Biology subjects

Ting, A. H.

Publications and source records attributed to Ting, A. H..

6 recordsLinked to original sources

bioRxiv2025

A poly(A) isoform-aware single-cell and spatial atlas defines fibroblast niches in the human bladder

Bladder function relies on coordinated interactions among epithelial, stromal, vascular, and neural compartments, but high-resolution molecular and spatial features remain undefined. We generated a publicly accessible, poly(A) isoform-aware single-nucleus and spatial reference of the adult human bladder spanning four anatomical regions and both sexes. Integrating 74,694 snRNA-seq profiles with 168,476 Xenium-resolved cells, we identified 22 cell types and 23,489 polyadenylation sites, with isoform usage improving stromal resolution beyond gene expression alone. Spatial mapping revealed layered fibroblast niches aligned with epithelial, vascular, and neural structures, supported by Visium data. This multimodal reference links isoform regulation to anatomical context and provides a reusable framework for cell-type annotation, cross-study integration, and analyses of bladder physiology and disease.

molecular biology↗

bioRxiv2025

A TP53 Intron-Derived Peptide Promotes Tumor Survival

During transcription, alternative cleavage and polyadenylation (APA) of transcripts produces mRNAs that differ in their 3 ends. We previously found that leukemia cells cleave and polyadenylate transcripts within introns (intronic APA, IPA) to generate truncated RNA isoforms, which perturb the expression and function of corresponding genes. In addition to protein-coding RNA, we found that leukemia cells express numerous putative long non-coding RNAs generated by IPA, with most uncharacterized. Here, we identify an IPA isoform encoded within intron 1 of the TP53 tumor suppressor gene that is translated into a non-canonical protein termed IPADP1 (IPA-derived protein 1). IPADP1 expression was detected in patient leukemia cells and human blood cancer cell lines. We uncovered an oncogenic role for IPADP1 in enhancing cancer cell survival during drug treatments, as well as promoting tumor formation in vivo. Using proteomic and functional studies, our data suggest that IPADP1 increases cell viability by regulating apoptotic signaling, cell cycle, and DNA damage responses. Furthermore, we observed that the expression of p53-IPA is significantly associated with SF3B1 mutations in leukemia patients, suggesting mechanisms for the genesis of this isoform. Our study demonstrates that an IPA isoform could have a function different from its host gene.

cancer biology↗

bioRxiv2025

Alternative polyadenylation regulates human urothelial differentiation

The urothelium is stratified into progenitor basal cells, intermediate cells, and terminally differentiated umbrella cells. Proper renewal of umbrella cells is necessary for maintaining urinary tract barrier integrity. To investigate whether mRNA alternative cleavage and polyadenylation (APA) regulates urothelial differentiation, we developed a single-cell polyadenylation site usage (scPASU) computational pipeline to map cell state-specific polyadenylation sites in single-cell RNA-seq data from 13,544 urothelial cells. Leveraging single-cell spatial imaging, we directly visualized APA events in situ, revealing their spatial specificity within the adult human ureter. APA shaped urothelial differentiation, independent of gene expression changes. Furthermore, key APA-regulated genes shared conserved motifs in their 3 UTRs, often containing Alu elements, suggesting a potential mechanism regulating poly(A) site selection. Our study establishes APA as a driver of urothelial transcriptome diversity.

systems biology↗

bioRxiv2025

Single Cell RNA-sequencing of BCG naive and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM mediated immune-suppressive pathway

Non-muscle invasive bladder cancer (NMIBC) represents 70-80% patients with newly diagnosed bladder cancer, and Bacillus Calmette-Guerin (BCG) remains a cornerstone treatment for intermediate-and high-risk NMIBC to prevent disease recurrence and progression. However, many patients experience recurrence after induction BCG, posing significant challenges in the management of the disease. We conducted single cell RNA sequencing on freshly collected NMIBC samples, distinguishing between those naive to BCG treatment and those that recurred post-BCG treatment. We observed a clear activation of inflammatory pathways across cell types during recurrence, but these were not associated with canonical immune checkpoint or T cell exhaustion phenotypes. Analysis of cell-to-cell communication revealed enhanced interactions between T cells and urothelial cells in BCG-recurrence, predominantly modulated by CD6 and ALCAM. Furthermore, we found CD6hi T cells to be immunosuppressed and enriched in recurrent samples, suggesting a potential role for CD6 as an immune evasion signal in NMIBC. SIGNIFICANCEThese findings uncover a novel mechanism responsible for bladder cancer recurrence after BCG treatment. Enhanced T cell-urothelial cell communication in recurrent tumors mediated by CD6 and ALCAM leads to an immunosuppressed state. Thus, CD6 may have potential as a therapeutic target to augment BCG response in non-muscle invasive bladder cancer.

cancer biology↗

bioRxiv2023

Heat shock induces alternative polyadenylation through dynamic DNA methylation-regulated chromatin looping

Alternative cleavage and polyadenylation (APA) is a gene regulatory mechanism used by cells under stress to upregulate proteostasis-promoting transcripts, but how cells achieve this remains poorly understood. Previously, we elucidated a DNA methylation-regulated APA mechanism, in which gene body DNA methylation enhances distal poly(A) isoform expression by blocking CTCF binding and chromatin loop formation at APA control regions. We hypothesized that DNA methylation-regulated APA is one mechanism cells employ to induce proteostasis-promoting poly(A) isoforms. At the DNAJB6 co-chaperone gene locus, acute heat shock resulted in binding of stress response transcription factors HSF1, ATF6, and YY1 at the APA control region and an increase in the expression of the proximal poly(A) isoform known to prevent protein aggregation. Furthermore, TET1 was recruited to rapidly demethylate DNA, facilitating CTCF binding and chromatin loop formation, thereby reinforcing preferential proximal poly(A) isoform expression. As cells recovered, the transcription factors vacated the APA control region, and DNMT1 was recruited to remethylate the region. This process resolved chromatin looping and reset the poly(A) isoform expression pattern. Our findings unveil an epigenetic mechanism enabling cells to dynamically modulate poly(A) isoforms in response to stress while shedding light on the interplay between DNA methylation, transcription factors, and chromatin looping.

cell biology↗

bioRxiv2021

Ureter single-cell and spatial mapping reveal cell types, architecture, and signaling networks

Tissue engineering offers a promising treatment strategy for ureteral strictures, but its success requires an in-depth understanding of the architecture, cellular heterogeneity, and signaling pathways underlying tissue regeneration. Here we define and spatially map cell populations within the human ureter using single-cell RNA sequencing, spatial gene expression, and immunofluorescence approaches. We focused on the stromal and urothelial cell populations to enumerate distinct cell types composing the human ureter and inferred potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Furthermore, we analyzed and experimentally validated the importance of Sonic Hedgehog (SHH) signaling pathway in adult stem cell maintenance. The SHH-expressing basal cells supported organoid generation in vitro and accurately predicted the differentiation trajectory from basal stem cells to terminally differentiated umbrella cells. Our results highlight essential processes involved in adult ureter tissue homeostasis and provide a blueprint for guiding ureter tissue engineering.

developmental biology↗