Regulation Of Epithelial Cell Proliferation Research Articles

Characterizing the role of exosomal miRNAs in metastasis.

Exosomal microRNAs (exomiRs), transported via exosomes, play a pivotal role in intercellular communication. In cancer, exomiRs influence tumor progression by regulating key cellular processes such as proliferation, angiogenesis, and metastasis. Their role in mediating communication between cancer cells and the tumor microenvironment highlights their significance as potential diagnostic and therapeutic targets. In this study, we aimed to characterize the role of exomiRs in influencing the pre-metastatic niche (PMN). Across 7 tumor types, including 4 cell lines and three tumors, we extracted high confidence exomiRs (Log FC >= 2 in exosomes relative to control) and their targets (experimentally identified and targeted by at least 2 exomiRs). Subsequently, we identified enriched pathways and selected the top 100 high-confidence exomiR targets based on the frequency of their appearance in the enriched pathways. These top 100 targets were consistently used throughout the analysis. Cancer cell line and tumor derived ExomiRs have significantly higher GC content relative to genomic background. Pathway enriched among the top exomiR targets included general cancer-associated processes such as "wound healing" and "regulation of epithelial cell proliferation", as well as cancer-specific processes, such as "regulation of angiogenesis in kidney" (KIRC), "ossification" in lung (LUAD), and "positive regulation of cytokine production" in pancreatic cancer (PAAD). Similarly, 'Pathways in cancer' and 'MicroRNAs in cancer' ranked among the top 10 enriched KEGG pathways in all cancer types. ExomiR targets were not only enriched for cancer-specific tumor suppressor genes (TSG) but are also downregulated in pre-metastatic niche formed in lungs compared to normal lung. Motif analysis shows high similarity among motifs identified from exomiRs across cancer types. Our analysis recapitulates exomiRs associated with M2 macrophage differentiation and chemoresistance such as miR-21 and miR-222-3p, regulating signaling pathways such as PTEN/PI3/Akt, NF-κB, etc. Cox regression indicated that exomiR targets are significantly associated with overall survival of patients in TCGA. Lastly, a Support Vector Machine (SVM) model using exomiR target gene expression classified responders and non-responders to neoadjuvant chemotherapy with an AUROC of 0.96 (in LUAD), higher than other previously reported gene signatures. Our study characterizes the pivotal role of exomiRs in shaping the PMN in diverse cancers, underscoring their diagnostic and therapeutic potential.

Integrated network pharmacology and experimental verification to reveal the role of Shezhi Huangling Decoction against glioma by inactivating PI3K/Akt-HIF1A axis

Shezhi Huangling Decoction (SHD) has been proven clinically effective in regulating metabolic and immune homeostasis in the treatment of glioma. The investigation aimed to deconstruct the active constituents and mechanisms of SHD. Effects of SHD on malignant characteristics of HS683 and KNS89 cells have been investigated by CCK-8, clone formation, flow cytometry, and Transwell assays. A mouse xenograft model was established to assess the effect of SHD or SHD + temozolomide (TMZ) in vivo. A total of 461 constituents were found from SHD in UPLC/Q-TOF-MS/MS analysis. Functional enrichment analysis showed that pathway in cancer, proteoglycans in cancer, regulation of epithelial cell proliferation, inflammation/immune, gliogenesis, brain development, cell adhesion, and autophagy could participate in the treatment of SHD. Additionally, 9 hub genes (AKT1, TP53, CTNNB1, STAT3, EGFR, VEGFA, PIK3CA, ERBB2, and HIF1A) were identified as hub genes. Moreover, we found that SHD may greatly reduce the migration and accelerate apoptosis of HS683 and KNS89 cells. Additionally, SHD coordinates TMZ to restrict tumor growth were found in the mice. Our results suggest that the malignant behaviors of glioma cells are suppressed by SHD and the mechanism may be closing on the inhibition of the PI3K/Akt-HIF1A axis. SHD may serve as a synergistic therapeutic choice for TMZ to suppress glioblastoma growth.

