Biology subjects

Lo, Y.-H.

Publications and source records attributed to Lo, Y.-H..

7 recordsLinked to original sources

bioRxiv2026

ARID1A deficiency unleashes centromeric RNA transcription to drive chromosomal instability and boosts PKMYT1 inhibitor efficacy via RNA sensing

Cancer gene-associated mutations and molecular hallmarks of chromosomal instability (CIN) are unexpectedly common in histologically normal cells and tissues. These emerging findings challenge the binary distinction between "normal" and "cancerous" cells and suggest that early tumorigenesis may commence against a background of widespread yet largely tolerated genomic instability. However, it remains largely unexplored how a cancer gene-associated mutation can initiate the development of CIN-like states in non-malignant cells and drive tumor evolution. ARID1A, a chromatin remodeling factor, was identified as the most frequently mutated gene in both gastric normal epithelium and tumors. This distinctive molecular convergence presents an opportunity to elucidate the mechanisms by which a cancer-associated gene facilitates the initiation of early CIN phenotypes and develop effective antitumor strategies. In the present study, using primary human gastric organoids, we employed optical genome mapping (OGM) and live-imaging technologies to demonstrate that ARID1A depletion induced a wide spectrum of structural variants (SVs), copy number variants (CNVs), and chromosomal segregation errors, characteristic features of CIN at a very early stage of gastric tumorigenesis. Mechanistically, ARID1A bound centromere repetitive satellite DNA (satDNA) sequences. Its SWI/SNF-associated chromatin remodeling activity was required for suppressing satDNA transcription and the production of -SatRNA, through restricting RNAPII elongation. Consequently, ARID1A depletion led to overexpression of -SatRNA, and a higher incidence of sister chromatid exchange (SCE), a sensitive indicator of CIN. Importantly, the elevated -SatRNA expression in ARID1A-deficient cells further established a dual therapeutic vulnerability for G2/M checkpoint blockade, such as PKMYT1 inhibitor (PKMYTi), by concurrently aggregating CIN-induced cell death and activating self-dsRNA sensing-mediated innate immune response. Notably, PKMYTi markedly promoted -SatRNA expression, aberrant release of these self-derived dsRNAs into the cytosol and a robust activation of the RIG/MDA5-MAVS-depenent type-I interferon response in ARID1A-depleted cells. As expected, PKMYTi potentiated the efficacy of immunotherapy in ARID1A-deficient gastric tumors. Together, our findings reveal that ARID1A deficiency unleashes centromeric -SatRNA transcription, which sets the molecular stage for tumor evolution and targeted therapy by coordinately inducing CIN and self-dsRNA-induced innate immune responses.

cancer biology↗

bioRxiv2022

A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids

Organoids are powerful experimental models for studying the ontogeny and progression of diseases including cancer. Organoids are conventionally cultured in bulk using an extracellular matrix mimic. However, organoids in bulk culture physically overlap, making it impossible to track the growth of individual organoids over time in high throughput. Moreover, local spatial variations in bulk matrix properties make it difficult to assess whether observed phenotypic heterogeneity between organoids results from intrinsic cell differences or microenvironment variability. Here, we developed a microwell-based method that enables high-throughput quantification of image-based parameters for organoids grown from single cells, which can be retrieved from their microwells for sequencing and molecular profiling. Coupled with a deep-learning image processing pipeline, we characterized phenotypic traits including growth rates, cellular movement, and apical-basal polarity in two CRISPR-engineered human gastric organoid models, identifying genomic changes associated with increased growth rate and changes in accessibility and expression correlated with apical-basal polarity.

bioengineering↗

bioRxiv2022

Experimental evolution in TP53 deficient gastric organoids recapitulates tumorigenesis

