Biology subjects

Rojas, A.

Publications and source records attributed to Rojas, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Causal analysis of rock-biodiversity relationships over the global Phanerozoic challenges rock record bias and common cause hypothesis

Sampled marine biodiversity covaries strongly with sedimentary rock quantity over the Phanerozoic, but the respective contributions of different potential causes remain unsettled. Although regional studies show that rock-record bias accounts for more variation in sampled marine biodiversity than common-cause mechanisms, evaluating this relationship across the global Phanerozoic record remains difficult because fossil databases are inherently biased toward fossiliferous strata. To address this limitation, we compiled literature-derived measures of global marine biodiversity and sedimentary strata, along with an existing sea-level curve. Using an information-theoretic causal framework, we then evaluated the relative contributions of rock-record bias and common-cause hypotheses to Phanerozoic-scale variation in sampled marine biodiversity. Our results show a strong contemporaneous causality of marine strata on sampled biodiversity, indicating that rock record bias detected at regional scales extends to the global scale. However, neither rock record bias nor common-cause mechanisms accounts for most Phanerozoic-scale patterns in sampled biodiversity, and additional unmeasured factors likely contribute. Finally, we find tentative evidence that synergistic causality between geologically mediated sampling biases and forces shaping the underlying biological signal contributes to global Phanerozoic patterns in sampled biodiversity.

paleontology↗

bioRxiv2026

Deletion of the MALAT1 RNA 3' end Promotes Transcript Decay, TALAM1 downregulation, and Inhibits Proliferation in Gastric and Breast Cancer Cells

The long non-coding RNA MALAT1 is a conserved oncogenic driver whose function relies on a 3 triple-helix motif. While its biochemistry is well-characterized in vitro, the endogenous requirement for this motif in regulating the stability of the transcript and other genes residing in its locus remains unclear. In this study, we employed a dual-sgRNA CRISPR-Cas9 approach to systematically excise triple-helix-forming sequences from the native MALAT1 locus in gastric (AGS) and breast (MCF7) cancer cells. Our findings demonstrate that the 3 end strongly contributes to MALAT1 stability. Perturbations ranging from genomic deletions to a single-base changes trigger transcript collapse and rapid exonucleolytic decay, while the biogenesis of the small RNA mascRNA (a byproduct of MALAT1, also involved in cancer) remains decoupled and unaffected. In cellulo, DMS probing reveals that edited transcripts retain structural complexity in the 3 region. Phenotypically, structural disruption of the 3 end significantly impairs proliferation of both cancer cellular models. These results identify the 3 triple-helix as a determinant of MALAT1 stability and provide endogenous validation for its role in the analyzed AGS and MCF7 cells.

molecular biology↗

bioRxiv2025

Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway

During tumor progression, it has been assumed that individual cells that have acquired advantageous mutations overtake the population. Cancers driven by extrachromosomal DNA (ecDNA) do not follow this paradigm. Instead, these tumors have a spectrum of oncogene copy numbers across cells, and graded ecDNA variation may function as a form of bet-hedging that equips tumors with a broad range of phenotypes. Using imaging, single-cell multiomics, and multiplexed proteomics, we systematically characterized ecDNA levels across thousands of single cells. Higher ecDNA dosage produces proportional changes in transcript abundance, chromatin accessibility, protein levels, cell-cycle progression, and proliferation. Genes amplified on ecDNA exhibit distinct transcriptional scaling regimes that shift when the same genes are reintegrated into chromosomal homogeneous staining regions. When we experimentally disrupted the continuum of ecDNA dosage by sorting cells into low- and high-copy number states, the population rapidly recovered its original, continuous distribution. Our time-course data, live-cell imaging, and stochastic models collectively show that restoring this spectrum is an active, deterministic process rather than the passive outcome of random segregation. Together, these findings position ecDNA-mediated expression as a distinct evolutionary mechanism that endows tumors with rapid, population-level adaptability. These findings offer insight into why ecDNA-driven cancers are among the most aggressive and treatment-resistant.