Abstract LB013: Characterizing the role of exosomal miRNAs in metastasis

Abstract Background: Exosomal microRNAs (Ex-miRs) play a pivotal role in intercellular communication, being transported via extracellular vesicles. In cancer, Ex-miRs influence tumor progression by regulating key cellular processes such as proliferation, angiogenesis, and metastasis. Their role in mediating communication between cancer cells and the tumor microenvironment highlights their significance as potential diagnostic and therapeutic targets. Methodology: In this study, we aimed to characterize the role of Ex-miRs in influencing the pre-metastatic niche (PMN) across 7 tumor types. We extracted high-confidence Ex-miRs (Log FC >= 2 in exosomes relative to expectation) and their targets (experimentally proven and targeted by at least 2 Ex-miRs) from various studies. Subsequently, we conducted gene ontology analysis to identify enriched pathways and selected the top 100 high-confidence Ex-miR targets based on the frequency of their appearance in the enriched pathways. These top 100 targets were consistently used throughout the analysis. Results: Pathway enriched among the top Ex-miR targets included common ones such as “wound healing” and “regulation of epithelial cell proliferation”, as well as cancer-specific, like “regulation of angiogenesis in kidney” (KIRC), “ossification” in lung (LUAD), and “positive regulation of cytokine production” in pancreatic cancer (PAAD). Similarly, 'Pathways in cancer' and 'MicroRNAs in cancer' ranked among the top 10 enriched KEGG pathways for all cancer types. Ex-miR targets exhibited cancer-specific downregulation of gene expression in TCGA-Normal Adjacent Tumors (NATs), taken as proxy for PMN, compared to healthy tissue samples in GTEx. We further examined the 3’UTR GC content of these targets and found that Ex-miR targets are GC-rich, consistent with the previous findings stating that Ex-miR bind to the 3’UTR region of the target gene, downregulating their expression. Fisher’s exact test revealed a significant overlap of cancer-specific tumor suppressor genes (TSG) with Ex-miR targets. Cox regression indicated that Ex-miR targets are associated with better survival in certain cancer types, such as BRCA, COAD and KIRC. Lastly, a Support Vector Machine (SVM) model using Ex-miR target gene expression classified responders and non-responders to neoadjuvant chemotherapy with a high AUROC compared to other gene signatures. Conclusion: Our study unveils the pivotal role of exosomal microRNAs in shaping the PMN in diverse cancers, underscoring the diagnostic and therapeutic potential of Ex-miRs. Citation Format: Piyush Agrawal, Gulden Olgun, Arashdeep Singh, Vishaka Gopalan, Sridhar Hannenhalli. Characterizing the role of exosomal miRNAs in metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB013.

Biomarkers of UVB radiation-related senescent fibroblasts

Excessive exposure to ultraviolet (UV) light is known to induce photoaging in the skin, necessitating the development of effective anti-photoaging strategies to mitigate the adverse effects of UV radiation. Understanding the biofunctional characteristics of diverse skin cell types and unraveling the molecular modifications implicated in the aging process are pivotal in comprehending the intricacies of photoaging in human skin. Such insights are essential for paving the way for innovative interventions to counteract the deleterious impact of UV radiation on the skin. The single-cell RNA sequencing data of UVB-irradiated and normal control mouse skin in GSE173385 were downloaded from the Gene Expression Omniniub (GEO) database. First, cell types were identified using Seurat for normalization, dimensionality reduction and clustering. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis were executed on these cell subpopulations. Using FindAllMarkers in the Seurat package to identify differential gene expression and Monocle2 cell trajectory analysis, we screened out hub genes related to the development trajectory of senescent fibroblasts during photoaging, and then combined it with 307 aging-related genes collected in the HAGR library, we finally identified two biomarkers. The efficiency of biomarkers in diagnosing UV radiation photoaging was also evaluated in the dataset. Concurrently, the immune infiltration of identified biomarkers under UV radiation has also been further explored. Moreover, we employed the Enrichr platform to conduct a comprehensive screening of drug molecules associated with the identified biomarkers. Our comprehensive analysis, employing Seurat for normalization, dimensionality reduction, and clustering, successfully identified ten distinct cell types within the samples. Then GO functional enrichment analysis showed that senescent fibroblasts are mainly involved in the regulation of immune effector processes such as cytokine-mediated signaling pathways, regulation of epithelial cell proliferation and intercellular adhesion. Afterwards, KEGG analysis determined the main biological pathways are: IL-17 signaling pathway, Cytokine–cytokine receptor interaction, Metabolism of xenobiotics by cytochrome P450. After differential gene expression and Monocle2 cell trajectory analysis, we matched the obtained hub genes with the aging-related genes collected in the HAGR library, and finally screened out two relevant biomarkers: Apoe and Gdf15 which are related to the development trajectory of senescent fibroblasts during photoaging. Meanwhile, the immune infiltration further implied that the expression of these two biomarkers was significantly correlated with immune cells. In addition, the Enrichr platform was used to screen the drug molecules related to these biomarkers. This strategic approach aimed to pinpoint effective molecular targets for the prevention and treatment of photoaging. Our investigation has effectively characterized biomarkers associated with fibroblast senescence during photoaging at the single-cell level, We have validated their correlation with cellular immune inflammation and identified potential drug targets through the utilization of the Enrichr platform. This foundational research establishes a robust basis for the development of therapeutic interventions targeting skin diseases resulting from photoaging.

Differential dependence on microbiota of IL-23/IL-22-dependent gene expression between the small- and large-intestinal epithelia.

In the intestine, interleukin (IL)-23 and IL-22 from immune cells in the lamina propria contribute to maintenance of the gut epithelial barrier through the induction of antimicrobial production and the promotion of epithelial cell proliferation. Several previous studies suggested that some of the functions of the IL-23/IL-22 axis on intestinal epithelial cells are shared between the small and large intestines. However, the similarities and differences of the IL-23/IL-22 axis on epithelial cells between these two anatomical sites remain unclear. Here, we comprehensively analyzed the gene expression of intestinal epithelial cells in the ileum and colon of germ-free, Il23-/- , and Il22-/- mice by RNA-sequencing. We found that while the IL-23/IL-22 axis is largely dependent on gut microbiota in the small intestine, it is much less dependent on it in the large intestine. In addition, the negative regulation of lipid metabolism in the epithelial cells by IL-23 and IL-22 in the small intestine was revealed, whereas the positive regulation of epithelial cell proliferation by IL-23 and IL-22 in the large intestine was highlighted. These findings shed light on the intestinal site-specific role of the IL-23/IL-22 axis in maintaining the physiological functions of intestinal epithelial cells.

