Identification of the Dysregulated Pathways and Key Gene in Prostate Cancer by Transcriptome Analysis and Cell Biology Experiments

Background: Prostate cancer (PCa) is a common cancer in elderly men with the first increasing new cases and the second leading cause of cancer death, but the molecular mechanisms underlying the pathogenesis of prostate cancer remain unclear. Methods: Here we mainly used Weight gene co-expression network analysis (WGCNA), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein to protein interaction (PPI), gene set enrichment analysis (GSEA) and cell biology experiments to analyze prostate cancer data in GEO and The Cancer Genome Atlas (TCGA) databases and revealed the main dysregulated pathways and key genes in prostate carcinogenesis. Results: We found that the focal adhesion pathway was the main pathway in PCa. FERMT2 was shown to be the key gene for prostate tumorigenesis both in GSE6919 and TCGA datasets. By using WGCNA and GSEA analysis, we found that FERMT2 was related to the focal adhesion pathway and the ECM interaction pathway. Cell biology experiments demonstrated that FERMT2 inhibited tumor cell proliferation and migration. Conclusion: Our findings revel that downregulation of FERMT2 and the focal adhesion pathway are the main characteristics of PCa and FERMT2 might be the potential biomarker or treatment target for PCa.Trial registration: The study is not a clinical trial.

Transcriptome analysis to identify the downstream genes of androgen receptor in dermal papilla cells

Background Testosterone signaling mediates various diseases, such as androgenetic alopecia and prostate cancer. Testosterone signaling is mediated by the androgen receptor (AR). In this study, we fortuitously found that primary and immortalized dermal papilla cells suppressed AR expression, although dermal papilla cells express AR in vivo. To analyze the AR signaling pathway, we exogenously introduced the AR gene via a retrovirus into immortalized dermal papilla cells and comprehensively compared their expression profiles with and without AR expression. Results Whole-transcriptome profiling revealed that the focal adhesion pathway was mainly affected by the activation of AR signaling. In particular, we found that caveolin-1 gene expression was downregulated in AR-expressing cells, suggesting that caveolin-1 is controlled by AR. Conclusion Our whole transcriptome data is critical resources for discovery of new therapeutic targets for testosterone-related diseases.

Baicalein Inhibits Metastatic Phenotypes in Nasopharyngeal Carcinoma Cells via a Focal Adhesion Protein Integrin β8

Baicalein, a prominent flavonoid from the indigenous herbal plant Scutellaria baicalensis Georgi, possesses broad-spectrum anticancer activities. However, the biological effects of baicalein on nasopharyngeal carcinoma (NPC) and its underlying mechanisms remain unclarified. Thus, in this study, we examined the effects of baicalein on NPC cell lines and investigated the corresponding molecular mechanism through transcriptome profiling. In the study, four NPC cell lines were treated with various concentrations of baicalein at different time points. Cellular toxicity and proliferative inhibition of baicalein were examined by MTT assay. Metastatic phenotypes of NPC cells were investigated by wound healing, transwell, and adhesion assays. Additionally, microarray experiments were performed to determine the cellular pathways affected by baicalein. The expression and localization of the integrin β8 were validated by western immunoblotting and immunofluorescence. Our results revealed that baicalein exhibited its cytotoxicity and antiproliferative activity on all tested NPC cell lines. It also significantly inhibited metastatic phenotypes at sub-lethal concentrations. Transcriptomic analysis showed that baicalein significantly affected the focal adhesion pathway in NPC, where integrin β8 was greatly diminished. Thus, the present study results suggested that baicalein inhibits the metastatic phenotypes of NPC cells by modulating integrin β8, one of the major molecules in a focal adhesion pathway.

LKB1 Regulates Goat Intramuscular Adipogenesis Through Focal Adhesion Pathway

Intramuscular fat (IMF) deposition is one of the most important factors to affect meat quality in livestock and induce insulin resistance and adverse metabolic phenotypes for humans. However, the key regulators involved in this process remain largely unknown. Although liver kinase B1 (LKB1) was reported to participate in the development of skeletal muscles and classical adipose tissues. Due to the specific autonomic location of intramuscular adipocytes, deposited between or within muscle bundles, the exact roles of LKB1 in IMF deposition need further verified. Here, we cloned the goat LKB1 coding sequence with 1,317 bp, encoding a 438 amino acid peptide. LKB1 was extensively expressed in detected tissues and displayed a trend from decline to rise during intramuscular adipogenesis. Functionally, knockdown of LKB1 by two individual siRNAs enhanced the intramuscular preadipocytes differentiation, accompanied by promoting lipid accumulation and inducing adipogenic transcriptional factors and triglyceride synthesis-related genes expression. Conversely, overexpression of LKB1 restrained these biological signatures. To further explore the mechanisms, the RNA-seq technique was performed to compare the difference between siLKB1 and the control group. There were 1,043 differential expression genes (DEGs) were screened, i.e., 425 upregulated genes and 618 downregulated genes in the siLKB1 group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis predicted that the DEGs were mainly enriched in the focal adhesion pathway and its classical downstream signal, the PI3K-Akt signaling pathway. Specifically, knockdown of LKB1 increased the mRNA level of focal adhesion kinase (FAK) and vice versa in LKB1-overexpressed cells, a key component of the activated focal adhesion pathway. Convincingly, blocking this pathway by a specific FAK inhibitor (PF573228) rescued the observed phenotypes in LKB1 knockdown adipocytes. In conclusion, LKB1 inhibited goat intramuscular adipogenesis through the focal adhesion pathway. This work expanded the genetic regulator networks of IMF deposition and provided theoretical support for improving human health and meat quality from the aspect of IMF deposition.

