scholarly journals BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas

2017 ◽  
Vol 12 (4) ◽  
pp. 724-733 ◽  
Author(s):  
Noémie Leblay ◽  
Frédéric Leprêtre ◽  
Nolwenn Le Stang ◽  
Amandine Gautier-Stein ◽  
Laurent Villeneuve ◽  
...  
2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e20548-e20548
Author(s):  
Longfeng Zhang ◽  
Weijin Xiao ◽  
Fangjun Wu ◽  
Ran Peng ◽  
Jialong Shi ◽  
...  

e20548 Background: SMARCA4 gene is one of the catalytic subunits of the SWI/SNF chromosomal remodeling complex, which can regulate important cellular processes and functions and is closely associated to tumors. The clinical features, therapeutic efficacy, prognosis and pathological features of lung adenocarcinoma with this genetic variation are still unknown and controversial. Methods: The study recruited 274 patients (pts) with lung adenocarcinoma whose samples were sent to perform parallel hybridization-based next-generation sequencing. Two categories of SMARCA4 mutations were divided into Type1 mutations (frameshift mutations, nonsense mutations, splice-3 mutations, copy number amplification) and Type2 mutations (missense mutations and copy number loss) based on whether the mutation may result in defective protein. Furthermore, comparative analysis by using the clinical outcome data, the genomic and pathological characteristics were be performed in SMARCA4 Type 1 alterations corhort and Type 2 alterations corhort. Results: Among 274 pts were recruited, the mutation rate of SMARCA4 gene in lung adenocarcinoma was 9.1%. Furthermore, the presence of SMARCA4 alteration was associated with smoking (P<0.05). Missense, nonsense, frameshift and splice were the most common types of mutations (92%). The pts with SMARCA4 Type1 alterations which probably lead to defective protein expression, had a worse prognosis compared with pts with SMARCA4 Type1 alterations (The role leading to defective protein expression is uncertain) and SMARCA4 Wild groups (P<0.05). In addition, EGFR alterations were strongly associated with SMARCA4 Wild corhort compared to SMARCA4 Type1 alterations corhort (67% vs. 31% ), and SMARCA4 Type1 alterations was more associated with the absence of TP53, RB1, and Robo3 alterations. GO enrichment analysis suggested that the differentiated mutated genes between SMARCA4 Type1 alterations corhort and SMARCA4 Wild corhort were mainly enriched in cell cycle regulation. Pathologically, The SMARCA4 Type1 alterations was mostly poorly or moderately differentiated and strongly accompanied by the loss of expression of TTF-1(83.3%) and BRG1(80%) in immunohistochemistry. Conclusions: SMARCA4 Type1 alterations which probably lead to abnormality of protein was associated with poor prognosis and having different the genomic and pathological characteristics.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2421-2421
Author(s):  
Tsuyoshi Nakamaki ◽  
Kunihiko Fukuchi ◽  
Hidetoshi Nakashima ◽  
Hirotsugu Ariizumi ◽  
Takashi Maeda ◽  
...  

