METHOD AND KIT FOR THE PREDICTIVE PROGNOSIS OF RESPONSIVENESS TO TREATMENTS OF AUTOIMMUNE DISEASES
20170261505 · 2017-09-14
Inventors
Cpc classification
A61K39/395
HUMAN NECESSITIES
G01N33/564
PHYSICS
G01N2800/102
PHYSICS
G01N2800/52
PHYSICS
International classification
Abstract
The present invention relates to the use of one or more MHC class I molecules dextramers (Dextramers®) associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells for the predictive prognosis of responsiveness or non-responsiveness to treatments and/or for monitoring the therapeutic effectiveness of treatments with biological medicaments that block and/or inhibit TNF, and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation in patients affected by autoimmune diseases, together with methods and kits for said predictive prognosis.
Claims
1. Use of one or more MHC class I molecules dextramers) (Dextranners®) associated with peptides corresponding to Apoptotic Epitopes of human CD8+ T cells for the predictive prognosis of responsiveness or non-responsiveness to treatments and/or for monitoring the therapeutic effectiveness of treatments with biological medicaments that block and/or inhibit TNFα and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors, and/or biological medicaments against B cells, and/or biological medicaments that inhibit T cell co-stimulation in patients affected by autoimmune diseases.
2. The use according to claim 1, wherein said one or more peptides corresponding to Apoptotic Epitopes of human CD8+ T cells are selected from the group consisting of peptides having SEQ ID NOS from 1 to 90.
3. The use according to claim 2 wherein said one or more peptides corresponding to Apoptotic Epitopes of human CD8+ T cells are selected from the group consisting of peptides having SEQ ID NO 3, SEQ ID NO 31, SEQ ID NO 37, SEQ ID NO 64, and SEQ ID NO 65.
4. The use according to claim 1, wherein said autoimmune diseases are selected from the group consisting of Rheumatoid arthritis (RA), Systemic lupus erythematosus (SLE), scleroderma, Crohn's disease, ulcerative colitis, dermatomyositis, Anti-phospholipid antibody syndrome, Burger's disease, and Hashimoto's thyroiditis.
5. The use according to claim 1 wherein said biological medicaments that block and/or inhibit TNFα are selected from the group consisting of adalimumab, certolizumab pegol, etanercept, golimumab, and infliximab.
6. The use according to claim 1 wherein said biological medicaments that block and/or inhibit cytokines or cytokine receptors are selected from the group consisting of tocilizumab and anakinra.
7. The use according to claim 1 wherein said biological medicaments against B cells are selected from the group consisting of rituximab.
8. The use according to claim 1 wherein said biological medicaments that inhibit T cell co-stimulation are selected from the group consisting of abatacept.
9. The use according to claim 1 wherein said monitoring is carried out on patients that are responsive to said treatments.
10. An ex vivo method for the predictive prognosis of responsiveness or non-responsiveness to treatments with biological medicaments that block and/or inhibit TNF, and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors, and/or biological medicaments against B cells, and/or biological medicaments that inhibit T cell co-stimulation in patients affected by autoimmune diseases, comprising the following steps: a. contacting a biological sample to be analysed, comprising CD8+ T cells and a control biological sample comprising CD8+ T cells representative of patients affected by autoimmune diseases that are responsive or non-responsive to said treatments, with one or more dextramers (Dextranners®)of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8+ T cells; b. quantifying the percent of CD8+ T cells specifically binding said one or more dextramers in each sample against the total of CD8+ T cells; c. comparing the percent of CD8+ T cells specifically binding said one or more dextramers in the analysed samples and predicting the responsiveness or non-responsiveness to said treatments of the patient associated with said biological sample to be analysed on the basis of the percentage of CD8+ T cells specifically binding said one or more dextramers detected.
11. An ex vivo method according to claim 10 wherein said control biological sample is representative of patients affected by autoimmune diseases that are responsive to said treatments and wherein the detection of a percent of CD8+ T cells specifically binding said dextramers in the sample to be analysed similar to the percent of CD8+ T cells specifically binding said dextramers in the control sample is predictive of responsiveness to said treatments, whereas the detection of a percent of CD8+ T cells specifically binding said dextramers in the sample to be analysed lower than the percent of CD8+ T cells specifically binding said dextramers in the control sample is predictive of non-responsiveness to said treatments.
12. An ex vivo method according to claim 10 wherein said control biological sample is representative of patients affected by autoimmune diseases that are not responsive to said treatments and wherein the detection of a percent of CD8+ T cells specifically binding said dextramers in the sample to be analysed higher than the percent of CD8+ T cells specifically binding said dextramers in the control sample is predictive of responsiveness to said treatments, whereas the detection of a percent of CD8+ T cells specifically binding said dextramers in the sample to be analysed similar to the percent of CD8+ T cells specifically binding said dextramers in the control sample is predictive of non-responsiveness to said treatments.
13. An ex vivo method according to claim 10 wherein said step a. comprises contacting said one or more dextramers with a biological sample to be analysed comprising CD8+ T cells and, concomitantly, a control biological sample comprising CD8.sup.+ T cells representative of patients affected by autoimmune diseases that are responsive to said treatments and a control biological sample comprising CD8+ T cells representative of patients affected by autoimmune diseases that are non-responsive to said treatments.
14. An ex vivo method for the predictive prognosis of responsiveness or non-responsiveness to treatments with biological medicaments that block and/or inhibit TNF, and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors, and/or biological medicaments against B cells, and/or biological medicaments that inhibit T cell co-stimulation in patients affected by autoimmune diseases, comprising the following steps: a. contacting a biological sample to be analysed comprising CD8+ T cells with one or more dextramers (Dextranners®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of Human CD8+ T cells; b. quantifying the percent of CD8+ T cells specifically binding said one or more dextramers in the sample against the total of CD8+ T cells, wherein the presence of a percent of CD8+ T cells specifically binding said dextramers against the total number of CD8+ T cells ≧0.5% is predictive of responsiveness to said treatments.
15. An ex vivo method for the predictive prognosis of responsiveness or non-responsiveness to treatments with biological medicaments that block and/or inhibit TNF, and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation in patients affected by autoimmune diseases, comprising the following steps: a. contacting a biological sample to be analysed comprising CD8+ T cells with one or more dextramers (Dextranners®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8+ T cells b. quantifying the percent of CD8+ T cells specifically binding said one or more dextramers in the sample against the total of CD8+ T cells, wherein the presence of a percent of CD8+ T cells specifically binding said dextramers against the total number of CD8+ T cells ≧0.235% has a predictive value of a 78% responsiveness to said treatments whereas a percent <0.235% has a predictive value of a 75% non-responsiveness to said treatments.
16. An ex vivo method for monitoring the therapeutic effectiveness of treatments with biological medicaments that block and/or inhibit TNFα and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation in a patient affected by an autoimmune disease, comprising the following steps: a. contacting biological samples comprising CD8+ T cells obtained in subsequent moments of time before and during said treatments with one or more dextramers (Dextranners®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8+ T cells b. quantifying the percent of CD8+ T cells specifically binding said one or more dextramers in each sample against the total of CD8+ T cells c. evaluating the variation of said percent of CD8+ T cells specifically binding said one or more dextramers in said samples in time, wherein a decrease in the percent of CD8+ T cells bound by said one or more dextramers in said samples in time indicates an effective therapy.
17. A method according to claim 10 wherein said one or more peptides corresponding to Apoptotic Epitopes of human CD8+ T cells are selected from the group consisting of peptides having SEQ ID NOS from 1 to 90.
18. A method according to claim 17 wherein said one or more peptides corresponding to Apoptotic Epitopes of human CD8+ T cells are selected from the group consisting of peptides having SEQ ID NO 3, SEQ ID NO 31, SEQ ID NO 37, SEQ ID NO 64, and SEQ ID NO 65.
19. The method according to claim 10 wherein said autoimmune diseases are selected from the group consisting of Rheumatoid arthritis (RA), Systemic lupus erythematosus (SLE), Scleroderma, Crohn's disease, ulcerative colitis, dermatomyositis, anti-phospholipid antibody syndrome, Burger's disease, DEL Hashimoto's thyroiditis.
20. The method according to claim 10 wherein said biological medicaments that block and/or inhibit TNFα are selected from the group consisting of adalimumab, certolizumab pegol, etanercept, golimumab, and infliximab.
21. The method according to claim 10 wherein said biological medicaments that block and/or inhibit cytokines or cytokine receptors are selected from the group consisting of tocilizumab, and anakinra.
22. The method according to claim 10 wherein said biological medicaments against B cells are selected from the group consisting of rituximab.
23. The method according to claim 10 wherein said biological medicaments that inhibit T cell co-stimulation are selected from the group consisting of abatacept.
24. A kit for the predictive prognosis of the responsiveness to treatment of one or more diseases with biological medicaments that block and/or inhibit TNFα, and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit cell T co-stimulation and/or for monitoring the effectiveness of said treatment with said medicaments in responsive patients, comprising one or more MHC class I molecules dextramers (Dextranners®) associated with peptides corresponding to Apoptotic Epitopes of human CD8+ T cells in one or more aliquots, one or more aliquots of a control sample comprising human CD8+ T cells representative of healthy individuals, one or more aliquots of a sample comprising human CD8+ T cells representative of individuals affected by an autoimmune disease that are responsive to said treatments and one or more aliquots of a sample comprising human CD8+ T cells representative of individuals affected by said autoimmune disease that are non-responsive to said treatments.
25. The kit according to claim 24 wherein said one or more peptides corresponding to Apoptotic Epitopes of human CD8+ T cells are selected from the group consisting of peptides having SEQ ID NOS from 1 to 90.
26. The kit according to claim 25 wherein said one or more peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells are selected from the group consisting of peptides having SEQ ID NO 3, SEQ ID NO 31, SEQ ID NO 37, SEQ ID NO 64, and SEQ ID NO 65.
27. The kit according to claim 24 wherein autoimmune diseases are selected from the group consisting of Rheumatoid arthritis (RA), Systemic lupus erythematosus (SLE), scleroderma, Crohn's disease, ulcerative colitis, dermatomyositis, anti-phospholipid antibody syndrome, Burger's disease, and Hashimoto's thyroiditis.
28. The kit according to claim 24 wherein said biological medicaments that block and/or inhibit TNFα are selected from the group consisting of adalimumab, certolizumab pegol, etanercept, golimumab, and infliximab.
29. The kit according to claim 24 wherein said biological medicaments that block and/or inhibit cytokines or cytokine receptors are selected from the group consisting of tocilizumab and anakinra.
30. The kit according to claim 24 wherein said biological medicaments against B cells are selected from the group consisting of rituximab.
31. The kit according to claim 24 wherein said biological medicaments that inhibit T cell co-stimulation are selected from the group consisting of abatacept.
Description
DETAILED DESCRIPTION OF THE FIGURES
[0029]
[0038] ACT B=Actin cytoplasmic 1
[0039] Numbers in parentheses correspond to the pool number shown in Table 1 below.
[0040]
[0041] (A) Representative flow cytometry analysis of dextramer®.sup.+ CD8.sup.+ T cells specific to Apoptotic Epitopes in an RA patient and an HD. PBMCs were stained with a PeCy7-labeled mAb to CD8, APC-labeled-HLA-A*0201 dextramers® expressing the indicated AE, and the dump channel APC-Cy7-labeled reagents so as to exclude CD4.sup.+ T cells, monocytes, B cells, NK cells and dead cells from the analysis. Zebra plot analyses show the percentage of dextramer®.sup.+ CD8.sup.+ T cells. The percentage of cells is indicated in the appropriate quadrant. (B) Percentage of dextramer®.sup.+ CD8.sup.+ T cells specific to a single epitope in 14 HLA-A2.sup.+ HD and in 15 HLA-A2.sup.+ patients (each symbol represents the percentage of dextramer®.sup.+ CD8.sup.+ T cells specific to a single epitope in HD or patients). (C) Sum of the percentages of all dextramer®.sup.+ CD8.sup.+ T cells detected in the single HD or patient (each symbol represents the sum of percentages of the 5 dextramers® tested in the single individual). (D). Percentage of dextramer®.sup.+ CD8.sup.+ T cells specific to a single epitope in 14 HLA-A2.sup.+ HD, 9 HLA-A2.sup.+ R to TNF-α inhibitor therapy, and 6 HLA-A2.sup.+ NR (each symbol represents the percentage of dextramer®.sup.+ CD8.sup.+ T cells specific to a single epitope in HD or patients). (E) Sum of the percentages of all dextramer®.sup.+ CD8.sup.+ T cells detected in the single HD, R, and NR (each symbol represents the sum of percentages of the 5 dextramers® tested in the single individual). Statistical analysis was performed with the Mann-Whitney test. **p<0,001; ***p<0,0001. (F) ROC (Receiver-operator characteristic) curve analyses for R and NR RA patients.
[0042] AUC=area under receiver-operator characteristic curve.
[0043] *=Predictive value of positive test.
[0044] #=Predictive value of negative test.
[0045]
[0046]
[0047] (A) Representative flow cytometry analysis of PD-1, HLA-DR and CD69 in AE-specific dextramer®.sup.+ CD8.sup.+ T cells from a R and a NR. (B) Percentage of AE-specific dextramer®.sup.+ CD8.sup.+ T cells expressing PD-1, HLA-DR, or CD69 in all R and NR studied. Statistical analysis was performed with the Mann-Whitney test. *p<0,01; **p<0,001; ns=not significant. (C) Correlation between AE-specific dextramer®.sup.+ CD8.sup.+ T cells expressing PD-1 and total AE-specific dextramer®.sup.+ CD8.sup.+ T cells (Spearman correlation analysis). **p<0,001.
[0048]
[0049] (A) Representative flow cytometry analyses of cells producing IL-17 or IFN-γ in Dextramer®.sup.+ CD8.sup.+ T cells in response to a relevant AE pool (5 peptides). (B)
[0050] Percentage of cytokine-producing cells in dextramer®.sup.+ CD8.sup.+ T cells from R and NR. Statistical analysis was performed with the Mann-Whitney test. ns=not significant. (C) Correlation between cytokine-producing dextramer®.sup.+ CD8.sup.+ T cells and those expressing PD-1 (Spearman correlation analysis).
