Biology subjects

Chi, C.

Publications and source records attributed to Chi, C..

18 recordsLinked to original sources

bioRxiv2026

Ferroptosis is executed through caspase-5 cleavage of gasdermin E in ovarian cancer cells

Ferroptosis, an intracellular iron-catalyzed form of programmed cell death (PCD) driven by lipid reactive oxygen species induced membrane damage, is mechanistically uncharacterized in its execution process. Here, we investigated ferroptosis execution in mesenchymal-like ovarian cancer cells treated with ferroptosis inducers ML162 and erastin. We showed that YVAD (a pyroptosis-associated inflammatory caspase inhibitor) and disulfiram (preventing gasdermin pore formation on plasma membrane) deterred ferroptotic cell death. Moreover, we also observed LDH release and IL-1{beta} secretion from ferroptotic cells, suggesting that ferroptosis involves a pore-forming process. Intriguingly, ferroptosis is independent of the canonical inflammasome pathway because caspase-1 is dispensable and not activated upon ferroptosis induction. In contrast, we found that caspase-5 was activated while caspase-4 was not during ferroptosis. In addition, depletion of caspase-5 rendered cells not responding to ferroptosis inducers. Also intriguingly, GSDMD, the well-established caspase-5 substrate, was not involved in ferroptosis. We instead detected GSDME cleavage upon ferroptosis induction and knockdown of GSDME reduced cell death induced by ferroptosis inducers. As caspase-5 activity was necessary for ferroptosis and caspase-5 directly cleaved GSDME, we conclude that the axis of caspase-5/GSDME executes ferroptosis in ovarian cancer cells.

cell biology↗

bioRxiv2026

G4 Eurasian avian-like H1N1 swine influenza viruses exhibit enhanced pathogenicity potential in mice and pigs

Currently circulating swine influenza viruses (SIVs) mainly include H1N1, H1N2, and H3N2 subtypes. In this study, two G4 genotype Eurasian avian-like (EA) H1N1 SIVs were isolated from 556 samples collected between 2023 and 2026. A systematic analysis was conducted on the two EA H1N1 isolates (FYD30 and YZF69) to assess their pandemic potential. The hemagglutinin (HA) proteins of both H1N1 viruses possessed residues 225E and 228S, indicating enhanced affinity for human-like -2,6-linked sialic acid receptors, which was confirmed by receptor-binding assays. Polymerase activity tests demonstrated that the two SIVs exhibited significantly higher activity in mammalian cells, relative to avian cells, which is consistent with the efficient replication in mammalian cells. Challenge experiments revealed that both H1N1 caused significant pathogenicity in mice and pigs, with YZF69 exhibited higher virulence than FYD30. The higher virulence of YZF69 may be attributed to its molecular features, including the NP Q357K mutation, and an additional glycosylation site in HA. In conclusion, currently circulating EA H1N1 SIVs have acquired key molecular signatures of mammalian adaptation, exhibit enhanced virulence in mammals, and continue to undergo extensive reassortment driven by international swine trade. These findings highlight the potential pandemic risk of SIVs and underscore the urgent need for strengthened surveillance.

microbiology↗

bioRxiv2026

An underlying bistability sets amplitude and explains temperature compensation in the cyanobacterial circadian clock

Circadian clocks create free-running biological rhythms with a period close to 24 hours. A universal property of these systems is temperature compensation, where the period of oscillation remains nearly invariant even as the amplitude changes with temperature. In the cyanobacterial system, where the core oscillator can be reconstituted from purified KaiABC proteins, we identify a key temperature-dependent positive feedback process: antagonism between KaiA and KaiB creates a bistable switch in protein-protein interaction. The region of bistability is strongly temperature dependent and correlated with oscillator amplitude. Combining this bistable mechanism with the temperature scaling of phosphorylation and dephosphorylation rates in a mathematical model recapitulates the overall temperature compensation of the oscillator. This capacity for history-dependent switching suggests that bistable dynamics underpin the generation of circadian rhythms. Significance StatementCircadian clocks are biological oscillators that anticipate the day-night cycle. The 24-hour time scale of the clock is remarkably insensitive to temperature owing to compensatory changes in amplitude and speed with temperature. In the cyanobacterial clock, we identify a bistability of the protein interaction network which determines oscillator amplitude and depends strongly on temperature, balancing the temperature dependence of dephosphorylation rates. This bistability indicates that oscillations arise from a combination of positive and negative feedback loops, a design principle used to maintain temperature compensation.

