Biology subjects

Chan, C.

Publications and source records attributed to Chan, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

A Way Through the Trees: Molecular Phylogenies Consistently Recover Two Clades of Aedes Mosquitoes

Phylogenetic analyses of molecular data have been critical in resolving deep and shallow relationships across the tree of life. Such analyses have provided clarity where traditional morphological analyses may not have, and have been instrumental in a range of evolutionary, systematic, and taxonomic studies for providing clarity to evolutionary relationships. One such case where evolutionary relationships are poorly understood is in the mosquito genus Aedes. Although this medically important genus of insects has received significant study, the majority of research has focused on those relatively few species that are invasive and transmit pathogens which cause disease. As a result, evolutionary relationships between Aedes mosquitoes are poorly understood, and the classification of the genus has been contentious, with numerous taxonomic changes over the last two decades being undertaken and reversed based entirely on analyses of somewhat limited morphological data. As a result, we conducted a literature review of molecular phylogenies and evaluated classificatory hypotheses under a framework based on observations of frequently occurring relationships among mosquito genera and subgenera. We found that molecular phylogenies consistently reflect two distinct clades of Aedes mosquitoes, each with other Aedini genera within them. We discuss these results in the context of ongoing debates over Aedes nomenclature. Our review demonstrates the ability for molecular phylogenies to aid in resolving long-standing debates on nomenclature. HighlightsO_LIThe genus Aedes, in the tribe Aedini, contains many of the worlds most important disease vector mosquitoes, such as the yellow fever mosquito Aedes aegypti. C_LIO_LIThe phylogeny of the genus Aedes remains contentious, leading to repeated and often confusing changes in taxonomy and nomenclature. C_LIO_LINo comprehensive molecular phylogenies of the genus Aedes have been published the, but Aedes species have been included in many phylogenetic analyses. C_LIO_LIMolecular phylogenies demonstrate consistent results: There are two major clades of Aedes mosquitoes, neither of which are monophyletic. C_LI Graphical Abstract

evolutionary biology↗

bioRxiv2025

Landscape and mutational dynamics of G-quadruplexes in the complete human genome and in haplotypes of diverse ancestry

G-quadruplexes (G4s) are alternative DNA structures with diverse biological roles, but their examination in highly repetitive parts of the human genome has been hindered by the lack of reliable sequencing technologies. Recent long-read based genome assemblies have enabled their characterization in previously inaccessible parts of the human genome. Here, we examine the topography and genomic instability of potential G4-forming sequences in the gap-less, reference human genome assembly and in 88 haplotypes of diverse ancestry. We report that G4s are highly enriched in specific repetitive regions, including in certain centromeric and pericentromeric repeat types, and in ribosomal DNA arrays, and experimentally validate the most prevalent G4s detected. G4s tend to have lower methylation than expected throughout the human genome and are genomically unstable, showing an excess of all mutation types, including substitutions, insertions and deletions and most prominently structural variants. Finally, we show that G4s are consistently enriched at PRDM9 binding sites, a protein involved in meiotic recombination. Together, our findings establish G4s as dynamic and functionally significant elements of the human genome and highlight new avenues for investigating their contributions to human disease and evolution.

