Biology subjects

Chaves, G.

Publications and source records attributed to Chaves, G..

6 recordsLinked to original sources

bioRxiv2023

Geographic risk assessment of Batrachochytrium salamandrivorans invasion in Costa Rica as a means of informing emergence management and mitigation

Remotely-sensed risk assessments of emerging, invasive pathogens are key to targeted surveillance and outbreak responses. The recent emergence and spread of the fungal pathogen, Batrachochytrium salamandrivorans (Bsal), in Europe has negatively impacted multiple salamander species. Scholars and practitioners are increasingly concerned about the potential consequences of this lethal pathogen in the Americas, where salamander biodiversity is higher than anywhere else in the world. Although Bsal has not yet been detected in the Americas, certain countries have already proactively implemented monitoring and detection plans in order to identify areas of greatest concern and enable efficient contingency planning in the event of pathogen detection. To predict areas in Costa Rica with a high Bsal transmission risk, we employed ecological niche modeling combined with biodiversity and tourist visitation data to ascertain the specific risk to a country with world renowned biodiversity. Our findings indicate that approximately 23% of Costa Ricas landmass provides suitable conditions for Bsal, posing a threat to 37 salamander species. The Central and Talamanca mountain ranges, in particular, have habitats predicted to be highly suitable for the pathogen. To facilitate monitoring and mitigation efforts, we identified eight specific protected areas that we believe are at the greatest risk due to a combination of high biodiversity, tourist visitation, and suitable habitat for Bsal. We advise regular monitoring utilizing remotely-sensed data and ecological niche modeling to effectively target in-situ surveillance and as places begin implementing educational efforts.

ecology↗

bioRxiv2023

Human proton channels accumulate in cholesterol dependent membrane domains via direct interaction with stomatin

Many membrane proteins are modulated by cholesterol. Here we report strong effects of cholesterol depletion and restoration on the human voltage gated proton channel, hHV1 in excised patches but negligible effects in whole-cell configuration. Despite the presence of a putative cholesterol binding site, a CARC domain in the human voltage gated proton channel, hHV1, mutation of this domain did not affect cholesterol effects. The murine HV1 lacks a CARC sequence but displays similar cholesterol effects. These three results all argue against a direct effect of cholesterol on HV1. We propose that the data are explainable if HV1 preferentially associates with cholesterol-dependent lipid domains, or "rafts." The rafts would be expected to concentrate in the membrane/glass interface and to be depleted from the electrically-accessible patch membrane. This idea is supported by evidence that HV1 channels can diffuse between seal and patch membranes when suction is applied. Suction pulls membrane constituents including HV1 into the patch. In whole-cell studies moderate osmotic stretch does not noticeably alter H+ currents. Simultaneous truncation of the large intracellular N- and C-termini greatly attenuated the cholesterol effect, but C-truncation only did not. We conclude that the N-terminus is the region of attachment to lipid domains. Searching for abundant raft-associated molecules led to stomatin. Co-immunoprecipitation experiments showed that hHV1 binds to stomatin. The stomatin-mediated association of HV1 with cholesterol-dependent lipid domains provides a mechanism for cells to direct HV1 to subcellular location where it is needed, such as the phagosome in leukocytes. SignificanceMany membrane proteins are modulated by cholesterol. Here we explore effects of cholesterol on the human voltage-gated proton channel, hHV1. Although we find little evidence for a direct effect, cholesterol was found to exert a strong influence over H+ current in excised membrane patches. These effects are explainable by hypothesizing that HV1 preferentially associates with cholesterol-dependent membrane lipid domains. We postulate that HV1 diffuses within the membrane and is concentrated in such domains that are anchored to the pipette glass by large membrane proteins. We find that HV1 co-immunoprecipitates with stomatin, a typical component of cholesterol dependent lipid domains. The association of HV1 with lipid domains provides a mechanism for directing HV1 to specific subcellular locations to perform specific functions.

physiology↗

bioRxiv2023

Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma

BackgroundCell free DNA (cfDNA) profiles of 5-hydroxymethylcytosine (5-hmC), an epigenetic marker of open chromatin and active gene expression, are correlated with metastatic disease burden in patients with neuroblastoma. Neuroblastoma tumors are comprised of adrenergic (ADRN) and mesenchymal (MES) cells, and the relative abundance of each in tumor biopsies has prognostic implications. We hypothesized that ADRN and MES specific signatures could be quantified in cfDNA 5-hmC profiles and would augment the detection of metastatic burden in patients with neuroblastoma. MethodsWe previously performed an integrative analysis to identify ADRN and MES specific genes (n=373 and n=159, respectively). Purified DNA from cell lines was serial diluted with healthy donor cfDNA. Using Gene Set Variation Analysis (GSVA), ADRN and MES signatures were optimized. We then quantified signature scores, and our prior neuroblastoma signature, in cfDNA from 84 samples from 46 high-risk patients including 21 patients with serial samples. ResultsSamples from patients with higher metastatic burden had increased GSVA scores for both ADRN and MES gene signatures (p < 0.001). While ADRN and MES signature scores tracked together in serially collected samples, we identified instances of patients with increases in either MES or ADRN score at relapse. ConclusionsWhile it is feasible to identify ADRN and MES signatures using 5-hmC profiles of cfDNA from neuroblastoma patients and correlate these signatures to metastatic burden, additional data are needed to determine the optimal strategies for clinical implementation. Prospective evaluation in larger cohorts is ongoing.

