T-Cell Epitopes and Neo-epitopes in Type 1 Diabetes: A Comprehensive Update and Reappraisal

James, Eddie A.; Mallone, Roberto; Kent, Sally C.; DiLorenzo, Teresa P.

doi:10.2337/dbi19-0022

The autoimmune disease type 1 diabetes is characterized by effector T-cell responses to pancreatic β-cell–derived peptides presented by HLA class I and class II molecules, leading ultimately to β-cell demise and insulin insufficiency. Although a given HLA molecule presents a vast array of peptides, only those recognized by T cells are designated as epitopes. Given their intimate link to etiology, the discovery and characterization of T-cell epitopes is a critical aspect of type 1 diabetes research. Understanding epitope recognition is also crucial for the pursuit of antigen-specific immunotherapies and implementation of strategies for T-cell monitoring. For these reasons, a cataloging and appraisal of the T-cell epitopes targeted in type 1 diabetes was completed over a decade ago, providing an important resource for both the research and the clinical communities. Here we present a much needed update and reappraisal of this earlier work and include online supplementary material where we cross-index each epitope with its primary references and Immune Epitope Database (IEDB) identifier. Our analysis includes a grading scale to score the degree of evidence available for each epitope, which conveys our perspective on several useful criteria for epitope evaluation. While providing an efficient summary of the arguably impressive current state of knowledge, this work also brings to light several deficiencies. These include the need for improved epitope validation, as few epitopes score highly by the criteria employed, and the dearth of investigations of the epitopes recognized in the context of several understudied type 1 diabetes–associated HLA molecules.

Introduction

The key role of autoimmune CD8⁺ and CD4⁺ T cells in the orchestration and final effector phase of β-cell destruction in type 1 diabetes is widely accepted (1). Based on this knowledge, T cells are expected to provide useful biomarkers, complementary to autoantibodies, for staging type 1 diabetes progression and monitoring regression following immunotherapy. The specificity of the autoimmune T cells toward β-cells is shaped through their recognition of peptides presented by HLA class I and class II molecules expressed on the surface of β-cells and/or antigen-presenting cells. The identification of the T-cell epitopes, i.e., those HLA-bound peptides recognized by autoreactive T cells, is therefore a matter of major effort in the field, as it provides critical information for detecting the corresponding T cells for disease-staging purposes, for developing antigen-specific immunotherapies, and for understanding disease pathogenesis. The increasing number of articles reporting the identification, characterization, or use of human islet–derived T-cell epitopes throughout recent years reflects these efforts (Fig. 1A and D), as does the continued discovery of new epitopes (Fig. 1B, C, E, and F). The pace of growth of this literature calls for a comprehensive assessment of the information available, as the first and only systematic review compiling this information dates back to 2007 (2). Additional reasons for updating this body of data include the advent of three relevant advances that were not available at that time. The first advance is the discovery of neo-epitopes generated by different mechanisms (3). The second is the efforts launched by the Network for Pancreatic Organ Donors with Diabetes (nPOD) and others, which have provided increased access to disease-proximal tissues, i.e., pancreas, isolated islets, and pancreatic lymph nodes (pLNs), while previous studies were largely confined to peripheral blood (4). This development also calls for a reappraisal of the strategy used to grade the level of evidence that defines a given epitope as such. Third, the Immune Epitope Database (IEDB) (www.iedb.org) now provides a comprehensive and prospective compilation of T-cell (and B-cell) epitopes relevant not only to type 1 diabetes and other autoimmune conditions but also to allergy, infectious disease, and transplantation (5). An updated assessment therefore should not be redundant with the IEDB information but, rather, complement it with additional elements, e.g., by grading the level of evidence for the epitopes and cross-referencing them with IEDB entries. These considerations have guided the epitope analysis presented herein.

Figure 1

View large Download slide

Year-by-year and cumulative summary of the articles and epitopes examined in this work. A–C: HLA class I–restricted epitopes. D–F: HLA class II–restricted epitopes. A: The articles represented in Table 1 were categorized by year of publication and the corresponding cumulative article numbers are depicted in A. For articles having both an e-publication date and a print date in PubMed, the earlier date was used to assign the year of publication. See Supplementary Table 1 for the PMID numbers for all of the 65 articles included in A. B and C: The number of new HLA class I–restricted epitopes reported in each of the indicated years is depicted in B, with the corresponding cumulative epitope numbers shown in C, for a total of 140 epitopes reported by the end of 2018. D: The articles represented in Table 2 were categorized by year of publication and the corresponding cumulative article numbers are depicted in D. See Supplementary Table 2 for the PMID numbers for all of the 100 articles included in D. E and F: The number of new HLA class II–restricted epitopes reported in each of the indicated years is depicted in E, with the corresponding cumulative epitope numbers shown in F, for a total of 418 epitopes reported by the end of 2018. Note that the cutoff for inclusion in our analysis was a publication date up to 9 July 2019. Given the partial nature of the data for 2019, the corresponding articles and epitopes are not included in Figure 1.

Epitope Cataloguing

To catalog all reported T-cell epitopes of potential relevance to human type 1 diabetes, we used a combination of search strategies, based on both PubMed and IEDB. Our goal was not to validate a single search strategy that would capture all published relevant T-cell epitopes but, rather, to use a combination of approaches to ensure a comprehensive coverage. Although IEDB includes T-cell epitopes that are submitted by individual investigators in addition to those extracted from the published literature by IEDB staff, we limited our analysis to published epitopes. In addition to the increased confidence afforded by peer reviewing, our detailed description of each epitope often required information not available in IEDB to be extracted from each reporting article, e.g., in the case of ex vivo T-cell studies, whether T-cell frequency differences between patients with type 1 diabetes and control subjects were statistically supported.

To harvest T-cell epitopes of potential relevance to type 1 diabetes from the IEDB, we first conducted a search at the level of protein antigens (rather than at the level of peptide epitopes) that included the following criteria: human proteins, T-cell assays only, positive assays only, MHC class I (for CD8⁺ T-cell epitopes) or MHC class II only (for CD4⁺ T-cell epitopes), any host, and insulin-dependent diabetes related. In some instances, we made the judgment to omit certain epitope sources. For example, peptides derived from claudin-17, tafazzin, and glucose-6-phosphatase were only reported as cross-reactive targets of T cells specific for GAD65 (6) or islet-specific glucose-6-phosphatase catalytic subunit–related protein (IGRP) (7) and were thus excluded. The proteins returned from our IEDB searches were then individually queried to compile epitope lists using similar criteria: T-cell assays only, positive assays only, MHC class I or class II only, and any host (to capture epitopes of human proteins discovered in model systems such as HLA-transgenic [Tg] mice). Epitopes with nonhuman MHC restrictions or disease associations other than insulin-dependent diabetes, e.g., stiff person syndrome, were eliminated. We then supplemented this information by searching PubMed for publications reporting relevant epitopes that had not yet been included in the IEDB, using various combinations of these search terms: diabetes, T cell, peptide, epitope, and CD8 or CD4. These epitopes were referred to IEDB staff for curation to ensure that each epitope in our analysis could be cross-referenced with an IEDB identification number. To minimize issues of reproducibility and conflicts in T-cell epitope data (8), we recommend inclusion of the indicated IEDB numbers in future publications. All epitopes and supporting references were then compiled into comprehensive epitope tables (Supplementary Tables 1 and 2), organized by the antigen from which they were derived. The cutoff for inclusion in our analysis was a publication date up to 9 July 2019. Differing from the previous work (2), we included all references providing important information about a given epitope, which are listed in chronological order of publication, including multiple references from a single group. Summary tables, in which each epitope was collapsed to a single line, were then constructed (Tables 1 and 2). In all of these tables, the names of the parent antigens are abbreviated according to the manner in which they are generally referred to in the literature. Supplementary Table 3 provides complete nomenclature information for each antigen, including the protein name prescribed by the UniProt consortium (www.uniprot.org) (9).

Table 1

CD8⁺ T-cell epitopes in type 1 diabetes

Antigen (gene)	Position	Sequence	IEDB#a	MHC	Human islets, pLNsb	Human blood, spleenb	HLA-Tg mouseb	NPPc	Evidenced	Reporting articlese
CHGA (CHGA)	10–19	LLCAGQVTAL	880821	A*02:01		Yes			D+	1
	43–52	TLSKPSPMPV	884674	A*02:01		Yes			D+	1
	344–352	KMDQLAKEL	952211	A*02:01		Yes		Yes	B+	1
GAD65 (GAD2)	3–11	SPGSGFWSF	177987	B*07:02		Yes	Yes	Yes	B+	1
	100–108	ACDGERPTL	177585	B*07:02		Yes	Yes	Yes	B+	1
	110–118	FLQDVMNIL	102433	A*02:01		Yes	Yes	Yes	B+	2
	114–122	VMNILLQYV	104336	A*02:01		Yes			C−	5
	114–123	VMNILLQYVV	102908	A*02:01	Yes	Yes	Yes	Yes	A+	16
	141–149	LLQEYNWEL	102620	A*02:01		Yes	Yes	Yes	B+	2
	159–167	ILMHCQTTL	104844	A*02:01		Yes	Yes	Yes	B+	1
	175–184	HPRYFNQLST	177734	B*07:02		Yes	Yes	Yes	B+	1
	255–263	RFKMFPEVK	104218	A3		Yes			C−	1
	255–263	RFKMFPEVK	104218	A11		Yes			C−	1
	269–277	ALP(R→Cit)LIAFT	436368	A2		Yes			C–	1
	277–285	TSEHSHFSL	104317	B15		Yes			C–	1
	277–285	TSEHSHFSL	104317	B35		Yes			C–	1
	311–320	IPSDLERRIL	177779	B*07:02		Yes	Yes	Yes	B+	1
	476–484	ELAEYLYNI	104767	A*02:01		Yes	Yes	Yes	B+	1
	498–506	KPQHTNVCF	177813	B*07:02		Yes	Yes	Yes	B+	1
	530–538	APVIKARMM	177606	B*07:02		Yes	Yes	Yes	B+	1
	536–545	RMMEYGTTMV	102769	A*02:01		Yes	Yes	Yes	B+	5
GFAP (GFAP)	143–151	NLAQDLATV	115871	A*02:01		Yes			D+	1
	192–200	SLEEEIRFL	115968	A*02:01		Yes			D+	1
	214–222	QLARQQVHV	115919	A*02:01		Yes			D+	1
IA-2 (PTPRN)	172–180	SLSPLQAEL	101245	A*02:01		Yes			D+	2
	180–188	LLPPLLEHL	101026	A*02:01		Yes			D+	1
	482–490	SLAAGVKLL	101237	A*02:01		Yes			D+	1
	790–798	TIADFWQMV	102844	A*02:01		Yes	Yes	Yes	B+	2
	797–805	MVWESGCTV	140054	A*02:01	Yes	Yes			C+	8
	805–813	VIVMLTPLV	102899	A*02:01		Yes	Yes	Yes	B+	5
	830–839	SLYHVYEVNL	102811	A*02:01		Yes	Yes	Yes	B+	2
	925–933	VLN(R→Cit)MAKGV	441419	A2		Yes			C–	1
	962–970	ALTAVAEEV	102306	A*02:01		Yes	Yes	Yes	B+	2
IAPP (IAPP)	5–13	KLQVFLIVL	100981	A*02:01	Yes	Yes			C	7
	9–17	FLIVLSVAL	100844	A*02:01		Yes			D+	2
IGRP (G6PC2)	152–160	FLWSVFWLI	105191	A*02:01		Yes			D+	3
	211–219	NLFLFLFAV	105409	A2		Yes			D+	1
	215–223	FLFAVGFYL	100843	A*02:01		Yes	Yes		D+	5
	222–230	YLLLRVLNI	105617	A2		Yes			D+	1
	228–236	LNIDLLWSV	103368	A*02:01		Yes			D+	4
	258–266	GLV(R→Cit)NLGVL	437684	A2		Yes			C–	1
	265–273	VLFGLGFAI	103705	A*02:01	Yes	Yes	Yes		C+	18
	293–301	RLLCALTSL	101199	A*02:01		Yes	Yes		D+	2
INS (INS)	2–10 (L2–L10)	ALWMRLLPL	100725	A*02:01		Yes			D+	6
	2–11 (L2–L11)	ALWMRLLPLL	105674	A*02:01		Yes	Yes	Yes	A–	4
	2–11 (L2–L11)	ALWMRLLPLL	105674	A24		Yes		Yes	B+	1
	2–11 (L2–L11)	ALWMRLLPLL	105674	B8		Yes		Yes	B+	1
	3–11 (L3–L11)	LWMRLLPLL	105950	A*24:02		Yes		Yes	A–	2
	4–13 (L4–L13)	WMRLLPLLAL	106187	B7		Yes		Yes	B+	2
	6–14 (L6–L14)	RLLPLLALL	103557	A*02:01		Yes	Yes	Yes	A–	7
	6–16 (L6–L16)	RLLPLLALLAL	115471	A2		Yes		Yes	B+	1
	8–16 (L8–L16)	LPLLALLAL	105936	B*07:02		Yes			D+	1
	9–18 (L9–L18)	PLLALLALWG	159293	A3		Yes		Yes	B+	1
	14–23 (L14–L23)	LALWGPDPAA	115337	A2		Yes	Yes	Yes	A–	1
	15–24 (L15–L24)	ALWGPDPAAA	103041	A*02:01	Yes	Yes	Yes	Yes	A+	21
	15–25 (L15–B1)	ALWGPDPAAAF	115182	A1		Yes		Yes	B+	1
	15–25 (L15–B1)	ALWGPDPAAAF	115182	A24		Yes		Yes	B+	1
	17–24 (L17–L24)	WGPDPAAA	103728	A*02:01		Yes		Yes	B+	1
	29–38 (B5–B14)	HLCGSHLVEA	102515	A*02:01		Yes	Yes	Yes	B+	3
	30–39 (B6–B15)	LCGSHLVEAL	106593	A*02:01		Yes			D+	1
	33–42 (B9–B18)	SHLVEALYLV	104248	A*02:01		Yes	Yes	Yes	A–	3
	34–42 (B10–B18)	HLVEALYLV	100920	A*02:01	Yes	Yes	Yes	Yes	A+	22
	38–46 (B14–B22)	ALYLVCGER	103803	A3		Yes		Yes	B+	1
	38–46 (B14–B22)	ALYLVCGER	103803	A11		Yes		Yes	B+	1
	39–47 (B15–B23)	LYLVCGERG	102639	A*24:02		Yes			C–	1
	39–48 (B15–B24)	LYLVCGERGF	106637	A24		Yes		Yes	B+	1
	41–50 (B17–B26)	LVCGERGFFY	106631	A1		Yes		Yes	B+	1
	41–50 (B17–B26)	LVCGERGFFY	106631	A3		Yes		Yes	B+	1
	41–50 (B17–B26)	LVCGERGFFY	106631	A11		Yes		Yes	B+	1
	42–51 (B18–B27)	VCGERGFFYT	102877	A1		Yes		Yes	B+	1
	42–51 (B18–B27)	VCGERGFFYT	102877	A*02:01		Yes	Yes	Yes	B+	5
	42–51 (B18–B27)	VCGERGFFYT	102877	B8		Yes		Yes	B+	1
	42–51 (B18–B27)	VCGERGFFYT	102877	B18		Yes		Yes	B+	1
	44–51 (B20–B27)	GERGFFYT	105816	A1		Yes		Yes	B+	1
	44–51 (B20–B27)	GERGFFYT	105816	B8		Yes		Yes	B+	1
	45–53 (B21–B29)	ERGFFYTPK	106399	A3		Yes		Yes	B+	1
	49–57 (B25–C1)	FYTPKTRRE	105799	B8		Yes		Yes	B+	1
	51–61 (B27–C5)	TPKTRREAEDL	106918	B8		Yes		Yes	B+	1
	76–84 (C20–C28)	SLQPLALEG	101242	A*02:01		Yes	Yes	Yes	A–	2
	76–84 (C20–C28)	SLQPLALEG	101242	A3		Yes		Yes	B+	2
	79–88 (C23–C32)	PLALEGSLQK	159292	A3		Yes		Yes	B+	2
	81–89 (C25–C33)	ALEGSLQKR	104727	A*02:01			Yes	Yes	B	1
	85–94 (C29–A5)	SLQKRGIVEQ	101241	A*02:01		Yes	Yes	Yes	A–	3
	90–99 (A1–A10)	GIVEQCCTSI	100882	A*02:01		Yes	Yes	Yes	A–	3
	101–109 (A12–A20)	SLYQLENYC	101248	A*02:01		Yes	Yes	Yes	A–	8
ISL-1 (ISL1)	276–284	GLQANPVEV	952138	A*02:01	Yes	Yes		Yes	A	1
KCNK16 (KCNK16)	129–137	ALLGIPLNV	952014	A*02:01		Yes		Yes	B+	1
KIF1A (KIF1A)	1347–1355	VLDTSVAYV	779283	A*02:01		Yes		Yes	B+	1
PC2 (PCSK2)	30–38	FTNHFLVEL	952113	A*02:01		Yes		Yes	B+	1
S100β (S100B)	10–18	ALIDVFHQY	562065	A*02:01		Yes	Yes	Yes	B+	1
	20–28	GREGDKHKL	910732	A*02:01		Yes	Yes	Yes	B+	1
SCG5 (SCG5)	186–195	YLQGQRLDNV	952620	A*02:01		Yes		Yes	B+	1
UCN3 (UCN3)	1–9	MLMPVHFLL	952274	A*02:01	Yes	Yes		Yes	A	1
VTDB (GC)	211–219	LLTTLSNRV	767640	A*02:01		Yes	Yes		D+	1
	235–243	NLIKLAQV	767652	A*02:01		Yes	Yes		D+	1
ZnT8 (SLC30A8)	16–24	KMYAFTLES	171844	A*02:01		Yes	Yes	Yes	B+	1
	16–25	KMYAFTLESV	504008	A*02:01		Yes			D+	1
	93–101	HIAGSLAVV	168764	A2		Yes	Yes	Yes	B+	1
	107–115	LLIDLTSFL	169149	A*02:01		Yes	Yes		C–	3
	107–116	LLIDLTSFLL	504015	A*02:01		Yes	Yes	Yes	B+	2
	110–118	DLTSFLLSL	168356	A*02:01		Yes			D+	1
	114–123	FLLSLFSLWL	168578	A*02:01		Yes	Yes	Yes	B+	2
	115–123	LLSLFSLWL	172188	A*02:01		Yes	Yes	Yes	A–	3
	140–148	EILGALLSI	168356	A*02:01		Yes			D+	1
	141–149	ILGALLSIL	168867	A*02:01		Yes			D+	1
	145–153	LLSILCIWV	172186	A*02:01			Yes		D	1
	153–161	VVTGVLVYL	170038	A*02:01		Yes	Yes	Yes	B+	5
	165–173	RLLYPDYQI	173061	A*02:01		Yes	Yes	Yes	B+	2
	173–181	IQATVMIIV	171556	A*02:01		Yes	Yes	Yes	B+	1
	177–186	VMIIVSSLAV	504065	A*02:01		Yes	Yes	Yes	B+	1
	185–194	AVAANIVLTV	168235	A*02:01		Yes	Yes	Yes	A–	2
	186–194	VAANIVLTV	173562	A*02:01	Yes	Yes	Yes	Yes	A+	4
	200–208	CLGHNHKEV	503971	A*02:01		Yes			D+	1
	221–229	ALGDLFQSI	168159	A*02:01		Yes	Yes	Yes	B+	3
	228–236	SISVLISAL	169725	A2		Yes	Yes	Yes	B+	1
	245–254	KIADPICTFI	504005	A*02:01		Yes			D+	1
	253–261	FIFSILVLA	171037	A*02:01		Yes	Yes	Yes	B+	1
	253–261	FIF(S→pS)ILVLA	437274	A2		Yes			C–	1
	257–266	ILVLASTITI	168881	A2		Yes	Yes	Yes	B+	1
	266–274	ILKDFSILL	168874	A*02:01		Yes	Yes	Yes	B+	2
	273–282	LLMEGVPKSL	169153	A*02:01		Yes			D+	1
	280–288	KSLNYSGVK	171933	A*02:01		Yes	Yes	Yes	B+	1
	281–290	SLNYSGVKEL	169744	A*02:01		Yes			D+	1
	291–300	ILAVDGVLSV	168865	A*02:01		Yes	Yes	Yes	B+	2
	292–300	LAVDGVLSV	172015	A*02:01		Yes			D+	1
	299–308	SVHSLHIWSL	169790	A*02:01		Yes			D+	1
	314–322	ILSAHVATA	168880	A*02:01		Yes			D+	1
	343–351	TMHSLTIQM	173491	A*02:01		Yes	Yes	Yes	B+	1

