Immunomodulation combined with antigen therapy holds great promise to arrest autoimmune type 1 diabetes, but clinical translation is hampered by a lack of prognostic biomarkers. Low-dose anti-CD3 plus Lactococcus lactis bacteria secreting proinsulin and IL-10 reversed new-onset disease in nonobese diabetic (NOD) mice, yet some mice were resistant to the therapy. Using miRNA profiling, six miRNAs (i.e., miR-34a-5p, miR-125a-3p, miR-193b-3p, miR-328, miR-365–3p, and miR-671–3p) were identified as differentially expressed in plasma of responder versus nonresponder mice before study entry. After validation and stratification in an independent cohort, plasma miR-193b-3p and miR-365–3p, combined with age and glycemic status at study entry, had the best power to predict, with high sensitivity and specificity, poor response to the therapy. These miRNAs were highly abundant in pancreas-infiltrating neutrophils and basophils with a proinflammatory and activated phenotype. Here, a set of miRNAs and disease-associated parameters are presented as a predictive signature for the L. lactis–based immunotherapy outcome in new-onset type 1 diabetes, hence allowing targeted recruitment of trial participants and accelerated trial execution.

Article Highlights

  • Low-dose anti-CD3 combined with oral gavage of genetically modified Lactococcus lactis bacteria secreting human proinsulin and IL-10 holds great promise to arrest autoimmune type 1 diabetes, but the absence of biomarkers predicting therapeutic success hampers clinical translation.

  • A set of cell-free circulation miRNAs together with age and glycemia at baseline predicts a poor response after L. lactis–based immunotherapy in nonobese mice with new-onset diabetes.

  • Pancreas-infiltrating neutrophils and basophils are identified as potential cellular sources of discovered miRNAs.

  • The prognostic signature could guide targeted recruitment of patients with newly diagnosed type 1 diabetes in clinical trials with the L. lactis–based immunotherapy.

Type 1 diabetes is an autoimmune disease characterized by the selective destruction of the insulin-producing pancreatic β-cells (1). Its heterogeneous presentation and course imply that a “one-size-fits-all” therapy is unlikely to provide the desired cure that can halt disease development in all patients (2). Thus, patient care should shift to precision medicine (3,4), based on the identification of specific patient endotypes with unique genetic, biological, and environmental properties (5).

Immunotherapies targeting T and B cells, using anti-CD3 (i.e., teplizumab and otelixizumab) (68) and anti-CD20 (i.e., rituximab) (9) monoclonal antibodies (mAbs), respectively, demonstrated acceptable safety and efficacy in maintaining functional β-cell mass, albeit temporarily, in patients with newly diagnosed type 1 diabetes. Hence, based on initial positive results, teplizumab (6,10,11), antithymocyte globulin (ATG) (1214), rituximab (9), and abatacept (CTLA4-Ig fusion protein) (15) therapies are further explored in late-stage prediabetes and type 1 diabetes onset, but they still face variable therapeutic outcomes differences in treatment response on an individual basis (16). Furthermore, little information is available on their long-term potential to restore peripheral tolerance or on the type of patient who would benefit most from these therapies.

Combinations of immunotherapies with disease-relevant antigens, delivered via tolerogenic routes, hold the potential of greater disease specificity, lower toxicity, and decreased risk of tumor susceptibility and infections, and are a putative solution for preventing or reversing autoimmunity (17). Our team demonstrated that a short course of low-dose anti-CD3 mAbs combined with an oral delivery of genetically modified Lactococcus lactis bacteria secreting full human proinsulin (PINS) and the anti-inflammatory cytokine IL-10 stably reversed new-onset type 1 diabetes in the nonobese diabetic (NOD) mouse model (1820). Preclinical success was related to glycemic status and insulin autoantibody titer at study entry, but these disease-associated parameters could not entirely identify which mice would respond to the therapy. A first-in-men study with a clinical L. lactis–based product (AG019 ActoBiotics) combined with teplizumab demonstrated stable C-peptide, HbA1c, and insulin-dose adjusted A1c values, in addition to an induction of antigen-specific immune responses in patients with newly diagnosed type 1 diabetes (21). These observations and the need to identify accurately those who will benefit from the treatment and those who will likely not respond underscore the exploration for highly specific biomarkers that can provide information not only on β-cell health and function but also on the complex immune signature at baseline.

miRNAs are evolutionarily conserved, small, noncoding RNA molecules that regulate gene expression at the posttranscriptional level in important cellular processes (2124). miRNAs have been found intracellularly but can also be selectively released from different cell types (25). These extracellular miRNAs can enter the bloodstream either encapsulated in small vesicles (26) or associated to Argonaute 2 complexes (27). They are present in a variety of biological specimens such as peripheral blood, saliva, urine, and feces. These relatively stable molecules hold great potential to be applied to disease diagnosis, monitoring, prognosis, and prediction of therapy response (reviewed by Sebastiani et al. (28)). Notably, certain circulating miRNAs, some of which have been linked to β-cell function and/or glucose homeostasis (reviewed by Dotta et al. (29)), were shown to be dysregulated in plasma or serum from patients with type 1 diabetes (30,31).

In this work, we aimed to identify cell-free circulating miRNAs in plasma of NOD mice with new-onset diabetes at study entry that are able to predict the outcome of the L. lactis–based immunotherapy. We found that an miR-193b-3p and miR-365–3p plasma profile improved the prognostic power of particular clinical parameters for therapeutic benefit. The composite biomarker signature could guide clinical decision-making in patients with newly diagnosed type 1 diabetes as well as accelerate future clinical trial execution.

Animals

Mice were bred and housed according to protocols approved by the KU Leuven Animal Care and Use Committee (Leuven, Belgium; project no. P116/2015 and P068/2019), and experiments complied with the European Union (EU) Directive 2010/63/EU for animal experiments. For details, see the Supplemental Material.

