Biology subjects

Kong, T.

Publications and source records attributed to Kong, T..

10 recordsLinked to original sources

bioRxiv2026

A Haplotype-resolved Telomere-to-Telomere Pig Genome

Haplotype-resolved telomere-to-telomere (T2T) pig genomes have not been reported, but may be essential for xenotransplantation and interspecies chimerism. Here we describe fully phased paternal and maternal T2T assemblies of an Erhualian pig (Ssc_EHL), enabling chromosome-scale reconstruction at base resolution. We uncover 2,498 (paternal haplotype) and 2,577 (maternal haplotype) protein-coding loci previously unresolved in Sscrofa11.1, while maintaining high concordance for anchored gene models between haplotypes. Applying this haplotype-resolved T2T annotation to publicly available pig-to-human kidney xenograft transcriptomes further allows the resolution of xenograft cell states and reveals newly resolved, cell-type-enriched genes. Cross-species synteny and orthology analyses against human identified a subset of high-confidence pig-specific genes with limited human counterparts, thus, refining the genomic basis of interspecies divergence. By integrating these orthology features with organ transcriptomes, we further defined an Interspecies Chimerism Compatibility score to prioritize organ-enriched, highly conserved loci with minimal redundancy imbalance, providing haplotype consistent targets for engineering organ-deficient pigs. Together, this haplotype-resolved T2T pig genome provides a foundational resource for mechanistic studies and rational genome engineering in xenotransplantation and interspecies chimerism.

genomics↗

bioRxiv2026

Single-Molecule Methods to Investigate Mechanisms of Transcription by RNA Polymerase of Mycobacterium tuberculosis

Single molecule methods have become prevalent tools in elucidating molecular processes across various life science fields over the past three decades, driving breakthroughs in understanding their underlying molecular mechanisms. In our study, we employed two single-molecule methods, Forster Resonance Energy Transfer (smFRET) and high-resolution optical tweezers, to investigate the transcription of Mycobacterium tuberculosis RNA polymerase (MtbRNAP) from initiation through to termination. We aim to provide a set of comprehensive biophysical tools to deepen our current understanding of MtbRNAP and its transcription factors. These experimental assays represent an important step towards unraveling the molecular dynamics and interactions that support transcription in Mycobacterium tuberculosis.

biophysics↗

bioRxiv2025

Pleomorphic effects of three small-molecule inhibitors on transcription elongation by Mycobacterium tuberculosis RNA polymerase

The Mycobacterium tuberculosis RNA polymerase (MtbRNAP) is the target of the first-line anti-tuberculosis inhibitor rifampin, however, the emergence of rifampin resistance necessitates the development of new antibiotics. Here, we communicate the first single-molecule characterization of MtbRNAP elongation and its inhibition by three diverse small-molecule inhibitors: N()-aroyl-N-aryl-phenylalaninamide (D-IX216), streptolydigin (Stl), and pseudouridimycin (PUM) using high-resolution optical tweezers. Compared to Escherichia coli RNA polymerase (EcoRNAP), MtbRNAP transcribes more slowly, has similar mechanical robustness, and only weakly recognizes E. coli pause sequences. The three small-molecule inhibitors of MtbRNAP exhibit strikingly different effects on transcription elongation. In the presence of D-IX216, which inhibits RNAP active-center bridge-helix motions required for nucleotide addition, the enzyme exhibits transitions between slowly and super-slowly elongating inhibited states. Stl, which inhibits the RNAP trigger-loop motions also required for nucleotide addition, inhibits RNAP primarily by inducing pausing and backtracking. PUM, a nucleoside analog of UTP, in addition to acting as a competitive inhibitor, induces the formation of slowly elongating RNAP inhibited states. Our results indicate that the three classes of small-molecule inhibitors affect the enzyme in distinct ways and show that the combination of Stl and D-IX216, which both target the RNAP bridge helix, has a strong synergistic effect on the enzyme.

biophysics↗

bioRxiv2025

ATR and PKMYT1 inhibition re-sensitize a subset of TNBC patient-derived models to carboplatin inducing mitotic catastrophe

