title: Bavachinin Suppresses Growth and Metastasis of Oral Squamous Cell Carcinoma through GSK-3β/β-Catenin Pathway: Potential for Synergistic Anticancer Therapy with Cisplatin

city: Taoyuan City

first: Chia-Yu

last: Yang

address: No.259, Wenhua 1st Rd., Guishan Dist.

department: Department of Microbiology & Immunology, Chang Gung University

country: Taiwan

institute: NGS Genomics Core Lab

summary:
Background: Oral squamous cell carcinoma (OSCC) is a highly aggressive malignancy with poor prognosis, often complicated by recurrence, metastasis, and chemoresistance. While cisplatin remains a cornerstone of OSCC treatment, its efficacy is limited by systemic toxicity and resistance. In search of safer, effective adjunctive strategies, we investigated bavachinin, a flavanone from Psoralea corylifolia L., for its antitumor potential in OSCC.

Materials and methods: Integrated in vitro, in silico, and in vivo approaches were employed. Functional assays evaluated cell viability, apoptosis, migration, and invasion. Transcriptomic profiling identified dysregulated pathways, with key targets validated by quantitative reverse transcription PCR (qRT-PCR). Molecular docking predicted protein targets, confirmed by Western blot. Toxicity and therapeutic efficacy were evaluated in C57BL/6 mice and OSCC cell line-derived xenograft (CDX) and patient-derived xenograft (PDX) models.

Results: Bavachinin significantly reduced cell viability, induced G2/M phase arrest, promoted apoptosis, and inhibited migration and invasion in OSCC cells. Transcriptomic profiling and qRT-PCR revealed suppression of genes involved in extracellular matrix remodeling and cell adhesion. Glycogen synthase kinase-3β (GSK-3β) was identified as a potential target by molecular docking analysis, confirmed by increased phosphorylation at Tyr216 and β-catenin degradation, leading to downregulation of matrix metalloproteinase-2 and fibronectin. As natural compounds are rarely used as monotherapies, bavachinin combined with cisplatin showed synergistic antitumor effects in OSCC CDX and PDX models, without systemic toxicity in mice.

Conclusion: Bavachinin exerts potent antitumor effects via modulation of the GSK-3β/β-catenin pathway and may serve as a promising adjunct to cisplatin in OSCC treatment.

overall_design: experimental design: By integrating in vitro, in silico, and in vivo (CDX/PDX) models, our experiments elucidate the role of bavachinin in oral cancer treatment.


title: Spinal signatures of entrenched and treated neuropathic pain in male mice [Xenium]

status: Public on Apr 28 2026

city: University of Sydney

first: Lipin

last: Loo

state: New South Wales

address: CHARLES PERKINS CENTRE D-17,

department: Charles Perkins Centre and School of Life & Environmental Sciences

country: Australia

institute: The University of Sydney

summary: Chronic pain arises from an imbalance between excitation and inhibition. For chronic pain caused by peripheral nerve injury, sensory neuron damage leads to changes in spinal pain transduction, where enhanced excitatory and/or loss of inhibitory pathways can drive pain diseases. At the cellular level, the transcriptional changes occurring in entrenched chronic pain are largely unknown. Here we use single nuclei and spatial transcriptomic approaches to investigate the cellular and molecular causes of entrenched and treated neuropathic pain.  Our data show that nerve injury leads to broad upregulation of spinal synaptic and excitatory pathways in dorsal neuronal and glial populations. We confirm these core populations are conserved in the human spinal cord, and show an effective pain therapy acts by dampening these neuropathic transcriptional programs. Overall, our data provides the first high resolution transcriptional analysis of the neuropathic spinal cord, highlighting known and novel pathways that may help us better manage pain diseases.

overall_design: Xenium imaging of Sham, SNI lumbar spinal cord samples. Sections were prepared on imaging slides at 28 days post SNI before imaging on Xenium.

