Biology subjects

Ling, R.

Publications and source records attributed to Ling, R..

6 recordsLinked to original sources

bioRxiv2026

Self-extending DNA recording with stochastic and programmed writing

Recording cellular histories requires new information to accumulate without erasing earlier records. Here we introduce Infinite Printer, a CRISPR recording architecture that couples self-extension to regeneration of a writable terminal context. A self-targeting prime-editing guide RNA (stpegRNA) directs repeat extension, while base editing generates diversity in situ without a separate insertion template for each character state. Earlier sequence remains upstream of the renewed terminus, linking substrate growth with record retention. Auxiliary pegRNAs specify payloads within a write-renew-write architecture. After three rounds of payload input, 4,436 distinct complete CCA-based records contained identities from all three pools. Longer AC/AT records retained shared upstream marks, and full-length sequence analysis resolved additional endpoint distinctions. Joint single-cell readout recovered 1,549 distinct records and 7,669 combinations across 12,302 transcriptome-linked cell labels from a single stpegRNA design. Spatial-transcriptomic readout recovered spacer records at 11,330 capture spots, linking record content to tissue coordinates and gene-expression profiles. Infinite Printer unites substrate renewal, sequence diversification and programmed writing with cell- and tissue-linked readout, providing a foundation for future lineage recording across large cell populations during mammalian development.

synthetic biology↗

bioRxiv2026

Rethinking Platelet Identity from an Extracellular Vesicle-Centric View: A Proof-of-Concept Study

The long-standing ambiguity surrounding whether platelets are cells or particles has hindered a unified understanding of their biology. In this study, we characterized the morphology of platelet-like particles (PLPs) using nanoparticle tracking analysis, transmission electron microscopy, and immunofluorescence. Notably, we observed that platelets can be endocytosed by living cells. We also indicate that platelets express the canonical extracellular vesicles (EVs) markers CD9, CD63, CD81, and TSG101. Our results demonstrate that platelets share six key similarities with EVs--in size, morphology, surface markers, function, biogenesis, and mode of action--leading us to propose a novel classification. Our findings suggest that platelets fulfill the current minimal criteria for EVs, raising the possibility that they could be conceptually viewed as a specialized EVs subset rather than conventional blood cells. Adopting this EVs-centric perspective could broaden the current conceptual framework for EVs and offer an alternative lens for interpreting platelet functions, which may in turn help guide future translational research and clinical exploration.

cell biology↗

bioRxiv2025

Diverse epigenomic mechanisms underpin transcriptional dysregulation in Polycomb-altered acute myeloid leukemia

BackgroundPolycomb Repressive Complex 2 (PRC2) modulates chromatin accessibility and architecture to direct tissue-specific gene expression. PRC2 function is frequently altered in cancer by loss-of-function mutation or deletion, but the downstream effects on transcriptional regulation are incompletely understood. ResultsTo gain insights into these mechanisms, we performed a holistic analysis of epigenomic and transcriptional changes in an isogenic model of acute myeloid leukemia (AML) with heterozygous EZH2 deletion that mimics reduced PRC2 function in patient leukemias. PRC2-depleted cells had diverse gene expression changes, including a bias towards more immature monocyte-lineage transcriptional signatures. PRC2 depletion also correlated with marked increases in chromatin accessibility genome-wide, with 10-45% increases in ATAC-seq peaks in EZH2+/- clones. These changes were accompanied by decreased H3K27me3 and increased H3K27ac levels in CUT+RUN assays that were incompletely linked to transcriptional activity. Despite these generalised changes, 3D chromatin architecture assessed by Hi-C was largely maintained, with H3K27me3 preferentially lost in regions with low DNA-DNA contact frequency. Surprisingly, some regions gained broad H3K27me3 domains at heavily compacted chromatin. We notably saw compartmentalisation changes upstream of the transcriptionally upregulated fetal hematopoiesis gene LIN28B in EZH2+/- cells, with corresponding activation of a LIN28B-specific transcriptional program, including upregulation of the CDK6 oncogene. These results correlated with EZH2+/- cell phenotype, including decreased cellular proliferation and increased resistance to CDK6 inhibitor palbociclib. ConclusionsOur findings suggest that PRC2 depletion pleiotropically affects AML transcriptional regulation to directly impact cell phenotype and treatment responsiveness, which may partially explain the aggressive biology seen in these cases.

