Biology subjects

Lander, A.

Publications and source records attributed to Lander, A..

8 recordsLinked to original sources

bioRxiv2025

Egyptian rousette bat macrophages elicit divergent interferon responses and cytokine storm signalling against Marburg and Sudan viruses

Egyptian rousette bats (ERBs) are the only known natural reservoir of Marburg virus (MARV), etiologic agent of a highly-pathogenic zoonotic viral hemorrhagic fever. In ERBs, evolutionary adaptations allow for fine-tuned discrete pro-inflammatory immune responses that control MARV infection, yet permit population-level viral maintenance. To look for exclusive co-adapted responses between ERBs and MARV, we compared macrophage (M{Phi}) responses to MARV and Sudan virus (SUDV), a related filovirus not hosted by ERBs. We queried whether MARV counters normal ERB M{Phi} responses, illuminating co-adapted host responses not observed upon infection with SUDV, which fails to establish a productive infection and is efficiently immunologically cleared by ERBs. We observed stark differences in M{Phi} transcriptional responses to MARV and SUDV, including differences in Type I and III interferon (IFN)-related genes, cytokines, chemokines, cell growth and proliferation genes. We show for the first time that while MARV-infected bat M{Phi}s undergo muted IFN responses and cytokine storm signalling, SUDV induces unperturbed Type I and III IFN gene expression, stronger cytokine and chemokine responses resembling typical host responses to a foreign viral pathogen. Our findings therefore corroborate growing evidence of unique coevolutionary relationships between bats and the specific viruses they harbor.

immunology↗

bioRxiv2025

Interaction between long-range chromatin regulators Nipbl & Isl1 synergistically drives heart defects in mice

Congenital heart defects (CHDs) are frequently observed in the most common form of Cornelia de Lange Syndrome (CdLS), which is caused by haploinsufficiency for NIPBL, a gene involved in chromatin looping and cis-regulatory control of gene expression. Here, we surveyed cardiac defects in mice made Nipbl-haploinsufficient in the second heart field using two Cre drivers: Mef2c-Cre and Isl1-Cre. Only Isl1-Cre-driven Nipbl-haploinsufficiency resulted in CHDs - a finding we traced to the additional contribution of Isl1-haploinsufficiency caused by the Isl1-Cre allele. To test whether combined reduction of Nipbl and Isl1 cause CHDs, we made mice globally haploinsufficient for both genes. Indeed, Nipbl+/-; Isl1+/- mice exhibited a substantially higher frequency and severity of CHDs than mice haploinsufficient for either gene alone. As a member of the LIM-homeodomain transcription factor family, Isl1 is involved in chromatin looping and enhancer-promoter communication via a mechanism distinct from that of Nipbl. Nevertheless, when we performed RNA sequencing on E10.5 hearts from wildtype, Nipbl+/-, Isl1+/-, and Nipbl+/-; Isl1+/- embryos, we observed that combined haploinsufficiency resulted in largely additive gene expression changes, including dysregulation of known cardiac regulators (Irx4, Tbx1, Foxo6, Heyl, Bnc1, Sox17) and novel candidates (Gbx1, Csdc2, Myrf, Pou6f1, Zfp579, ad Zfp763). A subset of additive changes arose from opposing regulatory influences in single mutants that restored gene expression to WT levels in Nipbl/-; Isl1/- hearts. For example, Hoxc4, Pitx2, Isl1 itself, and Pax6 (a known target of Isl1), were upregulated in Nipbl+/-hearts, downregulated in Isl1+/- hearts, but expressed at WT levels in Nipbl/-; Isl1/- hearts. Since loss of Isl1 upregulation from Nipbl+/- to Nipbl+/-; Isl1+/- hearts coincided with a marked increase in CHDs, we propose that Isl1 upregulation compensates for the loss of cis- regulatory interactions due to Nipbl-haploinsufficiency, and protects hearts from severe CHD risk. Supporting this model, other LIM-homeodomain transcription factors (Lhx2, Lhx3, Lhx9) were also upregulated in Nipbl+/- hearts, with Lhx3 and Lhx9 showing even greater upregulation in Nipbl+/-; Isl1+/- hearts. Despite this, CHDs resulting from the combined loss of Nipbl and Isl1 were particularly severe. These findings suggest that heart development is exquisitely sensitive to small changes in gene expression, leading to synergistic phenotypic interactions when relatively modest gene expression changes are combined.

