Compendium of Cancer Genome Aberrations

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{{DISPLAYTITLE:Subcutaneous panniculitis-like T-cell lymphoma}}
{{DISPLAYTITLE:Subcutaneous panniculitis-like T-cell lymphoma}}
[[HAEM5:Table_of_Contents|Haematolymphoid Tumours (WHO Classification, 5th ed.)]]
[[HAEM5:Table_of_Contents|Haematolymphoid Tumours (WHO Classification, 5th ed.)]]
{{Under Construction}}
<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)*==
==Primary Author(s)*==


Ian King, PhD  
Ian King, PhD  
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!Clinical Relevance Details/Other Notes
!Clinical Relevance Details/Other Notes
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==Individual Region Genomic Gain/Loss/LOH==
==Individual Region Genomic Gain/Loss/LOH==
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==Gene Mutations (SNV/INDEL)==
==Gene Mutations (SNV/INDEL)==
{| class="wikitable sortable"
{| class="wikitable sortable"
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|-
!Gene!!Genetic Alteration!!Tumor Suppressor Gene, Oncogene, Other!!Prevalence -
!Gene!!Genetic Alteration!!Tumor Suppressor Gene, Oncogene, Other!!Prevalence: Common >20%, Recurrent 5-20% or Rare <5% (Disease)
Common >20%, Recurrent 5-20% or Rare <5% (Disease)
!Diagnostic, Prognostic, and Therapeutic Significance
!Diagnostic, Prognostic, and Therapeutic Significance - D, P, T  
D, P, T  
!Established Clinical Significance Per Guidelines - Yes or No (Source)
!Established Clinical Significance Per Guidelines - Yes or No (Source)
!Clinical Relevance Details/Other Notes
!Clinical Relevance Details/Other Notes
|-
|-
|HAVCR2  
|''HAVCR2''


