LncRNA and mRNA expression in five paired lung tissues (lung cancer tissues versus nontumor tissues) from non-small cell lung cancer (NSCLC) patients
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ABSTRACT:
PROVIDER: PRJNA574971 | ENA |
REPOSITORIES: ENA
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Project description:To determine the LncRNA and mRNA expression profile in lung cancer tissues and matched nontumor tissues, we used LncRNA microarray analysis from Arraystar to examine the expression of LncRNAs and mRNAs in lung cancer tissues and matched nontumor tissues.
2021-09-30 | GSE138172 | GEO
Project description:Non-small cell lung cancer (NSCLC) is a common lung disorder.Recent studies have shown that circRNA plays critical roles in a myriad of biological processes and human diseases,Since the roles of circRNA in NSCLC remain unknown,they were investigated in the study.Our findings indicate that the expression profiles of circRNAs have changed in NSCLC as compared with normal lung, and may provide novel insight into the molecular mechanism underlying the disease and potential novel diagnostic or therapeutic targets for NSCLC.
2019-03-22 | GSE112214 | GEO
Project description:Background: MicroRNAs (miRNAs) are small noncoding RNAs about 22 nucleotides in length and regulate mRNA expression by binding to 3?UTR of mRNAs and causing translation repression or degradation of mRNAs. Recent studies have revealed that microRNAs play important regulatory roles in carcinogenesis. However, the complement of miRNAs involved in lung carcinogenesis and tumor biology is generally unknown. We used high-throughput sequencing technology to investigate miRNA expression profiles in a study of paired lung non-small cell carcinomas and remote noncancerous lung tissues. Methods: Total RNA was isolated by Trizol from patient lung tissues, including 1 non-pair of macroscopic lung adenocarcinoma tissue, and 20 pairs of macroscopic lung adenocarcinoma tissues and corresponding paired noncancerous lung tissues from the same patients, 1 non-pair of noncancerous lung tissues of squamous cell carcinoma patient, and 10 pairs of squamous cell carcinoma and corresponding paired noncancerous lung tissues from the same patients. Small RNA library of each total RNA was constructed with Illumina?s Small RNA Sample Prep Kit, followed by high-throughput sequencing. Statistical differences in microRNA expression between groups were analyzed by GenePattern software. Results: Using 2-fold threshold with FDR<0.05, there were ~90 miRNAs differentiated the lung cancers from nontumor lung tissues, both histologies. (a) The sets of microRNAs differentiating adenocarcinoma from paired nontumor tissues are largely different from those differentiating squamous tumors. There were 40 upregulated and 23 downregulated microRNAs differentiating adenocarcinoma Tvs.NT . For squamous cell, the numbers were 19 and 6, respectively. (b) In common between the two tumor histologies, there were six common upregulated microRNAs (miR-21, 135b, 200a, 494, 708. 1259), and four common down-regulated microRNAs (miR-144, 184, 516a, 1251). (c) Comparing our 22 miRNAs in common with Yanaihara/Harris Cancer Cell 2006 using spotted microarrays, we found similar direction of change in 19/22. (d) As a group, the top over-expressed miRNA in lung tumors (determined as fold change > 2, and comprising at least .01% of total miRNA) are able to predict mRNAs that are differentially expressed in those same samples (p=4.6x10^-6). Conclusions: This effort represents one of the more comprehensive surveys of the lung tumor micronome. (i) Tumor microRNA complement differs from far-adjacent lung; (ii) Histologies differ in their overall, and tumor-distinctive microRNA complement; (iii) Statistical correlations of individual microRNA:mRNA (putative) pairing from the same tissue sets are pending. (iv) Experimental confirmation of microRNA:mRNA targeting, using our microRNA affinity pull down assay is also pending.