biophysics↗

bioRxiv2026

ASFV early protein p30 suppresses antiviral type I IFN induction by targeting TRIM21 and RIG-I like receptor signaling adaptor MAVS

African swine fever (ASF) is a highly pathogenic disease caused by the African swine fever virus (ASFV) infection, which can affect pigs of all ages and breeds, posing significant threat to the global pig farming industry. The ASFV p30 protein is an early-expressed viral structural protein; however, its function is not fully understood. In this study, the interaction of viral p30 with host TRIM21 was identified. The ectopic TRIM21 inhibited ASFV replication, while knockdown or knockout of TRIM21 promoted ASFV replication. Further, p30 was found to interact with RIG-I-like receptor (RLR) signaling adaptor MAVS, and during ASFV infection, p30-TRIM21-MAVS interacted with each other. Mechanistically, TRIM21 activated the K27 polyubiquitination of MAVS to induce IRF3 mediated type I interferon (IFN) production, whereas p30 counteracted TRIM21 activated MAVS K27 polyubiquitination to evade RLR signaling mediated antiviral IFN induction. In summary, our study revealed a novel function of ASFV p30, and provided new insights into the immune evasion of ASFV.

immunology↗

bioRxiv2026

Species-specific regulation of porcine STING stability and antiviral signaling via its K61 mediated K48 ubiquitination and proteasome degradation

The cGAS-STING pathway has been widely recognized as a critical DNA-sensing pathway that plays a broad-spectrum antiviral role. Livestock, especially pigs, represents one of the most important meat sources. In this study, we identified a key lysine 61 (K61) of porcine STING (pSTING) that plays an essential role in its degradation and antiviral signaling in a species-specific manner, with K61 as the major lysine of pSTING for K48-linked ubiquitination. After virus infection, pSTING recruits the E3 ligase, RNF5, which specifically assembles a K48-linked ubiquitin chain at K61, thereby mediating pSTING proteasomal degradation and reducing its antiviral activity. Meanwhile, the deubiquitylation of K61 is mediated mainly by deubiquitinase USP20, which enhances the stability and antiviral activity of pSTING. Together, given the relatively few lysine numbers in livestock STINGs and species-specific K61 regulation of pSTING stability and antiviral function, the K61 and its specific regulatory enzymes of pSTING could serve as potential targets for breeding of antiviral pigs and design of antiviral drugs, respectively.

immunology↗

bioRxiv2025

Trsp is required by regulatory T cells to prevent lethal autoimmunity in mice

Selenoproteins are involved in immune cell metabolism, yet the roles of these proteins in T cell development and function remain largely unknown. The Trsp gene encodes the selenocysteine tRNA (tRNASec) required for translation of all selenoproteins. In this study, we found that Trsp was required for thymopoiesis, with the majority of tRNASec-deficient T cells not progressing beyond double negative 3 stage, with egressed thymocytes undergoing peripheral homeostatic expansion. Trsp-deficient CD4+ T cells exhibited impairments in TCR and IL-2 signaling and did not cause inflammation in experimental models. On the other hand, Trsp-deficient regulatory T (Treg) cells exhibited defects in suppressive function ex vivo and Treg-specific Trsp deletion using Trspfl/flFoxp3YFP-Cre (Trsp!{iota}Treg) mice caused fatal autoimmunity similar to FOXP3-deficient mice. Reducing oxidative stress via 2-HOBA administration prolonged survival in these Trsp!{iota}Treg mice. These findings indicate that tRNASec is required for T cell homeostasis and may be therapeutic targets in inflammation. One sentence summaryTrsp, a gene required for translation of all selenoproteins, is essential for all T cell development and function, especially regulatory T cells.

immunology↗

bioRxiv2025

PRRSV evades innate immune cGAS-STING antiviral function via its Nsp5 to deter STING translocation and activation