developmental biology↗

bioRxiv2025

Metabolically purified human stem cell-derived hepatocytes reveal distinct effects of Ebola and Lassa viruses

Ebola and Lassa viruses require biosafety-level-4 (BSL4) containment, infect the liver, and cause deadly hemorrhagic fevers. The cellular effects of these viruses, and whether different families of hemorrhagic-fever viruses elicit similar effects, remain fundamental questions in BSL4 virology. Here, we introduce a new metabolic selection approach to create nearly-pure hepatocytes from human pluripotent stem cells, killing non-liver cells by withholding essential nutrients. Unexpectedly, Ebola and Lassa exerted starkly different effects on human hepatocytes. Ebola infection activated the integrated stress response (ISR) and WNT pathways in hepatocytes in vitro and killed them, whereas Lassa did not. Within non-human primates, Ebola likewise infected hepatocytes and activated ISR signaling in vivo. In summary, we present a single-cell transcriptional and chromatin accessibility roadmap of human hepatocyte differentiation, purification, and viral infection.

cell biology↗

bioRxiv2022

Dynamic readout of the Hh gradient in the Drosophila wing disc reveals pattern-specific tradeoffs between robustness and precision

How patterning by morphogen gradients determine tradeoffs between robustness and precision is unclear. Gradients that exhibit self-enhanced ligand degradation provide robustness to perturbations in morphogen production rates. However, increased robustness achieved through this mechanism is traded off for lower precision to noise. Here we use a hypotheses-driven theoretical approach to show that Hedge-hog (Hh) signaling would confer the same robustness to all target genes established by the steady-state gradient, but when a dynamical interpretation of patterning is used, robustness is maintained for steady-state outputs, but is traded off for higher precision in outputs set prior to steady-state. As predicted by our model, the widths of decapentaplegic (dpp), and collier (col), two target genes established by the Hh gradient in the Drosophila wing disc, exhibit differential robustness to Hh dosage. Particularly, higher robustness in the col pattern is ensured by Hh-dependent upregulation of its receptor Patched, an evolutionary-conserved property of Hh signaling that results in self-promoted Hh degradation. In contrast, dpp expression that is determined by the transient overshoot gradient, is insensitive to self-enhanced ligand degradation and exhibits less robustness, in exchange for a more precise boundary. Our work reveals of how morphogen gradients can establish tunable patterning properties in a target-specific manner.

developmental biology↗

bioRxiv2022

Decreasing Wapl dosage partially corrects transcriptome phenotypes in Nipbl-/+ embryonic mouse brain

Cohesin rings interact with DNA and modulate expression of thousands of genes. NIPBL loads cohesin onto chromosomes and WAPL takes it off. Heterozygous mutations in NIPBL lead to a developmental disorder called Cornelia de Lange syndrome. Nipbl heterozygous mice are a good model for this disease but mutations in WAPL were not known to cause disease or gene expression changes in mammals. Here we show dysregulation of >1000 genes in Wapl{Delta}/+ embryonic mouse brains. The patterns of dysregulation are highly similar to Nipbl heterozygotes, suggesting that Wapl mutations may also cause disease in humans. Since WAPL and NIPBL have opposite effects on cohesins association with DNA, we asked whether a heterozygous Wapl mutation could correct phenotypes seen in Nipbl heterozygous mice. In fact, both gene expression and embryonic growth are partially corrected. Our data are consistent with the view that cohesin dynamics play a key role in regulating gene expression.