[0051]
[0052] (A) Percentages of the single AE-specific Dextramer®.sup.+ CD8.sup.+ T cells determined before (TO) and after 1 (T1) and 3 (T3) months from the start of TNF-a inhibitor therapy in R and NR (each symbol represents a single AE-specific Dextramer®.sup.+ CD8.sup.+ T cell population). Statistical analysis was performed with Wilcoxon matched pairs test. ***p<0,0001; ns=not significant. The § symbol indicates the percentages of single AE-specific dextramer®.sup.+ CD8.sup.+ T cells that were compared between R and NR at the t1 (**p<0,001) (B) Sum of percentages of the single AE-specific dextramer®.sup.+ CD8.sup.+ T cells in single R and NR (each symbol represents a single patient). Statistical analysis was performed by Wilcoxon matched pairs test. ***p<0,0001; ns=not significant. The # symbol indicates the percentages of single AE-specific dextramer®.sup.+ CD8.sup.+ T cells that were compared between R and NR at the t1 (**p<0,001) (C) Correlation between DAS28ESR and the percentage of AE-specific dextramer®.sup.+ CD8.sup.+ T cells in R (Spearman correlation analysis). (D) Parallel follow-up of AE-specific dextramer®.sup.+ CD8.sup.+ T cell analyses and DAS28ESR at T0, T1, and T3 from the start of the TNF-α inhibitor therapy in R.
[0053]
[0054] Patients were assessed for overall disease activity using the DAS28, and categorized in R or NR according to the EULAR criteria 6 months after the start of treatment. An improvement of the DAS28 >0,6 was considered a response to therapy. Statistical analysis was performed with Paired t test. ***p<0,0001. ns=not significant.
[0055]
[0056] DAS28 ESR values (A), DAS28 CRP values (B), and RA duration (months) (C), before the start of TNF-α inhibitor therapy, in R and NR. Statistical analysis was performed with the Mann-Whitney test. ns=not significant.
[0057]
[0058] Sum of IFN-γ.sup.+ cell spots formed in response to AE pools, analysed in R and NR at T0, T1, and T3 from the start of anti-TNF-α therapy. Statistical analysis was performed with Wilcoxon matched pairs test. *p<0,01; **p<0,001;
[0059] ***p <0,0001. ns=not significant.
[0060]
DETAILED DESCRIPTION OF THE INVENTION
[0061] As explained in the summary above, the present invention stems from the discovery that, in autoimmune diseases, the proportion of circulating apoptotic lymphocytes is correlated with the frequency of CD8 T lymphocytes specific for the peptides (epitopes) derived from apoptotic antigens, (i.e., from antigenic fragments derived from apoptotic T cells that are processed and cross-presented by dendritic cells (DC) to an enormous repertoire of specific CD8 T lymphocytes), and that the frequency of these CD8 T lymphocytes specific to Apoptotic Epitopes is correlated with disease activity, disease progression, and is predictive of the response to certain therapies. As already mentioned, the frequencies of CD8 T lymphocytes specific against Apoptotic Epitopes are significantly higher in patients affected by autoimmune diseases than in control healthy subjects and are correlated with disease activity, resulting significantly higher in patients that will respond (responsive) to certain therapies than in non-responsive patients. Therefore, determining the frequency of CD8 T lymphocytes specific for apoptotic peptides (autoreactive) enables to have a biomarker predictive of response to therapy.
[0062] In the present description, in all embodiments described, Apoptotic Epitopes of human CD8.sup.+ T cells are to be understood as epitopes derived from cleavage by caspases (caspase cleavage) to one or more human cellular proteins, therefore producing fragments processed by dendritic cells (DC) which subsequently present a high proportion of distinct epitopes in these fragments (Apoptotic Epitopes, or AE) by the classic MHC (major histocompatibility complex) class 1 pathway to a wide repertoire of autoreactive CD8.sup.+ T cells.
[0063] In other terms, T cell epitopes, generated by caspase cleavage of cellular proteins, recognized by CD8.sup.+ T cells, are defined as Apoptotic Epitopes of CD8.sup.+ T cells. This definition is known in the literature and is, for instance, described in detail in Rawson et al, 2007. Examples of such epitopes are represented by peptides listed in Table 1 in the present description.
[0064] Therefore, the Apoptotic Epitopes according to the present invention are antigenic peptides derived from apoptotic T cells, and can be peptides derived from proteins of apoptotic T lymphocytes and can bind MCH class I molecules belonging to the same HLA haplotype or to different HLA haplotypes.
[0065] The term “Apoptotic Epitopes” may be replaced throughout the present description and in the claims by any one of the definitions provided above, or even by one of the following terms: “antigenic peptides derived from apoptotic T cells”, “antigenic peptides derived by apoptotic T cells generated from caspase cleavage of cellular proteins”, or “Apoptotic Epitopes according to Table 1”; in other terms, those are antigenic fragments derived from apoptotic T cells, that are processed and cross-presented by dendritic cells to an enormous repertoire of specific CD8 T lymphocytes.
[0066] Such peptides can be identified by the expert in the field by analysis of T cells proteome, as described, e.g., in Apoptotic cells overexpress vinculin and induce vinculin-specific cytotoxic T cell cross-priming. Nature Med. 7:807-813, 2001., and in Rawson et al, Cross-presentation of caspase-cleaved apoptotic self antigens in HIV infection. Nat. Med. 13: 1431-9, 2007. In the paper by Rawson et al, Nat Med 2007, the method of isolation of proteins derived by apoptotic T lymphocytes is described in detail. In particular, in the supplementary information available online, there are described: preparation of apoptotic lymphocytes, two-dimensional electrophoresis (2DE) of apoptotic T cells, protein isolation from 2DE gels, and MALDI-TOF-MS analysis .
[0067] Caspase-cleaved cellular proteins identified herein are, e.g.: [0068] Actin cytoplasmic 1 (ACTB, reference sequence having accession number P02570); [0069] heterogeneous nuclear riboprotein k (ROK, reference sequence having accession number Q07244); [0070] lamin B1 (LAM1, reference sequence having accession number P20700) [0071] non-muscle myosin heavy chain 9 (MYH9 reference sequence having accession number P35579) [0072] vimentin (VIME reference sequence having accession number P08670) [0073] proteasome component C2 (PSA1 reference sequence having accession number P25786) [0074] rho GDP dissociation inhibitor 2 (GDIS reference sequence having accession number P52566) [0075] 60S acidic ribosomal protein C2 (RLA2 reference sequence having accession number P05387).
[0076] In the present description, in all embodiments, except where otherwise indicated, by “Apoptotic Epitopes bound by Human CD8.sup.+ T cells” short peptides of a length ranging from 8 and 12 amino acids are meant, capable of being bound by CD8 T lymphocytes specific for apoptotic peptides (autoreactive).
[0077] Such peptides may be short fragments (by caspase cleavage) of one or more of the above-listed proteins (ACTB, ROK, LAM1, MYH9, VIME, PSA1, GDIS, RLA2).
[0078] Concrete examples of such peptides are represented by sequences 1-90 of the sequence list attached to the present application and summarized in Table 1 below.