|Specific missense loss of function <ref name=":1">{{Cite journal|last=Gayden|first=Tenzin|last2=Sepulveda|first2=Fernando E.|last3=Khuong-Quang|first3=Dong-Anh|last4=Pratt|first4=Jonathan|last5=Valera|first5=Elvis T.|last6=Garrigue|first6=Alexandrine|last7=Kelso|first7=Susan|last8=Sicheri|first8=Frank|last9=Mikael|first9=Leonie G.|date=2018-12|title=Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome|url=https://pubmed.ncbi.nlm.nih.gov/30374066|journal=Nature Genetics|volume=50|issue=12|pages=1650–1657|doi=10.1038/s41588-018-0251-4|issn=1546-1718|pmid=30374066}}</ref>
|Specific missense loss of function <ref name=":1">{{Cite journal|last=Gayden|first=Tenzin|last2=Sepulveda|first2=Fernando E.|last3=Khuong-Quang|first3=Dong-Anh|last4=Pratt|first4=Jonathan|last5=Valera|first5=Elvis T.|last6=Garrigue|first6=Alexandrine|last7=Kelso|first7=Susan|last8=Sicheri|first8=Frank|last9=Mikael|first9=Leonie G.|date=2018-12|title=Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome|url=https://pubmed.ncbi.nlm.nih.gov/30374066|journal=Nature Genetics|volume=50|issue=12|pages=1650–1657|doi=10.1038/s41588-018-0251-4|issn=1546-1718|pmid=30374066}}</ref>
|Tumor suppressor
|Tumor suppressor
|Common >20%, <ref name=":0">{{Cite journal|last=Polprasert|first=Chantana|last2=Takeuchi|first2=Yasuhide|last3=Kakiuchi|first3=Nobuyuki|last4=Yoshida|first4=Kenichi|last5=Assanasen|first5=Thamathorn|last6=Sitthi|first6=Wimonmas|last7=Bunworasate|first7=Udomsak|last8=Pirunsarn|first8=Arunrat|last9=Wudhikarn|first9=Kitsada|date=2019-02-26|title=Frequent germline mutations of HAVCR2 in sporadic subcutaneous panniculitis-like T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/30792187|journal=Blood Advances|volume=3|issue=4|pages=588–595|doi=10.1182/bloodadvances.2018028340|issn=2473-9537|pmc=6391671|pmid=30792187}}</ref><ref name=":1" />
|Common >20%, <ref name=":0">{{Cite journal|last=Polprasert|first=Chantana|last2=Takeuchi|first2=Yasuhide|last3=Kakiuchi|first3=Nobuyuki|last4=Yoshida|first4=Kenichi|last5=Assanasen|first5=Thamathorn|last6=Sitthi|first6=Wimonmas|last7=Bunworasate|first7=Udomsak|last8=Pirunsarn|first8=Arunrat|last9=Wudhikarn|first9=Kitsada|date=2019-02-26|title=Frequent germline mutations of HAVCR2 in sporadic subcutaneous panniculitis-like T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/30792187|journal=Blood Advances|volume=3|issue=4|pages=588–595|doi=10.1182/bloodadvances.2018028340|issn=2473-9537|pmc=6391671|pmid=30792187}}</ref><ref name=":1" />
|P, T
|Yes; NCCN guidelines suggest germline testing in certain circumstances
|May have prognostic and therapeutic significance in patients presenting with severe hemophagocytic syndromes.<ref name=":3">{{Cite journal|last=Sonigo|first=Gabrielle|last2=Battistella|first2=Maxime|last3=Beylot-Barry|first3=Marie|last4=Ingen-Housz-Oro|first4=Saskia|last5=Franck|first5=Nathalie|last6=Barete|first6=Stéphane|last7=Boulinguez|first7=Serge|last8=Dereure|first8=Olivier|last9=Bonnet|first9=Nathalie|date=2020-03-26|title=HAVCR2 mutations are associated with severe hemophagocytic syndrome in subcutaneous panniculitis-like T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/32005988|journal=Blood|volume=135|issue=13|pages=1058–1061|doi=10.1182/blood.2019003811|issn=1528-0020|pmid=32005988}}</ref>
|May have prognostic and therapeutic significance in patients presenting with severe hemophagocytic syndromes.<ref name=":3">{{Cite journal|last=Sonigo|first=Gabrielle|last2=Battistella|first2=Maxime|last3=Beylot-Barry|first3=Marie|last4=Ingen-Housz-Oro|first4=Saskia|last5=Franck|first5=Nathalie|last6=Barete|first6=Stéphane|last7=Boulinguez|first7=Serge|last8=Dereure|first8=Olivier|last9=Bonnet|first9=Nathalie|date=2020-03-26|title=HAVCR2 mutations are associated with severe hemophagocytic syndrome in subcutaneous panniculitis-like T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/32005988|journal=Blood|volume=135|issue=13|pages=1058–1061|doi=10.1182/blood.2019003811|issn=1528-0020|pmid=32005988}}</ref>
|Not applicable
''HAVCR2'' encodes for T-cell immunoglobulin and mucin domain protein 3 (TIM-3), a membrane modulator of immune response resulting in hemophagocytosis and uncontrolled activation of the innate immune system.
|Homozygous p.Y82C pathogenic variant is more common in East Asian populations<ref name=":1" /><ref name=":0" />, with p.T101I being a variant in South Asian (Thai) populations<ref name=":0" />, and p.I97M  being more common in European and North African populations.<ref name=":1" /><ref name=":0" /><ref name=":3" />
Homozygous p.Y82C pathogenic variant is more common in East Asian populations<ref name=":1" /><ref name=":0" />, with p.T101I being a variant in South Asian (Thai) populations<ref name=":0" />, and p.I97M  being more common in European and North African populations.<ref name=":1" /><ref name=":0" /><ref name=":3" />
|}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==
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!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
!Gene; Genetic Alteration!!Pathway!!Pathophysiologic Outcome
|-
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|ARID1B<ref name=":0" /><ref name=":2" />, SMARCA4<ref name=":0" /><ref name=":2" />, NCOR1<ref name=":0" /><ref name=":2" />, KMT2C<ref name=":2" />, KMT2D<ref name=":2" />, DOTIL<ref name=":0" /><ref name=":2" />, CHD3<ref name=":0" /><ref name=":2" /><ref name=":4">{{Cite journal|last=Koh|first=Jiwon|last2=Jang|first2=Insoon|last3=Mun|first3=Seungchan|last4=Lee|first4=Cheol|last5=Cha|first5=Hee Jeong|last6=Oh|first6=Young Ha|last7=Kim|first7=Jin-Man|last8=Han|first8=Jae Ho|last9=Paik|first9=Jin Ho|date=2021-10-26|title=Genetic profiles of subcutaneous panniculitis-like T-cell lymphoma and clinicopathological impact of HAVCR2 mutations|url=https://pubmed.ncbi.nlm.nih.gov/34535012|journal=Blood Advances|volume=5|issue=20|pages=3919–3930|doi=10.1182/bloodadvances.2021004562|issn=2473-9537|pmc=8945616|pmid=34535012}}</ref>, CHD4<ref name=":0" /><ref name=":2" />, PBRM1<ref name=":2" />, CREBBP<ref name=":0" /><ref name=":2" />, ASXL1<ref name=":0" /><ref name=":2" /><ref name=":4" />, MBD1<ref name=":2" />, KMT2B<ref name=":0" /><ref name=":2" />, HIST1H3J<ref name=":2" />, CDC27<ref name=":4" />, TET2<ref name=":0" /><ref name=":4" />
|ARID1B<ref name=":0" /><ref name=":2" />, SMARCA4<ref name=":0" /><ref name=":2" />, NCOR1<ref name=":0" /><ref name=":2" />, KMT2C<ref name=":2" />, KMT2D<ref name=":2" />,  
DOTIL<ref name=":0" /><ref name=":2" />, CHD3<ref name=":0" /><ref name=":2" /><ref name=":4">{{Cite journal|last=Koh|first=Jiwon|last2=Jang|first2=Insoon|last3=Mun|first3=Seungchan|last4=Lee|first4=Cheol|last5=Cha|first5=Hee Jeong|last6=Oh|first6=Young Ha|last7=Kim|first7=Jin-Man|last8=Han|first8=Jae Ho|last9=Paik|first9=Jin Ho|date=2021-10-26|title=Genetic profiles of subcutaneous panniculitis-like T-cell lymphoma and clinicopathological impact of HAVCR2 mutations|url=https://pubmed.ncbi.nlm.nih.gov/34535012|journal=Blood Advances|volume=5|issue=20|pages=3919–3930|doi=10.1182/bloodadvances.2021004562|issn=2473-9537|pmc=8945616|pmid=34535012}}</ref>, CHD4<ref name=":0" /><ref name=":2" />, PBRM1<ref name=":2" />, CREBBP<ref name=":0" /><ref name=":2" />,  
 
