Global surveillance of somatic alterations in triple negative breast cancers by whole exon sequencing analyses
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE87479 | GEO | 2019/10/01
REPOSITORIES: GEO
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Project description:Introduction: The majority of pulmonary carcinoid (PC) tumors can be cured by surgical resection alone, but a significant proportion of patients experience recurrences. PC is insensitive to conventional chemotherapy, and it would be necessary to reveal the molecular mechanisms of metastasis and develop targeted therapeutics. Methods: We performed the comprehensive whole-exome sequencing (WES) of primary tumors and corresponding normal lung tissues from 14 PC patients (including 4 patients who developed postsurgical distant metastasis) and the RNA sequencing of primary tumors from 6 PC patients (including 4 patients who developed postsurgical distant metastasis). Exon array-based gene expression analysis was performed in 25 PC. Results: We identified a total of 139 alterations in 136 genes. MUC6 and SPTA1 were recurrently mutated with the frequency of 21 % (3/14) and 14% (2/14), respectively. The mucin protein family genes including MUC2, MUC4 and MUC6 were mutated in 36% (5/14) in a mutually exclusive manner. The pathway analysis of mutated genes revealed the enrichment of genes involved in the mitogen-activated protein kinase (MAPK) signaling, regulation of actin cytoskeleton and focal adhesion, and transforming growth factor (TGF)-β signaling pathways. RNA sequencing reveals a total of 8 novel fusion transcripts including one derived from chromosomal translocation between the TRIB2 and PRKCE genes. All the 8 fusion genes were detected in primary PC that had developed metastasis after surgical resection. We identified 14 genes (DENND1B, GRID1, CLMN, DENND1B, NRP1, SEL1L3, C5orf13, TNFRSF21, TES, STK39, MTHFD2, OPN3, MET, and HIST1H3C) up-regulated in 5 PC that had relapsed after surgical resection. Conclusions: In this study we identified novel somatic mutations and chromosomal rearrangements by examining clinically aggressive cases that had developed postsurgical metastasis. It is essential to validate their clinical significance in an independent larger patient cohort.
2020-08-04 | GSE142190 | GEO
Project description:Introduction: The majority of pulmonary carcinoid (PC) tumors can be cured by surgical resection alone, but a significant proportion of patients experience recurrences. PC is insensitive to conventional chemotherapy, and it would be necessary to reveal the molecular mechanisms of metastasis and develop targeted therapeutics. Methods: We performed the comprehensive whole-exome sequencing (WES) of primary tumors and corresponding normal lung tissues from 14 PC patients (including 4 patients who developed postsurgical distant metastasis) and the RNA sequencing of primary tumors from 6 PC patients (including 4 patients who developed postsurgical distant metastasis). Exon array-based gene expression analysis was performed in 25 PC. Results: We identified a total of 139 alterations in 136 genes. MUC6 and SPTA1 were recurrently mutated with the frequency of 21 % (3/14) and 14% (2/14), respectively. The mucin protein family genes including MUC2, MUC4 and MUC6 were mutated in 36% (5/14) in a mutually exclusive manner. The pathway analysis of mutated genes revealed the enrichment of genes involved in the mitogen-activated protein kinase (MAPK) signaling, regulation of actin cytoskeleton and focal adhesion, and transforming growth factor (TGF)-β signaling pathways. RNA sequencing reveals a total of 8 novel fusion transcripts including one derived from chromosomal translocation between the TRIB2 and PRKCE genes. All the 8 fusion genes were detected in primary PC that had developed metastasis after surgical resection. We identified 14 genes (DENND1B, GRID1, CLMN, DENND1B, NRP1, SEL1L3, C5orf13, TNFRSF21, TES, STK39, MTHFD2, OPN3, MET, and HIST1H3C) up-regulated in 5 PC that had relapsed after surgical resection. Conclusions: In this study we identified novel somatic mutations and chromosomal rearrangements by examining clinically aggressive cases that had developed postsurgical metastasis. It is essential to validate their clinical significance in an independent larger patient cohort.
