CC BY 4.0 · Global Medical Genetics 2020; 07(02): 051-063
DOI: 10.1055/s-0040-1715641
Original Article

From Anti-EBV Immune Responses to the EBV Diseasome via Cross-reactivity

Darja Kanduc
1  Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, Italy
,
Yehuda Shoenfeld
2  Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Aviv University School of Medicine, Tel-Hashomer, Israel
3  I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Sechenov University, Moscow, Russia
› Author Affiliations
Funding None.
 

Abstract

Sequence analyses highlight a massive peptide sharing between immunoreactive Epstein-Barr virus (EBV) epitopes and human proteins that—when mutated, deficient or improperly functioning—associate with tumorigenesis, diabetes, lupus, multiple sclerosis, rheumatoid arthritis, and immunodeficiencies, among others. Peptide commonality appears to be the molecular platform capable of linking EBV infection to the vast EBV-associated diseasome via cross-reactivity and questions the hypothesis of the “negative selection” of self-reactive lymphocytes. Of utmost importance, this study warns that using entire antigens in anti-EBV immunotherapies can associate with autoimmune manifestations and further supports the concept of peptide uniqueness for designing safe and effective anti-EBV immunotherapies.


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Introduction

The connection between Epstein-Barr virus (EBV) and Burkitt's lymphoma (BL) was discovered in 1964.[1] Almost contemporaneously, high anti-EBV antibody levels were found in BL.[2] [3] Since then, EBV infection has been associated with a wide spectrum of malignancies that, besides BL, comprehends different types of lymphomas, nasopharyngeal carcinoma (NPC), breast and brain cancer, and oral hairy leukoplakia,[4] [5] [6] [7] [8] among others. In addition, EBV has been implicated in a wide variety of diseases, including systemic lupus erythematosus (SLE), Sjögren's syndrome, multiple sclerosis (MS), myasthenia gravis (MG), rheumatoid arthritis (RA), autoimmune thyroid disorders, inflammatory bowel disease, celiac diseases, diabetes, Parkinson's disease, myopericarditis, dilated cardiomyopathy, and even death.[9] [10] [11] [12] [13] [14]

At the same time, anti-EBV antibody level was found to be higher in BL patients than in control subjects.[3] [15] [16] [17] High level of anti-EBV immunoglobulin G antibodies were also found in subjects with NPC,[18] [19] [20] [21] with IgG reactivity increasing significantly with tumor stage[21]; Hodgkin and non-Hodgkin lymphomas[22] [23] [24]; precancerous gastric lesions[25]; MS[26] [27] [28] [29]; RA[30] [31] [32]; MG[33] [34]; and SLE,[29] [31] [34] among others. In general, high antibody titers to EBV appeared to be related to a worse prognosis, a phenomenon that has been described by Coutinho's laboratory[35] as “the advantage of being low-respondents.” Currently, measurement of increased anti-EBV antibody titers is utilized to predict, to detect, and to monitor the progression of EBV-related cancers and progression of the various EBV-induced diseases.[36] [37] [38]

Today, in front of such well known clinical context, the molecular mechanism(s) by which anti-EBV immune responses relate to the EBV diseasome, from lymphomas to Parkinson's disease, are still obscure. From a logical point of view, a central question remains unanswered and perhaps, as far as we know, has never been clearly posed: why the powerful anti-EBV immune responses herald cancers, autoimmune diseases, and death instead of eradicating the viral infection and re-establishing a healthy status?

In the clinical frame exposed above and on the basis of previous scientific reports[39] [40] [41] [42] that have detailed a high level of peptide sharing between EBV and human proteins involved in crucial functions, this study investigates whether the immune responses that accompany active EBV infection have the potential to cross-react with and damage human proteins that, when altered, can lead to various cancer and autoimmune diseases. That is, the thesis is explored according to which the anti-EBV immune responses that should be a “protective defense” from EBV infection actually cross-react with human proteins, in this way setting up an anti-human protein assault with catastrophic pathologic sequelae in the body. Specifically, the present study used the pentapeptide as an antigenic and immunogenic unit,[43] [44] [45] [46] [47] [48] and analyzed 3,197 experimentally validated immunoreactive EBV-derived epitopes for pentapeptide matches with the human proteome. Data are reported on a vast peptide sharing between EBV epitopes and proteins involved in tumorigenesis, autoimmune disorders, diabetes, and death, among others. The data suggest that cross-reactivity is the mechanism underlying the causal connection between EBV infection, immune response, and the EBV-associated diseases.


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Methods

An EBV immunome formed by 3,197 immunopositive linear epitopes was assembled from Immune Epitope DataBase (IEDB, www.iedb.org).[49] The immunopositive EBV epitopes are listed in [Supplementary Table S1] (available in the online version). EBV epitope sequences were dissected into pentapeptides overlapped each other by four amino acid (aa) residues. The resulting 11,564 pentapeptides were analyzed for occurrence(s) within the human proteome using Pir Peptide Match Program.[50] Proteins related to EBV-induced diseases were annotated. UniProtKB database (http://www.uniprot.org/)[51] PubMed, and OMIM resources were used.