Circulating miRNA Expression Is Inversely Correlated with Tumor Tissue or Sentinel Lymph Nodes in Estrogen Receptor-Positive Early Breast Cancer Patients.

The deregulation of microRNAs (miRNAs) is associated with the various steps of the metastatic process. In addition, circulating miRNAs are remarkably stable in peripheral blood, making them ideal noninvasive biomarkers for disease diagnosis. Here, we performed a proof-of-principle study to determine whether tumor-tissue-derived miRNAs are traceable to plasma in ER-positive early breast cancer patients. We performed RNA-sequencing on 30 patients for whom plasma, sentinel lymph nodes (SLNs) and tumor tissue were available. We carried out differential expression, gene ontology and enrichment analyses. Our results show that circulating miRNAs are inversely expressed compared with tumor tissue or SLNs obtained from the same patients. Our differential expression analysis shows the overall downregulation of circulating miRNAs. However, the expression of miR-643a-3p and miR-223 was up-regulated in patients with positive SLNs. Furthermore, gene ontology analysis showed the significant enrichment of biological processes associated with the regulation of epithelial cell proliferation and transcriptional regulation commonly involved in the promotion of metastases. Our results suggest the potential role of several circulating miRNAs as surrogate markers of lymph node metastases in early breast cancer patients. Further preclinical and clinical studies are required to understand the biological significance of the most significant miRNAs and to validate our results in a larger cohort of patients.

Cancer-associated fibroblasts promote cancer stemness by inducing expression of the chromatin-modifying protein CBX4 in squamous cell carcinoma.

The chromobox-containing protein CBX4 is an important regulator of epithelial cell proliferation and differentiation, and has been implicated in several cancer types. The cancer stem cell (CSC) population is a key driver of metastasis and recurrence. The undifferentiated, plastic state characteristic of CSCs relies on cues from the microenvironment. Cancer-associated fibroblasts (CAFs) are a major component of the microenvironment that can influence the CSC population through the secretion of extracellular matrix and a variety of growth factors. Here we show CBX4 is a critical regulator of the CSC phenotype in squamous cell carcinomas of the skin and hypopharynx. Moreover, CAFs can promote the expression of CBX4 in the CSC population through the secretion of interleukin-6 (IL-6). IL-6 activates JAK/STAT3 signaling to increase ∆Np63α-a key transcription factor that is essential for epithelial stem cell function and the maintenance of proliferative potential that is capable of regulating CBX4. Targeting the JAK/STAT3 axis or CBX4 directly suppresses the aggressive phenotype of CSCs and represents a novel opportunity for therapeutic intervention.

1666-P: ScRNAseq–Based Analysis of the Stromal Immune Cell Composition in Murine Preweaning and Adult White Adipose Tissues

Early postnatal adipose growth is essential to establish a functional metabolism. Conversely, proportional adipose expansion in adults results in insulin resistance. Despite adipocytes, immune cells play a pivotal role in orchestrating adipose tissue function and expansion. To this end, we performed an in-depth analysis of scRNAseq data of immune cell populations of 2 weeks (pre-weaning) and 8 weeks old (adult) murine subcutaneous and perigonadal adipose depots. Our analysis revealed 15 distinct immune cell clusters. Most immune cell types were found in all depots and ages. Among the detected T-cell populations, we only observed differences in the abundance of naïve T cells, which were predominantly found in in subcutaneous white adipose tissue, irrespective of age. Similar to human, we could define several murine macrophage subtypes. Among them, perivascular macrophages (PVM) were predominantly found in subcutaneous white adipose tissue of 2 weeks old mice. RNA-velocity analysis and pseudotime trajectory construction suggested a developmental trajectory from lipid-associated macrophages (LAM) to PVM, which was further corroborated by analysis of gene expression dynamics resolved along latent time of white adipose tissue macrophages from 2 weeks old mice. Further analysis revealed that the top-ranked 100 genes of LAM were associated with the regulation of endothelial cell migration and proliferation (Nrp1, Grn, Glul, Sash1, Ccl24), blood vessel morphogenesis (Nrp1, Tgfbr2) and the regulation of epithelial cell proliferation. In summary, we provide a comprehensive overview of the immune cell composition of pre-weaning and adults murine adipose tissues. Moreover, we provide in-depth analysis of T-cell and macrophage populations and their relationship and dependency based on mRNA expression analysis. Disclosure X. Yan: None. V. Miok: None. R. Karlina: None. A. Böttcher: None. D. Lutter: None. H. Lickert: Research Support; Eli Lilly and Company. C. Garcia Caceres: None. S. Ussar: Research Support; Novo Nordisk. Funding China Scholarship Council (201908370218)

Comparison of gene expression profiles in healthy individuals and people with lung cancer using the meta-analysis method.

