Biology subjects

Reyes, A.

Publications and source records attributed to Reyes, A..

At least 19 recordsLinked to original sources

bioRxiv2026

A global signature of microbiome resilience to climate stress

As climate change accelerates, the microbial communities sustaining organisms and ecosystems worldwide face an uncertain future, with some proving resilient to stress while others collapse, yet no generalizable framework exists to distinguish the two beforehand. Using amplicon sequencing data from ~29,000 microbiomes, we constructed over 440 matched network pairs spanning three of the most pressing stressors: drought, warming, and salinity. We show that keystone microbes with high connectivity, functional redundancy, and metabolic flexibility, are disproportionately likely to survive stress, and that baseline network and functional properties predict community-level structural and functional stability even as taxonomic composition shifts stochastically. These relationships held across the diverse hosts, ecosystems, and regions we tested. Because these properties can be derived from standard, low-cost sequencing collected before disturbance occurs, our findings turn baseline microbiome data into an early-warning system for identifying which communities are most vulnerable to climate stress.

systems biology↗

bioRxiv2026

Casp1 and Ripk3 are required for homeostatic insulin secretion in mice

Objectives- Cell death and inflammatory pathways play important roles in adaptations to nutrient overload and metabolic dysfunction. This study investigates the metabolic consequences that arise from the dual disruption of both caspase 1 (Casp1) and receptor interacting protein kinase 3 (Ripk3) in mice fed a control or obesity-inducing diet. Methods- Male and female wild-type (WT), Casp1/11 knockout (KO), Ripk3 KO and Casp1/11/Ripk3 double knockout (DKO) mice were fed a matched low-fat or a 60% kcal high fat diet, followed by metabolic phenotyping. Islets were isolated from WT and DKO mice for measures of dynamic glucose-stimulated insulin and somatostatin (Sst) secretion. Islet architecture and cellular composition were assessed in WT and DKO mice by immunofluorescent staining of intact pancreatic sections. Pharmacological inhibition of Casp1 (Ac-YVAD-cmk) and Ripk3 (GSK872) was performed in WT and DKO mice using isolated islets and in vivo administration. Exogenous hormones were administered prior to glucose injection to test in vivo responses. Results- High-fat feeding resulted in increased adiposity in male, but not female mice, with single or double deletion of Casp1/11 and Ripk3. These mice also exhibited markers of impaired glucose tolerance and insulin sensitivity. Interestingly, when both Casp1 and Ripk3 were deleted or inhibited in mice fed a low-fat diet, mice experienced reductions in glucose excursion following administration of glucose due to increased plasma insulin levels. This increase in insulin secretion was recapitulated in isolated islets ex vivo and was independent of changes in the proportions of -, {beta}-, and {delta}-cells within the islet. There were significant reductions in the percentage of urocortin-3 (Ucn3)-positive {beta}-cells in DKO mice compared to control, suggesting altered Ucn3-Sst signaling; however, only exogenous Sst (Octreotide) and not Ucn3 was able to correct the decreased glucose excursion. Conclusions- Loss or inhibition of both Casp1 and Ripk3 fundamentally alter islet responses to glucose. Our findings highlight that endogenous Casp1 and Ripk3 act independently of inflammatory or cell death signals to coordinate normal glucose-stimulated insulin release.

physiology↗

bioRxiv2026

Temperate phage microdiversity reflects infant gut microbiome maturation independent of chronic undernutrition

