No abstract

The aim of the present study was to identify the hub genes and provide insight into the tumorigenesis and development of breast cancer. To examine the hub genes in breast cancer, integrated bioinformatics analysis was performed. Gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database and the differentially expressed genes (DEGs) were identified using the ‘limma’ package in R. Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis was used to determine the functional annotations and potential pathways of the DEGs. Subsequently, a protein-protein interaction network analysis and weighted correlation network analysis (WGCNA) were conducted to identify hub genes. To confirm the reliability of the identified hub genes, RNA gene expression profiles were obtained from The Cancer Genome Atlas (TCGA)-breast cancer database, and WGCNA was used to screen for genes that were markedly correlated with breast cancer. By combining the results from the GEO and TCGA datasets, 15 hub genes were identified to be associated with breast cancer pathophysiology. Overall survival analysis was performed to examine the association between the expression of hub genes and the overall survival time of patients with breast cancer. Higher expression of all hub genes was associated with significantly shorter overall survival in patients with breast cancer compared with patients with lower levels of expression of the respective gene.

Background Colorectal cancer (CRC) is a major cancer type whose mechanism of metastasis remains elusive. Methods In this study, we characterised the evolutionary pattern of metastatic CRC (mCRC) by analysing bulk and single-cell exome sequencing data of primary and metastatic tumours from 7 CRC patients with liver metastases. Here, 7 CRC patients were analysed by bulk whole-exome sequencing (WES); 4 of these were also analysed using single-cell sequencing. Results Despite low genomic divergence between paired primary and metastatic cancers in the bulk data, single-cell WES (scWES) data revealed rare mutations and defined two separate cell populations, indicative of the diverse evolutionary trajectories between primary and metastatic tumour cells. We further identified 24 metastatic cell-specific-mutated genes and validated their functions in cell migration capacity. Conclusions In summary, scWES revealed rare mutations that failed to be detected by bulk WES. These rare mutations better define the distinct genomic profiles of primary and metastatic tumour cell clones.

Background Mediator complex subunit 12 (MED12) is an essential hub for transcriptional regulation, in which mutations and overexpression were reported to be associated with several kinds of malignancies. Nevertheless, the role of MED12 in non-small cell lung cancer (NSCLC) remains to be elucidated. Methods MED12 mutation was detected by Next-generation sequencing. The expression of MED12 in 179 human NSCLC tissue samples and 73 corresponding adjacent normal lung tissue samples was measured by immunohistochemistry (IHC). CRISPR-Cas9 was used to knock out MED12 in PC9 and SPC-A1 cells. MED12 rescued stable cell lines were generated by lentivirus infection. We traced cell division process by live cell imaging. The molecular mechanism of aborted cytokinesis resulted by MED12 knockout was investigated by RNA-seq. Effects of MED12 deletion on the proliferation of NSCLC cells were determined by MTT assay and Colony-formation assay in vitro and xenograft tumor model in nude mouse. Cell senescence was measured by SA-β-gal staining. Results In our study, no MED12 exon mutation was detected in NSCLC samples, whereas we found that MED12 was overexpressed in human NSCLC tissues, which positively correlated with the tumor volume and adversely affected patient survival. Furthermore, knockout MED12 in NSCLC cell lines resulted in cytokinesis failure, displayed a multinuclear phenotype, and disposed to senescence, and become non-viable. Lack of MED12 decreased the proliferative potential of NSCLC cells and limited the tumor growth in vivo. Mechanism investigations revealed that MED12 knockout activated LIMK2, caused aberrant actin cytoskeleton remodeling, and disrupted the abscission of intercellular bridge, which led to the cytokinesis failure. Reconstitution of exogenous MED12 restored actin dynamics, normal cytokinesis and cell proliferation capacity in MED12 knockout cells. Conclusions These results revealed a novel role of MED12 as an important regulator for maintaining accurate cytokinesis and survival in NSCLC cells, which may offer a therapeutic strategy to control tumor growth for NSCLC patients especially those highly expressed MED12. Electronic supplementary material The online version of this article (10.1186/s12943-019-1020-4) contains supplementary material, which is available to authorized users.

Abstract:The tumor microenvironment is composed of numerous cell types, including tumor, immune and stromal cells. Cancer cells interact with the tumor microenvironment to suppress anticancer immunity. In this study, we molecularly dissected the tumor microenvironment of breast cancer was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/368605 doi: bioRxiv preprint first posted online Jul. 13, 2018; 3 Breast cancer is the most common cancer and the leading cause of death from cancer in women worldwide(1). Four subtypes of breast cancer with distinct expression profiles have been classified based on gene expression signatures associated with highly variable clinical characteristics(2, 3).To design targeted treatment for such a diverse disease, understanding its molecular mechanism of initiation and progression is essential(4). Several studies have shown that the presence of tumor-5 infiltrating lymphocytes (TILs) is associated with breast cancer progression and neoadjuvant chemotherapy response(5-7). TIL levels within and between different subtypes of breast cancer vary(8). Based on the CD8 + T cell infiltration phenotype, tumors can be categorized as T-cellinflamed and non-T-cell-inflamed tumors(9). In T-cell-inflamed tumors, the tumor cells act together with the tumor microenvironment (TME) to inhibit the antitumor functions of T cells. 10This process results in an exhausted T cell phenotype. Non-T-cell-inflamed tumors escape immune system clearance by preventing T cell infiltration into the TME(10). Cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs) and oncogenic pathway alterations in tumor cells are reportedly responsible for the non-T-cell-inflamed phenotype(10-14). However, the mechanism of immune evasion in breast cancer remains unclear. A recent study showed that a 15 high number of TILs was beneficial for triple negative breast cancer (TNBC) and HER-2-positive breast cancer patient survival, but this parameter was an adverse prognostic factor for luminal HER2-negative breast cancer patient survival(15). High-resolution mapping of the TME composition and cell states of different breast cancer subtypes will help us understand the different effects of TILs and the mechanism of tumor immune evasion in breast cancer. 20In the past five years, the development of high-throughput single-cell RNA sequencing has enabled high-resolution studies of biological processes(16). Single-cell transcriptome profiling of tumor cells has been used to characterize heterogeneous tumor cells and tumor-associated stromal All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/368605 doi: bioRxiv preprint first posted online Jul. 13, 2018; 4 and immune cells (17)(18)(19). To un...