Table 1

Numerical description of the pentapeptide sharing between the set of 3,197 immunopositive EBV epitopes and the human proteome

Pentapeptides composing the 3,197 EBV epitope immunome

11,564

EBV epitope pentapeptides not shared with the human proteome

798

EBV epitope pentapeptides shared with the human proteome

10,766

Human proteins sharing pentapeptides with EBV epitopes

18,744

Occurrences of EBV epitope pentapeptides in the human proteome (including multiple occurrences)

137,805

Abbreviation: EBV, Epstein-Barr virus.



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Results

Quantitation of the Peptide Sharing between EBV Epitopes and the Human Proteome

Following matching analyses of the 11,564 pentapeptides composing the 3,197 experimentally validated immunoreactive EBV epitopes, it was found that almost all of the epitope-derived pentapeptides (i.e., 93%) are widespread among thousands of human proteins ([Table 1]). From a mathematical point of view, if one considers that the probability of a pentapeptide to occur in two proteins is 20−5 (or 1 out of 3,200,000 or 0.0000003125), then the peptide overlap existing between the EBV immunome and the human proteome is staggering.


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Distribution of the Peptide Sharing among EBV Epitopes

A synthetic snapshot (i.e., 201 EBV epitopes) of the immunoreactive peptide sharing is shown in [Table 2], where peptide sequences shared with the human proteins are given in capital format and peptide fragments uniquely present in EBV are given with aa in small bold format. [Table 2] clearly shows that the immunoreactive EBV epitopes are predominantly composed by peptide sequences common to human proteins.

Table 2

Pentapeptide sharing between 201 immunoreactive EBV epitopes and human proteins[a]

IEDB ID[b]

EPITOPE[c] [d]

IEDB ID[b]

EPITOPE[c] [d]

IEDB ID[b]

EPITOPE[c] [d]

