Identification and molecular characterization of two recurrente gene fusions in acute myeloid leukemia : ETV6-ANLN and NPM1-HAUS1

Orientador: Fernando Ferreira CostaTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências MédicasResumo: Leucemia Mielóide Aguda (LMA) é uma neoplasia hematológica associada a alta morbidade e mortalidade. Os mecanismos genômicos causadores da LMA são diversos e incluem mutações em ponto, inserções, deleções, alterações do número de cópias, na metilação e translocações cromossômicas. Enquanto os genes envolvidos nas translocações cromossômicas mais frequentemente encontradas em LMA já tenham sido identificados, ainda existem dezenas de translocações cromossômicas recorrentes cujos genes envolvidos nos pontos de quebra cromossômicos não são conhecidos. Esta identificação é essencial para a melhor compreensão dos mecanismos da leucemogênese e muitas vezes podem ter um impacto clínico, modificando a estratificação prognóstica ou a conduta terapêutica. No presente trabalho, através da técnica de sequenciamento de DNA de nova geração, identificamos os genes envolvidos em duas translocações cromossômicas recorrentes em LMA: t(7;12)(p15:p13) e t(5;18)(q35;q21) que levam aos genes de fusão ETV6-ANLN e NPM1-HAUS1 respectivamente. A fusão ETV6-ANLN justapõe o exon 1 do gene ETV6 aos exons 2 a 25 do gene ANLN, gerando uma proteína bastante similar ao ANLN selvagem. Esta fusão gênica é expressa em precursores hematopoiéticos CD34+ e nas linhagens granulocítica e linfoide T, tendo provavelmente ocorrido em uma célula tronco hematopoiética ou em um precursor comum linfóide e mielóide. A fusão NPM1-HAUS1 justapõe os exons 1 a 11 do gene NPM1 ao exon 9 do gene HAUS1, gerando uma proteína similar ao NPM1, porém com a presença de um sinal de exportação nuclear na porção C-terminal da proteína. Como consequência, a proteína híbrida NPM1-HAUS1 localiza-se no núcleo e no citoplasma, ao contrário da NPM1 selvagem que tem localização exclusivamente nuclear. Como a localização citoplasmática da proteína NPM1 é leucemogênica em outros contextos, esse é provavelmente o mecanismo leucemogênico inicial associado a esta translocação cromossômica. Em conclusão, nós identificamos e caracterizamos duas novas fusões gênicas recorrentes em LMAAbstract: Acute Myeloid Leukemia (AML) is a neoplastic myeloid disease characterized by progressive substitution of normal hematopoiesis by leukemic blasts that is associated with high morbidity and mortality. AML is a genomic disease caused by distinct genomic mechanisms such as single nucleotide substitutions, insertions, deletions, copy number variations and chromosomal translocations. While the genes involved in common chromosomal translocations have been well studied, there are several recurrent chromosomal translocations for which the affected genes have not been characterized. The identifications of such genes is essential for better understanding of AML pathophysiology and has the potential to improve diagnostic, prognostic and the therapeutic approach of patients harboring such chromosomal translocations. In the present study we have identified the genes involved in two recurring chromosomal translocations in AML by means of next generation DNA sequencing: t(7;12)(p15:p13) and t(5;18)(q35;q21) that lead to the gene fusions ETV6-ANLN and NPM1-HAUS1 respectively. The gene fusion ETV6-ANLN juxtaposes ETV6 exon 1 to ANLN exons 2 to 25, culminating with a putative protein highly similar to wild type ANLN. This gene fusion is expressed in hematopoietic precursors, granulocytes and T cell lymphocytes, probably occurring in a hematopoietic stem cell or a common myeloid lymphoid precursor. The gene fusion NPM1-HAUS1 leads to the fusion of NPM1 exons 1 to 11 to HAUS1 exon 9, generetaing a putative protein similar to wild type NPM1 with the addition of a novel nuclear export signal (NES) in the C-terminal region of the protein. Regarding subcellular localization, NPM1-HAUS1 localizes in the nucleus and cytoplasm in opposition to wild type NPM1 that localizes exclusively in the nucleus. Since NPM1 cytoplasmic localization has been shown to be associated with leukemogenesis, this is probably the neoplastic mechanism associated with this gene fusion. In conclusion, we have described and characterized two novel gene fusions associated with recurrent chromosomal translocations in AMLDoutoradoPatologia ClinicaDoutor em Ciências Médica

Identification Of Anln As Etv6 Partner Gene In Recurrent T(7;12)(p15;p13): A Possible Role Of Deregulated Anln Expression In Leukemogenesis

The ETV6 gene encodes an ETS family transcription factor that is involved in a myriad of chromosomal rearrangements found in hematological malignancies and other neoplasms. A recurrent ETV6 translocation, previously described in patients with acute myeloid leukemia (AML) (Genes Chromosomes Cancer 51:328-337,2012, Leuk Res 35:e212-214, 2011), whose partner has not been identified is t(7; 12)(p15; p13). We herein report that the t(7; 12)(p15; p13) fuses ETV6 to ANLN, a gene not previously implicated in the pathogenesis of hematological malignancies, and we demonstrate that this translocation leads to high expression of the fusion transcript in the myeloid and lymphoid lineages.1