genomics↗

bioRxiv2025

In vivo generation of chimeric antigen receptor T cells using optimally retargeted and functionalized lentiviral vectors with reduced immune clearance

Despite striking efficacy against hematologic malignancies, the cost and complexity of CAR T manufacturing present significant barriers to broader patient access. Beyond manufacturing challenges, ex vivo expansion of T cells may be detrimental for their function and persistence. Thus, delivery of CARs to reprogram host cells in vivo would represent a significant advance toward "off-the-shelf" therapy but has been limited by low efficiency, low specificity, and immunogenicity of viral vectors. Here we describe the design of pseudotyped lentiviral vectors (LV) with superior functionality and high target specificity. We show that LV pseudotyped with chimeric envelope glycoproteins from dolphin morbillivirus (DMV) can be engineered to selectively infect human T cells and evade neutralizing antibody responses in measles-vaccinated human serum. We further demonstrate that camelid-derived nanobodies are a superior retargeting domain, overcoming limitations inherent to the use of single chain variable fragment antibodies. Using a chimeric DMV-pseudotyped virus targeting the CD7 receptor, we demonstrate efficient and highly specific infection of T cells both in vitro and in vivo, generating functional CAR T cells and inducing therapeutic efficacy in a preclinical B cell lymphoma model.

bioengineering↗

bioRxiv2025

Insights on Chamelea gallina growth dynamics from the Holocene climate optimum in the Northern Adriatic Sea (Italy)

The fossil record documents ecological responses to past climate transitions, providing insights into future scenarios of marine ecosystems and taxa under climate change. In this study, we compared shell growth dynamics, specifically linear extension and net calcification rates, of the bivalve Chamelea gallina between Northern Adriatic Sea (NAS) assemblages from the Holocene Climate Optimum (HCO, 9-5 kyr cal. B.P.) and today. This species is a valuable economic resource, currently threatened by climate warming and numerous anthropogenic stressors. During the HCO, regional sea surface temperatures were warmer than today, making it a potential analog for exploring ecological responses to increasing seawater temperatures predicted in the coming decades. By combining standard aging methods with reconstructed sea surface temperatures, we observed a significant reduction in linear extension and net calcification rates in warmer HCO assemblages. During the HCO, immature C. gallina specimens developed a denser shell, especially during their early growth stages, at the expense of a linear extension rate, which was lower than modern specimens. This resulted in an average delay of 3-4 months in reaching sexual maturity, which is currently reached after ~ 13-14 months or at a length of ~18 mm. Several environmental factors are probably responsible for these differences between fossil and modern assemblages. Temperature indirectly impacted the geomorphologic evolution of the NAS over the Early-Mid Holocene, shaping the outlet structure of the Po and other NAS rivers. This, in turn, affected environmental factors such as nutrient load, seawater transparency, salinity, and phytoplankton. In addition, recent anthropogenically-derived decreases in natural NAS predators of infaunal bivalves may have reduced the natural predation pressure on modern C. gallina, thus favoring those populations characterized by faster linear extension rates (at the expense of a higher shell density), especially during the initial stages of life, hence facilitating a quicker attainment of sexual maturity.

paleontology↗

bioRxiv2025

Spatial patterns of trematode-induced pits on bivalve skeletons: Challenges and prospects for research on parasite-host dynamics