Advances in the early detection of cancer are a way for treatment to be effective. However, due to the inability of early diagnose and treatment for lung cancer, the death rate of this type of cancer is high. Usually, a high percentage of patients are diagnosed at a stage where they are not able to receive treatment. The purpose of this study was the comparison of gene expression profiles in healthy individuals and people with lung cancer. The raw data sets GSE10072 and GSE19804 were taken from the GEO online database. Differentially expressed genes (DEGs) were identified between the non-tumor and tumor tissue samples using a meta-analysis investigation. Then, gene ontology and biological pathway analysis were performed with the Enrichr online server. The protein-protein interaction network of genes obtained from the meta-analysis investigation was drawn and analyzed using the String Online database and Cytoscape Software. Meta-analysis results showed a total of 515 differentially expressed genes. The results of the functional processes and biological pathway revealed that differentially expressed genes were mainly enriched in positive regulation of cell differentiation, regulation of cell population proliferation, regulation of epithelial cell differentiation, positive regulation of epithelial cell proliferation, response to growth factor, defense response to the tumor cell, cellular response to UV, regulation of cell cycle process, cell adhesion molecules, PPAR signaling pathway, TNF signaling pathway, ECM-receptor interaction, p53 signaling pathway, PI3K-Akt signaling pathway, and Cell cycle. Finally, key genes related to lung cancer, including IL6, MMP9, VWF, PECAM1, FOS, and CAV1 were identified. In conclusion, comparisons of gene expression profiles in healthy individuals and people with lung cancer identified some key genes that can act as lung cancer markers and can be used to predict new findings on cancer. These genes can play an important role in diagnosis and early cancer treatment.

YAP regulates intestinal epithelial cell proliferation through activation of STAT3 in DSS-induced colitis and associated cancer.

Ulcerative colitis (UC) is a chronic, relapsing inflammation of the colon. Impaired epithelial repair is an important biological features of UC. Accelerating intestinal epithelial repair to achieve endoscopic mucosal healing has become a key goal in UC. Yes-associated protein (YAP) is a key transcriptional coactivator that regulates organ size, tissue growth and tumorigenesis. Growing studies have focused on the role of YAP in intestinal epithelial regeneration. This study explore the molecular mechanism for the role YAP in modulating colonic epithelial proliferation, repair, and the development of colitis associated cancer. We constructed the acute colitis mouse model through successive 5 days of 3% dextran sulfate sodium salt (DSS) induction. Then YAP-overexpressed mouse model was constructed by intraperitoneal injection the YAP overexpressed and negative control lentivirus into DSS mice. On the 5th day of DSS induction and the 5th day of normal drinking water after removing DSS (5+5 d), the mice were killed by spinal dislocation. The colon was taken to measure the length, and the bowel 1-2 cm near the anal canal was selected for immunohistochemical and Western blotting. We used YAP over-expressed colonic epithelial cells and small interfering signal transducer and activator of transcription 3 (STAT3) RNA to probe the regulation of YAP on STAT3, using cell counting kit-8 and scratch assays to explore the role of YAP on colonic epithelial cell proliferation. Finally, we conducted co-immunoprecipitation to test the relationship between YAP and STAT3. After DSS treatment, the expression of YAP was dramatically diminished in crypts. Compared with the empty control mice, overexpression of YAP drastically accelerated epithelial regeneration after DSS induced colitis, presenting with more intact of structural integrity in intestinal epithelium and a reduction in the number of inflammatory cells in the mucosa. Further Western blotting, functional experiment and co-immunoprecipitation analyses showed that the expression of YAP in nucleus was significantly increased by 2 h post DSS cessation, accompanied with up-regulated total protein levels of STAT3 and phosphorylated-STAT3 (p-STAT3). Overexpression of YAP enhanced the expression of STAT3, p-STAT3, and their transcriptional targets including c-Myc and Cyclin D1. In addition, it promoted the proliferation and the "wound healing" of colonic cells. However, these effects were reversed when silencing STAT3 on YAP-overexpressed FHC cells. Moreover, protein immunoprecipitation indicated that YAP could directly interact with STAT3 in the nucleus, up-regulatvng the expressvon of STAT3. Finally, during the process of CAC, overexpression of YAP mutant caused the down-regulated expression of STAT3 and inhibited the development and progress of CAC. YAP activates STAT3 signaling in regulation of epithelial cell proliferation and promotes mucosal regeneration after DSS induced colitis, which may serve as a potential therapeutic target in UC. However, persistent and excessive YAP activation may promote CAC development.

Correlation of H3K9ac and H4K12ac With Cell Proliferation Marker Ki-67 in Oral Leukoplakia: An Immunohistochemical Study.