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is an important pathogen that seriously endangers pig breeding, causing significant economic losses to the global swine industry. Our previous study found that the DNA sensing innate cGAS-STING signaling pathway plays an important role in inducing interferon (IFN) upon PRRSV infection and inhibition of PRRSV replication. However, the immune evasion and its mechanism by PRRSV is still unclear. In current study, we found that PRRSV Non-structural protein 5 (Nsp5) strongly inhibits the cGAS-STING-IFN antiviral response. Further, we found that Nsp5 interacts with STING, blocking STING transport from ER to Golgi apparatus and interfering with STING recruitment of TBK1/IKK{varepsilon}/IRF3. Finally, we demonstrated that the Nsp5 36-47 and 58-67 amino acid regions are critical regions for inhibiting STING activity and PRRSV replication. The study describes a novel mechanism by PRRSV for suppression of the host innate antiviral response and have implications for our understanding of PRRSV pathogenesis. Author summaryThe innate immune system is the first line of host defense against infections. PRRSV is an immunosuppressive pathogen that has developed different strategies to evade the host innate immune responses. Here, we demonstrate for the first time that PRRSV utilizes its non-structural protein Nsp5 to inhibit the innate immune cGAS-STING-IFN signaling pathway, promoting the viral replication. Nsp5 can inhibit the cGAS-STING pathway by interacting with STING, blocking STING transport from ER to Golgi apparatus and interfering with STING recruitment of TBK1/IKK{varepsilon}/IRF3. In particular, the 36-47 and 58-67 amino acid regions of the Nsp5 is indispensable. This information will help us understand PRRSV-host interactions and provides new insights into the prevention and control of PRRSV.

immunology↗

bioRxiv2024

Mitochondrial Fatty Acid Synthesis and Mecr Regulate CD4+ T Cell Function and Oxidative Metabolism

SummaryWe show that the mitochondrial fatty acid synthesis gene Mecr shapes CD4+ T cell metabolism and function. It may be targeted in inflammatory diseases and provides rationale to consider the immunological state of patients with mitochondrial disease. Lipid metabolism is fundamental to CD4+ T cell metabolism yet remains poorly understood across subsets. Therefore, we performed targeted in vivo CRISPR/Cas9 screens to identify lipid-associated genes essential for T cell subset functions. These screens established mitochondrial fatty acid synthesis (mtFAS) genes Mecr, Mcat and Oxsm as highly impactful. Of these, the inborn error of metabolism gene Mecr was most dynamically regulated. Effector and memory T cells were reduced in Mecrfl/fl; Cd4cre mice, and MECR was required for activated CD4+ T cells to efficiently proliferate, differentiate, and survive. Mecr-deficient T cells also had decreased mitochondrial respiration, reduced TCA intermediates, and accumulated intracellular iron, which contributed to cell death and sensitivity to ferroptosis. Importantly, Mecr-deficient T cells exhibited fitness disadvantages in inflammatory, tumor, and infection models. mtFAS and MECR thus play important roles in activated T cells and may provide targets to modulate immune functions in inflammatory diseases. The immunological state of MECR- and mtFAS-deficient patients may also be compromised.

immunology↗

bioRxiv2024

YmoA functions as a molecular stress sensor in Yersinia

Pathogenic bacteria sense and respond to environmental fluctuations, a capability essential for establishing successful infections. The YmoA/Hha protein family are conserved transcription regulators in Enterobacteriaceae, playing a critical role in these responses. Specifically, YmoA in Yersinia adjusts the expression of virulence-associated traits upon temperature shift. Still, the molecular mechanisms transducing environmental signal through YmoA remain elusive. Our study employed nuclear magnetic resonance spectroscopy, biological assays and RNA-seq analysis to elucidate these mechanisms. We demonstrated that YmoA underwent structural fluctuations and conformational dynamics in response to temperature and osmolarity changes, correlating with changes in plasmid copy number, bacterial fitness and virulence function. Notably, chemical shift analysis identified key roles of a few specific residues and of the C-terminus region in sensing both temperature and salt-driven switch. These findings demonstrate that YmoA acts as a central stress sensor in Yersinia, fine-tuning virulence gene expression and balancing metabolic trade-offs.