Antigen (gene)	Position	Sequence	IEDB#a	MHC	Human islets, pLNsb	Human blood, spleenb	HLA-Tg mouseb	NPPc	Evidenced	Reporting articlese
CHGA (CHGA)	10–19	LLCAGQVTAL	880821	A*02:01		Yes			D+	1
	43–52	TLSKPSPMPV	884674	A*02:01		Yes			D+	1
	344–352	KMDQLAKEL	952211	A*02:01		Yes		Yes	B+	1
GAD65 (GAD2)	3–11	SPGSGFWSF	177987	B*07:02		Yes	Yes	Yes	B+	1
	100–108	ACDGERPTL	177585	B*07:02		Yes	Yes	Yes	B+	1
	110–118	FLQDVMNIL	102433	A*02:01		Yes	Yes	Yes	B+	2
	114–122	VMNILLQYV	104336	A*02:01		Yes			C−	5
	114–123	VMNILLQYVV	102908	A*02:01	Yes	Yes	Yes	Yes	A+	16
	141–149	LLQEYNWEL	102620	A*02:01		Yes	Yes	Yes	B+	2
	159–167	ILMHCQTTL	104844	A*02:01		Yes	Yes	Yes	B+	1
	175–184	HPRYFNQLST	177734	B*07:02		Yes	Yes	Yes	B+	1
	255–263	RFKMFPEVK	104218	A3		Yes			C−	1
	255–263	RFKMFPEVK	104218	A11		Yes			C−	1
	269–277	ALP(R→Cit)LIAFT	436368	A2		Yes			C–	1
	277–285	TSEHSHFSL	104317	B15		Yes			C–	1
	277–285	TSEHSHFSL	104317	B35		Yes			C–	1
	311–320	IPSDLERRIL	177779	B*07:02		Yes	Yes	Yes	B+	1
	476–484	ELAEYLYNI	104767	A*02:01		Yes	Yes	Yes	B+	1
	498–506	KPQHTNVCF	177813	B*07:02		Yes	Yes	Yes	B+	1
	530–538	APVIKARMM	177606	B*07:02		Yes	Yes	Yes	B+	1
	536–545	RMMEYGTTMV	102769	A*02:01		Yes	Yes	Yes	B+	5
GFAP (GFAP)	143–151	NLAQDLATV	115871	A*02:01		Yes			D+	1
	192–200	SLEEEIRFL	115968	A*02:01		Yes			D+	1
	214–222	QLARQQVHV	115919	A*02:01		Yes			D+	1
IA-2 (PTPRN)	172–180	SLSPLQAEL	101245	A*02:01		Yes			D+	2
	180–188	LLPPLLEHL	101026	A*02:01		Yes			D+	1
	482–490	SLAAGVKLL	101237	A*02:01		Yes			D+	1
	790–798	TIADFWQMV	102844	A*02:01		Yes	Yes	Yes	B+	2
	797–805	MVWESGCTV	140054	A*02:01	Yes	Yes			C+	8
	805–813	VIVMLTPLV	102899	A*02:01		Yes	Yes	Yes	B+	5
	830–839	SLYHVYEVNL	102811	A*02:01		Yes	Yes	Yes	B+	2
	925–933	VLN(R→Cit)MAKGV	441419	A2		Yes			C–	1
	962–970	ALTAVAEEV	102306	A*02:01		Yes	Yes	Yes	B+	2
IAPP (IAPP)	5–13	KLQVFLIVL	100981	A*02:01	Yes	Yes			C	7
	9–17	FLIVLSVAL	100844	A*02:01		Yes			D+	2
IGRP (G6PC2)	152–160	FLWSVFWLI	105191	A*02:01		Yes			D+	3
	211–219	NLFLFLFAV	105409	A2		Yes			D+	1
	215–223	FLFAVGFYL	100843	A*02:01		Yes	Yes		D+	5
	222–230	YLLLRVLNI	105617	A2		Yes			D+	1
	228–236	LNIDLLWSV	103368	A*02:01		Yes			D+	4
	258–266	GLV(R→Cit)NLGVL	437684	A2		Yes			C–	1
	265–273	VLFGLGFAI	103705	A*02:01	Yes	Yes	Yes		C+	18
	293–301	RLLCALTSL	101199	A*02:01		Yes	Yes		D+	2
INS (INS)	2–10 (L2–L10)	ALWMRLLPL	100725	A*02:01		Yes			D+	6
	2–11 (L2–L11)	ALWMRLLPLL	105674	A*02:01		Yes	Yes	Yes	A–	4
	2–11 (L2–L11)	ALWMRLLPLL	105674	A24		Yes		Yes	B+	1
	2–11 (L2–L11)	ALWMRLLPLL	105674	B8		Yes		Yes	B+	1
	3–11 (L3–L11)	LWMRLLPLL	105950	A*24:02		Yes		Yes	A–	2
	4–13 (L4–L13)	WMRLLPLLAL	106187	B7		Yes		Yes	B+	2
	6–14 (L6–L14)	RLLPLLALL	103557	A*02:01		Yes	Yes	Yes	A–	7
	6–16 (L6–L16)	RLLPLLALLAL	115471	A2		Yes		Yes	B+	1
	8–16 (L8–L16)	LPLLALLAL	105936	B*07:02		Yes			D+	1
	9–18 (L9–L18)	PLLALLALWG	159293	A3		Yes		Yes	B+	1
	14–23 (L14–L23)	LALWGPDPAA	115337	A2		Yes	Yes	Yes	A–	1
	15–24 (L15–L24)	ALWGPDPAAA	103041	A*02:01	Yes	Yes	Yes	Yes	A+	21
	15–25 (L15–B1)	ALWGPDPAAAF	115182	A1		Yes		Yes	B+	1
	15–25 (L15–B1)	ALWGPDPAAAF	115182	A24		Yes		Yes	B+	1
	17–24 (L17–L24)	WGPDPAAA	103728	A*02:01		Yes		Yes	B+	1
	29–38 (B5–B14)	HLCGSHLVEA	102515	A*02:01		Yes	Yes	Yes	B+	3
	30–39 (B6–B15)	LCGSHLVEAL	106593	A*02:01		Yes			D+	1
	33–42 (B9–B18)	SHLVEALYLV	104248	A*02:01		Yes	Yes	Yes	A–	3
	34–42 (B10–B18)	HLVEALYLV	100920	A*02:01	Yes	Yes	Yes	Yes	A+	22
	38–46 (B14–B22)	ALYLVCGER	103803	A3		Yes		Yes	B+	1
	38–46 (B14–B22)	ALYLVCGER	103803	A11		Yes		Yes	B+	1
	39–47 (B15–B23)	LYLVCGERG	102639	A*24:02		Yes			C–	1
	39–48 (B15–B24)	LYLVCGERGF	106637	A24		Yes		Yes	B+	1
	41–50 (B17–B26)	LVCGERGFFY	106631	A1		Yes		Yes	B+	1
	41–50 (B17–B26)	LVCGERGFFY	106631	A3		Yes		Yes	B+	1
	41–50 (B17–B26)	LVCGERGFFY	106631	A11		Yes		Yes	B+	1
	42–51 (B18–B27)	VCGERGFFYT	102877	A1		Yes		Yes	B+	1
	42–51 (B18–B27)	VCGERGFFYT	102877	A*02:01		Yes	Yes	Yes	B+	5
	42–51 (B18–B27)	VCGERGFFYT	102877	B8		Yes		Yes	B+	1
	42–51 (B18–B27)	VCGERGFFYT	102877	B18		Yes		Yes	B+	1
	44–51 (B20–B27)	GERGFFYT	105816	A1		Yes		Yes	B+	1
	44–51 (B20–B27)	GERGFFYT	105816	B8		Yes		Yes	B+	1
	45–53 (B21–B29)	ERGFFYTPK	106399	A3		Yes		Yes	B+	1
	49–57 (B25–C1)	FYTPKTRRE	105799	B8		Yes		Yes	B+	1
	51–61 (B27–C5)	TPKTRREAEDL	106918	B8		Yes		Yes	B+	1
	76–84 (C20–C28)	SLQPLALEG	101242	A*02:01		Yes	Yes	Yes	A–	2
	76–84 (C20–C28)	SLQPLALEG	101242	A3		Yes		Yes	B+	2
	79–88 (C23–C32)	PLALEGSLQK	159292	A3		Yes		Yes	B+	2
	81–89 (C25–C33)	ALEGSLQKR	104727	A*02:01			Yes	Yes	B	1
	85–94 (C29–A5)	SLQKRGIVEQ	101241	A*02:01		Yes	Yes	Yes	A–	3
	90–99 (A1–A10)	GIVEQCCTSI	100882	A*02:01		Yes	Yes	Yes	A–	3
	101–109 (A12–A20)	SLYQLENYC	101248	A*02:01		Yes	Yes	Yes	A–	8
ISL-1 (ISL1)	276–284	GLQANPVEV	952138	A*02:01	Yes	Yes		Yes	A	1
KCNK16 (KCNK16)	129–137	ALLGIPLNV	952014	A*02:01		Yes		Yes	B+	1
KIF1A (KIF1A)	1347–1355	VLDTSVAYV	779283	A*02:01		Yes		Yes	B+	1
PC2 (PCSK2)	30–38	FTNHFLVEL	952113	A*02:01		Yes		Yes	B+	1
S100β (S100B)	10–18	ALIDVFHQY	562065	A*02:01		Yes	Yes	Yes	B+	1
	20–28	GREGDKHKL	910732	A*02:01		Yes	Yes	Yes	B+	1
SCG5 (SCG5)	186–195	YLQGQRLDNV	952620	A*02:01		Yes		Yes	B+	1
UCN3 (UCN3)	1–9	MLMPVHFLL	952274	A*02:01	Yes	Yes		Yes	A	1
VTDB (GC)	211–219	LLTTLSNRV	767640	A*02:01		Yes	Yes		D+	1
	235–243	NLIKLAQV	767652	A*02:01		Yes	Yes		D+	1
ZnT8 (SLC30A8)	16–24	KMYAFTLES	171844	A*02:01		Yes	Yes	Yes	B+	1
	16–25	KMYAFTLESV	504008	A*02:01		Yes			D+	1
	93–101	HIAGSLAVV	168764	A2		Yes	Yes	Yes	B+	1
	107–115	LLIDLTSFL	169149	A*02:01		Yes	Yes		C–	3
	107–116	LLIDLTSFLL	504015	A*02:01		Yes	Yes	Yes	B+	2
	110–118	DLTSFLLSL	168356	A*02:01		Yes			D+	1
	114–123	FLLSLFSLWL	168578	A*02:01		Yes	Yes	Yes	B+	2
	115–123	LLSLFSLWL	172188	A*02:01		Yes	Yes	Yes	A–	3
	140–148	EILGALLSI	168356	A*02:01		Yes			D+	1
	141–149	ILGALLSIL	168867	A*02:01		Yes			D+	1
	145–153	LLSILCIWV	172186	A*02:01			Yes		D	1
	153–161	VVTGVLVYL	170038	A*02:01		Yes	Yes	Yes	B+	5
	165–173	RLLYPDYQI	173061	A*02:01		Yes	Yes	Yes	B+	2
	173–181	IQATVMIIV	171556	A*02:01		Yes	Yes	Yes	B+	1
	177–186	VMIIVSSLAV	504065	A*02:01		Yes	Yes	Yes	B+	1
	185–194	AVAANIVLTV	168235	A*02:01		Yes	Yes	Yes	A–	2
	186–194	VAANIVLTV	173562	A*02:01	Yes	Yes	Yes	Yes	A+	4
	200–208	CLGHNHKEV	503971	A*02:01		Yes			D+	1
	221–229	ALGDLFQSI	168159	A*02:01		Yes	Yes	Yes	B+	3
	228–236	SISVLISAL	169725	A2		Yes	Yes	Yes	B+	1
	245–254	KIADPICTFI	504005	A*02:01		Yes			D+	1
	253–261	FIFSILVLA	171037	A*02:01		Yes	Yes	Yes	B+	1
	253–261	FIF(S→pS)ILVLA	437274	A2		Yes			C–	1
	257–266	ILVLASTITI	168881	A2		Yes	Yes	Yes	B+	1
	266–274	ILKDFSILL	168874	A*02:01		Yes	Yes	Yes	B+	2
	273–282	LLMEGVPKSL	169153	A*02:01		Yes			D+	1
	280–288	KSLNYSGVK	171933	A*02:01		Yes	Yes	Yes	B+	1
	281–290	SLNYSGVKEL	169744	A*02:01		Yes			D+	1
	291–300	ILAVDGVLSV	168865	A*02:01		Yes	Yes	Yes	B+	2
	292–300	LAVDGVLSV	172015	A*02:01		Yes			D+	1
	299–308	SVHSLHIWSL	169790	A*02:01		Yes			D+	1
	314–322	ILSAHVATA	168880	A*02:01		Yes			D+	1
	343–351	TMHSLTIQM	173491	A*02:01		Yes	Yes	Yes	B+	1

Nonconventional epitopes, excluding posttranslational modifications, which are included above
Epitope sourcef	Position	Sequence	IEDB#a	MHC	Human islets, pLNsb	Human blood, spleenb	HLA-Tg mouseb	NPPc	Evidenced	Reporting articlese
CCNI-008	14–22	KLNWDLHTA	952207	A*02:01		Yes			D+	1
GAD2-003	179–187	KIIKLFFRL	952200	A*02:01		Yes			D+	1
GNAS-036	67–75	YMCTHRLLL	952623	A*02:01		Yes			D+	1
	124–132	AMSNLVPPV	952026	A*02:01		Yes			D+	1
IAPP-002	33–42	VLSRNILLEL	952582	A*02:01		Yes			D+	1
IAPP hybrid	15–17/5–10	VALKLQVFL	952568	A*02:01	Yes	Yes		Yes	A	1
INS-DRiP	1–9	MLYQHLLPL	606356	A*02:01		Yes			C–	2
PTPRN-021	392–402	SLAAGVKLLEI	952381	A*02:01		Yes			D+	1
	398–407	KLLEILAEHV	952204	A*02:01		Yes			D+	1
PTPRN2-005	11–19	LLLLLPPRV	101025	A*02:01		Yes			D+	1
	19–27	VLPAAPSSV	952581	A*02:01		Yes			D+	1
REXO2-020	2–10	SVANALWIV	952401	A*02:01		Yes			D+	1
SCG5-009	186–194	FLSGAVNRL	952103	A*02:01	Yes	Yes		Yes	A	1
SLC30A8-002	16–25	KMYAFTLESV	504008	A*02:01		Yes			D+	1

Nonconventional epitopes, excluding posttranslational modifications, which are included above
Epitope sourcef	Position	Sequence	IEDB#a	MHC	Human islets, pLNsb	Human blood, spleenb	HLA-Tg mouseb	NPPc	Evidenced	Reporting articlese
CCNI-008	14–22	KLNWDLHTA	952207	A*02:01		Yes			D+	1
GAD2-003	179–187	KIIKLFFRL	952200	A*02:01		Yes			D+	1
GNAS-036	67–75	YMCTHRLLL	952623	A*02:01		Yes			D+	1
	124–132	AMSNLVPPV	952026	A*02:01		Yes			D+	1
IAPP-002	33–42	VLSRNILLEL	952582	A*02:01		Yes			D+	1
IAPP hybrid	15–17/5–10	VALKLQVFL	952568	A*02:01	Yes	Yes		Yes	A	1
INS-DRiP	1–9	MLYQHLLPL	606356	A*02:01		Yes			C–	2
PTPRN-021	392–402	SLAAGVKLLEI	952381	A*02:01		Yes			D+	1
	398–407	KLLEILAEHV	952204	A*02:01		Yes			D+	1
PTPRN2-005	11–19	LLLLLPPRV	101025	A*02:01		Yes			D+	1
	19–27	VLPAAPSSV	952581	A*02:01		Yes			D+	1
REXO2-020	2–10	SVANALWIV	952401	A*02:01		Yes			D+	1
SCG5-009	186–194	FLSGAVNRL	952103	A*02:01	Yes	Yes		Yes	A	1
SLC30A8-002	16–25	KMYAFTLESV	504008	A*02:01		Yes			D+	1

a

IEDB identifier (www.iedb.org).

b

Yes, T-cell responses observed using the indicated T-cell sources. See Supplementary Table 1 for details.

c

NPP, natural processing/presentation; yes, evidence is available. See Supplementary Table 1 for details.

d

See Fig. 2 for epitope scoring criteria.

e

See Supplementary Table 1 for details.

f

Gene names followed by a hyphen and three numbers refer to splice variants derived from the indicated genes. DRiP, defective ribosomal product.

