Biology subjects

Larios-Serrato, V.

Publications and source records attributed to Larios-Serrato, V..

5 recordsLinked to original sources

bioRxiv2025

Determination of Copy Number Variations and Affected Gene Networks in Breast Cancer from Mexican Patients

Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options and high molecular heterogeneity. In this study, we performed a genome-wide analysis of copy number variations (CNVs) using high-density microarrays in tumor tissue (TUM), tumor adjacent tissue (ADJ), and leukocytes (LEU) from five Mexican TNBC patients. We identified both unique and shared CNVs across tissues, including alterations in key chromosomal regions such as 1q23.3, 1q32.1, and 8q24.3, which harbor oncogenes like MYC, MCL1, and BCL9. Losses in 6q25.2 affecting ESR1 were also detected. CNVs were enriched in genes related to the Hallmarks of Cancer, with TUM samples showing profiles associated with proliferation, metastasis, and immune evasion; ADJ samples with growth suppression; and LEU samples with genomic instability. Pathway enrichment analyses revealed disrupted functions in DNA repair, extracellular matrix organization, and TP53 signaling in TUM. Notably, EGFR, ERCC4, and HSP90AB1 emerged as central nodes in interaction networks and may serve as markers or therapeutic targets. This is the first CNV profiling study of its kind in TNBC from Mexican patients, highlighting the importance of including underrepresented populations in genomic research to uncover distinct molecular signatures and potential diagnostic or therapeutic avenues. ImplicationsMolecular signatures of breast cancer (BC), predicted bioinformatically, involve common and distinct CNV-Hallmarks of Cancer genes, which are suitable candidates for screening as potential BC markers.

genomics↗

bioRxiv2025

The oral cavity of chronically homeless adults is home for unusual extremophile environmental bacteria

Chronically homeless adults (CHA) often face limited healthcare access, poor nutrition, frequent substance use, and close contact with stray animals. These factors can significantly alter their oral microenvironment. This study aimed to characterize the oral microbiota of this vulnerable and understudied population. We analyzed saliva samples from 60 chronically homeless men and 40 asymptomatic men with no history of homelessness, all living in Mexico City. DNA was extracted, and the V1-V3 regions of the 16S rRNA gene were sequenced. Taxonomic classification was performed using human and non-human databases. Diversity metrics were calculated using the vegan v2.6-4 package in R, and informative species were identified through machine learning and statistical approaches. Microbial correlation networks were inferred using NetCoMi in RStudio. Bacterial diversity was significantly higher in the CHA group. While both groups shared 369 species, only eight were exclusive to the control group, and 149 were unique to CHA. Several of these taxa had never been reported in humans and are typically found in extreme environments. For example, Megasphaera cerevisiae, adapted to high ethanol and low pH, was the most abundant species. Syntrophocurvum alkaliphilum, from a hypersaline lake in Siberia, and Sinanaerobacter chloroacetimidivorans, from anaerobic bioreactors, were also prevalent. Marked differences in microbial network structure were observed between groups. These findings highlight the adaptability of extremophile bacteria to human environments under chronic stress and poor hygiene. This study provides a first look into the oral microbiota of individuals experiencing chronic homelessness, emphasizing the need for more research into marginalized populations.

bioinformatics↗

bioRxiv2024

Composition of saliva metabolome is significantly associated with SARS-CoV2 infection and with severity of COVID-19 disease