Interactions between the parasitic larvae of digenean trematodes (mainly gymnophallids) and bivalves often result in characteristic shell malformations, i.e., pit-like traces. Tracking these traces through the Holocene and modern marine death assemblages has made studying parasite-host responses to natural and anthropogenic environmental change possible. Despite major breakthroughs, empirical explorations of parasite-host dynamics in the geological record are primarily based on trace occurrence data, overlooking that trace spatial patterns on the host skeleton could carry ecological information and potentially document different aspects of the parasite-host interactions (e.g., infective behavior, association with specific host anatomy, spatial relationships of traces with different qualitative properties such as size class, etc.). The Spatial Point Pattern Analysis of Traces (SPPAT) has been increasingly employed to overcome similar challenges in studying predatory traces on bivalve prey. Although this approach holds considerable promise for research on trematode-host dynamics, several assumptions and caveats need to be considered (e.g., the number of traces required to capture the parasite-host dynamics accurately, the reliability of point patterns constructed from multiple host skeletons in describing parasite interactions). Here, we introduce a spatially explicit framework for extracting information from spatial patterns of trematode-induced pits on bivalve shells using SPPAT, address methodological questions involved in assembling a point pattern of traces from multiple host specimens, and discuss critical issues related to drawing inferences from pooled point data. We illustrate our approach using a case study on late Holocene samples of the commercially relevant bivalve Chamelea gallina from the northern Adriatic of Italy. This species holds high value in the seafood industry and is increasingly used in climate change research. Our results reveal that trematode-induced malformations on bivalve shells are not random; they show an aggregated pattern for metacercaria traces of the same size classes, while an independent pattern arises when examining traces of two distinct size classes. This study highlights the potential value of spatial information from parasite-induced traces in enhancing our understanding of parasite-host dynamics over time.

paleontology↗

bioRxiv2025

The Single-Cell Landscape of Peripheral and Tumor-infiltrating Immune Cells in HPV- HNSCC

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. HPV-negative HNSCC, which arises in the upper airway mucosa, is particularly aggressive, with nearly half of patients succumbing to the disease within five years and limited response to immune checkpoint inhibitors compared to other cancers. There is a need to further explore the complex immune landscape in HPV-negative HNSCC to identify potential therapeutic targets. Here, we integrated two single-cell RNA sequencing datasets from 29 samples and nearly 300,000 immune cells to investigate immune cell dynamics across tumor progression and lymph node metastasis. Notable shifts toward adaptative immune cell populations were observed in the 14 distinct HNSCC-associated peripheral blood mononuclear (PBMCs) and 21 tumor-infiltrating immune cells (TICs) considering disease stages. All PBMCs and TICs revealed unique molecular signatures correlating with lymph node involvement; however, broadly, TICs increased ligand expression among effector cytokines, growth factors, and interferon-related genes. Pathway analysis comparing PBMCs and TICs further confirmed active cell signaling among Monocyte-Macrophage, Dendritic cell, Natural Killer (NK), and T cell populations. Receptor-ligand analysis revealed significant communication patterns shifts among TICs, between CD8+ T cells and NK cells, showing heightened immunosuppressive signaling that correlated with disease progression. In locally invasive HPV-negative HNSCC samples, highly multiplexed immunofluorescence assays highlighted peri-tumoral clustering of exhausted CD8+ T and NK cells, alongside their exclusion from intra-tumoral niches. These findings emphasize cytotoxic immune cells as valuable biomarkers and therapeutic targets, shedding light on the mechanisms by which the HNSCC sustainably evades immune responses.

cancer biology↗

bioRxiv2024

Population genomics reveals an ancient origin of heartworms in canids

Heartworms (Dirofilaria immitis) are parasitic nematodes that cause significant cardiopulmonary-associated morbidity and mortality in canids worldwide. The global spread of heartworms is believed to have occurred alongside the dispersal of domesticated dogs. To test this theory, we analysed the genomes of 127 specimens collected from mammalian carnivore hosts across four continents. Here we show distinct genetic differences between heartworms from different continents, indicating a more ancient dispersal in canid hosts than previously recognised. Using admixture analyses, we find an Asian origin for Australian heartworms, consistent with the arrival of dingoes thousands of years ago. Finally, the genetic relatedness between European and Central American heartworms suggests that modern dispersal, likely associated with human colonisation of the Americas by Europeans, occurred with domesticated dogs. This work sheds light on the population dynamics and deep evolutionary history of a globally widespread parasite of veterinary significance.

