Compendium of Cancer Genome Aberrations

HAEM5:Hepatosplenic T-cell lymphoma: Difference between revisions

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|D, P
|D, P
|No
|No
|Considered a primary aberration<ref name=":2" />, seen in 40-70% of cases<ref name=":1" />
|Considered a primary aberration<ref name=":2">Yabe M, Miranda RN, Medeiros LJ. Hepatosplenic T-cell Lymphoma: a review of clinicopathologic features, pathogenesis, and prognostic factors. ''Hum Pathol''. 2018;74:5‐16. doi:10.1016/j.humpath.2018.01.005</ref>, seen in 40-70% of cases<ref name=":1">{{Cite journal|displayauthors=1|last=Medeiros|first=Jeffrey|date=2024|title=Hepatosplenic T-cell lymphoma. In: WHO Classification of Tumours Editorial Board. Haematolymphoid tumours [Internet]|url=https://tumourclassification.iarc.who.int/chaptercontent/63/229|journal=WHO classification of tumours series, 5th ed.|volume=vol. 11|pages=|via=Lyon (France): International Agency for Research on Cancer}}</ref>
|-
|-
|8
|8
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|Unknown
|Unknown
|P
|P
|No
|Seen in 10-15% of cases<ref name=":1" />
|}
{| class="wikitable sortable"
|-
!Chr #!!Gain / Loss / Amp / LOH!!Minimal Region Genomic Coordinates [Genome Build]!!Minimal Region Cytoband
!Diagnostic Significance (Yes, No or Unknown)<ref name=":2">Yabe M, Miranda RN, Medeiros LJ. Hepatosplenic T-cell Lymphoma: a review of clinicopathologic features, pathogenesis, and prognostic factors. ''Hum Pathol''. 2018;74:5‐16. doi:10.1016/j.humpath.2018.01.005</ref><ref name=":4">McKinney, M., Moffitt, A.B., Gaulard, P., Travert, M., De Leval, L., Nicolae, A., Raffeld, M., Jaffe, E.S., Pittaluga, S., Xi, L. and Heavican, T., 2017. The genetic basis of hepatosplenic T-cell lymphoma. ''Cancer discovery'', ''7''(4), pp.369-379.</ref>
!Prognostic Significance (Yes, No or Unknown)<ref name=":2" /><ref name=":4" />
!Therapeutic Significance (Yes, No or Unknown)
!Notes
|-
|7q
|Gain
|
|Constant loss of 7p22.1p14.1
Gain of 7q22.11q31.1
|Yes
|Yes
|No
|Considered a primary aberration<ref name=":2" />, seen in 40-70% of cases<ref name=":1">{{Cite journal|title=Hepatosplenic T-cell lymphoma. In: WHO Classification of Tumours Editorial Board. Haematolymphoid tumours [Internet]|url=https://tumourclassification.iarc.who.int/chaptercontent/63/229|displayauthors=1|last=Medeiros|first=Jeffrey|date=2024|journal=WHO classification of tumours series, 5th ed.|volume=vol. 11|pages=|via=Lyon (France): International Agency for Research on Cancer}}</ref>
|-
|8
|Gain (trisomy)
|
|Chr8
|Yes
|Yes
|No
|Considered a secondary aberration<ref name=":2" />, seen in 10-50% of cases<ref name=":1" />
|-
|Y
|Loss
|
|ChrY
|No
|No
|No
|Seen in 20-25% of cases<ref name=":1" />
|-
|10q
|Loss
|
|Chr10
|No
|Yes
|No
|Seen in 10-20% of cases<ref name=":1" />
|-
|1q
|Gain
|
|Chr1
|No
|Yes
|No
|No
|Seen in 10-15% of cases<ref name=":1" />
|Seen in 10-15% of cases<ref name=":1" />
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!Clinical Relevance Details/Other Notes
!Clinical Relevance Details/Other Notes
|-
|-
|Isochromosome 7q<ref name=":8" /> and chromosome 7 imbalances including ring chromosome 7.
|Isochromosome 7q<ref name=":8">{{Cite journal|last=Wlodarska|first=Iwona|last2=Martin-Garcia|first2=Nadine|last3=Achten|first3=Ruth|last4=De Wolf-Peeters|first4=Chris|last5=Pauwels|first5=Patrick|last6=Tulliez|first6=Micheline|last7=de Mascarel|first7=Antoine|last8=Brière|first8=Josette|last9=Patey|first9=Martine|date=2002-03|title=Fluorescence in situ hybridization study of chromosome 7 aberrations in hepatosplenic T-cell lymphoma: isochromosome 7q as a common abnormality accumulating in forms with features of cytologic progression|url=https://pubmed.ncbi.nlm.nih.gov/11807981|journal=Genes, Chromosomes & Cancer|volume=33|issue=3|pages=243–251|doi=10.1002/gcc.10021|issn=1045-2257|pmid=11807981}}</ref> and chromosome 7 imbalances including ring chromosome 7.
Can be seen in conjunction with trisomy 8
Can be seen in conjunction with trisomy 8
|Cases with chromosome 7 abnormalities show:
|Cases with chromosome 7 abnormalities show:
*Constant loss of 7p22.1p14.1 (34.88 Mb; 3506316-38406226 bp)<ref name=":3" />
*Constant loss of 7p22.1p14.1 (34.88 Mb; 3506316-38406226 bp)<ref name=":3">{{Cite journal|last=Finalet Ferreiro|first=Julio|last2=Rouhigharabaei|first2=Leila|last3=Urbankova|first3=Helena|last4=van der Krogt|first4=Jo-Anne|last5=Michaux|first5=Lucienne|last6=Shetty|first6=Shashirekha|last7=Krenacs|first7=Laszlo|last8=Tousseyn|first8=Thomas|last9=De Paepe|first9=Pascale|date=2014|title=Integrative genomic and transcriptomic analysis identified candidate genes implicated in the pathogenesis of hepatosplenic T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/25057852|journal=PloS One|volume=9|issue=7|pages=e102977|doi=10.1371/journal.pone.0102977|issn=1932-6203|pmc=4109958|pmid=25057852}}</ref>