This study aimed to analyze the immunohistochemical expression of H3K9ac and H4K12ac in oral leukoplakia (OL) and its association with cell proliferation marker Ki-67 and clinicopathologic data. Paraffin-embedded, formalin-fixed tissue samples from 50 OLs and 15 fragments of the normal oral mucosa (NOM) were submitted to immunohistochemical assay using the streptavidin-biotin-peroxidase method. Quantitative analysis of the antigen-antibody reaction was performed by obtaining integrated optical density (IOD) and the percentage of positive nuclei (PPN) with ImageJ software. OL samples presented higher PPN ( P =0.02) and lower IOD values ( P =0.007) for H4K12ac in comparison to NOM. The area under the receiver operating characteristic curve for PPN and IOD values of H4K12ac immunostaining were 0.70 ( P =0.02) and 0.73 ( P =0.007), respectively. No differences were found between OL and NOM for H3K9ac. Cell proliferation marker Ki-67 had a positive correlation with PPN ( P <0.0001) and IOD ( P =0.0007) for H3K9ac expression and with IOD values ( P =0.002) for H4K12ac expression. The present findings suggest that alterations in the acetylation pattern of H4K12 occur in the early stages of oral carcinogenesis and that both H3K9ac and H4K12ac might have a role in the regulation of epithelial cell proliferation of OL.

Low expression of CHRDL1 and SPARCL1 predicts poor prognosis of lung adenocarcinoma based on comprehensive analysis and immunohistochemical validation

PurposeExploring the molecular mechanisms of lung adenocarcinoma (LUAD) is beneficial for developing new therapeutic strategies and predicting prognosis. This study was performed to select core genes related to LUAD and to analyze their prognostic value.MethodsMicroarray datasets from the GEO (GSE75037) and TCGA-LUAD datasets were analyzed to identify differentially coexpressed genes in LUAD using weighted gene coexpression network analysis (WGCNA) and differential gene expression analysis. Functional enrichment analysis was conducted, and a protein–protein interaction (PPI) network was established. Subsequently, hub genes were identified using the CytoHubba plug-in. Overall survival (OS) analyses of hub genes were performed. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Human Protein Atlas (THPA) databases were used to validate our findings. Gene set enrichment analysis (GSEA) of survival-related hub genes were conducted. Immunohistochemistry (IHC) was carried out to validate our findings.ResultsWe identified 486 differentially coexpressed genes. Functional enrichment analysis suggested these genes were primarily enriched in the regulation of epithelial cell proliferation, collagen-containing extracellular matrix, transforming growth factor beta binding, and signaling pathways regulating the pluripotency of stem cells. Ten hub genes were detected using the maximal clique centrality (MCC) algorithm, and four genes were closely associated with OS. The CPTAC and THPA databases revealed that CHRDL1 and SPARCL1 were downregulated at the mRNA and protein expression levels in LUAD, whereas SPP1 was upregulated. GSEA demonstrated that DNA-dependent DNA replication and catalytic activity acting on RNA were correlated with CHRDL1 and SPARCL1 expression, respectively. The IHC results suggested that CHRDL1 and SPARCL1 were significantly downregulated in LUAD.ConclusionsOur study revealed that survival-related hub genes closely correlated with the initiation and progression of LUAD. Furthermore, CHRDL1 and SPARCL1 are potential therapeutic and prognostic indicators of LUAD.

A Computational Study to Predict Wound Healing Agents from the Peel of the Mangosteen (Garcinia mangostana L.) Extract

This study aimed to identify potentially active compounds from mangosteen peel extracts that heal skin burns and to evaluate their molecular mechanisms. There are about 120 compounds that have been identified in mangosteen peel by datamining, including 60 types of xanthones. The SMILE format of each compound was downloaded from the PubChem database. The compound data was then analyzed for potential anti-inflammatory, antioxidant, and antibacterial activities with PASS SERVER. To prediction mechanisms, firstly, target protein predictions were made with Swiss target prediction and HitPick. Target Protein data was then analyzed by interaction with STRING to determine its molecular mechanism. Further analysis of the shortest pathway was done with Cytoscape. The screening process of fifty compounds, which are predicted to have anti-inflammatory, antioxidant, and antibacterial activities by PASS SERVER. The four highest potency compounds were Smeaxanthone A, Garcinone E, γ-mangosteen, and Gartanin, which were types of xanthone. Based on the result of computational study these four compounds have potential targets prediction related to interleukin 6, epidermal growth factor, and transforming growth factor beta 1, that are involved in the regulation of epithelial cell proliferation which plays a role in the healing process of skin burns.

Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain

BackgroundFew somatic mutations have been linked to breast cancer metastasis, whereas transcriptomic differences among primary tumors correlate with incidence of metastasis, especially to the lungs and brain. However, the epigenomic alterations and transcription factors (TFs) which underlie these alterations remain unclear.MethodsTo identify these, we performed RNA-seq, Chromatin Immunoprecipitation and sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) of the MDA-MB-231 cell line and its brain (BrM2) and lung (LM2) metastatic sub-populations. We incorporated ATAC-seq data from TCGA to assess metastatic open chromatin signatures, and gene expression data from human metastatic datasets to nominate transcription factor biomarkers.ResultsOur integrated epigenomic analyses found that lung and brain metastatic cells exhibit both shared and distinctive signatures of active chromatin. Notably, metastatic sub-populations exhibit increased activation of both promoters and enhancers. We also integrated these data with chromosome conformation capture coupled with ChIP-seq (HiChIP) derived enhancer-promoter interactions to predict enhancer-controlled pathway alterations. We found that enhancer changes are associated with endothelial cell migration in LM2, and negative regulation of epithelial cell proliferation in BrM2. Promoter changes are associated with vasculature development in LM2 and homophilic cell adhesion in BrM2. Using ATAC-seq, we identified a metastasis open-chromatin signature that is elevated in basal-like and HER2-enriched breast cancer subtypes and associates with worse prognosis in human samples. We further uncovered TFs associated with the open chromatin landscapes of metastatic cells and whose expression correlates with risk for metastasis. While some of these TFs are associated with primary breast tumor subtypes, others more specifically correlate with lung or brain metastasis.ConclusionsWe identify distinctive epigenomic properties of breast cancer cells that metastasize to the lung and brain. We also demonstrate that signatures of active chromatin sites are partially linked to human breast cancer subtypes with poor prognosis, and that specific TFs can independently distinguish lung and brain relapse.

CeRNA regulatory network-based analysis to study the roles of noncoding RNAs in the pathogenesis of intrahepatic cholangiocellular carcinoma.

To explore and understand the competitive mechanism of ceRNAs in intrahepatic cholangiocarcinoma (ICC), we used bioinformatics analysis methods to construct an ICC-related ceRNA regulatory network (ceRNET), which contained 340 lncRNA-miRNA-mRNA regulatory relationships based on the RNA expression datasets in the NCBI GEO database. We identified the core regulatory pathway RP11-328K4.1-hsa-miR-27a-3p-PROS1, which is related to ICC, for further validation by molecular biology assays. GO analysis of 44 differentially expressed mRNAs in ceRNET revealed that they were mainly enriched in biological processes including “negative regulation of epithelial cell proliferation” and "positive regulation of activated T lymphocyte proliferation.” KEGG analysis showed that they were mainly enriched in the “complement and coagulation cascade” pathway. The molecular biology assay showed that lncRNA RP11-328K4.1 expression was significantly lower in the cancerous tissues and peripheral plasma of ICC patients than in normal controls (p<0.05). In addition, hsa-miR-27a-3p was found to be significantly upregulated in the cancer tissues and peripheral plasma of ICC patients (p<0.05). Compared to normal controls, the expression of PROS1 mRNA was significantly downregulated in ICC patient cancer tissues (p<0.05) but not in peripheral plasma (p>0.05). Furthermore, ROC analysis revealed that RP11-328K4.1, hsa-miR-27a-3p, and PROS1 had significant diagnostic value in ICC. We concluded that the upregulation of lncRNA RP11-328K4.1, which might act as a miRNA sponge, exerts an antitumor effect in ICC by eliminating the inhibition of PROS1 mRNA expression by oncogenic miRNA hsa-miR-27a.

Abstract 5084: Characterizing heterogeneity in the cancer-associated fibroblast population in non-small cell lung cancer: Relating phenotype to function

Abstract The aim of this work is to examine the heterogeneity in the cancer-associated fibroblast (CAF) population in non-small cell lung cancer through single-cell RNA sequencing. Fresh primary lung tissue was obtained directly from surgery, and the disaggregation process optimised to extract the highest number of fibroblasts (using collagenase P for sixty minutes). Single-cell RNA sequencing was performed using a droplet-barcoded sequencing (Drop-seq) platform. Quality control was performed on the raw sequencing data and the resulting digital gene expression matrix. Initial bioinformatic analysis, including cluster identification, was performed using the Seurat package in R. Subsequent cell type identification and gene set enrichment analysis were carried out with the ToppFun tool and GSEA program respectively. Correlations between the presence of fibroblast subtypes and clinical parameters were analysed using CIBERSORT. Our preliminary analysis of 11 non-small cell lung cancer (NSCLC) tumors and 5 samples of matched non-involved lung revealed the presence of 6 discrete CAF subtypes with differential prognostic impact. Four of the subgroups showed transcriptomic overlap with normal fibroblasts. Of the distinct CAF subtypes, one showed higher expression of genes normally associated with the ‘myofibroblastic' CAF phenotype, including multiple collagens, and was enriched for genes associated with the ‘extracellular structure organisation' gene ontology (GO) term. The second CAF cluster showed higher expression of genes encoding growth factors and regulators of cell growth, with enrichment of genes in the ‘regulation of epithelial cell proliferation' and ‘negative regulation of cell death' GO terms. The remaining four subtypes also showed enrichment of genes in keeping with previously-described fibroblast functions: two subtypes were enriched for genes associated with tissue remodelling, including in the ‘regulation of proteolysis' and ‘regulation of peptidase activity' GO terms. The fifth and sixth clusters showed enrichment for genes in the ‘innate immune response' and ‘angiogenesis' GO terms, respectively. Despite their abundance in most solid cancers, CAF remain a poorly characterised cell population. No single molecular marker identifies all CAF, and it is not yet clear whether different CAF phenotypes exist or whether such subgroups have different functions. Our analysis has identified six discrete CAF subtypes in NSCLC. These subtypes have differential gene set enrichment, suggestive of functional differences. In keeping with this, we found that the CAF subgroups differentially impact on patient prognosis. Identification of CAF subgroups associated with aggressive tumor progression may facilitate the development of more specific stromal targeting strategies. Citation Format: Sara Waise, Christopher Hanley, Rachel Parker, Matthew Rose-Zerilli, Christian Ottensmeier, Gareth Thomas. Characterizing heterogeneity in the cancer-associated fibroblast population in non-small cell lung cancer: Relating phenotype to function [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5084.