Table 2

CD4⁺ T-cell epitopes in type 1 diabetes

Antigen (gene)	Position	Sequence	IEDB#^a	MHC	Human islets, pLNs^b	Human blood, spleen^b	HLA-Tg mouse^b	NPP^c	Evidence^d	Reporting articles^e
CHGA (CHGA)	342–355	WSKMDQLAKELTAE	226405	DQ8		Yes		Yes	B+	1
DMK (DMPK)	9–28	RLQQLVLDPGFLGLEPLLDL	138808	DR0401		Yes			C–	1
GAD65 (GAD2)	1–20	MASPGSGFWSFGSEDGSGDS	101054	Class II		Yes			D+	1
	1–20	MASPGSGFWSFGSEDGSGDS	101054	DR0401		Yes			C–	1
	47–66	LLYGDAEKPAESGGSQPPRA	105302	Class II		Yes			D+	1
	73–92	CACDQKPCSCSKVDVNYAFL	142554	DR		Yes			C–	1
	73–92	CACDQKPCSCSKVDVNYAFL	142554	DR0401		Yes			C–	1
	81–100	SCSKVDVNYAFLHATDLLPA	104234	DR		Yes			C–	1
	86–103	DVNYAFLHATDLLPACDG	186992	DR4		Yes			D+	1
	88–99	NYAFLHATDLLP	104163	DR0101		Yes		Yes	A–	3
	88–99	NYAFLHATDLLP	104163	DRB5		Yes			C–	1
	89–108	YAFLHATDLLPACDGE(R→Cit)PTL	230433	DR0401		Yes			C–	1
	101–115	CDGERPTLAFLQDVM	6101	DQ		Yes			D+	1
	105–124	RPTLAFLQDVMNILLQYVVK	143044	DR0401		Yes			C–	1
	108–129	LAFLQDVMNILLQYVVKSFDRS	105275	Class II		Yes			D+	1
	113–132	DVMNILLQYVVKSFDRSTKV	138762	DR0401		Yes		Yes	A–	3
	113–132	DVMNILLQYVVKSFDRSTKV	138762	DR		Yes			C–	1
	113–132	DVMNILLQYVVKSFDRSTKV	138762	DRB4		Yes			D+	1
	115–127	MNILLQYVVKSFD	100311	DR0401	Yes		Yes	Yes	A+	3
	115–127	MNILLQYVVKSFD	100311	Class II		Yes			D+	1
	115–127	MNILL(Q→E)YVVKSFD	230399	DR0401		Yes			C–	1
	115–130	MNILLQYVVKSFDRST	104903	DR0401			Yes	Yes	B	1
	116–129	NILLQYVVKSFDRS	102675	DRB4		Yes			C–	1
	116–127	NILLQYVVKSFD	104150	DRB4		Yes			C–	2
	121–140	YVVKSFDRSTKVIDFHYPNE	102974	DQ8		Yes	Yes	Yes	A–	2
	126–140	FDRSTKVIDFHYPNE	103164	DQ		Yes			D+	1
	146–165	NWELADQPQNLEEILMHCQT	103455	DR1601		Yes		Yes	A–	1
	153–172	P(Q→E)NLEEILMHC(Q→E)TTLKYAIK	230405	DR0401		Yes			C–	1
	157–176	EEILMHCQTTLKYAIKTGHP	105161	Class II		Yes			D+	1
	172–191	KTGHPRYFNQLSTGLDMVGL	105271	Class II		Yes			D+	1
	173–187	TGHPRYFNQLSTGLD	104649	Class II		Yes			D+	1
	174–185	GHPRYFNQLSTG	103219	DR0401		Yes		Yes	A–	1
	175–190	HPRYFNQLSTGLDMVG	187007	DR4		Yes			D+	1
	177–196	RYFNQLSTGLDMVGLAADWL	143056	DR		Yes			C–	1
	200–217	ANTNMFTYEIAPVFVLLE	103808	DR8 or DR9		Yes			C–	1
	201–220	NTNMFTYEIAPVFVLLEYVT	102698	DQ8			Yes	Yes	B–	1
	201–220	NTNMFTYEIAPVFVLLEYVT	102698	DR0401		Yes		Yes	A–	1
	202–221	TNMFTYEIAPVFVLLEYVTL	105004	Class II		Yes			D+	1
	203–226	NMFTYEIAPVFVLLEYVTLKKMRE	187017	DR4		Yes			D+	1
	206–220	TYEIAPVFVLLEYVT	67328	DQ		Yes			D+	1
	209–228	IAPVFVLLEYVTLKKMREII	142728	DRB4		Yes			D+	1
	217–236	EYVTLKKMREIIGWPGGSGD	104481	DR		Yes			C–	1
	225–244	REIIGWPGGSGDGIFSPGGA	143023	DR		Yes			C–	1
	231–250	PGGSGDGIFSPGGAISNMYA	102715	DQ8			Yes	Yes	B–	1
	232–251	GGSGDGIFSPGGAISNMYAM	105216	Class II		Yes			D+	1
	243–267	GAISNMYAMMIARFKMFPEVKEKGM	186999	DR4		Yes			D+	1
	247–266	NMYAMMIARFKMFPEVKEKG	45043	DR3		Yes			C–	1
	247–266	NMYAMMIARFKMFPEVKEKG	45043	Class II		Yes			C–	2
	247–279	NMYAMMIARFKMFPEVKEKGMAALPRLIAFTSE	101931	Class II		Yes			D+	1
	248–257	MYAMMIARFK	104140	DRB5		Yes		Yes	A–	2
	248–259	MYAMMIARFKMF	104141	DR0101		Yes		Yes	A–	1
	249–268	YAMMIARFKMFPEVKEKGMA	143224	DR		Yes			C–	1
	250–266	AMMIARFKMFPEVKEKG	234479	DQ8		Yes			C–	1
	251–270	MMIARFKMFPEVKEKGMAAL	104118	DR12		Yes			C–	1
	252–266	MIARFKMFPEVKEKG	104114	DR0404		Yes			C–	1
	252–266	MIARFKMFPEVKEKG	104114	Class II		Yes			D+	1
	254–276	ARFKMFPEVKEKGMAALPRLIAF	118749	Class II		Yes			D+	1
	260–279	PEVKEKGMAALPRLIAFTSE	105471	Class II		Yes			D+	2
	261–275	EVKEKGMAALPRLIA	186666	Class II		Yes			D+	1
	261–280	EVKEKGMAALPRLIAFTSEH	103893	DQ8		Yes			C–	1
	264–287	EKGMAALPRLIAFTSEHSHFSLKK	186995	DR4		Yes			D+	1
	265–284	KGMAALPRLIAFTSEHSHFS	142811	DR0401		Yes		Yes	A–	2
	265–284	KGMAALP(R→Cit)LIAFTSEHSHFS	230391	DR0401		Yes			C–	2
	265–284	KGMAALPRLIAFTSEHSHFS	142811	DR		Yes			C–	1
	266–285	GMAALPRLIAFTSEHSHFSL	104502	DR0401		Yes			D+	1
	270–283	LPRLIAFTSEHSHF	103379	DR0401		Yes		Yes	A–	2
	270–284	LPRLIAFTSEHSHFS	103380	DRB4		Yes		Yes	A–	1
	270–287	LPRLIAFTSEHSHFSLKK	157610	DR0401		Yes			D+	1
	271–285	PRLIAFTSEHSHFSL	104934	DR0401			Yes	Yes	B	1
	272–283	RLIAFTSEHSHF	103556	DRB4		Yes		Yes	A–	1
	273–292	LIAFTSEHSHFSLKKGAAAL	138782	DR0401		Yes		Yes	A–	3
	273–292	LIAFTSEHSHFSLKKGAAAL	138782	DR		Yes			C–	1
	274–286	IAFTSEHSHFSLK	25275	DR0401	Yes	Yes	Yes	Yes	A+	4
	274–286	IAFTSEHSHFSLK	25275	Class II		Yes			D+	1
	276–284	FTSEHSHFS	231904	DR0404		Yes			C–	1
	289–303	AAALGIGTDSVILIK	130713	Class II		Yes			D+	1
	290–309	AALGIGTDSVILIKCDERGK	104403	Class II		Yes			D+	1
	297–316	DSVILIKCDERGKMIPSDLE	142591	DR0401		Yes			C–	1
	305–324	DERGKMIPSDLERRILEAKQ	105133	DR0401		Yes		Yes	A–	1
	320–339	LEAKQKGFVPFLVSATAGTT	105281	Class II		Yes			D+	1
	321–340	EAKQKGFVPFLVSATAGTTV	103867	DR0401		Yes		Yes	A–	1
	335–352	TAGTTVYGAFDPLLAVAD	226392	DR3		Yes			D+	1
	338–352	TTVYGAFDPLLAVAD	187030	DR4		Yes			D+	1
	353–372	ICKKYKIWMHVDAAWGGGLL	142730	Class II		Yes			C–	1
	353–372	ICKKYKIWMHVDAAWGGGLL	142730	DRB4		Yes			D+	1
	354–372	CKKYKIWMHVDAAWGGGLL	186990	DR4		Yes			D+	1
	356–370	KYKIWMHVDAAWGGG	104868	DR0401			Yes	Yes	B	1
	368–388	GGGLLMSRKHKWKLSGVERAN	103921	DPw2		Yes			C–	1
	369–388	GGLLMSRKHKWKLSGVERAN	142674	DR		Yes			C–	1
	369–392	GGLLMSRKHKWKLSGVERANSVTW	187001	DR4		Yes			D+	1
	376–390	KHKWKLSGVERANSV	104852	DR0401			Yes	Yes	B	1
	377–396	HKWKLSGVERANSVTWNPHK	142717	DR0401		Yes			C–	1
	377–396	HKWKLSGVERANSVTWNPHK	142717	DR		Yes			C–	1
	385–404	ERANSVTWNPHKMMGVPLQC	105169	Class II		Yes			D+	1
	405–424	SALLVREEGLMQNCNQMHAS	187026	DR4		Yes			D+	1
	413–431	GLMQNCNQMHASYLFQQDK	103939	DR0101		Yes			C–	1
	416–435	QNCNQMHASYLFQQDKHYDL	105488	Class II		Yes			D+	1
	431–445	KHYDLSYDTGDKALQ	103306	DQ		Yes			D+	1
	433–452	YDLSYDTGDKALQCGRHVDV	143226	DR0401		Yes		Yes	A–	1
	433–452	YDLSYDTGDKALQCGRHVDV	143226	Class II		Yes			C–	1
	446–466	CGRHVDVFKLWLMWRAKGTTG	105120	Class II		Yes			D+	1
	450–470	VDVFKLWLMWRAKGTTGFEAH	187032	DR4		Yes			D+	1
	461–473	AKGTTGFEAHVDK	103035	DQ		Yes			D+	1
	462–483	KGTTGFEAHVDKCLELAEYLYN	105261	Class II		Yes			D+	1
	471–490	VDKCLELAEYLYNIIKNREG	102882	DQ8			Yes	Yes	B–	1
	473–492	KCLELAEYLYNIIKNREGYE	142807	DR0401		Yes		Yes	A–	1
	479–498	EYLYNIIKNREGYEMVFDGK	105173	Class II		Yes			D+	1
	480–496	YLYNIIKNREGYEMVFD	187035	DR4		Yes			D+	1
	481–495	LYNIIKNREGYEMVF	104898	DR0401			Yes	Yes	B	1
	491–510	YEMVFDGKPQHTNVCFWYIP	104352	DR3		Yes			C–	1
	491–510	YEMVFDGKPQHTNVCFWYIP	104352	DQ5		Yes			C–	1
	493–507	MVFDGKPQHTNVCFW	104575	Class II		Yes			D+	1
	494–513	VFDGKPQHTNVCFWYIPPSL	119539	Class II		Yes			D+	1
	501–520	HTNVCFWYIPPSLRTLEDNE	103978	DR1		Yes			C–	1
	501–520	HTNVCFWYIPPSLRTLEDNE	103978	DR4		Yes			C–	1
	504–518	VCFWYIPPSLRTLED	187031	DR4		Yes			D+	1
	505–519	CFWYIPPSLRTLEDN	101509	Class II		Yes			C–	1
	505–519	CFWYIPPSLRTLEDN	101509	DQ8		Yes			D+	1
	506–518	FWYIPPSLRTLED	103913	Class II		Yes			D+	1
	509–528	IPPSLRTLEDNEERMSRLSK	102537	Class II		Yes			D+	1
	511–525	PSLRTLEDNEERMSR	104602	DR0401			Yes	Yes	B	1
	511–525	PSLRTLEDNEERMSR	104602	DR4		Yes			D+	1
	511–530	PSLRTLEDNEERMSRLSKVA	104189	DR3		Yes			C–	1
	521–535	ERMSRLSKVAPVIKA	101609	Class II		Yes			C–	1
	521–535	ERMSRLSKVAPVIKA	101609	DQ8		Yes			D+	1
	524–543	SRLSKVAPVIKARMMEYGTT	102085	Class II		Yes			D+	2
	529–548	VAPVIKARMMEYGTTMVSYQ	143155	DRB4		Yes			D+	1
	533–547	IKARMMEYGTTMVSY	104522	Class II		Yes			D+	1
	536–550	RMMEYGTTMVSYQPL	103560	DQ		Yes			D+	1
	536–550	RMMEYGTTMVSYQPL	103560	DQ8			Yes		D–	1
	539–558	EYGTTMVSYQPLGDKVNFFR	105172	Class II		Yes			D+	1
	545–564	VSYQPLGDKVNFFRMVISNP	143204	DR0401		Yes		Yes	A–	1
	545–585	VSYQPLGDKVNFFRMVISNPAATHQDIDFLIEEIERLGQDL	102216	Class II		Yes			D+	1
	546–560	SYQPLGDKVNFFRMV	104994	DR0401			Yes	Yes	B	1
	550–570	LGDKVNFFRMVISNPAATHQD	187013	DR4		Yes			D+	1
	551–565	GDKVNFFRMVISNPA	104792	DR0401			Yes	Yes	B	1
	552–572	DKVNFFRMVISNPAATHQDID	119442	DR0401		Yes			C–	1
	553–570	KVNFFRMVISNPAATHQD	102589	DR4		Yes		Yes	A–	1
	553–572	KVNFFRMVISNPAATHQDID	138779	DR0401		Yes		Yes	A–	2
	553–572	KVNFFRMVISNPAATHQDID	138779	Class II		Yes			C–	1
	553–572	KVNFFRMVISNPAATHQDID	138779	DRB4		Yes			D+	1
	553–572	KVNFF(R→Cit)MVISNPAATHQDID	230397	DR0401		Yes			C–	3
	554–573	VNFFRMVISNPAATHQDIDF	119541	Class II		Yes			D+	1
	554–567	VNFFRMVISNPAAT	158453	DR0401		Yes			D+	1
	554–575	VNFFRMVISNPAATHQDIDFLI	226402	DR4		Yes			D+	1
	555–567	NFFRMVISNPAAT	101067	DR0401	Yes	Yes			C+	5
	555–567	NFFRMVISNPAAT	101067	DR0404		Yes			C–	2
	555–567	NFFRMVISNPAAT	101067	DR4		Yes			D+	1
	556–570	FFRMVISNPAATHQD	104775	DR0401			Yes	Yes	B	1
	556–575	FFRMVISNPAATHQDIDFLI	103167	DR0401		Yes		Yes	A–	2
	563–575	NPAATHQDIDFLI	102684	DRB4		Yes		Yes	A–	1
	565–580	AATHQDIDFLIEEIER	104721	DR0401			Yes	Yes	B	1
	566–585	ATHQDIDFLIEEIERLGQDL	103818	Class II		Yes			D+	1
	566–585	ATHQDIDFLIEEIERLGQDL	103818	DRB4		Yes			D+	1
GRP78 (HSPA5)	195–209	VMRIINEPTAAAIAY	546164	DR0401		Yes			D+	1
	195–209	VM(R→Cit)IINEPTAAAIAY	858100	DR0401		Yes			D+	1
	292–305	VEKAK(R→Cit)ALSSQHQA	590605	Class II	Yes				C+	1
	498–512	EVTFEIDVNGILRVT	857879	DR0401		Yes			D+	1
	498–512	EVTFEIDVNGIL(R→Cit)VT	857878	DR0401		Yes			C–	1
	500–514	TFEIDVNGIL(R→Cit)VTAE	858056	DR0401		Yes			D+	1
HSP60 (HSPD1)	31–50	KFGADARALMLQGVDLLADA	79582	Class II		Yes			D+	1
	136–155	NPVEIRRGVMLAVDAVIAEL	102687	Class II		Yes			D+	1
	242–256	AYVLLSEKKISSIQS	114753	DR		Yes			D+	1
	255–275	QSIVPALEIANAHRKPLVIIA	102750	Class II		Yes			D+	1
	280–294	GEALSTLVLNRLKVG	114829	DR		Yes			D+	1
	286–305	LVLNRLKVGLQVVAVKAPGF	40453	Class II		Yes			D+	1
	394–408	LAKLSDGVAVLKVGG	104547	Class II		Yes			D+	1
	436–455	IVLGGGCALLRCIPALDSLT	79579	Class II		Yes			D+	1
	466–485	EIIKRTLKIPAMTIAKNAGV	79540	Class II		Yes			D+	1
	511–530	VNMVEKGIIDPTKVVRTALL	102911	Class II		Yes			D+	1
HSP70 (HSPA1B)	1–20	MAKAAA(I→V)GIDLGTTYSCVGV	102642	Class II		Yes			D+	1
	166–185	GLNVLRIINEPTAAAIAYGL	102794	Class II		Yes			D+	1
	211–230	TIDDGIFEVKATAGDTHLGG	102846	Class II		Yes			D+	1
	226–245	THLGGEDFDNRLVNHFVEEF	102842	Class II		Yes			D+	1
	271–290	KRTLSSSTQASLEIDSLFEG	102579	Class II		Yes			D+	1
	391–410	LLLLDVAPLSLGLETAGGVM	102619	Class II		Yes			D+	1
	421–440	PTKQTQIFTTYSDNQPGVLI	102728	Class II		Yes			D+	1
	497–516	KANKITITNDKGRLSKEEIE	102548	Class II		Yes			D+	1
	512–531	KEEIERMVQEAEKYKAEDEV	102553	Class II		Yes			D+	1
IA-2 (PTPRN)	142–159	LQDIPTGSAPAAQHRLPQ	536828	DQ8 or DQ8-trans		Yes		Yes	B+	1
	197–209	PSLSYEPALLQPY	104603	Class II		Yes			D+	1
	198–216	SLSYEPALL(Q→E)PYLFH(Q→E)FGS	914422	DQ8	Yes	Yes			C+	1
	264–284	LPGPSPAQLFQDSGLLYLAQE	534743	DR4		Yes		Yes	B+	1
	293–311	VPRLPEQGSSSRAEDSPEG	538314	DQ		Yes		Yes	B+	1
	318–333	GDRGEKPASPAVQPDA	535895	DQ		Yes		Yes	B+	1
	319–342	DRGEKPASPAVQPDAALQRLAAVL	534686	DR3		Yes		Yes	B+	1
	449–488	SPLGQSQPTVAGQPSARPAAEEYGYIVTDQKPLSLAAGVK	534789	DR3		Yes		Yes	B+	1
	467–482	AAEEYGYIVTD(Q→E)KPLS	914337	DQ8		Yes			C–	1
	490–502	LEILAEHVHMSSG	104552	Class II		Yes			D+	1
	502–514	GSFINISVVGPAL	104510	Class II		Yes			D+	1
	523–536	QNLSLADVT(Q→E)(Q→E)AGL	914404	DQ8		Yes			C–	1
	545–562	TGL(Q→E)IL(Q→E)TGVG(Q→E)REEAAA	914426	Class II	Yes				C+	1
	545–562	TGL(Q→E)IL(Q→E)TGVG(Q→E)REEAAA	914426	DQ8	Yes	Yes			C+	1
	575–587	RSVLLTLVALAGV	104618	Class II		Yes			D+	1
	601–618	RQHARQQDKERLAALGPE	104966	DQ8			Yes		D–	1
	608–620	DKERLAALGPEGA	910445	Class II		Yes			D+	1
	616–633	GPEGAHGDTTFEYQDLCR	104813	DQ8			Yes		D–	1
	646–663	EGPPEPSRVSSVSSQFSD	104764	DQ8			Yes		D–	1
	654–674	VSSVSSQFSDAAQASPSSHSS	933295	DR4		Yes		Yes	B+	1
	657–674	VSSQFSDAAQASPSSHSS	104677	DR0401		Yes			D+	1
	661–678	FSDAAQASPSSHSSTPSW	104781	DQ8			Yes		D–	1
	685–700	ANMDISTGHMILAYME	105676	DR4		Yes			D+	1
	709–731	LAKEWQALCAYQAEPNTCATAQG	104546	DR0401		Yes		Yes	B+	1
	709–733	LAKEWQALCAYQAEPNTCATAQGEG	874656	DR0401		Yes			D+	1
	709–736	LAKEWQALCAYQAEPNTCATAQGEGNIK	134126	Class II		Yes			D+	2
	713–728	WQALCAYQAEPNTCAT	106189	DR4		Yes			D+	1
	717–729	CAYQAEPNTCATA	104437	Class II		Yes			D+	1
	721–738	AEPNTCATAQGEGNIKKN	104723	DQ8			Yes		D–	1
	745–760	PYDHARIKLKVESSPS	106021	DR4		Yes			D+	1
	751–770	IKLKVESSPSRSDYINASPI	104523	DR0401		Yes			C–	1
	752–775	KLKVESSPSRSDYINASPIIEHDP	134118	Class II		Yes			D+	2
