Dataset Information

Colorectal Cancer-Associated Fibroblasts are Genotypically Distinct.

ABSTRACT: Cells in the stromal microenvironment facilitate colorectal cancer (CRC) progression and "co-evolve" with the epithelial cancer cells. Genetic and epigenetic differences between normal colorectal mucosa fibroblasts (NF) and carcinoma-associated fibroblasts (CAF) are not known. The aim of this study is to identify differentially expressed genes and promoter methylation between NF and CAF in human CRC. RNA and DNA were extracted from cultured NF and CAF from CRC resections. Genome-wide gene expression and methylation analyses were performed using the Illumina Human HT-12 v4.0 Expression and Illumina Human Methylation 27 BeadChips. Gene expression values between NF and CAF were compared and correlated with methylation patterns. Data was analyzed using Partek Genomics Suite using one-way ANOVA and p<0.05 as significant. Ingenuity iReport™ was performed to identify potential differences in biological functions and pathways between the NF and CAF. Paired methylation and gene expression analyses from 11 NF and 10 CAF colorectal samples are reported. Unsupervised analysis of differentially expressed genes using iReport™ identified "Top Diseases" as "Cancer" and "Colorectal Cancer". Previous genome wide studies have focused on the cancer cells. We have identified differentially expressed genes and differentially methylated promoter regions that are CAF-specific in CRC.

SUBMITTER: Mrazek AA

PROVIDER: S-EPMC4270051 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Colorectal Cancer-Associated Fibroblasts are Genotypically Distinct.

Mrazek Amy A AA Carmical Joseph R JR Wood Thomas G TG Hellmich Mark R MR Eltorky Mahmoud M Bohanon Frederick J FJ Chao Celia C

Current cancer therapy reviews 20140101 2

Cells in the stromal microenvironment facilitate colorectal cancer (CRC) progression and "co-evolve" with the epithelial cancer cells. Genetic and epigenetic differences between normal colorectal mucosa fibroblasts (NF) and carcinoma-associated fibroblasts (CAF) are not known. The aim of this study is to identify differentially expressed genes and promoter methylation between NF and CAF in human CRC. RNA and DNA were extracted from cultured NF and CAF from CRC resections. Genome-wide gene expres ...[more]

PMID: 25530743

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Project description:Recent studies have shown that the tumor microenvironment plays a significant role in the progression of solid tumors. As an abundant component of the tumor microenvironment, cancer-associated fibroblasts (CAFs) have been shown to promote tumorigenesis and cancer aggressiveness, but their molecular characteristics remain poorly understood. In the present study, paired CAFs and normal fibroblasts (NFs) were isolated from five colorectal cancer (CRC) tissues from patients who underwent surgical resection. The gene expression profiles of CAFs and NFs identified by RNA sequencing were compared to understand the complex role of CAFs in cancer progression. Gene Set Enrichment Analysis revealed that the gene sets related to the Wnt signaling pathway were highly enriched in CAFs, as well as TGFβ signaling, which is considered to be a regulator of CAFs. Among the components of this pathway, Wnt2 was specifically expressed. The observations led us to speculate that Wnt2 is extremely involved in regulating CRC progression by CAFs. Thus, we performed immunohistochemical analysis on Wnt2 in 171 patients who underwent surgery for colorectal adenocarcinoma. Positive staining for Wnt2 was mainly observed in cancer stroma, although the immunoreactivity was weak in cancer cells. Wnt2 expression in CAFs was significantly correlated with depth of tumor (P < .001), lymph node metastasis (P = .044), TNM stage (P = .010), venous invasion (P < .001), and recurrence (P = .013). Subsequent in vitro analyses were conducted using conditioned medium (CM) from immortalized CAFs transfected with siRNA targeting Wnt2. As a result, cancer cell invasion and migration were significantly decreased in the CM from immortalized CAFs transfected with siRNA targeting Wnt2. Our findings indicated that Wnt2 protein released from CAFs enhances CRC cell invasion and migration. In conclusion, Wnt2 secreted by CAFs plays a key role in cancer progression and is a potential therapeutic target for CRC.

Project description:BACKGROUND: Anopheles arabiensis, an important malaria vector in Sudan and other countries in sub-Saharan Africa, exhibits considerable ecological and behavioural plasticity allowing it to survive in the harsh conditions of arid regions. It has been shown that adult populations of An. arabiensis in the semi-desert habitat of western Khartoum State survive through the long dry season in a state of partial aestivation, characterized by limited feeding activity and a degree of arrested ovarian development. Anopheles arabiensis in these sites occurs in two phenotypic forms. One is large and heavily melanized, the other has the typical characteristics of An. arabiensis as found elsewhere in Africa. The extent of genetic variation in these forms was examined in widely separated locations in Sudan, including Kassala, Gedaref and the Northern States between 1998 and 1999 and 2004 and 2006. METHODS: Each mosquito specimen was identified using standard morphological keys and a species-specific PCR test. Sequence variation in a 660 bp fragment of the mtDNA ND5 coding region was examined and the extent of genetic divergence between the forms was estimated from FST values using DNASP version 4.9. TCS 1.13 software was used to determine the genealogical relationships and to reflect clustering among mtDNA haplotypes. RESULTS: The melanic and normal forms were found in sympatry in Kassala, Gedaref and Khartoum states, with the melanic form commonest in the hottest and most arid areas. Both forms were encountered in the periods of study: 1998-1999, and 2004-2006. Only ten specimens of An. arabiensis were collected from the Northern State in February 2006, all of which were of the normal form.Based on the ND5 analysis, there was a marked subdivision between the normal and melanic forms (FST?=?0.59). Furthermore, the melanic form showed more genetic variability, as measured by haplotype diversity (0.95) compared with the normal form (0.57), suggesting larger effective population. CONCLUSIONS: This is the first demonstration of correspondent phenotypic and genetic structuring in An. arabiensis. The high level of genetic differentiation shown by the mtDNA ND5 locus suggests that the two forms may represent separate species. It is hypothesized that the melanic form is better adapted to hot and arid environments.