Regulation of Epithelial Cell Proliferation, Differentiation, and Plasticity by Grainyhead-Like 2 During Oral Carcinogenesis.

Grainyhead-Like 2 (GRHL2) was originally described as one of the three mammalian isoforms with sequence homology to Grainyhead (GRH) in Drosophila, which determines the cuticle formation in fruit flies. Earlier studies characterized GRHL2 as an epithelial-specific transcription factor that regulates epithelial morphogenesis and differentiation. Using a high-throughput proteomic approach, we discovered GRHL2 as a novel trans-regulator of the hTERT gene, which codes for the catalytic subunit of the human telomerase. GRHL2 was found to be necessary and sufficient for hTERT expression and telomerase activity in human oral squamous cell carcinomas (OSCCs) and in primary normal human keratinocytes. Subsequently, we found numerous other direct transcription targets of GRHL2, including p63, microRNA (miR)-200 family genes, FoxM1, and epidermal differentiation complex (EDC) genes. These target molecules mediate the phenotypic effects of GRHL2 on epithelial cell proliferation, differentiation, and epithelial plasticity. The pro-carcinogenic role of GRHL2 was implicated by its aberrant overexpression in OSCC cells and tissues, although several other studies also suggested the tumor suppressive effects of GRHL2. Using the novel Grhl2 cKO model, we recently reported the first genetic study in which Grhl2 knockout completely abolished oral carcinogenesis induced by a potent carcinogen, 4-nitroquinoline N-oxide (NQO). In this review, we discuss the mechanistic insights underlying the phenotypic effects of GRHL2 on epithelial cell proliferation and differentiation, as well as possibly mechanisms by which GRHL2 may promote oral carcinogenesis.

Bioinformatics analysis of fibroblasts exposed to TGF‑β at the early proliferation phase of wound repair.

The aim of the current study was to identify gene signatures during the early proliferation stage of wound repair and the effect of TGF-β on fibroblasts and reveal their potential mechanisms. The gene expression profiles of GSE79621 and GSE27165 were obtained from GEO database. Differentially expressed genes (DEGs) were identified using Morpheus and co-expressed DEGs were selected using Venn Diagram. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Protein-protein interaction (PPI) networks of the DEGs were constructed using Cytoscape software. PPI interaction network was divided into subnetworks using the MCODE algorithm and the function of the top one module was analyzed using DAVID. The results revealed that upregulated DEGs were significantly enriched in biological process, including the Arp2/3 complex-mediated actin nucleation, positive regulation of hyaluronan cable assembly, purine nucleobase biosynthetic process, de novo inosine monophosphate biosynthetic process, positive regulation of epithelial cell proliferation, whereas the downregulated DEGs were enriched in the regulation of blood pressure, negative regulation of cell proliferation, ossification, negative regulation of gene expression and type I interferon signaling pathway. KEGG pathway analysis showed that the upregulated DEGs were enriched in shigellosis, pathogenic Escherichia coli infection, the mitogen-activated protein kinase signaling pathway, Ras signaling pathway and bacterial invasion of epithelial cells. The downregulated DEGs were enriched in systemic lupus erythematosus, lysosome, arachidonic acid metabolism, thyroid cancer and allograft rejection. The top 10 hub genes were identified from the PPI network. The top module analysis revealed that the included genes were involved in ion channel, neuroactive ligand-receptor interaction pathway, purine metabolism and intestinal immune network for IgA production pathway. The functional analysis revealed that TGF-β may promote fibroblast migration and proliferation and defend against microorganisms at the early proliferation stage of wound repair. Furthermore, these results may provide references for chronic wound repair.

Meta-analysis of miRNA expression profiles for prostate cancer recurrence following radical prostatectomy.

