5524 results for "*oma"

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• Comprehensive sequencing analyses of uterine and ovarian carcinosarcoma

  We collected 109 primary tumor and mached normal samples of uterine and ovarian carcinosarcoma. The purpose of this study is to find novel therapeutic options for carcinosarcoma as well as a clue to understand the molecular histogenic mechanism.

  Study JGAS000172

• Whole exome and ChIP sequencing of external auditory canal squamous cell carcinoma (EACSCC)

  We performed whole exome sequencing of the primary tumor tissues, peripheral blood mononuclear cells from an EACSCC patient as well as the cell line established from the primary tumor tissues. We performed ChIP sequencing of primary tumor tissues and noncancerous ear skin tissues from EACSCC patients as well.

  Study JGAS000645

• Development of Novel Synovial Sarcoma Organoids Models for Drug Discovery

  Although synovial sarcoma has been studied using established cell lines and mouse models, effective treatments remain limited. We treated five patients with synovial sarcoma between 2022 and 2023 and established organoid cultures from resected tumor specimens using a modified air-liquid interface method. After serial passaging, organoids were successfully xenografted into NOD-scid IL2Rgnull (NSG) mice in three cases. The established organoids retained SS18-SSX fusion transcripts and demonstrated histological and genetic similarities to the original tumors. These organoid models provide a reliable platform for studying synovial sarcoma biology and hold promise for the development of novel therapeutic strategies.

  Study JGAS000806

• Comprehensive molecular and clinicopathological profiling of glioma

  Various molecular profiles are needed to classify malignant brain tumors, including gliomas, based on the latest classification criteria of the World Health Organization, and their poor prognosis necessitates new therapeutic targets. The Todai OncoPanel 2 RNA Panel (TOP2-RNA) is a custom-target RNA-sequencing (RNA-seq) using the junction capture method to maximize the sensitivity of detecting 455 fusion gene transcripts and analyze the expression profiles of 1,390 genes. This study aimed to classify gliomas and identify their molecular targets using TOP2-RNA. A total of 124 frozen samples of malignant gliomas were subjected to TOP2-RNA for classification based on their molecular profiles and the identification of molecular targets.

  Study JGAS000671

• Target sequencing of 27 cancer-predisposing genes and 13 renal cell carcinoma-related genes in Japanese renal cell carcinoma patients

  Identifying causative genes via genetic testing is useful for the screening, prevention, and treatment of cancer. Several hereditary syndromes are known to occur in renal cell carcinoma (RCC). However, these evidences came from the European population; it remains unclear how the RCC-related genes and other cancer-predisposing genes contribute to the development RCC in the Japanese population. A case-control study of 14 RCC-related genes and 26 cancer-predisposing genes was performed using 1,563 Japanese patients with RCC and 6,016 controls. Patients were divided into two major histological subtypes of clear cell RCC (ccRCC) or non-clear cell RCC (nccRCC). Gene-based analysis of germline pathogenic variants in patients with each subtype and cancer-free subjects was performed. Following quality control, 1,532 patients with RCC and 5,996 controls were further analyzed. For ccRCC, 52 of 1,283 (4.05%) patients carried pathogenic variants mainly in the cancer-predisposing genes such as TP53 (P = 1.73 �� 10-4; OR, 5.8; 95% CI, 2.2���15.7). Approximately 80% of patients with pathogenic variants in TP53 had p.Ala189Val that was specific in East Asian population. For nccRCC, 14 of 249 (5.62%) patients carried pathogenic variants mainly in the RCC-related genes such as BAP1 (P = 6.27 �� 10-5; OR, Inf; 95% CI, 10.0���Inf), and FH (P = 6.27 �� 10-5; OR, Inf; 95% CI, 10.0���Inf). Our study showed different and population-specific contributions of risk genes between ccRCC and nccRCC in Japanese for better-personalized medicine.

  Study JGAS000414

• CAGE analysis for endometrial carcinoma

  For endometrial cancer patients, lymphadenectomy is recommended to exclude rarely metastasized cancer cells. This procedure is performed even in patients with low risk of recurrence despite the risk of complications such as lymphedema. A method to accurately identify cases with no lymph node metastases (LN-) before lymphadenectomy is therefore highly required. We approached this clinical problem by examining primary lesions of endometrial cancers with CAGE (Cap Analysis Gene Expression), which quantifies promoter-level expression across the genome. Fourteen profiles delineated distinct transcriptional networks between LN?+?and LN- cases, within those classified as having the low or intermediate risk of recurrence.

