Gujar, H. | Search bioRxiv

bioRxiv2026

Age-associated transcriptional programs in tumor-associated macrophages are associated with tumor progression in HPV-negative oral cancer

Aging and tobacco exposure are major determinants of risk and outcome in HPV-negative oral cavity squamous cell carcinoma (OSCC), yet the cellular programs linking host factors to tumor immunity remain poorly defined. We reprocessed and reanalyzed previously published single-cell RNA-seq data from 19 HPV-negative OSCC tumors and we identified a robust age- and smoking-associated expansion of SPP1high tumor-associated macrophages (TAMs), accompanied by a shift toward a myeloid-dominant and lymphocyte-reduced tumor microenvironment. SPP1high TAMs exhibit a distinct transcriptional state enriched for extracellular-matrix remodeling and metabolic programs and reduced antigen-presentation pathways. They also express inflammatory chemokines such as CXCL2 and CXCL3 and down-regulate the cytotoxic mediator TNFSF10, suggesting a broadly protumor TAM phenotype. Ligand-receptor modeling suggests that SPP1high TAMs act as key communication hubs, with dominant SPP1-CD44 signaling to T-cell subsets. Transcription-factor analysis further implicates a POU2F1/POU2F2/SP1 module in maintaining this state. In the TCGA HNSCC cohort, the association between SPP1 expression and overall survival did not reach statistical significance after adjustment for age and tumor purity. These findings demonstrate that aging and tobacco exposure converge to expand an SPP1high TAM population that remodels the extracellular matrix and suppresses antitumor immunity, highlighting the SPP1-CD44 axis and its upstream regulators as potential therapeutic targets in high-risk OSCC.

immunology↗

bioRxiv2017

Profiling DNA Methylation Differences Between Inbred Mouse Strains on the Illumina Human Infinium MethylationEPIC Microarray

The Illumina Infinium MethylationEPIC provides an efficient platform for profiling DNA methylation in humans at over 850,000 CpGs. Model organisms such as mice do not currently benefit from an equivalent array. Here we used this array to measure DNA methylation in mice. We defined probes targeting conserved regions and performed a comparison between the array-based assay and affinity-based DNA sequencing of methyl-CpGs (MBD-seq). Mouse samples consisted of 11 liver DNA from two strains, C57BL/6J (B6) and DBA/2J (D2), that varied widely in age. Linear regression was applied to detect differential methylation. In total, 13,665 probes (1.6% of total probes) aligned to conserved CpGs. Beta-values ({beta}-value) for these probes showed a distribution similar to that in humans. Overall, there was high concordance in methylation signal between the EPIC array and MBD-seq (Pearson correlation r = 0.70, p-value < 0.0001). However, the EPIC probes had higher quantitative sensitivity at CpGs that are hypo-({beta}-value < 0.3) or hypermethylated ({beta}-value > 0.7). In terms of differential methylation, no EPIC probe detected significant difference between age groups at a Benjamini-Hochberg threshold of 10%, and the MBD-seq performed better at detecting age-dependent change in methylation. However, the top most significant probe for age (cg13269407; uncorrected p-value = 1.8 x 10-5) is part of the clock CpGs used to estimate the human epigenetic age. For strain, 219 Infinium probes detected significant differential methylation (FDR cutoff 10%) with [~]80% CpGs associated with higher methylation in D2. This higher methylation profile in D2 compared to B6 was also replicated by the MBD-seq data. To summarize, we found only a small subset of EPIC probes that target conserved sites. However, for this small subset the array provides areliable assay of DNA methylation and can be effectively used to measure differential methylation in mice.

bioinformatics↗