The association of novel recurrent in-frame gene fusions with prognosis of diffuse gastric cancer.

2019 ◽  
Vol 37 (4_suppl) ◽  
pp. 34-34
Author(s):  
Hark K. Kim
Keyword(s):  
Gastric Cancer ◽  
Rna Sequencing ◽  
Young Patients ◽  
Diffuse Gastric Cancer ◽  
Prognostic Impact ◽  
Gene Fusions ◽  
Histologic Subtype ◽  
Cdh1 Mutation ◽  
Frame Fusion ◽  
Worse Prognosis

34 Background: Among the two histologic subtype of gastric cancer (GC), diffuse gastric cancer (DGC) is increasingly being considered distinct from intestinal type gastric cancer (IGC). Despite the relative importance of DGC, few whole transcriptomic analyses have been performed for this histological subtype. We therefore conducted an RNA-sequencing study to search for novel driver fusions in DGC. Methods: We conducted a whole transcriptomic and targeted RNA sequencing study of 384 Korean DGCs to identify gene fusions that may be novel prognostic markers or therapeutic targets. Targeted DNA sequencing and SNP6.0 array analyses were conducted in parallel. Results: Whole transcriptomic analyses were conducted in 80 discovery dataset tumors collected from young patients with DGC who had not been treated with chemotherapy or radiation. Twenty-five in-frame fusions were associated with DGC, four of which were recurrent in 384 DGCs based on targeted RNA sequencing and RT-PCR sequencing analyses. Three of the four recurrent fusions contained a RhoGAP domain in their 3’ partner genes. Patients with one of these three fusions have a significantly worse prognosis than those without (HR, 2.8 [95% CI, 1.5‒5.3]). The fusion that harbored a PAP2 domain in the 3’ partner gene was also identified as recurrent and poor prognostic in-frame fusions. Overall, RhoGAP and PAP2 domain-containing fusions were present in 7.5% of DGCs, but not in adjacent normal tissue, and clearly defined the worst prognosis subgroup. Their prognostic impact (adjusted HR 4.1 [95% CI, 2.1‒7.9]) was higher than, and independent of, chromosomal instability (CIN) and CDH1 mutation, which we previously identified as the strongest adverse prognostic genomic abnormalities in DGCs (adjusted HRs, 2.5 (1.5‒4.4) and 2.4 (1.3‒4.4), respectively). Our comprehensive in-frame fusion screen also identified several clinically-actionable fusions amenable to ALK or FGFR inhibition, which had not been previously associated with gastric cancer. Conclusions: Our findings may provide novel genomic insights guiding future personalized strategies for managing DGCs, given the strong prognostic impact of RhoGAP and PAP2 domain-containing gene fusions.

Unexpected CDH1 Mutations Identified on Multigene Panels Pose Clinical Management Challenges

2017 ◽  
pp. 1-12 ◽  
Author(s):  
Katrina Lowstuter ◽  
Carin R. Espenschied ◽  
Duveen Sturgeon ◽  
Charité Ricker ◽  
Rachid Karam ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Medical Management ◽  
Cancer Genetics ◽  
Medical Center ◽  
Academic Medical Center ◽  
Lifetime Risk ◽  
Diffuse Gastric Cancer ◽  
Mutation Carriers ◽  
Cdh1 Mutation ◽  
Testing Criteria

Purpose Mutations in the CDH1 gene confer up to an 80% lifetime risk of diffuse gastric cancer and up to a 60% lifetime risk of lobular breast cancer. Testing for CDH1 mutations is recommended for individuals who meet the International Gastric Cancer Linkage Consortium (IGCLC) guidelines. However, the interpretation of unexpected CDH1 mutations identified in patients who do not meet IGCLC criteria or do not have phenotypes suggestive of hereditary diffuse gastric cancer is clinically challenging. This study aims to describe phenotypes of CDH1 mutation carriers identified through multigene panel testing (MGPT) and to offer informed recommendations for medical management. Patients and Methods This cross-sectional prevalence study included all patients who underwent MGPT between March 2012 and September 2014 from a commercial laboratory (n = 26,936) and an academic medical center cancer genetics clinic (n = 318) to estimate CDH1 mutation prevalence and associated clinical phenotypes. CDH1 mutation carriers were classified as IGCLC positive (met criteria), IGCLC partial phenotype, and IGCLC negative. Results In the laboratory cohort, 16 (0.06%) of 26,936 patients were identified as having a pathogenic CDH1 mutation. In the clinic cohort, four (1.26%) of 318 had a pathogenic CDH1 mutation. Overall, 65% of mutation carriers did not meet the revised testing criteria published in 2015. All three CDH1 mutation carriers who had risk-reducing gastrectomy had pathologic evidence of diffuse gastric cancer despite not having met IGCLC criteria. Conclusion The majority of CDH1 mutations identified on MGPT are unexpected and found in individuals who do not fit the accepted diagnostic testing criteria. These test results alter the medical management of CDH1-positive patients and families and provide opportunities for early detection and risk reduction.

