Biology subjects

Hsieh, K.

Publications and source records attributed to Hsieh, K..

6 recordsLinked to original sources

bioRxiv2025

Divergent viral phosphodiesterases for immune signaling evasion

Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to humans. In response, viruses use phosphodiesterase-mediated oligonucleotide cleavage for immune evasion, a strategy whose diversity has not yet been explored. We used a canonical 2H phosphodiesterase (2H PDE) structure-based search of prokaryotic and eukaryotic viral sequences to identify an exceptional diversity of 2H PDEs across the virome, including enzymes not detectable with sequence search methods alone. Despite active site conservation, biochemical experiments revealed remarkable substrate specificity of these PDEs that corresponds to variation in the core 2H fold. This nuanced specificity allows 2H PDEs to selectively degrade oligonucleotide messengers to avoid interfering with host immune signaling. Together, these findings nominate viral 2H PDEs as key regulators of CDN signaling across the tree of life.

biochemistry↗

bioRxiv2025

Recurrent acquisition of nuclease-protease pairs in antiviral immunity

Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin-like protease repeatedly acquired by multiple, otherwise unrelated antiviral immune systems in bacteria. Cell-based and biochemical assays revealed the nuclease is a proenzyme that cleaves DNA only after activation by its partner protease. Phylogenetic analysis showed that two distinct immune systems, Hachiman and AVAST, use the same mechanism of proteolytic activation despite their independent evolutionary origins. Examination of nuclease-protease inheritance patterns identified caspase-nuclease (canu) genomic loci that confer antiviral defense in a pathway reminiscent of eukaryotic caspase activation. These results uncover the coordinated activities of pronucleases and their activating proteases within different immune systems and show how coevolution enables defense system innovation.

microbiology↗

bioRxiv2025

A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway

Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signaling that share mechanistic features with human anti-viral systems1. In these pathways, including CBASS and type III CRISPR systems in bacteria and cGAS-STING in humans, oligonucleotide synthesis occurs upon detection of virus or foreign genetic material in the cell, triggering the antiviral response2-4. In a surprising inversion of this process, we show here that the CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as part of an active mechanism that maintains cell health. Cell-based experiments demonstrated that the absence or loss of mCpol-produced cyclic oligonucleotides triggers cell death, preventing spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Structural and mechanistic investigation revealed mCpol to be a di-adenylate cyclase whose product, c-di-AMP, prevents toxic oligomerization of the effector protein 2TM{beta}. Analysis of cells by fluorescence microscopy showed that lack of mCpol allows 2TM{beta}-mediated cell death due to inner membrane collapse. These findings unveil a powerful new defense strategy against virus-mediated immune suppression, expanding our understanding of oligonucleotides in cell health and disease. These results raise the possibility of similar protective roles for cyclic oligonucleotides in other organisms including humans.

biochemistry↗

bioRxiv2024

A Multi-Modal Deep Learning Framework with Both Sequence and Structure for Tumor Antigens Prediction

Tumor antigens are key targets in cancer immunotherapies that can be recognized by T cell receptor and induce immune responses. However, precision screening of immunogenic tumor antigens remains a great challenge due to human leukocyte antigen (HLA) restriction and tumor antigen escape. Here, we introduce MultiTAP (Multi-modal Tumor Antigen Predictor), a pioneering multi-modal framework with TCR-peptide-HLA sequence and structure features incorporating an attention mechanism designed to accurately identify tumor antigens with immunogenic properties. By constructing the multi-modal TCR-peptide-HLA Dataset (TPHD) and integrating its sequence and structure, we perform antigen feature enhancement using peptide-HLA (pHLA) structural features at the residue level, achieving interpretable prediction of immunogenicity for tumor antigens. Relative to existing baseline models, the MultiTAP framework has exhibited superior efficacy in predicting the immunogenicity of tumor antigens. Through comprehensive out-of-distribution (OOD) assessments, MultiTAP has maintained predictive robustness across diverse HLA phenotypes and the continuously evolving landscape of epitope distributions. Overall, MultiTAP presents a brand-new and promising approach for cancer immunotherapies that target tumor antigens.

biophysics↗

bioRxiv2019

Machine Learning-Assisted Digital PCR and Melt Enables Broad Bacteria Identification and Pheno-Molecular Antimicrobial Susceptibility Test

Toward combating infectious diseases caused by pathogenic bacteria, there remains an unmet need for diagnostic tools that can broadly identify the causative bacteria and determine their antimicrobial susceptibilities from complex and even polymicrobial samples in a timely manner. To address this need, a microfluidic- and machine learning-based platform that performs broad bacteria identification (ID) and rapid yet reliable antimicrobial susceptibility testing (AST) is developed. Specifically, this new platform builds on \"pheno-molecular AST\", a strategy that transforms nucleic acid amplification tests (NAATs) into phenotypic AST through quantitative detection of bacterial genomic replication, and utilizes digital PCR and digital high-resolution melt (HRM) to quantify and identify bacterial DNA molecules. Bacterial species are identified using integrated experiment-machine learning algorithm via HRM profiles. Digital DNA quantification allows for rapid growth measurement that reflects susceptibility profiles of each bacterial species within only 30 min of antibiotic exposure. As a demonstration, multiple bacterial species and their susceptibility profiles in polymicrobial urine specimen were correctly identified with a total turnaround time of ~4 hours. With further development and clinical validation, this new platform holds the potential for improving clinical diagnostics and enabling targeted antibiotic treatments.\n\nTable of Contents Graphic\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC=\"FIGDIR/small/587543_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@184e367org.highwire.dtl.DTLVardef@16db02forg.highwire.dtl.DTLVardef@49e48corg.highwire.dtl.DTLVardef@13bb1d6_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2017

Pharmacological inhibition of the DNA damage checkpoint prevents radiation-induced oocyte death

Ovarian function is directly correlated with survival of the primordial follicle reserve. Women diagnosed with cancer have a primary imperative of treating the cancer, but since the resting oocytes are hypersensitive to the DNA-damaging modalities of certain chemo- and radiotherapeutic regimens, such patients face the collateral outcome of premature loss of fertility and ovarian endocrine function. Current options for fertility preservation primarily include collection and cryopreservation of oocytes or in vitro fertilized oocytes, but this necessitates a delay in cancer treatment and additional assisted reproductive technology (ART) procedures. Here, we evaluated the potential of pharmacological preservation of ovarian function by inhibiting a key element of the oocyte DNA damage checkpoint response, checkpoint kinase 2 (CHK2; CHEK2). Whereas non-lethal doses of ionizing radiation (IR) eradicate immature oocytes in wild type mice, irradiated Chk2-/- mice retain their oocytes and thus, fertility. Using an ovarian culture system, we show that transient administration of the CHK2 inhibitor 2-(4-(4-Chlorophenoxy)phenyl)-1H-benzimidazole-5-carboxamide-hydrate (\"CHK2iII\") blocked activation of the CHK2 targets TRP53 and TRP63 in response to sterilizing doses of IR, and preserved oocyte viability. After transfer into sterilized host females, these ovaries proved functional and readily yielded normal offspring. These results provide experimental evidence that chemical inhibition of CHK2 is a potentially valid treatment for preserving fertility and ovarian endocrine function of women exposed to DNA-damaging cancer therapies such as IR.\n\nSummary sentenceOocytes, which are highly sensitive to DNA damage caused by certain cancer treatments, can be protected from radiation-induced death by an inhibitor of the checkpoint protein CHK2.

cancer biology↗