*Gain of 7q22.11q31.1 (38.77 Mb; 86259620–124892276 bp)<ref name=":3" />
*Gain of 7q22.11q31.1 (38.77 Mb; 86259620–124892276 bp)<ref name=":3" />
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|P
|P
|No
|No
|occur in a significant minority of HSTL cases<ref name=":4" />
|occur in a significant minority of HSTL cases<ref name=":4">McKinney, M., Moffitt, A.B., Gaulard, P., Travert, M., De Leval, L., Nicolae, A., Raffeld, M., Jaffe, E.S., Pittaluga, S., Xi, L. and Heavican, T., 2017. The genetic basis of hepatosplenic T-cell lymphoma. ''Cancer discovery'', ''7''(4), pp.369-379.</ref>
|}
|}


*7q aberrations and trisomy 8 are considered specific for HSTL, but not sensitive<ref name=":2" />
*7q aberrations and trisomy 8 are considered specific for HSTL, but not sensitive<ref name=":2" />
 
<br />
{| class="wikitable sortable"
|-
!Chromosomal Pattern
!Diagnostic Significance (Yes, No or Unknown)
!Prognostic Significance (Yes, No or Unknown)<ref name=":2" /><ref name=":4" />
!Therapeutic Significance (Yes, No or Unknown)
!Notes
|-
|Isochromosome 7q<ref name=":8">{{Cite journal|last=Wlodarska|first=Iwona|last2=Martin-Garcia|first2=Nadine|last3=Achten|first3=Ruth|last4=De Wolf-Peeters|first4=Chris|last5=Pauwels|first5=Patrick|last6=Tulliez|first6=Micheline|last7=de Mascarel|first7=Antoine|last8=Brière|first8=Josette|last9=Patey|first9=Martine|date=2002-03|title=Fluorescence in situ hybridization study of chromosome 7 aberrations in hepatosplenic T-cell lymphoma: isochromosome 7q as a common abnormality accumulating in forms with features of cytologic progression|url=https://pubmed.ncbi.nlm.nih.gov/11807981|journal=Genes, Chromosomes & Cancer|volume=33|issue=3|pages=243–251|doi=10.1002/gcc.10021|issn=1045-2257|pmid=11807981}}</ref> and chromosome 7 imbalances including ring chromosome 7.
Cases with chromosome 7 abnormalities show:
 