2012-03-31 | GSE33858 | GEO
Project description:Alterations in cellular antigen processing and presenting machinery has gained increased interest as a hallmark of cancer-related inflammation. Growing evidence suggest that proteasome composition and immunoproteasome expression can influence the efficacy of cancer therapies. By applying proteasome foot-printing to clinical samples of Non Small Cell lung Cancer (NSCLC), we found tumor specific alterations in degradation products and increased expression of the proteasome regulator, PA200. We show that increased levels of PA200 alter the cleavage specificities of proteasomal-cleaved peptides and reduce antigenicity. We found that smoking-induced expression of PA200 abrogated immunoproteasome activity and is associated with poor survival. As immunotherapy is becoming a common treatment of NSCLC, we hypothesized that PA200 expression may contribute to resistance mechanism to immunotherapy. Consistent with this possibility, we found that the ratio between PA200 and the immunoproteasome subunit PSMB10, and not their absolute levels, were significantly associated with poor response to Durvalamab. Induced reduction in PA200 in vivo was associated with increased immune infiltration and attenuated tumor growth.
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2016-05-18 | E-GEOD-74706 | biostudies-arrayexpress
Project description:Genome-wide analysis of circRNA expression profile in non-small cell lung cancer (NSCLC) tissues and matched adjacent normal tissues
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Project description:Lung cancer is the leading cause of cancer-related death worldwide, and non-small cell lung cancer (NSCLC) accounts for approximately 85% of lung cancers. Lymphatic metastasis serves as a predominant NSCLC metastatic route and an essential predictor of patient prognosis. Recently, circular RNA (circRNA) has emerged as critical mediator in various tumor initiation and progression. To identify essential circRNA that involves in the lymphatic metastasis of NSCLC, Next generation sequencing (NSG) was performed in 6 paired NSCLC tissues and normal adjacent tissues (NAT).
2023-12-01 | GSE235634 | GEO
Project description:The stromal microenvironment plays a vital role in cancer initiation and progression. We performed a comparative expression profiling of pulmonary MSC derived from NSCLC and corresponding normal lung tissue of 5 newly diagnosed patients. The analysis indicated variable expression of genes involved in DNA repair, apoptosis, proliferation or angiogenesis between NSCLC-MSC and NLT-MSC. MSC were derived from NSCLC and corresponding normal lung tissue of 5 patients. Paired SAM test was performed to screen for differentially expressed genes between NSCLC-MSC and NLT-MSC.
2013-02-07 | E-GEOD-23066 | biostudies-arrayexpress
Project description:Lung cancer is the leading cause of cancer-related deaths world-wide. ~85% of lung carcinomas are non–small cell lung carcinoma (NSCLC). Tumor cell heterogeneity is very poorly defined. However, it is known to be important for tumor response to cancer therapy and cancer agressivenes. We subjected three NSCLC tumors resected from different patients to Drop-seq in order to 1) elucidate the capability of scRNA-seq analysis in identifying different tumor cell populations; and 2) ascertain the clinical value of the genes which distinguish cancer cells from other cells in the tissue. As anticipated, the tissue composition of independently collected samples varied. Despite deficient populations in some samples, both donor and patient samples contributed to the majority of cell populations. However, cancer cells were all patient-specific. These findings emphasize the utility of single cell gene expression data in identification of tumor cell populations. The collected data might be further used for predicting of drugs specific to the biology of activated pathways and patient outcome.
2020-12-19 | GSE148466 | GEO
Project description:T lymphocytes can efficiently counteract the growth of tumors within the tumor microenvironment. Specialized immune-interacting fibroblasts, termed fibroblastic reticular cells (FRC) are responsible for the formation of specialized niches promoting immune cell activation in secondary lymphoid organs and originate from embryonic progenitors. FRCs have also been identified in tertiary lymphoid structures (TLS) in tumor tissues. However, the identity and differentiation of TLS-associated FRC subsets that promote intra-tumoral T cell activity have remained unexplored. Here, we employed single cell RNA-sequencing of fibroblasts and immune cells, sampled from subpleural margin, central margin and unaffected lung tissue in non small cell lung cancer (NSCLC), demonstrating the formation of specific tumor T cell environments (TTEs) underpinned by CCL19-expressing FRCs. We detected tumor-specific FRC subsets namely CCL19-expressing TRCs and perivascular reticular cells (PRCs) interacting with intratumoral T cells, and thus regulating FRC differentiation and T cell activation. Our results highlight a remarkable functionality of FRCs to efficiently determine protective antitumoral T cell responses in NSCLC.
2024-11-19 | E-MTAB-13710 | biostudies-arrayexpress