Laboratory Assays and Analyses

Here we briefly describe various assays and analyses we conducted for this study. For additional details, see the Supplemental Material.

Pancreatic islets were isolated from C57BL/6 mice (18–20 weeks old) using intraductal collagenase digestion and then handpicked. Genetically modified L. lactis bacteria secreting the human full PINS antigen and human IL-10 were generated by Precigen ActoBio (Zwijnaarde (Ghent), Belgium) and grown as described (18,19). NOD mice with new-onset diabetes were bled via the submandibular vein and treated for 5 consecutive days with 2.5 μg/d of hamster anti–mouse CD3 mAb (clone 145–2C11; BioXCell, West Lebanon, NH), combined with an oral gavage of L. lactis bacteria secreting human PINS and IL-10 (2 × 109 CFU/d) 5 times per week for 42 days (Fig. 1A).

Figure 1

Glycemic status at disease onset moderately predicts L. lactis–based immunotherapy outcome. A: Experimental design in which NOD mice with new-onset diabetes were treated with a CT consisting of anti-CD3 and genetically modified L. lactis bacteria secreting full human PINS and IL-10. Glycemia was monitored three times per week until 42 days after study entry. B: Percentage of diabetic mice after 42 days of CT treatment, shown as Kaplan-Meier survival curves. White symbols indicate untreated diabetic mice; black symbols indicate mice treated with CT. C: The three curves show the percentage of NOD mice with new-onset diabetes after CT treatment, stratified by sex (left panel), age at disease onset (middle panel), and glycemia at disease onset (right panel). Light and dark symbols indicate male or female mice (left panel), mice < or >16 weeks of age at onset (middle panel), and mice with < or >19.4 mmol/L glycemia at onset, respectively. In all panels, Mantel-Cox log-rank test was used for statistical comparison between groups. *P < 0.05, **P < 0.005, ***P < 0.0005, ****P < 0.0001. hIL, human interleukin; i.v., intravenous; LL, L. lactis; PINS, proinsulin.

Figure 1

Glycemic status at disease onset moderately predicts L. lactis–based immunotherapy outcome. A: Experimental design in which NOD mice with new-onset diabetes were treated with a CT consisting of anti-CD3 and genetically modified L. lactis bacteria secreting full human PINS and IL-10. Glycemia was monitored three times per week until 42 days after study entry. B: Percentage of diabetic mice after 42 days of CT treatment, shown as Kaplan-Meier survival curves. White symbols indicate untreated diabetic mice; black symbols indicate mice treated with CT. C: The three curves show the percentage of NOD mice with new-onset diabetes after CT treatment, stratified by sex (left panel), age at disease onset (middle panel), and glycemia at disease onset (right panel). Light and dark symbols indicate male or female mice (left panel), mice < or >16 weeks of age at onset (middle panel), and mice with < or >19.4 mmol/L glycemia at onset, respectively. In all panels, Mantel-Cox log-rank test was used for statistical comparison between groups. *P < 0.05, **P < 0.005, ***P < 0.0005, ****P < 0.0001. hIL, human interleukin; i.v., intravenous; LL, L. lactis; PINS, proinsulin.

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Total RNA, including miRNAs, was extracted from 50 µL of mouse plasma or from cytokine-treated mouse islets, using an miRNeasy micro kit (Qiagen, Hilden, Germany). For plasma samples, single-assay, stem-loop RT-qPCR was used to validate miRNA expression from TaqMan miRNA array analysis (32).

Single-cell suspensions from NOD pancreas and whole blood were stained and sorted directly into Trizol-LS (Thermo Fisher Scientific, Waltham, MA). Droplet digital PCR (ddPCR) was performed using the QX200 Droplet Digital PCR System (Bio-Rad Laboratories, Hercules, CA) to quantify miR-193b-3p and miRNA-365–3p in flow-sorted immune cells derived from NOD pancreas and whole blood. We performed cellular indexing of transcriptomes and epitopes (CITE) sequencing, as described by Stoeckius et al. (33), with small modifications. Data were analyzed using Seurat, version 4.1.0. To investigate potential relationships between upregulated differentially expressed genes (DEGs) in pancreas-infiltrating neutrophils and basophils, the STRING (version 11.5) tool (https://string-db.org) was used.

Statistical Analysis

All statistical analyses were performed using GraphPad Prism software, version 9.0 (GraphPad, San Diego, CA). For details, see the Supplemental Material.

Data and Resource Availability

All data sets generated and analyzed in this study are available from the corresponding authors on reasonable request. All mouse CITE-sequencing raw data and mouse gene-cell count matrices are deposited at Gene Expression Omnibus (National Center for Biotechnology Information) under accession number GSE214031.

Glycemic Status at Disease Onset Moderately Predicts L. lactis–Based Immunotherapy Response

Based on a large data set of NOD mice with new-onset diabetes (n = 110; Supplementary Table 1) treated with a combination therapy (CT) of low-dose anti–CD3 mAbs (clone 145–2C11) and genetically modified L. lactis bacteria secreting full human PINS and IL-10, we evaluated the influence of sex, age, and glycemic status at disease onset on the responsiveness to the L. lactis–based immunotherapy (Fig. 1A). The CT-treated group had an overall disease remission rate of 45% compared with untreated diabetic controls (P < 0.01) that remained hyperglycemic and were sacrificed on the basis of human end points (Fig. 1B).