	752–775	KLKVESSPSRSDYINASPIIEHDP	134118	DR4		Yes		Yes	B+	1
	766–783	NASPIIEHDPRMPAYIAT	104909	DQ8			Yes		D–	1
	778–790	PAYIATQGPLSHT	104590	Class II		Yes			D+	1
	787–802	LSHTIADFWQMVWESG	105943	DR4		Yes			D+	1
	793–808	DFWQMVWESGCTVIVM	105709	DR4		Yes			D+	1
	793–817	DFWQMVWESGCTVIVMLTPLVEDGV	233467	Class II		Yes			D+	1
	797–809	MVWESGCTVIVML	910496	Class II		Yes			D+	1
	797–817	MVWESGCTVIVMLTPLVEDGV	104578	DR0401		Yes			D+	1
	799–814	WESGCTVIVMLTPLVE	106184	DR3-DQ2		Yes			D+	1
	799–814	WESGCTVIVMLTPLVE	106184	DR4		Yes			D+	1
	803–815	CTVIVMLTPLVED	104441	Class II		Yes			D+	1
	804–816	TVIVMLTPLVEDG	910528	Class II		Yes			D+	1
	805–817	VIVMLTPLVEDGV	133730	Class II		Yes			C–	1
	805–820	VIVMLTPLVEDGVKQC	106162	DR3-DQ2		Yes			D+	1
	805–820	VIVMLTPLVEDGVKQC	106162	DR4		Yes			D+	1
	826–843	DEGASLYHVYEVNLVSEH	922741	DQ8			Yes		D–	1
	830–842	SLYHVYEVNLVSE	104629	Class II		Yes			D+	1
	831–850	LYHVYEVNLVSEHIWCEDFL	104566	DP0401		Yes			C–	1
	841–856	SEHIWCEDFLVRSFYL	106100	DR3-DQ2		Yes			D+	1
	841–856	SEHIWCEDFLVRSFYL	106100	DR4		Yes			D+	1
	841–860	SEHIWCEDFLVRSFYLKNVQ	104620	DP0401		Yes			C–	1
	841–860	SEHIWCEDFLVRSFYLKNVQ	104620	DR4		Yes			D+	2
	845–860	WCEDFLVRSFYLKNVQ	106182	DR4		Yes			D+	2
	847–862	EDFLVRSFYLKNVQTQ	105741	DR3-DQ2		Yes			D+	1
	847–862	EDFLVRSFYLKNVQTQ	105741	DR4		Yes			D+	1
	853–872	SFYLKNVQTQETRTLTQFHF	134229	DR4		Yes			D+	1
	854–866	FYLKNVQTQETRT	910467	Class II		Yes			D+	1
	854–872	FYLKNVQTQETRTLTQFHF	104493	DR0401		Yes			D+	1
	889–904	DFRRKVNKCYRGRSCP	105708	DR4-DQ8		Yes			D+	1
	918–930	TYILIDMVLNRMA	104662	Class II		Yes			D+	1
	919–934	YILIDMVLNRMAKGVK	106198	DR3-DQ2		Yes			D+	1
	919–934	YILIDMVLNRMAKGVK	106198	DR4		Yes			D+	1
	931–948	KGVKEIDIAATLEHVRDQ	922742	DQ8			Yes		D–	1
	933–945	VKEIDIAATLEHV	910531	Class II		Yes			D+	1
	955–975	SKDQFEFALTAVAEEVNAILK	104626	DR0401		Yes			D+	1
	957–969	DQFEFALTAVAEE	104447	Class II		Yes			D+	1
	959–974	FEFALTAVAEEVNAIL	105774	DR4		Yes			D+	1
	961–979	FALTAVAEEVNAILKALPQ	104772	DQ8			Yes		D–	1
IAPP (IAPP)	65–84	VGSNTYGK(R→Cit)NAVEVLK(R→Cit)EPL	590688	Class II	Yes				C+	1
	65–84	VGSNTYGK(R→Cit)NAVEVLK(R→Cit)EPL	590688	DQ8		Yes			C–	1
ICA69 (ICA1)	36–47	AFIKATGKKEDE	104413	Class II		Yes			D+	1
IGRP (G6PC2)	13–25	QHLQKDYRAYYTF	106039	DR0301		Yes			C–	1
	17–36	KDYRAYYTFLNFMSNVGDPR	138777	DR0401		Yes			D+	1
	23–35	YTFLNFMSNVGDP	106206	DR0401		Yes			C–	2
	177–196	HQVILGVIGGMLVAEAFEHT	644404	Class II		Yes			C–	1
	226–238	RVLNIDLLWSVPI	106096	DR0301		Yes			C–	1
	241–260	KWCANPDWIHIDTTPFAGLV	138780	DR0401		Yes			D+	2
	241–260	KWCANPDWIHIDTTPFAGLV	138780	Class II		Yes			C–	1
	247–259	DWIHIDTTPFAGL	105736	DR0401		Yes			C–	3
	305–324	QLYHFLQIPTHEEHLFYVLS	648592	DR		Yes			C–	1
INS (INS)	1–15 (L1–L15)	MALWMRLLPLLALLA	840899	DQ8			Yes	Yes	B–	1
	1–16 (L1–L16)	MALWMRLLPLLALLAL	103406	Class II		Yes			D+	1
	1–24 (L1–L24)	MALWMRLLPLLALLALWGPDPAAA	105962	DQ8			Yes		D–	1
	1–24 (L1–L24)	MALWMRLLPLLALLALWGPDPAAA	105962	DQ6			Yes		D–	1
	5–20 (L5–L20)	MRLLPLLALLALWGPD	923548	Class II		Yes			D+	1
	8–23 (L8–L23)	LPLLALLALWGPDPAA	840893	DQ8			Yes	Yes	B–	1
	9–24 (L9–L24)	PLLALLALWGPDPAAA	923645	Class II		Yes			D+	1
	9–28 (L9–B4)	PLLALLALWGPDPAAAFVNQ	142953	DRB4		Yes			D+	1
	11–26 (L11–B2)	LALLALWGPDPAAAFV	104548	DR0401			Yes	Yes	B–	1
	13–28 (L13–B4)	LLALWGPDPAAAFVNQ	923488	Class II		Yes			D+	1
	14–33 (L14–B9)	LALWGPDPAAAFVNQHLCGS	105917	DQ8			Yes		D–	1
	14–33 (L14–B9)	LALWGPDPAAAFVNQHLCGS	105917	DQ6			Yes		D–	1
	16–30 (L16–B6)	LWGPDPAAAFVNQHL	933452	DQ8			Yes	Yes	B–	1
	17–24 (L17–24)	WGPDPAAA	103728	DQ8-trans		Yes		Yes	B+	1
	17–32 (L17–B8)	WGPDPAAAFVNQHLCG	923967	Class II		Yes			D+	1
	18–30 (L18–B6)	GPDPAAAFVNQHL	933381	DQ8			Yes	Yes	B–	1
	20–35 (L20–B11)	DPAAAFVNQHLCGSHL	840818	DQ8			Yes	Yes	B–	1
	21–36 (L21–B12)	PAAAFVNQHLCGSHLV	104589	DR0401			Yes	Yes	B–	1
	21–36 (L21–B12)	PAAAFVNQHLCGSHLV	104589	Class II		Yes			D+	1
	25–40 (B1–B16)	FVNQHLCGSHLVEALY	840840	Class II		Yes			D+	2
	25–40 (B1–B16)	FVNQHLCGSHLVEALY	840840	DQ8			Yes	Yes	B–	1
	25–41 (B1–B17)	FVNQHLCGSHLVEALYL	103908	Class II		Yes			D+	1
	30–46 (B6–B22)	LCGSHLVEALYLVCGER	104030	Class II		Yes			D+	1
	30–46 (B6–B22)	LCGSHLVEALYLVCGER	104030	DQ8		Yes			C–	1
	31–47 (B7–B23)	CGSHLVEALYLVCGERG	933280	Class II		Yes			D+	1
	33–47 (B9–B23)	SHLVEALYLVCGERG	58388	DQ8-trans	Yes				C+	1
	33–47 (B9–B23)	SHLVEALYLVCGERG	58388	DQ8	Yes	Yes	Yes	Yes	A+	3
	34–49 (B10–B25)	HLVEALYLVCGERGFF	102517	Class II		Yes			C–	1
	34–53 (B10–B29)	HLVEALYLVCGERGFFYTPK	105241	DQ8			Yes		D–	1
	34–53 (B10–B29)	HLVEALYLVCGERGFFYTPK	105241	DQ6			Yes		D–	1
	35–47 (B11–B23)	LVEALYLVCGERG	104895	DQ8		Yes			C–	1
	35–49 (B11–B25)	LVEALYLVCGERGFF	104062	DQ8	Yes				C+	1
	35–51 (B11–B27)	LVEALYLVCGERGFFYT	103394	DR1601		Yes			C–	1
	35–51 (B11–B27)	LVEALYLVCGERGFFYT	103394	Class II		Yes			D+	2
	37–47 (B13–B23)	EALYLVCGERG	104759	DQ8		Yes			D+	1
	38–54 (B14–B30)	ALYLVCGERGFFYTPKT	933279	Class II		Yes			D+	1
	40–55 (B16–B31)	YLVCGERGFFYTPKTR	840972	DQ8			Yes	Yes	B–	1
	40–56 (B16–B32)	YLVCGERGFFYTPKTRR	923983	Class II		Yes			D+	1
	42–71 (B18–C15)	VCGERGFFYTPKTRREAEDLQVGQVELGGG	105563	Class II		Yes			D+	1
	44–60 (B20–C4)	GERGFFYTPKTRREAED	103917	Class II		Yes			D+	2
	44–63 (B20–C7)	GERGFFYTPKTRREAEDLQV	105818	DQ8			Yes		D–	1
	44–63 (B20–C7)	GERGFFYTPKTRREAEDLQV	105818	DQ6			Yes		D–	1
	45–61 (B21–C5)	ERGFFYTPKTRREAEDL	933281	Class II		Yes			D+	1
	46–61 (B22–C5)	RGFFYTPKTRREAEDL	418483	DQ8			Yes	Yes	B–	1
	48–60 (B24–C4)	FFYTPKTRREAED	103168	DR0301		Yes			D+	1
	48–60 (B24–C4)	FFYTPKTRREAED	103168	Class II		Yes			D+	1
	49–64 (B25–C8)	FYTPKTRREAEDLQVG	102451	Class II		Yes			C–	1
	49–65 (B25–C9)	FYTPKTRREAEDLQVGQ	103191	Class II		Yes			D+	1
	52–68 (B28–C12)	PKTRREAEDLQVGQVEL	933289	Class II		Yes			D+	1
	54–69 (B30–C13)	TRREAEDLQVGQVELG	538096	DQ2/DQ8		Yes			C–	1
	54–69 (B30–C13)	TRREAEDLQVG(Q→E)VELG	910786	DQ2/DQ8		Yes			C–	1
	54–69 (B30–C13)	TRREAEDL(Q→E)VG(Q→E)VELG	910787	DQ2/DQ8		Yes			C–	1
	54–70 (B30–C14)	TRREAEDLQVGQVELGG	104316	Class II		Yes			D+	2
	55–70 (B31–C14)	RREAEDLQVGQVELGG	840928	DQ8			Yes	Yes	B–	1
	57–87 (C1–C31)	EAEDLQVGQVELGGGPGAGSLQPLALEGSLQ	104452	Class II		Yes			D+	1
	57–70 (C1–C14)	EAEDLQVGQVELGG	857864	DQ8		Yes			D+	1
	58–67 (C2–C11)	AEDLQVGQVE	174367	DQ8		Yes			D+	1
	59–74 (C3–C18)	EDLQVGQVELGGGPGA	102379	Class II		Yes			C–	1
	59–75 (C3–C19)	EDLQVGQVELGGGPGAG	103869	Class II		Yes			D+	2
	61–76 (C5–C20)	LQVGQVELGGGPGAGS	840894	DQ8			Yes	Yes	B–	1
	64–76 (C8–C20)	GQVELGGGPGAGS	952145	DQ8		Yes			D+	1
	64–80 (C8–C24)	GQVELGGGPGAGSLQPL	103948	Class II		Yes			D+	2
	64–83 (C8–C27)	GQVELGGGPGAGSLQPLALE	105845	DQ6			Yes		D–	1
	65–73 (C9–C17)	QVELGGGPG	174710	DQ8	Yes				C+	2
	65–75 (C9–C19)	QVELGGGPGAG	858014	DQ8	Yes				C+	2
	66–73 (C10–C17)	VELGGGPG	858095	DQ8	Yes				C+	1
	66–74 (C10–C18)	VELGGGPGA	174788	DQ8	Yes				C+	2
	66–82 (C10–C26)	VELGGGPGAGSLQPLAL	933294	Class II		Yes			D+	1
	69–85 (C13–C29)	GGGPGAGSLQPLALEGS	103922	Class II		Yes			D+	1
	69–88 (C13–C32)	GGGPGAGSLQPLALEGSLQK	134060	DR0401			Yes	Yes	B–	1
	69–88 (C13–C32)	GGGPGAGSLQPLALEGSLQK	134060	Class II		Yes			D+	1
	69–88 (C13–C32)	GGGPGAGSLQPLALEGSLQK	134060	DR4		Yes		Yes	B+	1
	70–86 (C14–C30)	GGPGAGSLQPLALEGSL	103215	DQ8			Yes	Yes	B–	1
	72–83 (C16–C27)	PGAGSLQPLALE	857990	DQ8		Yes			D+	1
	72–86 (C16–C30)	PGAGSLQPLALEGSL	913900	DQ8/DQ8-trans		Yes			D+	1
	73–82 (C17–C26)	GAGSLQPLAL	174496	DQ8-trans		Yes			D+	1
	73–89 (C17–C33)	GAGSLQPLALEGSLQKR	604401	Class II		Yes			D+	1
	73–89 (C17–C33)	GAGSLQPLALEGSLQKR	604401	DQ8-trans	Yes				C+	1
	73–90 (C17–A1)	GAGSLQPLALEGSLQKRG	102454	DR0401		Yes	Yes	Yes	B+	2
	73–92 (C17–A3)	GAGSLQPLALEGSLQKRGIV	138770	DR0401		Yes			D+	1
	74–82 (C18–C26)	AGSLQPLAL	174376	DQ8	Yes				C+	2
	74–83 (C18–C27)	AGSLQPLALE	174377	DQ8	Yes				C+	2
	74–90 (C18–A1)	AGSLQPLALEGSLQKRG	103791	Class II		Yes			D+	2
	74–90 (C18–A1)	AGSLQPLALEGSLQKRG	103791	DR0401		Yes			D+	1
	74–93 (C18–A4)	AGSLQPLALEGSLQKRGIVE	105666	DQ8			Yes		D–	1
	74–93 (C18–A4)	AGSLQPLALEGSLQKRGIVE	105666	DQ6			Yes		D–	1
	75–92 (C19–A3)	GSLQPLALEGSLQKRGIV	104511	DR0401		Yes	Yes	Yes	B+	3
	75–92 (C19–A3)	GSLQPLALEGSLQKRGIV	104511	DR4		Yes		Yes	B+	2
	76–85 (C20–C29)	SLQPLALEGS	174743	DQ8-trans	Yes	Yes			C+	1
	76–86 (C20–C30)	SLQPLALEGSL	858046	DQ8-trans	Yes				C+	2
	76–86 (C20–C30)	SLQPLALEGSL	858046	DR0401		Yes			D+	1
	76–87 (C20–C31)	SLQPLALEGSLQ	858047	DQ2-trans		Yes			D+	1
	76–90 (C20–A1)	SLQPLALEGSLQKRG	101243	DR0401	Yes	Yes			C+	5
	78–94 (C22–A5)	QPLALEGSLQKRGIVEQ	462422	DR0401			Yes	Yes	B–	1
	78–94 (C22–A5)	QPLALEGSLQKRGIVEQ	462422	DR4		Yes		Yes	B+	1
	78–86 (C22–C30)	QPLALEGSL	174706	DQ2		Yes			D+	1
	78–87 (C22–C31)	QPLALEGSLQ	174707	DR0401		Yes			D+	1
	79–95 (C23–A6)	PLALEGSLQKRGIVEQC	104177	Class II		Yes			D+	1
	80–86 (C24–C30)	LALEGSL	857935	DQ2		Yes			D+	1
	80–86 (C24–C30)	LALEGSL	857935	DQ2-trans		Yes			D+	1
	80–86 (C24–C30)	LALEGSL	857935	DQ8		Yes			D+	1
	80–88 (C24–C32)	LALEGSLQK	103335	DR0401		Yes			D+	1
	80–96 (C24–A7)	LALEGSLQKRGIVEQCC	933284	Class II		Yes			D+	1
	80–97 (C24–A8)	LALEGSLQKRGIVEQCCT	840879	DQ8			Yes	Yes	B–	1
	84–100 (C28–A11)	GSLQKRGIVEQCCTSIC	103953	Class II		Yes			D+	2
	85–101 (C29–A12)	SLQKRGIVEQCCTSICS	104628	DR0401			Yes	Yes	B–	1
	87–103 (C31–A14)	QKRGIVEQCCTSICSLY	933290	Class II		Yes			D+	1
	88–102 (C32–A13)	KRGIVEQCCTSICSL	103321	DR4		Yes			C–	1
	90–101 (A1–A12)	GIVEQCCTSICS	104808	DR		Yes			D+	1
	90–101 (A1–A12)	GIVEQCCTSICS	104808	DQ		Yes			D+	1
	90–102 (A1–A13)	GIVEQCCTSICSL (vicinal disulfide 95–96)	910744	DR		Yes			C–	1
	90–104 (A1–A15)	GIVEQCCTSICSLYQ	103926	DR0401	Yes				C+	1
	90–105 (A1–A16)	GIVEQCCTSICSLYQL	923350	Class II		Yes			D+	1
	92–104 (A3–A15)	VEQCCTSICSLYQ	102889	Class II		Yes			D+	1
	92–110 (A3–A21)	VEQCCTSICSLYQLENYCN	840960	DQ8			Yes	Yes	B−	1
	94–105 (A5–A16)	QCCTSICSLYQL	104945	Class II		Yes			D+	1
	94–110 (A5–A21)	QCCTSICSLYQLENYCN	106028	Class II		Yes			D+	1
	94–110 (A5–A21)	QCCTSICSLYQLENYCN	106028	DQ8			Yes		D–	1
	94–110 (A5–A21)	QCCTSICSLYQLENYCN	106028	DQ6			Yes		D–	1
	95–110 (A6–A21)	CCTSICSLYQLENYCN	103824	Class II		Yes			D+	2
	98–110 (A9–A21)	SICSLYQLENYCN	104979	Class II		Yes			D+	1
S100β (S100B)	6–25	KAMVALIDVFHQYSGREGDK	422018	DR0401		Yes		Yes	B+	1
	21–36	REGDKHKLKKSELKEL	422069	DR0401		Yes		Yes	B+	1
	25–46	KHKLKKSELKELINNELSHFLE	422020	DR0401		Yes		Yes	B+	1
	68–92	ECDFQEFMAFVAMVTTACHEFFEHE	421964	DR0401		Yes		Yes	B+	1
ZnT8 (SLC30A8)	1–27	MEFLERTYLVNDKAAKM(Y→H)AFTLESVEL	174655	DR4		Yes			D+	1
	5–19	ERTYLVNDKAAKM(Y→H)A	186664	Class II		Yes			D+	1
	15–41	AKM(Y→H)AFTLESVELQQKPVNKDQCPRER	174379	DR4		Yes			D+	1
	64–90	ANEYAYAKWKLCSASAICFIFMIAEVV	174388	DR4		Yes			D+	1
	67–80	YAYAKWKLCSASAI	186722	Class II		Yes			D+	1
	78–104	SAICFIFMIAEVVGGHIAGSLAVVTDA	174730	DR4		Yes			D+	1
	106–132	HLLIDLTSFLLSLFSLWLSSKPPSKRL	174539	DR4		Yes			D+	1
	120–146	SLWLSSKPPSKRLTFGWHRAEILGALL	174745	DR3		Yes			D+	1
	120–146	SLWLSSKPPSKRLTFGWHRAEILGALL	174745	DR4		Yes			D+	1
	124–138	SSKPPSKRLTFGWHR	186707	Class II		Yes			D+	1
	134–174	FGWHRAEILGALLSILCIWVVTGVLVYLACERLLYPDYQIQ	174484	DR3		Yes			D+	1
	134–174	FGWHRAEILGALLSILCIWVVTGVLVYLACERLLYPDYQIQ	174484	DR4		Yes			D+	1
	162–188	ACERLLYPDYQIQATVMIIVSSCAVAA	174364	DR4		Yes			D+	1
	197–223	HQRCLGHNHKEVQANASVRAAFVHALG	174542	DR4		Yes			D+	1
	211–237	NASVRAAFVHALGDLFQSISVLISALI	174667	DR4		Yes			D+	1
	244–258	YKIADPICTFIFSIL	186725	Class II		Yes			D+	1
	253–279	FIFSILVLASTITILKDFSILLMEGVP	174486	DR4		Yes			D+	1
	254–268	IFSILVLASTITILK	186680	Class II		Yes			D+	1
	266–285	ILKDFSILLMEGVPKSLNYS	644825	DR		Yes			C–	1
	267–293	LKDFSILLMEGVPKSLNYSGVKELILA	174637	DR4		Yes			D+	1
	271–283	SILLMEGVPKSLN	138810	DR0401		Yes			D+	1
	295–321	DGVLSVHSLHIWSLTMNQVILSAHVAT	174440	DR4		Yes			D+	1
	309–335	TMNQVILSAHVATAASRDSQVVRREIA	174759	DR4		Yes			D+	1
	323–356	ASRDSQVVRREIAKALSKSFTMHSLTIQMESPVD	174399	DR3		Yes			D+	1
	323–356	ASRDSQVVRREIAKALSKSFTMHSLTIQMESPVD	174399	DR4		Yes			D+	1
	326–340	DSQVVRREIAKALSK	186661	Class II		Yes			D+	1
	330–349	VRREIAKALSKSFTMHSLTI	651976	DR		Yes			C−	1
	352–366	ESPVDQDPDCLFCED	186665	Class II		Yes			D+	1