The earliest events during human tumor initiation, while poorly characterized, may hold clues to malignancy detection and prevention1. Here we model occult pre-neoplasia by bi-allelically inactivating TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over two years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single cell sequencing of TP53 deficient gastric organoids similarly indicates progression towards malignant transcriptional programs. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programs repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference, and a striking degree of phenotypic convergence in pre-malignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and reveal evolutionary constraints and barriers to malignant transformation with implications for earlier detection and interception of aggressive, genome instable tumors.

cancer biology↗

bioRxiv2021

Prevalent sex ratio bias in Caenorhabditis nematodes

Although equal sex ratio is ubiquitous and represents an equilibrium in evolutionary theory, biased sex ratios are predicted for certain local conditions. Cases of sex ratio bias have been mostly reported for single species, but little is known about its evolution above the species level. Here, we surveyed progeny sex ratios in 23 species of the nematode genus Caenorhabditis, including 19 for which we tested multiple strains. For the species with multiple strains, 5 species had female-biased and 2 had non-biased sex ratios in all strains, respectively. The other 12 species showed polymorphic sex ratios across strains. Female-biased sex ratios could be due to sperm competition whereby X-bearing sperm outcompete nullo-X sperm during fertilization. In this model, when sperm are limited allowing all sperm to be used, sex ratios are expected to be equal. However, in assays limiting mating to a few hours, most strains showed similarly biased sex ratios compared to unlimited mating experiments, except that one C. becei strain showed significantly reduced female bias compared to unlimited mating. Our study shows frequent polymorphism in sex ratios within Caenorhabditis species and that sperm competition alone cannot explain the sex ratio bias.

evolutionary biology↗

bioRxiv2018

Gfi1-expressing Paneth cells revert to stem cells following intestinal injury

BackgroundAimChemotherapy drugs harm rapidly dividing normal healthy cells such as those lining the gastrointestinal tract, causing morbidity and mortality that complicates medical treatment modalities. Growth Factor-Independent 1 (GFI1) is a zinc finger transcriptional repressor implicated in the differentiation of secretory precursors into Paneth and goblet cells in the intestinal epithelium. We hypothesize that stimulating the reversion of Gfi1+ secretory cells into stem cells will improve intestinal epithelial regeneration and mitigate injury.\n\nMethodsGfi1 reporter mice (Gfi1cre/+; ROSA26 LSL-YFP) were treated with Doxorubicin, radiation, anti-CD3 antibody, and rotavirus to induce intestinal injury. Mice and intestinal organoids (enteroids) were used to investigate cellular repair mechanisms following injury.\n\nResultsUnder homeostatic conditions, Gfi1-lineage cells are Paneth and goblet cells, which were non-proliferative and not part of the stem cell pool. After injury, Gfi1+ secretory cells can re-enter the cell cycle and give rise to all cell lineages of the intestinal epithelium including stem cells. Reversion of Gfi1-lineage cells was observed in other injury model systems, including irradiation and anti-CD3 treatment, but not in ISC-sparing rotavirus infection. Our results also demonstrated that PI3kinase/AKT activation improved cell survival, and elevated WNT signaling increased the efficiency of Gfi1+ cell reversion upon injury.\n\nConclusionsThese findings indicate that Gfi1+ secretory cells display plasticity and reacquire stemness following severe damage. Moreover, PI3kinase/AKT and WNT are key regulators involved in injury-induced regeneration. Our studies identified potential therapeutic intervention strategies to mitigate the adverse effects of chemotherapy-induced damage to normal tissues and improve the overall effectiveness of cancer chemotherapy.