The assembly and maturation of the infant gut microbiome is a critical developmental process. Yet the dynamics of the viral community, particularly in the context of stunting (chronic malnutrition) remain underexplored. Leveraging longitudinal fecal metagenomes from Zimbabwean infants with normal and stunted growth trajectories, we characterized the development of the gut bacterial and temperate phage communities from birth to 18 moths old. We found that infant gut temperate phages target hallmark early-life bacterial taxa, such as Bifidobacteriaceae, and exhibit an age-dependent maturation that parallels bacterial succession. Notably, both bacterial and temperate phage alpha diversity increased with age. This contrasts with previous studies focused on the extracellular viral fraction and highlights a strong coupling between prophage early-life dynamics and during bacterial gut colonization. Using abundance-based maturation models, we identified successional phases of colonization for both bacteria and their associated temperate viral clusters. Importantly, a viral microdiversity maturation model provided a stronger prediction of chronological age than viral abundance-based model, revealing within-phage genomic variation as a key signal of virome assembly, particularly around weaning. Contrary to findings in wasting (or severe acute malnutrition), stunted growth trajectories were not associated with a significant delay in either bacterial or temperate phage maturation. These results demonstrate that viral genomic variation is a new, informative dimension of early-life gut microbial assembly and that stunting may not impair infants gut maturation process. ImportanceThe early-life period represents a critical window for the establishment of the gut microbial communities, a process that is often affected by environmental factors such as diet. While severe acute malnutrition (SAM) is known to delay bacterial maturation, the impact of chronic, moderate undernutrition, such as stunting is poorly understood. Stunting is a highly prevalent global health condition with irreversible consequences on long-term host health, yet its implications on gut microbiome assembly remain unclear. Our study provides novel insights into the maturation of temperate phages, which to prime the infant gut by colonizing alongside their bacterial hosts and acting as drivers of bacterial evolution via lysogeny. By demonstrating that viral strain-level (genomic) variation captures a stronger age-related signal than viral abundance, we identified an underexplored dimension of microbial assembly. The finding that stunting, in contrast to SAM, does not impact microbial maturation provides essential context for public health interventions and future studies addressing this condition.

bioinformatics↗

bioRxiv2026

Leptin Receptor+ cells create a perisinusoidal niche for thrombopoiesis in the bone marrow by synthesizing CXCL14

Leptin Receptor-expressing (LepR+) stromal cells in the bone marrow are a critical source of growth factors for the maintenance of hematopoietic stem cells (HSCs) and most restricted hematopoietic progenitors. An important unresolved question is whether they also regulate terminal differentiation in some hematopoietic cells. We found that LepR+ cells promote thrombopoiesis by synthesizing the chemokine CXCL14, which is expressed in the bone marrow by a subset of LepR+ cells. Cxcl14-expressing LepR+ cells extend fine processes that wrap around perisinusoidal megakaryocytes. Deletion of Cxcl14 from LepR+ cells did not significantly alter HSC function or most aspects of bone marrow hematopoiesis, including megakaryocyte generation; however, it significantly reduced the numbers of proplatelet-forming megakaryocytes in the bone marrow and platelets in the blood. CXCL14 promoted platelet formation by remodeling lipid metabolism in megakaryocytes, increasing fatty acid transporter expression and enabling megakaryocytes to take up more polyunsaturated fatty acids from circulation. A high fat diet rescued the formation of proplatelet-forming megakaryocytes and platelets in Lepr-cre; Cxcl14 fl/fl mice. CXCL14 protein was sufficient to promote platelet formation by megakaryocytes in vitro and in vivo. LepR+ cells thus create a perisinusoidal niche for thrombopoiesis by producing CXCL14, which regulates lipid metabolism and terminal differentiation in megakaryocytes. Key pointsO_LILeptin Receptor+ stromal cells regulate terminal differentiation in megakaryocytes in addition to maintaining stem and progenitor cells C_LIO_LICXCL14 from Leptin Receptor+ cells promotes the formation of platelets by remodeling lipid metabolism in megakaryocytes in the bone marrow C_LI

