Biology subjects

Acevedo, A.

Publications and source records attributed to Acevedo, A..

12 recordsLinked to original sources

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

Contrasting Impacts of the Anthropogenic Environment on the Diet of Long-tailed Macaques (Macaca fascicularis) in Southeast Asia

Human expansion will only increase access to anthropogenic food resources for wildlife species. Access to these resources can have positive and negative impacts on wildlife species. It is generally assumed that access to anthropogenic resources will decrease diet diversity, although recent work questions this. Our research uses metabarcoding to assess the diet detected in fecal samples from long-tailed macaques (Macaca fascicularis) on the islands of Singapore and Bali, Indonesia. We gathered information about multiple parameters to characterize the distinctly different anthropogenic environments on the two islands. Then, we used a leave one out cross validation model selection procedure and linear regressions to determine which environmental parameters impact various diet metrics for the macaques in these two different anthropogenic contexts. Macaques in both island contexts increased their usage of crop diet items with greater anthropogenic access, but with different resulting patterns. We found that as food provisioning of the macaques increases in Bali, multiple measures of diet richness decrease, as generally expected, yet diet stability within a group also decreases, indicating that although diet richness decreases with provisioning, individuals do not experience similar levels of access to these resources. In contrast to Bali, there were no significant differences in diet stability across groups in Singapore with increases in anthropogenic resources. These differing impacts on diet, seen in a single species, highlight the need to consider more closely the details of the spatial and temporal distribution of anthropogenic resource access when making predictions about how a species diet will be impacted.

ecology↗

bioRxiv2023

Ketogenic diet administration later in life improves memory and regulates the synaptic cortical proteome through the cAMP/PKA signaling pathway in aging mice.

Aging is a complex biological process that compromises brain function and neuronal network activity, leading to cognitive decline and synaptic dysregulation. In recent years, a cyclic Ketogenic Diet (KD) has emerged as a potential treatment to ameliorate cognitive decline by improving memory in aged mice after long-term administration. However, the molecular mechanisms that govern such changes remains unclear. Additionally, whether short-term cyclic KD administration later in life preserves memory has not been addressed in detail. Accordingly, here we investigated how a short-term cyclic KD starting at 20-23 months-old regulates brain function of aged mice. Behavioral testing and long-term potentiation (LTP) recordings revealed that a cyclic KD improves working memory and hippocampal LTP in 24-27 months-old mice after 16 weeks of treatment. Moreover, the diet also promotes higher dendritic arborization complexity and dendritic spine density in the prefrontal cortex. Furthermore, to elucidate the molecular mechanisms underlying the memory improvements elicited by a cyclic KD, cortical synaptosomes of aged mice fed with this diet for 1 year were analyzed by mass spectrometry. Bioinformatics analysis revealed that long-term cyclic KD administration predominantly modulates the presynaptic compartment by inducing changes in the cAMP/PKA signaling pathway, the synaptic vesicle cycle, and the actin/microtubule cytoskeleton. To test these findings in vivo, synaptic proteins from cortices of 24-27-month-old mice fed with control or cyclic KD for 16 weeks were analyzed by western blot. Interestingly, increased Brain Derived Neurotrophic Factor abundance, MAP2 phosphorylation and PKA activity were observed. Overall, we show that a cyclic KD regulates brain function and memory even when it is administered at late mid-life and significantly triggers several molecular features of long-term administration, including the PKA signaling pathway and cytoskeleton dynamics, thus promoting synaptic plasticity at advanced age.

neuroscience↗

bioRxiv2023

The BCKDK inhibitor BT2 is a chemical uncoupler that lowers mitochondrial ROS production and de novo lipogenesis

Elevated levels of branched chain amino acids (BCAAs) and branched-chain -ketoacids (BCKAs) are associated with cardiovascular and metabolic disease, but the molecular mechanisms underlying a putative causal relationship remain unclear. The branched-chain ketoacid dehydrogenase kinase (BCKDK) inhibitor BT2 is often used in preclinical models to increase BCAA oxidation and restore steady-state BCAA and BCKA levels. BT2 administration is protective in various rodent models of heart failure and metabolic disease, but confoundingly, targeted ablation of Bckdk in specific tissues does not reproduce the beneficial effects conferred by pharmacologic inhibition. Here we demonstrate that BT2, a lipophilic weak acid, can act as a mitochondrial uncoupler. Measurements of oxygen consumption, mitochondrial membrane potential, and patch-clamp electrophysiology show BT2 increases proton conductance across the mitochondrial inner membrane independently of its inhibitory effect on BCKDK. BT2 is roughly five-fold less potent than the prototypical uncoupler 2,4-dinitrophenol (DNP), and phenocopies DNP in lowering de novo lipogenesis and mitochondrial superoxide production. The data suggest the therapeutic efficacy of BT2 may be attributable to the well-documented effects of mitochondrial uncoupling in alleviating cardiovascular and metabolic disease.