Triple negative breast cancer (TNBC) is associated with poor prognosis and is mainly treated with chemotherapy-based regimens, often including carboplatin. Resistance to carboplatin is a common clinical issue that is either initially present or develops with treatment. Overcoming this resistance is a significant clinical challenge, which highlights the need for novel therapeutic strategies. We used a pooled shRNA screening approach with a chemoresistant TNBC patient-derived xenograft (PDX) cell (PDXC) line to identify targets whose knockdown would enhance the efficacy of carboplatin. This screening led to the identification of the ATR (ataxia telangiectasia and Rad3-related) gene as a key therapeutic vulnerability. Inhibiting ATR with BAY1895344 or AZD6738 re-sensitized carboplatin-resistant PDXCs and PDXs to carboplatin, resulting in an increase in DNA damage, and apoptosis. ATR inhibition disrupts the dependence of carboplatin-resistant cells on the S and G2/M checkpoints for DNA repair, leading to mitotic catastrophe. We further found that the addition of ATR inhibitors to carboplatin reversed a FOXM1-targeted gene program enabling premature passage into mitosis. Moreover, targeting PKMYT1, a regulator of cyclin-dependent kinase 1 (CDK1) controlling the G2/M checkpoint, through knockdown or with the novel PKMYT1 inhibitor RP-6306, also enhanced carboplatin efficacy in our TNBC PDXC. Molecular factors associated with response to the ATR inhibitor/carboplatin combination included low RNA levels of PKMYT1. These results underscore the pivotal roles of ATR and PKMYT1 in mediating resistance to carboplatin in TNBC and support targeting these pathways to overcome carboplatin resistance in this disease.

cancer biology↗

bioRxiv2024

Self-Assembled Chambered Cardiac Organoids for Modeling Cardiac Chamber Formation and Cardiotoxicity Assessment

The human heart, crucial for health and longevity, is a primary focus of medical research. Despite advancements in cardiac organoid technology, replicating early cardiac chamber formation stages remains challenging. Here, we develop chambered cardiac organoids (CCOs) by orchestrating cardiac signaling pathways, including the synergistic modulation of FGF and Wnt signaling via the HAND1 transcription factor. These CCOs exhibit stable chambers with self-organized outer myocardial and inner endocardial layers, and express developmental markers such as NKX2.5, TNNT2, and NAPPA, demonstrating physiological functionality including spontaneous contractions and calcium transients. Immunofluorescence and single-cell RNA sequencing confirmed the presence and stability of cardiomyocytes within CCOs. Further validation showed CCOs involvement in critical processes like endothelial-mesenchymal transition (EndoMT) and valvulogenesis. Ultrastructural and electrophysiological analysis revealed organized myofibrils and atrial-like action potentials. Importantly, CCOs proved effective in assessing cardiotoxicity through observable morphological changes, demonstrating specific cellular responses to established cardiotoxic compounds, thereby highlighting their potential for drug testing and safety evaluations. Our findings offer insights into cardiac chamber formation mechanisms and establish a robust platform for drug testing, disease modeling, and personalized medicine, representing a significant advancement in functional cardiac organoid development for both basic research and translational applications.

cell biology↗

bioRxiv2023

A telomere-to-telomere genome assembly of Zhonghuang 13, a widely-grown soybean variety from the original center of Glycine max

Soybean (Glycine max) stands as a globally significant agricultural crop, and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary history. Nevertheless, previous soybean genome assemblies have harbored gaps and incompleteness, which have constrained in-depth investigations into soybean. Here, we present the first Telomere-to-Telomere (T2T) assembly of the Chinese soybean cultivar "Zhonghuang 13" (ZH13) genome, termed ZH13-T2T, utilizing PacBio Hifi and ONT ultralong reads. We employed a multi-assembler approach, integrating Hifiasm, NextDenovo, and Canu, to minimize biases and enhance assembly accuracy. The assembly spans 1,015,024,879 bp, effectively resolving all 393 gaps that previously plagued the reference genome. Our annotation efforts identified 50,564 high-confidence protein-coding genes, 707 of which are novel. ZH13-T2T revealed longer chromosomes, 421 not-aligned regions (NARs), 112 structure variations (SVs), and a substantial expansion of repetitive element compared to earlier assemblies. Specifically, we identified 25.67 Mb of tandem repeats, an enrichment of 5S and 48S rDNAs, and characterized their genotypic diversity. In summary, we deliver the first complete Chinese soybean cultivar T2T genome. The comprehensive annotation, along with precise centromere and telomere characterization, as well as insights into structural variations, further enhance our understanding of soybean genetics and evolution.

plant biology↗

bioRxiv2023

xRead: a coverage-guided approach for scalable construction of read overlapping graph