2020-08-04 | GSE142186 | GEO
Project description:Introduction: The majority of pulmonary carcinoid (PC) tumors can be cured by surgical resection alone, but a significant proportion of patients experience recurrences. PC is insensitive to conventional chemotherapy, and it would be necessary to reveal the molecular mechanisms of metastasis and develop targeted therapeutics. Methods: We performed the comprehensive whole-exome sequencing (WES) of primary tumors and corresponding normal lung tissues from 14 PC patients (including 4 patients who developed postsurgical distant metastasis) and the RNA sequencing of primary tumors from 6 PC patients (including 4 patients who developed postsurgical distant metastasis). Exon array-based gene expression analysis was performed in 25 PC. Results: We identified a total of 139 alterations in 136 genes. MUC6 and SPTA1 were recurrently mutated with the frequency of 21 % (3/14) and 14% (2/14), respectively. The mucin protein family genes including MUC2, MUC4 and MUC6 were mutated in 36% (5/14) in a mutually exclusive manner. The pathway analysis of mutated genes revealed the enrichment of genes involved in the mitogen-activated protein kinase (MAPK) signaling, regulation of actin cytoskeleton and focal adhesion, and transforming growth factor (TGF)-β signaling pathways. RNA sequencing reveals a total of 8 novel fusion transcripts including one derived from chromosomal translocation between the TRIB2 and PRKCE genes. All the 8 fusion genes were detected in primary PC that had developed metastasis after surgical resection. We identified 14 genes (DENND1B, GRID1, CLMN, DENND1B, NRP1, SEL1L3, C5orf13, TNFRSF21, TES, STK39, MTHFD2, OPN3, MET, and HIST1H3C) up-regulated in 5 PC that had relapsed after surgical resection. Conclusions: In this study we identified novel somatic mutations and chromosomal rearrangements by examining clinically aggressive cases that had developed postsurgical metastasis. It is essential to validate their clinical significance in an independent larger patient cohort.
2020-08-04 | GSE141755 | GEO
Project description:Up to 80% of endometrial and breast cancers express the oestrogen receptor ERa. Unlike breast cancer, anti-oestrogen therapy has had limited success in endometrial cancer, raising the possibility that oestrogen has different effects in the two cancer types. We investigated the role of oestrogen in endometrial and breast cancers using cell lines and found that oestrogen-responsive genes were predominantly unique between the two cancer types.
2018-08-29 | GSE107693 | GEO
Project description:Breast cancer is the most common malignancy that develops in women, responsible for the highest cancer-associated death rates. Triple negative breast cancers (TNBC) represent an important subtype that have an aggressive clinical phenotype, are associated with a higher likelihood of metastasis and are not responsive to current targeted therapies. miRNAs have emerged as an attractive candidate for molecular biomarkers and treatment targets in breast cancer, but their role in the progression of TNBC remains largely unexplored. This study has investigated miRNA expression profiles in 31 primary TNBC cases and in 13 lymph node metastases compared with 23 matched normal breast tissues to determine miRNAs associated with the initiation of this disease subtype and those associated with its metastasis. 71 miRNAs were differentially expressed in TNBC, the majority of which have previously been associated with breast cancer, including members of the miR-200 family and the miR-17-92 oncogenic cluster, suggesting that miRNAs involved in the initiation of TNBC are not subtype specific. However, the repertoire of miRNAs expressed in lymph node negative and lymph node positive TNBCs were largely distinct from one another. In particular, miRNA profiles associated with lymph node negative disease tended to be up-regulated, while those associated with lymph node positive disease were down-regulated and largely overlapped with the profiles of their matched lymph node metastases. miRNA expression profiles were examined in 31 primary TNBC cases and in 13 lymph node metastases compared with 23 matched normal breast tissues
2014-11-24 | E-GEOD-38167 | biostudies-arrayexpress
Project description:AML with mutated NPM1 usually carries normal karyotype (NK) but it may harbor chromosomal aberrations whose significance remains unclear. We addressed this question in 631 AML patients with mutated/cytoplasmic NPM1. An abnormal karyotype (AK) was present in 93/631 cases (14.7%), the most frequent abnormalities being +8, +4, -Y, del(9q), +21. Chromosome aberrations in NPM1-mutated AML were similar to, but occurred less frequently than additional chromosome changes found in other AML with recurrent cytogenetic abnormalities according to WHO classification. Four of the 31 NPM1-mutated AML patients karyotyped at different time points had NK at diagnosis but AK at relapse: del(9q) (n=2), t(2;11) (n=1), inv(12) (n=1). NPM1-mutated AML with NK or AK showed overlapping morphological, immunophenotypic (CD34-negativity) and gene expression profile (downregulation of CD34 and upregulation of HOX genes). No difference in survival was observed among NPM1-mutated AML patients independently of whether they carried a normal or abnormal karyotype, the NPM1-mutated/FLT3-ITD negative cases showing the better prognosis. Findings in our patients point to chromosomal aberrations as secondary events, reinforce the concept that NPM1 mutation is a founder genetic lesion and indicate that NPM1-mutated AML should be clinically handled as one entity, irrespective of the karyotype.