NOD mice develop type 1 diabetes with a heterogeneous presentation and course. Mean (±SD) age and glycemia at disease onset were 16 (±3.4) weeks of age (range, 9–27 weeks) and 19.5 (±5.15) mmol/L (range, 11.7–33.3 mmol/L) respectively, in the studied cohort. Based on this information and previous studies (34), we used 16 weeks of age and 19.4 mmol/L blood glycemia as cutoff values to investigate the impact of age and disease presentation at study entry on therapy outcome. Although we found no significant sex- or age-dependent differences in the outcome of the CT response, mice with mild hyperglycemia (<19.4 mmol/L) at disease onset had a superior response to the CT compared with mice with severe hyperglycemia (>19.4 mmol/L; 65% vs. 29% remission, respectively; P < 0.0001)(Fig. 1C). Receiver operating characteristic (ROC) curves compared sensitivity versus specificity for predicting therapy response, with a range of values from age and glycemia, alone or in combination (Supplementary Fig. 1, Supplementary Table 2). Although age at disease onset by itself did not influence therapy outcome, it significantly increased the predictability of therapy response when combined with glycemic status at disease onset (area under the curve [AUC]: 0.8; sensitivity, 64%; specificity, 86%; P < 0.001).

Screening for Candidate Plasma miRNAs Related to Therapy Response

To investigate circulating miRNAs as potential biomarkers to predict responsiveness to the L. lactis–based immunotherapy, we profiled expression values of 378 miRNAs in plasma samples collected at study entry. A detailed work flow depicts the experimental design and data analysis (Supplementary Fig. 2). The initial profiling was carried out using a TaqMan miRNA array on plasma samples obtained from six responder (R) and six nonresponder (NR) mice to the L. lactis–based immunotherapy, with even numbers of mice having mild (<19.4 mmol/L) and severe (>19.4 mmol/L) hyperglycemia at disease onset in each of the outcome groups. Through this analysis, we identified 236 miRNAs that were consistently expressed in at least one group, and we generated a hierarchically clustered heat map. Overall, we did not observe any significant differences in the number of detected miRNAs (Supplementary Fig. 3). Color-scale representation of the expression values allowed us to identify samples characterized by high or low miRNA expression in plasma (Fig. 2A).

Figure 2

Plasma miRNA signature of the L. lactis–based immunotherapy at study entry. A: Hierarchical clustering analysis of miRNA expression using a distance metric based on 1 − the Pearson correlation coefficient. miRNA clusters are reported in rows; samples are reported in columns. B: Volcano plot showing the differential expression of plasma miRNAs between NR and R mice at disease onset. The x axis shows the log-transformed values of fold change, and the y axis shows −log10 transformed values of the P value. Cutoff thresholds of the P value (P < 0.05) and fold change (≥0.7) are depicted by dashed lines. Green dots represent miRNAs that are significantly and differentially expressed with Student t test and Mann-Whitney U test; P < 0.05. C: Validation of differentially expressed miRNAs by stem-loop RT-qPCR in plasma derived from R (black; n = 6) and NR (red; n = 6) mice of the profiling cohort. D: Validation of differentially expressed miRNAs by stem-loop RT-qPCR in plasma derived from R (black; n = 44) and NR (red; n = 54) mice of an independent cohort. E: Prognostic potential of miR-125a-3p represented by ROC curve. C and D: Statistics were performed using Mann-Whitney U test on comparative cycle threshold method (2-ΔCt) values and are expressed as the mean ± SEM. *P < 0.05, **P < 0.005. PRE, pretreatment.

Figure 2

Plasma miRNA signature of the L. lactis–based immunotherapy at study entry. A: Hierarchical clustering analysis of miRNA expression using a distance metric based on 1 − the Pearson correlation coefficient. miRNA clusters are reported in rows; samples are reported in columns. B: Volcano plot showing the differential expression of plasma miRNAs between NR and R mice at disease onset. The x axis shows the log-transformed values of fold change, and the y axis shows −log10 transformed values of the P value. Cutoff thresholds of the P value (P < 0.05) and fold change (≥0.7) are depicted by dashed lines. Green dots represent miRNAs that are significantly and differentially expressed with Student t test and Mann-Whitney U test; P < 0.05. C: Validation of differentially expressed miRNAs by stem-loop RT-qPCR in plasma derived from R (black; n = 6) and NR (red; n = 6) mice of the profiling cohort. D: Validation of differentially expressed miRNAs by stem-loop RT-qPCR in plasma derived from R (black; n = 44) and NR (red; n = 54) mice of an independent cohort. E: Prognostic potential of miR-125a-3p represented by ROC curve. C and D: Statistics were performed using Mann-Whitney U test on comparative cycle threshold method (2-ΔCt) values and are expressed as the mean ± SEM. *P < 0.05, **P < 0.005. PRE, pretreatment.

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A volcano plot depicting differential expression revealed six miRNAs (i.e., miR-34a-5p, miR-125a-3p, miR-193b-3p, miR-328, miR-365–3p, and miR-671–3p) upregulated at study entry in plasma of NR versus R mice in the discovery cohort (Fig. 2B, Supplementary Table 3). Four of the six miRNAs were further confirmed by single-assay stem-loop RT-qPCR (Fig. 2C). Remarkably, these miRNAs were not overexpressed in plasma collected at study entry in NR compared with R mice given anti-CD3 monotherapy (Supplementary Fig. 4).

Validation of miR-34a-5p, miR-125a-3p, miR-193b-3p, and miR-365–3p as Circulating Biomarkers of Therapy Response

Plasma samples collected at study entry from an independent cohort of 54 NR and 44 R mice to the L. lactis–based immunotherapy were used to validate the differentially expressed plasma miRNAs from the discovery phase. miR-125a-3p expression was significantly increased in plasma of NR compared with R mice subjected to the L. lactis–based immunotherapy (Fig. 2D). ROC analysis revealed that miR-125a-3p could predict therapy response (P = 0.02); however, its prognostic power (AUC: 0.6; sensitivity, 65%; specificity, 64%) was inferior to the use of the aforementioned clinical parameters (Fig. 2E).

miR-193b-3p and miR-365–3p Together With Age and Glycemic Status at Study Entry Outperformed in the Prediction of the L. lactis–Based Immunotherapy Response

We hypothesized that a combined signature composed of differentially expressed miRNAs and clinical parameters could improve the prognostic power for therapy response. We stratified mice at study entry on the basis of glycemic status (< or >19.4 mmol/L), age (< or >16 weeks old), or a combination thereof (Fig. 3A), and evaluated miR-34a-5p, miR-125a-3p, miR-193b-3p, and miR-365–3p expression in these subgroups (Supplementary Fig. 5). Although miR-125a-3p in combination with younger age at study entry with or without severe hyperglycemia (Fig. 3B and C) had superior prognostic power for therapy response compared with values obtained in the unstratified group (Fig. 3F and G, Supplementary Table 4), miR-193b-3p and miR-365–3p combined with older age and severe hyperglycemia at study entry (Fig. 3D and E) outperformed all other combinations in predicting poor response to the L. lactis–based immunotherapy (AUC: 0.9; sensitivity, 94%; specificity, 75%) (Fig. 3H–J, Table 1, Supplementary Table 4).