genomics↗

bioRxiv2025

Ammonia-mediated Conformational Dynamics in SCAP for SREBP Activation

Cholesterol homeostasis is regulated by the sterol regulatory element-binding protein (SREBP) pathway, with the membrane-embedded SREBP-cleavage-activating protein (SCAP) and insulin-inducible gene protein (Insig)-1/2 acting as sterol sensors. Our previous studies unveiled a critical role of ammonia in activating the SREBP pathway. Here, we performed extensive molecular dynamics (MD) simulations to elucidate the structural mechanisms through which ammonia binding triggers SCAP/Insig dissociation and subsequently activate SREBP. The SCAP S4 helix exists in two distinct conformations: a partially unfolded S4 and an intact S4; the transition between these states may constitute a crucial aspect of SCAP activation. We first studied the binding of ammonia to SCAP in different S4 conformational states. We then explored how the binding of ammonia or 25-hydroxycholesterol (25-HC) affects the conformational transition of S4 using targeted MD simulations. Finally, we performed comparative analysis of the 25-HC-bound inactive SCAP and the ammonia-bound active SCAP. Collectively, our findings highlight the importance of S4 helix conformation in activating the SCAP protein. Our simulations suggest that ammonia and 25-HC act as an agonist and antagonist of SCAP activation, respectively. Specifically, ammonia binding facilitates the transition of S4 from the unfolded to the straight conformation, triggering subsequent conformational changes in the transmembrane domain of SCAP. These changes eventually promote the SCAP/Insig dissociation and alter the position of the MELADL motif at the membrane surface. Significant StatementCellular cholesterol homeostasis is tightly regulated by the SREBP pathway, which relies on the membrane proteins SCAP and Insig to sense sterol levels. While ammonia has recently been identified as a novel activator of this pathway, its structural mechanism of action remained unknown. Here, extensive molecular dynamics simulations reveal that ammonia binding promotes a critical conformational transition in the SCAP S4 helix, facilitating SCAP activation and its dissociation from Insig. Our findings show that ammonia and cholesterol act as opposing modulators--agonist and antagonist--of SCAP activity. This work uncovers a previously unrecognized structural switch in SCAP and provides new molecular insight into small-molecule regulation of cholesterol sensing.

molecular biology↗

bioRxiv2025

Chromosomal Aneuploidy in Normal, Non-Neuronal Brain Nuclei of Glioblastoma Patients is Not a Cancer Driver

Aneuploidy is a hallmark of cancers, including high-grade glioma (GBM), one of the most aggressive brain tumors. To assess whether increased aneuploidy already occurs in normal brain tissue of GBM patients, we performed single-nucleus whole-genome sequencing on 225 non-neuronal cortical nuclei from 12 disease-free individuals and 6 GBM patients, in the latter analyzing both tumor and non-tumor distal regions. Somatic aneuploidy was found in approximately 15% of non-neuronal nuclei in the adult human cortex, with recurrent chromosome 16p aneuploidy in up to 4% of nuclei. In contrast, about 51% of GBM tumor nuclei showed frequent aneuploidy of chromosomes 7 and 10, consistent with known GBM profiles. Notably, non-tumor brain regions from GBM patients exhibited aneuploidy frequencies and patterns similar to controls, including recurrent 16p involvement. These findings indicate that somatic aneuploidy in non-neuronal cells is a normal feature of the adult human brain and not linked to increased GBM risk.

cancer biology↗

bioRxiv2025

A functional map of phosphoprotein phosphatase regulation identifies an evolutionary conserved reductase for the catalytic metal ions

Serine/Threonine phosphoprotein phosphatases (PPPs, PP1-PP7) are conserved metalloenzymes and central to intracellular signaling in eukaryotes, but the details of their regulation is poorly understood. To address this, we performed genome-wide CRISPR knockout and focused base editor screens in PPP perturbed conditions to establish a high-resolution functional map of PPP regulation that pinpoints novel regulatory mechanisms. Through this, we identify the orphan reductase CYB5R4 as an evolutionarily conserved activator of PP4 and PP6, but not the closely related PP2A. Heme binding is essential for CYB5R4 function and mechanistically involves the reduction of the metal ions in the active site. Importantly, CYB5R4-mediated activation of PP4 is critical for cell viability when cells are treated with DNA damage-inducing agents known to cause oxidative stress. The discovery of a dedicated PPP reductase points to shared regulatory principles with protein tyrosine phosphatases, where specific enzymes dictate activity by regulating the active site redox state. In sum, our work provides a resource for understanding PPP function and the regulation of intracellular signaling.

cell biology↗

bioRxiv2025

A nonhuman primate model mirrors human congenital cytomegalovirus infection and reveals a spectrum of vertical transmission outcomes