Searching for CDH1 gene mutations in early-onset diffuse gastric cancer in Chinese patients.

2014 ◽  
Vol 32 (3_suppl) ◽  
pp. 23-23
Author(s):  
Xu Yanjun ◽  
Cao Wenming ◽  
Xu Qi ◽  
Guo Jianmin ◽  
Wang Xinbao ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Overall Survival ◽  
Lymph Node ◽  
Gene Mutations ◽  
Germline Mutations ◽  
Chinese Patients ◽  
Diffuse Gastric Cancer ◽  
Cdh1 Gene ◽  
Node Metastasis ◽  
Cdh1 Mutation

23 Background: CDH1 germline mutations are found to be associated with the development of hereditary diffuse gastric cancer (HDGC) and the early-onset diffuse gastric cancer (EODGC). But the impact of CDH1 gene mutations and large deletions on HDGC and EODGC has not been fully determined in Asians. Although the incidence of gastric cancer is relatively high in China, the detection rate of CDH1 germline mutations in Chinese patients with EODGC is rare compared to that in European patients. Methods: We investigated the mutation status of the CDH1 gene in 57 Chinese EODGC patients younger than 40 years old who met the clinical criteria for HDGC. Polymerase chain reaction-direct sequencing was performed, and multiplex ligation-dependent probe amplification (MLPA) was used to evaluate the patients with negative sequencing results. Associations between mutation, clinicopathologic, and overall survival data were analyzed by SPSS 19. Results: The germline mutations of CDH1gene were identified in 51 (89.5%) of the 57 EODGC patients. The nonsense mutation in exon 13 (c.2200T>C, p.Ala692*) occurred in fourty-six EODGC patients. The missense mutations were detected in twenty patients (Eighteen in exon 5: c.778G>C, p.Glu218Asp; Two in exon 12: c.2012C>G, p.Leu630Val). No deletion or duplication in any patient. Most of the patients carrying the CDH1 mutation in exon 13 had lymph node metastasis when compared with patients lacking CDH1 mutation (87.2% vs 60.0%) ( P < 0.05 ). EODGC patients, lacking germline CDH1 alterations, showed a longer median overall survival (mOS) than patients carrying CDH1 mutation in exon 13 ( P < 0.05 ). Moreover, the presence of CDH1 mutation in exon 13 was associated with the incidence of neural invasion ( P < 0.05 ). Conclusions: This study reveals novel CDH1 mutations in Chinese EODGC patients which had been poorly investigated. The presence of CDH1 mutation in EODGC patients may result in lymph node metastasis and poor prognosis. More research is needed to determine additional genetic targets that trigger EODGC.

scholarly journals Change of natural history of hereditary diffuse gastric cancer after identification of a novel CDH1 mutation

2017 ◽  
Vol 28 ◽  
pp. v503
Author(s):  
N. Stjepanovic ◽  
S. Castro ◽  
N. Gadea ◽  
E. Carrasco ◽  
M. Codina ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Natural History ◽  
Hereditary Diffuse Gastric Cancer ◽  
Diffuse Gastric Cancer ◽  
Cdh1 Mutation ◽  
History Of

scholarly journals Estrogen Aggravates Tumor Growth in a Diffuse Gastric Cancer Xenograft Model

2021 ◽  
Vol 27 ◽  
Author(s):  
Sunyi Lee ◽  
Kyoung Mee Kim ◽  
Seung Yeon Lee ◽  
Joohee Jung
Keyword(s):  
Gastric Cancer ◽  
Tumor Growth ◽  
Rna Sequencing ◽  
Xenograft Model ◽  
Diffuse Gastric Cancer ◽  
Diffuse Type ◽  
Female Mice ◽  
Exogenous Estrogen ◽  
Endogenous Estrogen ◽  
Diffuse Type Gastric Cancer

Gastric cancer has the fifth-highest incidence rate and is the third leading cause of cancer-related deaths worldwide. The incidence of gastric cancer is higher in men than in women, but for the diffuse types of gastric cancer, the trend is opposite. Estrogen is considered the prime culprit behind these differences. Nevertheless, the action of estrogen in gastric cancers remains unclear. In this study, we investigated the effect of estrogen on diffuse-type gastric cancer. Human female diffuse gastric cancer SNU-16 cells were transplanted into male and female mice to analyze the effect of endogenous estrogen on tumor growth. Furthermore, the effect of exogenous estrogen was evaluated in ovariectomized mice. Expressed genes were compared between female and male xenograft models using RNA sequencing analysis. Furthermore, human gene expression omnibus databases were utilized to examine the effect of our target genes on overall survival. SNU-16-derived tumor growth was faster in female mice than in male mice. In total RNA sequencing, interferon gamma receptor 2 (IFNGR2), IQ motif containing E (IQCE), transient receptor potential cation channel subfamily M member 4 (TRPM4), and structure-specific endonuclease subunit SLX4 (SLX4) were found. These genes could be associated with the tumor growth in female diffuse-type gastric cancer which was affected by endogenous estrogen. In an ovariectomized gastric cancer xenograft model, exogenous estrogen promoted tumor growth. Especially, our results indicated that estrogen induced G protein-coupled estrogen receptor expression in these mice. These results suggest that estrogen aggravates tumor progression in female diffuse gastric cancer.

