Biology subjects

Faden, D. L.

Publications and source records attributed to Faden, D. L..

3 recordsLinked to original sources

bioRxiv2025

Orphan Non-Coding RNAs Drive Tumorigenesis and Enable Pre-Diagnostic Detection in HPV-Negative Head and Neck Cancer

HPV-negative head and neck squamous cell carcinoma (HNSCC) lacks reliable biomarkers for early detection and molecular stratification. We recently described orphan non-coding RNAs (oncRNAs) as a class of cancer-emergent small RNAs that arise from cryptic promoters largely silent in normal tissues. Here, we define the comprehensive landscape of oncRNAs in HNSCC. Using TCGA and CPTAC-3 data, we demonstrate that these transcripts are not only tumor-specific but provide digital fingerprints that accurately stratify tumors by anatomical site. Moving from association to function, we investigated whether these emergent transcripts actively drive tumorigenesis. We focused on oncRNA64585, a transcript highly enriched in oral cavity tumors and associated with tumor progression. Its depletion significantly impaired proliferation in vitro and suppressed tumor growth in syngeneic murine models. Mechanistically, transcriptomic and chromatin accessibility profiling revealed that oncRNA64585 regulates transcriptional programs governing cell cycle progression and apoptosis through interaction with the Polycomb Repressive Complex 2 (PRC2). Finally, we demonstrate the clinical utility of these signatures: oncRNA profiles in plasma predicted oral cavity cancer with >90% accuracy up to four years prior to clinical diagnosis. These findings establish oncRNAs as active drivers of HNSCC biology and potent tools for early detection and therapeutic targeting.

cancer biology↗

bioRxiv2024

Dendritic cell effector mechanisms and tumor immune microenvironment infiltration define TLR8 modulation and PD-1 blockade

The potent immunostimulatory effects of toll-like receptor 8 (TLR8) agonism in combination with PD-1 blockade have resulted in various preclinical investigations, yet the mechanism of action in humans remains unknown. To decipher the combinatory mode of action of TLR8 agonism and PD-1 blockade, we employed a unique, open-label, phase 1b pre-operative window of opportunity clinical trial (NCT03906526) in head and neck squamous cell carcinoma (HNSCC) patients. Matched pre- and post-treatment tumor biopsies from the same lesion were obtained. We used single-cell RNA sequencing and custom multiplex staining to leverage the unique advantage of same-lesion longitudinal sampling. Patients receiving dual TLR8 agonism and anti-PD-1 blockade exhibited marked upregulation of innate immune effector genes and cytokines, highlighted by increased CLEC9A+ dendritic cell and CLEC7A/SYK expression. This was revealed via comparison with a previous cohort from an anti-PD-1 blockade monotherapy single-cell RNA sequencing study. Furthermore, in dual therapy patients, post-treatment mature dendritic cells increased in adjacency to CD8+ T-cells. Increased tumoral cytotoxic T-lymphocyte densities and expanded CXCL13+CD8+ T- cell populations were observed in responders, with increased tertiary lymphoid structures (TLSs) across all three patients. This study provides key insights into the mode of action of TLR8 agonism and anti-PD-1 blockade immune targeting in HNSCC patients.

immunology↗

bioRxiv2021

APOBEC Mutagenesis is Concordant Between Tumor and Viral Genomes in HPV Positive Head and Neck Squamous Cell Carcinoma

APOBEC (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like) is a major mutagenic source in human papillomavirus positive oropharyngeal squamous cell carcinoma (HPV+ OPSCC). Why APOBEC mutations predominate in HPV+OPSCC remains an area of active investigation. Prevailing theories focus on APOBECs role as a viral restriction agent. APOBEC-induced mutations have been identified in both human cancers and HPV genomes, but whether they are directly linked in HPV+OPSCCs remains unknown. We performed sequencing of host somatic exomes, transcriptomes and HPV16 genomes from 79 HPV+ OPSCC samples, quantifying APOBEC mutational burden and activity in both the host and virus. APOBEC was the dominant mutational signature in somatic exomes. APOBEC vulnerable PIK3CA hotspot mutations were exclusively present in APOBEC enriched samples. In viral genomes, there was a mean (range) of 5 (0-29) mutations per genome. Mean (range) of APOBEC mutations in the viral genomes was 1 (0-5). Viral APOBEC mutations, compared to non-APOBEC mutations, were more likely to be low-variant allele frequency mutations, suggesting that APOBEC mutagenesis is actively occurring in viral genomes during infection. Paired host and viral analyses revealed that APOBEC-enriched tumor samples had higher viral APOBEC mutation rates (p=0.028), and APOBEC-associated RNA editing (p=0.008) suggesting that APOBEC mutagenesis in host and viral genomes are directly linked. Using paired sequencing of host somatic exomes, transcriptomes, and viral genomes from HPV+OPSCC samples, here, we show concordance between tumor and viral APOBEC mutagenesis, suggesting that APOBEC-mediated viral restriction results in off-target host-genome mutations. These data provide a missing link connecting APOBEC mutagenesis in host and virus and support a common mechanism driving APOBEC dysregulation.

genomics↗