Congenital cytomegalovirus (cCMV) is the leading infectious cause of birth defects worldwide, yet immune determinants of protection to inform design of a maternal vaccine remain elusive. Here, we characterized the outcome of primary rhesus CMV (RhCMV) infection during pregnancy in an immune competent nonhuman primate (NHP) model. RhCMV DNA was detected in amniotic fluid and/or fetal tissues in six of 12 (50% placental transmission) CMV-naive rhesus macaque dams inoculated intravenously with RhCMV in early second trimester gestation. Widespread tissue dissemination dominated by one of two inoculated RhCMV strains was present in one fetus (8.3% cCMV disease). Placental RhCMV transmission was associated with elevated fetal and maternal plasma TNF-alpha and reduced maternal brain-derived neurotrophic factor and IL-10 levels. CMV exposure during pregnancy had a broad impact on the placenta and fetus even in the absence of congenital infection as evidenced by RhCMV infection at the maternal-fetal interface in all 12 dams, along with significantly reduced placental efficiency and fetal growth metrics compared to gestation-matched control pregnancies. This NHP model recapitulates key aspects of human cCMV and provides new insight into barriers and biomarkers of successful vertical transmission. One sentence summary: The nonhuman primate model mirrors the epidemiology of human congenital CMV (cCMV) after primary infection and reveals its transmission bottlenecks.

immunology↗

bioRxiv2024

LAG3 marks activated but hyporesponsive NK cells.

Natural Killer (NK) cells are critical for immunosurveillance yet become dysfunctional in contexts such as chronic stimulation by viral infections or cancer. This phenomenon is similar to T cell exhaustion but less well characterized, which limits therapeutic interventions. As shown for T cells, NK cells often display an increased expression of immune checkpoint proteins (ICP) following chronic stimulation, and ICP blockade therapies are currently being explored for several cancer types, which have remarkable patient benefits. Nevertheless, the nature of ICP expression in NK cells is still poorly documented. In this study, we aimed to identify the conditions that lead to and the phenotype of immune checkpoint LAG3 (Lymphocyte-activation gene 3) expressing NK cells. Using various experimental models, we found that LAG3 is expressed by murine NK cells upon activation in different contexts, including in response to cancer and acute viral infections. LAG3 marks a subset of immature, proliferating and activated cells, which, despite activation, have a reduced capacity to respond to a broad range of stimuli. Further characterization also revealed that LAG3+ NK cells exhibit a transcriptional signature similar to that of exhausted CD8+ T cells. Taken together, our results support the use of LAG3 as a marker of dysfunctional NK cells across diverse chronic and acute inflammatory conditions.

immunology↗

bioRxiv2024

Marker gene fishing for single-cell data with complex heterogeneity

In single-cell studies, cells can be characterized with multiple sources of heterogeneity such as cell type, developmental stage, cell cycle phase, activation state, and so on. In some studies, many nuisance sources of heterogeneity (SOH) are of no interest, but may confound the identification of the SOH of interest, and thus affect the accurate annotate the corresponding cell subpopulations. In this paper, we develop B-Lightning, a novel and robust method designed to identify marker genes and cell subpopulations correponding to a SOH (e.g., cell activation status), isolating it from other sources of heterogeneity (e.g., cell type, cell cycle phase). B-Lightning uses an iterative approach to enrich a small set of trustworthy marker genes to more reliable marker genes and boost the signals of the SOH of interest. Multiple numerical and experimental studies showed that B-Lightning outperforms existing methods in terms of sensitivity and robustness in identifying marker genes. Moreover, it increases the power to differentiate cell subpopulations of interest from other heterogeneous cohorts. B-Lightning successfully identified new senescence markers in ciliated cells from human idiopathic pulmonary fibrosis (IPF) lung tissues, new T cell memory and effector markers in the context of SARS-COV-2 infections, and their synchronized patterns which were previously neglected. This paper highlights B-Lightnings potential as a powerful tool for single-cell data analysis, particularly in complex data sets where sources of heterogeneity of interest are entangled with numerous nuisance factors.

bioinformatics↗

bioRxiv2024

Immune Checkpoint Blockade Delays Cancer and Extends Survival in Murine DNA Polymerase Mutator Syndromes