TABLE-US-00001 TABLE 1 HLA-A2 binding peptides derived from apoptotic cell-associated proteins detected by proteomic analyses. PROTEIN SEQ (ACCESSION Position ID NUMBER) of 1.sup.st aa SEQUENCE 1 ACTB (P02570) 131 AMYVAIQAV 2 Pool 1 319 ALAPSTMKI 3 266 FLGMESCGI 4 312 RMQKEITAL 5 348 SLSTFQQMWI 6 46 GMGQKDSYV 7 ROK (Q07244) 154 SLAGGIIGV 8 Pool 2 67 ALRTDYNASV 9 193 VLIGGKPDRV 10 209 ILDLISESPI 11 122 QLPLESDAV 12 LAM1 (P20700) 496 TIWAANAGV 13 Pool 3 41 RLAVYIDKV 14 301 SLSSQLSNL 15 361 QLLDVKLAL 16 291 ELMESRMRI 17 355 QLNDYEQLL 18 388 KLSPSPSSRV 19 488 VLKAGQTVTI 20 378 KLLEGEEERL 21 MYH9 (P35579) 9 YLYVDKNFI 22 Pool 4 108 GLIYTYSGL 23 111 YTYSGLFCV 24 145 EMPPHIYAI 25 186 KVIQYLAYV 26 478 QLFNKHTMFI 27 584 WLMKNMDPL 28 653 QLAKLMATL 29 111 YTYSGLFCVV 30 MYH9 (P35579) 424 RMFRWLVLRI 31 Pool 5 478 QLFMHTMFIL 32 302 FLSNGHVTI 33 338 GLLRVISGV 34 412 FAIEALAKA 35 450 ILDIAGFEI 36 733 FMDGKQACV 37 741 VLMIKALEL 38 1277 KLQVELDNV 39 MYH9 (P35579) 1843 KLKDVLLQV 40 Pool 6 279 YLLSGAGEHL 41 733 FMDGKQACVL 42 1920 KLRRGDLPFV 43 210 QLLQANPIL 44 847 MMAKEEELV 45 877 QLMAEKLQL 46 1726 RLEARIAQL 47 1793 KLQEMEGTV 48 MYH9 (P35579) 660 TLRNTNPNFV 49 Pool 7 688 VLDQLRCNGV 50 752 NLYRIGQSKV 51 248 YIVGANIET 52 1540 QLEELEDEL 53 161 MMQDREDQSI 54 821 KLRNWQWWRL 55 846 EMMAKEEELV 56 GDIS (P52566) 100 VLKEGSEYRV 57 Pool 8 186 HLSWEWNLSI 58 37 EMDKDDESL 59 51 TLLGDGIVV 60 VIME (P08670) 176 NLAEDIMRL 61 Pool 9 50 SLIASSPGGD 62 68 RLRSSVPGV 63 129 ILLAELEQL 64 225 SLQEEIAFL 65 78 LLQDSVDFSL 66 79 LQDSVDFSL 67 419 SLNLRETNL 68 122 FLEQQNKILL 69 370 NMKEEMARHL 70 PSA1 (P25786) 179 FMECNLNEL 71 Pool 10 183 NLNELVKHGL 72 175 HMSEFMECNL 73 63 ILHVDNHIGI 74 37 GLKSKTHAV 75 110 SLIGSKTQI 76 179 FMECNLNELV 77 48 ALKRAQSEL 78 76 GLTADARLL 79 PSA1 (P25786) 102 PLPVSRLVSL 80 Pool 11 204 DLTTKNVSI 81 45 ELNGKNIEDV 82 55 ELAAHQKKI 83 186 ELVKHGLRAL 84 37 GLKSKTHAVL 85 191 GLRALRETL 86 55 ELAAHQKKIL 87 97 FVFDRPLPV 88 RLA2 (P05387) 3 YVASYLLAA 89 Pool 12 26 ILDSVGIEA 90 3 YVASYLLAAL
[0079] In the present invention such peptides are preferably associated with dextramers of MHC class I molecules by dextramers (dextramer®) technology, which can be costumed by Immudex, Copenhagen, Denmark, for each desired HLA haplotype, like e.g. HLA-A and its allelic forms, HLA-B and its allelic forms, or HLA-C and its allelic forms.
[0080] For the purposes of the present description, in any embodiment, the term “biological sample” indicates a sample containing CD8.sup.+ T cells (CD8.sup.+ T lymphocytes) and could be, e.g., a blood sample, or a PBMC (peripheral blood mononucleated cells) sample.
[0081] For the purposes of the present description, in any embodiment, the term dextramers (dextramer®) denotes a molecular complex comprised of multiple MHC class I molecules, each of which conjugated with fluorescein and complexed to the synthetic apoptotic peptides identified by the Inventors and described above.
[0082] As described on the Immunodex site, http://www.immudex.com/technology/dextramer-technology.aspx, MHC Dextramer™ reagents consist in a dextran polymer backbone carrying an optimized number of MHC and fluorochrome molecules. Dextramer reagents carry more MHC molecules and fluorochromes than conventional MHC multimers. This enhances their avidity for specific T cells and enhances their labeling intensity, thereby increasing the resolution and the signal/background ratio. The dextran polymer backbone stabilizes the shape of bound proteins, i.e. the MHC-peptide complexes and the fluorochromes, and are therefore highly stable reagents. The site also shows a clear diagram of dextramers, reported below:
[0083] In other terms, using the definition provided by Wikipedia reported herein, dextramers are reagents fluorescently labeled with FITC, PE or APC, and contain MHC molecules attached to a dextran backbone, which are used to detect antigen-specific T-cells in fluid cells and solid tissue samples using flow cytometry.
[0084] For the purposes of the present description, in any embodiment, the term “biological medicaments that block and/or inhibit TNF” (Tumour Necrosis Factor) includes biological medicaments that block/inhibit TNFα, like, e.g., adalimumab, certolizumab pegol, etanercept, golimumab, infliximab;
[0085] By “biological medicaments that block and/or inhibit cytokines or cytokine receptors” are meant biological medicaments that block/inhibit one or more cytokines or cytokine receptors, like, e.g., tocilizumab, anakinra; by “biological medicaments against activated B cells” are meant biological medicaments that inhibit the functions of B lymphocytes and deplete them, like, e.g., rituximab, consisting of an antibody that recognizes molecule CD20 on B lymphocytes and destroys them; and, by “biological medicaments that inhibit T cell co-stimulation” are meant biological medicaments that inhibit T lymphocytes, like e.g. abatacept, which is comprised of IgG1 Fc region fused with the extracellular domain of molecule CTLA-4, that by binding molecules CD80 and CD86 on T lymphocytes prevents the latter molecules from being co-stimulated by antigen-presenting cells (i.e., DCs) thereby becoming anergic.
[0086] The term “biological medicaments” in the present description has the meaning recognized in the state of the art, i.e. it denotes medicaments that mime or inhibit the effects of natural substances present in the body, but are produced in laboratory.
[0087] In one embodiment, the present invention relates to the use of one or more MHC class I molecules dextramers (Dextramers®) associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells, for the predictive prognosis of responsiveness or non-responsiveness to certain therapeutic treatments, or even for monitoring the effectiveness of said therapeutic treatments, in patients affected by autoimmune diseases.
[0088] The therapeutic treatments according to the invention are treatments with biological medicaments that block and/or inhibit TNFα and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation. Said predictive prognosis can be carried out with the methods described below, by determination of the frequencies or of the number of CD8.sup.+ T lymphocytes specific for dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells and comparing this number with that obtained from control patients with known responsivity or relative to a cutoff value reported below.
[0089] The monitoring of the effectiveness of the therapeutic treatments can be carried out in patients, in which there are determined, in time, the frequencies (or the number) of CD8.sup.+ T lymphocytes specific for dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells at different times before and during the treatment, wherein a decrease of said T lymphocytes indicates effectiveness of therapy.