first: Gregory

middle: G

last: Neely


title: UBA1-CDK16: A Female-Specific Chimeric RNA Emerging Through Evolution and Involved in Immune Regulation

status: Public on Apr 20 2026

city: Charlottesville

first: Shafaque

last: Zahra

state: VA

address: MR6, 345 Crispell Drive

department: Pathology

country: USA

institute: University of Virginia

type: Expression profiling by high throughput sequencing

summary: Chimeric RNAs resulting from intergenic splicing represent a novel mechanism for transcriptome expansion. To explore the role of this new layer of the transcriptome in sex-specific immunity, we analyzed RNA-seq data from 425 blood samples and identified the first female-specific chimeric RNA, UBA1-CDK16, which was further validated in over 1,200 blood samples. This chimeric RNA forms via cis-splicing between two adjacent X-linked parental genes, UBA1 and CDK16, despite both being expressed in both sexes. We demonstrated that a female-specific chromatin loop at the UBA1-CDK16 junction sites facilitates the intergenic splicing. Evolutionary analysis revealed that UBA1-CDK16 became female-specific in humans through at least two independent paths. Functional studies suggested UBA1-CDK16 is enriched in the myeloid lineage and may regulate myeloid cell development and inflammatory responses. Notably, its abnormal expression in female COVID-19 patients correlates with altered neutrophil counts, highlighting its potential role in disease pathogenesis.

overall_design: The experiment compares single-cell transcriptomes of CD34+ female cells: non-targeting control (shGFP) and targeted knockdown (shUBA1-CDK16). Both populations are harvested at the same time point, Day 3 of in vitro myeloid differentiation, to identify gene expression changes driven by the knockdown.

first: Xinrui

last: Shi

first: Loryn

last: Facemire

first: Sandeep

last: Singh

first: Shailesh

last: Kumar

first: Robert

last: Cornelison

first: Chen

last: Liang

first: Fujun

last: Qin

first: Aiqun

last: Liu

first: Shitong

last: Lin

first: Yue

last: Tang

first: Justin

last: Elfman

first: Thomas

last: Manley

first: Martyna

last: Glowczyk

first: Anam

last: Tajammal

first: Timothy

last: Bullock

first: Doris M

last: Haverstick

first: Peng

last: Wu

first: Hui

last: Li


title: Filamin–ETV4/5 acts as mechanosensor–mechanotransducer axis that drives cell competition-mediated elimination of transformed cells

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

summary: Cell competition is a fundamental surveillance mechanism that preserves epithelial integrity by eliminating aberrant “loser” cells through interactions with surrounding “winner” cells. However, how winner cells sense and eliminate transformed neighbours remains poorly understood. Here, using a synNotch-based transcriptomic screen, we identify a mechanosensor–mechanotransducer axis linking the actin crosslinker filamin to the ETV4/5–PRKG2 pathway that mediates extrusion of oncogenically transformed cells through cell competition. Within an epithelial monolayer, transformed cells increase their volume, inducing membrane stretching. In adjacent normal cells, filamin senses the increased membrane tension and triggers activation of ETV4/5. Activated ETV4/5 then upregulate PRKG2, which promotes volume expansion of normal cells, consequently pushing back and driving the extrusion of transformed cells. These findings reveal that dynamic changes in cell volume can trigger mechanotransduction-driven cell competition, uncovering a fundamental pathway by which epithelial tissues maintain homeostasis and defend against oncogenic transformation.

overall_design: Transcriptome analysis of EpH4 cells directly contacting RasV12-transformed cells using the synNotch system

first: Jiaying

last: Wen

first: Kazuhito

last: Sai

first: Suzuka

last: Masutani

first: Yuki

last: Aoshima

first: Kotaro

last: Yumi

first: Tomoki

last: Kyo

first: Junya

last: Hasegawa

first: Toshiki

last: Itoh

first: Ken

last: Mizuta

first: Tomonori

last: Nakamura

first: Mitinori

last: Saitou

first: Satoshi

last: Toda

first: Yasuyuki

last: Fujita


title: DNA-PK Mediated CRTC2 Phosphorylation Promotes CRTC2 Relocation from Transcription to Repair Complexes Enhancing NHEJ and Suppressing Abscopal Effect