Antigen (gene)	Position	Sequence	IEDB#^a	MHC	Human islets, pLNs^b	Human blood, spleen^b	HLA-Tg mouse^b	NPP^c	Evidence^d	Reporting articles^e
CHGA (CHGA)	342–355	WSKMDQLAKELTAE	226405	DQ8		Yes		Yes	B+	1
DMK (DMPK)	9–28	RLQQLVLDPGFLGLEPLLDL	138808	DR0401		Yes			C–	1
GAD65 (GAD2)	1–20	MASPGSGFWSFGSEDGSGDS	101054	Class II		Yes			D+	1
	1–20	MASPGSGFWSFGSEDGSGDS	101054	DR0401		Yes			C–	1
	47–66	LLYGDAEKPAESGGSQPPRA	105302	Class II		Yes			D+	1
	73–92	CACDQKPCSCSKVDVNYAFL	142554	DR		Yes			C–	1
	73–92	CACDQKPCSCSKVDVNYAFL	142554	DR0401		Yes			C–	1
	81–100	SCSKVDVNYAFLHATDLLPA	104234	DR		Yes			C–	1
	86–103	DVNYAFLHATDLLPACDG	186992	DR4		Yes			D+	1
	88–99	NYAFLHATDLLP	104163	DR0101		Yes		Yes	A–	3
	88–99	NYAFLHATDLLP	104163	DRB5		Yes			C–	1
	89–108	YAFLHATDLLPACDGE(R→Cit)PTL	230433	DR0401		Yes			C–	1
	101–115	CDGERPTLAFLQDVM	6101	DQ		Yes			D+	1
	105–124	RPTLAFLQDVMNILLQYVVK	143044	DR0401		Yes			C–	1
	108–129	LAFLQDVMNILLQYVVKSFDRS	105275	Class II		Yes			D+	1
	113–132	DVMNILLQYVVKSFDRSTKV	138762	DR0401		Yes		Yes	A–	3
	113–132	DVMNILLQYVVKSFDRSTKV	138762	DR		Yes			C–	1
	113–132	DVMNILLQYVVKSFDRSTKV	138762	DRB4		Yes			D+	1
	115–127	MNILLQYVVKSFD	100311	DR0401	Yes		Yes	Yes	A+	3
	115–127	MNILLQYVVKSFD	100311	Class II		Yes			D+	1
	115–127	MNILL(Q→E)YVVKSFD	230399	DR0401		Yes			C–	1
	115–130	MNILLQYVVKSFDRST	104903	DR0401			Yes	Yes	B	1
	116–129	NILLQYVVKSFDRS	102675	DRB4		Yes			C–	1
	116–127	NILLQYVVKSFD	104150	DRB4		Yes			C–	2
	121–140	YVVKSFDRSTKVIDFHYPNE	102974	DQ8		Yes	Yes	Yes	A–	2
	126–140	FDRSTKVIDFHYPNE	103164	DQ		Yes			D+	1
	146–165	NWELADQPQNLEEILMHCQT	103455	DR1601		Yes		Yes	A–	1
	153–172	P(Q→E)NLEEILMHC(Q→E)TTLKYAIK	230405	DR0401		Yes			C–	1
	157–176	EEILMHCQTTLKYAIKTGHP	105161	Class II		Yes			D+	1
	172–191	KTGHPRYFNQLSTGLDMVGL	105271	Class II		Yes			D+	1
	173–187	TGHPRYFNQLSTGLD	104649	Class II		Yes			D+	1
	174–185	GHPRYFNQLSTG	103219	DR0401		Yes		Yes	A–	1
	175–190	HPRYFNQLSTGLDMVG	187007	DR4		Yes			D+	1
	177–196	RYFNQLSTGLDMVGLAADWL	143056	DR		Yes			C–	1
	200–217	ANTNMFTYEIAPVFVLLE	103808	DR8 or DR9		Yes			C–	1
	201–220	NTNMFTYEIAPVFVLLEYVT	102698	DQ8			Yes	Yes	B–	1
	201–220	NTNMFTYEIAPVFVLLEYVT	102698	DR0401		Yes		Yes	A–	1
	202–221	TNMFTYEIAPVFVLLEYVTL	105004	Class II		Yes			D+	1
	203–226	NMFTYEIAPVFVLLEYVTLKKMRE	187017	DR4		Yes			D+	1
	206–220	TYEIAPVFVLLEYVT	67328	DQ		Yes			D+	1
	209–228	IAPVFVLLEYVTLKKMREII	142728	DRB4		Yes			D+	1
	217–236	EYVTLKKMREIIGWPGGSGD	104481	DR		Yes			C–	1
	225–244	REIIGWPGGSGDGIFSPGGA	143023	DR		Yes			C–	1
	231–250	PGGSGDGIFSPGGAISNMYA	102715	DQ8			Yes	Yes	B–	1
	232–251	GGSGDGIFSPGGAISNMYAM	105216	Class II		Yes			D+	1
	243–267	GAISNMYAMMIARFKMFPEVKEKGM	186999	DR4		Yes			D+	1
	247–266	NMYAMMIARFKMFPEVKEKG	45043	DR3		Yes			C–	1
	247–266	NMYAMMIARFKMFPEVKEKG	45043	Class II		Yes			C–	2
	247–279	NMYAMMIARFKMFPEVKEKGMAALPRLIAFTSE	101931	Class II		Yes			D+	1
	248–257	MYAMMIARFK	104140	DRB5		Yes		Yes	A–	2
	248–259	MYAMMIARFKMF	104141	DR0101		Yes		Yes	A–	1
	249–268	YAMMIARFKMFPEVKEKGMA	143224	DR		Yes			C–	1
	250–266	AMMIARFKMFPEVKEKG	234479	DQ8		Yes			C–	1
	251–270	MMIARFKMFPEVKEKGMAAL	104118	DR12		Yes			C–	1
	252–266	MIARFKMFPEVKEKG	104114	DR0404		Yes			C–	1
	252–266	MIARFKMFPEVKEKG	104114	Class II		Yes			D+	1
	254–276	ARFKMFPEVKEKGMAALPRLIAF	118749	Class II		Yes			D+	1
	260–279	PEVKEKGMAALPRLIAFTSE	105471	Class II		Yes			D+	2
	261–275	EVKEKGMAALPRLIA	186666	Class II		Yes			D+	1
	261–280	EVKEKGMAALPRLIAFTSEH	103893	DQ8		Yes			C–	1
	264–287	EKGMAALPRLIAFTSEHSHFSLKK	186995	DR4		Yes			D+	1
	265–284	KGMAALPRLIAFTSEHSHFS	142811	DR0401		Yes		Yes	A–	2
	265–284	KGMAALP(R→Cit)LIAFTSEHSHFS	230391	DR0401		Yes			C–	2
	265–284	KGMAALPRLIAFTSEHSHFS	142811	DR		Yes			C–	1
	266–285	GMAALPRLIAFTSEHSHFSL	104502	DR0401		Yes			D+	1
	270–283	LPRLIAFTSEHSHF	103379	DR0401		Yes		Yes	A–	2
	270–284	LPRLIAFTSEHSHFS	103380	DRB4		Yes		Yes	A–	1
	270–287	LPRLIAFTSEHSHFSLKK	157610	DR0401		Yes			D+	1
	271–285	PRLIAFTSEHSHFSL	104934	DR0401			Yes	Yes	B	1
	272–283	RLIAFTSEHSHF	103556	DRB4		Yes		Yes	A–	1
	273–292	LIAFTSEHSHFSLKKGAAAL	138782	DR0401		Yes		Yes	A–	3
	273–292	LIAFTSEHSHFSLKKGAAAL	138782	DR		Yes			C–	1
	274–286	IAFTSEHSHFSLK	25275	DR0401	Yes	Yes	Yes	Yes	A+	4
	274–286	IAFTSEHSHFSLK	25275	Class II		Yes			D+	1
	276–284	FTSEHSHFS	231904	DR0404		Yes			C–	1
	289–303	AAALGIGTDSVILIK	130713	Class II		Yes			D+	1
	290–309	AALGIGTDSVILIKCDERGK	104403	Class II		Yes			D+	1
	297–316	DSVILIKCDERGKMIPSDLE	142591	DR0401		Yes			C–	1
	305–324	DERGKMIPSDLERRILEAKQ	105133	DR0401		Yes		Yes	A–	1
	320–339	LEAKQKGFVPFLVSATAGTT	105281	Class II		Yes			D+	1
	321–340	EAKQKGFVPFLVSATAGTTV	103867	DR0401		Yes		Yes	A–	1
	335–352	TAGTTVYGAFDPLLAVAD	226392	DR3		Yes			D+	1
	338–352	TTVYGAFDPLLAVAD	187030	DR4		Yes			D+	1
	353–372	ICKKYKIWMHVDAAWGGGLL	142730	Class II		Yes			C–	1
	353–372	ICKKYKIWMHVDAAWGGGLL	142730	DRB4		Yes			D+	1
	354–372	CKKYKIWMHVDAAWGGGLL	186990	DR4		Yes			D+	1
	356–370	KYKIWMHVDAAWGGG	104868	DR0401			Yes	Yes	B	1
	368–388	GGGLLMSRKHKWKLSGVERAN	103921	DPw2		Yes			C–	1
	369–388	GGLLMSRKHKWKLSGVERAN	142674	DR		Yes			C–	1
	369–392	GGLLMSRKHKWKLSGVERANSVTW	187001	DR4		Yes			D+	1
	376–390	KHKWKLSGVERANSV	104852	DR0401			Yes	Yes	B	1
	377–396	HKWKLSGVERANSVTWNPHK	142717	DR0401		Yes			C–	1
	377–396	HKWKLSGVERANSVTWNPHK	142717	DR		Yes			C–	1
	385–404	ERANSVTWNPHKMMGVPLQC	105169	Class II		Yes			D+	1
	405–424	SALLVREEGLMQNCNQMHAS	187026	DR4		Yes			D+	1
	413–431	GLMQNCNQMHASYLFQQDK	103939	DR0101		Yes			C–	1
	416–435	QNCNQMHASYLFQQDKHYDL	105488	Class II		Yes			D+	1
	431–445	KHYDLSYDTGDKALQ	103306	DQ		Yes			D+	1
	433–452	YDLSYDTGDKALQCGRHVDV	143226	DR0401		Yes		Yes	A–	1
	433–452	YDLSYDTGDKALQCGRHVDV	143226	Class II		Yes			C–	1
	446–466	CGRHVDVFKLWLMWRAKGTTG	105120	Class II		Yes			D+	1
	450–470	VDVFKLWLMWRAKGTTGFEAH	187032	DR4		Yes			D+	1
	461–473	AKGTTGFEAHVDK	103035	DQ		Yes			D+	1
	462–483	KGTTGFEAHVDKCLELAEYLYN	105261	Class II		Yes			D+	1
	471–490	VDKCLELAEYLYNIIKNREG	102882	DQ8			Yes	Yes	B–	1
	473–492	KCLELAEYLYNIIKNREGYE	142807	DR0401		Yes		Yes	A–	1
	479–498	EYLYNIIKNREGYEMVFDGK	105173	Class II		Yes			D+	1
	480–496	YLYNIIKNREGYEMVFD	187035	DR4		Yes			D+	1
	481–495	LYNIIKNREGYEMVF	104898	DR0401			Yes	Yes	B	1
	491–510	YEMVFDGKPQHTNVCFWYIP	104352	DR3		Yes			C–	1
	491–510	YEMVFDGKPQHTNVCFWYIP	104352	DQ5		Yes			C–	1
	493–507	MVFDGKPQHTNVCFW	104575	Class II		Yes			D+	1
	494–513	VFDGKPQHTNVCFWYIPPSL	119539	Class II		Yes			D+	1
	501–520	HTNVCFWYIPPSLRTLEDNE	103978	DR1		Yes			C–	1
	501–520	HTNVCFWYIPPSLRTLEDNE	103978	DR4		Yes			C–	1
	504–518	VCFWYIPPSLRTLED	187031	DR4		Yes			D+	1
	505–519	CFWYIPPSLRTLEDN	101509	Class II		Yes			C–	1
	505–519	CFWYIPPSLRTLEDN	101509	DQ8		Yes			D+	1
	506–518	FWYIPPSLRTLED	103913	Class II		Yes			D+	1
	509–528	IPPSLRTLEDNEERMSRLSK	102537	Class II		Yes			D+	1
	511–525	PSLRTLEDNEERMSR	104602	DR0401			Yes	Yes	B	1
	511–525	PSLRTLEDNEERMSR	104602	DR4		Yes			D+	1
	511–530	PSLRTLEDNEERMSRLSKVA	104189	DR3		Yes			C–	1
	521–535	ERMSRLSKVAPVIKA	101609	Class II		Yes			C–	1
	521–535	ERMSRLSKVAPVIKA	101609	DQ8		Yes			D+	1
	524–543	SRLSKVAPVIKARMMEYGTT	102085	Class II		Yes			D+	2
	529–548	VAPVIKARMMEYGTTMVSYQ	143155	DRB4		Yes			D+	1
	533–547	IKARMMEYGTTMVSY	104522	Class II		Yes			D+	1
	536–550	RMMEYGTTMVSYQPL	103560	DQ		Yes			D+	1
	536–550	RMMEYGTTMVSYQPL	103560	DQ8			Yes		D–	1
	539–558	EYGTTMVSYQPLGDKVNFFR	105172	Class II		Yes			D+	1
	545–564	VSYQPLGDKVNFFRMVISNP	143204	DR0401		Yes		Yes	A–	1
	545–585	VSYQPLGDKVNFFRMVISNPAATHQDIDFLIEEIERLGQDL	102216	Class II		Yes			D+	1
	546–560	SYQPLGDKVNFFRMV	104994	DR0401			Yes	Yes	B	1
	550–570	LGDKVNFFRMVISNPAATHQD	187013	DR4		Yes			D+	1
	551–565	GDKVNFFRMVISNPA	104792	DR0401			Yes	Yes	B	1
	552–572	DKVNFFRMVISNPAATHQDID	119442	DR0401		Yes			C–	1
	553–570	KVNFFRMVISNPAATHQD	102589	DR4		Yes		Yes	A–	1
	553–572	KVNFFRMVISNPAATHQDID	138779	DR0401		Yes		Yes	A–	2
	553–572	KVNFFRMVISNPAATHQDID	138779	Class II		Yes			C–	1
	553–572	KVNFFRMVISNPAATHQDID	138779	DRB4		Yes			D+	1
	553–572	KVNFF(R→Cit)MVISNPAATHQDID	230397	DR0401		Yes			C–	3
	554–573	VNFFRMVISNPAATHQDIDF	119541	Class II		Yes			D+	1
	554–567	VNFFRMVISNPAAT	158453	DR0401		Yes			D+	1
	554–575	VNFFRMVISNPAATHQDIDFLI	226402	DR4		Yes			D+	1
	555–567	NFFRMVISNPAAT	101067	DR0401	Yes	Yes			C+	5
	555–567	NFFRMVISNPAAT	101067	DR0404		Yes			C–	2
	555–567	NFFRMVISNPAAT	101067	DR4		Yes			D+	1
	556–570	FFRMVISNPAATHQD	104775	DR0401			Yes	Yes	B	1
	556–575	FFRMVISNPAATHQDIDFLI	103167	DR0401		Yes		Yes	A–	2
	563–575	NPAATHQDIDFLI	102684	DRB4		Yes		Yes	A–	1
	565–580	AATHQDIDFLIEEIER	104721	DR0401			Yes	Yes	B	1
	566–585	ATHQDIDFLIEEIERLGQDL	103818	Class II		Yes			D+	1
	566–585	ATHQDIDFLIEEIERLGQDL	103818	DRB4		Yes			D+	1
GRP78 (HSPA5)	195–209	VMRIINEPTAAAIAY	546164	DR0401		Yes			D+	1
	195–209	VM(R→Cit)IINEPTAAAIAY	858100	DR0401		Yes			D+	1
	292–305	VEKAK(R→Cit)ALSSQHQA	590605	Class II	Yes				C+	1
	498–512	EVTFEIDVNGILRVT	857879	DR0401		Yes			D+	1
	498–512	EVTFEIDVNGIL(R→Cit)VT	857878	DR0401		Yes			C–	1
	500–514	TFEIDVNGIL(R→Cit)VTAE	858056	DR0401		Yes			D+	1
HSP60 (HSPD1)	31–50	KFGADARALMLQGVDLLADA	79582	Class II		Yes			D+	1
	136–155	NPVEIRRGVMLAVDAVIAEL	102687	Class II		Yes			D+	1
	242–256	AYVLLSEKKISSIQS	114753	DR		Yes			D+	1
	255–275	QSIVPALEIANAHRKPLVIIA	102750	Class II		Yes			D+	1
	280–294	GEALSTLVLNRLKVG	114829	DR		Yes			D+	1
	286–305	LVLNRLKVGLQVVAVKAPGF	40453	Class II		Yes			D+	1
	394–408	LAKLSDGVAVLKVGG	104547	Class II		Yes			D+	1
	436–455	IVLGGGCALLRCIPALDSLT	79579	Class II		Yes			D+	1
	466–485	EIIKRTLKIPAMTIAKNAGV	79540	Class II		Yes			D+	1
	511–530	VNMVEKGIIDPTKVVRTALL	102911	Class II		Yes			D+	1
HSP70 (HSPA1B)	1–20	MAKAAA(I→V)GIDLGTTYSCVGV	102642	Class II		Yes			D+	1
	166–185	GLNVLRIINEPTAAAIAYGL	102794	Class II		Yes			D+	1
	211–230	TIDDGIFEVKATAGDTHLGG	102846	Class II		Yes			D+	1
	226–245	THLGGEDFDNRLVNHFVEEF	102842	Class II		Yes			D+	1
	271–290	KRTLSSSTQASLEIDSLFEG	102579	Class II		Yes			D+	1
	391–410	LLLLDVAPLSLGLETAGGVM	102619	Class II		Yes			D+	1
	421–440	PTKQTQIFTTYSDNQPGVLI	102728	Class II		Yes			D+	1
	497–516	KANKITITNDKGRLSKEEIE	102548	Class II		Yes			D+	1
	512–531	KEEIERMVQEAEKYKAEDEV	102553	Class II		Yes			D+	1
IA-2 (PTPRN)	142–159	LQDIPTGSAPAAQHRLPQ	536828	DQ8 or DQ8-trans		Yes		Yes	B+	1
	197–209	PSLSYEPALLQPY	104603	Class II		Yes			D+	1
	198–216	SLSYEPALL(Q→E)PYLFH(Q→E)FGS	914422	DQ8	Yes	Yes			C+	1
	264–284	LPGPSPAQLFQDSGLLYLAQE	534743	DR4		Yes		Yes	B+	1
	293–311	VPRLPEQGSSSRAEDSPEG	538314	DQ		Yes		Yes	B+	1
	318–333	GDRGEKPASPAVQPDA	535895	DQ		Yes		Yes	B+	1
	319–342	DRGEKPASPAVQPDAALQRLAAVL	534686	DR3		Yes		Yes	B+	1
	449–488	SPLGQSQPTVAGQPSARPAAEEYGYIVTDQKPLSLAAGVK	534789	DR3		Yes		Yes	B+	1
	467–482	AAEEYGYIVTD(Q→E)KPLS	914337	DQ8		Yes			C–	1
	490–502	LEILAEHVHMSSG	104552	Class II		Yes			D+	1
	502–514	GSFINISVVGPAL	104510	Class II		Yes			D+	1
	523–536	QNLSLADVT(Q→E)(Q→E)AGL	914404	DQ8		Yes			C–	1
	545–562	TGL(Q→E)IL(Q→E)TGVG(Q→E)REEAAA	914426	Class II	Yes				C+	1
	545–562	TGL(Q→E)IL(Q→E)TGVG(Q→E)REEAAA	914426	DQ8	Yes	Yes			C+	1
	575–587	RSVLLTLVALAGV	104618	Class II		Yes			D+	1
	601–618	RQHARQQDKERLAALGPE	104966	DQ8			Yes		D–	1
	608–620	DKERLAALGPEGA	910445	Class II		Yes			D+	1
	616–633	GPEGAHGDTTFEYQDLCR	104813	DQ8			Yes		D–	1
	646–663	EGPPEPSRVSSVSSQFSD	104764	DQ8			Yes		D–	1
	654–674	VSSVSSQFSDAAQASPSSHSS	933295	DR4		Yes		Yes	B+	1
	657–674	VSSQFSDAAQASPSSHSS	104677	DR0401		Yes			D+	1
	661–678	FSDAAQASPSSHSSTPSW	104781	DQ8			Yes		D–	1
	685–700	ANMDISTGHMILAYME	105676	DR4		Yes			D+	1
	709–731	LAKEWQALCAYQAEPNTCATAQG	104546	DR0401		Yes		Yes	B+	1
	709–733	LAKEWQALCAYQAEPNTCATAQGEG	874656	DR0401		Yes			D+	1
	709–736	LAKEWQALCAYQAEPNTCATAQGEGNIK	134126	Class II		Yes			D+	2
	713–728	WQALCAYQAEPNTCAT	106189	DR4		Yes			D+	1
	717–729	CAYQAEPNTCATA	104437	Class II		Yes			D+	1
	721–738	AEPNTCATAQGEGNIKKN	104723	DQ8			Yes		D–	1
	745–760	PYDHARIKLKVESSPS	106021	DR4		Yes			D+	1
	751–770	IKLKVESSPSRSDYINASPI	104523	DR0401		Yes			C–	1
	752–775	KLKVESSPSRSDYINASPIIEHDP	134118	Class II		Yes			D+	2
	752–775	KLKVESSPSRSDYINASPIIEHDP	134118	DR4		Yes		Yes	B+	1
	766–783	NASPIIEHDPRMPAYIAT	104909	DQ8			Yes		D–	1
	778–790	PAYIATQGPLSHT	104590	Class II		Yes			D+	1
	787–802	LSHTIADFWQMVWESG	105943	DR4		Yes			D+	1
	793–808	DFWQMVWESGCTVIVM	105709	DR4		Yes			D+	1
	793–817	DFWQMVWESGCTVIVMLTPLVEDGV	233467	Class II		Yes			D+	1
	797–809	MVWESGCTVIVML	910496	Class II		Yes			D+	1
	797–817	MVWESGCTVIVMLTPLVEDGV	104578	DR0401		Yes			D+	1
	799–814	WESGCTVIVMLTPLVE	106184	DR3-DQ2		Yes			D+	1
	799–814	WESGCTVIVMLTPLVE	106184	DR4		Yes			D+	1
	803–815	CTVIVMLTPLVED	104441	Class II		Yes			D+	1
	804–816	TVIVMLTPLVEDG	910528	Class II		Yes			D+	1
	805–817	VIVMLTPLVEDGV	133730	Class II		Yes			C–	1
	805–820	VIVMLTPLVEDGVKQC	106162	DR3-DQ2		Yes			D+	1
	805–820	VIVMLTPLVEDGVKQC	106162	DR4		Yes			D+	1
	826–843	DEGASLYHVYEVNLVSEH	922741	DQ8			Yes		D–	1
	830–842	SLYHVYEVNLVSE	104629	Class II		Yes			D+	1
	831–850	LYHVYEVNLVSEHIWCEDFL	104566	DP0401		Yes			C–	1
	841–856	SEHIWCEDFLVRSFYL	106100	DR3-DQ2		Yes			D+	1
	841–856	SEHIWCEDFLVRSFYL	106100	DR4		Yes			D+	1
	841–860	SEHIWCEDFLVRSFYLKNVQ	104620	DP0401		Yes			C–	1
	841–860	SEHIWCEDFLVRSFYLKNVQ	104620	DR4		Yes			D+	2
	845–860	WCEDFLVRSFYLKNVQ	106182	DR4		Yes			D+	2
	847–862	EDFLVRSFYLKNVQTQ	105741	DR3-DQ2		Yes			D+	1
	847–862	EDFLVRSFYLKNVQTQ	105741	DR4		Yes			D+	1
	853–872	SFYLKNVQTQETRTLTQFHF	134229	DR4		Yes			D+	1
	854–866	FYLKNVQTQETRT	910467	Class II		Yes			D+	1
	854–872	FYLKNVQTQETRTLTQFHF	104493	DR0401		Yes			D+	1
	889–904	DFRRKVNKCYRGRSCP	105708	DR4-DQ8		Yes			D+	1
	918–930	TYILIDMVLNRMA	104662	Class II		Yes			D+	1
	919–934	YILIDMVLNRMAKGVK	106198	DR3-DQ2		Yes			D+	1
	919–934	YILIDMVLNRMAKGVK	106198	DR4		Yes			D+	1
	931–948	KGVKEIDIAATLEHVRDQ	922742	DQ8			Yes		D–	1
	933–945	VKEIDIAATLEHV	910531	Class II		Yes			D+	1
	955–975	SKDQFEFALTAVAEEVNAILK	104626	DR0401		Yes			D+	1
	957–969	DQFEFALTAVAEE	104447	Class II		Yes			D+	1
	959–974	FEFALTAVAEEVNAIL	105774	DR4		Yes			D+	1
	961–979	FALTAVAEEVNAILKALPQ	104772	DQ8			Yes		D–	1
IAPP (IAPP)	65–84	VGSNTYGK(R→Cit)NAVEVLK(R→Cit)EPL	590688	Class II	Yes				C+	1
	65–84	VGSNTYGK(R→Cit)NAVEVLK(R→Cit)EPL	590688	DQ8		Yes			C–	1
ICA69 (ICA1)	36–47	AFIKATGKKEDE	104413	Class II		Yes			D+	1
IGRP (G6PC2)	13–25	QHLQKDYRAYYTF	106039	DR0301		Yes			C–	1
	17–36	KDYRAYYTFLNFMSNVGDPR	138777	DR0401		Yes			D+	1
	23–35	YTFLNFMSNVGDP	106206	DR0401		Yes			C–	2
	177–196	HQVILGVIGGMLVAEAFEHT	644404	Class II		Yes			C–	1
	226–238	RVLNIDLLWSVPI	106096	DR0301		Yes			C–	1
	241–260	KWCANPDWIHIDTTPFAGLV	138780	DR0401		Yes			D+	2
	241–260	KWCANPDWIHIDTTPFAGLV	138780	Class II		Yes			C–	1
	247–259	DWIHIDTTPFAGL	105736	DR0401		Yes			C–	3
	305–324	QLYHFLQIPTHEEHLFYVLS	648592	DR		Yes			C–	1
INS (INS)	1–15 (L1–L15)	MALWMRLLPLLALLA	840899	DQ8			Yes	Yes	B–	1
	1–16 (L1–L16)	MALWMRLLPLLALLAL	103406	Class II		Yes			D+	1
	1–24 (L1–L24)	MALWMRLLPLLALLALWGPDPAAA	105962	DQ8			Yes		D–	1
	1–24 (L1–L24)	MALWMRLLPLLALLALWGPDPAAA	105962	DQ6			Yes		D–	1
	5–20 (L5–L20)	MRLLPLLALLALWGPD	923548	Class II		Yes			D+	1
	8–23 (L8–L23)	LPLLALLALWGPDPAA	840893	DQ8			Yes	Yes	B–	1
	9–24 (L9–L24)	PLLALLALWGPDPAAA	923645	Class II		Yes			D+	1
	9–28 (L9–B4)	PLLALLALWGPDPAAAFVNQ	142953	DRB4		Yes			D+	1
	11–26 (L11–B2)	LALLALWGPDPAAAFV	104548	DR0401			Yes	Yes	B–	1
	13–28 (L13–B4)	LLALWGPDPAAAFVNQ	923488	Class II		Yes			D+	1
	14–33 (L14–B9)	LALWGPDPAAAFVNQHLCGS	105917	DQ8			Yes		D–	1
	14–33 (L14–B9)	LALWGPDPAAAFVNQHLCGS	105917	DQ6			Yes		D–	1
	16–30 (L16–B6)	LWGPDPAAAFVNQHL	933452	DQ8			Yes	Yes	B–	1
	17–24 (L17–24)	WGPDPAAA	103728	DQ8-trans		Yes		Yes	B+	1
	17–32 (L17–B8)	WGPDPAAAFVNQHLCG	923967	Class II		Yes			D+	1
	18–30 (L18–B6)	GPDPAAAFVNQHL	933381	DQ8			Yes	Yes	B–	1
	20–35 (L20–B11)	DPAAAFVNQHLCGSHL	840818	DQ8			Yes	Yes	B–	1
	21–36 (L21–B12)	PAAAFVNQHLCGSHLV	104589	DR0401			Yes	Yes	B–	1
	21–36 (L21–B12)	PAAAFVNQHLCGSHLV	104589	Class II		Yes			D+	1
	25–40 (B1–B16)	FVNQHLCGSHLVEALY	840840	Class II		Yes			D+	2
	25–40 (B1–B16)	FVNQHLCGSHLVEALY	840840	DQ8			Yes	Yes	B–	1
	25–41 (B1–B17)	FVNQHLCGSHLVEALYL	103908	Class II		Yes			D+	1
	30–46 (B6–B22)	LCGSHLVEALYLVCGER	104030	Class II		Yes			D+	1
	30–46 (B6–B22)	LCGSHLVEALYLVCGER	104030	DQ8		Yes			C–	1
	31–47 (B7–B23)	CGSHLVEALYLVCGERG	933280	Class II		Yes			D+	1
	33–47 (B9–B23)	SHLVEALYLVCGERG	58388	DQ8-trans	Yes				C+	1
	33–47 (B9–B23)	SHLVEALYLVCGERG	58388	DQ8	Yes	Yes	Yes	Yes	A+	3
	34–49 (B10–B25)	HLVEALYLVCGERGFF	102517	Class II		Yes			C–	1
	34–53 (B10–B29)	HLVEALYLVCGERGFFYTPK	105241	DQ8			Yes		D–	1
	34–53 (B10–B29)	HLVEALYLVCGERGFFYTPK	105241	DQ6			Yes		D–	1
	35–47 (B11–B23)	LVEALYLVCGERG	104895	DQ8		Yes			C–	1
	35–49 (B11–B25)	LVEALYLVCGERGFF	104062	DQ8	Yes				C+	1
	35–51 (B11–B27)	LVEALYLVCGERGFFYT	103394	DR1601		Yes			C–	1
	35–51 (B11–B27)	LVEALYLVCGERGFFYT	103394	Class II		Yes			D+	2
	37–47 (B13–B23)	EALYLVCGERG	104759	DQ8		Yes			D+	1
	38–54 (B14–B30)	ALYLVCGERGFFYTPKT	933279	Class II		Yes			D+	1
	40–55 (B16–B31)	YLVCGERGFFYTPKTR	840972	DQ8			Yes	Yes	B–	1
	40–56 (B16–B32)	YLVCGERGFFYTPKTRR	923983	Class II		Yes			D+	1
	42–71 (B18–C15)	VCGERGFFYTPKTRREAEDLQVGQVELGGG	105563	Class II		Yes			D+	1
	44–60 (B20–C4)	GERGFFYTPKTRREAED	103917	Class II		Yes			D+	2
	44–63 (B20–C7)	GERGFFYTPKTRREAEDLQV	105818	DQ8			Yes		D–	1
	44–63 (B20–C7)	GERGFFYTPKTRREAEDLQV	105818	DQ6			Yes		D–	1
	45–61 (B21–C5)	ERGFFYTPKTRREAEDL	933281	Class II		Yes			D+	1
	46–61 (B22–C5)	RGFFYTPKTRREAEDL	418483	DQ8			Yes	Yes	B–	1
	48–60 (B24–C4)	FFYTPKTRREAED	103168	DR0301		Yes			D+	1
	48–60 (B24–C4)	FFYTPKTRREAED	103168	Class II		Yes			D+	1
	49–64 (B25–C8)	FYTPKTRREAEDLQVG	102451	Class II		Yes			C–	1
	49–65 (B25–C9)	FYTPKTRREAEDLQVGQ	103191	Class II		Yes			D+	1
	52–68 (B28–C12)	PKTRREAEDLQVGQVEL	933289	Class II		Yes			D+	1
	54–69 (B30–C13)	TRREAEDLQVGQVELG	538096	DQ2/DQ8		Yes			C–	1
	54–69 (B30–C13)	TRREAEDLQVG(Q→E)VELG	910786	DQ2/DQ8		Yes			C–	1
	54–69 (B30–C13)	TRREAEDL(Q→E)VG(Q→E)VELG	910787	DQ2/DQ8		Yes			C–	1
	54–70 (B30–C14)	TRREAEDLQVGQVELGG	104316	Class II		Yes			D+	2
	55–70 (B31–C14)	RREAEDLQVGQVELGG	840928	DQ8			Yes	Yes	B–	1
	57–87 (C1–C31)	EAEDLQVGQVELGGGPGAGSLQPLALEGSLQ	104452	Class II		Yes			D+	1
	57–70 (C1–C14)	EAEDLQVGQVELGG	857864	DQ8		Yes			D+	1
	58–67 (C2–C11)	AEDLQVGQVE	174367	DQ8		Yes			D+	1
	59–74 (C3–C18)	EDLQVGQVELGGGPGA	102379	Class II		Yes			C–	1
	59–75 (C3–C19)	EDLQVGQVELGGGPGAG	103869	Class II		Yes			D+	2
	61–76 (C5–C20)	LQVGQVELGGGPGAGS	840894	DQ8			Yes	Yes	B–	1
	64–76 (C8–C20)	GQVELGGGPGAGS	952145	DQ8		Yes			D+	1
	64–80 (C8–C24)	GQVELGGGPGAGSLQPL	103948	Class II		Yes			D+	2
	64–83 (C8–C27)	GQVELGGGPGAGSLQPLALE	105845	DQ6			Yes		D–	1
	65–73 (C9–C17)	QVELGGGPG	174710	DQ8	Yes				C+	2
	65–75 (C9–C19)	QVELGGGPGAG	858014	DQ8	Yes				C+	2
	66–73 (C10–C17)	VELGGGPG	858095	DQ8	Yes				C+	1
	66–74 (C10–C18)	VELGGGPGA	174788	DQ8	Yes				C+	2
	66–82 (C10–C26)	VELGGGPGAGSLQPLAL	933294	Class II		Yes			D+	1
	69–85 (C13–C29)	GGGPGAGSLQPLALEGS	103922	Class II		Yes			D+	1
	69–88 (C13–C32)	GGGPGAGSLQPLALEGSLQK	134060	DR0401			Yes	Yes	B–	1
	69–88 (C13–C32)	GGGPGAGSLQPLALEGSLQK	134060	Class II		Yes			D+	1
	69–88 (C13–C32)	GGGPGAGSLQPLALEGSLQK	134060	DR4		Yes		Yes	B+	1
	70–86 (C14–C30)	GGPGAGSLQPLALEGSL	103215	DQ8			Yes	Yes	B–	1
	72–83 (C16–C27)	PGAGSLQPLALE	857990	DQ8		Yes			D+	1
	72–86 (C16–C30)	PGAGSLQPLALEGSL	913900	DQ8/DQ8-trans		Yes			D+	1
	73–82 (C17–C26)	GAGSLQPLAL	174496	DQ8-trans		Yes			D+	1
	73–89 (C17–C33)	GAGSLQPLALEGSLQKR	604401	Class II		Yes			D+	1
	73–89 (C17–C33)	GAGSLQPLALEGSLQKR	604401	DQ8-trans	Yes				C+	1
	73–90 (C17–A1)	GAGSLQPLALEGSLQKRG	102454	DR0401		Yes	Yes	Yes	B+	2
	73–92 (C17–A3)	GAGSLQPLALEGSLQKRGIV	138770	DR0401		Yes			D+	1
	74–82 (C18–C26)	AGSLQPLAL	174376	DQ8	Yes				C+	2
	74–83 (C18–C27)	AGSLQPLALE	174377	DQ8	Yes				C+	2
	74–90 (C18–A1)	AGSLQPLALEGSLQKRG	103791	Class II		Yes			D+	2
	74–90 (C18–A1)	AGSLQPLALEGSLQKRG	103791	DR0401		Yes			D+	1
	74–93 (C18–A4)	AGSLQPLALEGSLQKRGIVE	105666	DQ8			Yes		D–	1
	74–93 (C18–A4)	AGSLQPLALEGSLQKRGIVE	105666	DQ6			Yes		D–	1
	75–92 (C19–A3)	GSLQPLALEGSLQKRGIV	104511	DR0401		Yes	Yes	Yes	B+	3
	75–92 (C19–A3)	GSLQPLALEGSLQKRGIV	104511	DR4		Yes		Yes	B+	2
	76–85 (C20–C29)	SLQPLALEGS	174743	DQ8-trans	Yes	Yes			C+	1
	76–86 (C20–C30)	SLQPLALEGSL	858046	DQ8-trans	Yes				C+	2
	76–86 (C20–C30)	SLQPLALEGSL	858046	DR0401		Yes			D+	1
	76–87 (C20–C31)	SLQPLALEGSLQ	858047	DQ2-trans		Yes			D+	1
	76–90 (C20–A1)	SLQPLALEGSLQKRG	101243	DR0401	Yes	Yes			C+	5
	78–94 (C22–A5)	QPLALEGSLQKRGIVEQ	462422	DR0401			Yes	Yes	B–	1
	78–94 (C22–A5)	QPLALEGSLQKRGIVEQ	462422	DR4		Yes		Yes	B+	1
	78–86 (C22–C30)	QPLALEGSL	174706	DQ2		Yes			D+	1
	78–87 (C22–C31)	QPLALEGSLQ	174707	DR0401		Yes			D+	1
	79–95 (C23–A6)	PLALEGSLQKRGIVEQC	104177	Class II		Yes			D+	1
	80–86 (C24–C30)	LALEGSL	857935	DQ2		Yes			D+	1
	80–86 (C24–C30)	LALEGSL	857935	DQ2-trans		Yes			D+	1
	80–86 (C24–C30)	LALEGSL	857935	DQ8		Yes			D+	1
	80–88 (C24–C32)	LALEGSLQK	103335	DR0401		Yes			D+	1
	80–96 (C24–A7)	LALEGSLQKRGIVEQCC	933284	Class II		Yes			D+	1
	80–97 (C24–A8)	LALEGSLQKRGIVEQCCT	840879	DQ8			Yes	Yes	B–	1
	84–100 (C28–A11)	GSLQKRGIVEQCCTSIC	103953	Class II		Yes			D+	2
	85–101 (C29–A12)	SLQKRGIVEQCCTSICS	104628	DR0401			Yes	Yes	B–	1
	87–103 (C31–A14)	QKRGIVEQCCTSICSLY	933290	Class II		Yes			D+	1
	88–102 (C32–A13)	KRGIVEQCCTSICSL	103321	DR4		Yes			C–	1
	90–101 (A1–A12)	GIVEQCCTSICS	104808	DR		Yes			D+	1
	90–101 (A1–A12)	GIVEQCCTSICS	104808	DQ		Yes			D+	1
	90–102 (A1–A13)	GIVEQCCTSICSL (vicinal disulfide 95–96)	910744	DR		Yes			C–	1
	90–104 (A1–A15)	GIVEQCCTSICSLYQ	103926	DR0401	Yes				C+	1
	90–105 (A1–A16)	GIVEQCCTSICSLYQL	923350	Class II		Yes			D+	1
	92–104 (A3–A15)	VEQCCTSICSLYQ	102889	Class II		Yes			D+	1
	92–110 (A3–A21)	VEQCCTSICSLYQLENYCN	840960	DQ8			Yes	Yes	B−	1
	94–105 (A5–A16)	QCCTSICSLYQL	104945	Class II		Yes			D+	1
	94–110 (A5–A21)	QCCTSICSLYQLENYCN	106028	Class II		Yes			D+	1
	94–110 (A5–A21)	QCCTSICSLYQLENYCN	106028	DQ8			Yes		D–	1
	94–110 (A5–A21)	QCCTSICSLYQLENYCN	106028	DQ6			Yes		D–	1
	95–110 (A6–A21)	CCTSICSLYQLENYCN	103824	Class II		Yes			D+	2
	98–110 (A9–A21)	SICSLYQLENYCN	104979	Class II		Yes			D+	1
S100β (S100B)	6–25	KAMVALIDVFHQYSGREGDK	422018	DR0401		Yes		Yes	B+	1
	21–36	REGDKHKLKKSELKEL	422069	DR0401		Yes		Yes	B+	1
	25–46	KHKLKKSELKELINNELSHFLE	422020	DR0401		Yes		Yes	B+	1
	68–92	ECDFQEFMAFVAMVTTACHEFFEHE	421964	DR0401		Yes		Yes	B+	1
ZnT8 (SLC30A8)	1–27	MEFLERTYLVNDKAAKM(Y→H)AFTLESVEL	174655	DR4		Yes			D+	1
	5–19	ERTYLVNDKAAKM(Y→H)A	186664	Class II		Yes			D+	1
	15–41	AKM(Y→H)AFTLESVELQQKPVNKDQCPRER	174379	DR4		Yes			D+	1
	64–90	ANEYAYAKWKLCSASAICFIFMIAEVV	174388	DR4		Yes			D+	1
	67–80	YAYAKWKLCSASAI	186722	Class II		Yes			D+	1
	78–104	SAICFIFMIAEVVGGHIAGSLAVVTDA	174730	DR4		Yes			D+	1
	106–132	HLLIDLTSFLLSLFSLWLSSKPPSKRL	174539	DR4		Yes			D+	1
	120–146	SLWLSSKPPSKRLTFGWHRAEILGALL	174745	DR3		Yes			D+	1
	120–146	SLWLSSKPPSKRLTFGWHRAEILGALL	174745	DR4		Yes			D+	1
	124–138	SSKPPSKRLTFGWHR	186707	Class II		Yes			D+	1
	134–174	FGWHRAEILGALLSILCIWVVTGVLVYLACERLLYPDYQIQ	174484	DR3		Yes			D+	1
	134–174	FGWHRAEILGALLSILCIWVVTGVLVYLACERLLYPDYQIQ	174484	DR4		Yes			D+	1
	162–188	ACERLLYPDYQIQATVMIIVSSCAVAA	174364	DR4		Yes			D+	1
	197–223	HQRCLGHNHKEVQANASVRAAFVHALG	174542	DR4		Yes			D+	1
	211–237	NASVRAAFVHALGDLFQSISVLISALI	174667	DR4		Yes			D+	1
	244–258	YKIADPICTFIFSIL	186725	Class II		Yes			D+	1
	253–279	FIFSILVLASTITILKDFSILLMEGVP	174486	DR4		Yes			D+	1
	254–268	IFSILVLASTITILK	186680	Class II		Yes			D+	1
	266–285	ILKDFSILLMEGVPKSLNYS	644825	DR		Yes			C–	1
	267–293	LKDFSILLMEGVPKSLNYSGVKELILA	174637	DR4		Yes			D+	1
	271–283	SILLMEGVPKSLN	138810	DR0401		Yes			D+	1
	295–321	DGVLSVHSLHIWSLTMNQVILSAHVAT	174440	DR4		Yes			D+	1
	309–335	TMNQVILSAHVATAASRDSQVVRREIA	174759	DR4		Yes			D+	1
	323–356	ASRDSQVVRREIAKALSKSFTMHSLTIQMESPVD	174399	DR3		Yes			D+	1
	323–356	ASRDSQVVRREIAKALSKSFTMHSLTIQMESPVD	174399	DR4		Yes			D+	1
	326–340	DSQVVRREIAKALSK	186661	Class II		Yes			D+	1
	330–349	VRREIAKALSKSFTMHSLTI	651976	DR		Yes			C−	1
	352–366	ESPVDQDPDCLFCED	186665	Class II		Yes			D+	1

