STROLLO ROCKY (GB)
VINCI CHIARA (GB)
WINYARD PAUL (GB)
UNIV EXETER (GB)
WO2016115253A1 | 2016-07-21 | |||
WO2015023796A2 | 2015-02-19 | |||
WO2016146979A1 | 2016-09-22 | |||
WO2006132530A2 | 2006-12-14 | |||
WO2016146979A1 | 2016-09-22 |
US20140235789A1 | 2014-08-21 | |||
US20060115478A1 | 2006-06-01 | |||
US20210018520A1 | 2021-01-21 |
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CLAIMS 1. A peptide comprising an amino acid sequence selected from the group comprising: (i) SLYQLENYCN (SEQ ID NO: 1) or an oxidised version thereof; (ii) SL-dihydroxyphenylalanine-QLENY-Cysteate-N (SEQ ID NO: 2); (iii) SL-dihydroxyphenylalanine-QLEN-dihydroxyphenylalanine-cysteate-N (SEQ ID NO: 3); (iv) LVEALYLVCGERGFFYTPKT (SEQ ID NO: 4) or an oxidised version thereof; (v) ERGFFYTPKT (SEQ ID NO: 5) or an oxidised version thereof; (vi) ERGYYYTPKT (SEQ ID NO: 6); (vii) ERGYY-dihydroxyphenylalanine-TPKT (SEQ ID NO: 7); (viii) ERGFFYTPKTR (SEQ ID NO: 8) or an oxidised version thereof; (ix) ERGYYYTPKTR (SEQ ID NO: 9); (x) YLVCGERGFF (SEQ ID NO: 10) or an oxidised version thereof; (xi) LVEALYLVCGER (SEQ ID NO: 11) or an oxidised version thereof; and (xii) FVNQHLC (SEQ ID NO: 12) or an oxidised version thereof. 2. A method of diagnosing type 1 diabetes (T1D) in a subject comprising: testing a sample from the subject for the presence or absence of antibodies against one or more peptides as defined in claim 1; wherein the presence of antibodies against one or more peptides as defined in claim 1 in the sample is indicative of T1D in the subject. 3. A method according to claim 2, wherein the sample is tested for the presence or absence of antibodies against at least 2, at least 3, or 4 of the peptides as defined in claim 1. 4. A method according to any one of claims 1 to 3, wherein the sample is blood or serum or plasma. 5. A method according to any one of claims 1 to 4, wherein the presence or absence of antibodies against one or more peptides as defined in claim 1 is determined using an ELISA assay. 6. A method according to any one of claims 1 to 5, wherein the subject has not been diagnosed with diabetes. 7. A method according to any one of claims 1 to 6, wherein the subject has no insulin autoantibodies (IAA), ICA, GADA, IA2A and/or ZnT8A. 8. A method of treating type 1 diabetes (T1D) in a subject in need thereof, comprising: 45 6701955v1 testing a sample from the subject for the presence or absence of antibodies against one or more peptides as defined in claim 1; identifying the presence of antibodies against one or more peptides as defined in claim 1; and administering a therapeutic agent for T1D to the subject. 9. The method of claim 8, wherein the therapeutic agent is insulin, an immunotherapeutic administered as vaccine or an immunosuppressive drug. 10. A method of diagnosing latent autoimmune diabetes in adults (LADA) in a subject comprising: testing a sample from the subject for the presence or absence of antibodies against one or more peptides as defined in claim 1; wherein the presence of antibodies against one or more peptides as defined in claim 1 in the sample is indicative of LADA in the subject. 11. A method according to claim 10, wherein the subject has been diagnosed with type 2 diabetes. 12. A method according to claim 10 or 11, wherein the sample is blood or serum or plasma. 13. A method according to any one of claims 10 to 12, wherein the subject has no IAA, IA2A, GADA, ICA and/or ZnT8A. 14. A method of treating latent autoimmune diabetes in adults (LADA) in a subject in need thereof, comprising: testing a sample from the subject for the presence or absence of antibodies against one or more peptides as defined in claim 1; identifying the presence of antibodies against one or more peptides as defined in claim 1 in the sample; and administering a therapeutic agent for LADA to the subject. 15. The method of claim 14, wherein the therapeutic agent is insulin, an immunotherapeutic administered as vaccine or an immunosuppressive drug. 16. A method of determining the therapeutic effectiveness of a therapeutic agent in treating T1D or LADA in a subject diagnosed with T1D or LADA comprising: i) determining the level of antibodies against one or more peptides as defined in claim 1 in a first sample that has been obtained from a subject prior to administering the therapeutic agent to the subject; 46 6701955v1 ii) determining the level of antibodies against one or more peptides as defined in claim 1 in a second sample that has been obtained from the subject after administering the therapeutic agent to the subject; and iii) comparing the levels of antibodies against one or more peptides as defined in claim 1 between the first and second samples; wherein a decrease in the level of antibodies against one or more peptides as defined in claim 1 in the second sample when compared to the first sample is indicative of therapeutic effectiveness of the therapeutic agent. 17. A method of determining the therapeutic effectiveness of a therapeutic agent in treating T1D or LADA in a subject diagnosed with T1D or LADA comprising: i) obtaining a first sample from the subject; ii) determining the level of antibodies against one or more peptides as defined in claim 1 in the first sample; iii) administering the therapeutic agent to the subject; iv) obtaining a second sample from the subject; v) determining the level of antibodies against one or more peptides as defined in claim 1 in the second sample; and vi) comparing the levels of antibodies against one or more peptides as defined in claim 1 between the first and second samples; wherein a decrease in the level of antibodies against one or more peptides as defined in claim 1 in the second sample when compared to the first sample is indicative of therapeutic effectiveness of the therapeutic agent. 18. The method of claim 17, further comprising the step of administering a therapeutic agent for T1D or LADA to the subject. 19. The method of claim 18, wherein the therapeutic agent is insulin, an immunotherapeutic administered as vaccine or an immunosuppressive drug. 20. A kit for diagnosing T1D or LADA in a subject comprising at least two peptides as defined in claim 1. 21. A method of diagnosing type 1 diabetes (T1D) in a subject comprising: testing a sample from the subject for the presence or absence of T cells that are specific for one or more peptides as defined in claim 1; wherein the presence of T cells that are specific for one or more peptides as defined in claim 1 in the sample is indicative of T1D in the subject. 47 6701955v1 22. A method of treating type 1 diabetes (T1D) in a subject in need thereof, comprising: testing a sample from the subject for the presence or absence of T cells that are specific for one or more peptides as defined in claim 1; identifying the presence of T cells that are specific for one or more peptides as defined in claim 1; and administering a therapeutic agent for T1D to the subject. 