Figure 3

Plasma miR-193b-3p and miR-365–3p overexpression combined with glycemic status and age at study entry as a prognostic signature of the L. lactis–based immunotherapy. A: Stratification of an independent validation cohort by glycemia (< and >19.4 mmol/L) and age (< and >16 weeks) at study entry. BE: miRNAs displaying statistically significant expression in plasma from R (black) compared with NR (red) mice at study entry, stratified by age and glycemia. Results are reported as normalized comparative cycle threshold method (2-ΔCt) values; violin plots with median and quartile values are shown. Statistics were performed using the Mann-Whitney U test. *P < 0.05. ROC curves of (F) miR-125a-3p (<16 weeks of age), (G) miR-125a-3p (<16 weeks of age and >19.4mmol/L glycemia), (H) miR-193b-3p (>19.4 mmol/L glycemia), (I) miR-365–3p (>16 weeks of age and >19.4 mmol/L glycemia), and (J) miR-193b-3p and miR-365–3p in combination (>16 weeks of age and >19.4 mmol/L glycemia). AUC and P values for each ROC curve are provided. P < 0.05.

Figure 3

Plasma miR-193b-3p and miR-365–3p overexpression combined with glycemic status and age at study entry as a prognostic signature of the L. lactis–based immunotherapy. A: Stratification of an independent validation cohort by glycemia (< and >19.4 mmol/L) and age (< and >16 weeks) at study entry. BE: miRNAs displaying statistically significant expression in plasma from R (black) compared with NR (red) mice at study entry, stratified by age and glycemia. Results are reported as normalized comparative cycle threshold method (2-ΔCt) values; violin plots with median and quartile values are shown. Statistics were performed using the Mann-Whitney U test. *P < 0.05. ROC curves of (F) miR-125a-3p (<16 weeks of age), (G) miR-125a-3p (<16 weeks of age and >19.4mmol/L glycemia), (H) miR-193b-3p (>19.4 mmol/L glycemia), (I) miR-365–3p (>16 weeks of age and >19.4 mmol/L glycemia), and (J) miR-193b-3p and miR-365–3p in combination (>16 weeks of age and >19.4 mmol/L glycemia). AUC and P values for each ROC curve are provided. P < 0.05.

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Table 1

ROC curve statistics for each significant biomarker combination, including miRNAs* and clinical parameters reported as dicothomical features

Biomarker combinationSensitivity (%)Specificity (%)Likelihood ratioAUCP value
miR-125a-3p + miR-193b-3p + miR-365, >19.4 mmol/L 62 79 2.9 0.7 0.02 
miR-125a-3p + miR-365–3p, >19.4 mmol/L 64 64 1.8 0.7 0.04 
miR-193b-3p, >19.4 mmol/L 67 71 2.3 0.7 0.03 
miR-193b-3p + miR-365, >19.4 mmol/L 67 64 1.9 0.7 0.04 
miR-125a-3p + miR-193b-3p, >19.4 mmol/L 69 64 1.9 0.7 0.03 
miR-125a-3p + miR-193b-3p, <16 wk, >19.4 mmol/L 74 70 2.5 0.7 0.03 
miR-125a-3p, >19.4 mmol/L, <16 wk 74 80 3.7 0.7 0.03 
miR-125a-3p, <16 wk 76 69 2.4 0.7 0.03 
miR-365–3p, >19.4 mmol/L, >16 wk 88 75 3.5 0.9 0.01 
miR-193b-3p + miR-365–3p, >16 wk, >19.4 mmol/L 94 75 3.8 0.9 0.02 
Biomarker combinationSensitivity (%)Specificity (%)Likelihood ratioAUCP value
miR-125a-3p + miR-193b-3p + miR-365, >19.4 mmol/L 62 79 2.9 0.7 0.02 
miR-125a-3p + miR-365–3p, >19.4 mmol/L 64 64 1.8 0.7 0.04 
miR-193b-3p, >19.4 mmol/L 67 71 2.3 0.7 0.03 
miR-193b-3p + miR-365, >19.4 mmol/L 67 64 1.9 0.7 0.04 
miR-125a-3p + miR-193b-3p, >19.4 mmol/L 69 64 1.9 0.7 0.03 
miR-125a-3p + miR-193b-3p, <16 wk, >19.4 mmol/L 74 70 2.5 0.7 0.03 
miR-125a-3p, >19.4 mmol/L, <16 wk 74 80 3.7 0.7 0.03 
miR-125a-3p, <16 wk 76 69 2.4 0.7 0.03 
miR-365–3p, >19.4 mmol/L, >16 wk 88 75 3.5 0.9 0.01 
miR-193b-3p + miR-365–3p, >16 wk, >19.4 mmol/L 94 75 3.8 0.9 0.02 
*

Namely, miR-125a-3p, miR-193b-3p, and miR-365–3p.

Age and glycemic status at study entry.

