GS-168 / Gene Signal - LARVOL DELTA

Lumican is a potential predictor on the efficacy of concurrent chemoradiotherapy in cervical squamous cell carcinoma. (PubMed, Heliyon) - "Gene expression datasets GSE56363, GSE5787, and GSE168009 were analyzed to identify candidate genes to predict the efficacy of CCRT in CESC...Gene Set Enrichment Analysis (GSEA) revealed that possible mechanisms underlying resistance to CCRT might involve the PARs and IL1 signaling pathway affecting the immune landscape. High LUM expression is correlated with poor efficacy in CESC patients receiving CCRT, possibly through the PARs and IL1 signaling pathway affecting the immune landscape."

Journal • Cervical Cancer • Oncology • Squamous Cell Carcinoma • LUM

A novel DNA damage repair-related gene signature predicting survival, immune infiltration and drug sensitivity in cervical cancer based on single cell sequencing. (PubMed, Front Immunol) - "Differentially expressed genes were identified between high and low DDR groups of cells from the single-cell RNA sequencing dataset GSE168652 based on DDR scores...The high DDR group exhibited poorer prognosis, weaker immune cell infiltration in the immune microenvironment, lower expression of immune checkpoint-related genes, lower gene mutation frequencies and more sensitivity to drugs such as BI.2536, Bleomycin and etc. ITGB1, ZC3H13, and TOMM20 were expressed at higher levels in CaSki and HeLa cells compared to ECT1 cells...The 7 DDR-related gene signature was an independent and powerful prognostic biomarker that might effectively evaluate the prognosis of CC and provide supplementary information for a more personalized evaluation and precision therapy. ITGB1 was a potential candidate gene that may affect the DDR capacity of CC cells, and its mechanism of action was worth further in-depth study."

Gene Signature • Journal • Cervical Cancer • Immune Modulation • Oncology • Solid Tumor • ITGB1

N6AMT1 is a novel potential diagnostic, prognostic and immunotherapy response biomarker in pan-cancer. (PubMed, Aging (Albany NY)) - "N6AMT1 has shown excellent diagnostic and prognostic capabilities in a variety of cancers, and it may reshape the tumor microenvironment and contribute to the ability to predict response to immunotherapy."

Biomarker • IO biomarker • Journal • Pan tumor • Immune Modulation • Oncology • DNMT1

Single-cell sequencing analysis of peripheral blood in patients with moyamoya disease. (PubMed, Orphanet J Rare Dis) - "Our study can provide information for the diagnosis and treatment of moyamoya disease."

Journal • Vascular Neurology • GPX1 • LGALS3 • LGALS3BP • NDRG1 • PLAAT3 • SPINT2

Immune-pyroptosis-related genes predict the prognosis of kidney renal clear cell carcinoma. (PubMed, Transl Oncol) - "GSDMB and PYCARD are potential targets and effective prognostic biomarkers for the combination of immunotherapy and pyroptosis-targeted therapy in KIRC."

IO biomarker • Journal • Clear Cell Renal Cell Carcinoma • Genito-urinary Cancer • Immune Modulation • Kidney Cancer • Oncology • Renal Cell Carcinoma • Solid Tumor • Urology • GSDMB • PYCARD

Prediction and Verification of Potential Therapeutic Targets for Non-Responders to Infliximab in Ulcerative Colitis. (PubMed, J Inflamm Res) - "Colonic mucosal biopsies expression profiles of IFX-treated UC patients (GSE73661, GSE16879) were utilized to predict potential therapeutic targets. Their expression was confirmed in colonic mucosal biopsies of patients with UC. These results can help to further explore the mechanism of non-responders to IFX in UC and to provide potential targets for their subsequent treatment."

Journal • Gastroenterology • Gastrointestinal Disorder • Immunology • Inflammatory Bowel Disease • Ulcerative Colitis • CCL2 • CXCL8 • IL1B • IL6 • NF-κβ

Investigating the association of measures of epigenetic age with COVID-19 severity: evidence from secondary analyses of open access data. (PubMed, Swiss Med Wkly) - "Epigenetic age is a potentially useful tool in primary prevention, particularly as an incentive towards lifestyle changes that target reducing the risk of severe COVID-19 symptoms. However, additional research is needed to establish potential causal pathways and the directionality of this effect."