23. A method of diagnosing latent autoimmune diabetes in adults (LADA) in a subject comprising: testing a sample from the subject for the presence or absence of T cells that are specific for one or more peptides as defined in claim 1; wherein the presence of T cells that are specific for one or more peptides as defined in claim 1 in the sample is indicative of LADA in the subject. 24. A method of treating latent autoimmune diabetes in adults (LADA) in a subject in need thereof, comprising: testing a sample from the subject for the presence or absence of T cells that are specific for one or more peptides as defined in claim 1; identifying the presence of T cells that are specific for one or more peptides as defined in claim 1 in the sample; and administering a therapeutic agent for LADA to the subject. 25. A method of determining the therapeutic effectiveness of a therapeutic agent in treating T1D or LADA in a subject diagnosed with T1D or LADA comprising: i) determining the level of T cells that are specific for one or more peptides as defined in claim 1 in a first sample that has been obtained from a subject prior to administering the therapeutic agent to the subject; ii) determining the level of T cells that are specific for one or more peptides as defined in claim 1 in a second sample that has been obtained from the subject after administering the therapeutic agent to the subject; and iii) comparing the levels of T cells that are specific for one or more peptides as defined in claim 1 between the first and second samples; wherein a decrease in the level of T cells that are specific for one or more peptides as defined in claim 1 in the second sample when compared to the first sample is indicative of therapeutic effectiveness of the therapeutic agent. 26. A method of determining the therapeutic effectiveness of a therapeutic agent in treating T1D or LADA in a subject diagnosed with T1D or LADA comprising: i) obtaining a first sample from the subject; ii) determining the level of T cells that are specific for one or more peptides as defined in claim 1 in the first sample; 48 6701955v1 iii) administering the therapeutic agent to the subject; iv) obtaining a second sample from the subject; v) determining the level of T cells that are specific for one or more peptides as defined in claim 1 in the second sample; and vi) comparing the levels of T cells that are specific for one or more peptides as defined in claim 1 between the first and second samples; wherein a decrease in the level of T cells that are specific for one or more peptides as defined in claim 1 in the second sample when compared to the first sample is indicative of therapeutic effectiveness of the therapeutic agent. 49 6701955v1 |
Examples Example 1 – Analysis of oxidised insulin fragments by size exclusion chromatography The inventors tested a cohort of patients with T1D early in the onset for their reactivity to both native and oxidised insulin peptides. The later were exposed to reactive oxidants such as hydroxyl radicals ( ^ OH), hypochlorous acid (HOCl), and ribose. The structural modification was then analysed AKTA and mass spectrometry (MS). The inventors have used size exclusion chromatography using the AKTA purifier system (GE healthcare) to monitor the molecular profile of native versus oxidised insulin, collect the various fractions and test their activities by ELISA further to MS analysis. We used Superdex 30 increase 10/30 GE Healthcare that is suitable for detecting low molecular weights of 100-7000 Da (Figure 17). For native insulin, we observed a single peak at around 10ml which corresponded to 5900Da of insulin. Contrastingly, with the ^ OH and HOCl modification, the major native peak corresponding to native insulin disappeared but instead we observed a set of multiple peaks corresponding to small fragment towards the end of the column corresponding to small molecular weight (lower than 3kDa). Fractions correlating from individual peaks were collected for both ELISA. For HOCl insulin we collected fractions corresponding to native insulin fractions B (B10-B12) and the shoulder peak (B9 and B8). For ^ OH insulin we collected: I2, I3, I4, I5, I6, I7, I8, I9, I10, I11, I12, I13, I14, I15, J15, J14, J13, J12, J11, J10, J9, J8, J7, J6, J5 (Figure 17). ELISA showed reactivity to oxidised insulin in fraction B8 which corresponds to the shoulder peak of HOCl but not to fractions B10-B12 of native insulin. For the ^ OH modification, we observed reactivity to all the peaks corresponding to the small molecular weight modified fragments (Figure 17). Example 2 – Analysis of oxidised insulin fragments by mass spectrometry AKTA collected fractions that showed reactivity in ELISA were dried down and resuspended in around 30µl of 0.1% formic acid. The fractions were then analysed by LC-MS/MS (Orbitrap Velos, Thermo Scientific) at the Cambridge university UK core facility. The analysis has been more complex than we first anticipated due to the fact that ^ OH oxidation resulted in cleaved peptides that are relatively small and produce singly charged ions which are not ordinarily selected for MS/MS in a typical proteomic experiment. Secondly, the lack of specificity of the cleavage point makes the database searching more challenging. In a typical proteomic experiment, proteins are digested with specific enzymes such as trypsin and so the peptide cleavage sites are very well defined but in the current experiment, we are relying on the breakdown of the protein due to oxidation, which is a much more random. We are pleased to report that we found a way to overcome the problems and that the amino acid sequence of the active peaks following ^ OH modification, J12-14, I12-I14 and J9-J11 is ERGFFYTPKTR (SEQ ID NO: 8). Additional sequence that was identified with less hits and scoring is AAFVNQHLC (SEQ ID NO: 22). The amino acid sequence ERGFFYTPKTR (SEQ ID NO: 8) is at the C terminus end of the beta chain while AAFVNQHLC (SEQ ID NO: 22) is at the N terminus of beta chain. Additional AKTA fractionation and MS analysis identified in addition peptides from the beta chain that included; YLVCGERGFF (SEQ ID NO: 10); LVEALYLVCGER (SEQ ID NO: 11); and LVEALYLVCGERGFFYTPKT (SEQ ID NO: 4). One peptide was identified from the alpha chain: SLYQLENYCN (SEQ ID NO: 1). In total MS identified 6 peptides: (a) YLVCGERGFF (Peptide 1) (SEQ ID NO: 10); (b) LVEALYLVCGER (Peptide 2) (SEQ ID NO: 11); (c) SLYQLENYCN (Peptide 3) (SEQ ID NO: 1); (d) LVEALYLVCGERGFFYTPKT (Peptide 4) (SEQ ID NO: 4); (e) FVNQHLC (Peptide 5) (SEQ ID NO: 12); and (f) ERGFFYTPKT (Peptide 6) (SEQ ID NO: 5). The location of these peptides in the insulin amino acid sequence is shown in Figure 8. Example 3 - Antibody binding to native and oxidised peptides in sera from subjects with T1D. A competitive displacement assay was performed to map the exact epitope, namely the exact amino acid sequence binding specificities and to test the binding to native peptides versus oxidised insulin peptides. The binding to the peptide was done by direct ELISA on the native or modified peptides or by competition ELISA. Initially native synthetic peptide was oxidised by exposing to 0.05 mM CuCl2; 90 mM H2O2; 10 mM NaOCl. Native and modified peptides were fractionated by AKTA to evaluated