genomics↗

bioRxiv2023

T-cell inflammation is prognostic of survival in patients with high-risk neuroblastoma enriched for an adrenergic signature

PurposeT-cell inflammation (TCI) has been shown to be a prognostic marker in neuroblastoma, a tumor comprised of cells that can exist in two epigenetic states, adrenergic (ADRN) and mesenchymal (MES). We hypothesized that elucidating unique and overlapping aspects of these biologic features could serve as novel biomarkers. Patients and MethodsWe detected lineage-specific, single-stranded super-enhancers defining ADRN and MES specific genes. Publicly available neuroblastoma RNA-seq data from GSE49711 (Cohort 1) and TARGET (Cohort 2) were assigned MES, ADRN, and TCI scores. Tumors were characterized as MES (top 33%) or ADRN (bottom 33%), and TCI (top 67% TCI score) or non-inflamed (bottom 33% TCI score). Overall survival (OS) was assessed using the Kaplan-Meier method, and differences were assessed by the log-rank test. ResultsWe identified 159 MES genes and 373 ADRN genes. TCI scores were correlated with MES scores (R=0.56, p<0.001 and R=0.38, p<0.001) and anticorrelated with MYCN-amplification (R=-0.29, p<0.001 and -0.18, p=0.03) in both cohorts. Among Cohort 1 patients with high-risk, ADRN tumors (n=59), those with TCI tumors (n=22) had superior OS to those with non-inflammed tumors (n=37) (p=0.01), though this comparison did not reach significance in Cohort 2. TCI status was not associated with survival in patients with high-risk MES tumors in either cohort. ConclusionsHigh inflammation scores were correlated with improved survival in some high-risk patients with, ADRN but not MES neuroblastoma. These findings have implications for approaches to treating high-risk neuroblastoma.

cancer biology↗

bioRxiv2023

5-hydroxymethylcytosine profiling of cell-free DNA identifies bivalent genes that are prognostic of survival in high-risk neuroblastoma.

Neuroblastoma is the most common extra-cranial solid tumor in childhood and epigenetic dysregulation is a key driver of this embryonal disease. In cell-free DNA from neuroblastoma patients with high-risk disease, we found increased 5-hydroxymethylcytosine (5-hmC) deposition on Polycomb Repressive Complex 2 (PRC2) target genes, a finding previously described in the context of bivalent genes. As bivalent genes, defined as genes bearing both activating (H3K4me3) and repressive (H3K27me3) chromatin modifications, have been shown to play an important role in development and cancer, we investigated the potential role of bivalent genes in maintaining a de-differentiated state in neuroblastoma and their potential use as a biomarker. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogenous neuroblastoma cell lines. Through gene set variance analysis, we developed a clinically implementable bivalent signature. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in high-risk neuroblastoma patients. Thus, low expression of bivalent genes is a biomarker of ultra-high-risk disease and may represent a therapeutic opportunity in neuroblastoma.

genomics↗

bioRxiv2022

Trapped pore waters in the open proton channel HV1

The voltage-gated proton channel, HV1, is crucial for innate immune responses. According to alternative hypotheses, protons either hop on top of an uninterrupted water wire or bypass titratable amino acids, interrupting the water wire halfway across the membrane. To distinguish between both hypotheses, we estimate the water mobility for the putative case of an uninterrupted wire. The predicted single-channel water permeability 3x10-12cm3s-1 reflects the permeability-governing number of hydrogen bonds between water molecules in single-file configuration and pore residues. However, the measured unitary water permeability does not confirm the prediction, i.e., it is negligible. Osmotic deflation of reconstituted lipid vesicles reveals trapped water inside the HV1 wild-type channel and D174A mutant open at 0 mV. The conductance of 1400 H+ s-1 per wild-type channel agrees with the calculated diffusion limit for a ~2 [A] capture radius for protons. Removal of a charged amino acid (D174) at the pore mouth decreases H+ conductance, conceivably by reducing the capture radius. At least one intervening amino acid contributes to H+ conductance while blocking water flow.

biophysics↗