Abstract Abstract 2421 CD20 is not only a therapeutic target but also its expression has prognostic importance in B cell lymphoma. Decreased CD20 expression is often associated with refractory phenotypes, especially in lymphoma treated with therapy including rituximab, an anti-CD20 antibody. To address the molecular mechanism(s) of down-regulation of its expression and to find an alternative therapeutic target(s) in resistant lymphoma, we analyzed a CD20-negative B-cell lymphoma cell line (SD07). SD07 was established from lymphoma cells without expressing CD20, which appeared in pleural effusion in a patient with diffuse large B-cell lymphoma (DLBCL), after 2-years of repeated anti-lymphoma therapy including rituximab, While initial diagnosis was CD20 positive activated B cell-like DLBCL (ABCDLBCL). SD07 selectively lacks CD20 protein expression, but not other B cell antigens, such as CD19, CD21 and CD22 by flowcytometry(FCM). In SCID mice, subcutaneously transplanted SD07 developed tumors which are positive for B cell antigen such as CD79a, but not CD20 (L26) and EBER. Array CGH revealed 0.7 Mb region with copy number loss less than −1.0 of log2 ratios on chromosome 11q12 in SD07. Within this region, 30 kb segment, which showed further loss (less than −2.0),contained two genes, MS4A1(CD20) and MS4A5. Southern blot analysis using CD20 exon 1 as a probe showed homozygous deletion of CD20 gene in SD07. As expected, incubation with rituximab in culture failed to suppress the cell growth of SD07 up to 20 μg/ml(cell No. rituximab/control=0.98±0.04, P=NS). This suggests deletion of CD20 gene with genomic copy number loss in 11q12 produced the loss of CD20 expression and resulted in resistant to rituximab. It is currently studied whether the loss of CD20 expression is directly involved in the tumorigenicity of SD07. Array CGH also showed several genomic regions with copy number loss which are possibly involved in refractory phenotype of SD07. Those includes 10q23 (PTEN), 12q23 (APAF1) and 16q21 (NFATC3). Immunoblot analysis showed the absence of PTEN protein expression and constitutive AKT Ser473 phosphorylation in SD07. SDO7 also showed constitutive phosphorylation of both SykTyr525/526 and Btk Tyr223,however, those did not differ much in those in three germinal center B-like(GCB) cell lines, two Burkitt lymphoma cell lines, Daudi and N8, and a DLBCL cell line, TK, derived from follicular lymphoma. In SD07, somatic mutations of ITAM of either CD79A or CD79B was not detected. This suggests inactivation of PTEN, rather than chronic active BCR signaling, is likely to promote constitutive PI3K-AKT signaling in SD07. Nuclear NF-kB DNA binding by EMSA, SD07 showed constitutively higher binding signals of NF-kB, compared with either Daudi, N8 or TK (SD07=3.6±0.1,GCB cell lines(Daudi,N8,TK)=1.2±0.2, p<0.01, arbitrary density units). Supershift analysis showed increased NF-kB DNA binding in SD07 mainly consist of p50 and c-Rel. By immunoblot, SD07 showed steady-state increased accumulation of p50 protein, but not p65, in nuclear fraction, compared with either in Duadi,N8 or TK. Protein expression of BClxL, a NF-kB target gene, increased in SD07 (SD07=1.9±0.1, GCB cell lines=0.7±0.2, p<0.01, signal intensity, SI). Those suggest that oncogenic PI3K-AKT activation and/or constitutive activation of NF-kB pathway contribute pro-survival signaling in SD07 and those are possible therapeutic target in SD07. Incubation with LY294002(LY), selective PI3K inhibitor, at more than 0.1μM for 4 days, dose-dependently inhibited the cell growth of SD07(10μMLY/DMSO=0.35±0.01, P<0.01), without significant effects on cell viability. FCM analysis with PI showed that incubation with LY produced G1 accumulation and decrease of cells in the S (LY/DMSO,G1=1.5±0.1,S=0.2±0.1,G2M=0.4±0.1, P<0.05). 10 μM LY inhibited both AKT Ser473 phosphorylation (LY/DMSO=0.18±0.01,SI,P<0.01) and protein expression of BClxL (LY/DMSO=0.43±0.02,P<0.05) in SD07. LY increased p27 protein expression (LY/DMSO=1.83±0.04, P<0.05), without affecting NF-kB DNA binding in SD07. It may suggest PI3K are required for expression of some NF-kB target gene without suppressing nuclear NF-kB DNA binding. In summary, although a limited in a cell line, we clarify a novel molecular mechanism of acquired loss of expression of CD20 in DLBCL. In addition, we show that de-regulated PI3K-AKT pathway is a possible therapeutic target for CD20-negative refractory ABCDLBCL. Disclosures: No relevant conflicts of interest to declare.


2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 6060-6060 ◽  
Author(s):  
William S. Chen ◽  
Ranjit Bindra ◽  
Allen Mo ◽  
Thomas Hayman ◽  
Zain Husain ◽  
...  

