Faculty Opinions recommendation of Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma.

Author(s):  
Randy Gascoyne
2015 ◽  
Vol 47 (9) ◽  
pp. 1061-1066 ◽  
Author(s):  
Lu Jiang ◽  
Zhao-Hui Gu ◽  
Zi-Xun Yan ◽  
Xia Zhao ◽  
Yin-Yin Xie ◽  
...  

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 7549-7549 ◽  
Author(s):  
Soon Thye Lim ◽  
Tammy Song ◽  
Jing Quan Lim ◽  
Yurike Laurensia ◽  
Jane Wan Lu Pang ◽  
...  

7549 Background: Natural killer/T-cell lymphoma (NKTL) is a rare type of non-Hodgkin lymphoma that occurs more frequently in East Asia and Latin America and is associated with Epstein–Barr virus infection. Recent whole-exome sequencing studies in NKTL have reported recurrent somatic mutations in genes associated with JAK-STAT pathway, however the role of aberrant JAK-STAT signaling in tumor immune escape through PD-L1 regulation is unclear. Methods: To determine the prevalence of JAK-STAT pathway alteration in NKTL, we performed targeted sequencing of 188 genes associated with JAK-STAT pathway in 109 NKTL (22 Singapore cases, 79 China cases and 8 cell lines). Single nucleotide variants and micro-indels were called using Freebayes and candidate variants annotated using ANNOVAR. Ba/F3 model system was used to test the transformation capacity of identified variants. Cell lines were evaluated for PD-L1 expression by immunoblotting and flow cytometry. Tissue microarrays were examined for p-STAT3 and PD-L1 expression by immunohistochemistry. Results: We identified a total of 284 non-synonymous somatic mutations candidates in 114 genes, including 243 missense, 10 nonsense, 4 splice-site and 27 indel mutations. Recurrent mutations were most frequently located in STAT3 (25/109 cases, 23%) followed by TP53 (16/109 cases, 16%) and JAK3 (8/109 cases, 7%). A total of 18 STAT3 variants were identified including known hotspot mutations and novel mutations in the SH2, coiled coil and DNA-binding domains. Characterization of novel E616K mutant residing in the SH2 domain showed that E616K conferred IL3 independent growth to Ba/F3 cells, increased STAT3 phosphorylation and PD-L1 expression. Consistent with these findings, PD-L1 was over expressed in cell lines harboring STAT3 mutations. A positive correlation between PD-L1 and p-STAT3 expression was also observed in tumor tissue (R = 0.51, P = 0.02). Conclusions: We characterized a novel activating STAT3 mutant and demonstrated its ability to drive PD-L1 expression, which may promote tumor evasion from the antitumor immune response. The combination of PD-1/PD-L1 antibodies and STAT3 inhibitors might be a promising and novel therapeutic approach for NKTL in the future.


2020 ◽  
Author(s):  
Jing Quan Lim ◽  
Soon Thye Lim ◽  
Choon Kiat Ong

AbstractRecurrent GNAQ mutation encoding p.T96S in natural-killer/T cell lymphoma (NKTCL) was recently reported in 8.7% (11/127) of NKTCL patients. At the time of publication, this phenomenon was not observed in preceding genomic studies of NKTCL. We suspected that p.T96S was a false-positive somatic call due to misaligned sequencing reads that originated from the highly similar GNAQ-pseudogene (GNAQP) chr2q21.1 locus. Linkage disequilibrium analysis also revealed that GNAQP has high frequencies of co-occurring polymorphic mismatches which led to the preferential misalignment of sequencing reads to the GNAQ chr9q21.2 locus instead. This correspondence implicates our interpretation of true-positive somatic variants and many other studies which could be affected by similar suboptimal interpretation of somatic mutations.


Orbit ◽  
2021 ◽  
pp. 1-5
Author(s):  
Elzbieta Mechel ◽  
Ann. Q. Tran ◽  
Victoria S. North ◽  
Farnoush M. Moen ◽  
Andrea A. Tooley

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