ASXL1<ref name=":0" /><ref name=":2" /><ref name=":4" />, MBD1<ref name=":2" />, KMT2B<ref name=":0" /><ref name=":2" />, HIST1H3J<ref name=":2" />, CDC27<ref name=":4" />, TET2<ref name=":0" /><ref name=":4" />
|Epigenetic modifiers<ref name=":2" /><ref name=":4" />
|Epigenetic modifiers<ref name=":2" /><ref name=":4" />
|Unregulated cell division
|Unregulated cell division
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|Unregulated cell division
|Unregulated cell division
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|-
|TP53<ref name=":2" />; loss of tumor suppression
|TP53<ref name=":2" />
|TP53<ref name=":2" />
|Tumor suppression<ref name=":2" />
|Increased cell growth and proliferation
|Increased cell growth and proliferation
|-
|-
|NAV3<ref name=":0" /><ref name=":2" /><ref name=":4" /> ; microtubule dysfunction leading to unregulated cell growth
|NAV3<ref name=":0" /><ref name=":2" /><ref name=":4" />
|
|Microtubule activity and tumor suppression<ref name=":4" />
|
|Increased cell growth and proliferation
|}
|}
==Genetic Diagnostic Testing Methods==
==Genetic Diagnostic Testing Methods==
Put your text here <span style="color:#0070C0">(''Instructions: Include recommended testing type(s) to identify the clinically significant genetic alterations.'')</span>
'''Molecular Testing to detect detect clonal T-cell receptor (TCR) beta and/or gamma gene rearrangements:'''
 