950

AEGLRALLARSHVER

45499

NPTQAPVIQLVHAVY

127195

TEMYIMYAM

1518

AGGAGAGGGAGGA

46498

NVTQVGSEPISPEIG

127369

WEMRAGREI

1716

AGVFVYGGSKTSLYN

47613

PGAPGGSGSGP

127392

WPTPKTHPV

2390

ALAipqcrL

47760

PGTGPGNGLGEKGDT

127408

yamaiRQAI

2742

ALLVLYSFAL

48320

PLFDRKSDAK

137773

YNLRRGIAL

2743

ALLVLYSFALMLIIIILIIF

48486

PLSRLPFGM

138854

GAGAGAGA

3005

ALWNLHGQALFLGIVL

48852

PPPGRRPffhpvGE

138856

GRGRGRGR

3600

apifyPPVL

48876

PPPqapyqGY

138882

MTAASYARY

3782

APRLPDDPI

49864

PVFDRKSDAK

138873

LMARRARSL

3951

AQEILSDNSEISVFPK

50298

QAKWRLQTL

141342

LLDFVRMGV

5316

AVFDRKSDAK

51685

QNGALAINTF

144799

TLNLT

5317

AVFDRKSVAK

51946

QPRAPIRPI

167590

GPQRR

5326

AVFNRKSDAK

52142

QQrpvmfvSRVPAKK

186702

PQPRAPIRPIPT

5439

AVLLheesm

53195

RARGRGRGRGEKRP

191290

FIVFLQTHI

8120

DEPASTEPVHDQLL

54367

RKIYDLIEL

227777

HPVAEADYFEY

8905

DKIvqapifyPPVLQ

54728

RLRAEAQVK

230640

ASDYSQGAF

9644

DPhgpvqLSYYD

55251

RppifiRLL

230798

FYPPVLQPI

10448

DTPLIPLTIF

55298

RPQKRPSCI

231136

LAYArgqam

10858

DYDASTESEL

55327

RPRPPARSL

231402

RRVRRRVLV

10963

DYSQGAFTPL

55529

RRARSLSAERY

231547

TVFYnippm

11804

EENLLDFVRF

55619

RRIYDIEL

231696

YRTATLRTL

12183

EGGVGWRHW

56506

RYAREAEVRF

231699

YSQGAFTPL

13628

EPDVPPGAIEQGPAD

56523

RYEDPDAPL

231800

AQPAPQAPY

16876

FLRGRAYGI

56650

RYSIFFDY

231839

DSIMLTATF

17110

FMVFLQTHI

56651

RYSIFFDYM

231840

DTRaidqfF

17600

FRKAQIQGL

57755

SFFDRKSDAK

231880

FLQRTDLSY

18328

FVYGGSKTSL

59084

SLFDRKSDAK

231966

HVIQNAFRK

18438

FYnippmPL

59432

SLREWLLRI

232020

KPWLRAHPV

18946

GDDGDDGDEGGDGDE

62305

SVRDRLARL

232021

KQRKPGGPW

19674

GGAGGAGGAGAGGGAG

67456

TYSAGIVQI

232030

KTIGnfkpy

19737

GGGAGAGGAGAGGGGR

68561

VFSDGRVAC

232074

LPTPMQLAL

20023

GGSKTSLYNLRRGTA

69558

VLKDAIKDL

232076

LQALSNLIL

21719

GPPAA

70251

VPAPAGPIV

232078

LQSSSYPGY

21723

GPPAAGPPAAGPPAA

70624

VQPPQLTQV

232080

LSaerytLF

21870

GQGGSPTAM

70932

VSFIefvgw

232081

LSVIPSNPY

22159

GRPAVFDRKSDAKST

71968

VYAASFSPNL

232086

LTQAAGQAF

22976

GVFVYGGSKTSLYNL

72028

VYGGSKTSL

232095

LVSSGNTLY

23324

GydvghGPL

72251

WAPSV

232096

LVSSSAPSW

23449

GYRTATLRTL

73221

WVPSV

232103

MEQRVMATL

23994

Hhiwqnll

74120

yhlivDTDSL

232177

QEPGPVGPL

24170

HLAAQGMAY

75188

YNLRRGTAL

232178

QEQLSDTPL

24533

HPVgeady

75189

YNLRRGTALAIPQ

232199

RESIVCYFM

24666

HRCQAIRK

75356

YPLheqhgM

232214

RLHRLLLMR

24667

HRCQAIRKK

75360

YPLHKQHGM

232232

RPAPpkiam

26480

IIFIFRRDLLCPLGAL

75731

YSFALMLIIIILIIFIFRRD

232276

SEPCEALDL

26538

IIIILIIFI

79634

QPRAPIRPIT

232308

SQISNTEMY

27103

ILIIFIFRRDLLCPLGALCI

93251

LLARSHVER

232332

TEdnvppwl

27301

ILRQLLTGGVKKGRP

94034

THIFAEVLKD

232416

VTFSAGTFK

27375

ILTDFSVIK

97317

fwemrAGREITQ

232419

VTTQRQSVY

29618

IYLLEMLWRL

98084

GVFVYGGSK

232427

waqigHIPY

30430

KEHVIQNAF

101654

FVYGGSKTSLY

232437

WQRRYRRIY

30431

KEHVIQNAFRK

101878

LQTHIFAEV

232473

YQEPPAHGL

33207

KRppifiRR

102253

YPLheqygM

237896

QTAAAVVF

33866

KTSLYNLRRGTALA

106084

RPRSPSSQSSSSGSPPRRP

237920

RYKNRVASR

35162

LDFVRFMGV

107724

AARQRLQDI

540571

QPRLTPPQPL

35533

LEKARGSTY

107869

GPKVKRPPI

540583

RPTELQPTP

37153

LLDFVRFMGV

108006

LLDFVrfmgy

540628

TSSPSMPEL

38514

LPGPQVTAVLLHEES

108191

VMATLLPPV

548981

LLDFVRFMG

39102

lrgkwQRRYR

118970

PPPGRRP

548987

NGALAINTF

39634

LSRLPFGMA

124861

WNLHGQALFL

548994

QNGALAINT

41113

MARRARSLSaerytL

126528

LAsamrmLW

595247

FGLVLFPAQI

41147

MATLLPPVPQQPRAG

126967

RPRPrtpew

653929

AAQGMAY

41841

mkkawLSRAQQADAG

126980

RRAALSGHL

672845

PIFIRRL

42525

MSDEGPGTGPGNGLG

126985

RRLHRLLLM

674203

RamsfiATY

42941

MVFLQTHIFAEVLKD

126986

RRRRRRAAL

675184

RppifiR

44181

NIAEGLRAL

126991

RRYRRIYDL

676208

RRIYDLI

45378

NpkfenIAEGLRALL

127118

SQAAFGLPI

695961

QAPYPGYEE

Abbreviations: EBV, Epstein-Barr virus; IEDB, Immune Epitope DataBase.


a Epitopes assembled from IEDB (www.iedb.org).[49] Epitope experimental details and references are available at www.iedb.org.


b Epitopes listed according to IEDB ID number.[49]


c Epitope sequences given in 1-letter code.


d Pentapeptides shared between EBV epitopes and human proteins are given in capital letters, while pentapeptides present only in EBV are given in bold small format.


Immunologically, [Tables 1] and [2] document that the experimentally validated immunoreactive EBV epitopes mostly consist of pentapeptides that also occur in human proteins, in this way indicating a highest cross-reactivity potential, given the fact that a pentapeptide is a minimal immune determinant that contains the immunological information in terms of both immunogenicity and antigenicity.[43] [44] [45] [46] [47] [48]


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The Pathological Implications of the Peptide Sharing between EBV Epitopes and Human Proteins: Lymphomas and Leukemias