cell biology↗

bioRxiv2025

Specificity and exon target space of splicing modifying compounds

Modulation of splicing has become an established therapeutic strategy, with proven clinical applications and continued potential to target specific exons to influence gene expression. Recent advancements led to the identification of small molecule splicing modifiers such as Risdiplam and Branaplam. These compounds induce the inclusion of exons that are typically skipped due to their weak 5' splice site. While Risdiplam has a preference to induce exons with a N-3G-2A-1 sequence at the 3' exon end, Branaplam has a proclivity towards introducing A-3G-2A-1 -ending exons. However, the variables that determine the selectivity and specificity of splicing modulators are still not completely understood, as evidenced by the hundreds of unaffected N-3G-2A-1 -ending exons present in the human genome. In this study, we delve into the molecular mechanisms governing the specificity of splicing-modifying compounds, focusing on their interactions with RNA structures at splice sites. Using biochemical assays, whole transcriptome analyses, and genetic perturbation approaches, our findings reveal contributions of primary sequence codependencies that help determine the required secondary structural conformation, thus governing responsiveness to splicing modulator induction. Based on these learnings, we were able to reprogram the specificity of splicing modulators by genetic manipulation of the U1 snRNA component of the spliceosome. Our findings further the understanding of splicing modulators and might help to identify new targets and compounds.

molecular biology↗

bioRxiv2025

Antagonistic interactions between CLAVATA receptors shape maize ear development

Meristem activity is controlled by the CLAVATA (CLV) signaling pathway, which involves a suite of leucine rich receptor (LRR) receptors, receptor-like proteins and CLV- EMBRYO SURROUNDING REGION (CLE) peptide ligands. FASCIATED EAR 3 (FEA3) is a leucine rich receptor (LRR) receptor-like protein important for meristem maintenance in maize, and acts independently of canonical CLV receptors. Weak alleles of fea3 can increase yield-related traits in maize, so understanding how FEA3 controls inflorescence development can maximize its potential as a crop improvement target. To identify FEA3s interaction network, we used TurboID-based proximity labeling in maize meristems, and identified a putative co-receptor, BARELY ANY MERISTEM 1D (BAM1D). BAM1D and FEA3 proximity labeling proteomes shared over 100 proteins, including many signaling proteins, suggesting they feed into a common signaling pathway. fea3 was epistatic to bam1d in the control of IM size, supporting the idea that FEA3 and BAM1D interact physically. However, fea3 and bam1d act antagonistically, because fea3 mutants had larger inflorescence meristems (IMs), whereas bam1d mutants produced smaller IMs. Together, this study demonstrates how in vivo TurboID-based proximity labeling clarifies complex genetic interactions between CLV receptors and expands our knowledge of downstream signaling components of CLV signaling pathways, which are largely uncharacterized. Our findings support the notion that multiple, partially overlapping CLV receptor complexes coordinately control meristem maintenance.

plant biology↗

bioRxiv2025

Mitotic entry is controlled by the plant-specific phosphatase BSL1 and cyclin-dependent kinase B

Cell cycle regulation is well understood in opisthokonts (fungi and metazoans) but not in plants and Apicomplexa, as some cell cycle regulators are not conserved1-3. In opisthokonts, cell cycle progression requires dephosphorylation of cyclin-dependent kinase (CDK) by the CDC25 phosphatase4. Plants have no CDC25, and thus their mechanisms of cell cycle regulation remain elusive1,5,6. Here, we show that the BSL1 phosphatase dephosphorylates CDKB1 to promote mitotic entry in Chlamydomonas. Mutations of BSL1 or CDKB1 block mitotic entry after DNA replication. BSL1 shows dynamic localization through the cell cycle at the basal bodies, spindle poles, and cleavage furrow. CDKB1 is hyperphosphorylated at T14 and Y15 residues in the bsl1 mutant and in wild-type cells treated with DNA replication inhibitors. BSL1 binds to CDKB1 and dephosphorylates CDKB1 pT14/pY15 in vitro. Phospho-mimicking mutations of T14/Y15 inactivate CDKB1 function, whereas phospho-blocking mutations cause sensitivity to DNA replication inhibitors, which delay cytokinesis in wild-type cells more than cells expressing unphosphorylatable mutant CDKB1. These results indicate that CDKB1 T14/Y15 is phosphorylated to block mitotic entry before DNA replication is complete, and BSL1 dephosphorylates CDKB1 to promote mitosis. Our study demonstrates that BSL1, a phosphatase conserved in plants and Apicomplexa but absent in fungi and animals, is a CDKB1-activating mitosis-promoting factor that has evolved additional signaling functions in receptor kinase pathways in higher plants. One-Sentence SummaryBSL1 is a mitosis-promoting phosphatase that activates CDKB1 in plants.