genetics↗

bioRxiv2019

Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity

Bats are well known reservoir hosts for RNA and DNA viruses. The use of captive bats in research has intensified over the past decade as researchers aim to examine the virus-reservoir host interface. In this study, we investigated the effects of captivity on the fecal bacterial microbiome of an insectivorous microbat, Mops condylurus, a bat species that roosts in close proximity to humans and has likely transmitted viral infections to humans. Using amplicon 16S rRNA gene sequencing, we characterized changes in fecal bacterial community composition for individual bats directly at the time of capture and again after six weeks in captivity. We found that microbial community richness by measure of the number of observed operational taxonomic units (OTUs) in bat feces does increase significantly in captivity. Importantly, we found the similarity of microbial community structures of fecal microbiomes between different bats to converge during captivity. We propose a six week-acclimatization period prior to carrying out infection studies or other research influenced by the microbiome composition, which may be advantageous to reduce variation in microbiome composition and minimize biological variation inherent to in vivo experimental studies.

microbiology↗

bioRxiv2019

The cohesin loader NIPBL interacts with pre-ribosomal RNA and treacle to regulate ribosomal RNA synthesis

NIPBL is an essential loader of cohesin to mediate sister chromatid cohesion and chromatin loop organization. NIPBL mutations cause Cornelia de Lange Syndrome. How NIPBLs genomic localization is specified is not fully understood. We found that NIPBL localizes to the nucleolus in an RNA-dependent manner and binds directly to ribosomal RNA (rRNA). We identified two RNA binding domains in NIPBL in vitro, both of which are required for efficient rRNA binding in vivo. NIPBL binds to ribosomal DNA (rDNA) in an RNA-stimulated manner, recruits PAF1 and promotes pre-rRNA transcription. Stress that inhibits rRNA synthesis displaces NIPBL from the nucleolus and rDNA. Interestingly, treacle, mutated in Treacher Collins syndrome, tightly binds to and recruits NIPBL to the nucleolus, nucleolar organizer regions, and the stress-induced nucleolar cap. The results reveal that a subpopulation of NIPBL is recruited to the nucleolus through its interaction with RNA and treacle and regulates pre-rRNA transcription.

molecular biology↗

bioRxiv2017

The Effect Of Nipped-B-Like (Nipbl) Haploinsufficiency On Genome-Wide Cohesin Binding And Target Gene Expression: Modeling Cornelia de Lange Syndrome

Cornelia de Lange Syndrome (CdLS) is a multisystem developmental disorder frequently associated with heterozygous loss-of-function mutations of Nipped-B-like (NIPBL), the human homolog of Drosophila Nipped-B. NIPBL loads cohesin onto chromatin. Cohesin mediates sister chromatid cohesion important for mitosis, but is also increasingly recognized as a regulator of gene expression. In CdLS patient cells and animal models, the presence of multiple gene expression changes with little or no sister chromatid cohesion defect suggests that disruption of gene regulation underlies this disorder. However, the effect of NIPBL haploinsufficiency on cohesin binding, and how this relates to the clinical presentation of CdLS, has not been fully investigated. Nipbl haploinsufficiency causes CdLS-like phenotype in mice. We examined genome-wide cohesin binding and its relationship to gene expression using mouse embryonic fibroblasts (MEFs) from Nipbl +/- mice that recapitulate the CdLS phenotype. We found a global decrease in cohesin binding, including at CCCTC-binding factor (CTCF) binding sites and repeat regions. Cohesin-bound genes were found to be enriched for histone H3 lysine 4 trimethylation (H3K4me3) at their promoters; were disproportionately downregulated in Nipbl mutant MEFs; and displayed evidence of reduced promoter-enhancer interaction. The results suggest that gene activation is the primary cohesin function sensitive to Nipbl reduction. Over 50% of significantly dysregulated transcripts in mutant MEFs come from cohesin target genes, including genes involved in adipogenesis that have been implicated in contributing to the CdLS phenotype. Thus, decreased cohesin binding at the gene regions directly contributes to disease-specific expression changes. Taken together, our Nipbl haploinsufficiency model allows us to analyze the dosage effect of cohesin loading on CdLS development.

developmental biology↗