Numerous cancer-related proteins share peptides with the here analyzed self-reactive EBV epitopes. Reasons of space do not permit a detailed peptide-by-peptide description of the sharing and only a few examples are described in [Tables 3] and [4]. Specifically, [Table 3] shows the peptide sharing between the immunoreactive EBV epitopes and human proteins that—when mutated, modified, improperly functioning or deficient—are implicated in lymphomagenesis/leukemogenesis.[52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] It can be seen that the extent of the peptide sharing is very high and comes to the fore with glaring evidence when focusing on histone-lysine N-methyltransferase 2D (KMT2D), the disruption of which perturbs germinal center B cell development and promotes lymphomagenesis.[77] [78] KMT2D alterations are involved in follicular lymphoma and diffuse large B-cell lymphoma,[92] cutaneous T-cell lymphoma and Sézary syndrome,[93] ocular adnexal MALT-type marginal zone lymphomas,[79] and chronic myeloid leukemia.[94] Moreover, KMT2D alterations are involved in intraocular medulloepithelioma,[95] small cell lung cancer,[96] bladder cancer,[97] [98] and non-small-cell lung cancer.[99] Of not less importance, alterations of KMT2D have a causal role in Kabuki syndrome[100] that is characterized by skeletal and visceral abnormalities and cardiac anomalies,[101] hyperinsulinism,[102] epilepsy,[103] desmoid fibromatosis,[104] immunopathological manifestations,[105] lupus,[106] and oriental alterations,[107] among others.

Table 3

Pentapeptide sharing between immunoreactive EBV epitopes and human proteins implicated in lymphomagenesis/leukemogenesis

Shared peptides

Lymphoma/Leukemia-related proteins containing EBV epitope peptide(s)[a]

Ref[b]

LSPLL, RRQKR, LALRA, KEVLE, LGLGD, GNLVT, SLESV, LPTLL, PETVP, ALYLQ, ARVKE, PSLKL, KILLA, NPETL, EGLKD, LYLQQ, QKRPS, VAKVA, DRHSD, LQAIG, LSQVC, RPSCI

ATM: Serine-protein kinase ATM

[52]

PLPPP, PPLPP, LPTLL, REAIL, AERHG, CKKDH

BANK1: B-cell scaffold protein with ankyrin repeats

[53] [54]

EEEEE, PPLPP, GAGGG, AGAGG, GAGGA, AGGGA, GRGGG, PPPVS, LSAAS, PPLGP, PPVSP, EPGPA, PVSPG, SSLTP, TPPPQ, GDDDD, AVAQS, DPSLG, GNSST, PGLFP, SEPVE, DDAGG, DDDAG

BC11B: B-cell lymphoma/leukemia 11B

[55] [56] [57]

SSSEE, GPPSP, APAST, GPEAR, PCPQA, PQARL, RFIQA

BCL6B: B-cell/lymphoma 6 member B protein

[58] [59] [60] [61] [62]

SPSPP, PLPPV, GSGAG, PAGSL, PVPPP, EPGPA, EQASL, EGTRL, LDLDF, LNQNL, VLQKL

BIN1: Myc box-dependent-interacting protein 1

[63]

LLLLL, LRLLL, RLRLL, KEDDG, EGGQN

CADM1: Cell adhesion molecule 1

[64]

PPPPP, LPPPP, GSGSG, GGGSG, GAGGG, GSGGS, SGGSG, GGSGS, SGSGG, LPPVP, PPVPA, PVPPT, QQGSG, CTPGD, PYILD

CBL: E3 ubiquitin-protein ligase CBL

[65]

PPPLP, PPGPS, LSPLS, SSPQP, ATSGA, ENLLD, EENLL, SPVLG, AFEEV, GPQDP, YDAPG

CRTC2: CREB-regulated transcription coactivator 2

[66]

LLARL, GASGS, VAGLL, PLHAL, LARLR, SGASP, CGLLR, VPKPR, FIRRL, TDGKT, TPLLT, ALIKT, SSCNS

DAPK1: Death-associated protein kinase 1

[67] [68]

EEEAE, FGLSR, SDLSR, SLESV, KAIEE, VIQLV, IIAVV, VMDLL, IAVVA, IKAIE, ESFTQ, QDVGA, RLFAA, TTGGK, VIKAI, SFTQG

EPHA7: Ephrin type-A receptor 7 (998 aa)

[69]

LLLLL, PPPPP, LPPPP, ALLLL, LALLL, PPPPS, PPLPP, FPPPP, SLSST, GSPPR, PPQVP, SPSDS, TLSPS, TSEPV, SEDDP, ESVDV, GTPPQ, TDGGG, TSVVQ, VYAAS, EDDPQ, PSELD, DLRPL, FVGDY, KGTPP, PRLFA, VCSVA, HSPVV, ILQIS, LYEAS, PYEAF

FAT1: Protocadherin Fat 1

[70] [71]

PPPPP, GGGGG, EEEEA, AAAAV, SSSEE, GGSGS, GGGGD, RGGSG, GAPGG, ASGPG, LPGVP, VSPAV, PGGLG, VEAHV, GGDGD, LRAAT, ERPLA, FPEGV, GGDKV

HIC1: Hypermethylated in cancer 1 protein

[72]