# Polymerase Chain Reaction (PCR) fragment analysis '''(major diagnostic criteria)'''<ref name=":6" />
 
'''Molecular Genetic Testing for HAVCR2 variants:'''
 
# Next generation sequencing (NGS) - whole exome sequencing and whole genome sequencing.
# Sanger sequencing - to confirm or detect ''HAVCR2'' mutations.
# Droplet digital PCR (ddPCR): to confirm or detect presence of the ''HAVCR2'' p.Y82C variant<ref>{{Cite journal|last=Cheng|first=Jinjun|last2=Xi|first2=Liqiang|last3=Jang|first3=Yoon|last4=Kim|first4=Jung|last5=Wang|first5=Hao-Wei|last6=Pittaluga|first6=Stefania|last7=Jaffe|first7=Elaine S.|last8=Raffeld|first8=Mark|date=2024-10-01|title=An investigation of germline variants of HAVCR2 in subcutaneous panniculitis-like T-cell lymphoma and related lesions in a North American population|url=https://pubmed.ncbi.nlm.nih.gov/38867583|journal=Haematologica|volume=109|issue=10|pages=3363–3367|doi=10.3324/haematol.2023.284738|issn=1592-8721|pmc=11443401|pmid=38867583}}</ref>  
 
==Familial Forms==
==Familial Forms==
Hereditary germline mutations Autosomal recessive Familial disease in East Asian population: recessive. Hereditary form is Associated with severe HLH?.
Biallelic germline mutations in ''HAVCR2'' are inherited in an autosomal recessive pattern predominantly in individuals with East Asian ancestry.<ref name=":1" /><ref name=":0" /><ref name=":4" />
==Additional Information==
==Additional Information==
Suggestions that this entity is triggered by viral etiologies (EBV/COVID-19) or are associated with autoimmune conditions like HIV and systemic lupus erythematous can trigger
Subcutaneous panniculitis like T-cell lymphoma may be triggered or associated with viral etiologies including human immunodeficiency virus (HIV)<ref name=":0" />; with one case being reported after vaccination for SarsCoV2<ref>{{Cite journal|last=Kreher|first=Margaret Ann|last2=Ahn|first2=John|last3=Werbel|first3=Tyler|last4=Motaparthi|first4=Kiran|date=2022-10|title=Subcutaneous panniculitis-like T-cell lymphoma after COVID-19 vaccination|url=https://pubmed.ncbi.nlm.nih.gov/35966352|journal=JAAD case reports|volume=28|pages=18–20|doi=10.1016/j.jdcr.2022.08.006|issn=2352-5126|pmc=9364717|pmid=35966352}}</ref>. Typically, this entity is Epstein-Barr virus negative; however, it is rarely detected in Asian populations<ref name=":5">{{Cite journal|last=Kong|first=Yun-yi|last2=Dai|first2=Bo|last3=Kong|first3=Jin-cheng|last4=Zhou|first4=Xiao-yan|last5=Lu|first5=Hong-fen|last6=Shen|first6=Lei|last7=Du|first7=Xiang|last8=Shi|first8=Da-ren|date=2008-10|title=Subcutaneous panniculitis-like T-cell lymphoma: a clinicopathologic, immunophenotypic, and molecular study of 22 Asian cases according to WHO-EORTC classification|url=https://pubmed.ncbi.nlm.nih.gov/18708940|journal=The American Journal of Surgical Pathology|volume=32|issue=10|pages=1495–1502|doi=10.1097/PAS.0b013e31817a9081|issn=1532-0979|pmid=18708940}}</ref>. Association with autoimmune conditions such as systemic lupus erythematous have also been reported<ref name=":0" />.
 