cell biology↗

bioRxiv2018

Growth Factor Independent 1 is a tumor suppressor gene in colorectal cancer

Colorectal cancer (CRC) is the third most common cancer and the third leading cause of cancer death in the United States, causing about 50,000 deaths each year. Growth Factor-Independent 1 (GFI1) is a critical zinc finger transcriptional repressor responsible for controlling secretory cell differentiation in the small intestine and colon. GFI1 plays a significant role in the development of human malignancies, including leukemia, lung cancer and prostate cancer. However, the role of GFI1 in CRC progression is largely unknown. Our results demonstrate that RNA and protein expression of GFI1 are reduced in advanced stages of non-mucinous CRC. Subcutaneous tumor models demonstrated that the re-expression of GFI1 in 4 different human CRC cell lines inhibits tumor growth by 25-60%. To further investigate the role of Gfi1 in de novo colorectal tumorigenesis, we developed transgenic mice harboring a deletion of Gfi1 in the distal intestine driven by the CDX2cre (Gfi1F/F; CDX2cre/+) and crossed them with ApcMin/+ mice (ApcMin/+; Gfi1F/F; CDX2cre/+). Loss of Gfi1 significantly increased the total number of colorectal adenomas compared to littermate controls with an APC mutation alone. Furthermore, we found that compound (ApcMin/+; Gfi1F/F; CDX2cre/+) mice develop both adenomas as well as carcinoid-like tumors expressing the neuroendocrine marker chromogranin A, a feature that has not been previously described in APC-mutant tumors in mice. Collectively, these results demonstrate that Gfi1 deficiency promotes colorectal tumorigenesis, and suggest that loss of Gfi1 may promote formation of carcinoid cancers of the large intestines.\n\nSignificanceThese findings reveal that GFI1 functions as a tumor suppressor gene in colorectal tumorigenesis.

cancer biology↗

bioRxiv2017

Sox4 drives intestinal secretory differentiation toward tuft and enteroendocrine fates

Background & AimsThe intestinal epithelium is maintained by intestinal stem cells (ISCs), which produce post-mitotic absorptive and secretory epithelial cells. Initial fate specification toward enteroendocrine, goblet, and Paneth cell lineages is dependent on Atoh1, a master regulator of secretory differentiation. However, the origin of tuft cells, which participate in Type II immune responses to parasitic infection, is less clear and appears to occur in an Atoh1-independent manner. Here we examine the role of Sox4 in ISC proliferation and differentiation.\n\nMethodsWe used mice with intestinal epithelial-specific conditional knockout of Sox4 (Sox4fl/fl:vilCre; Sox4cKO) to study the role of Sox4 in the small intestine. Crypt- and single cell-derived organoids were used to assay proliferation and ISC potency between control and Sox4cKO mice. Lineage allocation and genetic consequences of Sox4 ablation were studied by immunofluorescence, RT-qPCR, and RNA-seq. In vivo infection with helminths and in vitro cytokine treatment in primary intestinal organoids were used to assess tuft cell hyperplasia in control and Sox4cKO samples. Atoh1GFP reporter mice and single cell RNA-seq (scRNA-seq) were used to determine co-localization of SOX4 and Atoh1. Wild-type and inducible Atoh1 knockout (Atoh1fl/fl:vilCreER; Atoh1iKO) organoids carrying an inducible Sox4 overexpression vector (Sox4OE) were used to determine the role of Atoh1 in Sox4 driven secretory differentiation.\n\nResultsLoss of Sox4 impairs ISC function and secretory differentiation, resulting in decreased numbers of enteroendocrine and tuft cells. In wild-type mice, SOX4+ cells are significantly upregulated following helminth infection coincident with tuft cell hyperplasia. Sox4 is activated by IL13 in vitro and Sox4cKO knockout mice demonstrate impaired tuft cell hyperplasia and parasite clearance following infection with helminths. A subset of Sox4-expressing cells colocalize with Atoh1 and enteroendocrine markers by scRNA-seq, while Sox4+/Atoh1-cells correlate strongly with tuft cell populations. Gain-of-function studies in primary organoids demonstrate that Sox4 is sufficient to drive both enteroendocrine and tuft cell differentiation, and can do so in the absence of Atoh1.\n\nConclusionOur data demonstrate that Sox4 promotes enteroendocrine and tuft cell lineage allocation independently of Atoh1. These results challenge long-standing views of Atoh1 as the sole regulator of secretory differentiation in the intestine and are relevant for understanding host epithelial responses to parasitic infection.

cell biology↗