changes in molecular profile. AKTA fractions were then tested by ELISA for reactivity (Figures 2 and 3). We next perform competition ELISA with the native peptides and peptides exposed to 0.05 mM CuCl 2 ; 90 mM H 2 O 2 ; 10 mM NaOCl. Serum samples were pre-incubated with either native insulin peptides or oxidised insulin peptides. Finally, based on the amino acid sequence of the identified peptides we predicted the amino acids that would be oxidised by ^ OH and HOCl and designed synthetic peptides that contain the oxidised amino acids in the synthesis. Synthetic peptides were produced by standard commercially available methods, specifically by Peptide Protein Research Ltd. Briefly, peptide synthesis was performed by automated solid phase peptide synthesis (SPPS), which was followed by purification. Each individual amino acid was added to the growing chain according to the sequence. Where specified, dihydroxyphenylalanine was added to replace Tyr or cysteate were added to replace Cys. Similarly, these peptides were tested by competition ELISA. The table below describe the different competition ELISA performed: Serum samples from children with type 1 diabetes were pre-incubated with the synthetic peptides before they were added to the native insulin or oxidised that were previously coated on the ELISA plate. If the antibodies in the serum sample bind to the peptide they will no longer bind to the insulin or oxidised insulin on the plate-competition ELISA. 1:200 dilutions of serum samples from T1D serum samples were pre- incubated for 2 hr at room temperature with the various peptides as shown in the table above. After incubation, serum/peptide mix was added to the ELISA plate previously coated overnight with either native insulin or oxidised insulin for an additional 2 hr incubation. Plates were then washed in a plate washer three times with PBS 0.05% tween. After washing, 100 ul of anti-human IgG diluted 1:1000 in 1% milk-PBS 0.05% tween were added for additional 1 hour and 30 min incubation. After washing, ELISA was developed by adding 100 ul of TMB (10 mg/ml in DMSO) in 10 ml of 0.1 M sodium acetate plus 2 ul of H2O2. Reaction was stopped by adding 0.5 M H 2 SO 4 (usually 20 min for insulin ELISA). When type 1 diabetes sera were pre-incubated with an excess amount of native insulin peptide no significant displacement occurred. In contrast, pre-incubation of sera with an excess of oxPTM-INS peptide whether they were oxidised in house or via oxidative synthesis we observed a strong reduction in binding (see Figures 2 and 3), indicating that oxidised peptides 6 and 3 are the neoepitope to which auto- antibodies in T1D bind. Oxidised peptide 3 reduced binding to oxidised whole insulin in the range of 40- 80% while peptide 6 reduce binding in the range of 35-70%. Nt-INSP-4, however, displayed a comparable inhibition compared to oxPTM-INSP-4 (Fig.11) Example 4 - Antibody binding combinations of oxidised peptides in sera from subjects with T1D When we used a combination of oxidised peptides we did not see a significant increase in blocking the binding to oxidised insulin compared to blocking by either oxidised peptide 3 or oxidised peptide 6 on its own. We used 5ug peptides and further analysis with reduced peptides need to be performed. We believe that we have used access of peptides in the current experiments and further reduction in the dose of each peptide competitor will give us a better outcome. Furthermore a combination of third competitor peptide will need to be tested. Example 5 - Autoantibody and T cell responses to oxidative post-translationally modified insulin neo- antigenic peptides in type 1 diabetes METHODS Study design. oxPTM-INS was generated in vitro by exposing human recombinant insulin to reactive oxidants. Size exclusion chromatography (ÄKTA) in combination with ELISA was employed to analyse the oxPTM-INS profile and to identify immunogenic fractions resulting from the oxPTM further to LC/MS-MS. Peptides discovered by ÄKTA/ELISA/LC/MS-MS were made and exposed to reactive oxidants, to generate oxPTM-INS peptides (oxPTM-INSP). We also synthesised oxPTM-INSP derivatives designed in silico with oxidised amino acids such as dihydroxyphenylalanine (DOPA) instead of tyrosine, cysteate instead of cysteine, or tyrosine instead of phenylalanine. Autoantibodies to oxPTM-INSPs (in house modified and in silico derivatives) were tested using sera from our biobanks of new onset type 1 diabetes (Study cohort 1). For T-cell stimulation we collected fresh blood samples from type 1 diabetes patients (Study cohort 2) to evaluate, in parallel, CD4 + and CD8 + T-cells and autoantibody responses to the oxPTM-INSPs (Fig.14). Patient cohorts. Study cohort 1: serum sample obtained from the following biobanks: (i) Linköping University (n=50), including sera from young patients at 10 days after type 1 diabetes diagnosis, under insulin therapy for 10 days; (ii) the Immunotherapy of Diabetes (IMDIAB) cohort (n=13) including sera from young subjects with newly diagnosed type 1 diabetes collected before insulin therapy. Thirty age- and sex-comparable non- diabetic subjects were used as controls (Table 1). Study cohort 2: fresh blood samples collected from 18 subjects with type 1 diabetes: 13 adults with disease duration ≤two years, and five newly-diagnosed children naive to insulin treatment. Eleven non-diabetic subjects were used as controls. Blood samples were collected at Università Campus Bio-Medico (Rome, Italy) and Università Federico II (Naples, Italy) (Table 1). Study cohort 3: fresh blood samples from five type 1 diabetes adult subjects with disease duration between 2 and 10 years (Table 3). Type 1 diabetes was diagnosed according to ADA criteria in most cases diagnosis was confirmed by islet- autoantibodies. The ethical committees at Università Campus Bio-Medico, Rome, Italy; Università Federico II, Naples, Italy; Linköping University, Linköping, Sweden and Benaroya Research Institute, Seattle, Washington, US have approved the use of blood samples for research with informed consent signed by the participants or their parents/caregivers. Insulin modifications. The insulin used for epitope mapping were from two different sources (i) human recombinant insulin from Sigma (product code #I2643) and (ii) human recombinant insulin Humulin R ® (Eli Lilly). Sigma insulin was dissolved in PBS (1mg/ml) while Humulin R ® was formulated by the manufacturer at a concentration of 3.47 mg/ml. Insulin was chemically modified as previously described [18] while testing a range of oxidation conditions with NaOCl (HOCl modification, BDH, Oxford, UK) and/or with CuCl2 (Sigma, Haverhill, UK) plus hydrogen peroxide ( ● OH modification, Sigma, Haverhill, UK) to further optimise modifications. ÄKTA pure protein purification. Size exclusion chromatography (ÄKTA purifier system) was used to fractionate the various insulin fragments obtained from oxPTM. Superdex 30 increase column (GE Healthcare) was suitable for the detection of low molecular weights (100-7000kDa). Chromatographic profiles at the absorbance wavelength of 280 nm were recorded