Nonconventional epitopes (excluding posttranslational modifications, which are included above)
Epitope type	Epitope source^f	Sequence	IEDB#^a	MHC	Human islets, pLNs^b	Human blood, spleen^b	HLA-Tg mouse^b	NPP^c	Evidence^d	Reporting articlese
INS hybrid	C-pep:INS A	GQVELGGGGIVEQCC	583306	Class II	Yes				C+	1
INS hybrid	C-pep:IAPP2	GQVELGGGNAVEVLK	505706	DQ8 (DR4?)	Yes				C+	2
INS hybrid	C-pep:NP-Y	GQVELGGGSSPETLI	505707	DQ8	Yes				C+	2
INS hybrid	C-pep:IAPP1	GQVELGGGTPIESHQ	583307	(DR4?)	Yes				C+	1

Nonconventional epitopes (excluding posttranslational modifications, which are included above)
Epitope type	Epitope source^f	Sequence	IEDB#^a	MHC	Human islets, pLNs^b	Human blood, spleen^b	HLA-Tg mouse^b	NPP^c	Evidence^d	Reporting articlese
INS hybrid	C-pep:INS A	GQVELGGGGIVEQCC	583306	Class II	Yes				C+	1
INS hybrid	C-pep:IAPP2	GQVELGGGNAVEVLK	505706	DQ8 (DR4?)	Yes				C+	2
INS hybrid	C-pep:NP-Y	GQVELGGGSSPETLI	505707	DQ8	Yes				C+	2
INS hybrid	C-pep:IAPP1	GQVELGGGTPIESHQ	583307	(DR4?)	Yes				C+	1

a

IEDB identifier (www.iedb.org).

b

Yes, T-cell responses observed using the indicated T-cell sources. See Supplementary Table 2 for details.

c

NPP, natural processing/presentation; yes, evidence is available. See Supplementary Table 2 for details.

d

See Fig. 2 for epitope scoring criteria.

e

See Supplementary Table 2 for details.

f

Underlining here and in the sequence column indicates the hybrid peptide extension. IAPP1 and IAPP2 are nonoverlapping regions of IAPP. NP-Y, neuropeptide Y.

HLA Nomenclature

The epitope discovery data covered by this review span many decades of work, diverse HLA-typing methods, and evolving standards for determining and reporting HLA restriction. Consequently, it was not possible for us to use a standardized set of HLA designations. For HLA class I, we consider typing with four-digit resolution to be definitive (e.g., HLA-A*02:01, HLA-B*07:02), with pairing of these chains with β2 microglobulin assumed. Two-digit nomenclature (e.g., HLA-A2, HLA-B15) is used as reported in original data (or to assess HLA coverage in Fig. 3, so that all of the compiled data could be included) and should be inferred to reflect a response with an unknown high-resolution subtyping.

For HLA class II, some assays did not attempt to define an HLA restriction, so these are designated as being “class II” restricted. Other studies used blocking antibodies to partially define an HLA restriction, so these are designated as being DR or DQ restricted (with no specific type or subtype implied). For HLA-DR, we consider typing of the β-chain with four-digit resolution to be definitive (e.g., HLA-DRB1*03:01, HLA-DRB1*04:04), with pairing of these chains to either of the dimorphic α-chains assumed. For convenience, DRB1 proteins are abbreviated DR0301, DR0401, etc. Two-digit nomenclature is always used for the rarely subtyped secondary DR proteins (e.g., HLA-DRB4, HLA-DRB5), for DRB1 restrictions as reported in original data, or to assess HLA coverage (so that all of the compiled data could be included). These designations should be inferred to reflect a response with an unknown high-resolution subtyping. For HLA-DP, definitive restriction would require both an α- and β-chain designated with four-digit resolution, but this was not done in the literature so we adopted a two-digit nomenclature (e.g., DP2), reflecting a response with an unknown α and no known high-resolution subtyping. For HLA-DQ, definitive restriction also requires both an α- and a β-chain designated with four-digit resolution. However, specific α-chain designations are often omitted in the literature. If available, we provide four-digit β-chain resolution (e.g., DQB1*02:01, DQB1*03:02). Pairing of these chains to the disease-associated α-chains (DQA1*05:01 and DQA1*03:01, respectively) is likely but cannot be assumed. When reported as such, we have retained historic serotype designations (e.g., DQ2 or DQ8, respectively, for the above examples) because further assignment was not available. For the few publications specifically addressing the formation of cross-haplotype trans-dimer pairings (e.g., DQ8-trans) as restriction elements, those designations are provided.