PPRPP, RRRKG, ATAAA, SVSQP, AEVLK, LLQTE, SHTAT

KDM6A: Lysine-specific demethylase 6A

[73] [74]

PPPPP, QPPPP, SPPPP, SSSSA, SSSAP, PTPPP, GAPAA, KKRKR, RGGRG, GGRGR, PPPPY, SSSAG, GRGGR, LPPTP, APPTP, PPLGP, PTPLP, SGSPP, PQPPL, SQASA, DDEDL, STSVP, LPGVS, SSGTA, LTPRP, RPRGA, RQRSR, SGLGT, TPRPP, TPRPS, TSVPS, VTLPL, DLILQ, GTPRP, TPRPV, IAVSS, LDTED, TPRPR, LGATI, SAPRK, EGVEV, LSPAN, LSSCP, MQPPP, SLIQL, AKIEA, EDLFG, EEVEN, QGVQV, TPRSQ, VEDLF, LGLYA, PQSGP, DSREG, VSTAD, GPADD, PADDP, QSLIQ, VFPKD, DTDSL, GTFKP, IPQTL, PLQHW, TGQGK, EQHGM, IDDNS, LRPQW, QRHSD, TFKPP, GPRHT

KMT2C: Histone-lysine N-methyltransferase 2C

[75] [76]

EEEEE, QPPPP, PLPPP, SAAAA, LRLLL, PAPAA, PAAAP, PTPPP, APPAP, GRGRG, PPSPG, PSPGS, PSPPP, RGRGR, SPLLP, AAPPA, GPAGP, LLAAL, PAQPP, SLGLA, LAPSP, LSPLL, PGPAG, SPSQS, SQSSS, GGRGR, GLPPP, PQGPP, RLRLL, LPPTP, LRSLG, PTLLL, SPSSQ, TPPPS, ALAPS, EGLRA, GPQPP, PEPPT, PLTEP, SSGSP, AASED, APVAP, AVGPP, DDEEL, ESPAR, GAHGG, GPPRL, KKRKR, LTPRP, PALDD, PPPGR, PPQGP, PPQVP, PPTQH, PTLGK, SDEAE, SPLLG, TPHTK, APYPG, ARPPE, ASDRL, CPSLD, DAAAR, EERPP, EGEGD, EGPST, EPRLA, FPDTK, FPEGL, GPLAI, GPWDP, GTQDP, IKVIE, LGLYA, LRLTP, LSPVI, PLLTV, PMSPP, PPTHP, PPVPQ, PQPLM, PQQPM, PSRPQ, QALAP, QEPPP, QTNQA, RGAFG, RPEFV, SDALG, SPVTP, SQTEL, SRVPA, SYTDP, TGSGG, TTPAG

KMT2D: Histone-lysine N-methyltransferase 2D

[77] [78] [79]

GGGGG, GGGGS, GGGGA, AGGGG, GGSGG, GGGSG, GAGGG, GGAGG, AGAGA, PPPEP, LRALL, LALRA, LTPPS, RALLA, RLLLK, PQAPE, TPLDL, GPETR, RVGAD

NFKB2: Nuclear factor NF-kappa-B p100 subunit

[80] [81] [82] [83]

AAAPA, GAAAS, PAPGL, LLGGG, TPSPS, SLPHP, PHLPP, GSPTA, PLTSE, RDSYA, TTLAA, YPGYA, HRDSY, SYPGY

PRDM1: PR domain zinc finger protein 1

[84]

EEEEE, PSPPP, APAAA, SPSPP, PSPSP, SPSPS, PLDLS, DEGEE, LDLSV, LLTPV, PTVSP, KQLLQ, VLDLS, LTPVT, TVSPS, VTEDL, AIEEE, TSEET, PAPTV, TPVTV, EAVSF, FKPPP, SFKPP, NIPQT, YSLRL, PALRD, RSQVK, PFVGD

PRDM2: domain zinc finger PR protein 2

[85] [86] [87] [88]

SSSSA, SPLLP, SSSAP, LSPLL, GTPSG, LQSET, PVSRF, AEGKL, PLRPT

SOCS6: Suppressor of cytokine signaling 6

[68]

KKRKR, AGAAR, LQSLA, TSPTS, RSLLT, LSLVF, AGPSV, DPVHG, GPSVA, QATLG, TQLTQ, DLQDP, LEKQS, PVQGE, QERDV, PKTAS, PLTQP, NIEEF, TPHQP, SHETP

TET1: Methylcytosine dioxygenase TET1

[89]

PPPLP, PPPPS, SPPPP, SSSEE, ELLEK, SASGS, QSSHL, APGGS, LQAPG, KLSSL, PPSQL, APPSQ, HLLQH, QQASV, VTKQE, VTVLT, PPTQH, PVTVL, GIKRT

TET2: Methylcytosine dioxygenase TET2

[90]

PPPPP, LPPPP, PLPPP, PPPLP, PPLPP, PPPPS, GGGRG, APGGG, GLPAP, QPPPQ, PAPGP, PRGPP, PPSSG, SLGLA, LPAPG, LPPVP, PLPPV, PPPSR, GGRPG, PPPGR, DLRSL, VGPLS, PMPPP, SEGLV, SGNGP, ADIGA, DIGAP, GGDQG, PVGPL

WASP: Wiskott-Aldrich syndrome protein

[91]

a Human proteins reported by UniProt entry names.


b Further references on the function/disease association at www.uniprot.org, OMIM, and PubMed resources.