Journal • Retrospective data • Infectious Disease • Novel Coronavirus Disease

DELETION OF ACONITATE DECARBOXYLASE 1 EXACERBATES EXPERIMENTAL COLITIS AND IS ASSOCIATED WITH A DYSBIOTIC MICROBIOME (DDW 2023) - " The GEO datasets GSE16879 and GSE75214 were interrogated for ACOD1 mRNA levels in ulcerative colitis (UC) and Crohn’s disease (CD) patients... ACOD1 is increased in human IBD tissues, and our data indicates that this enzyme has a protective role in acute and chronic experimental colitis. Notably, Acod1 deletion is associated with intestinal dysbiosis. Together our findings suggest that enhancement of ACOD1 activity may represent a new therapeutic strategy for IBD through an effect on the gut microbiota."

Colorectal Cancer • Crohn's disease • Gastroenterology • Gastrointestinal Disorder • Hematological Disorders • Immunology • Infectious Disease • Inflammatory Bowel Disease • Oncology • Solid Tumor • Ulcerative Colitis

IDENTIFICATION OF PYROPTOSIS-RELATED GENES LANDSCAPE TO IMPROVE DIAGNOSIS AND THERAPY FOR PATIENTS WITH INFLAMMATORY BOWEL DISEASE (DDW 2023) - "Finally, we analyzed the changes of hub genes during anti-TNF treatment according to response status based on GSE12251, GSE73661, GSE98820 and GSE16879... Our study identified AIM2, NLRP3, CASP1, CASP5, GSDMD as the critical pyroptosis-related biomarker in IBD and proposed the expression level of AIM2 and NLRP3 was related to the outcome of anti-TNF treatment. In addition, macrophages may be the main immune cells associated with cell pyroptosis, deserving further exploration."

Clinical • Crohn's disease • Gastroenterology • Gastrointestinal Disorder • Immunology • Inflammation • Inflammatory Bowel Disease • Ulcerative Colitis • IL1B • NLRP3

MicroRNA-Based Markers of Oral Tongue Squamous Cell Carcinoma and Buccal Squamous Cell Carcinoma: A Systems Biology Approach. (PubMed, Biochem Res Int) - "The dataset GSE168227 was downloaded and reanalyzed from the GEO database...These findings may benefit the prognosis and management of individuals with OTSCC/BSCC. However, additional experimental verification is required."

Journal • Head and Neck Cancer • Oncology • Oral Cancer • Solid Tumor • Squamous Cell Carcinoma • Squamous Cell Carcinoma of Head and Neck • Tongue Carcinoma • ANXA5 • CAV1 • DDX17 • EIF2S1 • HSP90AA1 • HSPA5 • MIR136 • NTRK2

Tumor Microenvironment CD8 T and Treg Cells-related Genes Signature Distinguishes Distinct Prognosis and Targeted Therapies Response in Endometrial Cancer. (PubMed, J Immunother) - "Furthermore, patients in the IRPRI-high group had lower tumor mutation burden, programmed death-ligand 1 expression, and Tumor Immune Dysfunction and Exclusion scores, indicating a poor response to immune checkpoint inhibitors therapy (P<0.05), which was also validated in the TCGA testing cohort and independent cohorts, GSE78200, GSE115821, and GSE168204. Also, the higher mutation frequencies of BRCA1, BRCA2, and genes enrolled in homologous recombination repair in the IRPRI-low group predicted a good response to PARP inhibitors. Finally, a nomogram integrating the IRPRI group and prognosis significant clinicopathological factors for EC OS prediction was developed and validated with good discrimination and calibration."

Biomarker • IO biomarker • Journal • Tumor microenvironment • Tumor mutational burden • Endometrial Cancer • Immune Modulation • Oncology • Solid Tumor • BRCA1 • BRCA2 • CD8 • E2F1 • FOXP3 • HRD • PD-L1 • TMB

Identification of ferroptosis-related genes in male mice with sepsis-induced acute lung injury based on transcriptome sequencing. (PubMed, BMC Pulm Med) - "This study identified two FR-DEGs (Ncf2 and Steap3) associated with sepsis-induced ALI via transcriptome analyses, as well as their functional and metabolic pathways."

Journal • Preclinical • Acute Lung Injury • Infectious Disease • Respiratory Diseases • Septic Shock • MIR15A

Gene Expression Omnibus (GEO) accession ID GSE168543. (PubMed, Hum Mol Genet) - "We now show that Sox7 and Wnt4 interact genetically in the development of VSDs through their additive effects on endocardial cushion development with Sox7+/-; Wnt4+/- double heterozygous embryos having hypocellular endocardial cushions and perimembranous and muscular VSDs not seen in their Sox7+/- and Wnt4+/- littermates. These results provide additional evidence that SOX7, WNT4 and BMP2 function in the same pathway during mammalian septal development and that their deficiency can contribute to the development of VSDs in humans."