molecular biology↗

bioRxiv2023

Tissue-Specific Dependence of Th1 Cells on the Amino Acid Transporter SLC38A1 in Inflammation

Amino acid (AA) uptake is essential for T cell metabolism and function, but how tissue sites and inflammation affect CD4+ T cell subset requirements for specific AA remains uncertain. Here we tested CD4+ T cell AA demands with in vitro and multiple in vivo CRISPR screens and identify subset- and tissue-specific dependencies on the AA transporter SLC38A1 (SNAT1). While dispensable for T cell persistence and expansion over time in vitro and in vivo lung inflammation, SLC38A1 was critical for Th1 but not Th17 cell-driven Experimental Autoimmune Encephalomyelitis (EAE) and contributed to Th1 cell-driven inflammatory bowel disease. SLC38A1 deficiency reduced mTORC1 signaling and glycolytic activity in Th1 cells, in part by reducing intracellular glutamine and disrupting hexosamine biosynthesis and redox regulation. Similarly, pharmacological inhibition of SLC38 transporters delayed EAE but did not affect lung inflammation. Subset- and tissue-specific dependencies of CD4+ T cells on AA transporters may guide selective immunotherapies. HIGHLIGHTSO_LIT cells dynamically regulate glutamine amino acid transporters when activated C_LIO_LISLC38A1 supports Th1 cell mTORC1 and proliferation by redox and hexosamine pathways C_LIO_LITargeting SLC38A1 does not affect lung inflammation but delays IBD and EAE C_LIO_LINutrient transporter needs of T cell subsets vary based on disease and tissue site C_LI

immunology↗

bioRxiv2023

Folded alpha helical putative new proteins from Apilactobacillus kunkeei

The emergence of new proteins is a central question in biology. Most tertiary protein folds known to date appear to have an ancient origin, but it is clear from bioinformatic analyses that new proteins continuously emerge in all organismal groups. However, there is a paucity of experimental data on new proteins regarding their structure and biophysical properties. We performed a detailed phylogenetic analysis and identified 48 putative open reading frames in the honeybee-associated bacterium Apilactobacillus kunkeei for which no homologs could be identified in closely-related species, suggesting that they could be relatively new on an evolutionary time scale and represent recently evolved proteins. Using circular dichroism-, fluorescence- and nuclear magnetic resonance spectroscopy we investigated five of these proteins and show that they are not intrinsically disordered, but populate alpha-helical dominated folded states with relatively low thermodynamic stability (0-3 kcal/mol). The data demonstrate that small new proteins readily adopt simple folded conformations suggesting that more complex tertiary structures can be continuously re-invented during evolution by fusion of such simple secondary structure elements. These findings have implications for the general view on protein evolution, where de novo emergence of folded proteins may be a common event.

molecular biology↗

bioRxiv2023

Androgen Signaling Restricts Glutaminolysis to Drive Sex-Specific Th17 Metabolism

Females have increased prevalence of many Th17-mediated diseases. While androgen signaling decreases Th17-mediated inflammation, the mechanisms are not fully understood. Th17 cells rely on glutaminolysis; however, it remains unclear whether androgen receptor (AR) signaling in males modifies glutamine metabolism to suppress Th17-mediated inflammation. We show that Th17 cells from male humans and mice had decreased glutaminolysis compared to females, and AR signaling attenuated Th17 cell mitochondrial respiration and glutaminolysis. Using allergen-induced airway inflammation models, we determined females, but not males, had a critical reliance upon glutaminolysis for Th17-mediated airway inflammation, and AR signaling attenuated glutamine uptake by reducing expression of glutamine transporters. These findings were confirmed in circulating human Th17 cells with minimal reliance on glutamine uptake in male compared to female Th17 cells. We found that AR signaling attenuates glutaminolysis, demonstrating sex-specific metabolic regulation of Th17 cells with implications for design and implementation of Th17 or glutaminolysis targeted therapeutics. HighlightsO_LIHuman male CD4+ T cells have decreased expression of metabolic enzymes and decreased reliance on glutaminolysis compared to female CD4+ T cells. C_LIO_LIAndrogen signaling decreased mitochondrial metabolism in Th17 cells and decreased airway inflammation. C_LIO_LIAndrogen signaling decreased glutamine uptake and utilization in Th17 cells. C_LI

immunology↗

bioRxiv2023

Functional Overlap of Inborn Errors of Immunity and Metabolism Genes Define T Cell Immunometabolic Vulnerabilities