Mutations in polymerases Pold1 and Pole exonuclease domains in humans are associated with increased cancer incidence, elevated tumor mutation burden (TMB) and response to immune checkpoint blockade (ICB). Although ICB is approved for treatment of several cancers, not all tumors with elevated TMB respond. Here we generated Pold1 and Pole proofreading mutator mice and show that ICB treatment of mice with high TMB tumors did not improve survival as only a subset of tumors responded. Similarly, introducing the mutator alleles into mice with Kras/p53 lung cancer did not improve survival, however, passaging mutator tumor cells in vitro without immune editing caused rejection in immune-competent hosts, demonstrating the efficiency by which cells with antigenic mutations are eliminated. Finally, ICB treatment of mutator mice earlier, before observable tumors delayed cancer onset, improved survival, and selected for tumors without aneuploidy, suggesting the use of ICB in individuals at high risk for cancer prevention. HighlightsO_LIGermline somatic and conditional Pold1 and Pole exonuclease domain mutations in mice produce a mutator phenotype. C_LIO_LISpontaneous cancers arise in mutator mice that have genomic features comparable to human tumors with these mutations. C_LIO_LIICB treatment of mutator mice with tumors did not improve survival as only a subset of tumors respond. C_LIO_LIIntroduction of the mutator alleles into an autochthonous mouse lung cancer model also did not produce immunogenic tumors, whereas passaging mutator tumor cells in vitro caused immune rejection indicating efficient selection against antigenic mutations in vivo. C_LIO_LIProphylactic ICB treatment delayed cancer onset, improved survival, and selected for tumors with no aneuploidy. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/597960v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@6cd159org.highwire.dtl.DTLVardef@243fd1org.highwire.dtl.DTLVardef@1d9da6borg.highwire.dtl.DTLVardef@192be51_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Assessing the impact of autologous neutralizing antibodies on rebound dynamics in postnatally SHIV-infected ART-treated infant Rhesus macaques

AO_SCPLOWBSTRACTC_SCPLOWThe presence of antibodies against HIV in infected children is associated with a greater capacity to control viremia in the absence of therapy. While the benefits of early antiretroviral treatment (ART) in infants are well documented, early ART may interfere with the development of antibody responses. In contrast to adults, early treated children lack detectable HIV-specific antibodies, suggesting a fundamental difference in HIV pathogenesis. Despite this potential adverse effect, early ART may decrease the size of the latent reservoir established early in infection in infants, which can be beneficial in viral control. Understanding the virologic and immunologic aspects of pediatric HIV is crucial to inform innovative targeted strategies for treating children living with HIV. In this study, we investigate how ART initiation time sets the stage for trade-offs in the latent reservoir establishment and the development of humoral immunity and how these, in turn, affect post-treatment dynamics. We also elucidate the biological function of antibodies in pediatric HIV. We employ mathematical modeling coupled with experimental data from an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model. Infant Rhesus macaques (RMs) were orally challenged with SHIV.C.CH505 375H dCT four weeks after birth and started treatment at different times after infection. In addition to viral load measurements, antibody responses and latent reservoir sizes were measured. We estimate model parameters by fitting viral load measurements to the standard HIV viral dynamics model within a nonlinear fixed effects framework. This approach allows us to capture differences between rhesus macaques (RMs) that develop antibody responses or exhibit high latent reservoir sizes compared to those that do not. We find that neutralizing antibody responses are associated with increased viral clearance and decreased viral infectivity but decreased death rate of infected cells. In addition, the presence of detectable latent reservoir is associated with less robust immune responses. These results demonstrate that both immune response and latent reservoir dynamics are needed to understand post-rebound dynamics and point to the necessity of a comprehensive approach in tailoring personalized medical interventions.