scholarly journals CDH1 Mutation Distribution and Type Suggests Genetic Differences between the Etiology of Orofacial Clefting and Gastric Cancer

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 391
Author(s):  
Arthavan Selvanathan ◽  
Cheng Yee Nixon ◽  
Ying Zhu ◽  
Luigi Scietti ◽  
Federico Forneris ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cleft Lip ◽  
Structural Characteristics ◽  
Molecular Data ◽  
Diffuse Gastric Cancer ◽  
Pathogenic Variants ◽  
Orofacial Clefting ◽  
Cleft Lip Palate ◽  
Cdh1 Mutation ◽  
Mutation Distribution

Pathogenic variants in CDH1, encoding epithelial cadherin (E-cadherin), have been implicated in hereditary diffuse gastric cancer (HDGC), lobular breast cancer, and both syndromic and non-syndromic cleft lip/palate (CL/P). Despite the large number of CDH1 mutations described, the nature of the phenotypic consequence of such mutations is currently not able to be predicted, creating significant challenges for genetic counselling. This study collates the phenotype and molecular data for available CDH1 variants that have been classified, using the American College of Medical Genetics and Genomics criteria, as at least ‘likely pathogenic’, and correlates their molecular and structural characteristics to phenotype. We demonstrate that CDH1 variant type and location differ between HDGC and CL/P, and that there is clustering of CL/P variants within linker regions between the extracellular domains of the cadherin protein. While these differences do not provide for exact prediction of the phenotype for a given mutation, they may contribute to more accurate assessments of risk for HDGC or CL/P for individuals with specific CDH1 variants.

Hereditary diffuse gastric cancer: Natural history, pathology, screening limitations, and prophylactic total gastrectomy in CDH1 mutation carriers

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 4500-4500 ◽  
Author(s):  
H. T. Lynch ◽  
C. Caldas ◽  
D. Wirtzfeld ◽  
C. Vaccaro ◽  
W. Rubinstein ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Genetic Counseling ◽  
Total Gastrectomy ◽  
Mutation Testing ◽  
Hereditary Diffuse Gastric Cancer ◽  
Diffuse Gastric Cancer ◽  
Mutation Carriers ◽  
Prophylactic Gastrectomy ◽  
Cdh1 Mutation ◽  
Prophylactic Total Gastrectomy

4500 Background: Hereditary diffuse gastric cancer (HDGC) is a potentially fatal disease that occurs due to mutations in the E- cadherin (CDH1) gene, as discovered in 1998. Its penetrance ranges between 70–80%. Its morbidity and mortality can be altered favorably through genetic counseling, germline mutation testing, and highly-targeted management that includes prophylactic total gastrectomy. Lobular breast cancer has been identified as an integral lesion in HDGC. Methods: This international collaborative group on HDGC is comprised of 56 mutation-positive families, which is the world’s largest resource of such families. Cancer diagnoses were verified with pathology slides/tissue block review when possible, or reports. Genetic counseling covering the pros and cons of mutation testing, screening and its limitations, and the option of prophylactic total gastrectomy was provided. Results: Findings on 56 HDGC mutation-positive families show carrier testing to have been performed on 267 individuals, of which 123 were CDH1 mutation positive. Prophylactic gastrectomies were performed on 14 families involving 50 individuals. Occult cancer was diagnosed in 31 (31/39=79.5%; results are pending on the remaining 11), based upon pathology and verbal reports. Five individuals underwent prophylactic gastrectomy prior to genetic counseling, 3 of whom later tested negative for mutations. In one of these remarkable HDGC families, 11 first cousins who tested positive for the CDH1 mutation underwent prophylactic total gastrectomy. On a post-surgery questionnaire, they each stated that the decision for the prophylactic procedure was the “right one” for them. In each case, a parent had died of HDGC sequelae, adding to the cousins’ acceptance of DNA testing and surgery. They considered their post-operative nutritional programs to have been acceptable. Conclusion: HDGC and its life-threatening sequelae were significantly ameliorated in CDH1 mutation carriers through total prophylactic gastrectomy in patients at enormous lifetime risk for HDGC. Decision for mutation testing and surgery may be more acceptable through intensive education in concert with a compassionate management team. No significant financial relationships to disclose.