*Constant loss of 7p22.1p14.1 (34.88 Mb; 3506316-38406226 bp)<ref name=":3">{{Cite journal|last=Finalet Ferreiro|first=Julio|last2=Rouhigharabaei|first2=Leila|last3=Urbankova|first3=Helena|last4=van der Krogt|first4=Jo-Anne|last5=Michaux|first5=Lucienne|last6=Shetty|first6=Shashirekha|last7=Krenacs|first7=Laszlo|last8=Tousseyn|first8=Thomas|last9=De Paepe|first9=Pascale|date=2014|title=Integrative genomic and transcriptomic analysis identified candidate genes implicated in the pathogenesis of hepatosplenic T-cell lymphoma|url=https://pubmed.ncbi.nlm.nih.gov/25057852|journal=PloS One|volume=9|issue=7|pages=e102977|doi=10.1371/journal.pone.0102977|issn=1932-6203|pmc=4109958|pmid=25057852}}</ref>
 
*Gain of 7q22.11q31.1 (38.77 Mb; 86259620–124892276 bp)<ref name=":3" />
 
Can be seen in conjunction with trisomy 8
|Yes
|Yes
|No
|See table under "Genomic Gain/Loss/LOH"
 
 
 
 
Co-occurrence of Isochromosome 7q and trisomy 8 can be seen in 8-53% of cases<ref name=":2" />
 
Cases without diagnostic detection of i(7q) or trisomy 8, often have detection of these abnormalities at the time of relapse or disease progression<ref name=":2" />
|-
|Loss of chromosome 10q
Gain of chromosome 1q
|No
|Yes
|No
|occur in a significant minority of HSTL cases<ref name=":4" />
|}<br />


==Gene Mutations (SNV/INDEL)==
==Gene Mutations (SNV/INDEL)==
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One study showed increased CD56 expression with ''STAT5b''<ref name=":9" />
One study showed increased CD56 expression with ''STAT5b''<ref name=":9">{{Cite journal|last=Nicolae|first=A.|last2=Xi|first2=L.|last3=Pittaluga|first3=S.|last4=Abdullaev|first4=Z.|last5=Pack|first5=S. D.|last6=Chen|first6=J.|last7=Waldmann|first7=T. A.|last8=Jaffe|first8=E. S.|last9=Raffeld|first9=M.|date=2014-11|title=Frequent STAT5B mutations in γδ hepatosplenic T-cell lymphomas|url=https://pubmed.ncbi.nlm.nih.gov/24947020|journal=Leukemia|volume=28|issue=11|pages=2244–2248|doi=10.1038/leu.2014.200|issn=1476-5551|pmc=7701980|pmid=24947020}}</ref>




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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.


