Compendium of Cancer Genome Aberrations

HAEM5:Systemic chronic active EBV disease: Difference between revisions

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[[HAEM5:Table_of_Contents|Haematolymphoid Tumours (WHO Classification, 5th ed.)]]
[[HAEM5:Table_of_Contents|Haematolymphoid Tumours (WHO Classification, 5th ed.)]]


{{Under Construction}}
==Primary Author(s)* ==
 
<span style="color:#0070C0">(General Instructions – The focus of these pages is the clinically significant genetic alterations in each disease type. This is based on up-to-date knowledge from multiple resources such as PubMed and the WHO classification books. The CCGA is meant to be a supplemental resource to the WHO classification books; the CCGA captures in a continually updated wiki-stye manner the current genetics/genomics knowledge of each disease, which evolves more rapidly than books can be revised and published. If the same disease is described in multiple WHO classification books, the genetics-related information for that disease will be consolidated into a single main page that has this template (other pages would only contain a link to this main page). Use [https://www.genenames.org/ <u>HUGO-approved gene names and symbols</u>] (italicized when appropriate), [https://varnomen.hgvs.org/ <u>HGVS-based nomenclature for variants</u>], as well as generic names of drugs and testing platforms or assays if applicable. Please complete tables whenever possible and do not delete them (add N/A if not applicable in the table and delete the examples); to add (or move) a row or column in a table, click nearby within the table and select the > symbol that appears. Please do not delete or alter the section headings. The use of bullet points alongside short blocks of text rather than only large paragraphs is encouraged. Additional instructions below in italicized blue text should not be included in the final page content. Please also see </span><u>[[Author_Instructions]]</u><span style="color:#0070C0"> and [[Frequently Asked Questions (FAQs)|<u>FAQs</u>]] as well as contact your [[Leadership|<u>Associate Editor</u>]] or [mailto:CCGA@cancergenomics.org <u>Technical Support</u>].)</span>
 