plant biology↗

bioRxiv2025

Phytochemical Screening, Radical Scavenging and Antimicrobial Activities of the Crude Ethanolic, Methanolic, Ethyl Acetate and Chloroform Leaf Extracts of Arayat Pitogo (Cycas riuminiana Porte ex Regel)

In the Philippines, Cycas spp. are found in Luzon Island particularly in Pampanga, Batangas, Bataan and Isabela provinces.. In this study, the bioactive potentials of the crude methanolic, ethanolic, ethyl acetate and chloroform leaf extracts of Cycas riuminiana Porte ex Regel were investigated. Based on the results of the four solvents used, the best extraction solvent for the phytochemicals is ethanol, followed by methanol, ethyl acetate and chloroform. The ethanolic and methanolic leaf extracts showed comparable antioxidant activity. The chloroform and ethyl acetate extracts also have comparable antioxidant activity but significantly lower than both methanolic and ethanolic extracts. However the greatest antimicrobial activity was exhibited by the ethyl acetate extract, followed by chloroform, methanolic and ethanolic extracts. The variation and similarity in the antioxidant and antimicrobial activities of the different extracts can be attributed to different mechanisms of interactions, namely, independent joint action, additive, synergistic, competitive or antagonistic interactions, among the bioactive compounds present in the crude extracts. Further studies are needed to elucidate the structure of the different phytochemicals present in the leaf extracts of Arayat Pitogo (C. riuminiana Porte ex Regel) and the specific mechanisms of interaction among these phytochemicals. SUMMARYThe extracts were tested for the presence (trace, moderate or abundant amounts) of flavonoids, saponins, tannins, triterpenes, alkaloids, sterols and glycosides. The ethanolic extract was positive for all phytochemicals screened with sterols, flavonoids, glycosides and tannins being abundant, alkaloids being moderate and triterpenes and saponins in trace amounts. The methanolic extract was also positive for all constituents but in trace amounts, except for flavonoids which were abundant. The ethyl acetate extract contained abundant sterols, moderate alkaloids and trace amounts of saponins, glycosides and tannins. Finally, the chloroform extract contained abundant sterols, and trace amounts of alkaloids, saponins and glycosides. The radical scavenging assay revealed that the highest percent inhibition was obtained for the ethanolic leaf extract (60.53{+/-}0.7801%), followed by methanolic extract (59.92{+/-}3.160%), chloroform extract (50.17{+/-}4.779%) and ethyl acetate extract (47.25{+/-}3.759%). In terms of antibacterial activity, the ethyl acetate extract registered the highest inhibition against the three test organisms, namely, Staphylococcus aureus, Bacillus subtilis and Escherichia coli. The chloroform extract inhibited S. aureus and B. subtilis. The methanol extract inhibited S. aureus only. Finally, the ethanolic extract failed to inhibit any of the test organisms despite its abundant phytochemicals and high antioxidant activity. In terms of antifungal activity, the different extracts inhibited Candida albicans with the ethyl acetate and chloroform extracts showing a high degree of inhibition followed by the methanolic and ethanolic extracts. However, none of the extracts showed any bioactivity against Aspergillus niger.

plant biology↗

bioRxiv2025

Malaria parasite population genomics during an elimination program in Eastern Myanmar