evolutionary biology↗

bioRxiv2024

In vivo CRISPR screens identify key modifiers of CAR T cell function in myeloma

Chimeric antigen receptor (CAR) T cells are highly effective in hematologic malignancies. However, loss of CAR T cells can contribute to relapse in a significant number of patients. These limitations could potentially be overcome by targeted gene editing to increase CAR T cell persistence. Here, we performed in vivo loss-of-function CRISPR screens in BCMA-targeting CAR T cells to investigate genes that influence CAR T cell persistence, function and efficacy in a human multiple myeloma model. We tracked the expansion and persistence of CRISPR-library edited T cells in vitro and then at early and late timepoints in vivo to track the performance of gene modified CAR T cells from manufacturing to survival in tumors. The screens revealed several context-specific regulators of CAR T cell expansion and persistence. Ablation of RASA2 and SOCS1 enhanced T cell expansion in vitro, while loss of PTPN2, ZC3H12A, and RC3H1 conferred early selective growth advantages to CAR T cells in vivo. Strikingly, we identified cyclin-dependent kinase inhibitor 1B (CDKN1B), a cell cycle regulator, as the most important factor limiting CAR T cell fitness at late timepoints in vivo. CDKN1B ablation increased BCMA CAR T cell proliferation and effector function in response to antigen, significantly enhancing tumor clearance and overall survival. Thus, our findings reveal differing effects of gene-perturbation on CAR T cells over time and in different selective environments, highlight CDKN1B as a promising target to generate highly effective CAR T cells for multiple myeloma, and underscore the importance of in vivo screening as a tool for identifying genes to enhance CAR T cell function and efficacy.

immunology↗

bioRxiv2024

Lineage-specific neutralising antibodies after SARS-CoV-2 mild disease. Immune boosting effect of vaccination

We followed a group of 105 non-vaccinated individuals after Alpha or Delta SARS-CoV-2 mild disease, measuring the viral shedding (qRT-PCR, dPCR and subgenomic RNA-E) and humoral response (commercial immunoassay and pseudovirus and live virus neutralisation) up to six months. Sixty nine patients received a vaccination boost during the follow-up period (n=95). Subgenomic RNA-E showed a shorter period until negativity (mean 2.2 weeks) compared to gRNA (mean 5.2 weeks). A high correlation between qRT-PCR and dPCR was found for viral load estimation, even when no nucleic acid extraction was used in dPCR (R2 = 0.87). Post-convalescent sera showed the strongest neutralisation against the variant of natural exposure, while the neutralisation capacity against Omicron variants was significantly lower compared to the other variants. Additionally, the results suggested that commercial immunoassays may not accurately predict protection against a different variant than the variant of exposure. An immune boosting effect of the SARS-CoV-2 vaccination was evident. Variant-specific neutralising antibodies were detected one month after natural infection. Although short lived, maximum igG response was observed after hybrid immunisation (natural infection + vaccination). This study also points to potential improvements in the clinical management of SARS-CoV-2 cases. Firstly, subgenomic RNA-E is a potentially more accurate biomarker of infectivity than current qRT-PCRs using genomic RNA as target. Secondly, accuracy of high-throughput immunoassays must be validated in order to estimate specific protection and organise vaccination campaigns. Our findings could play a role in the current implementation of SARS-CoV-2 vaccine programs. Author SummaryYears after SARS-CoV-2 related infections challenged the healthcare systems of the whole world, the optimal strategy to deal with diagnosis, quarantines or vaccination patterns is still a matter of debate. The interplay between infectivity and immunity in the different circulating variants is complex, and qPCR for diagnosis may extend quarantines, as detection of viral RNA does not necessarily mean that the virus remains infectious. We studied a group of patients infected with pre-Omicron variants to study how their variant-specific antibodies reacted to the past and present variants of SARS-CoV-2. In both Alpha and Delta, antibodies neutralise their own variants better than other variants that came before and after. Perhaps most importantly, neutralisation was lowest against Omicron variants. We followed the viral shedding dynamics of the patients, testing different PCR techniques and targets. Subgenomic RNA was detectable in nasopharyngeal samples for a shorter time than genomic RNA and it has been suggested as a good marker of infectivity. Using sgRNA instead of genomic RNA as a PCR target could reduce hospital bed occupation and quarantine time. Overall, we hope that these results could help guide pandemic and diagnostic control in the future.

microbiology↗

bioRxiv2024

Examining perfluorohexane sulfonate (PFHxS) impacts on sensorimotor and circadian rhythm development