Age: <16 wk or >16 wk; glycemia: <19.4 mmol/L or >19.4 mmol/L.

miR-193b-3p and miR-365–3p Are Highly Abundant in Pancreatic-Infiltrating Neutrophils and Basophils at Disease Onset

Because disease severity seemed to influence the response of NOD mice with new-onset diabetes to the L. lactis–based immunotherapy, we hypothesized that miR-193b-3p and miR-365–3p might originate from either the target organ or cells exposed to (or responsible for) disease-relevant inflammation. To investigate the cellular origin of miR-193b-3p and miR-365–3p, we first studied whether they originated from islet cells under inflammatory stress. We measured their expression in wild-type C57BL/6 mouse primary islet cells exposed to a cytokine mix (i.e., IL-1β plus IFN-γ) for 6 or 24 hours. We found no evidence of cytokine-mediated modulation of miR-193b-3p and miR-365–3p expression (Fig. 4A and B), making islet cells unlikely as a cellular source. These data are in line with previous reports on miRNAs expression in murine and human pancreatic islet cells upon cytokine treatment (35,36), which found no relevant changes in miR-193b-3p and miR-365–3p expression.

Figure 4

miR-193b-3p and miR-365–3p expression in different immune cells isolated from peripheral blood and pancreas of NOD mice with new-onset diabetes. Stem-loop RT-qPCR analyses of (A) miR-193b-3p and (B) miR-365–3p in pancreatic islets from C57BL/6 mice with or without IL-1β plus IFN-γ for 6 or 24 h. Data are presented as normalized comparative cycle threshold method (2-ΔCt) values from three independent experiments. The Mann-Whitney U test was used for statistics. *P < 0.05. C and D: ddPCR analyses of miR-193b-3p and miR-365–3p in immune cell subsets sorted from peripheral blood and pancreas of NOD mice with new-onset diabetes (n = 5 to ≤9 mice). Data are presented as box-and-whisker plots and range from the 2.7th to 97.5th percentiles. The median values are displayed. The Wilcoxon test was used. *P < 0.05, **P < 0.005. E: Ranking of miR-193b-3p and miR-365–3p expression in immune cell subsets from blood and pancreas of NOD mice with new-onset diabetes. The z-score ratio between each miRNA and the small nuclear RNA RNU6 is used to calculate the expression values, which range from low (blue) to high (red). cDC, conventional dendritic cell; CTR, control; NK, natural killer.

Figure 4

miR-193b-3p and miR-365–3p expression in different immune cells isolated from peripheral blood and pancreas of NOD mice with new-onset diabetes. Stem-loop RT-qPCR analyses of (A) miR-193b-3p and (B) miR-365–3p in pancreatic islets from C57BL/6 mice with or without IL-1β plus IFN-γ for 6 or 24 h. Data are presented as normalized comparative cycle threshold method (2-ΔCt) values from three independent experiments. The Mann-Whitney U test was used for statistics. *P < 0.05. C and D: ddPCR analyses of miR-193b-3p and miR-365–3p in immune cell subsets sorted from peripheral blood and pancreas of NOD mice with new-onset diabetes (n = 5 to ≤9 mice). Data are presented as box-and-whisker plots and range from the 2.7th to 97.5th percentiles. The median values are displayed. The Wilcoxon test was used. *P < 0.05, **P < 0.005. E: Ranking of miR-193b-3p and miR-365–3p expression in immune cell subsets from blood and pancreas of NOD mice with new-onset diabetes. The z-score ratio between each miRNA and the small nuclear RNA RNU6 is used to calculate the expression values, which range from low (blue) to high (red). cDC, conventional dendritic cell; CTR, control; NK, natural killer.

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To identify potential immune cell subsets that could contribute to the plasma miR-193b-3p and miR-365–3p pool in NOD mice with new-onset diabetes, we sorted by flow cytometry 11 major immune cell subsets (i.e., B cells, T cells, CD4+ T cells, CD8+ T cells, natural killers cells, γδ T cells, monocytes, dendritic cells, neutrophils, basophils, and myeloid cells) (Supplementary Fig. 6AD) from both peripheral blood and pancreas isolated from NOD mice with new-onset diabetes (Supplementary Table 5). miR-193b-3p and miR-365–3p expression values were then studied by ddPCR, measuring absolute copies, and expressing the data as a ratio to the standard small nuclear RNA RNU6 (Supplementary Fig. 7). Comparing the expression values of miR-193b-3p and miR-365–3p between peripheral blood and pancreas for each immune cell subset, we found that both miRNAs were more abundant in basophils infiltrating the pancreas than those isolated from peripheral blood (Fig. 4C and D). Remarkably, the same differential expression was observed in neutrophils for miR-193b-3p (Fig. 4C), whereas a trend was noticeable for miR-365–3p (Fig. 4D). When we ranked the immune cell subsets on the basis of the expression of miR-193b-3p and miR-365–3p in peripheral blood and pancreas, we found that basophils and neutrophils infiltrating the pancreas had the highest expression. Blood-circulating neutrophils also showed the highest expression of miR-365–3p compared with expression values in other immune cell subsets (Fig. 4E). Overall, these data suggest that neutrophils and basophils have the highest expression of miR-193b-3p and miR-365–3p in both peripheral blood and pancreas and that their expression was increased when these two immune cell populations were present in the pancreas compared with those from peripheral blood.