The development of long-read sequencing is promising to high-quality and comprehensive de novo assembly for various species around the world. However, it is still challenging for genome assemblers to well-handle thousands of genomes, tens of gigabase level genome sizes and terabase level datasets simultaneously and efficiently, which is a bottleneck to large de novo sequencing studies. A major cause is the read overlapping graph construction that state-of-the-art tools usually have to cost terabyte-level RAM space and tens of days for that of large genomes. Such lower performance and scalability are not suited to handle the numerous samples to be sequenced. Herein, we propose xRead, an iterative overlapping graph approach that achieves high performance, scalability and yield simultaneously. Under the guidance of its novel read coverage-based model, xRead uses heuristic alignment skeleton approach to implement incremental graph construction with highly controllable RAM space and faster speed. For example, it enables to process the 1.28 Tb A. mexicanum dataset with less than 64GB RAM and obviously lower time-cost. Moreover, the benchmarks on the datasets from various-sized genomes suggest that it achieves higher accuracy in overlap detection without loss of sensitivity which also guarantees the quality of the produced graphs. Overall, xRead is suited to handle numbers of datasets from large genomes, especially with limited computational resources, which may play important roles in many de novo sequencing studies.

bioinformatics↗

bioRxiv2021

DUSP6 mediates resistance to JAK2 inhibition and drives leukemic progression

Chronic myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which the underlying mechanisms remain poorly understood, resulting in limited treatment options and dismal clinical outcomes. Here, we performed bulk transcriptome profiling accompanied by single cell RNA-sequencing on CD34+ stem/progenitor cells from serial patient samples obtained at the chronic MPN and sAML phases, and identified aberrantly increased expression of dual-specificity phosphatase 6 (DUSP6) underlying disease transformation. Genetic and pharmacologic targeting of DUSP6 led to inhibition of S6 and JAK/STAT signaling, resulting in potent suppression of cell proliferation, while also reducing inflammatory cytokine production in primary samples. Furthermore, ectopic DUSP6 expression augmented proliferation and mediated JAK2 inhibitor resistance, while DUSP6 inhibition reduced colony-forming potential of JAK2 inhibitor-persistent patient cells. Mechanistically, DUSP6 perturbation dampened S6 signaling via inhibition of RSK1, which we identified as a second indispensable candidate associated with poor clinical outcome. Lastly, DUSP6 inhibition potently suppressed disease development across Jak2 V617F and MPL W515L MPN mouse models, and sAML patient-derived xenografts. These findings underscore DUSP6 in driving disease transformation and therapeutic resistance, and highlight the DUSP6-RSK1 axis as a novel, druggable pathway in myeloid malignancies.

cancer biology↗

bioRxiv2020

Exosome-mediated apoptosis pathway during WSSV infection in crustacean mud crab

MicroRNAs are regulatory molecules that can be packaged into exosomes to modulate recipients cellular response, while their role during viral infection is beginning to be appreciated. However, the involvement of exosomal miRNAs during immunoregulation in invertebrates has not been addressed. Here, we found that exosomes released from WSSV-injected mud crabs could suppress viral invasion by inducing apoptosis of hemocytes. Besides, miR-137 and miR-7847 were found to be less packaged in mud crab exosomes during viral infection, with both miR-137 and miR-7847 shown to be negative apoptosis regulators by targeting the apoptosis-inducing factor (AIF). Moreover, our data revealed that AIF did not only translocate to the nucleus to induce DNA fragmentation, but could also competitively bind to HSP70 to disintegrate the HSP70-Bax (Bcl-2-associated X protein) complex, which eventually activated the mitochondria apoptosis pathway via free Bax. Therefore, our findings provides a novel mechanism underlying the crosstalk between exosomal miRNAs and apoptosis pathway in innate immunity in invertebrates.

immunology↗

bioRxiv2019

Delving below the species level to characterize the ecological diversity within the global virome: An exploration of West Nile Virus

Efforts to describe the diversity of viruses have largely focused on classifying viruses at the species level. However, substantial ecological diversity, both in virulence level and host range, is known within virus species. Here we demonstrate a proof of concept for easily discovering ecological diversity within a virus species taxon. We have focused on the West Nile Virus to take advantage of its broad host range in nature. We produced a genome-based phylogeny of world diversity of WNV and then used Ecotype Simulation 2 to hypothesize demarcation of genomes into 69 putative ecotypes (ecologically distinct populations), based only on clustering of genome sequences. Then we looked for evidence of ecological divergence among ecotypes based on differences in host bird associations within the Connecticut-New York region. Our results indicated significant heterogeneity among ecotypes for their associations with different bird hosts. Ecological diversity within other zoonotic viruses could be easily discovered using this approach. Opportunities for extending this line of research to human associations of virus ecotypes are limited by missing geographic metadata on human samples.

microbiology↗