Epitope Grading

In development of an epitope scoring, or grading, system, our primary consideration was to devise a set of criteria that would succinctly reflect the current level of confidence that a given epitope is related to type 1 diabetes. While the grading system conveys our perspective on several useful and important criteria for epitope evaluation, we acknowledge the possibility of differing points of view. The key factors that were included in our scoring criteria (Fig. 2) were evidence of natural processing and presentation, the source of T cells used to define the epitope, and the isolation of T cells with confirmed recognition of the corresponding epitope. Natural processing and presentation were considered to be a critical factor for epitope relevance, primarily because, without such evidence, a putative T-cell epitope could be a mimotope peptide rather than a legitimate one. Consequently, evidence of natural processing and presentation was required for an epitope to be included in the upper grading strata (scores of B− or higher). Elution of the peptide from the corresponding HLA class I or class II molecule and identification by mass spectrometry are among the most stringent forms that this evidence could take, with arguably the ideal entry reporting such information for human β-cells and/or islet-associated antigen-presenting cells. However, we permitted processing and presentation evidence to take other less stringent forms as well, including T-cell responses to the protein source of the antigen or antigen-expressing cells and T-cell responses to DNA immunization in HLA-Tg mice. We acknowledge that some of these results are likely to be more reflective of in vivo processing and presentation than others, but weighting them differently would have resulted in an unwieldy grading system. However, to allow investigators to more heavily consider the evidence most relevant for their purposes, in the appropriate column of Supplementary Tables 1 and 2 we include the evidence for natural processing and presentation that supports each epitope.

Figure 2

View large Download slide

T-cell epitope grading rubric. Our epitope scoring criteria include the source of T cells used to define the epitope (human islets/pLNs, human blood/spleen, or HLA-Tg mice), evidence of natural processing/presentation, and the isolation of T cells with confirmed recognition of the corresponding epitope. The figure depicts the minimal criteria that must be met for an epitope to be assigned the corresponding evidence grade, ranging from A+ to D−. Evidence of natural processing/presentation of an epitope may include peptide elution from MHC and identification by mass spectrometry, response to antigen protein or antigen-expressing cells, protein/DNA immunization response in HLA-Tg mice, or in vitro proteasome digestion yielding the correct C-terminus. The T-cell isolation criterion can be fulfilled with the availability of an epitope-reactive T-cell clone, line, or hybridoma or T-cell receptor–transduced T-cell line (of human or mouse origin).

Within the upper (A+ to B−) and lower (C+ to D−) grading strata, the source of T cells used to identify the epitope source was employed to further subdivide epitopes. Common sources of T cells included spleens from HLA-Tg mice, as well as human peripheral blood or, occasionally, spleens. Only a minor proportion of epitopes were identified or validated using human pLN-derived or islet-infiltrating T cells. Confidence was deemed highest for epitopes defined or confirmed using human pLN- or islet-derived T cells, followed by those defined using human peripheral blood or spleen-derived T cells, followed by those defined using HLA-Tg mice. Successful isolation of a T-cell clone, polyclonal line, hybridoma, or T-cell receptor–transduced T-cell line was considered to provide additional confidence; thus, epitopes with such evidence were scored an additional half grade higher than those without. In doing so, we reasoned that a T-cell epitope discovered using peptide/MHC multimers (Mmr) or enzyme-linked immunospot (ELISpot) could be more confidently validated as such with further confirmation by isolation of an epitope-reactive T-cell line or clone, particularly if only very low numbers of reactive cells were observed.

Initial confidence scores were assigned to each epitope on an individual basis for each reference. For epitopes supported by multiple references, these individual scores were then combined into a final overall score that reflected the cumulative level of confidence afforded by available publications as a whole. In some cases, that aggregated score could be considerably higher than any individual score. For example, GAD65 115–127 was reported as a DRB1*04:01 (DR0401)-restricted epitope in multiple studies (with individual scores ranging from B to C+). However, those studies cumulatively documented natural processing and presentation of the epitope, its recognition by human islet-resident T cells, and the isolation of a peptide-reactive hybridoma derived from HLA-Tg mice, resulting in a cumulative score of A+. All the information used to assign a grade is included in Supplementary Tables 1 and 2 and summarized in Tables 1 and 2. The number of publications associated with each epitope was not incorporated into our grading strategy, as doing so would have unfairly disadvantaged those epitopes that were more recently discovered. Nonetheless, we recognize that some may find this metric useful; thus, the number of reporting articles for each epitope is included in Tables 1 and 2, and the PMID number for each article can be found in Supplementary Tables 1 and 2.

CD8⁺ T-Cell Antigens and Epitopes

Although the strongest genetic determinant for susceptibility to type 1 diabetes is the expression of predisposing class II MHC molecules (10), multiple studies have revealed that certain class I MHC alleles, e.g., HLA-A*24:02, -B*39:01, and -B*39:06, also contribute to susceptibility (11). These findings suggest that class I MHC–restricted CD8⁺ T cells are important contributors to β-cell elimination. Consistent with this notion, β-cell–specific CD8⁺ T cells are present in the peripheral blood and islets of patients with type 1 diabetes, with the seminal report of β-cell–specific islet-infiltrating CD8⁺ T cells appearing <10 years ago (12). Furthermore, CD8⁺ T cells specific for peptides derived from the important β-cell antigen preproinsulin (INS) are cytotoxic to human islets (13,14). Preclinical models also provide strong support for the importance of autoreactive CD8⁺ T cells in β-cell demise; e.g., in NOD mice lacking class I MHC expression only on their β-cells, which would prevent their interaction with cytotoxic CD8⁺ T cells, insulitis develops, but the animals are largely protected from hyperglycemia (15). Thus, autoreactive CD8⁺ T cells are now recognized as promising targets for immune intervention strategies, and knowledge of their specificities is of considerable interest and importance.

From our cataloguing of the CD8⁺ T-cell epitopes in type 1 diabetes (Table 1), it can be seen that 16 conventional antigens have been identified to date. Figure 3C reveals that five of these account for the majority of known epitopes: INS, 42 epitopes; zinc transporter 8 (ZnT8), 33; GAD65, 18; insulinoma-associated protein 2 (IA-2), 9; and IGRP, 8. Of these five antigens, IGRP is unique in having first been discovered as relevant to type 1 diabetes from studies in the NOD mouse model of the disease (16), which exemplifies the utility of animal models. Moreover, IGRP is also unique because, contrary to the other major antigens INS, ZnT8, GAD65, and IA-2, anti-IGRP autoantibodies have not been described to date. For the remaining 11 antigens, three or fewer epitopes have been defined in each. However, the majority of these antigens have only recently been discovered.

Figure 3

View large Download slide

HLA restriction and grade and antigen distributions for CD8⁺ and CD4⁺ T-cell epitopes of β-cell antigens. A–C: HLA class I–restricted epitopes. D–F: HLA class II–restricted epitopes. A and D: The HLA restrictions for the 142 CD8⁺ T-cell epitopes in Table 1 and the 143 CD4⁺ T-cell epitopes in Supplementary Table 4 are depicted as pie graphs in A and D, respectively. B and E: The grade distributions of the CD8⁺ T-cell epitopes in Table 1 and the 418 CD4⁺ T-cell epitopes in Table 2 are shown in B and E, respectively. Gray boxes summarize the grading criteria (see Fig. 2). C and F: The antigen sources of the CD8⁺ T-cell epitopes in Table 1 and the CD4⁺ T-cell epitopes in Table 2 are depicted as pie graphs in C and F, respectively. Epitopes arising from nonconventional antigens (bottom portions of Tables 1 and 2) are not included. For the eight antigens that are sources of both CD8⁺ and CD4⁺ T-cell epitopes (i.e., CHGA, GAD65, IA-2, IAPP, IGRP, INS, S100β, and ZnT8), the same color code is used in C and F.

One conclusion is that the known CD8⁺ T-cell epitopes provide only limited MHC coverage (Fig. 3A), with the vast majority of identified peptides being recognized in the context of HLA-A*02:01. This discovery bias stems, in large part, from the high prevalence of this allele among the Caucasian population, which is the most frequently studied. In addition, mice transgenic for HLA-A*02:01 have been available for over two decades (17), and many of the CD8⁺ T-cell epitopes were discovered and/or characterized using this model (Table 1). Despite the fact that HLA-B*39:06 and HLA-A*24:02 are predisposing for type 1 diabetes (11), no type 1 diabetes–related CD8⁺ T-cell epitopes have been reported for HLA-B*39:06, and only a handful are known for HLA-A*24:02, all derived from INS. For provision of broad population coverage, e.g., for T-cell monitoring efforts, which increasingly rely on peptide-MHC Mmr, epitope discovery that targets alleles other than HLA-A*02:01, especially HLA-B*39:06 and HLA-A*24:02, is a pressing need.

CD4⁺ T-Cell Antigens and Epitopes

Several lines of evidence support the importance of CD4⁺ T cells in type 1 diabetes. As mentioned, the disease has an overwhelming genetic association with specific HLA class II haplotypes, implying a role for CD4⁺ T cells in the disease. In addition, the development of type 1 diabetes is often marked by the presence of multiple islet-specific autoantibodies (18). The appearance of these high-affinity antibodies implies that self-reactive CD4⁺ T cells are also activated and provide help to autoreactive B cells. Convincing data from the NOD mouse model demonstrate that H2-A^g7–restricted responses to the INS 33–47 (B9–B23) epitope are crucial for disease development in this model (19); T cells that recognize that epitope were shown to be present in patients with recent-onset type 1 diabetes with frequencies that correlated with insulin autoantibody levels (20). Although CD8⁺ T cells are typically the predominant T-cell population in human insulitis (21), CD4⁺ T cells are also present within islets and a growing subset of HLA class II–restricted epitope specificities that were originally defined in peripheral blood have been shown to be recognized by islet-resident and pLN-derived T cells (21,22). Furthermore, a recent study (23) confirmed previous reports (24,25) that β-cells from the infiltrated islets of donors with type 1 diabetes express HLA class II on their cell surface, supporting the long-debated possibility of direct interactions between CD4⁺ T cells and islets.

A formidable number of studies have applied an array of methods and approaches to identify CD4⁺ T-cell epitopes derived from diabetes-associated antigens (Supplementary Table 2). The earliest of these studies focused on antigens that correspond to the most clearly defined autoantibody targets, i.e., INS, GAD65, and IA-2, and these remain the most extensively studied antigens both in terms of the quantity of individual reports and the number of unique epitopes identified (Table 2 and Fig. 3F). However, additional antigens of interest have emerged over time, including some that were addressed by multiple studies, e.g., ZnT8 and IGRP, and others that are only supported by single references to date, e.g., S100β and heat shock protein 70 (HSP70). We caution that the sizes of the slices in the pie graphs depicted in Fig. 3F (and Fig. 3C also) surely reflect some discovery bias rather than a simple correlation with the importance of each antigen.

A particular challenge for analyzing and compiling CD4⁺ T-cell epitopes is that the HLA class II binding groove readily accommodates peptides with variable lengths (typically 14–21 amino acids). Studies of the class II immunopeptidome indicate that nested sets of related peptides that share a consensus motif, but which have undergone varying degrees of proteolytic processing, decorate the surface of professional antigen-presenting cells (26). Furthermore, the synthetic peptide sets used for epitope discovery efforts by different groups at different times were designed with different lengths and degrees of overlap, leading to the definition of groups of highly similar peptide epitopes. For example, within GAD65 residues 265–292, seven partially overlapping peptides were defined as DR0401–restricted epitopes (Table 3). However, that segment of GAD65 includes only two plausible DR0401-binding motifs, suggesting that some of these peptides share the same minimal epitope. Thus, in order to graphically summarize the HLA restriction for the CD4⁺ T-cell epitopes (Fig. 3D) without overcounting the number of epitopes defined for well-studied HLA alleles, we first constructed an HLA-specific epitope table (Supplementary Table 4) in which we grouped “families” of epitopes into single lines. To achieve this, we sorted entries from Table 2 based on HLA, and those with unknown or ambiguous HLA information were excluded. The IEDB epitope prediction tool (http://tools.iedb.org/mhcii/) (5) was then used to define the most likely core nonamer for each epitope. All lines that shared the same HLA restriction and core nonamer were collapsed into a single line. While acknowledging that amino acids flanking the core peptide may influence T-cell recognition (27), we took this approach because failing to do so would likely overestimate the number of epitopes that have been discovered for well-studied alleles such as DR0401.

Table 3

Groups of overlapping DR0401-restricted GAD65 epitope “families”

Reported epitope	Peptide sequence	Epitope family A	Epitope family B
GAD65 265–284	KGMAALPRLIAFTSEHSHFS
GAD65 266–285	GMAALPRLIAFTSEHSHFSL
GAD65 270–283	LPRLIAFTSEHSHF	(KGMAAL)PRLIAFTSEHSHF(SLKK)
GAD65 270–287	LPRLIAFTSEHSHFSLKK
GAD65 271–285	PRLIAFTSEHSHFSL
GAD65 273–292	LIAFTSEHSHFSLKKGAAAL		(LPRL)IAFTSEHSHFSLK(KGAAAL)
GAD65 274–286	IAFTSEHSHFSLK

Reported epitope	Peptide sequence	Epitope family A	Epitope family B
GAD65 265–284	KGMAALPRLIAFTSEHSHFS
GAD65 266–285	GMAALPRLIAFTSEHSHFSL
GAD65 270–283	LPRLIAFTSEHSHF	(KGMAAL)PRLIAFTSEHSHF(SLKK)
GAD65 270–287	LPRLIAFTSEHSHFSLKK
GAD65 271–285	PRLIAFTSEHSHFSL
GAD65 273–292	LIAFTSEHSHFSLKKGAAAL		(LPRL)IAFTSEHSHFSLK(KGAAAL)
GAD65 274–286	IAFTSEHSHFSLK

Letters in boldface type indicate the amino acids that are shared among epitope family A members. Underlined letters indicate the predicted minimal 9mer for that family. Italicized letters indicate the amino acids that are shared among epitope family B members. Underlined letters indicate the predicted minimal 9mer for that family.

In examination of the HLA class II epitope knowledge accumulated to date, some clear discovery bias is evident. One striking bias is that, even after collapsing of closely related families of epitopes, there is clearly a preferential documentation of HLA-DR4–restricted epitopes (especially the DR0401 subtype) in comparison with HLA-DR3 (Fig. 3D), though both are associated with type 1 diabetes. DQ8 and DQ2 (and the trans-dimers that can form in heterozygous subjects) are also high-risk HLA allotypes, in linkage disequilibrium with DR4 and DR3, respectively. Thus, it is notable that for many antigens, e.g., IGRP and ZnT8, no T-cell epitopes have yet been defined to be recognized in the context of these two HLA molecules or DQ8-trans (α-chain of DQ2 and β-chain of DQ8) and DQ2-trans (α-chain of DQ8 and β-chain of DQ2) (28) (Table 2). In the case of ZnT8, peptide elution and mass spectrometry have suggested some candidates (29). Furthermore, for multiple antigens, including heat shock protein 60 (HSP60), HSP70, and 69-kDa islet cell autoantigen (ICA69), the restricting HLA for all epitopes remains undefined (Table 2). Another crucial gap is the lack of epitope discovery work for the HLA alleles that are associated with susceptibility to type 1 diabetes in non-Caucasian populations, e.g., DRB1*04:05-DQB1*04:01 and DRB1*09:01-DQB1*03:03 in Japanese and Korean populations (30).

CD8⁺ and CD4⁺ T-Cell Epitopes: A Common Need to Improve Their Grades

In addition to an HLA bias for both CD8⁺ and CD4⁺ T-cell epitopes, another gap that emerges from our analysis is a dearth of epitopes with high levels of evidence (Fig. 3B and E). Returning to our epitope scoring criteria (Fig. 2), 41% and 82% of CD8⁺ and CD4⁺ T-cell epitopes, respectively, do not have evidence of natural processing and presentation, relegating these epitopes to the lower strata (grades of C+ or lower) and leaving open the possibility that some of these peptides could be mimotopes rather than disease-associated epitopes. Though beyond the scope of our current efforts, mining of existing (e.g., 31) and future data sets arising from MHC purification followed by peptide elution and sequencing might help to establish natural processing and presentation for some of these epitopes.

Furthermore, while a growing number of specificities have been documented to be present among islet-infiltrating or pLN-derived T cells (8% of the HLA class I–restricted epitopes and 6% of class II), the vast majority of reported epitopes have not, having instead been defined in peripheral blood or HLA-Tg mice (Tables 1 and 2). Although the experimental work required to bridge this knowledge gap is intensive and relies on precious source material, determining which T-cell specificities are found in disease-proximal tissues will be crucial for our understanding of the disease (32).

Despite these limitations, 4 of 142 HLA class I–restricted epitopes earned grades of A+: GAD65 114–123, INS 15–24 (L15–L24), INS 34–42 (B10–B18), and ZnT8 186–194, all recognized by T cells in the context of HLA-A*02:01 (Table 1). Also, 3 of 418 class II–restricted epitopes scored as A+: GAD65 115–127 (DR0401), GAD65 274–286 (DR0401), and INS 33–47 (B9–23) (DQ8). It is noteworthy that, in two instances, there is overlap between the A+ class I and class II epitopes: GAD65 114–123/115–127 and INS 34–42/33–47 (B10–B18/B9–B23).

Emerging Neo-epitopes

In the context of type 1 diabetes, neo-epitopes were first defined as those generated by posttranslational modification of a DNA-encoded antigen, with the first reported modified epitope including an atypical vicinal disulfide modification of insulin and recognized by CD4⁺ T cells (33). Subsequent reports have highlighted additional mechanisms of epitope modification for both CD8⁺ and CD4⁺ T cells, including enzymatic citrullination (by peptidylarginine deiminase enzymes) and deamidation (by tissue transglutaminase) of self-proteins, which are reported to be triggered by endoplasmic reticulum stress in β-cells (34–37). The term “neo-epitopes” has more recently begun to be used to encompass other nonconventional epitopes. In the case of CD4⁺ T cells, these include hybrid insulin peptides (HIPs) that may form within β-cell secretory granules and consist of amino acid stretches from INS and a second protein or a noncontiguous segment of INS (38,39). For CD8⁺ T cells, other nonconventional epitopes include those derived from alternative splicing products (31) or defective ribosomal products (40) and hybrid epitopes potentially resulting from proteasomal splicing of two different regions of a protein (or proteins) (31). The universe of neo-epitopes represents a rapidly developing area of discovery. These developments complicate the landscape of antigens and epitopes but also reveal new mechanisms that may contribute to disease. Posttranslationally modified epitopes are included with conventional ones in Tables 1 and 2, with the posttranslational modifications indicated; other nonconventional epitopes are listed in a separate section of each table.

Discrimination Between Patients With Type 1 Diabetes and Control Subjects

Many studies have compared the ex vivo frequencies of circulating islet-reactive T cells between patients with type 1 diabetes and control subjects. This information is provided in the “Ex vivo type 1 diabetes > controls” columns of Supplementary Tables 1 and 2, in which we evaluated each epitope as enriched (or not) in patients with type 1 diabetes compared with control subjects—but only when this comparison was statistically supported. The control subjects used for nearly all of the studies were healthy donors, as opposed to first-degree relatives of patients with type 1 diabetes. Occasionally, patients with type 2 diabetes were used as control subjects. Overall, for CD8⁺ T cells, several studies are concordant at detecting a frequency difference between donors with type 1 diabetes and control donors for different epitopes when using a functional readout, most often an interferon (IFN)-γ ELISpot assay, for example (41). It is, however, noted that several publications failed to provide statistical evidence, either because they were underpowered or because they did not report statistical analyses. For CD4⁺ T cells, some consensus exists also when nonfunctional HLA class II Mmr assays were used. The agreement is less unanimous for CD8⁺ T cells detected by HLA class I (mostly HLA-A2) Mmr assays. Indeed, Mmr⁺CD8⁺ T cells were often (14,31,42,43), but not invariably (44,45), found at similar frequencies in the peripheral blood of individuals with type 1 diabetes and healthy individuals and have been variably reported to harbor more differentiated effector/memory phenotype in patients with type 1 diabetes (14,44), or a largely naive phenotype irrespective of disease status (31,42). Some islet-reactive CD8⁺ T cells that did not exhibit frequency differences between donors with type 1 diabetes and healthy donors in blood were enriched in the pancreas of donors with type 1 diabetes, suggesting that the fraction actively involved in disease may undergo preferential homing to the target organ (31,42).

Collectively, regarding the discrimination between patients with type 1 diabetes and control subjects, four matters emerge from our analysis. First, different findings were obtained when detecting T cells, notably CD8⁺ T cells, with functional ELISpot assays versus Mmr assays, which may reflect bystander activation or regulatory mechanisms at play in functional assays or a greater sensitivity of functional readouts for detecting low-avidity T cells (46). Second, large variations in the reported frequencies of T cells reactive to the same epitope are noted (likely due in part to different methods and/or variable reagent quality). These variations argue for a pressing need to reach a consensus on more stringent criteria to report T-cell frequencies and phenotype distributions, e.g., avoiding the potential bias of undersampling for these rare populations. Some of the challenges accompanying the standardization of T-cell biomarkers in type 1 diabetes have recently been reviewed (47). Third, different degrees of “benign” islet T-cell autoimmunity (42) seem to exist in individuals without diabetes, calling for efforts to define the features that shape the progression of this sometimes temporary benign state toward type 1 diabetes. Fourth, the analysis of more disease-proximal tissues, i.e., the pancreas and pLNs, adds important information and should be increasingly implemented (32).