city: tianjin

first: zhanjie

last: xiu

address: HUANHU XI ROAD, TIYUAN BEI, HEXI DISTRICT

country: China

institute: TIANJIN MEDICAL UNIVERSITY CANCER INSTITUTE & HOSPITAL

summary: DNA damage repair and transcription are antagonistic cellular processes that require precise spatiotemporal coordination to maintain genomic integrity. Transcriptional silencing at DSB sites is essential for efficient repair, mediated through localized histone modifications and direct inhibition of RNA polymerase II (Pol II). However, the role of transcriptional activators in coordinating DSB repair with transcriptional silencing remains elusive. Here, we identify the transcriptional coactivator CRTC2 as a key coordinator of DNA repair and transcriptional regulation. We demonstrate that CRTC2 promotes canonical non-homologous end joining (c-NHEJ) both in vitro and in vivo. Mechanistically, PARP1 activation recruits CRTC2 to DNA breaks, where it facilitates DNA-PKcs recruitment and assembly of the DNA-PK holoenzyme, thereby driving c-NHEJ. DNA-PK–mediated phosphorylation of CRTC2 at Ser433 dissociates it from transcriptional complexes, suppressing target gene transcription, and promoting its incorporation into DNA repair complexes. Thus, establishing a positive feedback loop that enhances NHEJ efficiency. CRTC2 loss radiosensitizes cancer cells, potentiates irradiation-induced cGAS–STING activation, promotes cytotoxic CD8⁺ T cell infiltration, and enhances the abscopal effect. Furthermore, AAV8-mediated targeting of CRTC2 sensitizes tumors to radioimmunotherapy. Our results reveal CRTC2 as bifunctional nodal effector coupling transcriptional silencing to DNA repair and propose its inhibition as a promising strategy for radioimmunotherapy sensitization in resistant malignancies.

overall_design: The Crtc2+/+ and Crtc2-/- mice were intraperitoneally injected with DEN (25 mg/ kg) at age of 2-weeks old. Mice maintain NASH diet from 8 to 26 week and sacrificed after 26 weeks. Tumors from liver were collected for single-cell RNA sequencing.

first: Fangdi

last: Zou


title: DNA-PK Mediated CRTC2 Phosphorylation Promotes CRTC2 Relocation from Transcription to Repair Complexes Enhancing NHEJ and Suppressing Abscopal Effect [RNA-Seq]

overall_design: RNA-seq profiling of  AiDIvA cells treated with doxycycline and in the absence or presence of 4-OHT were collected


title: Effects of loss of KAT6A on histone acetylation and methylation levels, as well as MLL1 and POLR2A occupancy

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heterozygous variants in the KAT6A gene encoding the histone lysine acetyltransferase KAT6A (MOZ, MYST3) cause Arboleda-Tham syndrome, an intellectual disability syndrome. The profound effects of pathogenic variants in only one allele of KAT6A on cognitive development and functions raises the question what effects heterozygous and homozygous loss of KAT6A may have on gene expression and chromatin modifications, specifically in a neural cell type that is functionally affected by loss of KAT6A. To address this question, we established that murine neural stem and progenitor cells form fewer neurons after loss of one and two alleles of Kat6a and used these cells to conduct automated chromatin profiling. We determined within the same cell preparation acetylation at histone H3 lysines 9, 14 and 23, RNA polymerase II (POLR2A) and MLL1 occupancy, as well as levels of methylation at histone H3 lysine 4 (H3K4), the MLL1 target, and compared these chromatin profiling results to the effects of loss of KAT6A on gene expression.

overall_design: We performed automated CUT&Tag chromatin profiling on NSPCs isolated from the dorsal telencephalon (the cerebral cortex precursor) of Kat6a+/+ (3 replicates), Kat6a+/– (4 replicates) and Kat6a–/– (3 replicates) E12.5 embryos, to detect in the same biological sample cell preparation multiple chromatin marks. These included the acetylation targets proposed for KAT6A, namely H3K9ac, H3K14ac and H3K23ac. We had previously observed MLL1 occupation of HOX genes to be dependent on the presence of KAT6A. Therefore, we assessed  MLL1. Within its four to five partite protein complex, MLL1 is a H3K4me2/3 methyltransferase. We assessed H3K4me3, which is the target of MLL1 that is most closely associated with mRNA levels. Lastly, we included RNA polymerase II subunit A phosphorylated on Ser2 [POLR2A; also known as Phospho-Rpb1 CTD]. Phosphorylation of POLR2A at Ser2 is required for elongation and allowed us to determine if the absence of KAT6A affected POLR2A progression through a gene locus.