[0090] For the purposes of the present invention, said peptides can be, for instance, one or more peptides derived from caspase cleavage of proteins ACTB, ROK, LAM1, MYH9, VIME, PSA1, GDIS, RLA2 as defined above.
[0091] In one embodiment, said peptides can be one or more peptides as indicated in Table 1 above, i.e. one or more peptides selected in the group of peptides having SEQ ID from 1 to 90.
[0092] According to one embodiment of the invention, said peptides are one or more peptides derived from caspase cleavage of proteins ACTB, MYH9 and VIME as defined above.
[0093] In a specific embodiment, said one or more peptides may be selected in the group of peptides having SEQ ID 3 (hereinafter also denoted as ACTB .sub.266-274) SEQ ID NO 31 (hereinafter also denoted as MYH9.sub.478-486) SEQ ID NO 37 (hereinafter also denoted as MYH9.sub.741-749) SEQ ID 64 (hereinafter also denoted as VIME .sub.225-233), SEQ ID NO 65 (hereinafter also denoted as VIME .sub.78-87).
[0094] In a further embodiment, said one or more peptides consist in the peptides having SEQ ID 3 (hereinafter also indicated as ACTB.sub.266-274) SEQ ID NO 31 (hereinafter also indicated as MYH9.sub.478-486) SEQ ID NO 37 (hereinafter also indicated as MYH9.sub.741-749), SEQ ID 64 (hereinafter also indicated as VIME.sub.225-233), SEQ ID NO 65 (hereinafter also indicated as VIME.sub.78-87).
[0095] As mentioned above, for the purposes of the present invention, the peptides in any one of the forms indicated above can be used for the predictive prognosis of responsiveness to certain therapeutic treatments (as defined in the present description) and/or the monitoring of the effectiveness of said therapeutic treatments in patients affected by autoimmune diseases. Said autoimmune diseases could be, e.g., diseases selected in the group comprising Rheumatoid arthritis (RA), Systemic lupus erythematosus (SLE), Scleroderma, Crohn's disease, Ulcerative colitis, Dermatomyositis, Anti-phospholipid antibody syndrome, Burger's disease, Hashimoto's thyroiditis.
[0096] According to the present invention, said therapeutic treatments could be therapeutic treatments with one or more biological medicaments selected among biological medicaments that block and/or inhibit TNF and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation.
[0097] Said biological medicaments that block and/or inhibit TNF may be, e.g., TNFα blockers/inhibitors selected in the group comprising adalimumab, certolizumab pegol, etanercept, golimumab, infliximab.
[0098] Said biological medicaments that block and/or inhibit cytokines or cytokine receptors are medicaments capable of blocking/inhibiting one or more cytokines or cytokine receptors, even indirecly. Said medicaments may be, e.g., blockers/inhibitors of any one of cytokines IL-1α, IL-1β, IL-17, IL-22, IL-18, IL-33 and IL-6 or of a receptor thereof and can be selected, e.g., in the group comprising, e.g., the blocker of IL-6 receptor (tocilizumab), the anti-IL-1 (anakinra).
[0099] Said biological medicaments against B cells are medicaments against activated B cells, i.e. biological medicaments that inhibit the functions of B lymphocytes and deplete them, like, e.g., rituximab, consisting of an antibody that recognizes the CD20 molecule on B lymphocytes and destroys them.
[0100] Said biological medicaments that inhibit T cell co-stimulation are medicaments like, e.g., abatacept, which is comprised of the IgG1 Fc region fused with the extracellular domain of the molecule CTLA-4, which by binding the molecules CD80 and CD86 on the T lymphocytes prevents the latter molecules from being co-stimulated by the antigen-presenting cells (i.e., DCs) thereby becoming anergic.
[0101] The responsiveness to said treatments or the effectiveness thereof, as emerges from what described above, can be ascertained by using the peptides and the methods described in the present description.
[0102] An ex vivo method for the predictive prognosis of responsiveness or non-responsiveness to treatments with biological medicaments that block and/or inhibit TNF, and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation in patients affected by autoimmune diseases, comprising the following steps: [0103] a. contacting a biological sample to be analysed comprising CD8.sup.+ T cells and, concomitantly, a control biological sample comprising CD8.sup.+ T cells representative of patients affected by autoimmune diseases that are responsive and/or representative of patients affected by autoimmune diseases that are non-responsive to said treatments, with one or more dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells; [0104] b. quantifying the number of CD8.sup.+ T cells specifically binding said one or more dextramers in each sample; [0105] c. comparing the amount of CD8.sup.+ T cells specifically binding said one or more dextramers in the analysed samples and predicting the responsiveness or non-responsiveness of the patient associated with said biological sample to be analysed to said treatments on the basis of the amount of CD8.sup.+ T cells specifically binding said one or more dextramers detected.
[0106] The term ex vivo, commonly used in scientific works, refers to testing, methods, measurements performed in or on tissues or cells outside of an organism, in an external environment, altering the natural conditions as little as possible. Ex vivo conditions enable testing on cells or tissues outside of the organism from which they originate. Therefore, the term ex vivo excludes in vivo embodiments. A main advantage of the use of ex vivo methods and techniques is the possibility of performing assays or measurements that otherwise, due to ethical or technical reasons, would not be possible on living organisms. For the purposes of the present invention, the term “sample to be analysed” refers to isolated samples, coming from patients affected by autoimmune diseases of whom the response to the above-indicated therapies is not known, and for whom the predictive method of the invention is to be applied before subjecting them to therapeutic treatments.
[0107] The amount of CD8.sup.+ T cells specifically binding Apoptotic Epitopes (i.e., the dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells according to the invention, also indicated herein as dextramer®.sup.+ CD8.sup.+ T cells) can be quantified by calculating the percentage of dextramer®.sup.+ CD8.sup.+ T cells relative to the total of CD8.sup.+ T cells.
[0108] This can be carried out by using markers specific for CD8.sup.+ T cells known in the state of the art and counting said cells by cytofluorimeter (e.g., by labeling cells with an anti-CD8 antibody).
[0109] When using a sample of responsive patients as control sample, if the sample to be analysed has a percentage of dextramer®.sup.+ CD8.sup.+ T cells, against the total of CD8.sup.+ T cells, comparable to that of the control, it will be a sample coming from a responsive patient (responder); if the percentage of dextramer®.sup.+ CD8.sup.+ T cells against the total of CD8.sup.+ T cells is instead significantly lower than that of the control, it will be a sample coming from a patient that will not respond effectively to the therapeutic treatment with biological medicaments as defined herein.
[0110] Conversely, when using a sample of non-responsive patients as control sample, if the sample to be analysed has a percentage of dextramer®.sup.+ CD8.sup.+ T cells against the total of CD8.sup.+ T cells comparable to that of the control, it will be a sample coming from a non-responsive patient; if instead the percentage of dextramer®.sup.+ CD8.sup.+ T cells against the total of CD8.sup.+ T cells in the sample to be analysed is instead significantly greater than that of the control, it will be a sample coming from a patient who will respond effectively to the therapeutic treatment with biological medicaments as defined herein. As mentioned above, the peptides of the present invention enable to quantify the number or the frequency of CD8.sup.+ T cells binding Apoptotic Epitopes; such quantifying enables to predict who will respond or not respond to the treatment before starting the same treatment. In particular, the data reported in the figures and in the examples below demonstrate that patients with frequencies of CD8.sup.+ T cells specific for Apoptotic Epitopes significantly higher than in the other patients will effectively respond to the therapeutic treatment as defined herein, whereas those with frequencies significantly lower than the former will not respond.