Knowledge Gaps and Unmet Needs

Major progress has been made in the past several years to define the target epitopes of islet-reactive T cells (Fig. 1). Besides the obvious merits of improving our understanding of type 1 diabetes pathogenesis, these efforts should continue in order to provide a comprehensive coverage of the overall autoimmune T-cell repertoire of a given individual. It is well established that the detection of multiple autoantibodies, as opposed to a single one, is more predictive of subsequent progression toward clinical type 1 diabetes (stage 3 [48]). Similarly, we may expect that analyzing autoreactive T cells recognizing more antigens rather than just a few may provide better prognostic stratification. In this respect, it will be critical to expand not only the panel of validated epitopes but also their HLA restrictions, as most epitopes already identified are restricted by HLA-A2 or -DR0401 (Fig. 3A and D). Other points for future improvement will be to increase the number of epitopes featuring an A+ level of evidence, as they are still too few at present, and to explore the utility of CD4⁺ versus CD8⁺ T-cell biomarkers (or combinations thereof) according to the application envisaged, as they may provide different and possibly complementary information. We recognize that periodic updates to the information presented here will be needed in the future, not only to add the epitopes that continue to be discovered, but also potentially to revise the epitope grading rubric based on advances in the field. For example, results from the clinic might also be considered for scoring in the future, e.g., the usefulness of an epitope in predicting disease, in measuring progression, or as a peptide therapeutic.

A novel view of type 1 diabetes as a disease continuum starting with β-cell autoimmunity, most commonly measured by autoantibody appearance, has been endorsed by the diabetes community (48). The corollary to this view is that type 1 diabetes prevention efforts should ideally target the underlying, early islet autoimmunity rather than its late consequence, i.e., hyperglycemia. This calls for novel biomarkers—including T-cell biomarkers—that may appear before autoantibodies and predict subsequent seroconversion and disease progression (49). The finding that less than half of patients with diabetes induced by immune checkpoint inhibitors have autoantibodies to GAD65, INS, IA-2, or ZnT8 supports the view that autoantibodies may be a consequence of islet autoimmunity rather than its first manifestation (50). A caveat to this reasoning is that checkpoint inhibitor diabetes remains a new and poorly characterized disease entity; it is possible that the antigens targeted by autoantibodies (and T cells) will differ from the usual suspects. Indeed, like the rare individuals who develop type 1 diabetes despite having protective HLA alleles (51), patients with checkpoint inhibitor diabetes may also offer new insights into important autoantigens in type 1 diabetes and/or alternative pathways of disease development.

The aforementioned knowledge gap about the differential features of islet-reactive T cells between the type 1 diabetes and healthy states (and anywhere in between) will be a priority area for future research. Indeed, defining the molecular switch between “benign” and progressive islet autoimmunity may provide the earliest biomarkers for type 1 diabetes staging and, possibly, new therapeutic targets to maintain or restore the benign state. In this regard, the scarcity of studies analyzing T-cell biomarkers in preclinical, stage 1–2, type 1 diabetes reveals another area for improvement. As many therapeutic strategies target T cells, T cell–based biomarkers are also expected to improve the selection of patients to enroll in clinical trials and their immune monitoring after treatment. Our update and reappraisal of the current state of knowledge regarding the T-cell epitopes of potential relevance to type 1 diabetes should help in the forwarding of each of these objectives.

E.A.J. and R.M. contributed equally to this work.

This article contains supplementary material online at https://doi.org/10.2337/figshare.12179796.

Article Information

Acknowledgments. The authors thank Nima Salimi (IEDB) for assistance with epitope data curation and for working with IEDB staff to ensure that all of the epitopes in this article were assigned identification numbers. The authors appreciate the Immunology of Diabetes Society T Cell Workshop for fostering discussions that launched this epitope reappraisal.

Funding. Work in the laboratory of E.A.J. is supported by grants from JDRF (1-SRA-2017-344-S-B and 2-SRA-2018-551-S-B). Work in the laboratory of R.M. is supported by grants from JDRF (2-SRA-2016-164-Q-R), The Leona M. and Harry B. Helmsley Charitable Trust (1901-03689), Fondation Francophone pour la Recherche sur le Diabète, Agence Nationale de la Recherche (ANR-19-CE15-0014-01), Fondation pour la Recherche Médicale (EQU20193007831), and the Innovative Medicines Initiative 2 Joint Undertaking (INNODIA, 115797), which receives support from the EU Horizon 2020 program, the European Federation of Pharmaceutical Industries and Associations, JDRF, and The Leona M. and Harry B. Helmsley Charitable Trust. Work in the laboratory of S.C.K. is supported by the National Institute of Diabetes and Digestive and Kidney Diseases (UC4 DK116284). S.C.K. is the George F. and Sybil H. Fuller Term Chair in Diabetes. Work in the laboratory of T.P.D. is supported by the National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK120420 and P30 DK020541, which supports the Einstein–Mount Sinai Diabetes Research Center), the National Institute of Allergy and Infectious Diseases (R01 AI123730), and the American Diabetes Association (1-16-IBS-069). T.P.D. is the Diane Belfer, Cypres & Endelson Families Faculty Scholar in Diabetes Research.

Duality of Interest. R.M. holds patents related to some of the antigens reviewed here. No other potential conflicts of interest relevant to this article were reported.

References

1.

Pugliese

A

.

Autoreactive T cells in type 1 diabetes

.

J Clin Invest

2017

;

127

:

2881

–

2891

Google Scholar

Crossref

2.

Di Lorenzo

TP

,

Peakman

M

,

Roep

BO

.

Translational mini-review series on type 1 diabetes: systematic analysis of T cell epitopes in autoimmune diabetes

.

Clin Exp Immunol

2007

;

148

:

1

–

16

Google Scholar

Crossref

3.

James

EA

,

Pietropaolo

M

,

Mamula

MJ

.

Immune recognition of β-cells: neoepitopes as key players in the loss of tolerance

.

Diabetes

2018

;

67

:

1035

–

1042

Google Scholar

Crossref

4.

Kaddis

JS

,

Pugliese

A

,

Atkinson

MA

.

A run on the biobank: what have we learned about type 1 diabetes from the nPOD tissue repository

?

Curr Opin Endocrinol Diabetes Obes

2015

;

22

:

290

–

295

Google Scholar

Crossref

5.

Vita

R

,

Mahajan

S

,

Overton

JA

, et al.

The Immune Epitope Database (IEDB): 2018 update

.

Nucleic Acids Res

2019

;

47

:

D339

–

D343

Google Scholar

Crossref

6.

Uemura

Y

,

Senju

S

,

Maenaka

K

, et al.

Systematic analysis of the combinatorial nature of epitopes recognized by TCR leads to identification of mimicry epitopes for glutamic acid decarboxylase 65-specific TCRs

.

J Immunol

2003

;

170

:

947

–

960

Google Scholar

Crossref

7.

Yang

J

,

Danke

NA

,

Berger

D

, et al.

Islet-specific glucose-6-phosphatase catalytic subunit-related protein-reactive CD4⁺ T cells in human subjects

.

J Immunol

2006

;

176

:

2781

–

2789

Google Scholar

Crossref

8.

Vita

R

,

Vasilevsky

N

,

Bandrowski

A

,

Haendel

M

,

Sette

A

,

Peters

B

.

Reproducibility and conflicts in immune epitope data

.

Immunology

2016

;

147

:

349

–

354

Google Scholar

Crossref

9.

UniProt Consortium

.

UniProt: a worldwide hub of protein knowledge

.

Nucleic Acids Res

2019

;

47

:

D506

–

D515

Crossref

10.

Cucca

F

,

Lampis

R

,

Congia

M

, et al.

A correlation between the relative predisposition of MHC class II alleles to type 1 diabetes and the structure of their proteins

.

Hum Mol Genet

2001

;

10

:

2025

–

2037

Google Scholar

Crossref

11.

Noble

JA

,

Valdes

AM

,

Varney

MD

, et al.;

Type 1 Diabetes Genetics Consortium

.

HLA class I and genetic susceptibility to type 1 diabetes: results from the Type 1 Diabetes Genetics Consortium

.

Diabetes

2010

;

59

:

2972

–

2979

Google Scholar

Crossref

12.

Coppieters

KT

,

Dotta

F

,

Amirian

N

, et al.

Demonstration of islet-autoreactive CD8 T cells in insulitic lesions from recent onset and long-term type 1 diabetes patients

.

J Exp Med

2012

;

209

:

51

–

60

Google Scholar

Crossref

13.

Kronenberg

D

,

Knight

RR

,

Estorninho

M

, et al.

Circulating preproinsulin signal peptide-specific CD8 T cells restricted by the susceptibility molecule HLA-A24 are expanded at onset of type 1 diabetes and kill β-cells

.

Diabetes

2012

;

61

:

1752

–

1759

Google Scholar

Crossref

14.

Skowera

A

,

Ellis

RJ

,

Varela-Calviño

R

, et al.

CTLs are targeted to kill beta cells in patients with type 1 diabetes through recognition of a glucose-regulated preproinsulin epitope

.

J Clin Invest

2008

;

118

:

3390

–

3402

Google Scholar

15.

Hamilton-Williams

EE

,

Palmer

SE

,

Charlton

B

,

Slattery

RM

.

Beta cell MHC class I is a late requirement for diabetes

.

Proc Natl Acad Sci U S A

2003

;

100

:

6688

–

6693

Google Scholar

Crossref

16.

Lieberman

SM

,

Evans

AM

,

Han

B

, et al.

Identification of the β cell antigen targeted by a prevalent population of pathogenic CD8⁺ T cells in autoimmune diabetes

.

Proc Natl Acad Sci U S A

2003

;

100

:

8384

–

8388

Google Scholar

Crossref

17.

Pascolo

S

,

Bervas

N

,

Ure

JM

,

Smith

AG

,

Lemonnier

FA

,

Pérarnau

B

.

HLA-A2.1-restricted education and cytolytic activity of CD8⁺ T lymphocytes from β2 microglobulin (β2m) HLA-A2.1 monochain transgenic H-2D^b β2m double knockout mice

.

J Exp Med

1997

;

185

:

2043

–

2051

Google Scholar

Crossref

18.

Endesfelder

D

,

Zu Castell

W

,

Bonifacio

E

, et al.;

TEDDY Study Group

.

Time-resolved autoantibody profiling facilitates stratification of preclinical type 1 diabetes in children

.

Diabetes

2019

;

68

:

119

–

130

Google Scholar

Crossref

19.

Nakayama

M

,

Abiru

N

,

Moriyama

H

, et al.

Prime role for an insulin epitope in the development of type 1 diabetes in NOD mice

.

Nature

2005

;

435

:

220

–

223

Google Scholar

Crossref

20.

Spanier

JA

,

Sahli

NL

,

Wilson

JC

, et al.

Increased effector memory insulin-specific CD4⁺ T cells correlate with insulin autoantibodies in patients with recent-onset type 1 diabetes

.

Diabetes

2017

;

66

:

3051

–

3060

Google Scholar

Crossref

21.

Babon

JA

,

DeNicola

ME

,

Blodgett

DM

, et al.

Analysis of self-antigen specificity of islet-infiltrating T cells from human donors with type 1 diabetes

.

Nat Med

2016

;

22

:

1482

–

1487

Google Scholar

Crossref

22.

Michels

AW

,

Landry

LG

,

McDaniel

KA

, et al.

Islet-derived CD4 T cells targeting proinsulin in human autoimmune diabetes

.

Diabetes

2017

;

66

:

722

–

734

Google Scholar

Crossref

23.

Russell

MA

,

Redick

SD

,

Blodgett

DM

, et al.

HLA class II antigen processing and presentation pathway components demonstrated by transcriptome and protein analyses of islet β-cells from donors with type 1 diabetes

.

Diabetes

2019

;

68

:

988

–

1001

Google Scholar

Crossref

24.

Bottazzo

GF

,

Dean

BM

,

McNally

JM

,

MacKay

EH

,

Swift

PG

,

Gamble

DR

.

In situ characterization of autoimmune phenomena and expression of HLA molecules in the pancreas in diabetic insulitis

.

N Engl J Med

1985

;

313

:

353

–

360

Google Scholar

Crossref

25.

Foulis

AK

,

Farquharson

MA

.

Aberrant expression of HLA-DR antigens by insulin-containing β-cells in recent-onset type I diabetes mellitus

.

Diabetes

1986

;

35

:

1215

–

1224

Google Scholar

Crossref

26.

Lippolis

JD

,

White

FM

,

Marto

JA

, et al.

Analysis of MHC class II antigen processing by quantitation of peptides that constitute nested sets

.

J Immunol

2002

;

169

:

5089

–

5097

Google Scholar

Crossref

27.

Carson

RT

,

Vignali

KM

,

Woodland

DL

,

Vignali

DA

.

T cell receptor recognition of MHC class II-bound peptide flanking residues enhances immunogenicity and results in altered TCR V region usage

.

Immunity

1997

;

7

:

387

–

399

Google Scholar

Crossref

28.

Eerligh

P

,

van Lummel

M

,

Zaldumbide

A

, et al.

Functional consequences of HLA-DQ8 homozygosity versus heterozygosity for islet autoimmunity in type 1 diabetes

.

Genes Immun

2011

;

12

:

415

–

427

Google Scholar

Crossref

29.

Zhou

Z

,

Reyes-Vargas

E

,

Escobar

H

, et al.

Type 1 diabetes associated HLA-DQ2 and DQ8 molecules are relatively resistant to HLA-DM mediated release of invariant chain-derived CLIP peptides

.

Eur J Immunol

2016

;

46

:

834

–

845

Google Scholar

Crossref

30.

Kawabata

Y

,

Ikegami

H

,

Kawaguchi

Y

, et al.

Asian-specific HLA haplotypes reveal heterogeneity of the contribution of HLA-DR and -DQ haplotypes to susceptibility to type 1 diabetes

.

Diabetes

2002

;

51

:

545

–

551

Google Scholar

Crossref

31.

Gonzalez-Duque

S

,

Azoury

ME

,

Colli

ML

, et al.

Conventional and neo-antigenic peptides presented by β cells are targeted by circulating naive CD8+ T cells in type 1 diabetic and healthy donors

.

Cell Metab

2018

;

28

:

946

–

960.e6

Google Scholar

Crossref

32.

Nakayama

M

,

Michels

AW

.

Determining antigen specificity of human islet infiltrating T cells in type 1 diabetes

.

Front Immunol

2019

;

10

:

365

Google Scholar

Crossref

33.

Mannering

SI

,

Harrison

LC

,

Williamson

NA

, et al.

The insulin A-chain epitope recognized by human T cells is posttranslationally modified

.

J Exp Med

2005

;

202

:

1191

–

1197

Google Scholar

Crossref

34.

Buitinga

M

,

Callebaut

A

,

Marques Câmara Sodré

F

, et al.

Inflammation-induced citrullinated glucose-regulated protein 78 elicits immune responses in human type 1 diabetes

.

Diabetes

2018

;

67

:

2337

–

2348

Google Scholar

Crossref

35.

Marre

ML

,

McGinty

JW

,

Chow

IT

, et al.

Modifying enzymes are elicited by ER stress, generating epitopes that are selectively recognized by CD4⁺ T cells in patients with type 1 diabetes

.

Diabetes

2018

;

67

:

1356

–

1368

Google Scholar

Crossref

36.

Rondas

D

,

Crèvecoeur

I

,

D’Hertog

W

, et al.

Citrullinated glucose-regulated protein 78 is an autoantigen in type 1 diabetes

.

Diabetes

2015

;

64

:

573

–

586

Google Scholar

Crossref

37.

van Lummel

M

,

Duinkerken

G

,

van Veelen

PA

, et al.

Posttranslational modification of HLA-DQ binding islet autoantigens in type 1 diabetes

.

Diabetes

2014

;

63

:

237

–

247

Google Scholar

Crossref

38.

Baker

RL

,

Rihanek

M

,

Hohenstein

AC

, et al.

Hybrid insulin peptides are autoantigens in type 1 diabetes

.

Diabetes

2019

;

68

:

1830

–

1840

Google Scholar

Crossref

39.

Delong

T

,

Wiles

TA

,

Baker

RL

, et al.

Pathogenic CD4 T cells in type 1 diabetes recognize epitopes formed by peptide fusion

.

Science

2016

;

351

:

711

–

714

Google Scholar

Crossref

40.

Kracht

MJ

,

van Lummel

M

,

Nikolic

T

, et al.

Autoimmunity against a defective ribosomal insulin gene product in type 1 diabetes

.

Nat Med

2017

;

23

:

501

–

507

Google Scholar

Crossref

41.

Mallone

R

,

Martinuzzi

E

,

Blancou

P

, et al.

CD8⁺ T-cell responses identify β-cell autoimmunity in human type 1 diabetes

.

Diabetes

2007

;

56

:

613

–

621

Google Scholar

Crossref

42.

Culina

S

,

Lalanne

AI

,

Afonso

G

, et al.

Islet-reactive CD8⁺ T cell frequencies in the pancreas, but not in blood, distinguish type 1 diabetic patients from healthy donors

.

Sci Immunol

2018

;3:

eaao4013

Google Scholar

43.

Wiedeman

AE

,

Muir

VS

,

Rosasco

MG

, et al.

Autoreactive CD8⁺ T cell exhaustion distinguishes subjects with slow type 1 diabetes progression

.

J Clin Invest

2020

;

130

:

480

–

490

Google Scholar

Crossref

44.

Luce

S

,

Lemonnier

F

,

Briand

JP

, et al.

Single insulin-specific CD8⁺ T cells show characteristic gene expression profiles in human type 1 diabetes

.

Diabetes

2011

;

60

:

3289

–

3299

Google Scholar

Crossref

45.

Velthuis

JH

,

Unger

WW

,

Abreu

JR

, et al.

Simultaneous detection of circulating autoreactive CD8⁺ T-cells specific for different islet cell-associated epitopes using combinatorial MHC multimers

.

Diabetes

2010

;

59

:

1721

–

1730

Google Scholar

Crossref

46.

Rius

C

,

Attaf

M

,

Tungatt

K

, et al.

Peptide-MHC class I tetramers can fail to detect relevant functional T cell clonotypes and underestimate antigen-reactive T cell populations

.

J Immunol

2018

;

200

:

2263

–

2279

Google Scholar

Crossref

47.

Ahmed

S

,

Cerosaletti

K

,

James

E

, et al.

Standardizing T-cell biomarkers in type 1 diabetes: challenges and recent advances

.

Diabetes

2019

;

68

:

1366

–

1379

Google Scholar

Crossref

48.

Insel

RA

,

Dunne

JL

,

Atkinson

MA

, et al.

Staging presymptomatic type 1 diabetes: a scientific statement of JDRF, the Endocrine Society, and the American Diabetes Association

.

Diabetes Care

2015

;

38

:

1964

–

1974

Google Scholar

Crossref

49.

Heninger

AK

,

Eugster

A

,

Kuehn

D

, et al.

A divergent population of autoantigen-responsive CD4⁺ T cells in infants prior to β cell autoimmunity

.

Sci Transl Med

2017

;

9

:eaaf8848

Google Scholar

50.

Quandt

Z

,

Young

A

,

Anderson

M

.

Immune checkpoint inhibitor diabetes mellitus: a novel form of autoimmune diabetes

.

Clin Exp Immunol

2020

;

200

:

131

–

140

Google Scholar

Crossref

51.

Graham

J

,

Kockum

I

,

Sanjeevi

CB

, et al.;

Swedish Childhood Diabetes Study Group

.

Negative association between type 1 diabetes and HLA DQB1*0602-DQA1*0102 is attenuated with age at onset

.

Eur J Immunogenet

1999

;

26

:

117

–

127

Google Scholar

2020

Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered. More information is available at https://www.diabetesjournals.org/content/license.

T-Cell Epitopes and Neo-epitopes in Type 1 Diabetes: A Comprehensive Update and Reappraisal

Introduction

Epitope Cataloguing

HLA Nomenclature

Epitope Grading

CD8⁺ T-Cell Antigens and Epitopes

CD4⁺ T-Cell Antigens and Epitopes

CD8⁺ and CD4⁺ T-Cell Epitopes: A Common Need to Improve Their Grades

Emerging Neo-epitopes

Discrimination Between Patients With Type 1 Diabetes and Control Subjects

Knowledge Gaps and Unmet Needs

Article Information

References

Email alerts

Journals

Books

Clinical Compendia

News

Podcasts

Other

About

Resources

T-Cell Epitopes and Neo-epitopes in Type 1 Diabetes: A Comprehensive Update and Reappraisal

Introduction

Epitope Cataloguing

HLA Nomenclature

Epitope Grading

CD8+ T-Cell Antigens and Epitopes

CD4+ T-Cell Antigens and Epitopes

CD8+ and CD4+ T-Cell Epitopes: A Common Need to Improve Their Grades

Emerging Neo-epitopes

Discrimination Between Patients With Type 1 Diabetes and Control Subjects

Knowledge Gaps and Unmet Needs

Article Information

References

Email alerts

Journals

Books

Clinical Compendia

News

Podcasts

Other

About

Resources

This Feature Is Available To Subscribers Only

CD8⁺ T-Cell Antigens and Epitopes

CD4⁺ T-Cell Antigens and Epitopes

CD8⁺ and CD4⁺ T-Cell Epitopes: A Common Need to Improve Their Grades