BackgroundThe metabolome of COVID-19 patients has been studied sparsely, with most research focusing on a limited number of plasma metabolites or small cohorts. This is the first study to test saliva metabolites in COVID-19 patients in a comprehensive way, revealing significant changes linked to disease severity and highlighting saliva is potential as a non-invasive diagnostic tool. MethodsWe included 30 asymptomatic subjects with no prior COVID-19 infection or vaccination, 102 patients with mild SARS-CoV-2 infection, and 61 hospitalized patients with confirmed SARS-CoV-2 status. Saliva samples were analyzed using hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS/MS) in positive and negative ionization modes. ResultsSignificant changes in metabolites were identified in COVID-19 patients, with distinct patterns based on disease severity. Healthy individuals exhibited a well-regulated bacterial network, while severe cases showed disordered microbial networks. Elevated dipeptides such as Val-Glu and Met-Gln in moderate cases suggest specific protease activity related to SARS-CoV-2. Increased acetylated amino acids like N-Acetylserine and N-Acetylhistidine indicate potential biomarkers for stress and disease severity. Bacterial metabolites, including muramic acid and indole-3-carboxaldehyde, were higher in mild-moderate cases, indicating oral microbiota changes. In severe cases, polyamines and organ damage-related metabolites, such as N-acetylspermine and 3-methylcytidine, were significantly increased. Interestingly, metabolites reduced in moderate cases were elevated in severe cases. ConclusionsSaliva metabolomics offers insight into disease progression and potential biomarkers for COVID-19.

bioinformatics↗

bioRxiv2021

Copy number alterations and epithelial-mesenchymal transition genes in diffuse and intestinal gastric cancers in Mexican patients

Gastric cancer (GC) is a malignancy with the highest mortality among diseases of the digestive system worldwide. The study of GC-alterations is crucial to understand tumor biology, to establish important aspects of cancer prognosis and treatment response. Here, we purified DNA and performed whole-genome analysis with high-density arrays in samples from Mexican patients diagnosed with GC: diffuse (DGC) or intestinal (IGC), or non-atrophic gastritis (NAG) samples that served as controls. We identified shared and unique copy number alterations (CNA) between these altered tissues involving key genes and signaling pathways associated with cancer, allowing their molecular distinction and identification of the most relevant molecular functions impacted. When focused on epithelial-mesenchymal transition (EMT) genes, our bioinformatic analysis revealed that the altered network associated with chromosomal alterations included 11 genes shared between DGC, IGC, and NAG, as well as 19 DGC- and 7 IGC-exclusive genes, whose main molecular functions included adhesion, angiogenesis, migration, metastasis, morphogenesis, proliferation, and survival. This study presents the first whole-genome high-density array study in GC from Mexican patients and reveals shared and exclusive CNA-genes in DGC and IGC. In addition, we provide a bioinformatically predicted network focused on CNA-altered genes involved in the EMT, associated with the hallmarks of cancer, as well as precancerous alterations that could lead to gastric cancer. ImplicationsMolecular signatures of diffuse and intestinal GC, predicted bioinformatically, involve common and distinct CNA-EMT genes related to the hallmarks of cancer that are potential candidates for screening GC biomarkers, including early stages.

cancer biology↗

bioRxiv2020

Independent Tryptophan pathway in Trichoderma asperellum and T koningiopsis: New insights with bioinformatic and molecular analysis

The synthesis of Indole Acetic Acid from tryptophan has been described in plants, fungi and bacteria; it is thus known as tryptophan-dependent indole acetic acid. Four possible pathways of IAA formation have been described, including the indole acetonitrile acid (IAN), indole acetamide (IAM), indole-pyruvic (IAP) and tryptamine (TRM) pathways. Of these, the indole acetonitrile pathway is particularly important because when this compound is transformed into IAA, a nitrogenated molecule is released. The microorganisms that have this pathway are thus called nitrogen fixers. There is another little-studied pathway called TRP-Independent, so-called because the IAA that is formed in it can have an exogenous origin, chorismic acid (CHA), and it enters the pathway through anthranilic acid (ANA). The TRP-Independent pathway is made up of three stages. The first from CHA to ANA, the second from AA to IAA and the third from TRP to ANA through Kynurenine (KYN). This work describes the different stages of the pathway, as well as the enzymes and the genes that control the production of IAA, using a bioinformatic analysis of the genes involved, which were identified by PCR. An expression analysis showed that only T asperellum has the necessary genes to incorporate ANA into the TRP-I pathway and synthesize IAA through it. The analysis also detected the gene that regulates anthranilate phosphoribosyl transferase (AFT), an enzyme necessary for the synthesis of AIA from ANA; the presence of this gene was confirmed in the two species analyzed.

microbiology↗