Holistic exploration of CHGA and hsa-miR-137 in colorectal cancer via multi-omic data Integration.

Colorectal cancer (CRC) ranks among the most widespread malignancies globally, with early detection significantly influencing prognosis. Employing a systems biology approach, we aimed to unravel the intricate mRNA-miRNA network linked to CRC pathogenesis, potentially yielding diagnostic biomarkers. Through an integrative analysis of microarray, Bulk RNA-seq, and single-cell RNA-seq data, we explored CRC-related transcriptomes comprehensively. Differential gene expression analysis uncovered crucial genes, while Weighted Gene Co-expression Network Analysis (WGCNA) identified key modules closely linked to CRC. Remarkably, CRC manifested its strongest correlation with the turquoise module, signifying its pivotal role. From the cohort of genes showing high Gene Significance (GS) and Module Membership (MM), and Differential Expression Genes (DEGs), we highlighted the downregulated Chromogranin A (CHGA) as a notable hub gene in CRC. This finding was corroborated by the Human Protein Atlas database, which illustrated decreased CHGA expression in CRC tissues. Additionally, CHGA displayed elevated expression in primary versus metastatic cell lines, as evidenced by the CCLE database. Subsequent RT-qPCR validation substantiated the marked downregulation of CHGA in CRC tissues, reinforcing the significance of our differential expression analysis. Analyzing the Space-Time Gut Cell Atlas dataset underscored specific CHGA expression in epithelial cell subclusters, a trend persisting across developmental stages. Furthermore, our scrutiny of colon and small intestine Enteroendocrine cells uncovered distinct CHGA expression patterns, accentuating its role in CRC pathogenesis. Utilizing the WGCNA algorithm and TargetScan database, we validated the downregulation of hsa-miR-137 in CRC, and integrated assessment highlighted its interplay with CHGA. Our findings advocate hsa-miR-137 and CHGA as promising CRC biomarkers, offering valuable insights into diagnosis and prognosis. Despite proteomic analysis yielding no direct correlation, our multifaceted approach contributes comprehensive understanding of CRC's intricate regulatory mechanisms. In conclusion, this study advances hsa-miR-137 and CHGA as promising CRC biomarkers through an integrated analysis of diverse datasets and network interactions.

Tumor-infiltrating CD8+ sub-populations in primary and recurrent glioblastoma: An in-silico study.

Background: Glioblastoma multiforme (GBM) remains an incurable primary brain tumor. CD8+ tumor-infiltrating lymphocytes (TILs) can target malignant cells; however, their anti-tumoral immune responses mostly do not lead to GBM rejection in GBM patients. We profiled the sub-populations of tumor-infiltrating CD8+ T-cells, i.e., naïve, cytotoxic, and exhausted cells, in primary and recurrent GBM tissues and provided a blueprint for future precision-based GBM immunotherapy. Method: We re-analyzed the raw data of single-cell RNA sequencing on the cells residing in the GBM microenvironment and leveraged tumor bulk RNA analyses to study the significance of CD8+ TILs sub-populations in primary and recurrent GBM. We investigated cell-cell interaction between exhausted CD8+ TILs and other immune cells residing in the primary and recurrent GBM microenvironments and profiled the expression changes following CD8+ TILs' transition from primary GBM to recurrent GBM. Results: Exhausted CD8+ TILs are the majority of CD8+ TILs sub-populations in primary and recurrent GBM, and cytotoxic CD8+ TILs display decreased expression of inhibitory immune checkpoint (IC) molecules in the primary and recurrent GBM. In the primary and recurrent GBM microenvironment, exhausted CD8+ TILs interact most with tumor-infiltrating dendritic cells. Conclusion: This study demonstrates the profiles of CD8+ TILs sub-populations in primary and recurrent GBM and provides a proof-of-concept for future precision-based GBM immunotherapy.

Deciphering the immune landscape of head and neck squamous cell carcinoma: A single-cell transcriptomic analysis of regulatory T cell responses to PD-1 blockade therapy.

Immunotherapy is changing the Head and Neck Squamous Cell Carcinoma (HNSCC) landscape and improving outcomes for patients with recurrent or metastatic HNSCC. A deeper understanding of the tumor microenvironment (TME) is required in light of the limitations of patients' responses to immunotherapy. Here, we aimed to examine how Nivolumab affects infiltrating Tregs in the HNSCC TME. We used single-cell RNA sequencing data from eight tissues isolated from four HNSCC donors before and after Nivolumab treatment. Interestingly, the study found that Treg counts and suppressive activity increased following Nivolumab therapy. We also discovered that changes in the CD44-SSP1 axis, NKG2C/D-HLA-E axis, and KRAS signaling may have contributed to the increase in Treg numbers. Furthermore, our study suggests that decreasing the activity of the KRAS and Notch signaling pathways, and increasing FOXP3, CTLA-4, LAG-3, and GZMA expression, may be mechanisms that enhance the killing and suppressive capacity of Tregs. Additionally, the result of pseudo-temporal analysis of the HNSCC TME indicated that after Nivolumab therapy, the expression of certain inhibitory immune checkpoints including TIGIT, ENTPD1, and CD276 and LY9, were decreased in Tregs, while LAG-3 showed an increased expression level. The study also found that Tregs had a dense communication network with cluster two, and that certain ligand-receptor pairs, including SPP1/CD44, HLA-E/KLRC2, HLA-E/KLRK1, ANXA1/FPR3, and CXCL9/FCGR2A, had notable changes after the therapy. These changes in gene expression and cell interactions may have implications for the role of Tregs in the TME and in response to Nivolumab therapy.