BackgroundProstate cancer (PCa) is a leading reason of death in men and the most diagnosed malignancies in the western countries at the present time. After radical prostatectomy (RP), nearly 30% of men develop clinical recurrence with high serum prostate-specific antigen levels. An important challenge in PCa research is to identify effective predictors of tumor recurrence. The molecular alterations in microRNAs are associated with PCa initiation and progression. Several miRNA microarray studies have been conducted in recurrence PCa, but the results vary among different studies.MethodsWe conducted a meta-analysis of 6 available miRNA expression datasets to identify a panel of co-deregulated miRNA genes and overlapping biological processes. The meta-analysis was performed using the ‘MetaDE’ package, based on combined P-value approaches (adaptive weight and Fisher's methods), in R version 3.3.1.ResultsMeta-analysis of six miRNA datasets revealed miR-125A, miR-199A-3P, miR-28-5P, miR-301B, miR-324-5P, miR-361-5P, miR-363*, miR-449A, miR-484, miR-498, miR-579, miR-637, miR-720, miR-874 and miR-98 are commonly upregulated miRNA genes, while miR-1, miR-133A, miR-133B, miR-137, miR-221, miR-340, miR-370, miR-449B, miR-489, miR-492, miR-496, miR-541, miR-572, miR-583, miR-606, miR-624, miR-636, miR-639, miR-661, miR-760, miR-890, and miR-939 are commonly downregulated miRNA genes in recurrent PCa samples in comparison to non-recurrent PCa samples. The network-based analysis showed that some of these miRNAs have an established prognostic significance in other cancers and can be actively involved in tumor growth. Gene ontology enrichment revealed many target genes of co-deregulated miRNAs are involved in “regulation of epithelial cell proliferation” and “tissue morphogenesis”. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that these miRNAs regulate cancer pathways. The PPI hub proteins analysis identified CTNNB1 as the most highly ranked hub protein. Besides, common pathway analysis showed that TCF3, MAX, MYC, CYP26A1, and SREBF1 significantly interact with those DE miRNA genes. The identified genes have been known as tumor suppressors and biomarkers which are closely related to several cancer types, such as colorectal cancer, breast cancer, PCa, gastric, and hepatocellular carcinomas. Additionally, it was shown that the combination of DE miRNAs can assist in the more specific detection of the PCa and prediction of biochemical recurrence (BCR).ConclusionWe found that the identified miRNAs through meta-analysis are candidate predictive markers for recurrent PCa after radical prostatectomy.

Abstract MIP-061: RAC 1 AND CDC42 GTPASES AS REGULATORS OF OVARIAN CANCER PROGRESSION AND NICHE INTERACTIONS

Abstract PURPOSE OF THE STUDY: The Ras-homologous (Rho) family GTPases Rac1 and Cdc42 contribute to metastatic dissemination through regulation of actin reorganization, cell motility, cell-cell and cell-extracellular matrix adhesion. The purpose of the study was to investigate the contributions of these GTPases in ovarian cancer progression. EXPERIMENTAL PROCEDURES: GTPase target expression and activity was determined by analysis of The Cancer Genome Atlas (TCGA), immunohistochemistry of ovarian cancer tissues and enzymatic assays of patient samples. The effects Rac1 and Cdc42 expression were investigated by comparing cell behaviors in vitro and in vivo in engineered cell lines and use of inhibitors of Rac1, Cdc42 or dual inhibition by the R-enantiomer of ketorolac. SUMMARY OF THE DATA: Expression of the constitutively active Rac1 splice variant Rac1b and elevation of Cdc42 protein were detected in advanced ovarian cancer specimens thus providing the first evidence for dysregulation of these GTPase targets in ovarian cancer. To confirm the importance of Rac1, RNA-seq gene expression data from 305 Stage III or IV ovarian cancer samples were downloaded from The Cancer Genome Atlas (TCGA) and evaluated for RAC1 gene expression. The samples with the highest Rac1 RNA levels had significantly worse (p=0.039) age adjusted survival than the patients with the lowest Rac1 levels. Additional analyses identified more than 4,000 genes that were differentially expressed (FDR corrected p &amp;lt;0.05) between these patient groups. Gene Ontology analysis revealed several highly enriched biological processes including: extracellular matrix organization (67 genes p=1.60E-25), multicellular organismal catabolic processes (29 genes p=4.30E-22), regulation of epithelial cell proliferation (30 genes p=6.10E-09 and regulation of cell migration (48 genes p=1.50E-08). Relevance of the pathway analyses is illustrated by experimental evidence that increased GTPase expression leads to enhanced homing and engraftment in the omental niche; suggesting that elevated activity detected in patients may contribute to disease progression. Conversely, dual inhibition of Rac1 and Cdc42 activity by R-ketorolac inhibits ovarian patient-derived tumor cell adhesion and invasion, omental homing and tumor implantation in a mouse xenograft model. CONCLUSIONS: These findings indicate that high expression of Rac1 is associated with late stage disease and/or poor patient survival and with genes involved in extracellular matrix, cell proliferation and cell migration. These functions of Rac1 were confirmed in experimental models and inhibition of protein activity provided anti-tumor benefit in vivo. Together, these data suggest that Rac1 and/or Cdc42 function as drivers of ovarian cancer and may represent novel therapeutic targets to improve ovarian cancer outcome. Citation Format: Hudson LG, Kenney SR, Rivera, M., Weisend, J. Luo, L., Ness, S., Gillette, JM, Wandinger-Ness A. RAC 1 AND CDC42 GTPASES AS REGULATORS OF OVARIAN CANCER PROGRESSION AND NICHE INTERACTIONS [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr MIP-061.