[0111] The percentage of CD8.sup.+ T cells specific for Apoptotic Epitopes conjugated with dextramers (in the present description also indicated as dextramer®.sup.+), and therefore of CD8.sup.+ T cells binding Apoptotic Epitopes, can be calculated by flow cytometry analysis. Therefore, according to an embodiment of the invention, in the above-indicated method there will be used a control biological sample representative of patients affected by autoimmune diseases that are responsive to said treatments, and the detection of a percent of CD8.sup.+ T cells specifically binding the dextramers Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells in the sample to be analysed similar to the percent of CD8.sup.+ T cells specifically binding said dextramers in the control sample is predictive of responsiveness to said treatments, whereas the detection of a percent of CD8.sup.+ T cells specifically binding said dextramers in the sample to be analysed lower than the percent of CD8.sup.+ T cells specifically binding said dextramers in the control sample is predictive of non-responsiveness to said treatments.
[0112] When referring to the percentage of CD8.sup.+ T cells specifically binding dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells (i.e., Apoptotic Epitopes) in any embodiment of the present invention, it is meant the percentage of such cells against the total of CD8.sup.+ T cells analysed.
[0113] According to another embodiment, said control biological sample is representative of patients affected by autoimmune diseases not responsive to said treatments, and the detection of a percent of CD8.sup.+ T cells specifically binding dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells of the invention in the sample to be analysed higher than the percent of CD8.sup.+ T cells specifically binding said dextramers in the control sample is predictive of responsiveness to said treatments, whereas the detection of a percent of CD8.sup.+ T cells specifically binding said dextramers in the sample to be analysed similar to the percent of CD8.sup.+ T cells specifically binding said dextramers in the control sample is predictive of non-responsiveness to said treatments.
[0114] Of course, the method according to the invention can comprise a step a. which comprises contacting said one or more dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells with a biological sample to be analysed comprising CD8.sup.+ T cells and, concomitantly, a control biological sample comprising CD8.sup.+ T cells representative of patients affected by autoimmune diseases that are responsive and a control biological sample comprising CD8.sup.+ T cells representative of patients affected by autoimmune diseases, that are non-responsive to said treatments.
[0115] Moreover, the method can also comprise the use of a control sample representative of healthy individuals, the percentage of CD8.sup.+ T cells specifically binding Apoptotic Epitopes in this sample will be substantially 0.
[0116] The invention also provides an ex vivo method for the predictive prognosis of responsiveness or non-responsiveness to treatments with biological medicaments that block and/or inhibit TNFα and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation in patients affected by autoimmune diseases, comprising the following steps: [0117] a. contacting a biological sample to be analysed comprising CD8.sup.+ T cells with one or more p dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells; [0118] b. quantifying the percent of CD8.sup.+ T cells specifically binding said one or more dextramers in the sample against the total of CD8.sup.+ T cells, wherein the presence of a percent of CD8.sup.+ T cells specifically binding said dextramers against the total number of CD8.sup.+ T cells ≧0.5% is predictive of responsiveness to said treatments.
[0119] Moreover, the invention also provides an ex vivo method for the predictive prognosis of responsiveness or non-responsiveness to treatments with biological medicaments that block and/or inhibit TNF, and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation in patients affected by autoimmune diseases, comprising the following steps: [0120] a. contacting a biological sample to be analysed, comprising CD8.sup.+ T cells, with one or more dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells; [0121] b. quantifying the percent of CD8.sup.+ T cells specifically binding said one or more dextramers in the sample against the total of CD8.sup.+ T cells, wherein the presence of a percent of CD8.sup.+ T cells specifically binding said dextramers against the total number of CD8.sup.+ T cells ≧0.235% has a predictive value of a 78% responsiveness to said treatments whereas a percent <0.235% has a predictive value of a 75% non-responsiveness to said treatments.
[0122] The invention further provides an ex vivo method for monitoring the therapeutic effectiveness of treatments with biological medicaments that block and/or inhibit TNFα and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation in a patient affected by autoimmune disease, comprising the following steps: [0123] a. contacting biological samples comprising CD8.sup.+ T cells obtained in subsequent moments of time before and during said treatments with one or more dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells; [0124] b. quantifying the percent of CD8.sup.+ T cells specifically binding said one or more dextramers in each sample against the total of CD8.sup.+ T cells; [0125] c. evaluating the variation of said percent of CD8.sup.+ T cells specifically binding said one or more dextramers in said samples in time, wherein a decrease in the percentage of CD8.sup.+ T cells bound by said one or more dextramers in said samples in time indicates an effective therapy.
[0126] The Authors of the present invention in fact demonstrated, as reported in
[0127] All indications provided above with regard to dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells, to peptides, to therapeutic treatments and the suitable biological samples, apply to all of the above-described methods.
[0128] However, in short, the peptides in the one or more dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells in the above-described methods can be prepared as described above, or can be selected in the group of peptides having SEQ ID from 1 to 90.
[0129] In a specific embodiment, the peptides can be selected in the group comprised of SEQ ID 3, SEQ ID NO 31, SEQ ID NO 37, SEQ ID 64, SEQ ID NO 65.
[0130] The methods of the invention can be applied to patients affected by autoimmune diseases in general; specifically, the autoimmune diseases can be those selected in the group comprising Rheumatoid arthritis (RA), Systemic lupus erythematosus (SLE), Scleroderma, Crohn's disease, Ulcerative colitis, Dermatomyositis, Anti-phospholipid antibody syndrome, Burger's disease, Hashimoto's thyroiditis.
[0131] The treatments to which the methods of the invention refer include treatments with biological medicaments that block and/or inhibit TNFα, like, e.g., medicaments selected in the group comprising adalimumab, certolizumab pegol, etanercept, golimumab, infliximab; treatments with biological medicaments that block and/or inhibit cytokines or cytokine receptors, like, e.g., medicaments selected in the group comprising tocilizumab, anakinra; treatments with biological medicaments against B cells, like, e.g., rituximab; treatments with biological medicaments that inhibit T cell co-stimulation, like, e.g., abatacept.
[0132] Moreover, the invention relates to a kit for the predictive prognosis of the responsiveness to treatment of one or more diseases with biological medicaments that block and/or inhibit TNFα and/or biological medicaments that block and/or inhibit cytokines or cytokine receptors and/or biological medicaments against B cells and/or biological medicaments that inhibit T cell co-stimulation and/or for monitoring the effectiveness of said treatments with said medicaments in responsive patients, comprising
[0133] one or more MHC class I molecules dextramers (Dextramers®) associated with peptides corresponding to Apoptotic Epitopes of human CD8+ T cells in one or more aliquots,
[0134] one or more aliquots of a sample representative of individuals affected by an autoimmune disease that are responsive to said treatments and one or more aliquots of a sample representative of individuals affected by said autoimmune disease that are non-responsive to said treatments and, optionally, one or more aliquots of a control sample representative of healthy individuals.
[0135] The one or more aliquots of a sample representative of individuals affected by an autoimmune disease that are responsive to said treatments and one or more aliquots of a sample representative of individuals affected by said autoimmune disease that are non-responsive to said treatment and, optionally, one or more aliquots of a control sample representative of healthy individuals are provided as control in order to enable the implementation of one or more of the methods of the invention by the use of the kit.
