De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide

Frontiers in Zoology, Год журнала: 2024, Номер 21(1)

Опубликована: Июнь 20, 2024

Abstract Many questions in biology benefit greatly from the use of a variety model systems. High-throughput sequencing methods have been triumph democratization diverse They allow for economical an entire genome or transcriptome interest, and with technical variations can even provide insight into organization expression regulation genes. The analysis biological interpretation such large datasets present significant challenges that depend on ‘scientific status’ system. While high-quality references are readily available well-established systems, establishment emerging system often requires extensive resources as finances, expertise computation capabilities. de novo assembly represents excellent entry point genetic molecular studies systems it efficiently assess gene content while also serving reference differential studies. However, process is non-trivial, rule must be empirically optimized every dataset. For researcher working system, little to no experience assembling quantifying short-read data Illumina platform, these processes daunting. In this guide we outline major faced when establishing advice how approach endeavor. We describe experimental bioinformatic steps, some broad recommendations cautions newcomer analyses. Moreover, initial selection tools assist journey raw assembled lists differentially expressed

Язык: Английский

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Combined inhibition of EZH2 and CDK4/6 perturbs endoplasmic reticulum-mitochondrial homeostasis and increases antitumor activity against glioblastoma

npj Precision Oncology, Год журнала: 2024, Номер 8(1)

Опубликована: Июль 25, 2024

Abstract Here, we show that combined use of the EZH2 inhibitor GSK126 and CDK4/6 abemaciclib synergistically enhances antitumoral effects in preclinical GBM models. Dual blockade led to HIF1α upregulation CalR translocation, accompanied by massive impairment mitochondrial function. Basal oxygen consumption rate, ATP synthesis, maximal respiration decreased, confirming disrupted endoplasmic reticulum-mitochondrial homeostasis. This was paralleled depolarization UPR sensors PERK, ATF6α, IRE1α. Notably, dual EZH2/CDK4/6 also reduced 3D-spheroid invasion, partially inhibited tumor growth ovo , impaired viability patient-derived organoids. Mechanistically, this due transcriptional changes genes involved mitotic aberrations/spindle assembly ( Rb, PLK1, RRM2, PRC1, CENPF, TPX2 ), histone modification HIST1H1B, HIST1H3G DNA damage/replication stress events TOP2A, ATF4 immuno-oncology DEPDC1 EMT-counterregulation PCDH1 ) a shift stemness profile towards more differentiated state. We propose for further investigation.

Язык: Английский

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Transcriptomic Approach for Investigation of Solanum spp. Resistance upon Early-Stage Broomrape Parasitism

Current Issues in Molecular Biology, Год журнала: 2024, Номер 46(8), С. 9047 - 9073

Опубликована: Авг. 18, 2024

Tomato (Solanum lycopersicum) is a major horticultural crop of high economic importance. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii, wild relative cultivated tomato, been utilized as breeding material S. lycopersicum. In the present study, it first time an in-depth analysis conducted these two specific introgression lines (ILs), IL6-2 IL6-3 (S. lycopersicum X pennellii), which were employed identify genes metabolic pathways associated resistance against broomrape. Comparative transcriptomic revealed multitude differentially expressed (DEGs) in roots, especially resistant genotype IL6-3, several validated by quantitative PCR. DEG pathway enrichment (PEA) diverse molecular mechanisms can potentially be implicated host’s defense response establishment resistance. The identified DEGs mostly up-regulated broomrape parasitism play crucial roles various processes different from strigolactone regulation. Our findings indicate that, addition essential role metabolism, multiple cellular may involved tomato’s broomrapes. insights gained this study will enhance our understanding facilitate methods regarding parasitism. Moreover, they assist developing strategies providing alternative solutions weed management tomatoes other agronomically important crops.

Язык: Английский

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Application of a high-throughput swarm-based deep neural network Algorithm reveals SPAG5 downregulation as a potential therapeutic target in adult AML

Functional & Integrative Genomics, Год журнала: 2025, Номер 25(1)

Опубликована: Янв. 6, 2025

Abstract Gene‒gene interactions play pivotal roles in disease pathogenesis and are fundamental the development of targeted therapeutics, particularly through elucidation oncogenic gene drivers cancer. The systematic analysis pathways is critical drug discovery process for various cancer subtypes. SPAG5, known its role spindle formation during cell division, has been identified as an oncogene several cancers, although specific impact on AML remains underexplored. This study leverages a high-throughput swarm-based deep neural network (SDNN) transcriptomic data—an approach that enhances predictive accuracy robustness collective intelligence—to augment, model, enhance understanding TP53 pathway cohorts. Our integrative systems biology SPAG5 uniquely downregulated driver adult AML, underscoring potential novel therapeutic target. interaction with key hub genes such MDM2 CDK1 not only reinforces tumour suppression negative regulation but also highlights moderating phenotypic genomic alterations associated progression. dynamics sets stage future research aimed at developing personalized treatment approaches utilizing capabilities genetic interventions.

Язык: Английский

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Plasma Proteomic Signatures of Physical Activity Provide Insights into Biological Impacts of Physical Activity and its Protective Role Against Dementia.

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 17, 2025

Physical activity (PA), including sedentary behavior, is associated with many diseases, Alzheimer's disease and all-cause dementia. However, the specific biological mechanisms through which PA protects against are not entirely understood. To address this knowledge gap, we first assessed conventional observational associations of three self-reported device-based measures circulating levels 2,911 plasma proteins measured in UK Biobank (n max =39,160) functional enrichment identified proteins. We then used bi-directional Mendelian randomization (MR) to further evaluate evidence for causal relationships protein levels. Finally, performed mediation analyses identify that may mediate relationship incident Our findings revealed 41 consistently all 1,027 at least one measure. Both MR study designs converged on appear increase as a result PA, integrin such ITGAV ITGAM, well MXRA8, CLEC4A, CLEC4M, GFRA1, ADGRG2; decrease LEP, LPL, INHBC, CLMP, PTGDS, ADM, OGN, PI3. Functional several relevant processes, cell-matrix adhesion, integrin-mediated signaling, collagen binding. proteins, GDF15, ITGAV, HPGDS, BCAN, MENT, were found dementia, implicating processes synaptic plasticity, neurogenesis inflammation, results provide insights into how affect protect from avenues future research health-promoting effects PA.