biochemistry↗

bioRxiv2023

Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens

Drug targets with human genetic evidence are expected to increase clinical success by at least two-fold. Yet, translating disease-associated genetic variants into functional knowledge remains a fundamental challenge of early drug discovery. A key issue is that, currently, the vast majority of complex disease associations cannot be cleanly mapped to a gene. Immune disease-associated variants are enriched within regulatory elements, such as distal enhancers, found in T cell-specific open chromatin regions. To identify the genes and thus the molecular programs modulated by these regulatory elements, we developed a CRISPRi-based single-cell functional screening approach in primary human CD4+ T cells. Our pipeline enables the interrogation of transcriptomic changes induced by the perturbation of regulatory elements at scale. We first optimised a highly efficient CRISPRi protocol in primary human CD4+ T cells via CROPseq vectors. Subsequently, we performed a proof-of-concept screen targeting 45 non-coding regulatory elements and 35 transcription start sites and profiled approximately 250,000 CD4+ T cell single-cell transcriptomes. We developed a bespoke analytical pipeline for element-to-gene (E2G) mapping and demonstrate that our method can identify both previously annotated and novel E2G links. Lastly, we integrated genetic association data for immune-related traits and demonstrate how our platform can aid in the identification of effector genes for GWAS loci.

genomics↗

bioRxiv2022

Metabolic switch in the aging astrocyte evidenced via integrative approach comprising network and transcriptome analyses

Dysregulated central-energy metabolism is a hallmark of brain aging. Supplying enough energy for neurotransmission relies on the neuron-astrocyte metabolic network. To identify genes contributing to age-associated brain functional decline, we formulated an approach to analyze the metabolic network by integrating flux, network structure and transcriptomic databases of neurotransmission and aging. Our findings support that during brain aging: 1) The astrocyte undergoes a metabolic switch from aerobic glycolysis to oxidative phosphorylation, decreasing lactate supply to the neuron, while the neuron suffers intrinsic energetic deficit by downregulation of Krebs cycle genes, including mdh1 and mdh2 (Malate-Aspartate Shuttle); 2) Branched-chain amino acid degradation genes were downregulated, identifying dld as a central regulator; 3) Ketone body synthesis increases in the neuron, while the astrocyte increases their utilization, in line with neuronal energy deficit in favor of astrocytes. We identified candidates for preclinical studies targeting energy metabolism to prevent age-associated cognitive decline.

neuroscience↗

bioRxiv2020

Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells

Dengue virus (DENV), an arbovirus infecting over 100 million annually, cycles between human and mosquito hosts1. Examining how DENV adapts to such different host environments could uncover principles of arbovirus transmission and emergence. Here we combine sequential passaging and ultra-deep sequencing to examine the sequence dynamics and fitness changes of DENV populations adapting to human and mosquito cells, identifying the contributions of beneficial and deleterious mutations in shaping the fitness landscape driving host-specific paths of viral adaptation. We find DENV phenotypic adaptation is best described by the collective fitness contributions of all the alleles present in the population. Accordingly, while increased fitness during adaptation to each host is driven by host-specific beneficial mutations, it is reduced by the consistently replenished genetic load of deleterious mutations. Of note, host-specific beneficial mutations are in discrete regions across the genome, revealing molecular mechanisms of adaptation. Some of these clusters comprise phenotypically redundant mutations that may provide evolutionary robustness to transmission bottlenecks. Our results also suggest DENV adaptation is facilitated through variation in intrinsically disordered protein regions while transmembrane and structured domains evolve under stronger biophysical constraints. Importantly, the adaptation strategies uncovered in our simple system mirror macro-evolutionary changes observed across DENV serotypes and Zika virus and may suggest general principles of evolvability in arbovirus evolution.

microbiology↗

bioRxiv2020

Genetic interactions shaping evolutionary trajectories in an RNA virus population

A quantitative understanding of evolution rests on the analysis of the mutation accumulation process in biological populations, but is largely limited to high-frequency mutations due to the resolution of conventional sequencing technologies. Here, we examine the mutation composition of a poliovirus population over multiple passages using a highly-accurate sequencing strategy, that enables detection of up to 99% of all possible mutations, most of which are present at low-frequency. This data informs a mathematical model describing trajectory patterns of individual mutations to understand the type of interactions shaping population dynamics. We identify mutations consistent with a locus-independent behavior, and others deviating from that simple model by interactions. Clonal interference, followed by hitchhiking, appear to be the most prevalent interactions in the virus population. Epistasis, while presents, but does not significantly affect the distribution of mutational fitness on the short time scale examined in our study. Our study provides a comprehensive analysis of the allelic composition and how mutation rate, fitness, epistasis, clonal interference and hitchhiking influence population dynamics and evolution.