CITE-Sequencing Profiling Establishes Immune Cell Repertoire in Peripheral Blood and Pancreas of New-Onset Diabetic NOD Mice

Because miR-193b-3p and miR-365–3p expression values were increased in pancreas-infiltrating neutrophils and basophils of NOD mice with new-onset diabetes, we used CITE-sequencing technology to further investigate their phenotype and frequency. CITE sequencing enabled us to perform a multimodal immune cell phenotyping by measuring cell surface proteins as well as the entire transcriptome at the single-cell level using a panel of 190 DNA-barcoded antibodies (Supplementary Table 6). This analysis was carried out on FACS-sorted CD45+ leukocytes isolated from peripheral blood and pancreas of four NOD mice with new-onset diabetes (Fig. 5A and B). We obtained a data set of 43,706 cells in total. Unsupervised uniform manifold approximation and projection (UMAP) analyses implemented in the Seurat pipeline were used to identify the major immune cell populations (Fig. 5C). All UMAPs based on RNA and protein showed a clear separation of the identified immune cell types (Supplementary Fig. 8A). The cellular identity of the different clusters was assigned on the basis of the differential expression of hallmark genes and surface proteins (Fig. 5E, Supplementary Fig. 8B, and Supplementary Fig. 9). Most gene–protein combinations had a strong correlation, although some markers (i.e., Ly6G, Itgax, and Fcer1a) showed variable expression in all cell types (Supplementary Fig. 9). The major populations identified were distributed differently in peripheral blood and pancreas. The pancreas was infiltrated primarily by lymphocytes, whereas myeloid-lineage cells predominated peripheral blood (Fig. 5D–F). In fact, the majority of basophils and neutrophils included in the CITE-sequencing analysis were found in peripheral blood rather than in the pancreas of NOD mice with new-onset diabetes. Neutrophils also represent the most abundant peripheral blood–circulating immune cell subset, while basophils contribute to a lesser extent (Fig. 5G).

Figure 5

CITE-sequencing analysis of sorted immune cells isolated from peripheral blood and pancreas of NOD mice with new-onset diabetes. A: Experimental design of CITE sequencing performed on FACS-sorted CD45+ leukocytes from peripheral blood and pancreas of NOD mice with new-onset diabetes (n = 4). B: FACS gating strategy of sorted CD45+ live immune cells used for CITE sequencing. C: Unsupervised UMAP map of 43,706 leukocytes; clusters are color coded to define the different cell types, identified using top variable genes and unsupervised clustering. D: UMAP of total leukocytes and their distribution between the two tissues of origin: blood (red), and pancreas (green). E: UMAP plots showing the expression values of selected hallmark genes (top) and their corresponding surface proteins (antibody-derived tag [ADT]) (bottom) used to identify the cellular identity of the different clusters. F: Bar plots representing, per cell type, the fraction of cells per tissue of origin. G: Box plot showing the frequency of each cell type normalized on total counts of CD45+ leukocytes in blood and pancreas. Mann-Whitney U test was used for statistical comparison. *P < 0.05. cDC, conventional dendritic cell; FSC-A, forward scatter-area; FSC-H, forward scatter-height; NK, natural killer; NKT, natural killer T cell; pDC, plasmacytoid dendritic cell; SSC-A, side scatter-area.

Figure 5

CITE-sequencing analysis of sorted immune cells isolated from peripheral blood and pancreas of NOD mice with new-onset diabetes. A: Experimental design of CITE sequencing performed on FACS-sorted CD45+ leukocytes from peripheral blood and pancreas of NOD mice with new-onset diabetes (n = 4). B: FACS gating strategy of sorted CD45+ live immune cells used for CITE sequencing. C: Unsupervised UMAP map of 43,706 leukocytes; clusters are color coded to define the different cell types, identified using top variable genes and unsupervised clustering. D: UMAP of total leukocytes and their distribution between the two tissues of origin: blood (red), and pancreas (green). E: UMAP plots showing the expression values of selected hallmark genes (top) and their corresponding surface proteins (antibody-derived tag [ADT]) (bottom) used to identify the cellular identity of the different clusters. F: Bar plots representing, per cell type, the fraction of cells per tissue of origin. G: Box plot showing the frequency of each cell type normalized on total counts of CD45+ leukocytes in blood and pancreas. Mann-Whitney U test was used for statistical comparison. *P < 0.05. cDC, conventional dendritic cell; FSC-A, forward scatter-area; FSC-H, forward scatter-height; NK, natural killer; NKT, natural killer T cell; pDC, plasmacytoid dendritic cell; SSC-A, side scatter-area.

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Single-Cell Transcriptomic Analysis Reveals an Inflammatory and Activated Phenotype in Pancreas-Infiltrating Neutrophils and Basophils of New-Onset Diabetic NOD Mice

Using DEG analysis, we further compared the transcriptome profiles of pancreas-infiltrating and blood-circulating neutrophils and basophils of NOD mice with new-onset diabetes. The volcano plots show that many genes in both cell types were upregulated in the pancreas compared with those in the circulation (Fig. 6A and B). According to an in silico coexpression analysis, the majority of these upregulated genes were part of different transcriptional networks of strong protein–protein interactions (PPIs). We found a group of 12 coregulated genes, including the activator protein-1 dimeric transcription factor components (i.e., Jun, Junb, Jund, Fos, and Fosb), members of the dimeric NF-κB signaling pathway (i.e., Nfkbia, Nfkbid, and Nfkbiz), in addition to Zfp36, Egr1, Ier2, and Nr4a1. These transcription factors act as master regulators of inducible gene transcription, modulating inflammatory responses and cell-fate decisions (37). Our data also revealed regulatory networks of the IL-1β signaling pathway in neutrophils and the IL-6 signaling pathway in basophils, both of which are known to be involved in inflammatory processes. Furthermore, neutrophils infiltrating the pancreas expressed high values of Cxcl2, a chemokine known to mediate recruitment and activation of immune cells in inflamed tissues (38). On the other hand, basophils infiltrating the pancreas expressed high values of activation and cytotoxic markers such as CD69 and Gzmb (Fig. 6C and D). A more detailed pathway analysis confirmed that the NF-κB and inflammatory pathways were upregulated in neutrophils and basophils infiltrating the pancreas compared with those in the circulation (Fig. 6E and F). These findings suggest that the plasma values of miR-193b-3p and miR-365–3p may be connected to the inflammatory and activation status of the pancreas-infiltrating granulocytes.

