Compendium of Cancer Genome Aberrations

HAEM5:Primary cutaneous gamma/delta T-cell lymphoma: Difference between revisions

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|'''CDKN2A'''||—||Homozygous or biallelic deletion → loss of  p16^INK4A/p14^ARF function (cell‑cycle control)||Tumour suppressor
|'''CDKN2A'''||—||Homozygous or biallelic deletion → loss of  p16^INK4A/p14^ARF function (cell‑cycle control)||Tumour suppressor
|'''Common''' (>20%) (~61% in cohort) (PubMed)
|'''Common''' (>20%) (~61% in cohort)<ref name=":0">{{Cite journal|last=Daniels|first=Jay|last2=Doukas|first2=Peter G.|last3=Escala|first3=Maria E. Martinez|last4=Ringbloom|first4=Kimberly G.|last5=Shih|first5=David J. H.|last6=Yang|first6=Jingyi|last7=Tegtmeyer|first7=Kyle|last8=Park|first8=Joonhee|last9=Thomas|first9=Jane J.|date=2020-04-14|title=Cellular origins and genetic landscape of cutaneous gamma delta T cell lymphomas|url=https://pubmed.ncbi.nlm.nih.gov/32286303|journal=Nature Communications|volume=11|issue=1|pages=1806|doi=10.1038/s41467-020-15572-7|issn=2041-1723|pmc=7156460|pmid=32286303}}</ref>
|P
|P
|No
|No
|High‐frequency  deletion, suggests aggressive biology and may be a prognostic marker
|High‐frequency  deletion, suggests aggressive biology and may be a prognostic marker<ref name=":0" />
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|'''ARID1A'''
|'''ARID1A'''
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|Other / P
|Other / P
|No
|No
|Indicates involvement of epigenetic/chromatin pathways in  PCGDTCL
|Indicates involvement of epigenetic/chromatin pathways in  PCGDTCL<ref name=":0" />
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|'''FAS'''
|'''FAS'''
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|Other / P
|Other / P
|No
|No
|Loss of FAS may contribute to immune‐escape of malignant γδ T‑cells
|Loss of FAS may contribute to immune‐escape of malignant γδ T‑cells<ref name=":0" />
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|'''PDCD1'''
|'''PDCD1'''
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|Other / P
|Other / P
|No
|No
|Suggests immune‐escape  mechanism; potential implications for checkpoint therapy though unproven
|Suggests immune‐escape  mechanism; potential implications for checkpoint therapy though unproven<ref name=":0" />
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|'''STAT5B'''
|'''STAT5B'''
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|T / P
|T / P
|No
|No
|JAK/STAT pathway dependency; early data suggest JAK‐inhibitor sensitivity in  analogous T‑cell neoplasms; investigational in PCGDTCL
|JAK/STAT pathway dependency; early data suggest JAK‐inhibitor sensitivity in  analogous T‑cell neoplasms; investigational in PCGDTCL<ref name=":1">{{Cite journal|last=Küçük|first=Can|last2=Jiang|first2=Bei|last3=Hu|first3=Xiaozhou|last4=Zhang|first4=Wenyan|last5=Chan|first5=John K. C.|last6=Xiao|first6=Wenming|last7=Lack|first7=Nathan|last8=Alkan|first8=Can|last9=Williams|first9=John C.|date=2015-01-14|title=Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells|url=https://pubmed.ncbi.nlm.nih.gov/25586472|journal=Nature Communications|volume=6|pages=6025|doi=10.1038/ncomms7025|issn=2041-1723|pmc=7743911|pmid=25586472}}</ref>
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|'''STAT3'''
|'''STAT3'''
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|T / P
|T / P
|No
|No
|Part of JAK/STAT alterations; less frequent than STAT5B  in PCGDTCL
|Part of JAK/STAT alterations; less frequent than STAT5B  in PCGDTCL<ref name=":1" />
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|'''JAK3'''
|'''JAK3'''
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|T
|T
|No
|No
|Supports JAK/STAT pathway involvement; therapeutic  relevance remains investigational in this disease
|Supports JAK/STAT pathway involvement; therapeutic  relevance remains investigational in this disease<ref name=":0" />
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|'''KRAS'''
|'''KRAS'''
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|T / P
|T / P
|No
|No
|MAPK pathway potentially targetable; mutations associated  with poorer outcome in the cohort studied
