Biology subjects

Shih, C.-H.

Publications and source records attributed to Shih, C.-H..

7 recordsLinked to original sources

bioRxiv2026

KMT5C-H4K20me3 drives changes in epigenetic landscape independent of H3K9me3

Histone H4 lysine 20 trimethylation (H4K20me3) is a histone modification that is critical in maintaining genome integrity. Dysregulation of H4K20me3 and KMT5C, the major methyltransferase for H4K20me3, occurs commonly in multiple types of cancer but the mechanisms surrounding how they contribute to shaping the epigenomic landscape remains unclear. Here, we show that KMT5C is involved in non-canonical deposition of H4K20me3, independent of H3K9me3, which was previously recognized as a prerequisite for H4K20me3. This novel subtype of H4K20me3 lacks canonical repressive epigenetic signatures and instead overlaps with multiple activating marks. These activating modifications likely contribute to the dynamic changes in transcript levels upon loss of H4K20me3. The mechanism involved in recruiting KMT5C to these loci is independent of HP1, the factor reported to be involved in recruitment of KMT5C to heterochromatin marked with H3K9me3. Instead, biochemical analyses revealed ZNF280C to be a novel interacting partner of KMT5C, with ZNF280C localizing specifically at H3K9me3-/H4K20me3+ sites. Together, these results suggest a novel, non-canonical function of KMT5C-H4K20me3 that protects vulnerable regions of the genome from uncontrolled expression.

genomics↗

bioRxiv2024

The circadian gene Dec2 promotes pancreatic cancer dormancy by regulating tumor cell antigen presentation to facilitate immune evasion

The mechanisms that regulate cancer dormancy remain poorly understood. Using a mouse model of resectable pancreatic adenocarcinoma (PDAC), we identified Dec2 as a gene that was upregulated in metastatic dormant tumor cells. Deletion of Dec2 from tumor cells substantially increased mouse survival after resection due to an immune-mediated mechanism as the survival benefit was abrogated in immunodeficient conditions. Dec2 promoted immune evasion by repressing multiple components of the MHC-I dependent antigen presentation pathway in tumor cells. Dec2 is a regulator of circadian rhythms, and we found several components of the antigen presentation pathway oscillated in a circadian manner that was lost upon deletion of Dec2. Moreover, T-cell mediated tumor cell killing varied depending on the time of day. We suggest that lowered MHC-I presentation of antigens during rest phase is a natural effect of the circadian clock, which is exploited by Dec2-overexpressing pancreatic tumors to evade the immune system.

cancer biology↗

bioRxiv2024

High-Throughput Empirical and Virtual Screening to Discover Novel Inhibitors of Polyploid Giant Cancer Cells in Breast Cancer

Therapy resistance in breast cancer is increasingly attributed to polyploid giant cancer cells (PGCCs), which arise through whole-genome doubling and exhibit heightened resilience to standard treatments. Characterized by enlarged nuclei and increased DNA content, these cells tend to be dormant under therapeutic stress, driving disease relapse. Despite their critical role in resistance, strategies to effectively target PGCCs are limited, largely due to the lack of high-throughput methods for assessing their viability. Traditional assays lack the sensitivity needed to detect PGCC-specific elimination, prompting the development of novel approaches. To address this challenge, we developed a high-throughput single-cell morphological analysis workflow designed to differentiate compounds that selectively inhibit non-PGCCs, PGCCs, or both. Using this method, we screened a library of 2,726 FDA Phase 1-approved drugs, identifying promising anti-PGCC candidates, including proteasome inhibitors, FOXM1, CHK, and macrocyclic lactones. Notably, RNA-Seq analysis of cells treated with the macrocyclic lactone Pyronaridine revealed AXL inhibition as a potential strategy for targeting PGCCs. Although our single-cell morphological analysis pipeline is powerful, empirically testing all existing compounds is impractical and inefficient. To overcome this limitation, we trained a machine learning model to predict anti-PGCC efficacy in silico, integrating chemical fingerprints and compound descriptions from prior publications and databases. The model demonstrated a high correlation with experimental outcomes and predicted efficacious compounds in an expanded library of over 6,000 drugs. Among the top-ranked predictions, we experimentally validated two compounds as potent PGCC inhibitors. These findings underscore the synergistic potential of integrating high-throughput empirical screening with machine learning-based virtual screening to accelerate the discovery of novel therapies, particularly for targeting therapy-resistant PGCCs in breast cancer.

bioengineering↗

bioRxiv2023

Reduced glutamate decarboxylase 1 underlies morphine-promoted lung metastasis of triple-negative breast cancer in mice

IntroductionMorphine is commonly used for cancer-related pain management. Long-term morphine use is not only addictive but also has been associated with risk factor for cancer. MethodsWe intraperitoneally administered morphine to mice for 14 days and then implanted EO771 cells, triple negative breast cancer cells, into their mammary fat pad. After primary tumors were removed on 38th day, a subset of mice were continuously giving saline or morphine until the 68th day. Tumor size, organ metastasis, and tumor RNA expression were analyzed. ResultsOur results revealed that long-term morphine treatment increased lung metastasis in the triple-negative breast cancer mouse model. To determine cellular pathways responsible for morphine-mediated metastasis, we performed RNA sequencing analysis to compare transcriptional profiles during metastasis. Transcriptional analysis revealed a significant number of genes down-regulated by morphine treatment. Based on pathway analysis, we focused on the novel effect of morphine on down-regulating taurine/hypotaurine biosynthesis. Considering that morphine, droperidol (dopamine receptor antagonist), and naloxone (opioid receptor antagonist) may act through opioid receptor or dopamine receptor, we further demonstrated that taurine reduced EO771 cell invasion caused by morphine, but not by droperidol, or naloxone treatment. In addition, morphine treatment significantly reduced the expression of GAD1, one of the enzymes required for biosynthesis of taurine, whereas droperidol and naloxone did not. ConclusionThese novel findings of morphine reduces GAD1 level and taurine reverses invasion suggest that taurine could potentially be employed as a supplement for triple negative breast cancer patients using morphine as pain management. Key MessagesO_LIMorphine usage has been implicated in modulating immune system and affecting cancer progression. C_LIO_LILong-term usage of morphine promotes metastasis of triple negative breast cancer through reducing taurine biosynthesis. C_LIO_LIThese novel findings of morphine reduces GAD1 level and taurine reverses invasion suggest that taurine could potentially be employed as a supplement for triple negative breast cancer patients using morphine as pain management. C_LI

cancer biology↗

bioRxiv2021

Cis-regulatory variants affect gene expression dynamics in yeast

Evolution of cis-regulatory sequences depends on how they effect gene expression and motivates both the identification and prediction of cis-regulatory variants responsible for expression differences within and between species. While much progress has been made in relating cis-regulatory variants to expression levels, the timing of gene activation and repression may also be important to the evolution of cis-regulatory sequences. We investigated allele-specific expression (ASE) dynamics within and between Saccharomyces species during the diauxic shift and found appreciable cis-acting variation in gene expression dynamics. Within species ASE is associated with intergenic variants, but ASE dynamics are more strongly associated with insertions and deletions than ASE levels. To refine these associations we used a high-throughput reporter assay to test promoter regions and individual variants. Within the subset of regions that recapitulated endogenous expression we identified and characterized cis-regulatory variants that affect expression dynamics. Between species, chimeric promoter regions generate novel patterns and indicate constraints on the evolution of gene expression dynamics. We conclude that changes in cis-regulatory sequences can tune gene expression dynamics and that the interplay between expression dynamics and other aspects expression are relevant to the evolution of cis-regulatory sequences.

evolutionary biology↗

bioRxiv2019

Integrative Functional Network Interactions Underlie the Association between Physical Activity and Cognition in Neurodegenerative Diseases

Physical activity (PA) has preventive and possibly restorative effects in aging-related cognitive decline, which relate to intrinsic functional interactions (functional connectivity, FC) in large-scale brain networks. Preventive and ameliorative effects of PA on cognitive decline have also been documented in neurodegenerative diseases, such as Parkinson's disease (PD). However, the neural substrates that mediate the association between PA and cognitive performance under such neurological conditions remain unknown. Here we set out to examine if the association between PA and cognitive performance in PD is mediated by FC in large-scale sensorimotor and association brain networks. Data from 51 PD patients were analyzed. Connectome-level analysis based on a whole-brain parcellation showed that self-reported levels of PA were associated with increased FC between, but not within the default mode (DMN) and salience networks (SAL) (p < .05, false discovery rate corrected). Additionally, multiple parallel mediation analysis further demonstrated that FC between left lateral parietal nodes in the DMN and rostral prefrontal nodes in the SAL mediated the association between PA and executive function performance. These findings are in line with previous studies linking FC in large-scale association networks with the effects of PA on cognition in healthy aging. Our results extend these previous results by demonstrating that the association between PA and cognitive performance in neurodegenerative diseases such as PD is mediated by integrative functional interactions in large-scale association networks.

neuroscience↗

bioRxiv2017

Comparative genomics approaches accurately predict deleterious variants in plants

Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but the approaches are nearly always assessed based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, their relative ranking differed from prior benchmarks in humans. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches does not necessarily translate from one species to another.

bioinformatics↗