Microbial and Molecular Differences According To The Location of Head and Neck Cancers

Background Microbiome has been shown to substantially contribute to some cancers. However, the diagnostic implications of microbiome in head and neck squamous cell carcinoma (HNSCC) remain unknown. Here, we report for the first time, the molecular difference in the microbiome of oral and non-oral HNSCC. Methods Primary data was downloaded from the Kraken-TCGA dataset. The molecular differences in the microbiome of oral and non-oral HNSCC were identified using the linear discriminant analysis effect size method. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUST) and ANOVA-like differential expression (ALDEx2), we predicted bacterial metabolic contributions of oral rich and non-oral rich bacteria, common rich bacteria in two groups and their pathways. A Correlation analysis was performed between RNA expression data and common bacteria data and protein-protein interaction (PPI) analysis was performed using correlated genes. Finally, to find out unique microbial signatures, we performed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene ontology (GO) analysis using the PPI results. Results The common microbiomes in oral and non-oral cancers were Fusobacterium, Treponema, and Selenomonas and Clostridium and Massilia, respectively. We found unique microbial signatures that positively and negatively correlated with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in oral cancer and negatively correlated KEGG pathways in non-oral cancer. In oral cancer, positively correlated genes were mostly found in bacterial infection pathways, while negative correlated genes were involved in HTLV-I infection, signal transduction, cell adhesion, and cancer-associated pathway. In non-oral cancer, positively correlated genes did not show any significant results, and negatively correlated genes showed results from focal adhesion pathway and regulation of actin cytoskeleton pathway. Conclusions These results could help in understanding the underlying biological mechanisms of the microbiome of oral and non-oral HNSCC. Microbiome-based oncology diagnostic tool warrants further exploration.

Transcriptome Analysis Revealed Potential Mechanisms of Resistance to Trichomoniasis gallinae Infection in Pigeon (Columba livia)

Trichomoniasis gallinae (T. gallinae) is one of the most pathogenic parasites in pigeon, particularly in squabs. Oral cavity is the main site for the host-parasite interaction. Herein, we used RNA-sequencing technology to characterize lncRNA and mRNA profiles and compared transcriptomic dynamics of squabs, including four susceptible birds (S) from infected group, four tolerant birds (T) without parasites after T. gallinae infection, and three birds from uninfected group (N), to understand molecular mechanisms underlying host resistance to this parasite. We identified 29,809 putative lncRNAs and characterized their genomic features subsequently. Differentially expressed (DE) genes, DE-lncRNAs and cis/trans target genes of DE-lncRNAs were further compared among the three groups. The KEGG analysis indicated that specific intergroup DEGs were involved in carbon metabolism (S vs. T), metabolic pathways (N vs. T) and focal adhesion pathway (N vs. S), respectively. Whereas, the cis/trans genes of DE-lncRNAs were enriched in cytokine-cytokine receptor interaction, toll-like receptor signaling pathway, p53 signaling pathway and insulin signaling pathway, which play crucial roles in immune system of the host animal. This suggests T. gallinae invasion in pigeon mouth may modulate lncRNAs expression and their target genes. Moreover, co-expression analysis identified crucial lncRNA-mRNA interaction networks. Several DE-lncRNAs including MSTRG.82272.3, MSTRG.114849.42, MSTRG.39405.36, MSTRG.3338.5, and MSTRG.105872.2 targeted methylation and immune-related genes, such as JCHAIN, IL18BP, ANGPT1, TMRT10C, SAMD9L, and SOCS3. This implied that DE-lncRNAs exert critical influence on T. gallinae infections. The quantitative exploration of host transcriptome changes induced by T. gallinae infection broaden both transcriptomic and epigenetic insights into T. gallinae resistance and its pathological mechanism.

