7153 results for "canc*"

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• Identification of genetic mutations characteristic for recurrence and metastasis of gastric cancer.

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

  Study JGAS000086

• Sequencing cancer mutations in various types of lung cancer using the long-read, portable sequencer

  In this study, we used a long-read and portable sequencer MinION to identify cancer mutations in lung adenocarcinoma cells. We performed cDNA amplicon sequencing for various types of mutations such as point mutations in EGFR and KRAS and oncogenic fusion transcripts in ALK and RET. Using the long reads of MinION, we also conducted mutation phasing of EGFR TKI-sensitive and resistant mutations, which would provide useful information to next thrapeutic approaches for cancers. We applied this method to identify mutation genotypes of eight clinical samples from Japanese lung adenocarcinomas. This method could provide new sequencing-based diagnostic approaches for lung cancers. Additinally we also performed cancer mutation identification of risk-dependent unique samples. Usual interstitial pneumonia (UIP) is a risk factor for lung carcinogenesis. This study was performed to characterize mutagenesis and mutational target genes underlying lung carcinogenesis in patients with UIP.We performed whole exome sequencing of lung adenocarcinoma with usual interstitial pneumonia.

  Study JGAS000065

• Identification of genetic mutations characteristic for recurrence of serous ovarian cancer.

  Establishment of novel therapeutic strategy to overcome intractable cancer by molecular profiling of serous ovarian cancer

  Study JGAS000104

• Genome and gene analysis of gastrointestinal cancer and elucidation of its clinicopathological significance

  Cancer develops through the accumulation of genetic and epigenetic aberrations. To identify sequential molecular alterations that occur during the development of hepatocellular carcinoma (HCC), we molecularly compared 52 early and 108 overt HCC samples by genome sequencing. Gene mutations in the p53/RB1 pathway, WNT pathway, MLLs, SWI/SNF complexes, and AKT/PI3K pathway were common in HCC. In the early phase of all entities, TERT was the most frequently upregulated gene owing to diverse mechanisms. Despite frequent somatic mutations in driver genes, including CTNNB1 and TP53, early HCC was a separate molecular entity from overt HCC as each had a distinct expression profile. Notably, WNT target genes were not activated in early HCC, regardless of CTNNB1 mutation status, because ?-catenin did not translocate into the nucleus due to the E-Cadherin/?-catenin complex at the membrane. Conversely, WNT targets were definitively upregulated in overt HCC with CTNNB1 mutation associated with downregulation of CDH1 and hypomethylation of CpG islands in the target genes. Similarly, cell cycle genes downstream of the p53/RB pathway were upregulated only in overt HCC with TP53 and/or RB1 gene mutations associated with chromosomal deletion of 4q and/or 16q. Differing from the expression profile, HCC was epigenetically distinguished into four subclasses: normal-like methylation, global-hypomethylation (favorable prognosis), stem-like methylation (poor prognosis), and CpG island methylation. These methylation statuses were globally maintained through HCC progression. Taken together, additional molecular events besides driver gene mutations cooperatively contribute to transcriptional activation of downstream targets as HCC progresses, according to the methylation status of the associated genes.

  Study JGAS000233

• Integrated copy number and expression analysis identifies profiles of whole-arm chromosomal alterations and subgroups with favorable outcome in ovarian clear cell carcinomas

  Ovarian clear cell carcinoma (CCC) is generally associated with chemoresistance and poor clinical outcome, even with early diagnosis; whereas high-grade serous carcinomas (SCs) and endometrioid carcinomas (ECs) are commonly chemosensitive at advanced stages. Although an integrated genomic analysis of SC has been performed, conclusive views on copy number and expression profiles for CCC are still limited. In this study, we performed single nucleotide polymorphism arrays in 57 (31 CCCs, 14 SCs, and 12 ECs) and expression microarrays in 55 epithelial ovarian cancers (25 CCCs, 16 SCs, and 14 ECs), and then evaluated PIK3CA mutations and ARID1A expression in CCCs. SNP array analysis classified 13% of CCCs into a cluster with high frequency and focal range of copy number alterations (CNAs), significantly lower than for SCs (93%, P < 0.01) and ECs (50%, P = 0.017). The ratio of whole-arm to all CNAs was higher in CCCs (46.9%) than SCs (21.7%) (P < 0.0001). SCs with loss of heterozygosity (LOH) of BRCA1 (85%) also had LOH of NF1 and TP53, and LOH of BRCA2 (62%) coexisted with LOH of RB1 and TP53. Microarray analysis classified CCCs into three clusters. One cluster (CCC-2, n = 10) showed more favorable prognosis than the others (CCC-1and CCC-3) (P = 0.041). Coexistent alterations of PIK3CA and ARID1A were more common in CCC-1 and CCC-3 (7/11, 64%) than in CCC-2 (0/10, 0%) (P < 0.01). Being in cluster CCC-2 was an independent favorable prognostic factor in CCC. In conclusion, CCC was characterized by a high ratio of whole-arm CNAs; whereas CNAs in SC were mainly focal, but preferentially caused LOH of well-known tumor suppressor genes. As such, expression profiles might be useful for sub-classification of CCC, and might provide useful information on prognosis.