Table 4

Quantitative pentapeptide matching between immunoreactive EBV epitopes and human proteins related to various cancers and diseases

Pentapeptides:

Human proteins sharing pentapeptides with EBV epitopes, and disease involvement[c] [d]

Refs.

A[a]

B[b]

3

ACHA: Acetylcholine receptor subunit α. MG.

[117]

7

ACHD: Acetylcholine receptor subunit delta. MG.

[117]

8

ACHE: Acetylcholine receptor subunit epsilon. MG.

[117]

9

11

ACHG: Acetylcholine receptor subunit gamma. MG.

[117]

31

42

AGRB1: Adhesion G protein-coupled receptor B1. Inhibits glioma growth.

[118] [119]

15

AKA12: A-kinase anchor protein 12. MG autoantigen. Involved in breast cancer.

[120]

27

APC: Adenomatous polyposis coli protein. Relates to colorectal adenomas and breast cancer.

[121] [122] [123]

64

68

APCL: Adenomatous polyposis coli protein 2. Its repression promotes ovarian cancer.

[123] [124]

57

68

ARI1A: AT-rich interactive domain-containing protein 1A. Bladder, colorectal, endometrial, esophageal, gastric, kidney, liver, lung, ovarian cancers.

[108]

68

92

ARI1B: AT-rich interactive domain-containing protein 1B. Liver cancer.

[108]

33

ARID2: AT-rich interactive domain-containing protein 2. Liver, lung, melanoma cancers.

[108]

23

BCOR: BCL-6 corepressor. Tumor suppressor in endometrial cancer and medulloblastoma.

[108] [125]

9

C1S: Complement C1s subcomponent precursor. SLE.

[126]

20

CHD4: Chromodomain-helicase-DNA-binding protein 4. Endometrial cancer.

[108]

32

34

CHD6. Chromodomain-helicase-DNA-binding protein 6. Bladder cancer.

[108]

38

CHD8: Chromodomain-helicase-DNA-binding protein 8. glioblastoma.

[108]

10

CLAT: Choline O-acetyltransferase. Myasthenic syndrome.

[127]

17

CO4A: Complement C4-A precursor. SLE.

[128]

29

56

CO4A1: Collagen α-1(IV) chain. Tumor suppressor; anti-angiogenic.

[129]

17

CO4B: Complement C4-B precursor. SLE.

[128]

12

13

CUL7: Cullin-7. 3M syndrome with growth restriction, skeletal abnormalities and dysmorphisms.

[130]

25

26

DCC: Netrin receptor DCC. Required for axon guidance. Colorectal cancer suppressor.

[131]

16

66

DMBT1: Deleted in malignant brain tumors 1 protein. Suppressed in human lung cancer.

[132] [133]

59

DYST: Dystonin. Bullous pemphigoid.

[134] [135]

42

FAT4: Protocadherin Fat 4. Involved in hepatocellular carcinoma. and in gastric cancer risk.

[136] [137]

34

38

FUBP2: Far upstream element-binding protein 2.

[138]

11

IGF1R: Insulin-like growth factor 1 receptor. Intrauterine and postnatal growth retardation.

[139]

14

INSR: Insulin receptor. Insulin resistance syndrome with pineal hyperplasia.

[140]

13

INSR2: Insulin, isoform 2. Diabetes.

[141]

27

31

IRS1: Insulin receptor substrate 1. Diabetes. cognitive impairment and Alzheimer's disease.

[142]

42

45

IRS2: Insulin receptor substrate 2. Diabetes. cognitive impairment and Alzheimer's disease.

[142] [143] [144]

38

50

IRS4: Insulin receptor substrate 4. Diabetes. cognitive impairment and Alzheimer's disease.

[142]

20

KDM5A: Lysine-specific demethylase 5A. Intellectual disability. Inhibits glioma cells migration.

[145] [146]

2

LA: Lupus La protein. SLE.

[147]

16

LRP1B: Low-density lipoprotein receptor-related protein 1B precursor 4599.

[148]

6

MAG: Myelin-associated glycoprotein precursor. MS.

[149]

4

MOG: Myelin-oligodendrocyte glycoprotein precursor. MS.

[150]

13

19

MYRF: Myelin regulatory factor. MS.

[151]

17

12

MYT1L: Myelin transcription factor 1-like protein. MS.

[152]

45

47

NBEL2: Neurobeachin-like protein 2 Role in neutrophil and NK cell function and pathogen defense.

[153]

27

NF1: Neurofibromin. neurofibromatosis.

[154]

44

47

NMDE4, Glutamate receptor ionotropic, NMDA 2D. Epileptic encephalopathy.