6060 Background: HPV infection is associated with high p16 expression and relatively good prognosis in head and neck cancers. Analysis of CDKN2A, the gene that encodes the p16 tumor suppressor protein, may further elucidate the association between HPV status and prognosis in head and neck squamous cell carcinomas (HNSCCs). We aimed to identify whether CDKN2A copy number loss was associated with poor survival in HNSCCs stratified by HPV status. Methods: We analyzed The Cancer Genome Atlas (TCGA) head and neck cancer data, integrating genomic measurements with clinical metadata. Patients 85 years old or younger with a primary tumor in the oral cavity, oropharynx, hypopharynx, or larynx were included. Defining CDKN2A copy number loss as a relative log2 copy number ratio < −0.6, CDKN2A mRNA and p16 protein expression levels were compared to confirm significant differences in gene transcription and translation between the copy number loss and non-copy number loss patient groups. Overall survival (OS) and disease-free survival (DFS) were evaluated to characterize prognostic differences between genomic groups. Results: 397 patients negative for HPV (HPV−) and 91 patients positive for HPV (HPV+) HNSCC were identified. 139 HPV− patients and 9 HPV+ patients demonstrated CDKN2A copy number loss. The CDKN2A copy number loss group expressed significantly lower levels of CDKN2A mRNA and p16 protein than did the non-copy number loss group in both HPV+ and HPV− disease. Median OS for HPV− patients with and without CDKN2A copy number loss was 21.8 months and 46.0 months (P = 0.02). Median DFS was 12.0 and 19.4 months respectively (P < 0.05). Median OS for HPV+ patients with and without CDKN2A copy number loss was 12.7 months and 57.4 months (P = 0.004) and median DFS was 7.0 and 36.6 months respectively (P = 0.02). Conclusions: CDKN2A copy number loss was associated with low CDKN2A mRNA and p16 protein expression, with poor prognosis in terms of disease-free and overall survival.


2010 ◽  
Vol 28 (13) ◽  
pp. 2174-2180 ◽  
Author(s):  
Rafal Dziadziuszko ◽  
Daniel T. Merrick ◽  
Samir E. Witta ◽  
Adelita D. Mendoza ◽  
Barbara Szostakiewicz ◽  
...  

PurposeThe purpose of this study was to characterize insulin-like growth factor-1 receptor (IGF1R) protein expression, mRNA expression, and gene copy number in surgically resected non–small-cell lung cancers (NSCLC) in relation to epidermal growth factor receptor (EGFR) protein expression, patient characteristics, and prognosis.Patients and MethodsOne hundred eighty-nine patients with NSCLC who underwent curative pulmonary resection were studied (median follow-up, 5.3 years). IGF1R protein expression was evaluated by immunohistochemistry (IHC) with two anti-IGF1R antibodies (n = 179). EGFR protein expression was assessed with PharmDx kit. IGF1R gene expression was evaluated using quantitative reverse transcription polymerase chain reaction (qRT-PCR) from 114 corresponding fresh-frozen samples. IGF1R gene copy number was assessed by fluorescent in situ hybridization using customized probes (n = 181).ResultsIGF1R IHC score was higher in squamous cell carcinomas versus other histologies (P < .001) and associated with stage (P = .03) but not survival (P = .46). IGF1R and EGFR protein expression showed significant correlation (r = 0.30; P < .001). IGF1R gene expression by qRT-PCR was higher in squamous cell versus other histologies (P = .006) and did not associate with other clinical features nor survival (P = .73). Employing criteria previously established for EGFR copy number, patients with IGF1R amplification/high polysomy (n = 48; 27%) had 3-year survival of 58%, patients with low polysomy (n = 87; 48%) had 3-year survival of 47% and patients with trisomy/disomy (n = 46; 25%) had 3-year survival of 35%, respectively (P = .024). Prognostic value of high IGF1R gene copy number was confirmed in multivariate analysis.ConclusionIGF1R protein expression is higher in squamous cell versus other histologies and correlates with EGFR expression. IGF1R protein and gene expression does not associate with survival, whereas high IGF1R gene copy number harbors positive prognostic value.


2021 ◽  
Vol 12 ◽  
Author(s):  
Chunrong Zhu ◽  
Liangjun Zhu ◽  
Yanhong Gu ◽  
Ping Liu ◽  
Xiaoling Tong ◽  
...  