''Immunohistochemical profile'': Subcutaneous panniculitis like T-cell lymphoma is a rare cytotoxic (CD3+, CD4-, CD8+, granzyme B +) T-cell lymphoma with atypical T-cells infiltrating subcutaneous tissue and rimming adipocytes in a "lace-like" pattern<ref name=":5" /><ref name=":6">{{Cite journal|last=Parveen|first=Zahida|last2=Thompson|first2=Karen|date=2009-02|title=Subcutaneous panniculitis-like T-cell lymphoma: redefinition of diagnostic criteria in the recent World Health Organization-European Organization for Research and Treatment of Cancer classification for cutaneous lymphomas|url=https://pubmed.ncbi.nlm.nih.gov/19195975|journal=Archives of Pathology & Laboratory Medicine|volume=133|issue=2|pages=303–308|doi=10.5858/133.2.303|issn=1543-2165|pmid=19195975}}</ref>. In one study, expression of CCR4 and FOXP3 was increased in tumor cells in sporadic cases with HAVCR2 wild-type genotypes.<ref name=":4" /> A major diagnostic criteria for is protein expression of TCRαβ and absence of TCRγδ <ref name=":6" />.
 
==Links==
==Links==


Put a link here or anywhere appropriate in this page <span style="color:#0070C0">(''Instructions: Highlight the text to which you want to add a link in this section or elsewhere, select the "Link" icon at the top of the wiki page, and search the name of the internal page to which you want to link this text, or enter an external internet address by including the "<nowiki>http://www</nowiki>." portion.'')</span>
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==References==
==References==
(use the "Cite" icon at the top of the page) <span style="color:#0070C0">(''Instructions: Add each reference into the text above by clicking where you want to insert the reference, selecting the “Cite” icon at the top of the wiki page, and using the “Automatic” tab option to search by PMID to select the reference to insert. If a PMID is not available, such as for a book, please use the “Cite” icon, select “Manual” and then “Basic Form”, and include the entire reference. To insert the same reference again later in the page, select the “Cite” icon and “Re-use” to find the reference; DO NOT insert the same reference twice using the “Automatic” tab as it will be treated as two separate references. The reference list in this section will be automatically generated and sorted''</span><span style="color:#0070C0">''.''</span><span style="color:#0070C0">)</span>
<references />
 
==Notes==
==Notes==
<nowiki>*</nowiki>Primary authors will typically be those that initially create and complete the content of a page.  If a subsequent user modifies the content and feels the effort put forth is of high enough significance to warrant listing in the authorship section, please contact the [[Leadership|''<u>Associate Editor</u>'']] or other CCGA representative.  When pages have a major update, the new author will be acknowledged at the beginning of the page, and those who contributed previously will be acknowledged below as a prior author.
<nowiki>*</nowiki>Primary authors will typically be those that initially create and complete the content of a page.  If a subsequent user modifies the content and feels the effort put forth is of high enough significance to warrant listing in the authorship section, please contact the [[Leadership|''<u>Associate Editor</u>'']] or other CCGA representative.  When pages have a major update, the new author will be acknowledged at the beginning of the page, and those who contributed previously will be acknowledged below as a prior author.


Prior Author(s):   
Prior Author(s): N/A  


       
<nowiki>*</nowiki>''Citation of this Page'': “Subcutaneous panniculitis-like T-cell lymphoma”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), updated {{REVISIONMONTH}}/{{REVISIONDAY}}/{{REVISIONYEAR}}, <nowiki>https://ccga.io/index.php/HAEM5:Subcutaneous_panniculitis-like_T-cell_lymphoma</nowiki>.
<nowiki>*</nowiki>''Citation of this Page'': “Subcutaneous panniculitis-like T-cell lymphoma”. Compendium of Cancer Genome Aberrations (CCGA), Cancer Genomics Consortium (CGC), updated {{REVISIONMONTH}}/{{REVISIONDAY}}/{{REVISIONYEAR}}, <nowiki>https://ccga.io/index.php/HAEM5:Subcutaneous_panniculitis-like_T-cell_lymphoma</nowiki>.
[[Category:HAEM5]][[Category:DISEASE]][[Category:Diseases S]]
[[Category:HAEM5]][[Category:DISEASE]][[Category:Diseases S]]
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