BackgroundWe investigated parasite population genomics during an intensive malaria elimination program in Kayin State (Myanmar), in which malaria posts were used for rapid detection and treatment of malaria cases, while mass drug administration (MDA) was used in villages with high submicroscopic reservoirs. MethodsWe collected 5014 dried blood spots from Plasmodium falciparum infected patients from 413 malaria posts, over 58-months (November 2015 - August 2020), and sequenced 2270 parasite genomes, each with geographic references (latitude and longitude). We used identity-by-descent (IBD) relationships to examine how control efforts impact parasite population structure. FindingsParasites were genetically depauperate: 1726 single-genotype infections comprised 166 unique genomes ([≥]90% IBD), while nine families ([≥]45% IBD) accounted for 62{middle dot}5% of parasites sampled. We observed localized, temporally stable transmission of unique parasite genotypes, identifying transmission chains. Parasite relatedness was positively correlated up to approximately 20 km revealing the scale of parasite subpopulations. Kelch13 diversity was stable from 2016-2019, but only one predominant clonal genotype (kelch13-R561H) remained in 2020. MDA resulted in parasite founder effects, providing genomic evidence for the efficacy of this malaria control tool. InterpretationOur genomic data show that parasite population size decreased over the study period, and we observed regional distribution of parasite genotypes, which can define operational units for parasite control. One parasite genotype (kelch13-R561H) from the north rose to high frequency in 2020, because transmission was halted elsewhere in the control area. Future surveillance will reveal whether this genotype spreads to neighboring regions. Genetic drift may have a stronger impact on parasite population structure than selection in low-transmission elimination settings. FundingNational Institutes of Health; Wellcome Trust; Global Fund to Fight against AIDS, Tuberculosis and Malaria; The Bill and Melinda Gates Foundation. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSThis study describes the genomic analysis of malaria parasites collected during a malaria elimination program targeting four townships (Myawaddy, Kawkareik, Hlaingbwe, and Hpapun) in Kayin State, eastern Myanmar. We searched PubMed on May 10, 2025, using the terms: "malaria", "transmission", "drug resistance", "southeast Asia" and "genetic surveillance" without any date or language restrictions. Our search yielded 58 publications, including reports on declined immunity to malaria and increased drug resistance in southeast Asia; genetic diversity and population structure shaped by mass drug administration, transmission intensity, human movement and mosquito ecology; and the spread of kelch13 and pfcrt mutations conferring dihydroartemimsinin-piperaquine resistance in east southeast Asia countries. Added value of this studyWe sequenced and analyzed 2270 Plasmodium falciparum whole genomes (each with geographic location) collected between November 2015 and August 2020 in Kayin State. We described fine-scale molecular epidemiology changes during intense malaria elimination interventions. We observed localized, temporally stable transmission of parasite genotypes, with different parasite families and kelch13 haplotypes predominating in different subregions over the 5-year period. We found kelch13 haplotypes with local or regional origin, but none originating from eastern southeast Asia. The genomic data indicated decreasing parasite population size, but we observed no selection towards drug-resistance parasites. In 2020, only one predominant lineage (kelch13-R561H) remained in our studying region, consistent with genetic drift in a pre-elimination setting. Implications of all the available evidenceThe parasite population was genetically depauperate, with a spatially localized and temporally stable distribution of parasite lineages, and declining population size. In this situation genetic drift may play a heightened role in parasite epidemiology. Consistent with this, parasites carrying kelch13-R561H rose to high frequency in 2020, because transmission was eliminated in all regions except the north of Kayin State, where parasites bearing this kelch13 genotype have predominated since 2017. Future surveillance will determine whether this parasite genotype is transmitted to neighboring regions, and thus related to changes in P. falciparum drug resistance dynamics on the Thailand Myanmar border. These data illustrate how genetic drift in small populations can result in instantaneous changes in the resistance status of parasite populations in near elimination settings.

genomics↗

bioRxiv2025

Large-Scale Genomic Analysis of CpG-Mediated Immunogenicity in Bacteriophages and a Novel Predictive Risk Index