evolutionary biology↗

bioRxiv2019

An RNA-based system to study hepatitis B virus replication and select drug-resistance mutations

Hepatitis B virus (HBV) chronically infects over 250 million people worldwide, increasing their risk of liver cirrhosis and hepatocellular carcinoma. There is a vaccine to prevent new infections, but no efficient cure for chronic infection. New insights into HBV biology are needed to improve cure rates for this widespread devastating disease. We describe a method to initiate replication of HBV, a DNA virus, using synthetic RNA. This approach has several advantages over existing systems: it eliminates contaminating background signal from input virus or plasmid DNA and can be easily adapted to multiple genotypes and mutants. Further, it can be applied to identify anti-HBV compounds, measure anti-HBV drug efficiency, study virus evolution, and, as we demonstrate, it can be uniquely applied to predict antiviral drug resistance.

microbiology↗

bioRxiv2018

LIPEA: Lipid Pathway Enrichment Analysis

MotivationAnalyzing associations among multiple omic variables to infer mechanisms that meaningfully link them is a crucial step in systems biology. Gene Set Enrichment Analysis (GSEA) was conceived to pursue this aim in computational genomics, unveiling significant pathways associated to certain gene signatures under investigation. Lipidomics is a rapidly growing omic field, and absolute quantification of lipid abundance by shotgun mass spectrometry is generating high-throughput datasets that depict lipid metabolism in a plethora of conditions and organisms. In addition, high-throughput lipidomics represents a new important ally to develop personalized medicine approaches, investigate the causes and predict effective biomarkers in metabolic diseases, and not only.\n\nResultsHere, we present Lipid Pathway Enrichment Analysis (LIPEA), a web-tool for over-representation analysis of lipid signatures and detection of the biological pathways in which they are enriched. LIPEA is a new valid resource for biologists and physicians to mine pathways significantly associated to a set of lipids, helping them to discover whether common and collective mechanisms are hidden behind those lipids. LIPEA was extensively tested and we provide two examples where our system gave successfully results related with Major Depression Disease (MDD) and insulin re-sistance.\n\nAvailabilityThe tool is available as web platform at https://lipea.biotec.tu-dresden.de.

bioinformatics↗

bioRxiv2018

Genetic recombination of poliovirus facilitates subversion of host barriers to infection

The contribution of RNA recombination to viral fitness and pathogenesis is poorly defined. Here, we isolate a recombination-deficient, poliovirus variant and find that, while recombination is detrimental to virus replication in tissue culture, recombination is important for pathogenesis in infected animals. Notably, recombination-defective virus exhibits severe attenuation following intravenous inoculation that is associated with a significant reduction in population size during intra-host spread. Because the impact of high mutational loads manifests most strongly at small population sizes, our data suggest that the repair of mutagenized genomes is an essential function of recombination and that this function may drive the long-term maintenance of recombination in viral species despite its associated fitness costs.\n\nSignificance StatementRNA recombination is a widespread but poorly understood feature of RNA virus replication. For poliovirus, recombination is involved in the emergence of neurovirulent circulating vaccine-derived poliovirus, which has hampered global poliovirus eradication efforts. This emergence illustrates the power of recombination to drive major adaptive change; however, it remains unclear if these adaptive events represent the primary role of recombination in virus survival. Here, we identify a viral mutant with a reduced rate of recombination and find that recombination also plays a central role in the spread of virus within animal hosts. These results highlight a novel approach for improving the safety of live attenuated vaccines and further our understanding of the role of recombination in virus pathogenesis and evolution.

microbiology↗

bioRxiv2017

Hsp90 dictates viral sequence space by balancing the evolutionary tradeoffs between protein stability, aggregation and translation rate

Acquisition of mutations is central to evolution but the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, are proposed to promote sequence diversification by buffering destabilizing mutations. However, whether and how chaperones directly control protein evolution remains poorly understood. Here, we examine the effect of reducing the activity of the key eukaryotic chaperone Hsp90 on poliovirus evolution. Contrary to predictions of a buffering model, inhibiting Hsp90 increases population sequence diversity and promotes accumulation of mutations reducing protein stability. Explaining this counterintuitive observation, we find that Hsp90 offsets the evolutionary tradeoff between protein stability and aggregation. Lower chaperone levels favor sequence variants of reduced hydrophobicity, thus decreasing protein aggregation propensity but at a cost to protein stability. Notably, reducing Hsp90 activity also promotes clusters of codon-deoptimized synonymous mutations at inter-domain boundaries, likely to promote local ribosomal slowdown to facilitate cotranslational domain folding. Our results reveal how a chaperone can shape the sequence landscape at both the protein and RNA levels to harmonize the competing constraints posed by protein stability, aggregation propensity and translation rate on successful protein biogenesis.

evolutionary biology↗