immunology↗

bioRxiv2024

RESPIRATION DEFECTS LIMIT SERINE SYNTHESIS REQUIRED FOR LUNG CANCER GROWTH AND SURVIVAL

Mitochondrial function is important for both energetic and anabolic metabolism. Pathogenic mitochondrial DNA (mtDNA) mutations directly impact these functions, resulting in the detrimental consequences seen in human mitochondrial diseases. The role of pathogenic mtDNA mutations in human cancers is less clear; while pathogenic mtDNA mutations are observed in some cancer types, they are almost absent in others. We report here that the proofreading mutant DNA polymerase gamma (PolGD256A) induced a high mtDNA mutation burden in non-small-cell lung cancer (NSCLC), and promoted the accumulation of defective mitochondria, which is responsible for decreased tumor cell proliferation and viability and increased cancer survival. In NSCLC cells, pathogenic mtDNA mutations increased glycolysis and caused dependence on glucose. The glucose dependency sustained mitochondrial energetics but at the cost of a decreased NAD+/NADH ratio that inhibited de novo serine synthesis. Insufficient serine synthesis, in turn, impaired the downstream synthesis of GSH and nucleotides, leading to impaired tumor growth that increased cancer survival. Unlike tumors with intact mitochondrial function, NSCLC with pathogenic mtDNA mutations were sensitive to dietary serine and glycine deprivation. Thus, mitochondrial function in NSCLC is required specifically to sustain sufficient serine synthesis for nucleotide production and redox homeostasis to support tumor growth, explaining why these cancers preserve functional mtDNA. In briefHigh mtDNA mutation burden in non-small-cell lung cancer (NSCLC) leads to the accumulation of respiration-defective mitochondria and dependency on glucose and glycolytic metabolism. Defective respiratory metabolism causes a massive accumulation of cytosolic nicotinamide adenine dinucleotide + hydrogen (NADH), which impedes serine synthesis and, thereby, glutathione (GSH) and nucleotide synthesis, leading to impaired tumor growth and increased survival. HighlightsO_LIProofreading mutations in Polymerase gamma led to a high burden of mitochondrial DNA mutations, promoting the accumulation of mitochondria with respiratory defects in NSCLC. C_LIO_LIDefective respiration led to reduced proliferation and viability of NSCLC cells increasing survival to cancer. C_LIO_LIDefective respiration caused glucose dependency to fuel elevated glycolysis. C_LIO_LIAltered glucose metabolism is associated with high NADH that limits serine synthesis, leading to impaired GSH and nucleotide production. C_LIO_LIMitochondrial respiration defects sensitize NSCLC to dietary serine/glycine starvation, further increasing survival. C_LI O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/596339v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@3dac07org.highwire.dtl.DTLVardef@e93401org.highwire.dtl.DTLVardef@555c48org.highwire.dtl.DTLVardef@1d7d31_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Comparative Analysis of Within-Host Dynamics of Acute Infection and Viral Rebound Dynamics in Postnatally SHIV-Infected ART-Treated Infant Rhesus Macaques

Viral dynamics of acute HIV infection and HIV rebound following suspension of antiretroviral therapy may be qualitatively similar but must differ given, for one, development of adaptive immune responses. Understanding the differences of acute HIV infection and viral rebound dynamics in pediatric populations may provide insights into the mechanisms of viral control with potential implications for vaccine design and the development of effective targeted therapeutics for infants and children. Mathematical models have been a crucial tool to elucidate the complex processes driving viral infections within the host. Traditionally, acute HIV infection has been modeled with a standard model of viral dynamics initially developed to explore viral decay during treatment, while viral rebound has necessitated extensions of that standard model to incorporate explicit immune responses. Previous efforts to fit these models to viral load data have underscored differences between the two infection stages, such as increased viral clearance rate and increased death rate of infected cells during rebound. However, these findings have been predicated on viral load measurements from disparate adult individuals. In this study, we aim to bridge this gap, in infants, by comparing the dynamics of acute infection and viral rebound within the same individuals by leveraging an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model. Ten infant Rhesus macaques (RMs) orally challenged with SHIV.C.CH505 375H dCT and given ART at 8 weeks post-infection. These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We use the HIV standard viral dynamics model fitted to viral load measurements in a nonlinear mixed effects framework. We find that the primary difference between acute infection and rebound is the increased death rate of infected cells during rebound. We use these findings to generate hypotheses on the effects of adaptive immune responses. We leverage these findings to formulate hypotheses to elucidate the observed results and provide arguments to support the notion that delayed viral rebound is characterized by a stronger CD8+ T cell response.