  Study JGAS000124

• Amplicon sequencing of duodenal adenoma

  The aim of this study is to analyze the methylation and mutation status of non-ampullary duodenal lesions in order to detect the genetic changes for predicting the progression to adenocarcinomas.

  Study JGAS000352

• Variant allele frequency changes in TP53 predict pembrolizumab response in patients with metastatic urothelial carcinoma

  Prognoses for patients with metastatic urothelial carcinoma (mUC) have strikingly improved with pembrolizumab, an immune checkpoint inhibitor (ICI), but clinical benefits are limited to a subset of patients. Therefore, a non-invasive biomarker to predict pembrolizumab response is urgently required. We retrospectively examined genomic alterations in 25 plasma circulating tumor DNA (ctDNA) samples using a targeted sequencing of 77 genes from 16 mUC patients during pembrolizumab treatment. Eleven (68.8%) patients had two or more genomic alterations, including TP53 mutations (as defined by ctDNA-positive status). The proportion of responders to pembrolizumab in the ctDNA-positive group was higher than the ctDNA-negative group (72.7% vs. 20.0%). Furthermore, among all detected genomic alterations, variant allele frequency decreases in TP53 during pembrolizumab treatment were mainly associated with therapeutic response. Collectively, we suggest that profiling of ctDNA in plasma, especially TP53, is useful for predicting and monitoring therapeutic responses to pembrolizumab in mUC patients.

  Study JGAS000622

• Genomic Structural Variants in Japanese Malignant mesothelioma patients

  We extracted genomic DNAs from established mesothelioma cell lines from Japanese malignant mesothelioma patients. We sequenced those genomic DNAs using 10X Genomics sequencing technologies, and analyzed genomic structural variations.

  Study JGAS000176

• Molecular Characterization of Large Cell Neuroendocrine Carcinoma of the Lung by Multilayered Omics Analysis

  Large cell neuroendocrine carcinoma (LCNEC) is a rare lung cancer type with a very poor prognosis. The underlying molecular features remain unclear. Here, we conducted a multi-omics analysis of 27 LCNEC cases along with 7 small cell lung carcinoma and aimed to propose new classification by extracting genomic and transcriptomic features in LCNEC, leading to the elucidation of the therapeutic approaches.

  Study JGAS000832

• Whole exome sequencing of patients with esophageal squamous cell carcinoma receiving chemoradiotherapy

  We performed multi-region whole exome sequencing (WES) of pre-treatment and recurrent esophageal cancer receiving chemoradiotherapy in order to characterize clonal evolution of treatment resistant clones. Furthermore, additional solitary pre-treatment tumor samples were subjected to WES to detect biomarkers predicting clinical outcome.

  Study JGAS000227

• Unraveling the heterogeneity of multiple myeloma identifies therapy resistant subpopulation with vulnerability to the splicing pathway intervention

  Intra-tumor heterogeneity underlies the therapy resistance of multiple myeloma (MM). However, its details remain unknown. Here, we performed single-cell RNA sequencing coupled with VDJ targeted sequencing on highly purified bone marrow lineage marker-negative CD38+ MM cells from patients at diagnosis and in remission. This approach successfully subdivided MM cells into distinct clusters, unraveling their heterogeneity and plasticity on the axis of cell surface CD138 expression. Notably, unique clusters were identified in the minor CD138-negative population that resisted therapies. CRISPR/Cas9 screening of upregulated genes in the resistant population identified their vulnerability to the splicing pathway inhibition, among which RNA-binding protein 39 (RBM39) appeared to be overexpressed in the resistant population and involved in aberrant splicing. Genetic and pharmacological inhibition of RBM39 exerted a profound synthetic lethal effect on them. Our results unveil an uncharacterized subpopulation associated with therapy resistance and provide a novel therapeutic strategy targeting the splicing pathway in MM.