Inborn Errors of Metabolism (IEM) and Immunity (IEI) are Mendelian diseases in which complex phenotypes and patient rarity can limit clinical annotations. Few genes are assigned to both IEM and IEI, but immunometabolic demands suggest functional overlap is underestimated. We applied CRISPR screens to test IEM genes for immunologic roles and IEI genes for metabolic effects and found considerable crossover. Analysis of IEM showed N-linked glycosylation and the de novo hexosamine synthesis enzyme, Gfpt1, are critical for T cell expansion and function. Interestingly, Gfpt1-deficient TH1 cells were more affected than TH17 cells, which had increased Nagk for salvage UDP-GlcNAc synthesis. Screening IEI genes showed the transcription factor Bcl11b promotes CD4+ T cell mitochondrial activity and Mcl1 expression necessary to prevent metabolic stress. These data illustrate a high degree of functional overlap of IEM and IEI genes and point to potential immunometabolic mechanisms for a previously unappreciated set of these disorders. HIGHLIGHTSO_LIInborn errors of immunity and metabolism have greater overlap than previously known C_LIO_LIGfpt1 deficiency causes an IEM but also selectively regulates T cell subset fate C_LIO_LILoss of Bcl11b causes a T cell deficiency IEI but also harms mitochondrial function C_LIO_LIMany IEM may have immune defects and IEI may be driven by metabolic mechanisms C_LI

immunology↗

bioRxiv2022

Subset-specific mitochondrial and DNA damage shapes T cell responses to fever and inflammation

Heat is a cardinal feature of inflammation. Despite temperature variability and dependence of enzymes and complexes, how heat and fever affect immune cells remains uncertain. We found that heat broadly increased inflammatory activity of CD4+ T cell subsets and decreased Treg suppressive function. Th1 cells, however, also selectively developed mitochondrial dysfunction with high levels of ROS production and DNA damage. This led Th1 cells to undergo Tp53-dependent death, which was required to minimize the accumulation of mutations in heat and inflammation. Th1 cells with similar DNA damage signatures were also detected in Crohns disease and rheumatoid arthritis. Fever and inflammation-associated heat thus selectively induce mitochondrial stress and DNA damage in activated Th1 cells that requires p53 to maintain genomic integrity of the T cell repertoire. One Sentence SummaryFever temperatures augment CD4+ T cell-mediated inflammation but induce differential metabolic stress and DNA damage in T cell subsets, with Th1 cells selectively sensitive and dependent on p53 to induce apoptosis and maintain genomic integrity.

immunology↗

bioRxiv2022

Interferon receptor gene dosage determines multiple hallmarks of Down syndrome

Trisomy 21 causes Down syndrome, a condition characterized by cognitive impairments, immune dysregulation, and atypical morphogenesis. Using whole blood transcriptome analysis, we demonstrate that specific overexpression of four interferon receptors encoded on chromosome 21 associates with chronic interferon hyperactivity and systemic inflammation in Down syndrome. To define the contribution of interferon receptor overexpression to Down syndrome phenotypes, we used genome editing to correct interferon receptor gene dosage in mice carrying triplication of a large genomic region orthologous to human chromosome 21. Normalization of interferon receptor copy number attenuated lethal antiviral responses, prevented heart malformations, decreased developmental delays, improved cognition and normalized craniofacial anomalies. Therefore, interferon receptor gene dosage determines major hallmarks of Down syndrome, indicating that trisomy 21 elicits an interferonopathy amenable to therapeutic intervention. One-Sentence SummaryCorrection of interferon receptor gene dosage rescues multiple key phenotypes in a mouse model of trisomy 21.