of both native insulin (Nt-INS) and oxPTM- INS. ELISA for autoantibody detection. The ELISA analysis of Nt-INS and oxPTM-INS autoantibodies was performed as previously described [18] (detailed in ESM methods, ELISA assay for antibody detection). Mass spectrometry. Fractions that showed reactivity in ELISA were dried and resuspended in 30 µl of 0.1% formic acid. Fractions were analysed by LC-MS/MS (Orbitrap Velos, Thermo Scientific) at the Cambridge University UK core facility. The analysis was based on the cleaved peptides following the oxidation producing singly charged ions which are not ordinarily selected for MS/MS in a typical proteomic experiment usually digested with specific enzymes resulting in well-defined peptide cleavage. The breakdown of the insulin was dependent on oxidation whereby cleavage sites are less-well defined and more as a result of random events. Analysis of insulin synthetic peptides (produced by Peptide Protein Research Ltd, ESM methods, Peptides synthesis-modification-assessment) was done by ultra-performance liquid chromatography coupled with an electrospray ionization quadrupole time-of flight mass spectrometry operating in MSE mode (UPLC- qTof/MS e ), which was used to identify all peptides, and to generate fragment ions upon collision induced dissociation (CID) to positively confirm their sequences (ESM methods, Peptide Fractionation and Mass Spectrometry). Structure changes induced by oxPTM were studied by circular dichroism data analysis using the BeStSel server [20] (ESM methods, Structural changes analysis by Circular dichroism). In vitro peptide stimulation and T-cell proliferation assay. Peripheral blood mononuclear cells (PBMCs) were freshly isolated from type 1 diabetes and healthy individuals using Ficoll-Hypaque density gradient centrifugation. PBMCs were labelled with the fluorescent dye CellTrace Violet (Invitrogen, Thermo Fisher Scientific) and cultured (2×10 5 cells/well) in round-bottom 96-well plates (Falcon, Becton Dickinson) with RPMI-1640 medium (Gibco, Thermo Fisher Scientific) supplemented with 5% autologous plasma in the presence or not of insulin peptides (20 µg/ml); PPD (10 µg/ml) and anti-CD3 (0.1 µg/ml; clone OKT3) were used as positive control. Two scrambled peptides: DNRDGNVYYF (SEQ ID NO: 17), GRKAETELLVYPTCVYLFFG (SEQ ID NO: 18), and the Exendin 9-39 fragment were used as negative controls. After 7 days, PBMCs were stained with PE-Cy7 anti-CD8 (clone RPA-T8, BD Pharmingen) and FITC anti-CD3 (clone UCHT1, BD Pharmingen). Samples were analysed by using a FACSCanto II (BD Bioscience) to evaluate T-cell proliferation measured as CellTrace Violet dilution. Cytofluorimetric analyses were performed using FlowJo Software (FlowJo, LLC). The results were given as stimulation index (SI), calculated as percentage of stimulated T-cell subset proliferation/percentage of unstimulated T-cell subset proliferation. Assay for detection of peptide specific T cells subsets was done as previously described [37] (detailed in ESM methods, Assay for detection of peptide specific T cells) Statistical analyses. Statistical analyses were performed using Prism Software 9.0 (GraphPad, San Diego, CA, USA). Cut-off points of positivity (binders) in the antibody ELISA for each peptide were defined by the mean of optical absorbance (O.D) of healthy controls to the corresponding Nt-INSP plus three times the standard error of the mean (SEM). Specificity and sensitivity were evaluated by receiver operating characteristic (ROC) curve analysis. Area under the curve (AUC) is reported as absolute value and was tested for equality according to DeLong et al [21]. Differences in antibody levels and T-cell stimulation indices (SI) between groups were tested by the One way ANOVA or Student’s t-tests as appropriate. Correlation analyses were tested by Pearson or Spearman’s test, as appropriate. Categorical analyses were performed by Chi-square or McNemar’s tests, as appropriate. For each set of experiments, p values were adjusted for multiple comparison using the Holm-Sidak’s test. Hierarchical cluster and Principal Component Analysis (PCA) was done using Clustvis software (https://biit.cs.ut.ee/clustvis/) and Prism Software 9.0, respectively. RESULTS Mapping of the oxidized amino acid hotspots in the oxPTM-INS. For the epitope mapping, we used multiple size exclusion chromatography (ÄKTA), ELISA and LC-MS/MS experiments for Sigma insulin and Humulin R ® insulin. We first confirmed that reactivity pattern of type 1 diabetes samples to Humulin R ® oxPTM-INS was similar to Sigma oxPTM-INS (Fig. 15). Size exclusion chromatography fractions of oxPTM-INS corresponding to small insulin fragments resulting from oxPTM were collected and analysed by ELISA. Fractions that showed reactivity by ELISA were dried and analysed by LC-MS/MS (Fig.7 and Fig. 16). We have previously reported that amino acids His 5 , Cys 7 , Tyr 16 , Phe 24 and Tyr 26 in the beta-chain are oxidized hotspots. In the current study, additional new oxidized amino acid modification hotspots were discovered: His 10 , Leu 17 , Cys 19 and Phe 25 of the beta-chain and Cys 6 , Cys 7 , Cys 11 , Tyr 14 and Cys 20 of the alpha-chain. Oxidation of Cys 6 in the alpha-chain was also seen in the Nt-INS (Fig.8). LC-MS/MS experiments data mapped neoepitopes to six potential oxPTM-INSP that span both insulin alpha- and beta-chains. Candidate insulin peptides (INSPs) included: SLYQLENYCN (SEQ ID NO: 1) (A:12-21, INSP-3) from the alpha-chain and additional five peptides from the beta-chain: YLVCGERGFF (SEQ ID NO: 10) (B:16-25, INSP-1), LVEALYLVCGER (SEQ ID NO: 11) (B:11-22, INSP-2), LVEALYLVCGERGFFYTPKT (SEQ ID NO: 4) (B:11-30, INSP-4), FVNQHLC (SEQ ID NO: 12) (B:1-7, INSP-5), ERGFFYTPKT (SEQ ID NO: 5) (B:21-30, INSP-6). We also included another version of INSP-6 with the addition of a C-terminal arginine (R) as this sequence was seen in several MS profiles and R is the amino acid in the junction with the proinsulin C-peptide (Table 2). Antibody reactivity of type 1 diabetes serum against the candidate oxPTM-INSP. Identified peptide candidates were synthesised and exposed to either HOCl or ● OH to generate oxPTM-INSPs that were first assessed by TOF-MS/ES+TIC to confirm modification (Fig. 17). Antibody response against native INSPs (Nt-INSPs) and oxPTM-INSPs was evaluated by ELISA using sera from Study cohort 1. Serum antibody binding experiments revealed the highest number of type 1 diabetes binders (cut-off defined as mean binding of healthy control to Nt-INSP-3 plus three times SEM) for ● OH-modified oxPTM-INSP-3 (86% binders, mean OD=0.667±0.044), HOCl-modified oxPTM-INSP-4 (66% binders, mean OD=0.563±0.053, (cut-off defined as mean binding of healthy control to Nt-INSP-4 plus three times SEM) and ● OH-modified oxPTM-INSP-6 (83% binders, mean OD=0.461±0.013, (cut-off defined as mean binding of healthy control to Nt-INSP-6 plus three times SEM) (Fig.9a-c, Table 4). No significant reactivity was observed for INSP-1, INSP-2 and INSP-5 (data not shown). For oxPTM-INSP-3 we observed high background binding of healthy controls (p>0.05, Fig. 9a, Table 