  Study JGAS000022

• Cancer genomics for elucidation of molecular mechanisms of carcinogenecis and progression in lung cancer

  The objective of this project is to analyze genomic aberrations and gene expression changes such as mutations, deletions, amplifications, and hypermethylation in human lung cancer cells at the somatic cell level, and to contrast these with clinicopathological information to elucidate the molecular mechanisms and characteristics of lung cancer development and progression at the genetic level.

  Study JGAS000756

• Geriatric Oncology Database of genotypes and methylation, gene expression, clinical data, and survey results on psychosocial and physical conditions in Japanese elderly cancer patients to establish truly effective treatment strategy

  Owing to the advent of super-aged society, cancer mortality in Japan is forecasted to become an all-time high. The management of elderly patients with cancer is a serious health issue and the need for specific care guidelines for this population is critical in Japan. The significant individual differences in comorbidity, physical and mental functioning, and social problems among aging individuals are obstacles to the progress. The response to cancer treatment varies significantly among patients, even in the same stage of the same type of cancer. Older aged patients are still less likely to be offered participation in clinical trials, thus the number of clinical evidences is limited. The molecular mechanisms regulating the physiological process of ageing and senescence, and cancer are far from understood. To establish a truly effective treatment algorithm, we attempted to develop a geriatric oncology database for genotypes and methylation, gene expression, clinical data, and survey results on psychosocial and physical conditions in Japanese elderly cancer patients in this retrospective study. The genomic analysis was performed in 62, 106, and 173 cases, respectively for gastric, colon and lung cancers. The clinical data and survey results on psychosocial and physical conditions were collected from 166, 313, and 344 patients respectively for gastric, colon and lung cancers, and also collected from 357, 49, and 300 benign cases respectively for cardiovascular disorder, respiratory dysfunction, diabetes and nephropathy as the analysis control.

  Study JGAS000061

• 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

• The impact of CCR8+ regulatory T cells on cytotoxic T cell function in human lung cancer

  Regulatory T cells (Tregs) suppress the host immune response and maintain immune homeostasis. Tregs also promote cancer progression and are involved in resistance to immune checkpoint inhibitor treatments. Recent studies identified selective CCR8 expression on tumor-infiltrating Tregs; CCR8+ Tregs have been indicated as a possible new target of cancer immunotherapy. Here, we investigated the features of CCR8+ Tregs in lung cancer patients. CCR8+ Tregs were highly activated and infiltration of CCR8+ Tregs in tumors was associated with poor prognosis in lung cancer patients. We also investigated their immune suppressive function, especially the influence on cytotoxic T lymphocyte cell function. The Cancer Genome Analysis revealed that CD8 T cell activities were suppressed in high CCR8-expressing tumors. Additionally, depletion of CCR8+ cells enhanced CD8 T cell function in an ex vivo culture of lung tumor-infiltrating cells. Moreover, CCR8+ Tregs, but not CCR8��� Tregs, induced from human PBMCs markedly suppressed CD8 T cell cytotoxicity. Finally, we demonstrated the therapeutic effect of targeting CCR8 in a murine model of lung cancer. These findings reveal the significance of CCR8+ Tregs for immunosuppression in lung cancer, especially via cytotoxic T lymphocyte cell suppression, and suggest the potential value of CCR8-targeted therapy for cancer treatment.

