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<h4>Introduction</h4>Tumor infiltrating lymphocytes (TIL) drive the anti-tumor activity of a broad class of immunotherapies. <i>In situ</i> TIL are composed of T cells that recognize tumor antigens (Tumor Reactive T cells, or TRTs) as well as …
Read PDFEvidence suggests that alternative RNA splicing (AS) plays a critical role in tumor biology and may contribute to the generation of tumor antigens. Here, we develop a method to detect AS in short-read single-cell 5'-RNA-sequencing …
Read PDF<i>Piscirickettsia salmonis</i> is a facultative intracellular pathogen and the causative agent of piscirickettsiosis, a systemic disease affecting salmonid fish. Successful replication within host phagocytes is central to disease progression, yet the intracellular niche supporting bacterial …
Read PDFRibosomal protein mutations are increasingly associated with cancer risk and thought to perturb ribosome function. At the same time, they reportedly activate p53, a critical anti-cancer barrier. To determine how these mutations overcome this protective …
Read PDF<h4>Background</h4>Lymphatic metastasis is strongly associated with poor prognosis. Although the chemokine receptor CCR7 is a well-established promoter of lymphatic dissemination, its prognostic relevance remains weak. We show that tumour cell plasticity, defined by podoplanin (PDPN)-expression …
Read PDFDrug-induced liver injury (DILI) is a major clinical and regulatory challenge, with cholestasis representing a frequent mechanism of hepatotoxicity. Conventional two-dimensional (2D) hepatocyte cultures often fail to predict such effects, underscoring the need for advanced …
Read PDFMitochondrial regulators are increasingly recognized for their influence on immune signaling within the tumor microenvironment (TME). In glioma, where immunosuppression limits therapeutic efficacy, we investigate how targeting the mitochondrial protein MIRO1 alters the TME. We …
Read PDFExtracellular or cell-free RNAs (exRNAs) derived from biofluids are utilized in biomarker studies to study health and diseases. Here, we present a protocol for total RNA sequencing analysis of blood plasma exRNA using the Switching …
Read PDFTransposable elements (TEs) comprise nearly half of mammalian genomes and drive species-specific regulatory innovation, but their contributions to the first lineage segregation-establishing trophectoderm versus inner cell mass (ICM)-remain largely unexplored. Here, we identify IAPEz, a …
Read PDF<h4>Introduction</h4>Respiratory coinfections involving Influenza viruses, including Influenza A viruses (IAV) and bacteria, significantly worsen disease severity and remain a major public health concern, particularly during seasonal and pandemic flu outbreaks. Among bacterial pathogens, <i>Streptococcus pneumoniae</i> …
Read PDFEndothelial cells (ECs) are crucial in cancer development and progression, partly by regulating tumor angiogenesis and immune modulation. As a key component of the RNA-induced silencing complex, Argonaute 1 (AGO1) regulates tumor biology, yet the …
Read PDFAlthough viruses are often studied in relation to disease, they can also offer valuable insights into RNA functionality. Due to their vast range of hosts and high mutation rates, viruses can quickly adapt to changing …
Read PDFParkinson's disease (PD) involves selective degeneration of midbrain dopaminergic neurons (mDANs), yet the regulatory networks governing their development remain incompletely understood. ZFHX4 has been linked to neurodevelopment across species and shows reduced expression in the …
Read PDF<h4>Objectives</h4>Brown adipose tissue (BAT) dissipates energy via non-shivering thermogenesis, but durable thermogenic benefit requires sustained cold remodeling that stabilizes a cold-adapted tissue state. While most studies have focused on adipocyte-intrinsic pathways that drive acute activation, …
Read PDF<h4>Motivation</h4>Predicting phenotypes from gene expression data is a crucial task in biomedical research, enabling insights into disease mechanisms, drug responses, and personalized medicine. Traditional machine learning and deep learning rely on supervised learning, which requires …
Read PDFKDM5B, a member of the KDM5 family of histone demethylases, plays a critical role in transcriptional repression by demethylating H3K4me2/3. It regulates key biological processes such as development, stem cell maintenance, and oncogenesis, and its …
Read PDFAccurate detection of driver gene fusions is essential for the diagnosis, treatment, and prognostic prediction of hematologic malignancies. Despite increasing reliance on RNA sequencing (RNA-seq) for fusion detection, its algorithms have not been sufficiently examined …
Read PDF<h4>Background</h4>Phosphatidylinositol transfer protein-1 (pitp-1) is involved in the phosphoinositide (PIP) cycle. The role of pitp-1 in promoting healthy longevity remains unknown. Our previous work showed that the PIP cycle-related genes diacylglycerol lipase-1 (dagl-1) and diacylglycerol …
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