Background: Leukocyte infiltration plays an critical role in outcome of various diseases including Lung adenocarcinoma (LUAD).
Objectives: To understand the genetic and epigenetic factors affecting leukocyte infiltration and identification and validation of immune based biomarkers.
Method: Correlation analysis was done to get the associations of the factors. CIBERSORT analysis was done for immune cell infiltration. Genetic and epigenetic analysis were performed. Cox regression was carried out for survival.
Results: We categorized the TCGA-LUAD patients based on Leukocyte fraction (LF) and performed extensive immunogenomic analysis. Interestingly, we showed that LF has a negative correlation with copy number variation (CNV) but not with mutational load. However, several individual genetic mutations, including KRAS and KEAP1, were significantly linked with LF. Also, as expected, patients with high LF showed significantly increased expression of genes involved in leukocyte migration and activation. DNA methylation changes also showed a strong association with LF and regulated a significant proportion of genes associated with LF. We also developed and validated an independent prognostic immune signature using the top six prognostic genes associated with LF.
Conclusion: Together, we have identified clinical, genetic, and epigenetic variations associated with LUAD LF and developed an immune gene-based signature for disease prognostication.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.3233/CBM-203071 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Visceral fat distribution: Interracial studies.
Adv Clin Chem
January 2025
Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, China. Electronic address:
Visceral adipose tissue, a type of abdominal adipose tissue, is highly involved in lipolysis. Because increased visceral adiposity is strongly associated with the metabolic complications related with obesity, such as type 2 diabetes and cardiovascular disease, there is a need for precise, targeted, personalized and site-specific measures clinically. Existing studies showed that ectopic fat accumulation may be characterized differently among different populations due to complex genetic architecture and non-genetic or epigenetic components, ie, Asians have more and Africans have less visceral fat vs Europeans.
View Article and Find Full Text PDFc-FLIP/Ku70 complex; A potential molecular target for apoptosis induction in hepatocellular carcinoma.
Arch Biochem Biophys
January 2025
Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Experimental Cancer Medicine, Institution for Laboratory Medicine, Karolinska Institute, Stockholm, Sweden. Electronic address:
Hepatocellular carcinoma (HCC) is one of the most lethal malignancies worldwide and the most common form of liver cancer. Despite global efforts toward early diagnosis and effective treatments, HCC is often diagnosed at advanced stages, where conventional therapies frequently lead to resistance and/or high recurrence rates. Therefore, novel biomarkers and promising medications are urgently required.
View Article and Find Full Text PDFDissection of type 2 diabetes: a genetic perspective.
Lancet Diabetes Endocrinol
January 2025
Université de Lille, Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France; Department of Metabolism, Imperial College London, London, UK. Electronic address:
Diabetes is a leading cause of global mortality and disability, and its economic burden is substantial. This Review focuses on type 2 diabetes, which makes up 90-95% of all diabetes cases. Type 2 diabetes involves a progressive loss of insulin secretion often alongside insulin resistance and metabolic syndrome.
View Article and Find Full Text PDFThe effects of mitoquinol mesylate on post-thaw characteristics and fertilizing ability of rooster semen cryopreserved in the Beltsville medium.
Theriogenology
January 2025
Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.
Cryopreservation of rooster semen is a reproductive technology carried out to boost genetic gain and productivity in commercial flocks of chicken. However, semen freezing significantly reduces the quality and fertilizing potential of spermatozoa. This study examined cryoprotective effects of the mitochondria-targeted antioxidant mitoquinol mesylate added to the freezing extender by assessing post-thaw characteristics of rooster sperm.
View Article and Find Full Text PDFAn epigenetic pathway regulates MHC-II expression and function in B cell lymphoma models.
J Clin Invest
January 2025
Department of Biochemistry and Molecular Genetics and.
Mutations or homozygous deletions of MHC class II (MHC-II) genes are commonly found in B cell lymphomas that develop in immune-privileged sites and have been associated with patient survival. However, the mechanisms regulating MHC-II expression, particularly through genetic and epigenetic factors, are not yet fully understood. In this study, we identified a key signaling pathway involving the histone H2AK119 deubiquitinase BRCA1 associated protein 1 (BAP1), the interferon regulatory factor interferon regulatory factor 1 (IRF1), and the MHC-II transactivator class II transactivator (CIITA), which directly activates MHC-II gene expression.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!