immunology↗

bioRxiv2024

Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity

Starvation triggers bacterial spore formation, a committed differentiation program that transforms a vegetative cell into a dormant spore. Cells in a population enter sporulation non-uniformly to secure against the possibility that favorable growth conditions, which puts sporulation-committed cells at a disadvantage, may resume. This heterogeneous behavior is initiated by a passive mechanism: stochastic activation of a master transcriptional regulator. Here, we identify a cell-cell communication pathway that actively promotes phenotypic heterogeneity, wherein Bacillus subtilis cells that start sporulating early utilize a calcineurin-like phosphoesterase to release glycerol, which simultaneously acts as a signaling molecule and a nutrient to delay non-sporulating cells from entering sporulation. This produced a more diverse population that was better poised to exploit a sudden influx of nutrients compared to those generating heterogeneity via stochastic gene expression alone. Although conflict systems are prevalent among microbes, genetically encoded cooperative behavior in unicellular organisms can evidently also boost inclusive fitness.

microbiology↗

bioRxiv2024

Rhesus Cytomegalovirus-encoded Fcγ-binding glycoproteins facilitate viral evasion from IgG-mediated humoral immunity

Human cytomegalovirus (HCMV) encodes four viral Fc-gamma receptors (vFc{gamma}Rs) that counteract antibody-mediated activation in vitro, but their role in infection and pathogenesis is unknown. To examine the in vivo function of vFc{gamma}Rs in animal hosts closely related to humans, we identified and characterized vFc{gamma}Rs encoded by rhesus CMV (RhCMV). We demonstrate that Rh05, Rh152/151 and Rh173 represent the complete set of RhCMV vFc{gamma}Rs, each displaying functional similarities to their respective HCMV orthologs with respect to antagonizing host Fc{gamma}R activation in vitro. When RhCMV-naive rhesus macaques were infected with vFc{gamma}R-deleted RhCMV, peak plasma viremia levels and anti-RhCMV antibody responses were comparable to wildtype infections. However, the duration of plasma viremia was significantly shortened in immunocompetent, but not in CD4+ T cell-depleted animals. Since vFc{gamma}Rs were not required for superinfection, we conclude that vFc{gamma}Rs delay control by virus-specific adaptive immune responses, particularly antibodies, during primary infection.

microbiology↗

bioRxiv2024

Substrate recognition principles for PP2A-B55

The PP2A-B55 phosphatase regulates a plethora of signaling pathways throughout eukaryotes. How PP2A-B55 selects its substrates presents a severe knowledge gap. By integrating AlphaFold modelling with comprehensive high resolution mutational scanning, we show that -helices in substrates bind B55 through an evolutionary conserved mechanism. Despite a large diversity in sequence and composition, these -helices share key amino acid determinants that engage discrete hydrophobic and electrostatic patches. Using deep learning protein design, we generate a specific and potent competitive peptide inhibitor of PP2A-B55 substrate interactions. With this inhibitor, we uncover that PP2A-B55 regulates the nuclear exosome targeting complex by binding to an -helical recruitment module in RBM7. Collectively, our findings provide a framework for the understanding and interrogation of PP2A-B55 in health and disease. One sentence summary-helices in PP2A-B55 substrates bind a conserved pocket on B55 through a common mechanism that is conserved in eukaryotes.

cell biology↗

bioRxiv2023

PARP inhibitors enhance reovirus-mediated cell killing through the death-inducing signaling complex (DISC) with an associated NF-kappa B-regulated immune response.

