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T cell receptor gene repertoire profiles in subgroups of patients with lymphocytic leukemia bearing distinct genomic aberrations

ABSTRACT: Immunogenetic studies in CLL revealed clonal expansions of T cells and shared T cell clonotypes between different patients, strongly implying clonal selection by antigens. Recurrent genomic aberrations associated with distinct abnormal expression profiles could represent an alternative source of potent immunogenic neoepitopes that might shape the T cell receptor (TR) gene repertoire in CLL. On these grounds, here we interrogated the TR gene repertoire of CLL patients with different genomic aberration profiles with the aim to identify unique signatures that would allude to distinct antigen selection pressures.The study group included 44 untreated CLL patients with who were categorized in 5 subgroups defined by a unique genomic aberration, as follows: +12, n=17; del(11q), n=10; del(13q), n=7; TP53mut, n=5; NOTCH1mut, n=5. Starting material was RNA extracted from blood mononuclear cells. TRBV-TRBD-TRBJ gene rearrangements were RT-PCR amplified and subjected to paired-end next generation sequencing (NGS). Bioinformatics analysis with a purpose-build pipeline and in silico prediction models were used for the profiling of the TR gene repertoire and the identification of neoepitope-specific TR clonotypes, respectively.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Homo sapiens

SUBMITTER: Elisavet Vlachonikola

PROVIDER: E-MTAB-12216 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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