==Primary Author(s)*==


Karin Miller, MD<span style="color:#0070C0"> </span>
Karin Miller, MD<span style="color:#0070C0"> </span>
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|Monoclonality detected in ~47% of cases<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Ito|first2=Yoshinori|last3=Kawabe|first3=Shinji|last4=Gotoh|first4=Kensei|last5=Takahashi|first5=Yoshiyuki|last6=Kojima|first6=Seiji|last7=Naoe|first7=Tomoki|last8=Esaki|first8=Shinichi|last9=Kikuta|first9=Atsushi|date=2012-01-19|title=EBV-associated T/NK-cell lymphoproliferative diseases in nonimmunocompromised hosts: prospective analysis of 108 cases|url=https://pubmed.ncbi.nlm.nih.gov/22096243|journal=Blood|volume=119|issue=3|pages=673–686|doi=10.1182/blood-2011-10-381921|issn=1528-0020|pmid=22096243}}</ref>
|Monoclonality detected in ~47% of cases<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Ito|first2=Yoshinori|last3=Kawabe|first3=Shinji|last4=Gotoh|first4=Kensei|last5=Takahashi|first5=Yoshiyuki|last6=Kojima|first6=Seiji|last7=Naoe|first7=Tomoki|last8=Esaki|first8=Shinichi|last9=Kikuta|first9=Atsushi|date=2012-01-19|title=EBV-associated T/NK-cell lymphoproliferative diseases in nonimmunocompromised hosts: prospective analysis of 108 cases|url=https://pubmed.ncbi.nlm.nih.gov/22096243|journal=Blood|volume=119|issue=3|pages=673–686|doi=10.1182/blood-2011-10-381921|issn=1528-0020|pmid=22096243}}</ref>
|D
|D
|The WHO 5<sup>th</sup> edition notes that, "cases with monomorphic and monoclonal proliferation have a poorer outcome than those with polymorphic and polyclonal proliferation."<ref name=":0">{{Cite journal|title=BlueBooksOnline|url=https://tumourclassification.iarc.who.int/chapters/63}}</ref><ref>{{Cite journal|last=Ohshima|first=Koichi|last2=Kimura|first2=Hiroshi|last3=Yoshino|first3=Tadashi|last4=Kim|first4=Chul Woo|last5=Ko|first5=Young H.|last6=Lee|first6=Seung-Suk|last7=Peh|first7=Suat-Cheng|last8=Chan|first8=John K. C.|last9=CAEBV Study Group|date=2008-04|title=Proposed categorization of pathological states of EBV-associated T/natural killer-cell lymphoproliferative disorder (LPD) in children and young adults: overlap with chronic active EBV infection and infantile fulminant EBV T-LPD|url=https://pubmed.ncbi.nlm.nih.gov/18324913|journal=Pathology International|volume=58|issue=4|pages=209–217|doi=10.1111/j.1440-1827.2008.02213.x|issn=1440-1827|pmid=18324913}}</ref>
|The WHO 5<sup>th</sup> edition notes that, "cases with monomorphic and monoclonal proliferation have a poorer outcome than those with polymorphic and polyclonal proliferation."<ref name=":5">The WHO Classification of Tumours Editorial Board, ed. ''Haematolymphoid Tumours: Who Classification of Tumours''. 5th ed. International Agency for Research on Cancer; 2024.</ref><ref name=":0">{{Cite journal|title=BlueBooksOnline|url=https://tumourclassification.iarc.who.int/chapters/63}}</ref><ref>{{Cite journal|last=Ohshima|first=Koichi|last2=Kimura|first2=Hiroshi|last3=Yoshino|first3=Tadashi|last4=Kim|first4=Chul Woo|last5=Ko|first5=Young H.|last6=Lee|first6=Seung-Suk|last7=Peh|first7=Suat-Cheng|last8=Chan|first8=John K. C.|last9=CAEBV Study Group|date=2008-04|title=Proposed categorization of pathological states of EBV-associated T/natural killer-cell lymphoproliferative disorder (LPD) in children and young adults: overlap with chronic active EBV infection and infantile fulminant EBV T-LPD|url=https://pubmed.ncbi.nlm.nih.gov/18324913|journal=Pathology International|volume=58|issue=4|pages=209–217|doi=10.1111/j.1440-1827.2008.02213.x|issn=1440-1827|pmid=18324913}}</ref>
|N/A
|N/A
|}
|}
==Individual Region Genomic Gain/Loss/LOH==
==Individual Region Genomic Gain/Loss/LOH==


*Multiple different chromosomal aberrations have been reported, approximately 7% of cases<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Ito|first2=Yoshinori|last3=Kawabe|first3=Shinji|last4=Gotoh|first4=Kensei|last5=Takahashi|first5=Yoshiyuki|last6=Kojima|first6=Seiji|last7=Naoe|first7=Tomoki|last8=Esaki|first8=Shinichi|last9=Kikuta|first9=Atsushi|date=2012-01-19|title=EBV-associated T/NK-cell lymphoproliferative diseases in nonimmunocompromised hosts: prospective analysis of 108 cases|url=https://pubmed.ncbi.nlm.nih.gov/22096243|journal=Blood|volume=119|issue=3|pages=673–686|doi=10.1182/blood-2011-10-381921|issn=1528-0020|pmid=22096243}}</ref>
* Multiple different chromosomal aberrations have been reported, approximately 7% of cases<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Ito|first2=Yoshinori|last3=Kawabe|first3=Shinji|last4=Gotoh|first4=Kensei|last5=Takahashi|first5=Yoshiyuki|last6=Kojima|first6=Seiji|last7=Naoe|first7=Tomoki|last8=Esaki|first8=Shinichi|last9=Kikuta|first9=Atsushi|date=2012-01-19|title=EBV-associated T/NK-cell lymphoproliferative diseases in nonimmunocompromised hosts: prospective analysis of 108 cases|url=https://pubmed.ncbi.nlm.nih.gov/22096243|journal=Blood|volume=119|issue=3|pages=673–686|doi=10.1182/blood-2011-10-381921|issn=1528-0020|pmid=22096243}}</ref>
* Frequent copy number alterations (CNAs) have recently been described in a subtype of NK-cell CAEBV with a poor prognosis that also showed a high CPG-island methylation pattern and higher tumor mutational burden (TMB).<ref name=":4" />
 