Oncolytic Reovirus type 3 Dearing (RT3D), is a naturally occurring double-stranded (ds) RNA virus that is under development as an oncolytic immunotherapy We used an unbiased high-throughput cytotoxicity screen of different targeted therapeutic agents with the aim of identifying potential drug-viral sensitizers to enhance RT3D tumour killing. Talazoparib, a clinical poly(ADP)-ribose polymerase 1 (PARP-1) inhibitor, was identified as a top hit and found to cause profound sensitisation to RT3D. This effect was not seen with other classes of oncolytic virus and was not mediated by enhanced viral replication or PARP inhibitor-related effects on the DNA damage response. RT3D interacts with retinoic acid-induced gene-1 (RIG-I) and activates PARP-1, with consequent PARylation of components of the extrinsic apoptosis pathway. Pharmacological and genetic inhibition of PARP-1 abrogates this PARylation and increases levels of extrinsic apoptosis, NF-kB signalling and pro-inflammatory cell death. Direct interaction between PARP-1 and RIG-I following RT3D/talazoparib treatment is a key factor in activating downstream signaling pathways that lead to IFN-{beta} and TNF-/TRAIL production which, in turn, amplify the therapeutic effect through positive feedback. Critically, it was possible to phenocopy the effect of RT3D through the use of non-viral ds-RNA therapy and RIG-I agonism. In in vivo studies, we demonstrated profound combinatorial efficacy of RT3D and talazoparib in human A375 melanoma in immunodeficient mice. More impressively, in immunocompetent mouse models of 4434 murine melanoma, we achieved 100% tumour control and protection from subsequent tumour rechallenge with the combination regimen. Correlative immunophenotyping confirmed significant innate and adaptive immune activation with the combination of RT3D and PARP inhibition. Taken together, these data provide a clear line of sight to clinical translation of combined regimens of PARP inhibition or ds-RNA agonism, with either viral or non-viral agents, in tumour types beyond the relatively narrow confines of current licensed indications for PARP inhibition.

cancer biology↗

bioRxiv2023

kmerDB: A Database Encompassing the Set of Genomic and Proteomic Sequence Information for Each Species

The rapid decline in sequencing cost has enabled the generation of reference genomes and proteomes for a growing number of organisms. However, at the present time, there is no established repository that provides information about organism-specific genomic and proteomic sequences of certain lengths, also known as kmers, that are either present or absent in each genome or proteome. In this article, we present kmerDB, a database accessible through an interactive web interface that provides kmer based information from genomic and proteomic sequences in a systematic way. kmerDB currently contains 202,340,859,107 base pairs and 19,304,903,356 amino acids, spanning 45,785 and 22,386 reference genomes and proteomes, respectively, as well as 14,658,776 and 149,264,442 genomic and proteomic species-specific sequences, termed quasi-primes. Additionally, we provide access to 5,186,757 nucleic and 214,904,089 peptide sequences that are absent from every genome and proteome, termed primes. kmerDB features a user-friendly interface offering various search options and filters for easy parsing and searching. The service is available at: www.kmerdb.com.

genomics↗

bioRxiv2023

Dengue virus exploits the host tRNA epitranscriptome to promote viral replication

The 40-50 RNA modifications of the epitranscriptome regulate posttranscriptional gene expression. Here we show that flaviviruses hijack the host tRNA epitranscriptome to promote expression of pro-viral proteins, with tRNA-modifying ALKBH1 acting as a host restriction factor in dengue virus infection. Early in the infection of human Huh-7 cells, ALKBH1 and its tRNA products 5-formylcytidine (f5C) and 2-O-methyl-5-formylcytidine (f5Cm) were reduced. ALKBH1 knockdown mimicked viral infection, but caused increased viral NS3 protein levels during infection, while ALKBH1 overexpression reduced NS3 levels and viral replication, and increased f5C and f5Cm. Viral NS5, but not host FTSJ1, increased f5Cm levels late in infection. Consistent with reports of impaired decoding of leucine UUA codon by f5Cm-modified tRNALeu(CAA), ALKBH1 knockdown induced translation of UUA-deficient transcripts, most having pro-viral functions. Our findings support a dynamic ALKBH1/f5Cm axis during dengue infection, with virally-induced remodeling of the proteome by tRNA reprogramming and codon-biased translation.

microbiology↗