[0136] The aliquots of samples representative of individuals affected by an autoimmune disease that are responsive, and of individuals that are non-responsive to the therapeutic treatments as defined herein, can be aliquots of samples representative of the two typologies of patients for patients affected by an autoimmune disease in general; in particular, said aliquots could be of patients affected by a disease selected in the group comprising Rheumatoid arthritis (RA), Systemic lupus erythematosus (SLE), Scleroderma, Crohn's disease, Ulcerative colitis, Dermatomyositis, Anti-phospholipid antibody syndrome, Burger's disease, Hashimoto's thyroiditis.
[0137] According to the invention, the kit could comprise pairs of control aliquots (responsive patients and non-responsive patients) for one or more of each of the above-listed diseases.
[0138] All indications given above with regard to the dextramers, peptides, therapeutic treatments and suitable biological samples apply also to the above-described kit. However, in short, the peptides in the dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells in the above-described methods can be prepared as described above, or can be selected in the group of peptides having SEQ ID from 1 to 90.
[0139] In a specific embodiment, the peptides can be selected in the group consisting of SEQ ID 3, SEQ ID NO 31, SEQ ID NO 37, SEQ ID 64, SEQ ID NO 65.
[0140] The treatments to which the kit of the invention relates include treatments with biological medicaments that block and/or inhibit TNFα, like, e.g., medicaments selected in the group comprising adalimumab, certolizumab pegol, etanercept, golimumab, infliximab; treatments with biological medicaments that block and/or inhibit cytokines or cytokine receptors, like, e.g., medicaments selected in the group comprising tocilizumab, anakinra; treatments with biological medicaments against B cells, like, e.g., rituximab; treatments with biological medicaments that inhibit T cell co-stimulation, like, e.g., abatacept.
[0141] In all of the above-indicated embodiments the term “comprising” can be replaced by the term “consisting in”.
[0142] The following examples aim at illustrating embodiments of the invention and technical data demonstrating the validity thereof.
EXAMPLES
[0143] Patients and Methods
[0144] Study Population
[0145] 16 selected HLA-A2+ biologic-naive patients (i.e., patients that had never previously been treated with biological medicaments) affected by selected RA (F/M=15/1; median age 53 years, range 36-69 years, mean disease duration 96.6 months, range 6-240 months), who had shown a satisfactory response to conventional DMARDs (disease-modifying antirheumatic drugs), including methotrexate (associated or not with other anti-inflammatory/immunosuppressive drugs) and submitted to a subsequent treatment with Etanercept (according to the 1987 ACR criteria) were included in the study (Table 2 below). Each patient was given a standard dose of 50 mg Etanercept per week subcutaneously, and followed for clinical parameters. Clinical response was set in the present study as an improvement of the 28-joint-count Disease Activity Score (DAS28)>0.6 after 6 months of therapy according to EULAR response criteria. Of the 16 patients, 9 resulted responders (R) and 7 non-responders (NR) (Table 2 and
[0146] All patients and controls gave written informed consent.
[0147] Preliminary data on Systemic lupus erythematosus (SLE), Ulcerative colitis, Burger's disease and Hashimoto's thyroiditis show that the predictive method described herein can also be applied to those autoimmune diseases, supporting the applicability of the method to autoimmune diseases in general.
TABLE-US-00002 TABLE 2 Disease duration DAS28 Clinical Gender Age (months) DMARDS* ACPA** ESR result 1 F 59 18 MTX, HCQ neg 3.85 Non-responder 2 F 59 84 MTX pos 6.01 Non-responder 3 F 54 72 MTX, HCQ, SSZ pos 5.82 Responder 4 F 36 48 MTX, HCQ neg 1.26 Non-responder 5 F 38 16 MTX, HCQ neg 4.7 Responder 6 F 68 120 MTX, HCQ neg 5.44 Non-responder 7 M 51 18 MTX, HCQ, SSZ pos 5.08 Responder 8 F 43 60 MTX pos 5.02 Non-responder 9 F 62 84 MTX, LEF neg 4.91 Non-responder 10 F 69 84 MTX pos 5.65 Responder 11 F 48 240 MTX, HCQ neg 5.18 Responder 12 F 60 6 MTX neg 7.08 Responder 13 F 53 48 MTX neg 5.44 Responder 14 F 56 156 MTX pos 5.84 Responder 15 F 66 216 MTX, HCQ neg 4.74 Non-responder 16 F 44 216 SO, CsA, MTX, pos 4.32 Responder HCQ *Disease Modifying Anti-Rheumatic Drugs **Anti-citrullinated protein autoantibodies
[0148] Sythetic Peptides
[0149] HLA-2 binding peptides (nonamers or decamers) reported in SEQ ID NO 1-90 were derived from caspase-cleaved fragment of proteins [0150] Actin cytoplasmic 1 (ACTB, reference sequence having accession number P02570); [0151] heterogeneous nuclear riboprotein (ROK, reference sequence having accession number Q07244); [0152] lamin B1 (LAM1, reference sequence having accession number P20700) [0153] non-muscle myosin heavy chain 9 (MYH9 reference sequence having accession number P35579) [0154] vimentin (VIME reference sequence having accession number P08670) [0155] proteasome component C2 (PSA1 reference sequence having accession number P25786) [0156] rho GDP dissociation inhibitor 2 (GDIS reference sequence having accession number P52566) [0157] 60S acidic ribosomal protein C2 (RLA2 reference sequence having accession number P05387).
[0158] The peptides have the sequences SEQ ID from 1 to 90 and are reported in Table 1 above.
[0159] The selected peptides were associated with dextramers of MHC class I molecules, thereby obtaining dextramers (Dextramers®) of MHC class I molecules associated with peptides corresponding to Apoptotic Epitopes of human CD8.sup.+ T cells by technology performed as commercial service by Immudex, Copenhagen, Denmark.
[0160] Cell Preparations
[0161] Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient. Spontaneous apoptosis of T cells from patients was determined by staining fresh PBMCs with fluorescein isothiocyanate (FITC)-labeled Annexin-V (Biolegend), propidium iodide (PI) (Biolegend) and allophycocyanin (APC)-labeled anti-CD3 monoclonal antibody (mAb) (Biolegend).
[0162] Enzyme-linked Immunospot (ELISPOT) Assay
[0163] PBMCs following stimulation with 12 independent pools of AE (see Table 1 above) were tested by enzyme-linked immunospot (ELISPOT) assay. Briefly, 96-well millimeter high-affinity plates (Millipore Corporation, Bedford, Mass.) were coated with 10 μg/ml of capture mAb against IFN-γ (BD Bioscience) at 4° C. overnight. The plates were blocked for 2 hours with blocking solution (PBS containing 2% bovine serum albumin [BSA]). A total of 1×10.sup.5 PBMCs were added to each well and stimulated for 18 hours (h) with peptides. Biotinylated anti-IFN-γ (BD Bioscience) diluted to 5 mg/ml in Blocking Solution as indicated by the manufacturer was added and incubated for 2 h in 5% CO.sub.2 at 37° C. Plates were washed, incubated with alkaline phosphatase (AKP)-streptavidin (BD Bioscience) and developed with Sigmafast BCIP®/NBT (Sigma). The reaction was stopped by rinsing the plates with distilled water. Each well was then examined for positive signals (dots). The number of dots in each well was counted by an ELISPOT reader system (AELVIS reader system). IFN-γ-secreting cells were expressed as IFN-γ spots per each 1×10.sup.6 cells. The IFN-γ spot values were subtracted from the background, which was below 10 IFN-γ spots in 1×10.sup.6 cells for each test.