4). For oxPTM-INSP-4 and oxPTM-INSP-6, binding of type 1 diabetes serum was significantly stronger compared to controls (p=0.0204, p=0.0176 and p=0.0005, for native, ● OH and HOCl oxPTM-INSP-4 and p<0.0001, p<0.0001 and p=0.0187, for native, ● OH and HOCl oxPTM- INSP-6; Fig.9b-c, Table 4). INSP-6 showed the highest specificity and sensitivity with AUC of 0.879, 0.875 and 0.740 for native, ● OH- and HOCl-modified INSP-6 (Table 4, Fig.18). Designing in silico oxPTM-INSPs. We designed in silico multiple oxPTM-INSP derivatives corresponding to one or more aminoacidic modifications. For INSP-3 (SLYQLENYCN (SEQ ID NO: 1)) we synthesised the following oxPTM-INSP-3 derivatives: SL-DOPA-QLENY-Cysteate-N (SEQ ID NO: 2) where tyrosine (Y) was converted to DOPA only in one position and cysteine (C) to Cysteate: SL-DOPA-QLENY-Cysteate-N (SEQ ID NO: 2). An additional oxPTM-INSP-3 was synthesised where both Y residues were converted to DOPA: SL-DOPA-QLEN-DOPA-Cysteate-N (SEQ ID NO: 3). To make the in silico oxPTM-INSP-6 of ERGFFYTPKT (SEQ ID NO: 5), phenylalanine (F) was converted to Y, and Y to DOPA. We thus synthesised two oxPTM-INSP-6 versions of ERGFFYTPKT (SEQ ID NO: 5): ERGYYYTPKT (SEQ ID NO: 6) and ERGYY-DOPA-TPKT (SEQ ID NO: 7). We also included another oxPTM-INSP-6 version with a C- terminal arginine (R), ERGYYYTPKTR (SEQ ID NO: 9), as this sequence was seen in several MS profiles and R is the amino acid in the junction with the proinsulin C-peptide (Fig. 7). Peptide sequence of native and their corresponding in silico oxPTM-peptides were confirmed by UPLC-qTOF/MS (detailed ESM Result section ‘Peptide sequence confirmation by UPLC-qTOF/MS e ‘, Fig. 19). Structure changes induced by oxPTM were then studied by circular dichroism analysis (ESM results, Structural changes in the oxPTM- INSPs compared to native peptides, Fig.20) Antibody reactivity of type 1 diabetes serum against in silico modified oxPTM-INSPs. In type 1 diabetes patients (study cohort 1), we observed a non-significant increase binding to SL-DOPA-QLENY- Cysteate-N (SEQ ID NO: 2) and SL-DOPA-QLEN-DOPA-Cysteate-N (SEQ ID NO: 3) (54% and 57% binders, respectively) compared to SLYQLENYCN (SEQ ID NO: 1) (49% binders, p>0.05); binding of type 1 diabetes samples was, however, significantly more frequent compared to healthy controls (9%, 17% and 30% controls bound to SLYQLENYCN (SEQ ID NO: 1), SL-DOPA-QLENY-Cysteate-N (SEQ ID NO: 2) and SL-DOPA-QLEN-DOPA-Cysteate-N (SEQ ID NO: 3), with p=0.0006, p=0.0112 and p=0.0029 versus type 1 diabetes, respectively) (Fig. 9d, Table 4). There was no increase in specificity/sensitivity in binding to oxPTM-INSP-3 derivatives compared to the Nt-INSP-3 with AUC 0.670, 0.707 and 0.664, for SLYQLENYCN (SEQ ID NO: 1), SL-DOPA-QLENY-Cysteate-N (SEQ ID NO: 2) and SL-DOPA-QLEN- DOPA-Cysteate-N (SEQ ID NO: 3), respectively (Table 4, Fig.18). We observed a significant increased binding of type 1 diabetes samples to both ERGYYYTPKT (SEQ ID NO: 6) and ERGYYYTPKTR (SEQ ID NO: 9) with 100% and 88% binders, respectively, compared to 25% and 48% binders in controls, respectively (p≤0.004). In type 1 diabetes patients, binding to oxPTM-INSP-6 derivatives ERGYYYTPKT (SEQ ID NO: 6) or ERGYYYTPKTR (SEQ ID NO: 9) was significantly higher compared to the native ERGFFYTPKT (SEQ ID NO: 5) (p≤0.008). Similarly, a significant increase in binding to ERGYY-DOPA-TPKT (SEQ ID NO: 7) was observed, compared to the native ERGFFYTPKT (SEQ ID NO: 5) (p=0.008, Fig. 9e). We did not observe a significant difference in specificity/sensitivity of Nt-INSP-6 vs. in silico modified oxPTM-INSP-6 derivatives with AUC 0.8686, 0.8542 and 0.8340, respectively (Table 4, Fig.18). A competitive displacement assay was performed to evaluate serum binding specificities to oxPTM-INSPs by pre-incubating sera with Nt- or oxPTM-INSPs. Interestingly, oxPTM-INSP-3 and oxPTM-INSP-6, but not Nt-INSP-3 or Nt-INSP-6, were able to inhibit the binding of type 1 diabetes samples to oxPTM-INS (p<0.001), but not to Nt-INS (Fig. 10 a-c; g-i). Competition with combined oxPTM-INSP-3 and oxPTM- INSP-6 did not increase blocking to oxPTM-INS binding compared to a single peptide (data not shown). Nt- INSP-4, however, displayed a comparable inhibition compared to oxPTM-INSP-4 (Fig.10 d-f). T-cell stimulation with oxPTM-INSPs. To evaluate the immune cell response against the oxPTM-INSPs, we performed CD4+ and CD8+ T cells proliferation experiments using freshly isolated PBMCs (Study cohort 2, Table 1). Response was calculated as stimulatory index (SI) over unstimulated T-cells. We found that Nt-INSP-4 (LVEALYLVCGERGFFYTPKT (SEQ ID NO: 4)) induced the strongest stimulation in type 1 diabetes compared to controls for both CD4 + (mean SI: 119.8±51.69 vs.6.89±3.4, p<0.001; Fig. 11a) and CD8 + T-cells (mean SI: 405.8±325.5 vs.5.948±3.125, p=0.049; Fig.11c). Of note, as highlighted by the heatmaps in Fig. 11b and 4d, heterogeneous response also to other peptides was evident across different type 1 diabetes individuals, with some patients preferentially responding to various derivatives of oxPTM-INSP-3 (SL-DOPA-QLENY-Cysteate-N (SEQ ID NO: 2), SL-DOPA-QLEN-DOPA-Cysteate-N (SEQ ID NO: 3)) and oxPTM-INSP-6 (ERGYYYTPKT (SEQ ID NO: 6), ERGYY-DOPA-TPKT (SEQ ID NO: 7), ERGYYYTPKTR (SEQ ID NO: 9)). To better assess specificity of T-cell stimulation in type 1 diabetes compared to controls, we analysed response according to different SI cut-offs. When using a SI>3, we found a larger number of type 1 diabetes subjects with a CD4 + response to oxPTM-INSP-6 derivatives compared to controls (66.7% vs. 27.3%; p=0.039), while response to Nt-INSP-4 and oxPTM-INSP-3 was similar between patients and controls (Nt-INSP-4: 66.7% vs. 45.5%; oxPTM-INSP-3 22.2% vs. 9.1%) (Table 5). When comparing response to oxPTM-INSPs and Nt-INSPs among type 1 diabetes patients, we found that CD4 + response to oxPTM-INSP-6 was more frequent compared to Nt-INSP-6 (66.7% vs 27.8%; p=0.045) (Figure 11a-b, Table 5). CD8 + T-cells responses to the tested peptides were also common in type 1 diabetes subjects, who responded with similar frequency to oxPTM-INSP-6 and Nt-INSP-4 (72.2% patients showed a SI>1 for both); such response was higher in type 1 diabetes compared to controls for oxPTM-INSP-6 (72.2% vs. 27.3%; p=0.02), but not for Nt-INSP-4 (72.2% vs. 63.6%; p=NS) (Table 6). Higher SI cut-offs did not reveal significant differences between groups (Table 6). Correlation analysis showed association between T-cell responses to the oxPTM-INS-6 derivative ERGYYYTPKTR (SEQ ID NO: 9) (but not Nt-INSP-6) and Nt-INSP-4, for both CD4 + (r= 0.59, p=0.12; Fig 5a) and CD8 + (r=0.83, p=0.002; Fig. 12b). The CD4 + T cell response to Nt-INSP-4 was also strongly correlated to the CD8 + T cell response of oxPTM-INSP derivatives ERGYYYTPKTR (SEQ ID NO: 9) and SL-DOPA-QLENY-Cysteate-N (SEQ ID NO: 2) (r≥0.83, p≤0.002), but not their native counterparts (Fig. 12c), suggesting an overlap in CD4 + and CD8 + T-cell responses involving Nt-INSP-4, oxPTM-INSP-3 and oxPTM-INSP-6. We next utilized surface staining for CD45RA and CCR7 on CD154+CD69+ T-cells to classify