Biology subjects

Amrit, F. R.

Publications and source records attributed to Amrit, F. R..

4 recordsLinked to original sources

bioRxiv2026

A TCER-1-siRNA Regulatory Axis Suppresses Antibacterial Innate Immunity in C. elegans

Small interfering RNA (siRNA) are important regulators of gene expression with well-established roles in pathogen defense. Yet, their specific roles in antibacterial immunity are not well understood. Here, we identify an siRNA pathway involved in repressing antibacterial innate immunity in Caenorhabditis elegans. We show that genes required for the biogenesis or function of WAGO Argonaute-associated siRNAs, called 22G-RNAs, function in a common genetic pathway with the immune-suppressive transcription elongation and splicing factor TCER-1 to inhibit immunity. Loss of tcer-1 reduced levels of 22G-RNAs from a subset of WAGO targets, while mutations in several WAGO 22G-RNA pathway genes phenocopied the enhanced immunoresistance of tcer-1 mutants, suggesting a shared regulatory module. Integrative 22G-RNA-mRNA analyses and molecular genetic studied show that this module does not induce widespread gene silencing, but instead targets a restricted set of immune-relevant effectors, including scrm-4, encoding a phospholipid translocase that promotes host resistance. Together, our findings establish endogenous WAGO 22G-RNAs as repressors of antibacterial immunity and identify TCER-1 as a physiological regulator that promotes 22G-RNA biogenesis to constrain host defense. The results uncover a previously unrecognized small RNA-dependent mechanism linking transcription, metabolism, and antibacterial innate immunity.

immunology↗

bioRxiv2026

Re-evaluating the Need for Double Centrifugation in Plasma Cell-Free DNA Analysis

Plasma cell-free DNA (cfDNA) is a central analyte in liquid biopsy applications spanning prenatal testing, oncology, and epigenomic profiling. To minimize contamination by high-molecular-weight genomic DNA (gDNA) released from nucleated blood cells, standard pre-analytical workflows typically mandate a double-centrifugation protocol prior to cfDNA extraction. This requirement has limited the use of many existing plasma biorepositories that were prepared using only a single low-speed centrifugation step. In this study, we evaluated whether single-spun plasma is sufficient for accurate cfDNA analysis when samples are processed under controlled conditions. Using paired single- and double-spun plasma aliquots derived from the same early-pregnancy maternal blood samples collected in EDTA tubes, we performed whole-genome DNA methylation sequencing and assessed cfDNA integrity across multiple orthogonal dimensions. These included cell-type proportion deconvolution using large and small DNA methylation reference signatures, CpG-level methylation rate estimation with explicit variance modeling, beta-binomial-corrected correlation analyses across libraries, cfDNA fragment length profiling, and genotype-based fetal fraction estimation. Across all analyses, we found no evidence that a second high-speed centrifugation step improved accuracy, reduced technical variability, or enhanced analytical fidelity. Cell-type proportion estimates and CpG-level methylation rates were statistically indistinguishable between single- and double-spun plasma, fragment length distributions were nearly identical, and fetal fraction estimates showed near-perfect concordance. Together, these results demonstrate that a single low-speed centrifugation step is sufficient for high-fidelity cfDNA methylation, fragmentomic, and genotyping analyses. Our findings support the expanded use of legacy single-spun plasma collections for liquid biopsy research and assay development and motivate a re-evaluation of rigid double-centrifugation requirements in cfDNA workflows.

genomics↗

bioRxiv2025

LIPL-1 and LIPL-2 are TCER-1-regulated Lysosomal Lipases with Distinct Roles in Immunity and Fertility

Reproduction and immunity are fundamental, energy intensive processes that often compete for resources, leading to trade-offs observed across diverse species. Lipid metabolism plays a crucial role in integrating these processes, particularly during stressful conditions such as pathogenic infections. Yet the molecular mechanisms governing this integration remain poorly understood. TCER-1, the C. elegans homolog of mammalian TCERG1, suppresses immunity and promotes fertility, especially upon maternal infection. Here, we show that TCER-1 regulates two conserved lysosomal lipases, lipl-1 and lipl-2, to balance reproduction, immunity and lifespan. Using transcriptomic, lipidomic, and molecular-genetic analyses, we demonstrate that while both lipl-1 and lipl-2 mediate infection-induced lipid remodeling, lipl-1 enhances immunity and catalyzes the accumulation of ceramide species linked to stress response and longevity, whereas, lipl-2 unexpectedly does not. Both lipases contribute towards fertility outcomes, but lipl-2 is especially critical for maintaining embryonic-eggshell integrity during maternal infection and aging. Strikingly, expression of human lysosomal acid lipase (LAL), the ortholog of lipl genes, rescues the immune defects triggered by lipl-l loss and enhances immune resilience. Together, these findings uncover functionally distinct roles for lipl-1 and lipl-2 in modulating lipid species that shape immune fitness, healthspan and reproductive health, and suggest a potentially conserved mechanism by which lipid metabolism links fertility and immunity.

genetics↗

bioRxiv2020

NHR-49 acts in distinct tissues to promote longevity versus innate immunity

Aging and immunity are inextricably linked and many genes that extend lifespan also enhance immunoresistance. However, it remains unclear if longevity-enhancing factors modulate immunity and longevity by distinct or shared mechanisms. Here, we demonstrate that the Caenorhabditis elegans pro-longevity factor, NHR-49, also promotes resistance against Pseudomonas aeruginosa, but modulates immunity and longevity by spatially and mechanistically distinct mechanisms. Fenofibrate, an agonist of NHR-49s mammalian functional homolog, PPAR, enhanced worm immunoresistance in an NHR-49-dependent manner. NHR-49 expression is increased by germline ablation, an intervention that extends lifespan, but lowered by pathogen exposure. NHR-49 acted in multiple somatic tissues to promote longevity, whereas, its pro-immunity function was mediated by neuronal expression. The canonical NHR-49 target genes, acs-2 and fmo-2, were upregulated by germline loss, but infection triggered fmo-2 downregulation and acs-2 upregulation. Interestingly, neither gene conferred resistance against Gram-negative Pseudomonas, unlike their reported roles in immunity against Gram-positive pathogens. Thus, NHR-49 is differentially regulated by interventions that bring about long-term changes (lifespan extension) vs. short-term stress (pathogen exposure) and in response it orchestrates distinct outputs, including pathogen-specific transcriptional programs. Overall, our study demonstrates the independent control of immunity and longevity by a conserved regulatory protein.

molecular biology↗