Bacteriophage (phage) therapy is a promising alternative to antibiotics, yet phage-induced immune responses can affect treatment efficacy. However, current methods for assessing phage immunogenicity are limited, hindering the development of safer, more effective therapies. Here, we introduce the Bacteriophage Risk Index (BRI), a novel metric that quantifies phage immunogenic potential based on CpG dinucleotide frequency, motif spacing, and sequence context, key factors influencing Toll-like receptor 9 (TLR9) activation. Applying the BRI to 7,011 phage genomes, we classified them into five risk tiers, revealing substantial immunogenic variability, even among phages targeting the same bacterial host. BRI scores correlated with immune responses in human lung epithelial cells, validating its predictive power. Experimental testing further confirmed this, as exposure of lung epithelial cells to two phages from distinct risk tiers showed that the high-risk phage (Category 4) induced a strong pro-inflammatory response, upregulating CXCL1, CXCL8, IRF7, and TNFAIP3, while the low-risk phage (Category 2) triggered minimal immune activation with limited cytokine expression. These findings confirm that higher BRI scores predict stronger immune responses, providing a robust tool for evaluating phage immunogenicity. By enabling the selection of phages with lower immunogenic potential, the BRI enhances the safety and efficacy of phage therapy while offering a framework for regulatory agencies, clinical researchers, and biologic drug development, with applications extending beyond phage therapy to other immunogenic biologics.

immunology↗

bioRxiv2025

Effects of Willow and Pine tree growth in bacterial abundance, interactions and metabolic profile in a copper mine tailing

The Cauquenes tailings is one of the largest mine tailings in Chile and represents a significant environmental hazard due to its high copper levels and acidic pH. However, there is evidence of willow and pine tree growth in these terrains, which is unexpected given the extreme conditions of this environment. Considering the importance of plants in restoration strategies, the objective of this study was to analyze the effect that willow and pine growth have on the heavy metal contents of their surrounding soil, and the abundance, interaction, metabolic profile and assembly of the bacterial community. In the Cauquenes tailing, we collected samples from willow and pine vegetated soils as well as the surrounding non-vegetated soils. We analyzed characteristics such as heavy metal concentrations and pH levels in all sampled soils, and in tree leaves and roots. Vegetated sites exhibited lower copper levels and a neutral pH, while both tree species accumulated heavy metals in their tissues. We also determined bacterial abundance in all soil samples, and co-occurrence networks were constructed to assess bacterial interactions. Both trees promoted a higher abundance of Proteobacteria and had networks with higher modularity compared to non-vegetated soils. Finally, we estimated the metabolic profile of the bacterial community using PICRUSt 2 analysis and determined carbon source utilization with BioLog Ecoplates. PICRUSt 2 predicted higher metabolic activity in vegetated soils, and BioLog Ecoplate analysis revealed the utilization of a greater number of carbon sources. The microbial communities from vegetated soils were assembled in a deterministic manner, while the community from non-vegetated soils were stochastically assembled. In conclusion, tree growth mitigated the extreme conditions of the tailing and promoted a more active and healthier bacterial community. HighlightsO_LIWillow and pine tree can grow and mitigate toxic metal conditions in the tailings C_LIO_LIBoth trees provoked a shift in bacterial abundance and interaction network C_LIO_LIThe provoked shift was tree-dependent C_LIO_LIMicrobial activity was higher in vegetated soils C_LI

microbiology↗

bioRxiv2024

HIV-1 infection promotes neuroinflammation and neuron pathogenesis in novel microglia-containing cerebral organoids.

Cerebral organoids (COs) are a valuable tool to study the intricate interplay between glial cells and neurons in brain development and disease, including HIV-associated neuroinflammation. We developed a novel approach to generate microglia containing COs (CO-iMs) by co-culturing hematopoietic progenitors and induced pluripotent stem cells. This approach allowed for the differentiation of microglia within the organoids concomitantly to the neuronal progenitors. CO- iMs exhibited higher efficiency in generation of CD45+/CD11b+/Iba-1+ microglia cells compared to conventional COs with physiologically relevant proportion of microglia ([~]7%). CO-iMs exhibited substantially higher expression of microglial homeostatic and sensome markers as well as markers for the complement cascade. CO-iMs showed susceptibility to HIV infection resulting in a significant increase in several pro-inflammatory cytokines/chemokines and compromised neuronal function, which were abrogated by addition of antiretrovirals. Thus, CO-iM is a robust model to decipher neuropathogenesis, neurological disorders, and viral infections of brain cells in a 3D culture system.