  Study JGAS000454

• Treg cell subset-specific gene expression patterns in human head and neck cancer

  Backgrand: The occurrence of head and neck cancer has been increased all over the world. Although the prognosis has been improved by using several treatment modalities including immunotherapy, it is still unsatisfying. It is still unclear why the immunotherapy is effective only for partial amount of patients. To resolve this problem and to make a new treatment strategy based on human immune system, further investigation of antitumor immunity is required. Regulatory T (Treg) cells play critical roles in human immune responses including antitumor immunity. Therefore, the research to elucidate Treg function is strongly urged to clarify the mechanisms of antitumor immunity. Methods: We performed RNA-seuencing analysis of regulatory T cells infiltrating head and neck cancer. We devided into four populations, DP, CD25+, CTLA4+, DN and analyzed gene expressions. Results: The gene expression patterns of Treg-related genes were different between CD25+ cells and CD25- cells. Furthermore, DP cells had unique gene expression pattern compared to other populations. Conclusions: We found Treg cells infiltrating head and neck cancer had high expression levels of Treg-related genes and DP cells had unique gene expression pattern that may become a target of new treatment strategy. Regulatory T (Treg) cells play critical roles in human immune responses including antitumor immunity. Therefore, the research to elucidate Treg function is strongly urged to clarify the mechanisms of antitumor immunity.

  Study JGAS000135

• intratumor heterogeneity in colorectal adenoma and carcinoma

  To investigate intratumor heterogeneity in precancerous lesions of colorectal cancers (PCRCs), we performed whole-exome sequencing of 53 tumor and 10 matched-normal samples from 10 laterally spreading tumors in the colon and rectum, which were histologically diagnosed as adenoma with/without adenocarcinoma.

  Study JGAS000092

• Loss of presentation of estimated neoantigens from mutated genes in ctDNA was essential for fostering primary to recurrent tumors in postoperative colorectal cancer cases

  Specific parameters regarding mutations at primary sites for the detection of postoperative recurrence using circulating tumor (ct)DNA liquid biopsy are lacking. In the current retrospective study, we conducted target resequencing of ctDNA using 47 plasma samples and established a cancer panel carrying the commonly mutated genes between primary and recurrent tumors. We found that mutated genes in ctDNA indicated immune-resistance traits with respect to the impaired ability to present neoantigens by loss of expression or binding affinity to HLA in the primary tumor. Compared with the estimated neoantigens from all mutated genes in primary tumors, the neoantigen peptides from commonly mutated genes between primary and recurrent tumors showed abundant and significant expression with no binding affinity to HLA. Therefore, ctDNA mutations can be frequently and postoperatively detected to identify recurrence; however, these mutated genes were derived from immune-tolerated clones owing to the loss of neoantigen presentation in primary CRC tumors.

  Study JGAS000549

• Identification of driver oncogenes in scirrhous-type gastric cancer cell lines

  Scirrhous type gastric cancer (SGC) is one of the most intractable cancer subtypes in human, and its therapeutic targets have been rarely identified to date. Exploration of somatic mutations in the SGC genome with the next generation sequencers has been hampered by low tumor contents by the markedly increased fibrous tissues. Thus, SGC cell lines may be useful resources to search for novel oncogenes in. Here we have conducted whole exome sequencing and RNA sequencing on two SGC cell lines, OCUM-8 and OCUM-9. Interestingly, most of the mutations thus identified have not been reported. In OCUM-8 cells, a novel CD44-IGF1R fusion gene is discovered, the protein product of which ligates the amino-terminus of CD44 to the transmembrane and the tyrosine-kinase domains of IGF1R. Further, both of CD44 and IGF1R are markedly amplified in the OCUM-8 genome and abundantly expressed. CD44-IGF1R has a transforming ability, and the suppression of its kinase activity leads to rapid cell death of OCUM-8. On the other hand, OCUM-9 seems to possess multiple oncogenic events in its genome. The MET gene is highly amplified, and the treatment of OCUM-9 with crizotinib, a MET inhibitor, results in cell death. Further, a novel BORCS5-ETV6 fusion gene is identified in the OCUM-9 genome. BORCS5-ETV6 possesses oncogenic activity, and suppression of its message partially inhibits cell growth. Prevalence of these novel fusion genes among SGC awaits further investigation, but we validate the significance of cell lines as appropriate reagents for detailed genomic analyses of SGC.