Treatment change as a predictor of outcome among patients with classic chronic graft-versus-host disease

We analyzed outcomes for 668 patients who had systemic treatment for chronic graft-versus-host disease (GVHD) to assess the utility of early treatment change for exacerbation of chronic GVHD as a surrogate for survival endpoints in clinical trials. Fifty-six percent of patients had treatment change within 2 years after diagnosis of chronic GVHD. The median onset of treatment change was 4.4 months (range, 0.3 – 50 months). The cumulative incidence of non-relapse mortality (NRM) at 2 years was 16%, and overall survival at 2 years was 74%. In time-dependent Cox models, treatment change was associated with an increase in risk of NRM (hazard ratio, 2.53; 95% CI, 1.7-3.7; p < .0001). The hazard ratio was attenuated by 6% per month of delay in treatment change. Our results confirm that exacerbation of chronic GVHD is associated with an increased risk of NRM and with decreased survival, but the strength of this association is not large enough to allow the use of early exacerbation as a surrogate for survival endpoints in clinical trials. Other measures of clinical benefit, such as response, will need to be developed as endpoints in phase II trials for patients with chronic GVHD

Identification Of Anln As Etv6 Partner Gene In Recurrent T(7;12)(p15;p13): A Possible Role Of Deregulated Anln Expression In Leukemogenesis.

The ETV6 gene encodes an ETS family transcription factor that is involved in a myriad of chromosomal rearrangements found in hematological malignancies and other neoplasms. A recurrent ETV6 translocation, previously described in patients with acute myeloid leukemia (AML) (Genes Chromosomes Cancer 51:328-337,2012, Leuk Res 35:e212-214, 2011), whose partner has not been identified is t(7;12)(p15;p13). We herein report that the t(7;12)(p15;p13) fuses ETV6 to ANLN, a gene not previously implicated in the pathogenesis of hematological malignancies, and we demonstrate that this translocation leads to high expression of the fusion transcript in the myeloid and lymphoid lineages.1419

Multi-center real-world comparison of the fully automated Idylla (TM) microsatellite instability assay with routine molecular methods and immunohistochemistry on formalin-fixed paraffin-embedded tissue of colorectal cancer

Microsatellite instability (MSI) is present in 15-20% of primary colorectal cancers. MSI status is assessed to detect Lynch syndrome, guide adjuvant chemotherapy, determine prognosis, and use as a companion test for checkpoint blockade inhibitors. Traditionally, MSI status is determined by immunohistochemistry or molecular methods. The Idylla (TM) MSI Assay is a fully automated molecular method (including automated result interpretation), using seven novel MSI biomarkers (ACVR2A, BTBD7, DIDO1, MRE11, RYR3, SEC31A, SULF2) and not requiring matched normal tissue. In this real-world global study, 44 clinical centers performed Idylla (TM) testing on a total of 1301 archived colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissue sections and compared Idylla (TM) results against available results from routine diagnostic testing in those sites. MSI mutations detected with the Idylla (TM) MSI Assay were equally distributed over the seven biomarkers, and 84.48% of the MSI-high samples had >= 5 mutated biomarkers, while 98.25% of the microsatellite-stable samples had zero mutated biomarkers. The concordance level between the Idylla (TM) MSI Assay and immunohistochemistry was 96.39% (988/1025); 17/37 discordant samples were found to be concordant when a third method was used. Compared with routine molecular methods, the concordance level was 98.01% (789/805); third-method analysis found concordance for 8/16 discordant samples. The failure rate of the Idylla (TM) MSI Assay (0.23%; 3/1301) was lower than that of referenced immunohistochemistry (4.37%; 47/1075) or molecular assays (0.86%; 7/812). In conclusion, lower failure rates and high concordance levels were found between the Idylla (TM) MSI Assay and routine tests.Peer reviewe

A Novel Assay for the Identification of NOTCH1 PEST Domain Mutations in Chronic Lymphocytic Leukemia

Aims. To develop a fast and robust DNA-based assay to detect insertions and deletions mutations in exon 34 that encodes the PEST domain of NOTCH1 in order to evaluate patients with chronic lymphocytic leukemia (CLL). Methods. We designed a multiplexed allele-specific polymerase chain reaction (PCR) combined with a fragment analysis assay to detect specifically the mutation c.7544 7545delCT and possibly other insertions and deletions in exon 34 of NOTCH1. Results. We evaluated our assay in peripheral blood samples from two cohorts of patients with CLL. The frequency of NOTCH1 mutations was 8.4% in the first cohort of 71 unselected CLL patients. We then evaluated a second cohort of 26 CLL patients with known cytogenetic abnormalities that were enriched for patients with trisomy 12. NOTCH1 mutations were detected in 43.7% of the patients with trisomy 12. Conclusions. We have developed a fast and robust assay combining allele-specific PCR and fragment analysis able to detect NOTCH1 PEST domain insertions and deletions