NEW YORK (GenomeWeb) – Studies by independent research teams are highlighting the somatic mutations and copy number changes behind a rare type of primary cutaneous T cell lymphoma (CTCL) known as Sézary syndrome.
For the first of the studies, researchers from the US and the Netherlands did exome sequencing on tumor and normal samples from more than two-dozen individuals with Sézary syndrome and another 17 individuals with other forms of CTCL. Along with recurrent mutations in genes involved in epigenetic regulation and signaling, their results pointed to an over-representation of copy number changes affecting tumor suppressor genes in Sézary syndrome tumors.
"Our results identify new genetic drivers in the pathogenesis of Sézary syndrome and point to [T cell receptor]-controlled signaling pathways as potential targets in treating this disease," co-corresponding authors Teresa Palomero, Adolfo Ferrando, and Raul Rabadan, all based at Columbia University, and their colleagues wrote.
"Extended analysis of clinically annotated series and further genetic characterization, including whole-genome sequencing and transcriptomic analysis, will be instrumental to elucidate the complete repertoire of genetic driver alterations in Sézary syndrome and CTCL," they noted.
Both Sézary syndrome and a related condition called mycosis fungoides are characterized by CD4+ T helper immune cell expansions, though individuals with Sézary syndrome tend to have more pronounced skin symptoms and far worse outcomes.
Palomero, Ferrando, Rabadan, and their collaborators focused on samples from 25 Sézary syndrome patients, eight individuals with mycosis fungoides, and nine individuals with other forms of CTCL who were treated at Northwestern University of the Leiden University Medical Center.
After capturing protein-coding sequences from each individual's tumor-normal pair using an Agilent SureSelect kit, the researchers sequenced the exomes to average depths of more than 30-fold coverage over around 95 percent of coding sequences with the Illumina HiSeq 2000 instrument.
Their analyses uncovered numerous copy number changes in the Sézary syndrome tumors, particularly chromosome 7, 8, and 17 gains as well as deletions affecting TP53, PTEN, CDKN1B, and other tumor suppressor genes — copy number changes not detected in mycosis fungiodes samples that were not leukemic.
Meanwhile, the team's sequence analysis pointed to recurrent Sézary syndrome mutations in not only TP53, but also epigenetic-related genes such as SMARCA4 and KMT2C, which were also mutated in some mycosis fungoides cases.
Likewise, both Sézary syndrome and other forms of CTCL were marked by mutations suspected of bumping up MAP kinase, NF-kappaB, and NFAT signaling in response to T cell receptor activation.
For their part, investigators from the Baylor College of Medicine and the University of Texas MD Anderson Cancer Center uncovered genetic glitches affecting T cell signaling processes, T cell differentiation, tumor suppressor genes, and other cell cycle checkpoint players when they did exome sequencing, transcriptome sequencing, array-based copy number profiling on tumor and matched normal samples from 37 individuals with stage IV Sézary syndrome.
The collaborators turned to Nimblegen capture kits and Illumina HiSeq 2000 paired-end sequencing to scrutinize protein-coding portions of the Sézary syndrome tumor genomes. They also used Illumina HiSeq 2500 and MiSeq instruments to generate and/or validate sequence data used to assess gene expression and fusion patterns in samples from 32 patients.
By comparing these sequences with those found in matched normal samples — fibroblast cultures generated from a sample of each individual's normal, sun-shielded skin — the researchers identified driver mutations in TP53, CCR4, ARID1A, CARD11, and FAS, genes involved in tumor suppression, T cell migration, cell cycle checkpoints, NF-kappaB signaling, and apoptosis, respectively.
Other glitches in signaling or cell cycle genes turned up, too, including mutations or copy number changes affecting the T cell receptor signaling gene PLCG1, the NF-kappaB gene, TNFRSF1B gene, and mitotic checkpoint contributors such as CDKN2A and RPS6KA1.
Roughly half of the tumors included changes to T cell receptor gene rearrangement patterns that seemed to be consistent with broader shifts in T cell receptor maturation during Sézary syndrome development.
The researchers noted that Sézary syndrome tumors often showed unusual expression in in other genes as well, including frequent jumps in IL32 and IL2RG interleukin receptor-coding gene expression. IL32 expression was especially high in tumor samples from African-American patients, they noted, who tended to have poor Sézary syndrome outcomes.
The team also saw abbreviated survival times in individuals with large cell transformation, a feature of the disease often found in conjunction with TP53 mutations and deletions involving chromosome 2, as well as those carrying independent chromosome 2 deletions or alterations affecting CCR4 or CDKN2A.