Perfluorohexane sulfonate (PFHxS) is a ubiquitous perfluoroalkyl substance known for its environmental persistence and potential toxicity. This study investigated PFHxSs impact on zebrafish embryos, focusing on sensorimotor behavior, circadian rhythm disruption, and underlying molecular mechanisms. Under 24 hr dark incubations, PFHxS exposure induced concentration-dependent hyperactivity within larval photomotor response, characterized by the distinctive "O-bend" response, strong light-phase hyperactive movement and seizure-like movements. It appears that PFHxS-treated embryos cannot sense light cues in a normal manner. Similar hyperactivity was seen for acoustic startle response assay, suggesting that the response is not merely visual, but sensorimotor. LC-MS studies confirmed detectable uptake of PFHxS into embryos. We then conducted mRNA-sequencing across multiple time points (48 and 120 hpf) and concentrations (0.00025, 0.0025 and 25 {micro}M). Data at the 25 {micro}M (2-120 hpf) exposure showed disrupted pathways associated with DNA and cell cycle. Interestingly, data at 0.00025 {micro}M - an environmentally relevant concentration- at 48 hpf showed disruption of MAPK and other signaling pathways. Immunohistochemistry of eyes showed reduced retinal stem cell proliferation, consistent with observed DNA replication pathway disruptions. To assess if these impacts were driven by circadian rhythm development, we manipulated light/dark cycles during PFHxS incubation; this manipulation altered behavioral patterns, implicating circadian rhythm modulation as a target of PFHxS. Since circadian rhythm is modulated by the pineal gland, we ablated the gland using metronidazole; this ablation partially rescued hyperactivity, indicating the glands role in driving the phenotype. Collectively, these findings underscore proclivity of PFHxS to cause neurodevelopmental toxicity, necessitating further mechanistic exploration and environmental health assessments.

pharmacology and toxicology↗

bioRxiv2024

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks

The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. In future publications, these data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.

genomics↗

bioRxiv2024

Tenascin-C in the early lung cancer tumor microenvironment promotes progression through integrin activation and FAK

Pre-cancerous lung lesions are commonly initiated by activating mutations in the RAS pathway, but do not transition to lung adenocarcinomas (LUAD) without additional oncogenic signals. Here, we show that expression of the extracellular matrix protein Tenascin-C (TNC) is increased in and promotes the earliest stages of LUAD development in oncogenic KRAS-driven lung cancer mouse models and in human LUAD. TNC is initially expressed by fibroblasts and its expression extends to tumor cells as the tumor becomes invasive. Genetic deletion of TNC in the mouse models reduces early tumor burden and high-grade pathology and diminishes tumor cell proliferation, invasion, and focal adhesion kinase (FAK) activity. TNC stimulates cultured LUAD tumor cell proliferation and migration through engagement of v-containing integrins and subsequent FAK activation. Intringuingly, lung injury causes sustained TNC accumulation in mouse lungs, suggesting injury can induce additional TNC signaling for early tumor cell transition to invasive LUAD. Biospecimens from patients with stage I/II LUAD show TNC in regions of FAK activation and an association of TNC with tumor recurrence after primary tumor resection. These results suggest that exogenous insults that elevate TNC in the lung parenchyma interact with tumor-initiating mutations to drive early LUAD progression and local recurrence.

cancer biology↗

bioRxiv2024

Assessing mechanisms driving phenol isopropylated phosphate (IPP)- induced larval photomotor response deficits in zebrafish