  Study JGAS000179

• Genome- and epigenome-driven evolutionary dynamics of tumour-immune coevolution within primary colorectal cancers

  This data includes targeting sequencing of the immunopeptidome from 94 samples, usually individual laser microdissected cancer glands, from 11 cases of colorectal cancer. The data were used to test for evidence of immunoediting (antigen depletion) in colorectal cancers. The full data description is provided in the original manuscript https://pmc.ncbi.nlm.nih.gov/articles/PMC10888923/. The 11 colorectal cancers had been previously multiomic profiled with data described in the parts of this disposition.

  Study EGAS50000001154

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Study EGAS50000001327

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Study EGAS50000001328

• single cell RNA-seq of small cell lung cancer tumors

  This study investigated the transcriptomic profile of small cell lung cancer from 10 patients. Tumors were rapidly dissociated after the surgical procedure. Libraries were constructed using the VDJ NextGEM v1.1 10x Genomics Chromium kit. Samples were sequenced on a NextSeq 550 sequencer (Illumina).

  Study EGAS50000001400

• single cell RNA-seq of small cell lung cancer circulating tumor cells

  This study investigated the transcriptomic profile of circulating tumor cells from three small cell lung cancer patients. CTCs were enriched from the blood of three SCLC patients using the CTC-iChip followed by magnetic depletion of RBCs. The enriched samples were processed with the 10x Genomics Chromium platform (Chromium GEM-X Single Cell 3' Kit v4) and sequenced on a NextSeq 2000 system.

  Study EGAS50000001401

• single cell RNA-seq data of 10 small cell lung cancer patients

  This dataset contains 10 paired fastq files sequenced on Illumina NextSeq 550 sequencer. Tumors were rapidly dissociated after the surgical procedure using the Miltenyi Biotec Human Tumor Dissociation kit (cat# 130-095-929). Libraries were constructed using the VDJ NextGEM v1.1 10x Genomics Chromium kit. Single cell RNA-seq analysis was performed using Seurat R package.

  Dataset EGAD50000002034

• single cell RNA-seq data of circulating tumor cells from three small cell lung cancer patients

  This dataset contains raw 10x Genomics single-cell RNA sequencing data from a total of eight runs of circulating tumor cells from three small cell lung cancer patients. Each run represented by four FASTQ files (R1, R2, I1, I2) generated using the Illumina NextSeq 2000 platform. These files include read pairs as well as sample and cellular barcode indices. Circulating tumor cells were enriched from the blood of three SCLC patients using the CTC-iChip followed by magnetic depletion of RBCs. The enriched samples were processed with the 10x Genomics Chromium platform (Chromium GEM-X Single Cell 3' Kit v4) and sequenced on a NextSeq 2000 system.

  Dataset EGAD50000002035

• Massachusetts General Hospital Cancer Center DAC for single cell RNA-seq data from small cell lung cancer primary tumors and CTCs

  single cell RNA-seq data from 10 small cell lung cancer primary tumors and circulating tumor cells of three small cell lung cancer patients

  Dac EGAC50000000808

• Single-cell RNA sequencing of human omental tissue in benign and metastatic ovarian cancer

  To elucidate the cellular and molecular mechanisms underlying omental homeostasis and its transformation during ovarian cancer metastasis, a human omental cell atlas was generated encompassing both benign and metastatic conditions. Single-cell RNA sequencing was performed on freshly dissociated omental tissue samples from patients with newly diagnosed benign and malignant disease. Samples collected during diagnostic surgery covered distinct anatomical regions, enabling comparison between non-metastasized omentum and sites along the metastatic gradient, including distant, peritumoral, and tumor core areas.

  Study EGAS50000001465

• Human omentum cell atlas

  This dataset contains single-cell RNA sequencing data derived from freshly dissociated human omental tissue. The study investigates the transcriptomic landscape of the omentum by comparing samples from patients with benign conditions against those with ovarian cancer metastasis. To capture the heterogeneity of the metastatic niche, sampling was performed across distinct anatomical sites, including non-metastasized tissue, distant omental regions, peritumoral zones, and the tumor core. This comprehensive profiling aims to define the cellular remodeling associated with malignant transformation

  Dataset EGAD50000002110

• Targeted gene panel sequencing of leiomyosarcoma

  We conducted MSK-IMPACT sequencing of leiomyosarcoma.

  Study EGAS50000000595

• Clinical Utility of BRCA Research by Inocras, CMC and SMC (CUBRICS)

  This dataset consists of transcriptome data available for most cases of the whole-genome sequences from 1,364 Korean breast cancers

  Dataset EGAD50000001993