cancer biology↗

bioRxiv2023

RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac4C modification

NAT10 is dysregulated and plays an essential role in various types of cancers. However, the exact machenism of how NAT10 regulates cancer progression remains debatable. In this report, we show that NAT10 affects tumorigeneis mainly based on its acetylation function on tRNA. In addition, we found NAT10 regulate the ac4C of tRNA in cancer via interaction with RNPS1, which in turn protect NAT10 from degradation by E3 ubiquitin ligase ZSWIM6. We developed TRMC-seq method to compreshensively profile tRNA ac4C sites and uncovered the presence of ac4C in a broader range of tRNA isoacceptors than previous studies. Multi-omics analysis identified AP-1 signaling pathway as a major downstream mediator of NAT10. Mechanistically, we found NAT10 is responsible for the translation efficiency genes which contain higher ac4C-tRNA codon. Importantly, our genetic mouse model validated our in vitro findings of NAT10 in cancer. Our study highlights a role of NAT10 in mediating tRNA ac4C to regulate the translation and tumorigenesis of cancer.

molecular biology↗

bioRxiv2021

Adipocyte Tribbles1 Regulates Plasma Adiponectin and Plasma Lipids in Mice

Multiple GWAS have identified SNPs in the 8q24 locus near the TRIB1 gene that significantly associate with plasma lipids and coronary artery disease. While subsequent studies have uncovered roles for hepatic and myeloid Trib1 in contributing to either plasma lipids or atherosclerosis, the causal tissue for these GWAS associations remains unclear. The same 8q24 SNPs significantly associate with plasma adiponectin levels in humans as well, suggesting a role for TRIB1 in adipose tissue. Here, we report that adipocyte-specific Trib1 knockout mice (Trib1_ASKO) have increased plasma adiponectin levels and decreased plasma cholesterol and triglycerides. We demonstrate that loss of Trib1 increases adipocyte production and secretion of adiponectin independent of the known TRIB1 function of regulating proteasomal degradation. RNA-seq analysis of adipocytes and livers from Trib1_ASKO mice suggests that alterations in adipocyte function underlie the plasma lipid changes observed in these mice. Secretomics and RNA-seq analysis revealed that Trib1_ASKO mice have increased production of Lpl and decreased production of Angptl4 in adipose tissue, and fluorescent substrate assays confirm an increase in adipose tissue Lpl activity, which likely underlies the observed triglyceride phenotype. In summary, we demonstrate here a novel role for adipocyte Trib1 in regulating plasma adiponectin, total cholesterol, and triglycerides in mice, confirming previous genetic associations observed in humans and providing a novel avenue through which Trib1 regulates plasma lipids and coronary artery disease.

physiology↗

bioRxiv2019

Effects of Large-Scale Oceanic Phenomena on Non-Cholera Vibriosis Incidence in the United States: Implications for Climate Change

PurposeEpidemics of diarrhea caused by toxigenic strains of Vibrio cholerae are of global public health concern, but non-cholera Vibrio (NCV) species are also important causes of disease. These pathogens are thermophilic, and climate change could increase the risk of NCV infection. The El Nino Southern Oscillation (ENSO) is a "natural experiment" that may presage ocean warming effects on disease incidence. MethodWe obtained vibriosis case counts in the United States by digitizing annual reports from the U.S. Cholera and Other Vibrio Illness Surveillance system. Trends and environmental impacts (of ENSO and the North Atlantic Oscillation) were evaluated using negative binomial and distributed nonlinear lag models. Associations between latitude and changing risk were evaluated with meta-regression. ResultsTrend models demonstrated significant seasonality (P < 0.001) and a 7% annual increase in disease risk from 1999 to 2014 (annual IRR 1.071, 95% CI 1.061-1.081). Distributed lag models demonstrated increased vibriosis risk following ENSO conditions over the subsequent 12 months (integrated RR 1.940, 95% CI 1.298-2.901). The rate of change in vibriosis risk increased with state latitude (RR per 10{degrees} increase 1.066, 95% CI 1.027-1.107). ConclusionVibriosis risk in the United States appears to be impacted by irregular large-scale ocean warming and exhibits a north-south gradient in rate of change as would be expected if changing disease incidence is attributable to ocean warming. Vulnerable populations, which include high-income countries with well-developed public health systems, may experience increased risk of this disease as a result of climate change.

epidemiology↗