Phenol isopropylated phosphates (IPP) are an additive organophosphate flame retardant (OPFR) which has been extensively used in furniture, electronics, automobiles, plastics, and childrens products to slow down the spread of fire. The processing and distribution of IPP-containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP-induced developmental toxicity using zebrafish embryos. We first conducted range finding experiments with embryonic zebrafish exposures to 0-200 M IPP from 6 to 120 h post fertilization and found significant morphological impacts like pericardial edema, yolk sac edema and spinal curvature at higher concentrations. For behavioral readouts, we performed larval photomotor response (LPR) assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Following this, relying on secondary analyses of our whole embryo mRNA-seq data, we conducted-1) retinoic acid receptor (RAR) signaling assay and 2) DNA methylation assays. In vitro assay for RA receptors indicate that IPP significantly inhibits RAR, but not RAR{beta} and RAR{gamma}. Whole-mount immunohistochemistry for 5-methylcytosine and global DNA methylation assay showed significant IPP-induced hypermethylation in situ. We conducted IPP co-exposure studies with a methylome modifier 5-azacytidine (Aza-c a methylation inhibitor) or retinoic acid signaling activators to assess if LPR phenotypes were mitigated by co-exposures. Data showed that Aza-c co-exposures partially reversed IPP-induced LPR hypoactivity and DNA hypermethylation, co-exposure with retinoic acid as well as AM580 (an RAR activator) were not able to reverse IPP-induced hypoactivity. Finally, based on RNA-seq data, we hypothesized that IPP affects the development of brain and eyes. Firstly, we performed global DNA methylation in brain and eyes, but did not find any significant effects. Then, we conducted mRNA sequencing on dissected brains and eyes, and found 2 and 135 differentially expressed genes, respectively. Gene ontology revealed that IPP affect phototransduction, voltage gated ion channels, synaptic and neurotransmitter signaling. Collectively, our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response, potentially through methylomic regulation. Finally, we observed that IPP affects gene expression within the developing eye, establishing synaptic transmission, vision and muscle contraction as a potential causative factor for LPR responses.

pharmacology and toxicology↗

bioRxiv2024

Quantification of rose rosette emaravirus (RRV) titers in eriophyoid mites: insights into viral dynamics and vector competency

Understanding the interaction between rose rosette emaravirus (RRV) and its vectors is pivotal in addressing the epidemic outbreak of rose rosette disease. This study employed quantitative real-time RT-PCR to assess RRV genome copy numbers in Phyllocoptes fructiphilus and P. adalius, providing insights into the viral dynamics and vector competency. Our findings suggest active virus replication within P. fructiphilus, a confirmed vector species, unlike P. adalius, highlighting its non-vector status. Furthermore, the study highlights the variability in virus concentration in mites over time, underlining possible developmental stage-specific response and influence of mite lifestyle on RRV retention and replication. This research is the first step in understanding the virus-mite interactome, which is essential for developing effective management strategies against rose rosette disease.

pathology↗

bioRxiv2024

Inbreeding and gallbladder cancer risk: Homozygosity associations adjusted for indigenous American ancestry, BMI and genetic risk of gallstone disease

Latin Americans have a rich genetic make-up that translates into heterogeneous fractions of the autosomal genome in runs of homozygosity (FROH), and heterogeneous types and proportions of indigenous American ancestry. While autozygosity has been linked to several human diseases, very little is known about the relationship between inbreeding, genetic ancestry and cancer risk in Latin Americans. Chile has one of the highest incidences of gallbladder cancer (GBC) in the world, and here we investigated the association between inbreeding, GBC, gallstone disease (GSD) and body mass index (BMI) in 4029 genetically admixed Chileans. We calculated individual FROH above 1.5 Mb and weighted polygenic risk scores for GSD, and applied multiple logistic regression to assess the association between homozygosity and GBC risk. We found that homozygosity was due to a heterogeneous mixture of genetic drift and consanguinity in the study population. Although we found no association between homozygosity and overall GBC risk, we detected interactions between FROH and sex, age, and genetic risk of GSD on GBC risk. Specifically, the increase in GBC risk per 1% FROH was 19% in men (P-value = 0.002), 30% in those under 60 years of age (P-value = 0.001), and 12% in those with a genetic risk of GSD above the median (P-value = 0.01). The present study highlights the complex interplay between inbreeding, genetic ancestry and genetic risk of GSD in the development of GBC. The applied methodology and our findings underscore the importance of considering the population-specific genetic architecture, along with sex- and age specific-effects, when investigating the genetic basis of complex traits in Latin Americans.