  Study JGAS000723

• Genetic mutation profiling of lymphomas arising in the uterine cervix and vagina

  Follicle center lymphoma (FCL) of the lower female genital tract (LFGT) is a rare lymphoma, with fewer than 20 cases reported to date. Since the genetic features of FCL of the LFGT have not been well characterized, we aimed to identify genetic alterations in this tumor through whole-exome sequencing or targeted gene panel analysis. Genomic DNA was extracted from a frozen tissue sample obtained from a surgically resected uterine cervical tumor. Whole-exome sequencing was performed using the Illumina NovaSeq X Plus platform. Library preparation was conducted with the SureSelect Human All Exon V6 kit, and sequencing was carried out with 150 bp paired-end reads.

  Study JGAS000823

• Identification of genetic mutations characteristic for recurrence and metastasis of lymphoma.

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent B cell lymphoma, and the purpose of this study is to find the characteristics of recurrent B cell lymphoma by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000087

• Whole-genome sequencing analysis for understanding of the stepwise progression of lung adenocarcinoma

  In this study, we performed long and short read whole-genome sequencing analysis of lung adenocarcinoma from early to advanced stages to identify molecular events associated with the stepwise progression of lung adenocarcinoma. We particularly focused on very early stage of lung adenocarcinoma, such as adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA). In addition to the whole-genome sequencing analysis, we conducted transcriptome and epigenome analysis, multiplex fluorescence immunostaining. This study would enable us to understand important molecular events of pathogenesis in detail during lung adenocarcinoma progression.

  Study JGAS000570

• Analysis of Large Cell Neuroendocrine Carcinoma Expressing HNF4alpha Using WGS

  Lung LCNEC (Large Cell Neuroendocrine Carcinoma) has a poor prognosis, and no effective treatment has yet been established. We have found that the gastrointestinal marker HNF4alpha is specifically expressed in some LCNEC cases. By performing Whole Genome Sequencing (WGS) on samples from 10 LCNEC patients, we aim to identify changes characteristic of LCNEC expressing HNF4alpha and explore new classifications and treatment options for LCNEC.

  Study JGAS000732

• Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance

  The treatment outcome of glioma patients remains disappointing, and more studies are needed to improve therapeutic strategies. In particular, it is crucial to understand the mechanisms underlying resistance to treatment and malignant transformation, as well as the intratumoral heterogeneity and interaction of tumor cells and host immunity. Recent advances in omics analysis techniques, such as next-generation sequencing (NGS), have enabled us to obtain omics data more easily and accelerated our ability to integrate this information and precisely characterize cases. In our project, we have already collected more than 100 pairs of human glioma/normal tissue samples, of which some are multiple specimens collected from initial and recurrent tumors, and some include multiple specimens collected from different regions within a single tumor. We used our in-house algorithms, composed of alignment and variant calling programs, to analyze omics data from multiple platforms, such as whole-exome sequencing (WES), RNA sequencing (RNA-seq), and methylation array, with our original cohort of glioma patients. Using several informatics tools, the information about genetic and epigenetic status and expression signatures were analyzed. Those data are expected to provide key information for investigating the mechanisms discussed above. Through this project, we hope to improve strategies for personalized therapy based on comprehensive omics data.

  Study JGAS000004

• Whole exome sequencing and RNA-seq of esophageal squamous cell carcinoma

  We perform integrative genome-wide analyses such as whole-exome sequencing, copy number variant(CNV) analysis, and gene expression analysis using next-generation sequencing and other methods to elucidate driver genes and signaling pathways causing tumorigenesis and cancer progression, leading novel molecular diagnostics and molecular therapies.

  Study JGAS000367

• Whole genome sequencing, single-cell RNA sequencing, and ATAC sequencing of mesothelioma (patient, patient-derived xenograft and cell line)

  Malignant pleural mesothelioma is an aggressive pleural tumor with a poor prognosis, and elucidating its molecular mechanisms is essential for improving diagnosis and treatment. This study investigates key genes and pathways involved in tumor progression, with particular attention to the involvement of neutrophils in the tumor ecosystem of mesothelioma. We performed whole-genome sequencing and single-cell RNA sequencing (scRNA-seq) of one pleural mesothelioma tumor specimen, scRNA-seq of matched patient-derived xenograft tumors, scRNA-seq of mesothelioma-free pleural tissues from three patients, and assay for transposase-accessible chromatin using sequencing (ATAC-seq) of a patient-derived cell line.