scholarly journals RNA Sequencing Reveals Novel and Rare Fusion Transcripts in Acute Myeloid Leukemia

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3627-3627 ◽  
Author(s):  
Antonella Padella ◽  
Giorgia Simonetti ◽  
Giulia Paciello ◽  
Anna Ferrari ◽  
Elisa Zago ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Rna Sequencing ◽  
Cytogenetic Analysis ◽  
Myeloid Leukemia ◽  
Fusion Transcript ◽  
Gene Fusions ◽  
Fusion Genes ◽  
Exon 2 ◽  
Frame Fusion ◽  
Acute Myeloid

Abstract Acute Myeloid Leukemia (AML) is a highly heterogeneous disease and a complex network of events contribute to its pathogenesis. Chromosomal rearrangements and fusion genes have a crucial diagnostic, prognostic and therapeutic role in AML. A recent RNA sequencing (RNAseq) study on 179 AML revealed that fusion events occur in 45% of patients. However, the leukemogenic potential of these fusions and their prognostic role are still unknown. To identify novel rare gene fusions having a causative role in leukemogenesis and to identify potential targets for personalized therapies, transcriptome profiling was performed on AML cases with rare and poorly described chromosomal translocations. Bone marrow samples were collected from 5 AML patients (#59810, #20 and #84 at diagnosis and #21 and #32 at relapse). RNAseq was performed using the Illumina Hiseq2000 platform. The presence of gene fusions was assessed with deFuse and Chimerascan. Putative fusion genes were prioritized using Pegasus and Oncofuse, in order to select biologically relevant fusions. Chimeras not supported by split reads, occurring in reactive samples, involving not annotated or conjoined genes were removed. The remaining fusions were prioritized according to mapping of partner genes to chromosomes involved in the translocation or to Chimerascan and deFuse concordance. The CBFβ-MYH11 chimera was identified in sample #84, carrying inv(16) aberration, thus confirming the reliability of our analysis. Sample #59810 carried the fusion transcript ZEB2-BCL11B (Driver Score, DS=0.7), which is an in-frame fusion and a rare event in AML associated with t(2;14)(q21;q32). The breakpoint of the fusion mapped in exon 2 of ZEB2 (ENST00000558170) and exon 2 of BCL11B (ENST00000357195). Differently from previous data, this fusion transcript showed 3 splicing isoforms. Type 1 isoform is the full-length chimera and it retains all exons of both genes involved in the translocation. Type 2 isoform was characterized by the junction of exon 2 of ZEB2 and exon 3 of BCL11B. In type 3 isoform, exon 2 and 3 of BCL11B were removed, resulting in an mRNA composed by exon 2 of ZEB2 and exon 4 of BCL11B. Gene expression profiling showed an upregulation of ZEB2 and BCL11B transcripts in the patient's blasts, compared to 53 AML samples with no chromosomal aberrations in the 14q32 region. The same samples showed the WT1-CNOT2 chimera, which is a novel out-of-frame fusion (DS= 0.008) related to t(11;12) translocation, identified by cytogenetic analysis. Two new in-frame fusion genes were identified in sample #20: CPD-PXT1 (DS=0.07), which appeared as the reciprocal fusion product of t(6;17) translocation, and SAV1-GYPB, which remained cryptic at cytogenetic analysis (DS=0.8, alternative splicing events are being investigated). SAV1 was downregulated in sample #20 compared to our AML cohort, suggesting the putative loss of a tumour-suppressor gene. Sample #21 carried a t(3;12) translocation and RNAseq identified a novel fusion event between chromosomes 19 and 7, involving the genes OAZ and MAFK (DS=0.9). Finally, no chimeras were confirmed in sample #32 having a t(12;18) translocation. Our data suggest that fusion events are frequent in AML and a number of them cannot be detected by current cytogenetic analyses. Gene fusions cooperate to AML pathogenesis and heterogeneity and we are further investigating the oncogenic potential of the identified translocations. Moreover, the results firmly indicate that different approaches, including G-banding, molecular biology, bioinformatics and statistics, need to be integrated in order to better understand AML pathogenesis and improve patients' stratification, High-resolution sequencing analysis currently represent the most informative strategy to tailor personalized therapies. Acknowledgments: ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), Fondazione del Monte di Bologna e Ravenna, FP7 NGS-PTL project. Disclosures Soverini: Novartis, Briston-Myers Squibb, ARIAD: Consultancy. Martinelli:BMS: Speakers Bureau; MSD: Consultancy; Roche: Consultancy; ARIAD: Consultancy; Novartis: Speakers Bureau; Pfizer: Consultancy.

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