[155]

97

113

Obscurin: Heart disease.

[156]

26

39

SMCA4: Transcription activator BRG1. Esophageal, medulloblastoma, lung cancers.

[157]

62

113

SRRM2: Serine/arginine repetitive matrix protein 2. Thyroid carcinoma; Parkinson's disease.

[158] [159]

15

STA13: StAR-related lipid transfer protein 13. Deleted in liver cancer 2 protein.

[160]

8

9

TGFB1: Transforming growth factor β-1 proprotein. Lupus nephritis in SLE Patients.

[161]

250

341

TITIN: Titin. Myocarditis, acute myocardial ischemia, cardiac arrest.

[162]

32

34

TRNK1: TPR and ankyrin repeat-containing protein 1. SLE. Neural development and differentiation.

[163]

12

TSP1: Thrombospondin-1. Inhibits tumor angiogenesis and suppresses tumor growth.

[164]

24

ZAN: Zonadhesin . Crucial role in sperm-zona adhesion. Sterility.

[165]

40

ZEP1: Zinc finger protein 40. Tum or-suppressive effects in prostate and nonsmall cell lung cancer.

[166] [167]

Abbreviations: EBV, Epstein-Barr virus; DNA, deoxyribonucleic acid; MG, myasthenia gravis; MS, multiple sclerosis; SLE, systemic lupus erythematosus.


a Column A: number of shared peptides.


b Column B: number of shared peptides including multiple occurrences.


c Human proteins reported by UniProt entry names. Protein details, sequence, and aa length available at www.uniprot.org.


d Further references on the function/associated disease are available at UniProt, OMIM, and PubMed resources.


Also, the intense peptide sharing between immunoreactive EBV epitopes and KMT2C is of relevance. KMT2C not only may act as a tumor suppressor in leukemias and T-cell lymphomas,[75] [76] but it is also implicated in bladder, breast, colorectal, endometrial, gastric, head and neck, lung, and liver cancer, and in medulloblastoma.[108]

Then, in spite of the lack of space, it is mandatory noting the harmful cross-reactivity platform represented by the peptide commonality between the immunoreactive EBV epitopes and Wiskott-Aldrich syndrome protein (WASP) ([Table 4]). The 29 pentapeptides shared with EBV epitopes mainly occur throughout the central and COOH regulatory domains of the WASP primary sequence ([Fig. 1], shared peptides in underlined bold character) and produce a “bull” for the EBV-activated immune system that is practically impossible not to hit. Hitting WASP can lead to lymphomagenesis. Indeed, WASP is a tumor suppressor frequently low or absent in anaplastic large cell lymphoma.[92] WASP deficiency relates to Wiskott-Aldrich syndrome (WAS).[109] [110] [111] [112] WAS is characterized by eczema, thrombocytopenia, recurrent infections, immunodeficiency, neutropenia, and bloody diarrhea.[113] A large proportion of WAS patients develop autoimmunity and allergy since WASP appears to play an important role in the activation of CD4(+)CD25(+)FOXP3(+) natural regulatory T cells.[114] Even in the absence of typical clinical manifestations of WAS, a low expression of WASP associates with the pathogenesis of a subtype of inflammatory bowel disease.[115] Furthermore, deficiency of WASP associates with exacerbated experimental arthritis.[116]

Zoom Image
Fig. 1 Distribution of EBV epitope-derived peptides throughout WASP primary aa sequence. WASP sequence from Uniprot (http://www.uniprot.org/).[51] EBV epitope-derived peptides are underlined and bold marked. EBV, Epstein-Barr virus; WASP, Wiskott-Aldrich syndrome protein.

Overall, the peptide sharing between the immunoreactive EBV epitopes and KMT2D, KMT2C, and WASP proteins suffices to define the constellation of human diseases associated with EBV infection.


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The Pathological Implications of the Peptide Sharing between EBV Epitopes and Human Proteins: Various Cancers and Diseases

[Table 4] illustrates that the EBV epitope-derived pentapeptides are widespread among the most disparate human proteins able to cause, when altered, a vast spectrum of diseases, from diabetes and sterility to myocarditis and death,[117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] the latter two being possibly associated with the Titin imposing peptide sharing (250 shared pentapeptides).


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Discussion

We summarize here the vast peptide platform that, with impressive mathematical unexpectedness, connects immunoreactive EBV epitopes and human proteins.

Quantitatively, [Table 1] shows that the peptide sharing does not obey to any theoretical probability expectations or constraints such as, for example, protein dimension. The case is best illustrated by the far upstream element-binding protein 2 (FUBP2; 711 aa) and the low-density lipoprotein receptor-related protein 1B (LRP1B; 4,599 aa). FUBP2 has 34 pentapeptides in common with the herpesviral proteome, whereas the much longer LRP1B shares 16 pentapeptides ([Table 4]). That is, a high number of shared pentapeptides can be found in a protein irrespective of the protein length.