*Intragenic deletions in the EBV genome may be detected (~35% of cases)<ref name=":2" />. Intragenic deletions in EBV were also detected in other EBV-associated neoplasms, but were not reported in patients with infectious mononucleosis or posttransplant lymphoproliferative disorder (PTLD)<ref name=":2" />
*Intragenic deletions in the EBV genome may be detected (~35% of cases)<ref name=":2" />. Intragenic deletions in EBV were also detected in other EBV-associated neoplasms, but were not reported in patients with infectious mononucleosis or posttransplant lymphoproliferative disorder (PTLD)<ref name=":2" />


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* Somatic mutations can be detected in a subset of CAEBV cases (~29%).<ref name=":2">{{Cite journal|last=Okuno|first=Yusuke|last2=Murata|first2=Takayuki|last3=Sato|first3=Yoshitaka|last4=Muramatsu|first4=Hideki|last5=Ito|first5=Yoshinori|last6=Watanabe|first6=Takahiro|last7=Okuno|first7=Tatsuya|last8=Murakami|first8=Norihiro|last9=Yoshida|first9=Kenichi|date=2019-03|title=Defective Epstein-Barr virus in chronic active infection and haematological malignancy|url=https://pubmed.ncbi.nlm.nih.gov/30664667|journal=Nature Microbiology|volume=4|issue=3|pages=404–413|doi=10.1038/s41564-018-0334-0|issn=2058-5276|pmid=30664667}}</ref>
* Somatic mutations can be detected in a subset of CAEBV cases (~29%).<ref name=":2">{{Cite journal|last=Okuno|first=Yusuke|last2=Murata|first2=Takayuki|last3=Sato|first3=Yoshitaka|last4=Muramatsu|first4=Hideki|last5=Ito|first5=Yoshinori|last6=Watanabe|first6=Takahiro|last7=Okuno|first7=Tatsuya|last8=Murakami|first8=Norihiro|last9=Yoshida|first9=Kenichi|date=2019-03|title=Defective Epstein-Barr virus in chronic active infection and haematological malignancy|url=https://pubmed.ncbi.nlm.nih.gov/30664667|journal=Nature Microbiology|volume=4|issue=3|pages=404–413|doi=10.1038/s41564-018-0334-0|issn=2058-5276|pmid=30664667}}</ref>
* ''DDX3X'' mutations are the most commonly implicated known driver mutations<ref name=":2" />
* ''DDX3X'' mutations are the most commonly implicated known driver mutations. <ref name=":2" />
** Mutations in KMT2D, KMT2B, BCOR/BCORL1, TET2, KDM6A, NFKB1, and ARID1a have also been described.<ref name=":2" /><ref>{{Cite journal|last=Akazawa|first=Ryo|last2=Mikami|first2=Takashi|last3=Yamada|first3=Masaki|last4=Kato|first4=Itaru|last5=Kubota|first5=Hirohito|last6=Saida|first6=Satoshi|last7=Uchihara|first7=Yoshinori|last8=Ishikawa|first8=Yuriko|last9=Kamitori|first9=Tatsuya|date=2025-11-06|title=Multiomics analysis reveals the genetic and epigenetic features of high-risk NK cell-type chronic active EBV infection|url=https://pubmed.ncbi.nlm.nih.gov/40737598|journal=Blood|volume=146|issue=19|pages=2336–2349|doi=10.1182/blood.2024026805|issn=1528-0020|pmid=40737598}}</ref>
* In one study, identical driver mutations were detected in different cell lineages (T, B, and NK), demonstrating that EBV infected a common lymphoid progenitor in CAEBV patients. Acquisition of somatic, driver mutations in these pre-malignant, EBV-infected cells subsequently leads to clonal evolution in multiple cell lines.<ref name=":2" />
* In one study, identical driver mutations were detected in different cell lineages (T, B, and NK), demonstrating that EBV infected a common lymphoid progenitor in CAEBV patients. Acquisition of somatic, driver mutations in these pre-malignant, EBV-infected cells subsequently leads to clonal evolution in multiple cell lines.<ref name=":2" />
* Presence of a driver mutation associated with shorter overall survival<ref name=":2" />
* Presence of a driver mutation associated with shorter overall survival<ref name=":2" />
* Mutations in DDX3X, KMT2D, BCOR/BCORL1, TET2, and KDM6A have been described.<ref name=":2" /> Mutations in KMT2B, NFKB1, and ARID1a have also recently been described.<ref>{{Cite journal|last=Akazawa|first=Ryo|last2=Mikami|first2=Takashi|last3=Yamada|first3=Masaki|last4=Kato|first4=Itaru|last5=Kubota|first5=Hirohito|last6=Saida|first6=Satoshi|last7=Uchihara|first7=Yoshinori|last8=Ishikawa|first8=Yuriko|last9=Kamitori|first9=Tatsuya|date=2025-11-06|title=Multiomics analysis reveals the genetic and epigenetic features of high-risk NK cell-type chronic active EBV infection|url=https://pubmed.ncbi.nlm.nih.gov/40737598|journal=Blood|volume=146|issue=19|pages=2336–2349|doi=10.1182/blood.2024026805|issn=1528-0020|pmid=40737598}}</ref>