genetics↗

bioRxiv2024

Flame retardant tetrabromobisphenol A (TBBPA) disrupts histone acetylation during zebrafish maternal-to-zygotic transition

3,3,5.5-Tetrabromobisphenol A (TBBPA) is a widely used brominated flame-retardant utilized in the production of electronic devices and plastic paints. The objective of this study is to use zebrafish as a model and determine the effects of TBBPA exposure on early embryogenesis. We initiated TBBPA exposures (0, 10, 20 and 40M) at 0.75 h post fertilization (hpf) and monitored early developmental events such as cleavage, blastula and epiboly that encompass maternal-to-zygotic transition (MZT) and zygotic genome activation (ZGA). Our data revealed that TBBPA exposures induced onset of developmental delays by 3 hpf (blastula). By 5.5 hpf (epiboly), TBBPA-exposed (10-20 M) embryos showed concentration-dependent developmental lag by up to 3 stages or 100% mortality at 40 M. Embryos exposed to sublethal TBBPA concentrations from 0.75-6 hpf and raised in clean water to 120 hpf showed altered larval photomotor response (LPR), suggesting a compromised developmental health. To examine the genetic basis of TBBPA-induced delays, we conducted mRNA-sequencing on embryos exposed to 0 or 40 M TBBPA from 0.75 hpf to 2, 3.5 or 4.5 hpf. Read count data showed that while TBBPA exposures had no overall impacts on maternal or maternal-zygotic genes, collective read counts for zygotically activated genes were lower in TBBPA treatment at 4.5 hpf compared to time-matched controls, suggesting that TBBPA delays ZGA. Gene ontology assessments for both time- and stage-matched differentially expressed genes revealed TBBPA-induced inhibition of chromatin assembly- a process regulated by histone modifications. Since acetylation is the primary histone modification system operant during early ZGA, we immunostained embryos with an H3K27Ac antibody and demonstrated reduced acetylation in TBBPA-exposed embryos. Leveraging in silico molecular docking studies and in vitro assays, we also showed that TBBPA potentially binds to P300- a protein that catalyzes acetylation- and inhibits P300 activity. Finally, we co-exposed embryos to 20 M TBBPA and 50 M n-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide (CTPB) -a histone acetyltransferase activator that promotes histone acetylation- and showed that TBBPA-CTPB co or pre-exposures significantly reversed TBBPA-only developmental delays, suggesting that TBBPA-induced phenotypes are indeed driven by repression of histone acetylation. Collectively, our work demonstrates that TBBPA disrupts ZGA and early developmental morphology, potentially by inhibiting histone acetylation. Future studies will focus on mechanisms of TBBPA-induced chromatin modifications.

pharmacology and toxicology↗

bioRxiv2023

Metabolic changes that allow Plasmodium falciparum artemisinin-resistant parasites to tolerate the oxidative stress

1.1.1 BackgroundArtemisinin-based treatments (ACTs) are the first therapy currently used to treat malaria produced by Plasmodium falciparum. However, in recent years increasing evidence shows that some strains of P. falciparum are less susceptible to ACT in the Southeast Asian region. 1.2 Materials & MethodsA data reanalysis of several omics approaches currently available about parasites of P. falciparum that have some degree of resistance to ACT was carried out. The data used was from transcriptomics and metabolomics studies. One mitochondrial carrier of the parasite possibly involved in the mechanisms of tolerance to oxidative stress was modelled and subjected to molecular dockings with citrate and oxoglutarate. 1.3 ResultsAn increase in glutathione production was detected, changing the direction of the flux of metabolites in the tricarboxylic acid cycle, and boosting glucose consumed. The models of the mitochondrial carrier, called PfCOCP, show that it may be important in transporting citrate and oxoglutarate from the mitochondrial matrix to cytosol. If so, it may allow the parasite to tolerate the oxidative stress produced by artemisinin. 1.4 ConclusionsThis in-silico analysis shows that P. falciparum may tolerate the artemisinins oxidative stress through metabolic changes not reported before, showing the need for further research on the many metabolic aspects linked to this phenotype.

bioinformatics↗