epitope specific T-cells as Naïve (CD45RA+CCR7+), central memory (TCM, CD45RA-CCR7+), effector memory (TEM, CD45RA-CCR7-) or effector memory cells re-expressing CD45RA (TEMRA, CD45RA+CCR7-). Across five representative subjects with established type 1 diabetes (Cohort 3, Table 3) we detected TCM, TEM and TEMRA, with naïve cells also present. Nt-INS and oxPTM-INS specific T-cells had a higher percentage of naïve cells than the influenza control (44.7% and 41.1%, respectively) but appreciable percentage of TCM and TEM were also present, suggesting that there is an existing pool of memory T-cells that recognized these insulin peptides in subjects with type 1 diabetes (Fig.21-22). Correlation between T-cell stimulation and antibody response. Subjects evaluated for T-cell stimulation were also tested for antibody reactivity to either oxPTM-INSPs or oxidised intact insulin (oxPTM-INS) to assess correlations between humoral and cellular responses (Fig.11-e-f). In study cohort 2, antibody reactivity to oxPTM-INSP-6 was the highest as observed in the study cohort 1, with 11/18 (61.1%) binding to at least one oxPTM-INSP-6 derivatives (p<0.001 oxPTM-INSP-6 vs. Nt-INSP-6). Detailed analysis of autoantibody response in this cohort is described in the ESM (ESM results Antibody binding to oxPTM-INSPs in Study cohort 2). We then analysed the extent of correlation between CD4 + , CD8 + and IgG antibody responses. CD4 + and CD8 + responses to oxPTM-INSP-3 overlapped in 9/18 (50.0%), but only 1/18 patients (5.5%) showed concordant antibody reactivity (Fig. 13a). The CD4 + T cell response to Nt-INSP-4 frequently overlapped with CD8 + (13/18 [72.2%]), and to a lesser extent to antibodies (7/18 [38.8%]). Overall, 4/18 (22.2%) patients had a concordant CD4 + , CD8 + and antibody response to Nt-INSP-4 (Fig.13b). CD4 + response to oxPTM-INSP-6 was linked to both CD8 + and/or antibodies: 12/18 (72.2%) patients had concordant CD4 + and CD8 + responses, while 9/18 (50%) patients had concordant CD4 + and antibody responses. Overall, 8/18 (44.4%) patients showed an immune response involving simultaneously CD4 + , CD8 + and antibodies (Fig.13c). CD4 + T-cell stimulation to Nt-INSP-4, oxPTM-INSP-6 and oxPTM-INSP-3 was associated with antibody reactivity to oxPTM-INS in 8/18 (44.4%), 8/18 (44.4%) and 7/18 (38.9%) type 1 diabetes patients. Concordant autoimmune response to oxPTM-INSP involving simultaneously CD4 + , CD8 + T-cells and autoantibodies to oxPTM-INS was seen in 5/18 (27.8%), 6/18 (33.3%), and 4/18 (22.2%) type 1 diabetes patients for Nt-INSP-4, oxPTM-INSP-6 and oxPTM-INSP-3, respectively (Figure 13d-f), suggesting that CD4 + T-cell response to these peptides is required to generate CD8 + and/or antibody responses to oxPTM- INS. We next performed hierarchical cluster analysis (Euclidean distance, Ward's method) of patients, and of peptides. Hierarchical cluster analysis and principal component analysis (PCA) revealed association between the responses to different oxPTM-INSP and identify clustering of type 1 diabetes versus healthy control samples. We observed association between Nt-INSP-4 and ox-PTM-INS-P6, ERGYYYTPKTR (SEQ ID NO: 9) for CD4 + and CD8 + . For IgG response ERGYY-DOPA-TPKT (SEQ ID NO: 7) is associated with ● OH -Insulin. We also observed clustering of response of type 1 diabetes samples using PCA analysis of all responses, CD4, CD8 and IgG. We observed cluster of 11 type 1 diabetes samples with PC1>0 while the rest clustered with healthy control samples with PC1<0 (Figure 23). SUMMARY In this study, we show that neo-antigenic insulin peptides generated by oxPTM are targeted by both circulating autoantibodies and T-cells in patients with type 1 diabetes. The main autoimmune response involved three insulin peptides: B:11-30, B:21-30, A:12-21 and their respective oxPTM-INSP derivatives: oxPTM-INSP-4 (B:11-30), oxPTM-INSP-6 (B:21-30) and oxPTM-INSP-3 (A:12-21). We identified multiple cleavage sites after exposure of insulin to oxidants ( ● OH and HOCl). Consistent with literature, cleavage resulting from oxidative damage occur preferentially between the residues phenylalanine, cysteine, glycine, leucine, valine, and tyrosine, as well as near the cysteine bridges, especially in the alpha-chain [23]. As previously described [22], we observed structural changes within insulin derived peptides oxPTM-INSP-3 and oxPTM-INSP-6 as a results of oxidations. It appears that the nature of the modification itself provides new interaction properties (e.g. additional hydrogen bonding potential), or opens the access to hidden epitopes that could contribute to the formation of immunogenic products. Peptide cleavage makes self-antigens more accessible to the immune system and represents a step required for antigen presentation. It has been shown that B:21-29 is a CD8 epitope generated by proteasome cleavage during antigen presentation [22]. Our data suggest that a similar epitope (B:21-30) can result from beta-chain cleavage by oxidation. We speculate that oxidative cleavage may facilitate antigen presentation via a proteasome independent pathway by providing readily accessible peptides to the immune system. We found antibodies to oxPTM-INSP-6 in most individuals with type 1 diabetes. Of note, we observed the same pattern of response for oxPTM-INSP-6 that was oxidised in house compared to in silico designed derivatives (ERGYYYTPKT (SEQ ID NO: 6) and ERGYY-DOPA-TPKT (SEQ ID NO: 7)), suggesting that oxidation of F to Y and Y to DOPA generates neoepitopes that are recognised by specific antibodies. Interestingly, methyldopa (an analogue of DOPA) can block the activation of insulin autoreactive T-cells in NOD mice and prevented beta cell loss and IAA in recent onset type 1 diabetes [24]. In contrast to oxPTM- INSP-6, oxPTM-INSP-3 was less specific revealing increased background in control subjects. This can be due to the spontaneous oxidation of cysteine or to the presence of a free thiol, which could result in non- specific interaction of SLYQLENYCN (SEQ ID NO: 1), SL-DOPA-QLENY-Cysteate-N (SEQ ID NO: 2) and SL-DOPA-QLEN-DOPA-Cysteate-N (SEQ ID NO: 3). Further chemistry studies will need to address this point in future work. Data from oxPTM-INSP-4 did not clearly substantiate the importance of oxPTM for antibody response to INSP-4. Indeed, Nt-INSP-4 blocked type 1 diabetes serum binding to oxPTM-INS like oxPTM-INSP-4. A similar result was observed for the T-cells, as stimulation with Nt-INSP-4 was stronger compared to other oxPTM-INSPs. Antibodies to oxPTM-INSP-6 coincided with cellular responses in most cases, implying that antibody reactivity to oxPTM-INS is dependent of CD4 + T-cell activation and often associates with CD8 + response. Antibody reactivity to oxPTM-INSP-6 (B:21-30) and Nt-INSP-4 (B:11-30) strongly correlated with antibodies to oxPTM-INS. Furthermore, immune responses to oxPTM-INSP-6 and Nt-INSP-4 often coexisted within patients. Sequence homology between the two peptides cannot fully explain the overlap in immune response, because the association was specific to oxPTM-INSP-6 rather than Nt-INSP-6. It is possible that, when