Figure 6

Pancreas infiltrating neutrophils and basophils show an inflammatory and activated gene expression signature. A: Volcano plot showing DEGs comparing pancreas-infiltrating and blood-circulating neutrophils. B: Volcano plot showing DEGs comparing pancreas-infiltrating and blood-circulating basophils. C: STRING PPI network of top upregulated DEGs in pancreas-infiltrating neutrophils. The network contains 42 nodes, 81 edges, a clustering coefficient of 0.499, and enrichment P < 1.0 × 10−16. D: STRING PPI network of top upregulated DEGs in pancreas-infiltrating basophils. The network contains 42 nodes, 97 edges, a clustering coefficient of 0.506, and enrichment P < 1.0 × 10−16. C and D: The STRING software added 10 additional proteins or nodes to show the network around the 32 DEGs used as input. The four different clusters of proteins (red, yellow, green, and blue) were defined on the basis of the K-means parameter. The line thicknesses indicate the confidence in the interaction. hypeR pathway analysis of genes upregulated in pancreas-infiltrating neutrophils (E) and basophils (F). The hallmark gene sets from Molecular Signatures Database were used as reference for the investigation of relevant pathways. A and B: Gray dots on the volcano plots represent P ≥ 0.05 (NS) values; red dots indicate P < 0.05; dark red dots indicate P < 0.05 and absolute log2 fold change ≥0.5. The log-transformed values of fold change are reported on the x axis, and −log10 transformed values of the adjusted P values are shown on the y axis. P values were obtained by Wilcoxon rank sum test and Bonferroni correction (Seurat function “FindMarkers”). C–F: P values of the upregulated DEGs in pancreas-infiltrating neutrophils and basophils were obtained by Wilcoxon rank sum test and Bonferroni correction (Seurat function “FindMarkers”). FDR, false discovery rate; UV, ultraviolet.

Figure 6

Pancreas infiltrating neutrophils and basophils show an inflammatory and activated gene expression signature. A: Volcano plot showing DEGs comparing pancreas-infiltrating and blood-circulating neutrophils. B: Volcano plot showing DEGs comparing pancreas-infiltrating and blood-circulating basophils. C: STRING PPI network of top upregulated DEGs in pancreas-infiltrating neutrophils. The network contains 42 nodes, 81 edges, a clustering coefficient of 0.499, and enrichment P < 1.0 × 10−16. D: STRING PPI network of top upregulated DEGs in pancreas-infiltrating basophils. The network contains 42 nodes, 97 edges, a clustering coefficient of 0.506, and enrichment P < 1.0 × 10−16. C and D: The STRING software added 10 additional proteins or nodes to show the network around the 32 DEGs used as input. The four different clusters of proteins (red, yellow, green, and blue) were defined on the basis of the K-means parameter. The line thicknesses indicate the confidence in the interaction. hypeR pathway analysis of genes upregulated in pancreas-infiltrating neutrophils (E) and basophils (F). The hallmark gene sets from Molecular Signatures Database were used as reference for the investigation of relevant pathways. A and B: Gray dots on the volcano plots represent P ≥ 0.05 (NS) values; red dots indicate P < 0.05; dark red dots indicate P < 0.05 and absolute log2 fold change ≥0.5. The log-transformed values of fold change are reported on the x axis, and −log10 transformed values of the adjusted P values are shown on the y axis. P values were obtained by Wilcoxon rank sum test and Bonferroni correction (Seurat function “FindMarkers”). C–F: P values of the upregulated DEGs in pancreas-infiltrating neutrophils and basophils were obtained by Wilcoxon rank sum test and Bonferroni correction (Seurat function “FindMarkers”). FDR, false discovery rate; UV, ultraviolet.

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Disease-modifying immunotherapies aimed at re-educating the host immune system to peripheral tolerance and maintaining residual functional β-cell mass have the potential to change the course of type 1 diabetes treatment and may offer the long-elusive prospect of a cure. Although single-agent therapies like teplizumab (6,10) and ATG (13) transiently preserved β-cell function in some individuals, most study participants had ongoing β-cell loss, suggesting that tolerance was not reached. The way forward is the rational design of combination therapies that not only improve therapeutic success with minimal toxicity but simultaneously reduce the likelihood of therapy unresponsiveness in an individual patient (39,40). The identification of patient endotypes based on demographic, genetic, histopathological, immune, and metabolic features will most probably accelerate the implementation of precision medicine and can influence trial design and execution (4).

We developed an experimental immunotherapy composed of a short course of low-dose anti-CD3 mAbs with a L. lactis–based delivery of full human PINS and IL-10. This combination therapy stably and permanently reverted new-onset type 1 diabetes in most, although not all, mice (1820). A first-in-human study with the L. lactis–based immunotherapy (ActoBiotics AG019) demonstrated, apart from acceptable safety and tolerability, favorable metabolic and antigen-specific immune responses (41). The next step to human translation is to better select those individuals who are likely to respond. Here, we propose that on top of clinical parameters, cell-free circulating miRNAs may support patient stratification but also accelerate future trial execution.

Previous and current data obtained with the L. lactis–based immunotherapy linked glycemic status at study entry to therapy response (19) but only with moderate sensitivity and specificity (70% and 70%, respectively). Thus, additional prognostic biomarkers are needed to improve patient selection and increase the therapeutic success rate. In the present study, using multiple mouse cohorts and optimized standard operating procedures with different validation and stratification steps (31,42), we uncovered circulating miRNAs differentially expressed between specific subgroups of NR and R mice subjected to the L. lactis–based immunotherapy. Although plasma miR-125a-3p expression could discriminate NR from R mice in both the discovery and validation cohorts, its prognostic power for therapy response was not superior when compared with ROC curves and corresponding AUC values when age and glycemic status at study entry were applied. Several reports highlight the role of miR-125a-3p in T-cell biology (reviewed by Wang et al. (43) and Sun et al. (44)). miR-125–3p was induced and highly expressed in T regulatory cells and not in effector T cells. miR-125–3p might affect effector T-cell differentiation. Hence, miR-125a-3p overexpression in plasma of NR mice remains of interest, especially given the T-cell–directed nature of the immunotherapy, even though its utility as a prognostic biomarker for therapy response was relatively low and outperformed by other biomarker signatures. Indeed, the combination of plasma miR-193b-3p and miR-365–3p overexpression, together with age and glycemic status at study entry, had the best prognostic power for therapy response (AUC: 0.9; sensitivity, 94%; specificity, 75%). Importantly, these observations highlight the importance of integrating multiple omics covariates with disease-associated parameters to obtain a robust therapy response signature. In this regard, consortia like INNODIA already drafted master protocols that, apart from metabolic parameters, integrate multiomics analyses on various biological samples (i.e., blood, urine, and feces) in their upcoming clinical trials with the intention to get a broader picture of the underlying pathological mechanisms in their study participants (45).