Project description:Outcomes for men with localized prostate cancer vary widely, with some men effectively managed without treatment on active surveillance, while other men rapidly progress to metastatic disease despite curative-intent therapies. One of the strongest prognostic indicators of outcome is grade groups based on the Gleason grading system. Gleason grade 4 prostate cancer with cribriform morphology is associated with adverse outcomes and can be utilized clinically to improve risk stratification. The underpinnings of disease aggressiveness associated with cribriform architecture are not fully understood. Most studies have focused on genetic and molecular alterations in cribriform tumor cells; however, less is known about the tumor microenvironment in cribriform prostate cancer. Cancer-associated fibroblasts (CAFs) are a heterogeneous population of fibroblasts in the tumor microenvironment that impact cancer aggressiveness. The overall goal of this study was to determine if cribriform prostate cancers are associated with a unique repertoire of CAFs. Radical prostatectomy whole-tissue sections were analyzed for the expression of fibroblast markers (ASPN in combination with FAP, THY1, ENG, NT5E, TNC, and PDGFRβ) in stroma adjacent to benign glands and in Gleason grade 3, Gleason grade 4 cribriform, and Gleason grade 4 noncribriform prostate cancer by RNAscope®. Halo® Software was used to quantify percent positive stromal cells and expression per positive cell. The fibroblast subtypes enriched in prostate cancer were highly heterogeneous. Both overlapping and distinct populations of low abundant fibroblast subtypes in benign prostate stroma were enriched in Gleason grade 4 prostate cancer with cribriform morphology compared to Gleason grade 4 prostate cancer with noncribriform morphology and Gleason grade 3 prostate cancer. In addition, gene expression was distinctly altered in CAF subtypes adjacent to cribriform prostate cancer. Overall, these studies suggest that cribriform prostate cancer has a unique tumor microenvironment that may distinguish it from other Gleason grade 4 morphologies and lower Gleason grades.

Project description:BackgroundLiver metastasis (LM) is a leading cause of cancer-related deaths in CRC patients, whereas the associated mechanisms have not yet been fully elucidated. Therefore, it is urgently needed to deeply explore novel metastasis accelerators and therapeutic targets of LM-CRC.MethodsThe bulk RNA sequencing data and clinicopathological information of CRC patients were enrolled from the TCGA and GEO databases. The single-cell RNA sequencing (scRNA-seq) datasets of CRC were collected from and analyzed in the Tumor Immune Single-cell Hub (TISCH) database. The infiltration levels of cancer-associated fibroblasts (CAFs) and macrophages in CRC tissues were estimated by multiple immune deconvolution algorithms. The prognostic values of genes were identified by the Kaplan-Meier curve with a log-rank test. GSEA analysis was carried out to annotate the significantly enriched gene sets. The biological functions of cells were experimentally verified.ResultsIn the present study, hundreds of differentially expressed genes (DEGs) were selected in LM-CRC compared to primary CRC, and these DEGs were significantly associated with the regulation of endopeptidase activity, blood coagulation, and metabolic processes. Then, SPP1, CAV1, ANGPTL2, and COLEC11 were identified as the characteristic DEGs of LM-CRC, and higher expression levels of SPP1 and ANGPTL2 were significantly associated with worse clinical outcomes of CRC patients. In addition, ANGPTL2 and SPP1 mainly distributed in the tumor microenvironment (TME) of CRC tissues. Subsequent scRNA-seq analysis demonstrated that ANGPTL2 and SPP1 were markedly enriched in the CAFs and macrophages of CRC tissues, respectively. Moreover, we identified the significantly enriched gene sets in LM-CRC, especially those in the SPP1+macrophages and ANGPTL2+CAFs, such as the HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION and the HALLMARK_COMPLEMENT. Finally, our in vitro experiments proved that ANGPTL2+CAFs and SPP1+macrophages promote the metastasis of CRC cells.ConclusionOur study selected four characteristic genes of LM-CRC and identified ANGPTL2+CAFs and SPP1+macrophages subtypes as metastasis accelerators of CRC which provided a potential therapeutic target for LM-CRC.

Dataset Information

Colorectal Cancer-Associated Fibroblasts are Genotypically Distinct.

Publications

Colorectal Cancer-Associated Fibroblasts are Genotypically Distinct.

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