bulk RNA-seq

Mechano-activated synovial cells instigate OA-like disease progression in the absence of joint injury

This study shows that altering synovial cell mechanotransduction drives OA-like disease without joint injury, with partial effects on symptoms versus structural damage.

Host Plant and Light Regime Shape Limited, Whole-Body Transcriptional Rhythmicity in the Bird Cherry-Oat Aphid (Rhopalosiphum padi)

This study examines transcriptional rhythmicity in aphids under different light and host conditions, finding limited rhythmic transcripts and host-dependent regulation.

Epstein-Barr viral product-containing exosome facilitates LIF-associated immunosuppressive polarization of macrophage in nasopharyngeal carcinoma

This study identifies exosome-delivered LMP1 from EBV in NPC as a driver of immunosuppressive macrophage polarization via LIF, promoting tumor progression and immune evasion.

Endothelial CD36 links arteriolar remodeling to metabolic and immune alterations in Alzheimer's disease

This study identifies CD36-associated vascular changes in Alzheimer's disease and shows CD36's role in regulating endothelial metabolic and immune programs, with potential for targeted therapies.

A false sense of circularity: hidden variability in RNase R enzymes confounds reliable circRNA validation

The paper shows that different RNase R enzymes from the same supplier can produce inconsistent results in circRNA validation, emphasizing the need for consistent verification with linear controls.

Early-onset spontaneous murine mammary tumors show increased lymphocyte representation and reduced MHC antigen presentation

This study shows that introducing the PWK/PhJ genetic background in HER2/neu-driven breast cancer mice leads to earlier tumor onset, increased immune cell presence, and reduced MHC antigen presentation.

Individual-Specific Gaussian Graphical Models for Heterogeneous Populations with Application to Epigenetic Gene Regulation in Lung Adenocarcinoma

SIREN estimates individual-specific gene regulatory networks from multi-omics data, revealing epigenetic heterogeneity in lung adenocarcinoma that correlates with patient survival.

Co-targeting KRAS and BCL-2 induces pyroptosis and antitumor tertiary lymphoid structures

This study shows that combining KRAS and BCL-2 inhibition induces pyroptosis and tertiary lymphoid structures in KRAS G12D-mutant lung cancer, enhancing B-cell-dependent antitumor immunity.

Mitochondrial respiratory complexes, excitation-contraction coupling and mTOR signaling transcriptional programs are dysregulated in cardiometabolic HFpEF

This study identifies transcriptomic changes in HFpEF mouse hearts, showing mitochondrial respiratory complex downregulation, mTOR activation, and excitation-contraction coupling disruption.

Anisomycin-induced ribosome collisions follow a dose-dependent positional rule, distinct from the UV-induced collision landscape

Low- and high-dose anisomycin confine ribosome collisions to a dose-shifted zone just past the start codon, whereas 30 min after UV, collisions appear more dispersed and favor highly translated mRNAs.

Inhibiting 2-oxoglutarate dehydrogenase reveals the mechanisms and limits of metabolic plasticity in developing maize kernels

This study investigates the role of 2-oxoglutarate dehydrogenase in maize kernels by knocking it down and analyzing metabolic changes and structural impacts.

Long-term effects of the early life environment on alternative splicing

This study shows that early life environment has long-term effects on alternative splicing in pea aphids, independent of morph identity.

The role of the NLRP3 inflammasome in a CLN2 mouse model of neuroinflammation

This study investigates the role of the NLRP3 inflammasome in a CLN2 mouse model, showing that inflammasome activation occurs at 3 months and that its inhibition reduces neuroinflammation.

Chromosome 7 gain establishes a just-right WNT signaling state during colorectal tumorigenesis

This study shows that chromosome 7 gain optimizes WNT signaling in colorectal cancer by counteracting excessive stemness from APC mutations.

Subchondral bone remodeling in knee osteoarthritis is coupled to lipid mobilization from bone marrow adipocytes

This study investigates the link between lipid mobilization from bone marrow adipocytes and bone formation in knee osteoarthritis, finding that lipolysis is associated with osteogenic activity and can be pharmacologically modulated.

DiffRhyShiny: A Benchmarking-Informed Platform for Differential Rhythmicity Analysis with Dependence-Aware Evidence Integration

The paper benchmarks differential rhythmicity analysis methods and introduces a web platform for robust analysis and visualization of rhythmicity changes.

Apoptosis at the optic fissure shapes transient retinal myeloid states

The paper identifies the optic fissure as the entry site for myeloid cells into the embryonic mouse retina, showing that apoptosis and CD206 expression are linked to transient myeloid states during development.

The nuclear membrane protein Samp1 links peripheral genome organization to the myogenic transcriptional program

This study shows Samp1 is essential for myogenic differentiation by linking its role in chromatin organization at the nuclear periphery to the transcriptional program of muscle development.

MetAR: A semi-automated meta-analysis of skeletal muscle androgen receptors association with age

This study uses a novel R-based pipeline, MetAR, to analyze RNA-seq datasets and finds that androgen receptor expression declines with age in human skeletal muscle.

A Trisomy 21 Model Atlas reveals conserved dosage effects and context-specific transcriptional responses across mouse and human models of Down syndrome

The paper presents a Trisomy 21 Model Atlas comparing mouse and human models to show conserved dosage effects and context-specific transcriptional responses across tissues and developmental stages.

Preoperative thymic output and T cell repertoire diversity are associated with recurrence after nephrectomy for localized renal cell carcinoma

Evolutionary insights into β-cyclocitral signaling in Physcomitrium patens

The paper investigates how β-cyclocitral signaling evolved in the moss Physcomitrium patens, finding that while it triggers a strong transcriptional response, it impairs photosynthesis and lacks protective effects.

Non-canonical IL-2 signaling facilitates peripheral regulatory T cell differentiation

This study identifies MACS as a non-canonical IL-2 signaling pathway that promotes Treg differentiation and function through AP-1-dependent mechanisms.

Keratinocyte FABP5 mediates saturated fat-induced MAPK/CCL20 signaling in psoriatic inflammation

Reference-Gene Stability for RT-qPCR in the Medial Prefrontal Cortex and Hippocampal Subregions of the 5xFAD Mouse Brain

The paper evaluates reference gene stability for RT-qPCR in specific brain regions of 5xFAD mice and recommends gene pairs for accurate normalization.

Cirrhosis-associated immune dysfunction reflects impaired intestinal CD8ab⁺ intraepithelial lymphocyte compartmentalization

The paper investigates immune dysfunction in cirrhosis by analyzing CD8ab⁺ intraepithelial lymphocytes and identifies CCL25-CCR9 axis disruption as a key factor.

The root knot nematode effector MiEFF186 interacts with a splicing factor to reshape plant transcriptome

This study identifies MiEFF186a as a nematode effector that interacts with GDP1/CIS2 to alter plant transcriptome splicing and gene expression, affecting susceptibility to nematode infection.

In Vivo Transcriptomics-Based Framework for Systematic Indication Expansion

This paper presents a drug repurposing framework using in vivo transcriptomics to expand indications by matching drug signatures with disease signatures, successfully recovering established uses of semaglutide and proposing new ones.

Endothelial CXCL12 is dispensable for adipose tissue function

This study investigates the role of CXCL12 in adipose tissue endothelial cells and finds it dispensable for adipose tissue function under normal and cold conditions, as well as during obesity.

Temporal RNA splicing dysregulation in a human multicellular model of C9orf72 ALS

This study uses human spinal cord organoids to model C9orf72 ALS, identifying early RNA splicing dysregulation and RBP network dysfunction as key features of the disease.