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{| class="wikitable sortable"
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Note: A more extensive list of mutations can be found in [https://www.cbioportal.org/ <u>cBioportal</u>], [https://cancer.sanger.ac.uk/cosmic <u>COSMIC</u>], and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.
Note: A more extensive list of mutations can be found in [https://www.cbioportal.org/ <u>cBioportal</u>], [https://cancer.sanger.ac.uk/cosmic <u>COSMIC</u>], and/or other databases. When applicable, gene-specific pages within the CCGA site directly link to pertinent external content.
==Epigenomic Alterations==
==Epigenomic Alterations==
A high CPG-island methylation pattern has been described in a subtype of NK-cell CAEBV with a poor prognosis.<ref name=":4">{{Cite journal|last=Akazawa|first=Ryo|last2=Mikami|first2=Takashi|last3=Yamada|first3=Masaki|last4=Kato|first4=Itaru|last5=Kubota|first5=Hirohito|last6=Saida|first6=Satoshi|last7=Uchihara|first7=Yoshinori|last8=Ishikawa|first8=Yuriko|last9=Kamitori|first9=Tatsuya|date=2025-11-06|title=Multiomics analysis reveals the genetic and epigenetic features of high-risk NK cell-type chronic active EBV infection|url=https://pubmed.ncbi.nlm.nih.gov/40737598|journal=Blood|volume=146|issue=19|pages=2336–2349|doi=10.1182/blood.2024026805|issn=1528-0020|pmid=40737598}}</ref>
A high CPG-island methylation pattern has been described in a subtype of NK-cell CAEBV with a poor prognosis; these high methylation cases also showed higher tumor mutational burden (TMB) and frequent copy number alterations (CNAs).<ref name=":4">{{Cite journal|last=Akazawa|first=Ryo|last2=Mikami|first2=Takashi|last3=Yamada|first3=Masaki|last4=Kato|first4=Itaru|last5=Kubota|first5=Hirohito|last6=Saida|first6=Satoshi|last7=Uchihara|first7=Yoshinori|last8=Ishikawa|first8=Yuriko|last9=Kamitori|first9=Tatsuya|date=2025-11-06|title=Multiomics analysis reveals the genetic and epigenetic features of high-risk NK cell-type chronic active EBV infection|url=https://pubmed.ncbi.nlm.nih.gov/40737598|journal=Blood|volume=146|issue=19|pages=2336–2349|doi=10.1182/blood.2024026805|issn=1528-0020|pmid=40737598}}</ref>
==Genes and Main Pathways Involved==
==Genes and Main Pathways Involved==
{| class="wikitable sortable"
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==Genetic Diagnostic Testing Methods==
==Genetic Diagnostic Testing Methods==