genetics↗

bioRxiv2021

HLA Allele Imputation with Multitask Deep Convolutional Neural Network

MotivationThe Human leukgocyte antigen (HLA) system is a highly polymorphic gene complex encoding the major histocompatibility complex proteins in humans. HLA alleles are of strong epidemiological interest for their large effect sizes in associations with autoimmune diseases, infectious diseases, severe drug reactions, and transplant medicine. Since HLA genotyping can be time-consuming and cost-prohibitive, methods to impute HLA alleles from SNP genotype data have been developed, including HLA Genotype Imputation with Attribute Bagging (HIBAG), HLA*IMP:02, and SNP2HLA. However, limitations of these imputation programs include imputation accuracy, computational runtime, and ability to impute HLA allele haplotypes. ResultsWe present a deep learning framework for HLA allele imputation using a multitask convolutional neural network (CNN) architecture. In this approach, we use phased SNP genotype data flanking {+/-}250 kb from each HLA locus to simultaneously impute HLA allele haplotyes across loci HLA-A, -B, -C, -DQA1, -DQB1, -DPA1, -DPB1, and -DRB1. We start by tokenizing phased genotype sequences into k-mers that serve as input to the model. The CNN architecture starts with a shared embedding layer for learning low-dimensional representations of k-mers, shared convolutional layers for detecting genotype motifs, and branches off into separate densely-connected layers for imputing each HLA loci. We present evidence that the CNN used information from known tag SNPs to impute HLA alleles, and demonstrate the architecture is robust against a selection of hyperparameters. On the T1DGC dataset, our model achieved 97.6% imputation accuracy, which was superior to SNP2HLAs performance and comparable to HIBAGs performance. However, unlike HIBAG, our method can impute an entire HLA haplotype sequence instead of imputing one locus at a time. Additionally, by separating the training and inference steps, our imputation program provides user flexibility to reduce usage time. AvailabilityThe source code is available at https://github.com/CalvinTChi/HLA_imputation Contactcalvin.chi@berkeley.edu

bioinformatics↗

bioRxiv2020

Suppression of canonical TGF-β signaling enables GATA4 to interact with H3K27me3 demethylase JMJD3 to promote cardiomyogenesis

Direct reprogramming of fibroblasts into cardiomyocytes (CMs) represents a promising strategy to regenerate CMs lost after ischemic heart injury. Overexpression of GATA4, HAND2, MEF2C, TBX5, miR-1, and miR-133 (GHMT2m) along with transforming growth factor beta (TGF-{beta}) inhibition efficiently promotes reprogramming. However, the mechanisms by which TGF-{beta} blockade promotes cardiac reprogramming remain unknown. Here, we identify interactions between the histone H3 lysine 27 trimethylation (H3K27me3) - demethylase JMJD3, the SWI/SNF remodeling complex subunit BRG1, and cardiac transcription factors. Furthermore, canonical TGF-{beta} signaling regulates the interaction between GATA4 and JMJD3. TGF-{beta} activation impairs the ability of GATA4 to bind target genes and prevents demethylation of H3K27 at cardiac gene promoters during cardiac reprogramming. Finally, a mutation in GATA4 (V267M) exhibits reduced binding to JMJD3 and impaired cardiomyogenesis. Thus, we have identified an epigenetic mechanism wherein canonical TGF-{beta} pathway activation impairs cardiac gene programming by interfering with GATA4-JMJD3 interactions.

cell biology↗

bioRxiv2020

Maturation of human induced pluripotent stem cell-derived cardiomyocytes for modeling hypertrophic cardiomyopathy

RationaleHuman induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) are a powerful platform for biomedical research. However, they are immature, which is a barrier to modeling adult-onset cardiovascular disease. ObjectiveWe sought to develop a simple method which could drive cultured hiPSC-CMs towards maturity across a number of phenotypes. Methods and resultsCells were cultured in fatty acid-based media and plated on micropatterned surfaces to promote alignment and elongation. These cells display many characteristics of adult human cardiomyocytes, including elongated cell morphology, enhanced maturity of sarcomeric structures, metabolic behavior, and increased myofibril contractile force. Most notably, hiPSC-CMs cultured under optimal maturity-inducing conditions recapitulate the pathological hypertrophy caused by either a pro-hypertrophic agent or genetic mutations. ConclusionsThe more mature hiPSC-CMs produced by the methods described here will serve as a useful in vitro platform for characterizing cardiovascular disease.

cell biology↗