Pathologically, the peptide sharing between the immunoreactive EBV epitopes and the human proteome implies the possibility of cross-reactions and of a consequent wide spectrum of diseases, from lymphomas and leukemias to diabetes and spermatogenesis ([Tables 3] and [4]). From this point of view, [Tables 3] and [4] offer a scientific explanation of the clinical fact that EBV infection can trigger so many and so various diseases in so different and distant parts of the body. Moreover, given the number of human proteins involved in the sharing, the possibility of cross-reacting with a specific protein or group of proteins and inducing a specific disease or group of diseases will depend on the “when and where” the disease-associated protein(s) will be expressed. Consequently, the EBV diseasome will manifest with different diseases depending on the age of the subjects and on the immunological imprinting by previous pathogen infections,[168] thus explaining also why, once the immune system has been activated by EBV, some subjects will develop a lymphoma while other subjects contract diabetes or lupus or will die.

Immunologically, the vast peptide sharing between immunoreactive EBV epitopes and human proteins fails to support the theory of microbial or of human immunological specificity and nullifies the current concept of self-tolerance. Indeed, it was advanced in the “50s and still persists today the Burnet's hypothesis according to which self-tolerance is achieved by the so-called negative selection” of self-reactive lymphocytes.[169] [170] [171] That is, lymphocytes with specificity for peptide sequences that are expressed in the human host are hypothesized to be deleted from the immunological repertoire during fetal or early life to avoid self-reactivity and the consequent autoimmunity. Clearly, such a hypothesis breaks down in front of the pervasive peptide overlap between immunoreactive EBV epitopes and human proteins. If the “negative selection” assumptions were true, the self-reactive lymphocytes targeting the experimentally validated EBV epitopes described here and almost exclusively composed by peptides common to human proteins would have had to be eliminated from the immunological repertoire in the fetal life. It seems that the postulated deletion of potentially self-reactive lymphocytes did not occur. Similar results have been obtained analyzing hepatitis C virus and human papillomavirus immunoreactive epitopes.[172] [173] Altogether, our data indicate that potentially self-reactive lymphocytes are regularly produced by the immune system. It seems that the immune system, under physiological conditions, does not engage reactions with self-proteins or pathogens just in virtue of their peptide commonality. As already discussed,[174] [175] [176] it seems that it is just the vast peptide commonality to confer or, better, to reify protein immunotolerance.

As a collateral note, we observe that, while [Tables 1] and [2] militate against the assumption of a “negative selection” of self-reactive lymphocytes, [Tables 3] and [4] also question the defensive role of the immune response. By definition, immune system attacks pathogenic enemies and protects self-entities. That is, it is assumed that the immune system is endowed with the capacity of discerning a pathogen antigen from a self-protein and of behaving consequentially by attacking the “foes” and defending the “friends.” Instead of being analyzed and defined as an aggregate of molecules organized into functional biological pathways, the immune system is considered as a “thinking entity” that sees, discriminates, decides, and then attacks. Against such an anthropomorphous view, the present mathematical and biochemical data document that pathogenic immune responses can routinely occur following infections, as already experimentally demonstrated.[177] [178] Pathogenic autoantibodies—that are usually considered as rare phenomena due to the so-called “immunological holes” deriving from an incomplete negative selection of the self-reactive lymphocytes[169] [170] [171] or that, even, have been denied as pure fantasies[179]—seem to be the rule.

[Tables 3] and [4] show that anti-EBV immunoreactivity can hit a myriad of human proteins that, when (epi)genetically altered, can lead to cancers, autoimmune diseases, and even death. Such cross-reactive potential explains why higher the anti-EBV IgG antibody titer, worse may be the disease prognosis and faster the disease progression as described by a continuum of reports since the 1970s.[16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] That is, autoimmunity is not a matter of “rare immunological holes,” but it is intrinsic to the immune response that involves most of the human proteome by being most of the human proteome shared with microbial entities as a result of a long evolutionary path that from viruses and bacteria led to the eukaryotic cell.[180]

In conclusion, this study highlights the necessity of reviewing the hypothesis of the “negative selection” of self-reactive lymphocytes and, at the same time, emphasizes the importance of the “peptide uniqueness” concept to develop immunotherapies against EBV infection, and infections in general. Only immunotherapies based on peptides uniquely owned by the infectious agents would offer high specificity as well as the advantage of a lack of adverse events in the human host.[39] [181] [182] [183]


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Conflict of Interest

D.K. declares no conflicts. Y.S. is a medical consultant in vaccine compensation court, United States.

Supplementary Material


Address for correspondence

Darja Kanduc, PhD
Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari
Via Orabona 4, Bari 70125
Italy   

Publication History

Publication Date:
31 August 2020 (online)

© 2020. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/).

Georg Thieme Verlag KG
Stuttgart · New York


Zoom Image
Fig. 1 Distribution of EBV epitope-derived peptides throughout WASP primary aa sequence. WASP sequence from Uniprot (http://www.uniprot.org/).[51] EBV epitope-derived peptides are underlined and bold marked. EBV, Epstein-Barr virus; WASP, Wiskott-Aldrich syndrome protein.