|MAPK pathway potentially targetable; mutations associated  with poorer outcome in the cohort studied<ref name=":0" />
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|'''NRAS'''
|'''NRAS'''
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|T / P
|T / P
|No
|No
|Part of same pathway as KRAS though less common
|Part of same pathway as KRAS though less common<ref name=":0" />
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|'''MYC'''
|'''MYC'''
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|P / T
|P / T
|No
|No
|MYC pathway involvement may contribute to more aggressive  phenotype; direct targeting not yet established
|MYC pathway involvement may contribute to more aggressive  phenotype; direct targeting not yet established<ref name=":0" />
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|'''MYCN'''
|'''MYCN'''
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|P / T
|P / T
|No
|No
|Highlights involvement of MYC family beyond MYC itself in  PCGDTCL
|Highlights involvement of MYC family beyond MYC itself in  PCGDTCL<ref name=":0" />
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|'''Arm‑level chromosomal alterations (e.g., 9p,  18q deletions; 1q, 7q,15q gains)'''
|'''Arm‑level chromosomal alterations (e.g., 9p,  18q deletions; 1q, 7q,15q gains)'''
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|D / P
|D / P
|No
|No
|These structural changes suggest genomic instability and  aggressive biology; may help risk stratification though not diagnostic per se
|These structural changes suggest genomic instability and  aggressive biology; may help risk stratification though not diagnostic per se<ref name=":0" />
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|'''Fusion: FYN :: (probable partner TRAF3IP2)'''
|'''Fusion: FYN :: (probable partner TRAF3IP2)'''
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|T
|T
|No
|No
|Very recently described; may represent novel  driver/target; further cases needed
|Very recently described; may represent novel  driver/target; further cases needed<ref>{{Cite journal|last=Azimpouran|first=Mahzad|last2=Bui|first2=Chau M.|last3=Balzer|first3=Bonnie|last4=Kitahara|first4=Sumire|date=2024-12-01|title=Rapidly Progressive Primary Cutaneous Gamma Delta T-Cell Lymphoma With FYN Gene Alteration|url=https://pubmed.ncbi.nlm.nih.gov/39412302|journal=The American Journal of Dermatopathology|volume=46|issue=12|pages=e120–e123|doi=10.1097/DAD.0000000000002856|issn=1533-0311|pmid=39412302}}</ref>
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|'''Fusion: PCM1 :: JAK2'''
|'''Fusion: PCM1 :: JAK2'''
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|T
|T
|No
|No
|Known in other T‑cell and myeloid neoplasms; in PCGDTCL  this double‐hit  case had PCM1::JAK2 + TBL1XR1::TP63 fusion; patient refractory to JAK  inhibitor
|Known in other T‑cell and myeloid neoplasms; in PCGDTCL  this double‐hit  case had PCM1::JAK2 + TBL1XR1::TP63 fusion; patient refractory to JAK  inhibitor<ref name=":2">{{Cite journal|last=Fadl|first=Amr|last2=Bennani|first2=N. Nora|last3=Comfere|first3=Nneka|last4=Durani|first4=Urshila|last5=Greipp|first5=Patricia T.|last6=Feldman|first6=Andrew L.|date=2023-09|title=Primary cutaneous gamma/delta T-cell lymphoma with simultaneous JAK2 and TP63 rearrangements: a new double-hit?|url=https://pubmed.ncbi.nlm.nih.gov/37308177|journal=Histopathology|volume=83|issue=3|pages=492–495|doi=10.1111/his.14973|issn=1365-2559|pmc=10524708|pmid=37308177}}</ref>
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|'''Fusion: TBL1XR1 :: TP63'''
|'''Fusion: TBL1XR1 :: TP63'''
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|P / T
|P / T
|No
|No
|Associated with aggressive behaviour in T‑cell lymphomas;  in the reported PCGDTCL case contributed to aggressive course and JAK  inhibitor resistance
|Associated with aggressive behaviour in T‑cell lymphomas;  in the reported PCGDTCL case contributed to aggressive course and JAK  inhibitor resistance<ref name=":2" />
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==Individual Region Genomic Gain/Loss/LOH==
==Individual Region Genomic Gain/Loss/LOH==
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