modified, oxPTM-INSP-6 gains a structural conformation similar to the C-terminal part of the longer Nt-INSP-4. A second possibility is that the B:11-30 peptide is autoxidised during the experimental procedures. We were not able to systematically design/analyse in silico derivatives of INSP-4. Within the INSP-4 sequence LVEALYLVCGERGFFYTPKT (SEQ ID NO: 4) there are at least 5 oxidatively modifiable amino acid residues corresponding to dozens of potential combinations, in which various numbers of the cysteine, tyrosines and phenylalanines are either oxidised or not oxidised at various locations within the peptide. Thus, we had to restrict our in silico oxidised peptides analysis to the shorter INSP-6 ERGFFYTPKT (SEQ ID NO: 5) and INSP-2 LVEALYLVCGER (SEQ ID NO: 11) containing lower numbers of oxidation-susceptible amino acid residues. No reactivity was observed against LVEALYLVCG (SEQ ID NO: 19). Previously, it has been shown that simple exposure to ambient air can induce oxidation of the insulin peptide B:9-23 [25], which is targeted by γδT-cells in the NOD mouse. Intermolecular epitope spreading, involving native and oxPTM-INS and their derived peptides (Nt-INSP-4 and oxPTM-INSP-6), is another potential mechanism. Taken together, these findings suggest that Nt-INSP-4 and oxPTM-INSP-6 peptides are potential T-cell and antibody neoepitopes in type 1 diabetes. We performed a pilot study to identify the T-cell subsets that are stimulated by oxPTM-INSPs finding an existing pool of memory T-cells that recognize oxPTM-INSPs in subjects with type 1 diabetes. Further studies with a larger sample size will be needed to confirm this observation. In conclusion, our findings support the concept that oxidative stress, and neo-antigenic epitopes generated by oxPTM of beta cell antigens such as insulin, may involve in the pathogenesis of type 1 diabetes. Table 1 – Clinical and biochemical features of the study populations. Table shows features related to serum samples of i) Study cohort 1 used for the neo-antigenic peptide discovery experiments, collected at the Linkoping and IMDIAB-Rome biobanks and ii) Study cohort 2 tested in the T cell stimulation experiments, newly recruited in Rome, Università Campus Bio-Medico, and Naples, Università Federico II. Categorical analyses were performed by Chi-square test. *p=0.0498
Table 2 – Six oxidative insulin neoantigenic peptides. List of insulin peptide (INSP) candidates that were detected by LC-MS/MS following insulin oxPTM. The table highlights the aminoacidic modifications detected by LC-MS/MS that are graphically represented in Figure 8. Electronic supplementary material (ESM) ESM methods ELISA assay for antibody detection. The ELISA analysis of native (Nt-INS) and modified insulin (oxPTM- INS) was performed as previously described [18-19]. Briefly, the ELISA plate was coated overnight at 4°C with 100µl per well of modified or native insulin in 0.05 M carbonate/bicarbonate buffer pH 9.6 at 10 µg/ml. The next day, the plates were washed 3 times with 0.1% Tween PBS, followed by blocking for 2 hours at room temperature with 200µl per well of 5% BSA in 0.1% Tween PBS. After washing, 100 μl of 1:200- diluted serum samples in 5% BSA-0.1% Tween PBS were added for additional 2 hours incubation. ELISA plates were then washed 3 times with 0.1% Tween PBS followed by probing with anti-human IgG horse radish peroxidase conjugated (HRP, Sigma) at 1:1,000 dilution in 5% BSA-0.1% Tween PBS for another 1.5 hours incubation. The ELISA plates were washed, and 100µg/ml TMB substrate in 0.1M sodium acetate pH 6.0 plus 2µl/10ml of H2O2, were added. Subsequently, the reaction was stopped with 20% v/v sulphuric acid. The optical density (O.D.) was measured at 450 nm using a GENios plate reader and Magellan software (TECAN, Dorset, UK). Binding of serum to for oxPTM-INS fragments was also done by ELISA. Fraction from the AKTA runs were collected further to 1:10 dilution in PBS before coating microtiter plates for further overnight incubation at 37 0 C which followed the assay as above. To assess the binding specificity of serum samples to identified peptides, a competitive ELISA was performed. The ELISA was carried out following the method described above, except that the serum samples were pre-incubated for 2h with and without 10 μg/ml peptides as competitors, before adding the serum samples to the insulin coated ELISA plate. Peptides synthesis-modification-assessment. The peptides were synthesized using standard Fmoc solid phase chemistry (Shepherd and Atherton). Peptides were cleaved from the appropriate resin using TFA containing silanes and ethane dithiol, which removed all side chain protecting groups. If the acetonide protecting group had not been fully cleaved using this methodology the peptide was dissolved in an aqueous buffer containing 0.1% TFA and the peptide monitored by MS until complete removal of the group was verified. The peptides were then purified using HPLC on a C18 column (Phenomenex) using a gradient elution profile of water:acetonitrile and 0.1% TFA. Peptides containing cysteate were synthesised using Fmoc-L-Cysteic acid (Carbosynth) and those containing dihydroxyphenylalanine (DOPA) were synthesised using Fmoc-DOPA (acetonide)-OH (Carbosynth). These two amino acids were treated the same as standard Fmoc amino acids. Peptide Fractionation and Mass Spectrometry. Ultra-performance liquid chromatography coupled with an electrospray ionization quadrupole time-of flight mass spectrometry operating in MSE mode (UPLC- qTof/MS e ) was used to identify all peptides, and to generate fragment ions upon collision induced dissociation (CID) to positively confirm their sequences. The analysis was executed on an ACQUITY H- Class UPLC system (Waters, Milford, USA) coupled to a qTOF High Definition Mass Spectrometer (HDMS) Synapt G2Si, equipped with an electrospray ionisation (ESI) interface (Waters, Milford, USA). All six peptide samples were separated chromatographically using a Waters Acquity UPLC BEH C18 column (1.7 μm, 2.1 mm × 50 mm). The mobile phases consisted of A (LCMS grade Water, 0.1% formic acid) and B (LCMS grade Acetonitrile, 0.1% formic acid), with the following gradient: 0–2 min, 5% B; 2.0–3.0 min, 5%−45% B; 3.0–3.1 min, 45%−90% B; 3.1–4.0 min, 90% B; 4.0–4.1 min, 90%–5% B, 4.1%−5% B. The flow rate was set at 0.45 mL/min. The temperature in the auto sampler and in the column oven was set at 10°C and 60°C, respectively. MS data were collected from m/z 100–1500 Da in positive MSE continuum mode. The electrospray ionization conditions were set as follows: capillary voltage, 3.5 kV; cone voltage, 40 V; cone gas flow, 50 L/h; source temperature, 120°C; desolvation gas flow, 800 L/h; and desolvation temperature, 450°C. Collision energy was set at 4 V in low energy acquisition; whereas high energy collision energy ramp wat set at 10–40 V. Leucine Encephalin (m/z 556.2771) was used for lock mass at a concentration of 200 pg/mL and a flow rate of 20 μl/min. Data acquisition was carried out with Masslynx v4.2 (Waters, Milford, USA), whereas data were processed using the UNIFI