{| class="wikitable sortable"
|-
!Gene; Genetic Alteration!!Presumed Mechanism (Tumor Suppressor Gene [TSG] / Oncogene / Other)!!Prevalence (COSMIC /  TCGA / Other)!!Concomitant Mutations!!Mutually Exclusive Mutations
!Diagnostic Significance (Yes, No or Unknown)<ref name=":4" />
!Prognostic Significance (Yes, No or Unknown)<ref name=":2" /><ref name=":4" />
!Therapeutic Significance (Yes, No or Unknown)<ref name=":2" /><ref>{{Cite journal|last=Pro|first=Barbara|last2=Allen|first2=Pamela|last3=Behdad|first3=Amir|date=2020-10-29|title=Hepatosplenic T-cell lymphoma: a rare but challenging entity|url=https://pubmed.ncbi.nlm.nih.gov/32756940|journal=Blood|volume=136|issue=18|pages=2018–2026|doi=10.1182/blood.2019004118|issn=1528-0020|pmc=7596851|pmid=32756940}}</ref>
!Notes
|-
|''STAT3''; missense mutation
|Oncogenic driver mutation
|9%
|
|''STAT5b''; Only 1 reported case with both mutations present<ref name=":4" />
|No
|No
|Yes
|Also seen in 40% of T-large granular lymphocyte leukemia<ref name=":2" />
|-
|''STAT5b''; missense mutation
|Oncogenic driver mutation
|31%
|
|''STAT3''; Only 1 reported case with both mutations present<ref name=":4" />
|Yes<ref name=":4" /><ref>{{Cite journal|last=Desmares|first=Anne|last2=Bouzy|first2=Simon|last3=Thonier|first3=Florian|last4=Goustille|first4=Julien|last5=Llamas-Gutierrez|first5=Francisco|last6=Genevieve|first6=Franck|last7=Cottin|first7=Laurane|last8=Baseggio|first8=Lucile|last9=Lemaire|first9=Pierre|date=2024-01-25|title=Hepatosplenic T-cell lymphoma displays an original oyster-shell cytological pattern and a distinct genomic profile from that of gamma-delta T-cell large granular lymphocytic leukemia|url=https://pubmed.ncbi.nlm.nih.gov/38268478|journal=Haematologica|doi=10.3324/haematol.2023.283856|issn=1592-8721|pmid=38268478}}</ref>
|No
|Yes
|Highest functional potency: ''STAT5B'' N642H and V712E mutations<ref name=":2" />
One study showed increased CD56 expression with ''STAT5b''<ref name=":9">{{Cite journal|last=Nicolae|first=A.|last2=Xi|first2=L.|last3=Pittaluga|first3=S.|last4=Abdullaev|first4=Z.|last5=Pack|first5=S. D.|last6=Chen|first6=J.|last7=Waldmann|first7=T. A.|last8=Jaffe|first8=E. S.|last9=Raffeld|first9=M.|date=2014-11|title=Frequent STAT5B mutations in γδ hepatosplenic T-cell lymphomas|url=https://pubmed.ncbi.nlm.nih.gov/24947020|journal=Leukemia|volume=28|issue=11|pages=2244–2248|doi=10.1038/leu.2014.200|issn=1476-5551|pmc=7701980|pmid=24947020}}</ref>
Also seen in ~2% of T-large granular lymphocyte leukemia<ref name=":2" />
|-
|''PIK3CD''
|Activate signaling
pathways important to cell survival<ref name=":4" />
|9%
|
|
|No
|No
|Yes
|
|-
|''SETD2''; biallelic LOF
|Tumor suppressor gene, chromatin modifier*<ref name=":4" />
|25%
|
|
|Yes
|No
|Yes
|''SET2–RPB1'' interacting domain (SRI) domain ( 31 ) at the COOH-terminus of the SETD2 protein product
Most frequently silenced gene and most frequent mutated chromatin modifier in HSTL<ref name=":4" />
71% of cases showing at least one LOF mutation<ref name=":4" />, and more than 44% of patients with ''SETD2'' mutations had more than 1 mutation detected<ref name=":2" />
|-
|''INO80''
|Chromatin modifier*
|21%
|
|
|Yes
|Yes<ref name=":2" />
|Yes
|
|-
|''ARID1B''
|Chromatin modifier*
|19%
|
|
|No
|No
|No
|
|-
|''TET3''
|Chromatin modifier*
|15%
|
|
|Yes
|No
|Yes
|
|-
|''SMARCA2''
|Chromatin modifier*
|10%
|
|
|No
|No
|No
|
|}
<nowiki>*</nowiki>Chromatin modifiers make up the most commonly mutated genes in HSTL, detected in 62% of cases. <ref name=":4" />
<nowiki>*</nowiki>Chromatin modifiers make up the most commonly mutated genes in HSTL, detected in 62% of cases. <ref name=":4" />


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