Although the role of the miR-125 family in the immune system is well addressed (by Wang et al. (43) and Sun et al. (44)), the putative origin and function of miR-193b-3p and miR-365–3p are less clear. miR-193b-3p and miR-365–3p are transcribed from a highly conserved cluster found on chromosome 16 in all vertebrates (46). Hence, their transcriptional regulation and expression may be controlled by similar mechanisms, and these miRNAs may originate from the same cell type. According to our observations in NOD mice with new-onset diabetes, both miR-193b-3p and miR-365–3p are expressed by neutrophils and basophils. Remarkably, these miRNAs were more abundant in neutrophils and basophils isolated from the pancreas compared with those isolated from peripheral blood. Although the involvement of basophils remains largely understudied in type 1 diabetes, neutrophils have become increasingly recognized key players in the initiation and perpetuation of type 1 diabetes (reviewed by Battaglia (47), Huang et al. (48), and Giovenzana et al. (49)). Some studies described diminished peripheral-blood neutrophil counts coinciding with increased migration of these cells in the pancreas, in at-risk participants and those with type 1 diabetes (50,51), whereas other reports revealed increased, circulating platelet–neutrophil aggregates implicated in innate immune activation and migration, in at-risk children and children with new-onset type 1 diabetes (52). In the present study, broad transcriptomic and proteomic profiling using CITE sequencing of peripheral blood and pancreas-infiltrating immune cells of NOD mice with new-onset diabetes uncovered a mature (i.e., Egr1, Spi1), inflammatory (i.e., IL-1/IL-6, NF-κB family members, MAPK family members), and activated (i.e., Trem1, Gzmb, CD69) phenotype in pancreas-infiltrating neutrophils and basophils at disease onset compared with their circulating counterparts. Furthermore, STRING PPI networks revealed a close interaction between NF-κB, MAPK, and IL-1/IL-6 inflammatory pathways in pancreas-infiltrating granulocytes in NOD mice with new-onset diabetes. Interestingly, a previous study already reported that MAPK and NF-κB signaling pathways contributed to the regulation of miR-365–3p expression (53). Pretreatment with the MAPK/ERK inhibitor U0126 significantly reduced miR-365–3p expression, whereas forced overexpression of the canonical NF-κB family member p65 markedly increased miR-365–3p transcription. Moreover, ample evidence suggests that miR-365–3p is a direct regulator of IL-6 translation, because forced overexpression of miR-365–3p repressed IL-6 protein expression in a dose-dependent manner (53). On the basis of these observations, we speculate that pancreas-infiltrating basophils and neutrophils with a proinflammatory and activated phenotype most probably released miR-193b-3p and miR-365–3p into the circulation in response to MAPK or NF-κB pathway–activating stimuli in the inflammatory milieu of the pancreas. These granulocyte subsets may thus play critical roles in the subsequent response to current immunotherapies in people with type 1 diabetes, underscoring the importance of integrating the identified miRNA profile in future trial design.

Overall, we report in this study a reliable and noninvasive composite biomarker signature for predicting response to the L. lactis–based immunotherapy in new-onset type 1 diabetes. Apart from having a strong prognostic value, this biomarker signature also provides insights into the mechanisms of therapy nonresponsiveness and could be prioritized for individualized clinical decisions for individuals with newly diagnosed type 1 diabetes.

This article contains supplementary material online at https://doi.org/10.2337/figshare.23737335.

G. Sassi, G.L., and G.V. share first authorship. C.G. and G. Sebastiani share senior authorship.

Acknowledgments. The authors thank Marijke Viaene and Jos Laureys for technical assistance, Jeroen Gilis for advice regarding statistical analysis, and Toon Ieven for assisting with blood collection. We also acknowledge Jana Roels, the VIB Single Cell Core Leuven, the VIB Flow Core Ghent, and the VIB Nucleomics Core Leuven for support regarding the single-cell technologies (vib.be/core-facilities). The authors thank the KU Leuven Flow and Mass Cytometry facility. The graphical abstract was created with BioRender.com.

Funding. This work was supported by grants from the Research Foundation Flanders (Fonds Wetenschappelijk Onderzoek [FWO] Vlaanderen, grant G.0C63.19N to C.M. and C.G.; FWO fellowship 1.1A02.20N to S.B.), the KU Leuven (C1/18/006), and by gifts for the Hippo & Friends type 1 diabetes and Carpe Diem funds for diabetes research.

Duality of Interest. No potential conflicts of interest relevant to this article were reported.

Author Contributions. All authors have contributed substantially to this study. G.Sa., G.L., G.V., C.G., and G.Se. designed the experiments. G.Sa., G.L., G.V., A.W., P.L., A.M., G.E.G., S.B., and G.Se. conducted the experiments and performed data analyses. G.Sa., R.S., N.V., and C.G. designed and carried out the bioinformatic analyses. D.E., S.C., and P.R. critically revised the article. G.Sa., C.G., and G.Se. wrote the manuscript. C.G. and G.Se. supervised the experimental design, data analysis and interpretation. C.M., F.D., C.G., and G.Se. revised the manuscript and supervised the study. The manuscript was approved for publication by all authors. G.Se. and C.G. are the guarantors of this work and, as such, had full access to all the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.

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