Scientific Information System v1.8 software (Waters, Milford, USA). Structural changes analysis by Circular dichroism. Structural changes were determined by Circular dichroism. Nt-INSP-6 and oxPTM-INSP-6 were resuspended in PBS buffer while Nt-INSP-3 was resuspended in 50% (v/v) methanol, 50% (v/v) PBS buffer, oxPTM-INSP-3 Ac-SL-DOPA-QLENY-Cysteate- N (SEQ ID NO: 15) peptide was resuspended in 25% (v/v) methanol, 75% (v/v) PBS buffer and oxPTM- INSP-3 Ac-SL-DOPA-QLEN-DOPA-Cysteate-N (SEQ ID NO: 16) peptide was resuspended in 15% (v/v) methanol, 85% (v/v) PBS buffer. Far-UV CD spectra were measured in a Chirascan (Applied Photophysics) spectropolarimeter thermostated at 20°C. The spectra of peptides (0.05 mg/ml) were recorded from 260 to 200nm, at 0.5nm intervals, 1 nm bandwidth, and a scan speed of 10nm/min. Three accumulations were averaged for each spectrum. Data analysis was carried out using the BeStSel server [20]. Assay for detection of peptide specific T cells. An activation induced marker (AIM) to label and characterize native (Nt-INS) and modified insulin (oxPTM-INS) responsive T cells and influenza specific T cells (as a positive control) was performed as previously described [37]. Briefly, PBMC from subjects with type 1 diabetes were plated at a density of 10 million cells per ml in 24 well plates and pulsed with solvent only (Mock) or specific peptides of interest (oxPTM-INSP, Nt-INSP, or an influenza peptide) in individual wells for 10-14 hours in the presence of an anti-CD40 blocking antibody (Miltenyi Biotec). Activated T cells were labelled with anti-CD154 APC (Miltenyi Biotec) followed by anti-APC beads (Miltenyi Biotec) and magnetically enriched using columns (Miltenyi Biotec), reserving a 1% fraction of the non-enriched cells to determine the total number of T cells in the sample. The enriched and reserved cells were labelled with anti-CD4 BUV395 (BD Biosciences), anti-CD69 PE-Cy7 (BioLegend), anti-CD45RA AF700 (BD Biosciences), anti-CCR7 APC-Cy7 (BioLegend), plus anti-CD14 PerCP-Cy5.5 (BD Biosciences) anti-CD19 PerCP-Cy5.5 (BD Biosciences) and Viaprobe (BD Biosciences) as cell exclusion markers acquired using an BD LSR II cytometer and analyzed using FlowJo software (Tree Star). ESM results Peptide sequence confirmation by UPLC-qTOF/MS e . Fig. 19 shows the fragmentation spectra of the three versions of synthetically oxidative modified peptides 3 (oxPTM-INSP-3) and 6 (oxPTM-INSP-6). Native and oxPTM-INSP-3 correspond to common sequence backbone of SLYQLENYCN (SEQ ID NO: 1), [R-NH3] + , m/z 1288.551); Ac-SL-DOPA-QLENY-cysteate-N (SEQ ID NO: 15), [R-NH3] + , m/z 1352.5162) and Ac-SL-DOPA-QLEN-DOPA-cysteate-N (SEQ ID NO: 16), [R-NH3] + , m/z 1368.5091). Fragmentation pattern of oxPTM-INSP-6 versions, ERGFFYTPKT (SEQ ID NO: 5)-NH2, [R-NH3] + , m/z 1286.6626; ERGYYYTPKT (SEQ ID NO: 6), [R-NH3]+, m/z 1277.6253 and ERGYY-DOPA-TPKT (SEQ ID NO: 7), [R- NH3]+, m/z 1293.6213 is also shown. Table in Fig.19 highlights the fragment ions identified with different m/z values as a result of modifications. Detailed CID spectra with 67%-83% matched first generation primary ions within a filtered upper limit of error of measurement of 30 ppm of peptide y and b assigned fragment ions positively identified against their respective putative sequences and expected modifications was collected (not shown). Structural changes in the oxPTM-INSPs compared to native peptides. Within the context of intact insulin, residues within native peptide 3 form a helix (Fig. 20a). However, the free peptide is significantly unstructured (52%) but with sheet forming propensity (27%) and minor helical conformations (6%). After oxPTM modification, the SL-DOPA-QLENY-cysteate-N (SEQ ID NO: 2) peptide became more structured with increased helicity (16%). However, the SL-DOPA-QLEN-DOPA-cysteate-N (SEQ ID NO: 3) peptide was more disordered (60%) with complete loss of helical structure. Residues corresponding to native peptide 6 are extended within intact insulin and the free peptide (ERGFFYTPKT (SEQ ID NO: 5)) showed both coil (54%) and sheet (29%) conformations. After oxPTM modification ERGYYYTPKT (SEQ ID NO: 6), ERGYY-DOPA-TPKT (SEQ ID NO: 7) and ERGYYYTPKTR (SEQ ID NO: 9) became significantly more sheet-like in structure (10 to 14% increase), while addition of arginine at the C-terminus in peptide Ac- ERGFFYTPKTR (SEQ ID NO: 21) had no effect. Antibody binding to oxPTM-INSPs in Study cohort 2. When analysing the IgG autoantibody reactivity in Study cohort 2, we found increased binding to NT-INS, ● OH-INS, and insulin peptides compared to healthy controls (p<0.001), with 6/18 (33.3%), 9/18 (50%), and 11/18 (61.1%) type 1 diabetes binders to Nt-INS, ● OH-INS, and insulin peptides, respectively. Of note, 11/18 (61.1%) bound to at least one oxPTM-INSP-6 derivatives, with ERGYY-Dopa-TPKT (SEQ ID NO: 7) being the most reactive peptide (10/18 [55.5%]), while none bound to the Nt-INSP-6 (p<0.001); among type 1 diabetes binders to oxPTM-INSP-6, two patients also showed reactivity to Nt-INSP-3 and oxPTM-INSP-3 (SL-Dopa-QLENY-Cysteate-N (SEQ ID NO: 2), respectively, while 7/18 (38.9%) type 1 diabetes patients showed reactivity to the Nt-INSP-4 peptide. Reactivity to the oxPTM-INSP-6 derivative ERGYY-dopa-TPKT (SEQ ID NO: 7), but not the Nt- INSP-6, displayed a positive correlation with Nt-INSP-4 (LVEALYLVCGERGFFYTPKT (SEQ ID NO: 4)) (r=0.92; p<0.001). Antibody reactivity to both ERGYY-DOPA-TPKT (SEQ ID NO: 7) and LVEALYLVCGERGFFYTPKT (SEQ ID NO: 4) correlated with ● OH-INS (r=0.75, p<0.001; and r=0.76, p<0.001). By contrast, neither Nt-INSP-6 or Nt-INSP-3 correlated with ● OH-INS antibody reactivity. Table 3 - Clinical features of subjects with established type 1 diabetes (T1D) from the Benaroya Research Institute.
Table 4 – Statistical analysis of binding of the various native and oxPTM- insulin peptides (INSP). The most significant binding observed is for insulin peptide 6 (INSP-6) that demonstrate the highest specificity with ROC-AUC >0.8 and 100% binding to the in silico modified oxPTM-INSP-6 (ERGYYYTPKT (SEQ ID NO: 6) and ERGYY-DOPA-TPKT (SEQ ID NO: 7)). Cut-off points of positivity (binders) for each peptide were defined by the mean absorbance of healthy controls to the corresponding Nt-INSP plus three times the standard error of the mean (SEM). All analyses were corrected for multiple comparisons using Holm Sidak’s test. In IN IN IN In IN IN
Table 5 – CD4 + T-cell response in subjects with type 1 diabetes and controls according to different stimulatory index (SI) cut-offs. Nt-INSP-3 SLYQLEN oxPTM-INSP SL-Dopa‐Q NO: 2) SL‐Dopa‐Q (SEQ ID NO: at least one Nt-INSP-4 LVEALYLV NO: 4) Nt-INSP-6 ERGFFYT oxPTM-INS- ERGYY‐Do ERGYYYT ERGYYYT at least one
Table 6 – CD8 + T-cell response in subjects with type 1 diabetes and controls according to different stimulatory index (SI) cut-offs. Nt-INSP-3 SLYQLENYV oxPTM-INSP- SL-Dopa‐QL NO: 2) SL-Dopa‐QL (SEQ ID NO: 3 at least one Nt-INSP-4 LVEALYLVC ID NO: 4) Nt-INSP-6 ERGFFYTPK oxPTM-INS-6 ERGYY‐Dop ERGYYYTP ERGYYYTP at least one *p vs. controls = 0.02
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