Academic Articles & Research Papers

Reporting and representation of population descriptors in public RNA-seq databases.

Progressive suppression of regulated cell death defines terminal macrophage states in liver cirrhosis

Background Macrophages are central regulators of liver immunity and fibrosis; Recent single-cell studies have characterized macrophage heterogeneity in cirrhosis; however, how regulated cell death programs shape their functional transitions...

Publisher Correction: A general and flexible method for signal extraction from single-cell RNA-seq data

The original PDF version of this Article contained errors in two equations. In Eq. (1), all Γ symbols were inadvertently omitted. In the second equation in the subsection entitled ‘1. Dispersion optimization’ within the Methods section ‘ZIN...

Lysosome blockade induces divergent metabolic programs in macrophages and tumours for cancer immunotherapy

Abstract Background Platinum-drugs based chemotherapy in clinic increases the potency of tumor cells to produce M2 macrophages, thus leading to poor anti-metastatic activity and immunosuppression. Lysosome metabolism is critical for cancer ...

Integrative omics analysis on phytohormones involved in oil palm seed germination

Abstract Background Heat treatment is widely used to break dormancy for seed germination and phytohormones could be deeply involved. However, effect of heat treatment on phytohormone related genes/proteins/metabolites and possible relations...

A large deletion conferring pale green leaves of maize

Abstract Background The structural basis of chloroplast and the regulation of chloroplast biogenesis remain largely unknown in maize. Gene mutations in these pathways have been linked to the abnormal leaf color phenotype observed in some mu...

An integrated analysis of multiple datasets reveals novel gene signatures in human granulosa cells

Abstract Granulosa cells (GCs) play crucial roles in oocyte maturation. Through gap junctions and extracellular vesicles, they mediate the exchange of molecules such as microRNAs and messenger RNAs. Different ovarian cell types exhibit uniq...

RNA-seq analysis of gene expression profiles in isolated stria vascularis from wild-type and Alport mice reveals key pathways underling Alport strial pathogenesis.

Previous work demonstrates that the hearing loss in Alport mice is caused by defects in the stria vascularis. As the animals age, progressive thickening of strial capillary basement membranes (SCBMs) occurs associated with elevated levels o...

Increased expression of glutathione peroxidase 3 prevents tendinopathy by suppressing oxidative stress

Tendinopathy, a degenerative disease, is characterized by pain, loss of tendon strength, or rupture. Previous studies have identified multiple risk factors for tendinopathy, including aging and fluoroquinolone use; however, its therapeutic ...

Identification of DDIT4 as a potential prognostic marker associated with chemotherapeutic and immunotherapeutic response in triple-negative breast cancer

Abstract Background Triple-negative breast cancer (TNBC) is the most heterogenous and aggressive subtype of breast cancer. Chemotherapy remains the standard treatment option for patients with TNBC owing to the unavailability of acceptable t...

Single-cell RNA sequencing to detect age-associated genes that identify senescent cells in the liver of aged mice

Abstract Senescent cells are predicted to occur and increase in animal tissues with aging. However, senescent cells in the tissues of aged animals remain to be identified. We refer to the marker genes to identify senescent cells in tissues ...

Cracking rare disorders: a new minimally invasive RNA-seq protocol

Abstract RNA sequencing (RNA-seq) has become key to complementing exome and genome sequencing for variant interpretation. We present a minimally invasive RNA-seq protocol using short-term cultured peripheral blood mononuclear cells (PBMCs) ...

Rap GTPase Interactor: A Potential Marker for Cancer Prognosis Following Kidney Transplantation

Post-transplant (post-Tx) kidney cancer has become the second-highest cause of death in kidney recipients. Late diagnosis and treatment are the main reasons for high mortality. Further research into early diagnosis and potential treatment i...

LADS: a powerful vaccine platform for cancer immunotherapy and prevention

Abstract Background The intracellular bacterium Listeria monocytogenes is an attractive vector for cancer immunotherapy as it can effectively deliver tumor antigens to antigen-presenting cells, leading to a robust antitumor response. Result...

Single-cell RNA-seq reveals the genesis and heterogeneity of tumor microenvironment in pancreatic undifferentiated carcinoma with osteoclast-like giant-cells

Abstract Background Undifferentiated carcinoma with osteoclast-like giant cells (OGCs) of pancreas (UCOGCP) is a rare subtype of pancreatic ductal adenocarcinoma (PDAC), which had poorly described histopathological and clinical features. Me...

Engineering protein translocation pathway to improve recombinant proteins in Pichia pastoris

Pichia pastoris is one of the most commonly used hosts for producing heterologous proteins, whereas production levels vary depending on the protein of interest and are also regulated by regulatory factors. We conducted RNA-seq by expressing...

A single-cell RNA sequencing dataset of cardiac aging in African Turquoise Killifish

Abstract Aging is a major contributor to functional decline of the heart and various cardiovascular diseases. Alterations across different cardiac cell types must be tightly orchestrated during the normative aging process that has begun to ...

CircUCK2(2,3) promotes cancer progression and enhances synergistic cytotoxicity of lenvatinib with EGFR inhibitors via activating CNIH4–TGFα–EGFR signaling

Abstract Background Circular (circ)RNAs have emerged as crucial contributors to cancer progression. Nonetheless, the expression regulation, biological functions, and underlying mechanisms of circRNAs in mediating hepatocellular carcinoma (H...

Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome

Abstract Background Hutchinson-Gilford progeria syndrome (HGPS) is a progeroid disease characterized by the early onset of age-related phenotypes including arthritis, loss of body fat and hair, and atherosclerosis. Cells from affected indiv...

The critical involvement of monocytes/macrophages in the pathogenesis of primary Sjögren's syndrome: New evidence from Mendelian randomization and single-cell sequencing

Background: Primary Sjögren's syndrome (pSS) stands as a chronic autoimmune disease characterized by an elusive pathogenesis. The synergy of single-cell RNA sequencing and Mendelian randomization (MR) analysis provides an opportunity to com...