Complex structural variants and formation of de novo fusion genes in chronic lymphocytic leukemia

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F65269705%3A_____%2F19%3A00071796" target="_blank" >RIV/65269705:_____/19:00071796 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.olhemdny.cz/sites/default/files/downloads/sbornik_abstrakt_ohd_2019.pdf" target="_blank" >https://www.olhemdny.cz/sites/default/files/downloads/sbornik_abstrakt_ohd_2019.pdf</a>

DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Complex structural variants and formation of de novo fusion genes in chronic lymphocytic leukemia

Popis výsledku v původním jazyce

Complex structural variants (cSVs) represented by chromothripsis have recently been identified in various tumor types, including chronic lymphocytic leukemia (CLL). They lead to extensive chromosomal rearrangements due to chromosome shattering and consequent random re-joining of scattered fragments. Substantial parts of DNA are typically lost, and other chromosomal parts potentially containing oncogenes are amplified. Importantly, albeit not common in CLL, de novo fusion gene variants with novel functions can be formed. Overall, it is associated with unfavorable prognosis, which can be in part attributed to the frequent co-occurrence with TP53 gene defects. In our study we aimed to perform a detailed analysis of cSVs in CLL and to identify putative de novo fusion genes and their possible functions. Using SNP arrays, we screened for cSVs among 93 CLL cases with various types of TP53 gene abnormalities and identified a subset of 20 patients bearing chromothripsis. In parallel, conventional cytogenetics, mFISH, iFISH and chromosome painting methods were used to supplement the array findings. We predominantly observed clustered deletions but in a third of cases, deletions and also amplifications were present in localized regions. Several chromosomes were affected recurrently with the most frequent being chr6 and chr13. The number of breakpoints ranged from 30 to 154 per case (median 54); a third of breakpoints was located in coding genes. In selected cases we performed whole genome sequencing and studied character of genomic breakpoints in detail, taking into account origins of replication, transposon localization and other factors potentially affecting DNA fragility. We identified recurrent genomic loci containing breakpoints and also genes mutated recurrently. Furthermore, we carried out transcriptome analysis of 10 cSV samples, which revealed gene expression profiles associated with certain genomic changes. In-house bioinformatic pipeline was applied to detect putative de novo fusion genes. Although a high number of genomic breakpoints was found in the tested cases, they mostly did not lead to formation of expressed fusion genes. For a set of 10 PCR validated fusion transcripts we studied whether they could be translated in proteins and found out that only 4 of them encoded abnormal proteins containing domains with predicted functions. In conclusion, using our comprehensive approach we showed that chromothripsis mostly leads to inactivation of genes present in genomic breakpoints. De novo fusion transcripts supposedly encoding abnormal proteins are expressed only to a limited extent.

Název v anglickém jazyce

Complex structural variants and formation of de novo fusion genes in chronic lymphocytic leukemia

Popis výsledku anglicky

Complex structural variants (cSVs) represented by chromothripsis have recently been identified in various tumor types, including chronic lymphocytic leukemia (CLL). They lead to extensive chromosomal rearrangements due to chromosome shattering and consequent random re-joining of scattered fragments. Substantial parts of DNA are typically lost, and other chromosomal parts potentially containing oncogenes are amplified. Importantly, albeit not common in CLL, de novo fusion gene variants with novel functions can be formed. Overall, it is associated with unfavorable prognosis, which can be in part attributed to the frequent co-occurrence with TP53 gene defects. In our study we aimed to perform a detailed analysis of cSVs in CLL and to identify putative de novo fusion genes and their possible functions. Using SNP arrays, we screened for cSVs among 93 CLL cases with various types of TP53 gene abnormalities and identified a subset of 20 patients bearing chromothripsis. In parallel, conventional cytogenetics, mFISH, iFISH and chromosome painting methods were used to supplement the array findings. We predominantly observed clustered deletions but in a third of cases, deletions and also amplifications were present in localized regions. Several chromosomes were affected recurrently with the most frequent being chr6 and chr13. The number of breakpoints ranged from 30 to 154 per case (median 54); a third of breakpoints was located in coding genes. In selected cases we performed whole genome sequencing and studied character of genomic breakpoints in detail, taking into account origins of replication, transposon localization and other factors potentially affecting DNA fragility. We identified recurrent genomic loci containing breakpoints and also genes mutated recurrently. Furthermore, we carried out transcriptome analysis of 10 cSV samples, which revealed gene expression profiles associated with certain genomic changes. In-house bioinformatic pipeline was applied to detect putative de novo fusion genes. Although a high number of genomic breakpoints was found in the tested cases, they mostly did not lead to formation of expressed fusion genes. For a set of 10 PCR validated fusion transcripts we studied whether they could be translated in proteins and found out that only 4 of them encoded abnormal proteins containing domains with predicted functions. In conclusion, using our comprehensive approach we showed that chromothripsis mostly leads to inactivation of genes present in genomic breakpoints. De novo fusion transcripts supposedly encoding abnormal proteins are expressed only to a limited extent.

Druh

O - Ostatní výsledky

CEP obor

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OECD FORD obor

30205 - Hematology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2019

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů