Biology subjects

Chao, T.-C.

Publications and source records attributed to Chao, T.-C..

6 recordsLinked to original sources

bioRxiv2025

Association of GADD45A and favorable outcome in hormone positive breast cancer

BackgroundHormone receptor-positive (HR(+)) breast cancer is the most prevalent subtype in breast cancer, and although treatment options are rapidly increasing, still poses as an unmet need in advanced cases. Growth arrest and DNA damage-inducible alpha (GADD45A) is a gene with known relationship with the cell cycle and DNA damage pathways. Conflicting roles in breast cancer biology have been reported for GADD45A. In our study, we investigate the clinical and molecular association of GADD45A in HR(+) breast cancer, evaluating its prognostic potential and relationship with estrogen signaling. MethodsGADD45A expression was assessed in 100 breast cancer tissue samples from a tissue microarray and correlated with clinicopathologic parameters. Public genomic datasets were analyzed to validate associations between GADD45A expression and clinical outcomes in HR(+)HER2(-) breast cancer. Gene set enrichment analysis (GSEA) was used to investigate pathway correlations. ResultsGADD45A protein levels were highest in HR(+)HER2(-) tumors and positively correlated with estrogen receptor (ER) levels, consistent with a luminal phenotype. No significant association was observed between GADD45A levels and progression-free survival in CDK4/6 inhibitor-treated patients, suggesting limited predictive utility in this context. However, higher GADD45A expression was significantly associated with improved overall and relapse-free survival in HR(+)HER2(-) breast cancer in the METABRIC cohort, but not in HER2(+) or triple- negative subtypes. GSEA revealed a positive association between GADD45A expression and the estrogen late response signature, suggesting a functional link with hormone signaling. ConclusionGADD45A expression is enriched in luminal-type HR(+) breast cancer and correlates with favorable clinical outcomes. While not predictive of CDK4/6 inhibitor response, GADD45A may serve as a surrogate marker of estrogen signaling and improved prognosis. These findings support further investigation into GADD45A as a biomarker for stratification and potentially as a therapeutic target in HR(+) breast cancer.

cancer biology↗

bioRxiv2024

3D printed microtissue cassettes enabling high throughput proton radiobiological assays

Uncertainties on proton relative biological effectiveness (RBE) across the spread out of Bragg peak (SOBP) (typically assumed to be 1.1) may lead to suboptimal treatment plan and unwarranted toxicity to organs-at-risk. Herein, we report a reliable analytical method to determine the proton RBE along the SOBP and distal fall-off region. The 3D microtissue cassette enables the high throughput assessment of biological assays including clonogenic assay and {gamma}-H2AX assay following a single proton irradiation. Clonogenic assay shows the RBE of 1.6 (10% cellular survival) which is consistent with the deter-mined RBE of 1.58 using the {gamma}-H2AX assay. Besides, we also show that the high spatial resolution of the cassette can distinguish the minute but significant foci changes (number, area) in response to small proton radiation dose fraction. The results validate the reliability of our setup in addressing critical proton radiobiological questions.

bioengineering↗

bioRxiv2024

Structural basis of the human transcriptional Mediator complex modulated by its dissociable Kinase module

The eukaryotic Mediator, comprising a large Core (cMED) and a dissociable CDK8 kinase module (CKM), regulates RNA Polymerase II (Pol II)-dependent transcription. cMED recruits Pol II and promotes pre-initiation complex (PIC) formation in a manner inhibited by the CKM, which is also implicated in post-initiation control of gene expression. Herein we report cryo-electron microscopy structures of the human complete Mediator and its CKM, which explains the basis for CKM inhibition of cMED-activated transcription. The CKM binds to cMED through an intrinsically disordered region (IDR) in MED13 and HEAT repeats in MED12. The CKM inhibits transcription by allocating its MED13 IDR to occlude binding of Pol II and MED26 to cMED and further obstructing cMED-PIC assembly through steric hindrance with TFIIH and the +1 nucleosome. Notably, MED12 binds to the cMED Hook, positioning CDK8 downstream of the transcription start site, which sheds new light on its stimulatory function in post-initiation events.

biochemistry↗

bioRxiv2019

Blocks in tricarboxylic acid cycle of Salmonella enterica cause global perturbation of carbon storage, motility and host-pathogen-interaction

The tricarboxylic acid cycle is a central metabolic hub in most cells. Virulence functions of bacterial pathogens such as facultative intracellular Salmonella enterica serovar Typhimurium (STM) are closely connected to cellular metabolism. During systematic analyses of mutant strains with defects in TCA cycle, a strain deficient in all fumarase isoforms ({Delta}fumABC) elicited a unique metabolic profile. Alongside fumarate STM {Delta}fumABC accumulates intermediates of glycolysis and pentose phosphate pathway. Analyses by metabolomics and proteomics revealed that fumarate accumulation redirects carbon fluxes towards glycogen synthesis due to high (p)ppGpp levels. In addition, we observed reduced abundance of CheY, leading to altered motility and increased phagocytosis of STM by macrophages. Deletion of glycogen synthase restored normal carbon fluxes and phagocytosis, and partially levels of CheY. We propose that utilization of accumulated fumarate as carbon source induces a status similar to exponential to stationary growth phase transition by switching from preferred carbon sources to fumarate, which increases (p)ppGpp levels and thereby glycogen synthesis. Thus, we observed a new form of interplay between metabolism of STM, and cellular functions and virulence.\n\nImportanceWe performed perturbation analyses of the tricarboxylic acid cycle of the gastrointestinal pathogen Salmonella enterica serovar Typhimurium. The defect of fumarase activity led to accumulation of fumarate, but also resulted in a global alteration of carbon fluxes, leading to increased storage of glycogen. Gross alterations were observed in proteome and metabolome compositions of fumarase-deficient Salmonella. In turn, these changes were linked to aberrant motility patterns of the mutant strain, and resulted in highly increased phagocytic uptake by macrophages. Our findings indicate that basic cellular functions and specific virulence functions in Salmonella critically depend on the proper function of the primary metabolism.

microbiology↗

bioRxiv2018

Finding reliable phenotypes and detecting artefacts among in vivo and in vitro assays to characterize the refractory transcriptional activator Sxy (TfoX) in Escherichia coli

The Sxy (TfoX) protein is required for expression of a distinct subset of the genes regulated by the cAMP receptor protein (CRP) in the model organisms Escherichia coli, Haemophilus influenzae, and Vibrio cholerae. Genetic studies have established that CRP and Sxy co-activate transcription at gene promoters containing DNA binding sites called CRP-S sites. In contrast, CRP acts without Sxy at gene promoters containing canonical CRP-N sites, suggesting that Sxy makes physical contacts with CRP and/or DNA to assist in transcriptional activation at CRP-S promoters. Despite growing interest in Sxys activity as a transcription factor, Sxy remains poorly characterized due to a lack of reliable phenotypes in E. coli. Experiments are further hampered by growth inhibition and formation of inclusion bodies when Sxy is overexpressed. In this study we applied diverse phenotypic and molecular assays to test for postulated Sxy functions and interactions. Mutations in conserved regions of Sxy and truncations in the Sxy C-terminus abolish transcriptional activation of a CRP-S promoter, and a 37 amino acid truncation of the C-terminus relieves the growth inhibition normally caused by Sxy overexpression. Sxy was unable to augment weakened CRP interactions to restore carbon metabolism phenotypes. Bandshift analysis and chromatin pull-down assays of Sxy-CRP-DNA interactions yielded intriguing evidence of CRP-Sxy and Sxy-DNA physical interactions. However, despite the careful application of standard protein purification protocols and quality control steps for nickel affinity column purification, protein mass spectrometry revealed the enrichment of additional DNA-binding proteins in nickel column eluates, presenting a probable source of artefactual protein-protein and protein-DNA interaction results. These findings highlight the importance of extensive controls and phenotypic assays for the study of poorly characterized and recalcitrant proteins like Sxy.

microbiology↗

bioRxiv2017

The primary transcriptome, small RNAs, and regulation of antimicrobial resistance in Acinetobacter baumannii

AO_SCPCAPBSTRACTC_SCPCAPWe present the first high-resolution determination of transcriptome architecture in the priority pathogen Acinetobacter baumannii. Pooled RNA from 16 laboratory conditions was used for differential RNA-seq (dRNA-seq) to identify 3731 transcriptional start sites (TSS) and 110 small RNAs, including the first identification in A. baumannii of sRNAs encoded at the 3 end of coding genes. Most sRNAs were conserved among sequenced A. baumannii genomes, but were only weakly conserved or absent in other Acinetobacter species. Single nucleotide mapping of TSS enabled prediction of -10 and -35 RNA polymerase binding sites and revealed an unprecedented base preference at position +2 that hints at an unrecognized transcriptional regulatory mechanism. To apply functional genomics to the problem of antimicrobial resistance, we dissected the transcriptional regulation of the drug efflux pump responsible for chloramphenicol resistance, craA. The two craA promoters were both down-regulated >1000-fold when cells were shifted to nutrient limited medium. This conditional down-regulation of craA expression renders cells sensitive to chloramphenicol, a highly effective antibiotic for the treatment of multidrug resistant infections. An online interface that facilitates open data access and visualization is provided as \"AcinetoCom\" (http://bioinf.gen.tcd.ie/acinetocom/).

microbiology↗