microbiology↗

bioRxiv2024

ZNF574 is a Quality Control Factor For Defective Ribosome Biogenesis Intermediates

Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that take part in numerous interdependent steps. This complexity creates a large genetic space in which pathogenic mutations can occur. "Dead-end" ribosome intermediates that result from biogenesis errors are rapidly degraded, affirming the existence of quality control pathway(s) that monitor ribosome assembly. However, the factors that differentiate between on-path and dead-end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway, which we term the Ribosome Assembly Surveillance Pathway (RASP). Loss of ZNF574 results in the accumulation of faulty biogenesis intermediates that interfere with global ribosome production, further emphasizing the role of RASP in protein homeostasis and cellular health.

cell biology↗

bioRxiv2024

Benchmarking tools for transcription factor prioritization

Spatiotemporal regulation of gene expression is controlled by transcription factor (TF) binding to regulatory elements, resulting in a plethora of cell types and cell states from the same genetic information. Due to the importance of regulatory elements, various sequencing methods have been developed to localise them in genomes, for example using ChIP-seq profiling of the histone mark H3K27ac that marks active regulatory regions. Moreover, multiple tools have been developed to predict TF binding to these regulatory elements based on DNA sequence. As altered gene expression is a hallmark of disease phenotypes, identifying TFs driving such gene expression programs is critical for the identification of novel drug targets. In this study, we curated 84 chromatin profiling experiments (H3K27ac ChIP-seq) where TFs were perturbed through e.g., genetic knockout or overexpression. We ran nine published tools to prioritize TFs using these real-world data sets and evaluated the performance of the methods in identifying the perturbed TFs. This allowed the nomination of three frontrunner tools, namely RcisTarget, MEIRLOP and monaLisa. Our analyses revealed opportunities and commonalities of tools that will help to guide further improvements and developments in the field.

bioinformatics↗

bioRxiv2024

The transcription factor ZNF469 regulates collagen production in liver fibrosis

Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the worlds population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.

molecular biology↗

bioRxiv2023

Apobec-Mediated Retroviral Hypermutation In Vivo is Dependent on Mouse Strain

Replication of the complex retrovirus mouse mammary tumor virus (MMTV) is antagonized by murine Apobec3 (mA3), a member of the Apobec family of cytidine deaminases. We have shown that MMTV-encoded Rem protein inhibits proviral mutagenesis by the Apobec enzyme, activation-induced cytidine deaminase (AID) during viral replication in BALB/c mice. To further study the role of Rem in vivo, we have infected C57BL/6 (B6) mice with a superantigen-independent lymphomagenic strain of MMTV (TBLV-WT) or a mutant strain (TBLV-SD) that is defective in Rem and its cleavage product Rem-CT. Unlike MMTV, TBLV induced T-cell tumors in {micro}MT mice, indicating that mature B cells, which express the highest AID levels, are not required for TBLV replication. Compared to BALB/c, B6 mice were more susceptible to TBLV infection and tumorigenesis. The lack of Rem expression accelerated B6 tumorigenesis at limiting doses compared to TBLV-WT in either wild-type B6 or AID-deficient mice. However, unlike proviruses from BALB/c mice, high-throughput sequencing indicated that proviral G-to-A or C-to-T changes did not significantly differ in the presence and absence of Rem expression. Ex vivo stimulation showed higher levels of mA3 relative to AID in B6 compared to BALB/c splenocytes, but effects of agonists differed in the two strains. RNA-Seq revealed increased transcripts related to growth factor and cytokine signaling in TBLV-SD-induced tumors relative to those from TBLV-WT, consistent with a third Rem function. Thus, Rem-mediated effects on tumorigenesis in B6 mice are independent of Apobec-mediated proviral hypermutation.