Journal • Cardiovascular • Congestive Heart Failure • Heart Failure

Identification of Differentially Methylated Genes Associated with Clear Cell Renal Cell Carcinoma and Their Prognostic Values. (PubMed, J Environ Public Health) - "The GSE168845 dataset was downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) between ccRCC tissues and paired tumor-free kidney tissues...Among these differentially methylated genes, TYROBP, BIRC5, BUB1B, CENPF, and MELK were significantly correlated with the survival of ccRCC patients (p < 0.001). Our study indicates the DNA methylation of TYROBP, BIRC5, BUB1B, CENPF, and MELK may be promising results for the prognosis of ccRCC."

Journal • Clear Cell Renal Cell Carcinoma • Genito-urinary Cancer • Oncology • Renal Cell Carcinoma • Solid Tumor • BIRC5 • BUB1B • CD4 • ITGAM • ITGB2 • KIF2C • MELK • PTPRC

Angiogenesis-related gene signatures reveal the prognosis of cervical cancer based on single cell sequencing and co-expression network analysis. (PubMed, Front Cell Dev Biol) - "First we screened the AG gene set from GeneCard website, and then performed angiogenesis-related scores (AGS) per cell from single cell sequencing dataset GSE168652, followed by performing weighted gene co-expression network analysis (WGCNA) for cervical cancer patients according to angiogenesis phenotype...Patients in the low-AGS group were more sensitive to AMG.706, Bosutinib, and Lenalidomide while Imatinib, Pazopanib, and Sorafenib were more recommended to patients in the high-AGS group...Meanwhile, the results showed that TXNDC12 promoted the migration of cervical cancer cells and the tubule-forming ability of endothelial cells. In conclusion, our model based on genes with AG features can effectively assess the prognosis of cervical cancer, and can also provide reference for clinicians to choose immune-related treatments."

Gene Signature • Journal • Tumor mutational burden • Cervical Cancer • Gynecologic Cancers • Immune Modulation • Inflammation • Oncology • Solid Tumor • TMB

Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn's disease. (PubMed, Front Immunol) - "The microarray-based transcriptomic data and corresponding clinical information of GSE100833 and GSE16879 were obtained from the Gene Expression Omnibus (GEO) database...Our findings indicate that NLRP3 inflammasome and its related genes could regulate immune cells and responses, as well as involve in the pathogenesis of Crohn's disease from transcriptomic aspects. These findings provide in silico insights into the diagnosis and treatment of Crohn's disease and might assist in the clinical decision-making process."

Journal • Crohn's disease • Gastroenterology • Immunology • Inflammatory Bowel Disease • NLRP3

CASP4 and CASP8 as newly defined autophagy-pyroptosis-related genes associated with clinical and prognostic features of renal cell carcinoma. (PubMed, J Cancer Res Ther) - "Gene expression data were downloaded from Gene Expression Omnibus (GSE168845), and autophagy-pyroptosis-related differentially expressed genes (DEGs) were identified...CASP4 and CASP8 were autophagy-pyroptosis-related genes associated with immunotherapy in RCC. CASP4 and CASP8 were identified as potential targets and effective prognostic biomarkers for RCC."

IO biomarker • Journal • Genito-urinary Cancer • Oncology • Renal Cell Carcinoma • Solid Tumor • CASP4 • CASP8

miR-125b-5p upregulation by TRIM28 induces cisplatin resistance in non-small cell lung cancer through CREB1 inhibition. (PubMed, BMC Pulm Med) - "Overall, our findings demonstrated novel functions and mechanisms underlying DDP resistance in NSCLC through the TRIM28/miR-125b-5p/CREB1 axis. These may serve as novel therapeutic targets to improve the treatment efficacy using DDP for NSCLC in the future."

Journal • Lung Cancer • Non Small Cell Lung Cancer • Oncology • Solid Tumor • CREB1 • miR-125b • TRIM28

Construction of a prognostic model related to copper dependence in breast cancer by single-cell sequencing analysis. (PubMed, Front Genet) - " CDRG were obtained by single-cell analysis of the GSE168410 dataset in the Gene Expression Omnibus (GEO) database. Veliparib, Selumetinib, Entinostat, and Palbociclib were found to be more sensitive medications for the high-risk group after drug sensitivity analysis. Our CDRG-based prognostic model can aid in the prediction of prognosis and treatment of BC patients."

Journal • Breast Cancer • Immunology • Oncology • Solid Tumor

Role of ARRB1 in prognosis and immunotherapy: A Pan-Cancer analysis. (PubMed, Front Mol Biosci) - "Finally, the relationship between ARRB1 and immunotherapeutic responses was assessed using three independent immunotherapy cohorts, namely, GSE67501, GSE168204, and IMvigor210... ARRB1 has prognostic value in malignant tumors, especially in KIRC and LUAD. At the same time, ARRB1 was closely correlated with the tumor immune microenvironment and indicators of immunotherapy efficacy, indicating its great potential as a reliable marker for predicting the efficacy of immunotherapy."