2009-06-01 | GSE16015 | GEO
Project description:AML with mutated NPM1 usually carries normal karyotype (NK) but it may harbor chromosomal aberrations whose significance remains unclear. We addressed this question in 631 AML patients with mutated/cytoplasmic NPM1. An abnormal karyotype (AK) was present in 93/631 cases (14.7%), the most frequent abnormalities being +8, +4, -Y, del(9q), +21. Chromosome aberrations in NPM1-mutated AML were similar to, but occurred less frequently than additional chromosome changes found in other AML with recurrent cytogenetic abnormalities according to WHO classification. Four of the 31 NPM1-mutated AML patients karyotyped at different time points had NK at diagnosis but AK at relapse: del(9q) (n=2), t(2;11) (n=1), inv(12) (n=1). NPM1-mutated AML with NK or AK showed overlapping morphological, immunophenotypic (CD34-negativity) and gene expression profile (downregulation of CD34 and upregulation of HOX genes). No difference in survival was observed among NPM1-mutated AML patients independently of whether they carried a normal or abnormal karyotype, the NPM1-mutated/FLT3-ITD negative cases showing the better prognosis. Findings in our patients point to chromosomal aberrations as secondary events, reinforce the concept that NPM1 mutation is a founder genetic lesion and indicate that NPM1-mutated AML should be clinically handled as one entity, irrespective of the karyotype. All bone marrow samples were obtained from untreated patients at the time of diagnosis. Cells used for microarray analysis were collected from the purified fraction of mononuclear cells after Ficoll density centrifugation.
2009-06-01 | E-GEOD-16015 | biostudies-arrayexpress
Project description:Current prognostic gene expression profiles for breast cancer mainly reflect proliferation status and are most useful in ER-positive cancers. Triple-negative breast cancers (TNBCs) are clinically heterogeneous, and prognostic markers and biology-based therapies are needed to better treat this disease. We assembled Affymetrix gene expression data for 579 TNBCs and performed unsupervised analysis to define metagenes that distinguish molecular subsets within TNBC. We used n=394 cases for discovery and n=185 cases for validation. Sixteen metagenes emerged that identified basal-like, apocrine and claudin-low molecular subtypes, or reflected various non-neoplastic cell populations including immune cells, blood, adipocytes, stroma, angiogenesis, and inflammation within the cancer. The expressions of these metagenes were correlated with survival and multivariate analysis was performed including routine clinical and pathological variables. 73% of TNBCs displayed basal-like molecular subtype that correlated with high histological grade and younger age. Survival of basal-like TNBC was not different from non-basal-like TNBC. High expression of immune cell metagenes was associated with good and high expression of inflammation and angiogenesis-related metagenes were associated with poor prognosis. A ratio of high B-cell and low IL-8 metagenes identified 32% of TNBC with good prognosis (HR 0.37, 95% CI 0.22-0.61; P<0.001) and was the only significant predictor in multivariate analysis including routine clincopathological variables. We describe a ratio of high B-cell presence and low IL-8 activity as a powerful new prognostic marker for TNBC. Inhibition of the IL-8 pathway also represents an attractive novel therapeutic target for this disease.
2011-09-13 | GSE31519 | GEO
Project description:We recently reported a truncating deletion in the NFKBIE gene, which encodes IκBε, a negative feedback regulator of NF-κB, in clinically aggressive chronic lymphocytic leukemia (CLL). Preliminary data indicate enrichment of NFKBIE aberrations in other lymphoid malignancies, hence we screened a large patient cohort (n=1460) diagnosed with different lymphoid neoplasms. We observed a a remarkably high frequency of NFKBIE aberrations (46/203 cases, 22,7%) in primary mediastinal B-cell lymphoma (PMBL). The deletion was associated with a particular aggressive clinical course and reduced survival in multivariate analysis. With gene expression profiling (GEP) via the NanoString nCounter hybridization system and the NanoString GX Human PanCancer Pathway Panel including 30 additional custom genes, the aim of this analysis was to study the differential activation of various oncogenic pathways including NFKB-signaling in NFKBIE mutated vs. non-mutated PMBL.
2016-10-09 | GSE86815 | GEO
Project description:Triple negative breast cancers (TNBCs) are characterised by a wide spectrum of genomic aberrations representing underlying repair defects that may be targeted therapeutically. However, means to measure these defects in tumours and an understanding of their effect on sensitivity to DNA damaging agents is limited. We sought to address this by establishing methods to trace underlying deficiencies in DNA repair processes using patterns of genomic instability. Here, we demonstrate that a pattern related to Homologous Recombination defects, allelic-imbalanced Copy Number Aberration, predicts response to platinum containing chemotherapeutics in TNBC patients. These patterns also enabled us to identify a meiotic gene HORMAD1, as a functional driver of allelic-imbalanced Copy Number Aberration and genomic instability in TNBC. Additionally, HORMAD1 expression is also a predictive marker of carboplatin response in TNBC. Mechanistically, expression of HORMAD1 in cell lines inhibited Homologous Recombination representing outÐof-context activation of its meiotic function.
2015-03-31 | E-MTAB-2626 | biostudies-arrayexpress