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The hallmarks of cancer describe stepwise changes in cellular functions and molecular pathways of tumour cells that undergo malignant progression. Although 14 hallmarks have been proposed, their manifestation at the molecular level across different tumour …
Read PDFSingle-nucleus RNA sequencing (snRNAseq) allows for the dissection of cell type-specific transcriptional profiles. We evaluated differential gene expression using snRNAseq data generated from hippocampal region tissue donated by 11 Boston University Alzheimer's Disease Research Center …
Read PDFAdenosine-to-inosine (A-to-I) RNA editing is a major epitranscriptomic mechanism, yet its contribution to non-coding RNA regulation during neurodegeneration is largely unknown. SINE B2 RNAs represent the dominant editing substrates in mice and have been shown …
Read PDFAlzheimer's disease (AD), a neurodegenerative disease primarily affecting older adults, is characterized by changes in memory, behavior, and language. Although gene expression varies during AD progression, the molecular mechanisms underlying this variation remain unclear. RNA …
Read PDFTranscriptome assembly and quantification are crucial steps in the differential expression analysis of RNA-seq data. As transcriptome assembly precedes quantification, its results inevitably influence the outcomes of quantification. This study investigates the impact of transcriptome …
Read PDFThe recent COVID-19 pandemic left behind the lingering question as whether new variants of concern might cause further waves of infection. Thus, it is important to investigate the long-term protection gained via vaccination or exposure …
Read PDFConjugation, the exchange of genetic material between different bacterial species, is an important process underlying adaptation. The reason for this is that conjugative elements carry additional genes potentially providing adaptive benefit to the host, such …
Read PDFIridosomes, the guanine crystal-forming organelles of pigment-producing iridophores, are among the most versatile, visually striking yet mechanistically uncharacterized organelles in vertebrate biology. Lysosome-related organelles (LROs) support cell type-specific functions by adapting endolysosomal pathways for specialized …
Read PDFPolycystic kidney diseases (PKD) are a group of inherited nephropathies marked by the formation of fluid-filled cysts along the nephron, which cause renal failure. Bulk RNA sequencing of microdissected renal cysts from Pkd1<sup>RC/RC</sup> mice identifies …
Read PDFUnderstanding how microorganisms adapt to novel physical and chemical environments requires integrating evolutionary, regulatory, and phenotypic perspectives. Here, we examined <i>Streptococcus mutans</i> populations previously evolved for 100 days under simulated microgravity (sMG) or combined microgravity …
Read PDFRett syndrome (RTT) is an X-linked neurological disorder caused by <i>MECP2</i> mutations, creating distinct cellular environments in females (mosaic) versus males (nonmosaic). Despite female patients representing most cases, how mosaicism contributes molecularly to RTT pathogenesis, …
Read PDF<i>Candida albicans</i>, a World Health Organization critical-priority fungal pathogen, represents the predominant cause of candidemia. Therapeutic failure is sometimes driven by antifungal tolerance, a phenotype distinct from resistance, whose underlying mechanisms remain incompletely defined. Here, …
Read PDF<h4>Purpose</h4>Alpha-enolase (ENO1), the enzyme catalyzing 2-phosphoglycerate conversion to phosphoenolpyruvate, is highly expressed in diffuse large B-cell lymphoma (DLBCL) and correlates with adverse clinical outcomes. Thus, understanding the relationship between ENO1-related gene (ERG) network and DLBCL …
Read PDF<h4>Background</h4>Ageing is associated with the loss of muscle mass and function, with consequences for metabolic health, frailty and independence in later life. The aim of this study was to investigate the transcriptional heterogeneity of human …
Read PDFIn this paper, we develop a heterogeneous graph neural network, STAMapper, to transfer the cell-type labels from single-cell RNA-sequencing (scRNA-seq) data to single-cell spatial transcriptomics (scST) data. We collect 81 scST datasets consisting of 344 …
Read PDFBACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with limited treatment options and a high recurrence rate. Recurrence often occurs with metastasis, for which cancer cells must adapt to isolation stress to …
Read PDFWheat (<i>Triticum aestivum</i> L.) resistance to Hessian fly (HF, <i>Mayetiola destructor</i>) conferred by HF resistance (<i>R</i>) genes, is often vulnerable to heat stress. This study aims to investigate the molecular basis of heat-induced susceptibility in …
Read PDFHeme is an essential molecule for most organisms, yet some parasites, like <i>Trypanosoma cruzi</i>, the causative agent of Chagas disease, cannot synthesize it. These parasites must acquire heme from their hosts, making this process critical …
Read PDFThe US is experiencing a major drug epidemic largely attributed to synthetic opioids including fentanyl. We considered how illicit fentanyl use in persons living with HIV impacted gene expression profiles in the peripheral blood. Whole …
Read PDF<b>Background</b>: Translocation morphology renal cell carcinoma (tRCC) accounts for nearly half of all pediatric RCC cases. Biological study AREN14B4-Q aimed to characterize the molecular landscape of tRCC using samples acquired from patients enrolled in the …
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