IO biomarker • Journal • Pan tumor • Immune Modulation • Immunology • Inflammation • Melanoma • Oncology • Solid Tumor • ARRB1 • BRCA • MSI • PD-L1 • TMB

LINKING LOCATION SPECIFIC GENE EXPRESSION PATTERNS TO POTENTIAL VEDOLIZUMAB OUTCOMES IN CROHN’S DISEASE PATIENTS (UEGW 2022) - "Aims & Patients’ gene-expression data were collected from the publicly available dataset GSE16879, which includes sixty patients with active IBD, (19 with colonic CD and 18 with ileal CD), and a control group of 12 CD patients (6 with colonic involvement and 6 with ileal involvement) who underwent endoscopy for polyp screening. Our results suggest a potential increased response to VDZ in the colon when compared to the ileum, likely due to gut regional-specific chemoattractant gene expression profiles."

Clinical • Crohn's disease • Gastroenterology • Gastrointestinal Disorder • Immune Modulation • Immunology • Inflammatory Bowel Disease • Ulcerative Colitis • ANXA1 • ICAM1 • VCAM1

UNDERSTANDING THE IMPACT OF PREVIOUS TNF-Α INHIBITORS ON VEDOLIZUMAB RESPONSE IN PATIENTS WITH ULCERATIVE COLITIS AND CROHN’S DISEASE USING SYSTEMATIC REVIEW AND GENE EXPRESSION DATA (UEGW 2022) - "In addition, gene-expression data in patients with active IBD treated with the TNF-α inhibitor infliximab and/or VDZ were collected from the publicly available Gene Expression Omnibus database, retrieving datasets GSE16879 and GSE73661.  Our analyses highlight potential pharmacological mechanisms behind the observed differences on VDZ outcomes when used first-line biologic or after TNF-α inhibitors in clinical practice."

Clinical • Review • Crohn's disease • Gastroenterology • Gastrointestinal Disorder • Immunology • Inflammatory Bowel Disease • Ulcerative Colitis • CCL20 • CXCL5

Alzheimer's disease-associated inflammatory pathways might contribute to osteoporosis through the interaction between PROK2 and CSF3. (PubMed, Front Neurol) - "The intersection of the three datasets (GSE97760, GSE168813, and GSE62402) was used to obtain 21 co-expressed targets in the peripheral blood samples in patients with Alzheimer's disease and osteoporosis...The interaction of PROK2 and CSF3, core genes related to osteoporosis inflammation, plays an important role in the mechanism of osteoporosis in patients with Alzheimer's. Therefore, abnormalities or alterations in the inflammatory pathways in the peripheral blood samples of Alzheimer's patients may affect the course of osteoporosis."

Journal • Alzheimer's Disease • CNS Disorders • Immunology • Inflammation • Osteoporosis • Rheumatology • CSF3 • PDGFB • PROK

A comprehensive pancancer analysis reveals the potential value of RAR-related orphan receptor C (RORC) for cancer immunotherapy. (PubMed, Front Genet) - "Furthermore, three CIT cohorts (GSE67501, GSE168204, and IMvigor210) from the Gene Expression Omnibus database and a previously published study were used to determine the association between RORC expression and CIT response...However, no significant association was found between RORC and CIT response in the three CIT cohorts. Conclusion Our findings revealed the potential immunotherapeutic value of RORC for various cancers and provides preliminary evidence for the application of RORC in CIT."

IO biomarker • Journal • Pan tumor • Brain Cancer • Clear Cell Renal Cell Carcinoma • CNS Tumor • Glioma • Immune Modulation • Immunology • Inflammation • Lung Cancer • Mesothelioma • Oncology • Renal Cell Carcinoma • Solid Tumor • MSI • PD-L1 • TMB

Presepsin Predicts Severity and Secondary Bacterial Infection in COVID-19 by Bioinformatics Analysis. (PubMed, Comput Math Methods Med) - "The differentially expressed genes (DEGs) between severe COVID-19 patients with SBI and without SBI were screened through the analysis of GSE168017 and GSE168018 datasets...The presepsin expression of COVID-19 patients in the nonsurvivors was significantly higher than that in the survivors (P < 0.05). Presepsin predicts severity and SBI in COVID-19 and may be associated with prognosis in COVID-19."

Journal • Infectious Disease • Novel Coronavirus Disease • Pneumonia • Respiratory Diseases • CD14 • NDUFA2