* The WHO 5<sup>th</sup> edition essential diagnostic criteria include:<ref name=":0" />
* '''Both the WHO 5<sup>th</sup> edition and International Consensus Classification (ICC) include detection of increased EBV DNA in the peripheral blood (>10,000 IU/mL in ICC criteria) and/or EBV RNA (EBER) or viral protein in T or NK-cells of affected tissues.'''<ref name=":5" />'''<ref name=":0" /><ref name=":1">Arber DA, Borowitz MJ, Cook JR, et al. ''The International Consensus Classification of Myeloid and Lymphoid Neoplasms''.; 2025.</ref>'''
** Persistent (greater than 3 months) infectious mononucleosis-like symptoms
** Increased EBV DNA in the peripheral blood or EBER-positive cells in affected organs with evidence of EBV infection in T or NK-cells
** Exclusion of known immunodeficiency, malignancy, or autoimmune disorders
 
* The International Consensus Classification (ICC) revised diagnostic criteria include:<ref name=":1">Arber DA, Borowitz MJ, Cook JR, et al. ''The International Consensus Classification of Myeloid and Lymphoid Neoplasms''.; 2025.</ref>
** Persistent (greater than 3 months) infectious mononucleosis-like symptoms
** Increased EBV DNA (>10,000 IU/mL) in the peripheral blood
** Histologic evidence of organ disease
** Detection of EBV RNA or viral protein in T or NK-cells in affected tissues
** Exclusion of known immunodeficiency, malignancy, or autoimmune disorders
 
* '''Both the WHO 5<sup>th</sup> edition and ICC include detection of increased EBV DNA in the peripheral blood and/or EBV RNA (EBER) or viral protein in T or NK-cells of affected tissues.<ref name=":0" /><ref name=":1" />'''
** Whole blood or peripheral blood mononuclear cells are preferred for EBV DNA PCR testing, as serum or plasma are less sensitive for CAEBV disease<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Cohen|first2=Jeffrey I.|date=2017|title=Chronic Active Epstein-Barr Virus Disease|url=https://pubmed.ncbi.nlm.nih.gov/29375552|journal=Frontiers in Immunology|volume=8|pages=1867|doi=10.3389/fimmu.2017.01867|issn=1664-3224|pmc=5770746|pmid=29375552}}</ref>
** Whole blood or peripheral blood mononuclear cells are preferred for EBV DNA PCR testing, as serum or plasma are less sensitive for CAEBV disease<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Cohen|first2=Jeffrey I.|date=2017|title=Chronic Active Epstein-Barr Virus Disease|url=https://pubmed.ncbi.nlm.nih.gov/29375552|journal=Frontiers in Immunology|volume=8|pages=1867|doi=10.3389/fimmu.2017.01867|issn=1664-3224|pmc=5770746|pmid=29375552}}</ref>
** In tissues, using a double stain for B, T, or NK-cell markers and EBV is recommended.
** In tissues, using a double stain for B, T, or NK-cell markers and EBV is recommended.
* TCR-gene rearrangements can be tested via PCR-Capillary Electrophoresis or NGS methods
* DNA mutations (SNV/Indels) can be detected using NGS


==Familial Forms==
==Familial Forms==
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==Additional Information==
==Additional Information==