first: Gordon

middle: K

last: Smyth

first: Anne

last: Voss

first: Tim

last: Thomas

first: Johannes

last: Wichmann


title: DNA-PK Mediated CRTC2 Phosphorylation Promotes CRTC2 Relocation from Transcription to Repair Complexes Enhancing NHEJ and Suppressing Abscopal Effect [CUT&Tag]

overall_design: CUT&Tag of CRTC2 and H2ax in AiDIvA cells treated with doxycycline and in the absence or presence of 4-OHT were collected


title: Aggravated cardiac dysfunction in CKD post-infarction

city: Aachen

first: Julia

last: Wollenhaupt

address: Pauwelsstraße 30

department: Institute for Molecular Cardiovascular Research

country: Germany

institute: Uniklinik RWTH Aachen

summary: Uremic cardiomyopathy is a clinically highly relevant cause of cardiovascular events in patients with chronic kidney disease (CKD). Additionally, after acute myocardial infarction (MI), CKD-patients exhibit an increased risk of death. To investigate the underlying molecular mechanisms causing the adverse effects of CKD on cardicac outcome after MI, male mice were fed with an adenine-supplemented diet combined with western type diet (CKD mice) or with western type diet only (control mice). Invasive heart function evaluation and histological analyses were performed 7 days after MI-induction through left anterior descending artery (LAD) ligation. For a deeper look on molecular level, RNA sequencing of heart tissue was performed.

overall_design: Heart tissue of male mice was studied with RNAseq, comparing adenine-fed mice (CKD mice) vs. control mice 7 days post-MI.

first: Heidi

last: Noels

first: Corinna

last: Schulte

first: Eva

last: Harlacher

first: Han

last: Jin


title: KCNN4 mediated potassium ion efflux maintains mitochondrial functions leading to platelet biogenesis

first: Koji

last: Eto

address: 53 Kawahara-cho, Shogoin Kawahara-cho, Sakyo-ku

department: CiRA

institute: Kyoto University

summary: Background: While potassium ion (K+) is known to be vital to platelet functions, we have limited knowledge about K+ channels involved in thrombopoiesis from imMKCLs, the iPSC-derived megakaryocyte progenitor cell lines that we have established for ex vivo manufacturing of platelet products for clinical use. Objective: We aimed to elucidate how K+ channels contribute to platelet biogenesis and focused on the role of Ca2+-activated K+ channel KCNN4 (also known as KCa3.1). Methods: Using imMKCLs and human cord blood hematopoietic stem cell-derived megakaryocytes (CB-megakaryocytes), we examined the dynamic changes of intracellular cations during platelet biogenesis. Along with RNA-seq profiling of K+ channels, we investigated the role of KCNN4 by using inhibitors or by direct gene knockdown in proplatelet formation or platelet production. We further examined its relationship with tubulin reorganization, mitochondrial functions, and reactive oxygen species (ROS) levels. Results: Continuous reduction of intracellular K+ levels ([K+]i) was observed during the 6-day of maturing imMKCLs. KCNN4 was expressed at the initiation of platelet generation in megakaryocytes and KCNN4 inhibition resulted in impaired proplatelet formation and reduced platelet productivity in imMKCLs and CB-megakaryocytes, accompanied by decreased [K+]i, diminished mitochondrial membrane potential and an elevated level of ROS. Conclusions: Our findings suggest that the decline of [K+]i via KCNN4 is a key mechanism linking tubulin regulation, ROS, and mitochondrial functions to proplatelet formation and intact thrombopoiesis. This study sheds new light on thrombopoiesis mechanism that contributes to improved ex vivo platelet manufacturing.

overall_design: RNA-seq profiling of imMKCLs at maturation stage (absent of doxcycline, Dox-OFF) from day 0 to day 4

first: Qihao

last: Chen

first: Takuya

last: Yamamoto

first: Sou


title: Gene expression profiling of tumor organoids of colorectal liver metastases.