[0164] Monoclonal Antibody and Dextramer® Staining
[0165] PBMCs were incubated with APC-labeled-HLA-A*0201 dextramer® complexed respectively to MYH9.sub.478-486 (QLFNHTMFI, SEQ ID NO 31), MYH9.sub.741-749 (VLMIKALEL SEQ ID NO 37), VIME.sub.78-87 (LLQDSVDFSL SEQ ID NO 65), VIME.sub.225-233 (SLQEEIAFL SEQ ID NO 64) or ACTB.sub.266-274 (FLGMESCGI SEQ ID NO 3) peptides (Immudex, Copenhagen, Denmark). The incubation was performed in FACS buffer (PBS containing 2% human AB serum) at room temperature for 10 min, followed by washing and further surface staining with FITC-labeled mAb to CD8 (eBioscience).
[0166] In order to distinguish the various CD8 cells, also phycoerythrin-cyanine (PeCy)7-labeled mAb to PD-1 (eBioscience), AlexaFluor700-labeled mAb to CD69, PECF594-labeled mAb to HLA-DR, and a cocktail of labeled-mAbs and -reagents (APC-Cy7-labeled mAbs to CD4, CD14, CD16, CD19, and CD56 [Biolegend]) and Fixable Viability Dye eFluor 780 [eBioscience]) (dump channel), for 20 min at 4° C., were used. Dextramer®.sup.+ cells were analysed within a CD8.sup.+ T cell gate, whereas CD69.sup.+, HLA-DR.sup.+, or 1 PD+cells within dextramer®.sup.+CD8.sup.+ cells, after exclusion of B cells, monocytes, natural killer T (NKT) cells, NK cells, cells CD4.sup.+ T cells (dump channel). Cells were acquired with LSRFortessa cytometer (Becton Dickinson) and analysed with FlowJo software version 7.5.5 (Tree star, Inc. San Carlos, Calif.).
[0167] Intracellular Cytokine Labeling
[0168] Cytokine production was analysed by intracellular staining assay (ICS). PBMCs were incubated with or without the relevant peptides (20 μg/ml) plus anti-CD28 mAb (4 μg/ml) (BD Biosciences) and Protein Transport Inhibitor Cocktail (Brefeldin A and Monensin) (eBioscience), or with Cell Stimulation Cocktail as positive control (PMA, ionomycin, brefeldin A and monensin) (eBioscience), for 18 h at 37° C. Cells were washed, and stained with APC-labeled-HLA-A*0201 dextramers® complexed to the above-indicated peptides, PeCy7-labeled mAb to CD8 (Biolegend) and the dump channel reagents. Cells were fixed and permeabilised using Cytofix/Cytoperm solution (BD Biosciences) at 4° C. for 20 min, re-washed with Perm Wash Buffer (BD Biosciences), and stained with different combinations of AlexaFluor700-labeled IL17A (Biolegend), fluorescein-conjugated anti-IFN-γ (Biolegend) for 20 min at 4° C. Cells were washed, acquired with LSRFortessa cytometer (Becton Dickinson) and analysed with FlowJo software. IL-17, IFN-γ or IL-17/IFN-γ producing cells were analysed in CD8.sup.+ dextramer®.sup.+ T cells after exclusion of B cells, monocytes, NKT cells, NK cells, CD4.sup.+ T cells (dump channel).
[0169] Statistical Analyses
[0170] The collected data underwent statistical analysis by GraphPad Prism version 4 software (GraphPad Software). The data of comparison between healthy donors and patients, comparison in patients at different times, correlation between different tests performed and correlation between tests and clinical data were analysed, respectively, with Mann-Whitney test, Wilcoxon matched pairs test, linear regression and Spearman's correlation. The significance threshold was set at p=0.05. Receiver Operating Characteristic (ROC) analysis was performed to assess the predictive power of AE-specific CD8.sup.+ T cells. The area under the ROC curve (AUC) was calculated along with 95% confidence intervals (CI). In the study reported herein, AUC value indicates the ability of Dextramer®.sup.+ T cells to distinguish R and NR.
[0171] Results
[0172] Multispecific CD8.sup.+ T cell Responses to Apoptotic Epitopes (AE)
[0173] Initially, the Inventors analysed longitudinally the effector responses by the capacity of freshly isolated CD8.sup.+ T cells from either 12 of the 16 HLA-A2.sup.+ patients or 24 HDs, to form IFN-γ spots (in an ELISPOT assay) within 4 to 6 hours (h) of contact with 12 pools containing a total of 90 synthetic HLA-A2-binding apoptotic peptides (Table 1). Therefore, the Inventors defined these CD8.sup.+ T cells as “T.sub.EM”, on the basis of their capacity to perform their effector functions promptly within few hours of antigenic stimulus. Each peptide pool was tested in triplicate. The synthetic peptides used were prepared according to the sequence of caspase-cleaved proteins that had been previously identified by the proteomic analyses of apoptotic T cells (e.g., fragments of ACTB, ROK, LAM1, MYH9, GDIS, VIME, PSA1, e RLA2 proteins as above-defined and described). From the study it emerged that the responses to AE by IFN-γ.sup.+ CD8.sup.+ T.sub.Em cells were significantly higher and wider in the patients' pool than in the HD pool (
[0174] AE-specific CD8.sup.+ T Cells as Detected by Dextramers® Peptides are Predictive of the Effect of TNF-α Inhibitor Therapy
[0175] To explore the possibility that the frequencies of CD8.sup.+ T cells specific to AE, as detected by ELISPOT assay, were not different between R and NR (
[0176] AE-specific CD8.sup.+ T cells (and in particular those expressing the PD-1 exhaustion marker) were more represented in NR than in R (
[0177] Importantly, PD-1 expression inversely correlated with the frequencies of the total AE-specific CD8.sup.+ T cells (
[0178] Follow-Up of AE-Specific CD8.sup.+ T Cells in Rheumatoid Arthritis (RA) Patients Treated with TNF-α Inhibitors
[0179] Time course analyses of the disease, performed longitudinally throughout the follow-up in patients treated with TNF-α inhibitors, revealed, first, a significant decline of ELISPOT responses (that were equally represented in R and NR at the time 0 [see
[0180] Discussion
[0181] The Inventors therefore demonstrated for the first time that frequency, multispecificity, and magnitude of CD8.sup.+ T cells directed to AE were significantly higher in RA patients as compared with HDs pool, and correlated with the disease activity, indicating, without wishing to be bound by theory, that they might contribute to its progression. Amazingly, the frequencies of AE-specific CD8.sup.+ T cells (as detected by dextramers® technology) were significantly higher in pool R than in pool NR at the time 0 (before the start of therapy), as indicated by the significant ROC sensitivity and specificity. This, together with the finding that no clinical criteria (including DAS28-ESR, DAS28-CRP, or ACPA) was capable to discriminate R from NR in many autoimmune diseases, suggest that the frequency of AE-specific CD8.sup.+ T cells represents a unique biomarker predicting the response to therapy with TNF-α inhibitors and other biological medicaments such as those listed in this description in patients with autoimmune diseases.
SEQUENCE DESCRIPTION
[0182] The sequences are described in Table 1 above.
REFERENCE
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