Biology subjects

Zambada-Moreno, O.

Publications and source records attributed to Zambada-Moreno, O..

4 recordsLinked to original sources

bioRxiv2025

SiteCELL enables on-site PBMCs purification and cryopreservation for immune single cell profiling of diverse ancestries

Single cell genomics has improved our knowledge of immune function and heterogeneity. In recent years, the steady increase in the number of cells and individuals profiled as part of large multinational projects has enabled the characterization of cellular differences across human populations and ancestries. However, methods for collecting and processing peripheral blood mononuclear cells (PBMCs) for downstream single cell sequencing are difficult to implement in remote and rural settings. This has resulted in a lack of representation of underserved communities across the Global South in current initiatives. Hence, we developed SiteCELL, a method that enables purification and cryopreservation of PBMCs from whole blood at the site of collection using minimal laboratory equipment and without electricity. By comparing matched samples of purified PBMCs, we showed that SiteCELL performs as well as ficoll density gradient (FDG), both in laboratory and rural settings. This method ensures accurate recovery of cell type proportions and excels in reducing stress and minimizing variability across sampling batches. These advantages make it particularly well suited for implementation in challenging settings across countries, thereby enabling the inclusion of underrepresented ancestries in cellular atlases.

immunology↗

bioRxiv2025

Evolutionary Reconstruction of Hormone-bHLH Regulatory Networks in Solanaceae: Phylogenomic Insights from PSTVd-Tomato Interactions

The evolutionary reconstruction of transcriptional regulatory networks play a crucial role in plant adaptation to biotic stress. In Solanaceae, basic helix-loop-helix (bHLH) transcription factors (TFs) regulate hormone signaling pathways that balance growth and defense responses. In this study, we investigated the phylogenomic evolution of bHLH-mediated hormone networks in response to Potato Spindle Tuber Viroid (PSTVd) infection in tomato (Solanum lycopersicum) and its wild relatives. Among them, the JA-associated bHLH Solyc08g076930, IA3/MYC2 exhibits strong evolutionary conservation across Solanaceae, whereas the auxin regulator Solyc03g113560 miP-bHLH-ARF8 is a tomato-specific gene raising from an ancestral duplication, indicating neofunctionalization. Under PSTVd infection, we observe extensive regulatory rewiring, with bHLH hubs assuming dominant control over target genes typically regulated by multiple TFs in healthy conditions. The JA regulon undergoes the most pronounced shift, with Solyc08g076930 directly regulating 91 genes, compared to shared regulation with over a thousand TFs in healthy plants. This rewiring reflects the adaptive plasticity of bHLH TFs in coordinating stress responses through hormonal crosstalk. These findings reveal key evolutionary pressures shaping Solanaceae stress responses, offering insights for improving viroid tolerance and crop resilience.

evolutionary biology↗

bioRxiv2023

Dynamic co-expression modular network analysis of bHLH transcription factors regulation in the potato spindle tuber viroid-tomato pathosystem

Viroids, minimalist plant pathogens, present significant threats to crops by causing severe diseases. The use of high-throughput sequencing technologies for analyzing the transcriptomes of viroid-infected host plants has yielded informative information on gene regulation by these pathogens, however a complete understanding of the transcriptome data suffers from the inclusion of numerous genes of unknown function. Co-expression analysis addresses this by clustering genes into modules based on global gene expression levels. Our previous study emphasized basic helix-loop-helix protein (bHLH) transcriptional reprogramming in tomato in response to different potato spindle tuber viroid (PSTVd) strains. In the current research, we delve into tissue-specific gene modules, particularly in root and leaf tissues, governed by bHLH transcription factors during PSTVd infections. Utilizing public datasets that span Control (C; (mock-inoculated), PSTVd-mild (M), and PSTVd-severe (S23) strains in time-course infections, we uncovered differentially expressed gene modules. These modules were functionally characterized, identifying essential hub genes. We identified the roles of bHLH transcription factors (TFs) in managing processes like photosynthesis and rapid membrane repair in infected roots. In leaves, external layer alterations influenced photosynthesis, linking bHLH TFs to distinct metabolic functions. Expanding on these findings, we explored bipartite networks, discerning both common and unique bHLH TF regulatory roles, notably highlighting the bifan motifs significance in these interactions. Through this holistic approach, we deepen our understanding of viroid-host interactions and the intricate regulatory mechanisms underpinning them.

systems biology↗

bioRxiv2022

Deciphering the tissue-specific regulatory role of intronless genes across cancers

Intronless genes (IGs) or single-exon genes lacking an intron are found across most Eukaryotes. Notably, IGs display a higher transcriptional fidelity as they are not regulated through alternative splicing, suggesting better predictability biomarkers and easier regulation as targets for therapy. Cancer is a complex disease that relies on progressive uncontrolled cell division linked with multiple dysfunctional biological processes. Tumor heterogeneity remains the most challenging feature in cancer diagnosis and treatment. Given the clinical relevance of IGs, we aim to identify their unique expression profiles and interactome, that may act as functional signatures across eight different cancers. We identified 940 protein-coding IGs in the human genome, of which about 35% were differentially expressed across the analyzed cancer datasets. Specifically, [~]78% of differentially expressed IGs were undergoing transcriptional reprogramming with elevated expression in tumor cells. Remarkably, in all the studied tumors, a highly conserved induction of a group of deacetylase-histones located in a region of chromosome 6 enriched in nucleosome and chromatin condensation processes. This study highlights that differentially expressed human intronless genes across cancer types are prevalent in epigenetic regulatory roles participating in specific PPI networks for ESCA, GBM, and LUAD tumors. We determine that IGs play a key role in the tumor phenotype at transcriptional and post-transcriptional levels, with important mechanisms such as interactomics rewiring.

genomics↗