Identification of Potential Crucial Immune-related Genes and Key Pathways in Oral Lichen Planus

Oral lichen planus (OLP) is a chronic autoimmune oral mucosal disease which seriously affect the life quality of the patients. But till now, the exact etiology and pathogenesis of OLP still remains unclear. The aim of our study was to find the key molecules and pathway involved in the pathogenesis mechanisms of OLP, therefore, provide reference for identifying more effective therapeutic strategies for OLP. Data from GSE52130 were downloaded from GEO data sets for analysis, and a total of 255 differentially expressed genes were selected out. Then by means of a series of gene enrichment analysis, we illustrated that most of these important genes were enriched in the focal adhesion pathway and metabolism pathways. In addition, we also constructed a protein-protein interaction (PPI) network and identified 8 hub genes which may play the important role in the development of OLP, including THBS2, COL3A1, IGFBP3, COL1A2, COL1A1, PTGS2, IL1B, ARG1. Lastly, we also predicted transcription factors of these hub genes, then constructed the corresponding transcription regulatory network. Taken together, our data indicated that the focal adhesion pathway and metabolism pathways, as well as 8 crucial immune-related genes might be most likely involved in the development of OLP, which would provide important information and objective basis for elucidating the pathogenesis of OLP and providing more effective targeted immunotherapy strategies for OLP.

DCBLD2 Affects the Development of Colorectal Cancer via EMT and Angiogenesis and Modulates 5-FU Drug Resistance

Background: DCBLD2 is highly expressed in various cancers, including colorectal cancer. DCBLD2 overexpression promotes tumor occurrence, development, and metastasis. However, DCBLD2 sensitivity to chemotherapy drugs and its mechanism on tumor development are unknown.Methods: DCBLD2 expression differences in cancer and normal tissues were obtained from GEO and TCGA databases. DCBLD2 influence on prognosis was also compared, and the database analysis results were verified via the analysis of clinical samples. GDSC database was used to analyze the effect of DCBLD2 expression difference on 5-FU drug sensitivity on tumor cells. CCK-8, clone formation, scratch, Transwell invasion and migration assays were used to assess DCBLD2 effects on the proliferation, metastasis, and 5-FU drug sensitivity on HCT116 and Caco-2 colorectal cancer cells. Angiogenesis and Matrigel plug assays were used to study the effect of DCBLD2 on angiogenesis. Q-RCR and Western Blot were used to analyze DCBLD2 impact on the EMT signaling pathway, and TAP-MS assay with Co-IP verification was used to identify the downstream target proteins binding to DCBLD2.Results: Both database and clinical sample validation results showed that the expression of DCBLD2 in colorectal cancer tissues was significantly higher than that in normal tissues, leading to poor prognosis of patients. GDSC database analysis showed that DCBLD2 overexpression caused tumor cell resistance to 5-FU. The results of in vitro and in vivo experiments showed that the inhibition of DCBLD2 reduced the proliferation, migration and invasion of colorectal cancer cells, inhibited the angiogenesis of endothelial cells, and enhanced the drug sensitivity to 5-FU. The results of q-RCR and Western Blot experiments showed that the inhibition of DCBLD2 can suppress the EMT signal. The results of TAP-MS assay showed that the proteins bound to DCBLD2 were enriched to the Focal adhesion pathway. The results of Co-IP assay show that DCBLD2 can combine with ITGB1, the key factor of Focal adhesion pathway.Conclusion: DCBLD2 may affect the development of colorectal cancer by regulating cell proliferation and motility, and modulate 5-FU resistance. Down-regulation of DCBLD2 can inhibit EMT signal and angiogenesis. DCBLD2 can combine with ITGB1, the key signal factor of the Focal adhesion pathway.

IRF8 Is an AML-Specific Susceptibility Factor That Regulates Signaling Pathways and Proliferation of AML Cells

Personalized treatment of acute myeloid leukemia (AML) that target individual aberrations strongly improved the survival of AML patients. However, AML is still one of the most lethal cancer diseases of the 21st century, demonstrating the need to find novel drug targets and to explore alternative treatment strategies. Upon investigation of public perturbation data, we identified the transcription factor IRF8 as a novel AML-specific susceptibility gene in humans. IRF8 is upregulated in a subset of AML cells and its deletion leads to impaired proliferation in those cells. Consistently, high IRF8 expression is associated with poorer patients’ prognoses. Combining gene expression changes upon IRF8 deletion and the genome-wide localization of IRF8 in the AML cell line MV4-11, we demonstrate that IRF8 directly regulates key signaling molecules, such as the kinases SRC and FAK, the transcription factors RUNX1 and IRF5, and the cell cycle regulator Cyclin D1. IRF8 loss impairs AML-driving signaling pathways, including the WNT, Chemokine, and VEGF signaling pathways. Additionally, many members of the focal adhesion pathway showed reduced expression, providing a putative link between high IRF8 expression and poor prognosis. Thus, this study suggests that IRF8 could serve as a biomarker and potential molecular target in a subset of human AMLs.