* CAEBV shows an increased prevalence in populations from Asia and natives from Central and South America, suggesting a potential for genetic polymorphisms in immune-modulating genes to play a role in disease pathogenesis.<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Cohen|first2=Jeffrey I.|date=2017|title=Chronic Active Epstein-Barr Virus Disease|url=https://pubmed.ncbi.nlm.nih.gov/29375552|journal=Frontiers in Immunology|volume=8|pages=1867|doi=10.3389/fimmu.2017.01867|issn=1664-3224|pmc=5770746|pmid=29375552}}</ref> <ref>{{Cite journal|last=Kimura|first=Hiroshi|date=2006|title=Pathogenesis of chronic active Epstein-Barr virus infection: is this an infectious disease, lymphoproliferative disorder, or immunodeficiency?|url=https://pubmed.ncbi.nlm.nih.gov/16791843|journal=Reviews in Medical Virology|volume=16|issue=4|pages=251–261|doi=10.1002/rmv.505|issn=1052-9276|pmid=16791843}}</ref>
* CAEBV shows an increased prevalence in populations from Asia and Latin America, suggesting a potential for genetic polymorphisms in immune-modulating genes to play a role in disease pathogenesis.<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Cohen|first2=Jeffrey I.|date=2017|title=Chronic Active Epstein-Barr Virus Disease|url=https://pubmed.ncbi.nlm.nih.gov/29375552|journal=Frontiers in Immunology|volume=8|pages=1867|doi=10.3389/fimmu.2017.01867|issn=1664-3224|pmc=5770746|pmid=29375552}}</ref> <ref>{{Cite journal|last=Kimura|first=Hiroshi|date=2006|title=Pathogenesis of chronic active Epstein-Barr virus infection: is this an infectious disease, lymphoproliferative disorder, or immunodeficiency?|url=https://pubmed.ncbi.nlm.nih.gov/16791843|journal=Reviews in Medical Virology|volume=16|issue=4|pages=251–261|doi=10.1002/rmv.505|issn=1052-9276|pmid=16791843}}</ref>
* EBV clonality testing showed monoclonality (84%), oligoclonality (11%), or polyclonality (5%).<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Ito|first2=Yoshinori|last3=Kawabe|first3=Shinji|last4=Gotoh|first4=Kensei|last5=Takahashi|first5=Yoshiyuki|last6=Kojima|first6=Seiji|last7=Naoe|first7=Tomoki|last8=Esaki|first8=Shinichi|last9=Kikuta|first9=Atsushi|date=2012-01-19|title=EBV-associated T/NK-cell lymphoproliferative diseases in nonimmunocompromised hosts: prospective analysis of 108 cases|url=https://pubmed.ncbi.nlm.nih.gov/22096243|journal=Blood|volume=119|issue=3|pages=673–686|doi=10.1182/blood-2011-10-381921|issn=1528-0020|pmid=22096243}}</ref> TCR clonality testing is described above (see gene rearrangements)
* EBV clonality testing showed monoclonality (84%), oligoclonality (11%), or polyclonality (5%).<ref>{{Cite journal|last=Kimura|first=Hiroshi|last2=Ito|first2=Yoshinori|last3=Kawabe|first3=Shinji|last4=Gotoh|first4=Kensei|last5=Takahashi|first5=Yoshiyuki|last6=Kojima|first6=Seiji|last7=Naoe|first7=Tomoki|last8=Esaki|first8=Shinichi|last9=Kikuta|first9=Atsushi|date=2012-01-19|title=EBV-associated T/NK-cell lymphoproliferative diseases in nonimmunocompromised hosts: prospective analysis of 108 cases|url=https://pubmed.ncbi.nlm.nih.gov/22096243|journal=Blood|volume=119|issue=3|pages=673–686|doi=10.1182/blood-2011-10-381921|issn=1528-0020|pmid=22096243}}</ref> TCR clonality testing is described above (see gene rearrangements)


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