microbiology↗

bioRxiv2023

Ontogeny of the organized nasopharynx-associated lymphoid tissue in rainbow trout

Understanding the ontogeny of teleost mucosa-associated lymphoid tissues (MALT) is critical for determining the earliest timepoint for effective mucosal vaccination of young fish. Here, we describe the developmental sequence that leads to the formation of an organized MALT structure in rainbow trout, the organized nasopharynx-associated lymphoid tissue (O-NALT). Control rainbow trout were sampled between 340 and 1860 degree days (DD) and routine histology and immunofluorescence staining were used to determine cellular changes in immune cells in the nasal cavity as well as O-NALT formation. We identified that O-NALT is first seeded by CD8+ T cells at 700DD followed by IgM+ B cells and CD4-2b+ T cells at 1000DD. Histomorphologically, trout O-NALT is fully formed at 1400DD when it is composed of 67% CD4-2b+ cells, 20% IgM+ cells, 13% CD8+ T cells, and no IgT+ B cells. Whole body gene expression analyses uncovered waves of igmh, cd4-2b, and cd8a expression that recapitulate the cellular seeding sequence of O-NALT by specific lymphocyte subsets. Our results indicate that 1) O-NALT formation results from a specific sequence of lymphocyte subset colonization pioneered by CD8+ T cells and 2) the presence of the full O-NALT structure at 1400DD may mark this timepoint as the earliest developmental stage at which mucosal vaccines can induce long lasting, specific immune responses.

immunology↗

bioRxiv2023

Using a P. falciparum genetic cross to dissect the relative contributions of pfcrt and plasmepsin II/III to piperaquine response-related traits

Piperaquine (PPQ) is widely used in combination with dihydroartemisinin (DHA) as a first-line treatment against malaria parasites. Multiple genetic drivers of PPQ resistance have been reported, including mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and increased copies of plasmepsin II/III (pm2/3). We generated a cross between a Cambodia-derived multi-drug resistant KEL1/PLA1 lineage isolate (KH004) and a drug susceptible parasite isolated in Malawi (Mal31). Mal31 harbors a wild-type (3D7-like) pfcrt allele and a single copy of pm2/3, while KH004 has a chloroquine-resistant (Dd2-like) pfcrt allele with an additional G367C substitution and four copies of pm2/3. We recovered 104 unique recombinant progeny and examined a targeted set of progeny representing all possible combinations of variants at pfcrt and pm2/3 for detailed analysis of competitive fitness and a range of PPQ susceptibility phenotypes, including PPQ survival assay (PSA), area under the dose-response curve (AUC), and a limited point IC50 (LP-IC50). We find that inheritance of the KH004 pfcrt allele is required for PPQ resistance, whereas copy number variation in pm2/3 further enhances resistance but does not confer resistance in the absence of PPQ-R-associated mutations in pfcrt. Deeper investigation of genotype-phenotype relationships demonstrates that progeny clones from experimental crosses can be used to understand the relative contributions of pfcrt, pm2/3, and parasite genetic background, to a range of PPQ-related traits and confirm the critical role of the PfCRT G367C substitution in PPQ resistance. ImportanceResistance to PPQ used in combination with DHA has emerged in Cambodia and threatens to spread to other malaria-endemic regions. Understanding the causal mutations of drug resistance and their impact on parasite fitness is critical for surveillance and intervention, and can also reveal new avenues to limiting the evolution and spread of drug resistance. An experimental genetic cross is a powerful tool for pinpointing the genetic determinants of key drug resistance and fitness phenotypes and have the distinct advantage of assaying the effects of naturally evolved genetic variation. Our study was significantly strengthened because the full a range of copies of KH004 pm2/3 was inherited among the progeny clones, allowing us to directly test the role of pm2/3 copy number on resistance-related phenotypes in the context of a unique pfcrt allele. Our multi-gene model suggests an important role for both loci in the evolution of this ACT resistant parasite lineage.

genomics↗