  Study JGAS000859

• exploration of biomarkers discriminating squamous cell carcinoma from other lung cancers

  Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. The most effective regimen in lung cancers is different between squamous cell carcinoma (SCC) and adenocarcinoma (AD). Therefore a precise diagnosis is crucial, but this has been difficult, particularly for poorly differentiated SCC (PDSCC) and AD without a lepidic growth component (non-lepidic AD). Biomarkers enabling a precise diagnosis are therefore urgently needed. To achieve this goal, we initially performed CAGE (Cap Analysis of Gene Expression) to quantify promoter activities on 97 frozen tissues from surgically resected lung cancers (22 SCC and 75 AD). We furhter expanded the transcriptome profiling to cover additional 48 malignant neoplasm of bronchus and lung, including mesothelioma and metastatic lung cancers derived from other tissues.

  Study JGAS000488

• Whole-genome sequencing of the parental tumor and established organoids from a patient with gastric-type cervical adenocarcinoma

  This study aims to evaluate the genetic characteristics of patient-derived organoids established from gastric-type cervical adenocarcinoma and to assess their similarity to the parental tumors using whole-genome sequencing.

  Study JGAS000796

• Clonal diversity analysis and inter/intra-organ heterogeneity in urothelial carcinoma under immunotherapy

  We studied a unique autopsy case of metastatic urothelial carcinoma with both sensitivity and resistance to anti-PD-1 therapy. We performed multiregional analyses of 58 paired whole exome sequencing and RNA sequencing samples of 8 different bulk tumor masses, 8 matched whole genome sequencing samples to identify structural abnormalities of each mass. Furthermore, we performed 7 whole exome sequencing from metastatic urothelial carcinoma patients who received anti-PD-1 therapy.

  Study JGAS000725

• Targeted Capture DNA Sequencing

  We performed targeted capture DNA sequencing for 29 genes in extranodal NK/T-cell lymphoma, nasal type (n=67).

  Study JGAS000548

• Recurrent COPA mutation drives R-spondin-independent Wnt activation in intestinal tumors

  The majority of intestinal tumors harbor mutations in canonical Wnt pathway genes such as APC, whereas the lack of such alterations in a subset of tumors implies alternative tumorigenic routes. Here, we identify recurrent in-frame deletion in COPA, frequently co-occurring with USP9X truncating mutation, in small intestinal adenoma and adenocarcinoma. Patient-derived and CRISPR-engineered small intestinal organoids carrying COPA in-frame deletions exhibit R-spondin-independent yet Wnt ligand-dependent growth, maintaining LGR5 expression without canonical Wnt drivers. Mechanistically, COPA mutation stabilizes frizzled co-receptor LRP6 irrespective of R-spondin, sustaining Wnt pathway activation under growth factor-restricted conditions. USP9X loss further potentiates this phenotype. Unlike canonical Wnt pathway members, COPA encodes the alpha-subunit of coatomer complex I, which engages in vesicle trafficking with little prior linkage to intestinal tumorigenesis. Our findings establish COPA mutation as a novel and atypical intestinal tumor driver and implicate USP9X loss as a cooperating lesion.

  Study JGAS000868

• 1. Identidication of molecular biological mechanism associated with the development and prognosis of uterine cancer, uterine sarcoma, and endometrial hyperplasia / 2. Identification of molecular biological mechanism associated with the development of endometriosis and malignant transformation, ovarian cancer, fallopian tubal cancer, peritoneal cancer, and other malignant tumors in gynecological organs

  To clarify the biological difference between clear cell carcinoma and other histological subtypes in ovarian carcinomas by comparing copy number variants, and to identify molecular subtypes and carcinogenesis in clear cell ovarian carcinomas by whole-exome sequencing and RNA-sequencing. Then, characterize high-grade serous carcinomas by NGS-based, integrative genomic analyses, with focus on homologous recombination deficiency, molecular subtypes, prognostic factors and effectiveness of PARP inhibitor. Based on the results of whole-exome sequencing, an investigator-initiated, phase 2 clinical trial will be conducted to evaluate the efficacy and safety of the PARP inhibitor olaparib in HRD-positive cases.

  Study JGAS000789