Gastrointestinal tract cancers have high incidence and mortality in China, but their molecular characteristics have not been fully investigated. We sequenced 432 tumor samples from the colorectum, stomach, pancreas, gallbladder, and biliary tract to investigate cancer-related mutations and detail the landscape of microsatellite instability (MSI), tumor mutation burden (TMB), and chromosomal instability (CIN). We observed the highest TMB in colorectal and gastric cancers and the lowest TMB in gastrointestinal stromal tumors (GISTs). Twenty-four hyper-mutated tumors were identified only in colorectal and gastric cancers, with a significant enrichment of mutations in the polymerase genes (POLE, POLD1, and POLH) and mismatch repair (MMR) genes. Additionally, CIN preferentially occurred in colorectal and gastric cancers, while pancreatic, gallbladder, and biliary duct cancers had a much lower CIN. High CIN was correlated with a higher prevalence of malfunctions in chromosome segregation and cell cycle genes, including the copy number loss of WRN, NAT1, NF2, and BUB1B, and the copy number gain of MYC, ERBB2, EGFR, and CDK6. In addition, TP53 mutations were more abundant in high-CIN tumors, while PIK3CA mutations were more frequent in low-CIN tumors. In colorectal and gastric cancers, tumors with MSI demonstrated much fewer copy number changes than microsatellite stable (MSS) tumors. In colorectal and gastric cancers, the molecular characteristics of tumors revealed the mutational diversity between the different anatomical origins of tumors. This study provides novel insights into the molecular landscape of Chinese gastrointestinal cancers and the genetic differences between tumor locations, which could be useful for future clinical patient stratification and targeted interventions.


2021 ◽  
Author(s):  
Hua-fu Zhao ◽  
Xiu-ming Zhou ◽  
Jing Wang ◽  
Fan-fan Chen ◽  
Chang-peng Wu ◽  
...  

Abstract Background Epidermal growth factor receptor (EGFR) and lanthionine synthetase C-like 2 (LanCL2) genes locate in the same amplicon, and co-amplification of EGFR and LANCL2 is frequent in glioblastoma. However, the prognostic value of LANCL2 and EGFR co-amplification, and their mRNA and protein expression in glioblastoma remain unclear yet. Methods This study analyzed the prognostic values of the copy number variations (CNVs), mRNA and protein expression of LANCL2 and EGFR in glioblastoma specimens from TCGA database or our tumor banks. Results The amplification of LANCL2 or EGFR, and their co-amplification were frequent in glioblastoma of TCGA database and our tumor banks. CNVs of LANCL2 or EGFR were significantly correlated with IDH1/2 mutation but not MGMT promoter methylation status. LANCL2 or EGFR amplification, and their co-amplification were significantly associated with reduced overall survival (OS) of glioblastoma patients, rather than IDH1/2-wild-type glioblastoma patients. mRNA and protein overexpression of LANCL2 and EGFR was also frequently found in glioblastoma. LANCL2, rather than EGFR, was overexpressed in relapsing glioblastoma, compared with newly diagnosed glioblastoma. However, mRNA or protein expression of EGFR and LANCL2 was not significantly correlated with OS of glioblastoma patients. In addition, the intracellular localization of LanCL2, not EGFR, was associated with the grade of gliomas. Conclusions Taken together, amplification and mRNA overexpression of LANCL2 and EGFR, and their co-amplification and co-expression were frequent in glioblastoma patients. Our findings suggest that CNVs of LANCL2 and EGFR were the independent diagnostic and prognostic biomarkers for histological glioblastoma patients, but not for IDH1/2-wild-type glioblastoma patients.


2021 ◽  
Author(s):  
Klaske Marijke Schukken ◽  
Jason Meyer Sheltzer

Aneuploidy is a hallmark of human cancers, but the effects of aneuploidy on protein expression remain poorly understood. To uncover how chromosome copy number changes influence the cancer proteome, we have conducted an analysis of hundreds of human cancer cell lines with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins exhibit dosage compensation and fail to change by the degree expected based on chromosome copy number alone. We uncovered a variety of gene groups that were recurrently buffered upon both chromosome gain and loss, including protein complex subunits and cell cycle genes. Several genetic and biophysical factors were predictive of protein buffering, highlighting complex post-translational regulatory mechanisms that maintain appropriate gene product dosage. Finally, we established that chromosomal aneuploidy has an unexpectedly moderate effect on the expression of oncogenes and tumor suppressors, demonstrating that these key cancer drivers can be subject to dosage compensation as well. In total, our comprehensive analysis of aneuploidy and dosage compensation across cancers will help identify the key driver genes encoded on altered chromosomes and will shed light on the overall consequences of aneuploidy during tumor development.


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