Язык: Английский

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Effects of light exposure during IVF: transcriptomic analysis of murine embryos and embryo-derived EVs

Frontiers in Immunology, Год журнала: 2025, Номер 16

Опубликована: Фев. 20, 2025

Light exposure of embryos during assisted reproduction affects embryo quality and implantation capacity in a wavelength dependent manner. We investigated the molecular mechanism these light-induced changes through comparative analysis gene expression regulatory miRNA profile murine cultured dark environment those exposed to white- or red filtered light. sequencing was used assess role embryo-derived extracellular vesicles endometrium-embryo dialogue. In vitro mouse at 3.5 days post coitum (dpc) were white After 24 hours mRNA content as well isolated RNA-sequencing performed. Differential functional enrichment for evaluating transcriptome results. caused transcriptomic embryos. White light upregulated apoptotic pathways, while gave rise activation regeneration including DNA repair mechanisms. Embryo-derived enclosed dependently unique cargos target genes which play implantation. upregulates both miRNAs levels. Red filtration partially counterbalances negative effects by shifting cellular processes towards regeneration, Extracellular blastocyst-decidua communication horizontal transfer miRNAs. Our data prove that fertilization modifies cell function might affect outcome

Язык: Английский

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A teaching proposal for a short course on biomedical data science

PLoS Computational Biology, Год журнала: 2025, Номер 21(4), С. e1012946 - e1012946

Опубликована: Апрель 14, 2025

As the availability of big biomedical data advances, there is a growing need university students trained professionally on analyzing these and correctly interpreting their results. We propose here study plan for master’s degree course science, by describing our experience during last academic year. In course, we explained how to find an open dataset, clean it prepare computational statistics or machine learning phase. By doing so, introduce common health science terms avoid mistakes in process. Moreover, clarified perform exploratory analysis (EDA) reasonably interpret its also described properly execute supervised unsupervised analysis, now understand outcomes. Eventually, validate findings obtained. illustrated all steps context principles, suggesting use only source programming languages (R Python particular), (if available), access scientific articles possible). believe teaching proposal can be useful interest anyone wanting start science.

Язык: Английский

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PathwayMind: An Innovative Tool and Database for Pathway Perturbation Analysis, Uncovering Critical Pathways for Drugs and Target Protein Sets

Computational Biology and Chemistry, Год журнала: 2025, Номер 118, С. 108466 - 108466

Опубликована: Апрель 15, 2025

Язык: Английский

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Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice – The Central Nucleus of the Amygdala

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Апрель 18, 2025

Abstract Alcohol use disorder (AUD) is a complex disease with heritability of ∼0.5, indicating genetic and non-genetic factors contribute to risk. Identifying gene expression networks contributing risk using post-mortem human brain tissue has the limitation conflating for AUD consequences alcohol use. We leveraged mice selectively bred differential ethanol preference from highly genetically diverse population overcome this limitation. Ethanol intake was correlated preference, high-preferring (HP) consumed more sweet-but not bitter-tasting solutions compared low-preferring (LP) mice, lines did differ in rate elimination. Adult, ethanol-naïve HP LP contributed central nucleus amygdala (CeA), region critical intake. Single-nuclei bulk RNA sequencing data were used identify cell types transcriptome changes related selective breeding preference. Single nuclei analysis identified populations inhibitory (∼48% cells) excitatory (∼23%) neurons, non-neuronal (∼29%) cells, but no differences cell-type composition or between lines. Bulk CeA for: (1) (2996 genes), (2) variability (426 (3) wiring (407 significant gene-gene correlations). Overall, lower variance found line. Reduced correlation, also suggested that selection high induced transcriptional regulation resulting reduced connectivity, specific enriched markers neurons expressing Isl1 Tac1 .

Язык: Английский

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The effect of fatty acid binding protein-3 exposure on endothelial transcriptomics

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Апрель 19, 2025

Abstract Background Fatty acid binding protein-3 (FABP3) is released in circulation following myocardial infarction and an increased level of circulatory FABP3 also reported peripheral artery disease patients exposing endothelial cells to higher FABP3. Recently, loss was shown protect against inflammation-induced dysfunction, however, the effect FABP3-exposure on unknown. Accordingly, study we performed transcriptomic profiling recombinant human (rhFABP3) treatment cells. Method Cultured were treated with either vehicle or rhFABP3 (50 ng/ml, 6h) then RNA-sequencing performed. Gene expression analysis followed by gene ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG) pathway analyses identify differentially expressed genes affected cellular functions pathways. Results Differential revealed kinesin family member 26b ( KIF26B ) as most upregulated survival motor neuron 2 SMN2 downregulated rhFABP3-treated comparison vehicle-treated Most associated cell motility, immune response, angiogenesis. GO KEGG indicated that exposure impacts several crucial pathways, prominently “Regulation leukocyte mediated cytotoxicity” “Natural killer cytotoxicity”, suggesting its involvement physiology response mechanisms cardiovascular stress. Conclusion This first evaluating rhFABP3-induced transcriptomics Our data reveal novel pathways Further research necessary validate these findings fully understand FABP3’s role biology diseases like disease.

Язык: Английский

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