Characterization of Wnt signaling pathway under treatment of Lactobacillus acidophilus postbiotic in colorectal cancer using an integrated in silico and in vitro analysis.

Colorectal cancer (CRC) is a prevalent and life-threatening cancer closely associated with the gut microbiota. Probiotics, as a vital microbiota group, interact with the host's colonic epithelia and immune cells by releasing a diverse range of metabolites named postbiotics. The present study examined the effects of postbiotics on CRC's prominent differentially expressed genes (DEGs) using in silico and in vitro analysis. Through single-cell RNA sequencing (scRNA-seq), we identified four DEGs in CRC, including secreted frizzled-related protein 1 (SFRP1), secreted frizzled-related protein 2 (SFRP2), secreted frizzled-related protein 4 (SFRP4), and matrix metallopeptidase 7 (MMP7). Enrichment analysis and ExpiMap, a novel deep learning-based method, determined that these DEGs are involved in the Wnt signaling pathway as a primary cascade in CRC. Also, spatial transcriptome analysis showed specific expression patterns of the SFRP2 gene in fibroblast cell type. The expression of selected DEGs was confirmed on CRC and normal adjacent tissues using Real-Time quantitative PCR (RT-qPCR). Moreover, we examined the effects of postbiotics extracted from Lactobacillus acidophilus (L. acidophilus) on the proliferation, migration, and cell cycle distribution of HT-29 cells using MTT, scratch, and flow cytometry assays. Our results showed that L. acidophilus postbiotics induce cell cycle arrest at G1 phase and also had anti-proliferative and anti-migration effects on HT-29 cells, while it did not exert anti-proliferative activity on control fibroblasts. Finally, we revealed that treating HT-29 cells with postbiotics can affect the expression of selected DEGs. We suggested that L. acidophilus postbiotics have therapeutic potential in CRC by modulating key genes in the Wnt pathway.

Putative role of glial cells in treatment resistance depression: An updated critical literation review and evaluation of single-nuclei transcriptomics data.

AIMS: Major depressive disorder (MDD) is a prevalent global mental illness with diverse underlying causes. Despite the availability of first-line antidepressants, approximately 10-30 % of MDD patients do not respond to these medications, falling into the category of treatment-resistant depression (TRD). Our study aimed to elucidate the precise molecular mechanisms through which glial cells contribute to depression-like episodes in TRD. MATERIALS AND METHODS: We conducted a comprehensive literature search using the PubMed and Scopus electronic databases with search terms carefully selected to be specific to our topic. We strictly followed inclusion and exclusion criteria during the article selection process, adhering to PRISMA guidelines. Additionally, we carried out an in-depth analysis of postmortem brain tissue obtained from patients with TRD using single-nucleus transcriptomics (sn-RNAseq). KEY FINDINGS: Our data confirmed the involvement of multiple glia-specific markers (25 genes) associated with TRD. These differentially expressed genes (DEGs) primarily regulate cytokine signaling, and they are enriched in important pathways such as NFκB and TNF-α. Notably, DEGs showed significant interactions with the transcription factor CREB1. sn-RNAseq analysis confirmed dysregulation of nearly all designated DEGs; however, only Cx30/43, AQP4, S100ß, and TNF-αR1 were significantly downregulated in oligodendrocytes (OLGs) of TRD patients. With further exploration, we identified the GLT-1 in OLGs as a hub gene involved in TRD. SIGNIFICANCE: Our findings suggest that glial dysregulation may hinder the effectiveness of existing therapies for TRD. By targeting specific glial-based genes, we could develop novel interventions with minimal adverse side effects, providing new hope for TRD patients who currently experience limited benefits from invasive treatments.

The expression pattern of VISTA in the PBMCs of relapsing-remitting multiple sclerosis patients: A single-cell RNA sequencing-based study.

Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS). Dysregulated immune responses have been implicated in MS development. Growing evidence has indicated that inhibitory immune checkpoint molecules can substantially regulate immune responses and maintain immune tolerance. V-domain Ig suppressor of T cell activation (VISTA) is a novel inhibitory immune checkpoint molecule that can suppress immune responses; however, its expression pattern in the peripheral blood mononuclear cells (PBMCs) of relapsing-remitting multiple sclerosis (RRMS) has not thoroughly been studied. Herein, we evaluated Vsir expression in PBMCs of RRMS patients and characterized the expression pattern of the Vsir in the PBMCs of MS patients. Besides, we investigated the effect of fingolimod, IFNß-1α, glatiramer acetate (GA), and dimethyl fumarate (DMF) on Vsir expression in PBMCs of RRMS patients. Our results have shown that Vsir expression is significantly downregulated in the PBMCs of patients with RRMS. Besides, the single-cell RNA sequencing results have demonstrated that Vsir expression is downregulated in classical monocyte, intermediate monocytes, non-classical monocytes, myeloid DCs (mDC), Plasmacytoid dendritic cells (pDCs), and naive B-cells of PBMCs of MS patients compared to the control. In addition, DMF, IFNß-1α, and GA have significantly upregulated Vsir expression in the PBMCs of RRMS patients. Collectively, the current study has shed light on Vsir expression in the PBMCs of MS patients; however, further studies are needed to elucidate the significance of VISTA in the mentioned immune cells.