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

summary: We have performed gene expression profiling of patient-derived tumor organoids (PDOs) and tissue samples of resected liver metastases from patients with metastatic colorectal cancer.

overall_design: This series consists of PDOs (n=119) cultured from resected liver metastases from patients with colorectal cancer, as well as corresponding tumor tissue samples for a subset (n=50). PDOs were cultured from multiple metastatic lesions from a subset of the patients. All samples were analyzed on Affymetrix Human Transcriptome 2.0 Arrays.

first: Kushtrim

last: Kryeziu

first: Ragnhild

middle: A

last: Lothe


title: Effects of D4-MASLD and D5-MASLD Diets on Rats: Pathway Alterations Similar to Human MASLD

city: Barcelona

first: Maria

last: Martell

state: Barcelona

address: Pg Vall Hebron 119

department: Liver Diseases

country: Spain

institute: Institut de Recerca Hospital Vall d'Hebron

summary: Animal models are essential to understand the mechanisms underlying the onset and progression of metabolic associated steatotic liver disease (MASLD), a rapidly growing form of chronic liver disease driven largely by the global rise in metabolic syndrome. However, existing animal models for MASLD often fail to accurately reproduce advanced human liver disease, and have varying degrees of clinical relevance. To address this, we have undertaken efforts to create a dietary translational model of MASLD in rats that closely replicates the full MASLD phenotype observed in humans, including advanced fibrosis, portal hypertension, and metabolic syndrome. Three MASLD rat models were developed by sequentially combining a high-fat glucose-fructose diet (HFGFD) with additional factors: lipopolysaccharide, increased cholesterol (Chol), and cholic acid (CA) at different concentrations. Of these, two diets—D4-MASLD (HFGFD + 2% Chol) and D5-MASLD (HFGFD + 2% Chol + 0.1% CA)—effectively replicated MASLD characteristics.  Transcriptomic analysis revealed that while both diets significantly altered gene expression compared to controls, D5-MASLD had a greater impact on the activation of inflammation and immune response pathways. The inclusion of CA in D5-MASLD exacerbated pathways related to microbiota changes, intestinal barrier dysfunction, and bacterial translocation. Additionally, comparison of the transcriptomic profiles of these diet-induced rat models with data from MASLD/MASH patients further validated the relevance of these models, establishing a robust platform for studying MASLD pathogenesis and evaluating potential therapeutic interventions.

overall_design:
To develop a dietary rat model replicating the full MASLD phenotype observed in human disease we performed three subsequent studies in rats with variations in diet and additional factors, like lipopolysacharides, cholesterol and cholic acid.
Variables analysed were, body weight changes, biochemical parameters (Glucose, ALT, AST, cholesterol, albumin, triglycerides), hemodynamic parameters (MAP, PP, SMABF and SMAR), histological fibrosis, gene expression markers of hepatic insulin resistance and protein markers of endothelial dysfunction and ductular reaction.
We then performed transcriptomic profiling analysis using data obtained from RNAseq of 15 different liver samples from rats feed with 3 diets (Controls, n=5; D4-MASLD, n=5; D5-MASLD, n=5).

first: María

last: Martínez-Gómez


title: Transcripts identified by microarray analysis that were deregulated in E15.5 Pax2-cre/+;Trp63(dN-flox/dN-flox) (ΔNp63-cKO) ureters

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E15.5 ureters upon loss of ΔNp63 in the ureteric epithelium.

overall_design: Total RNA from dissected ureters of E15.5 ΔNp63-cKO and control embryos was analyzed by microarray analysis.

first: Andreas

last: Kispert

first: Fairouz

last: Qasrawi


title: Transcripts identified by microarray analysis that were deregulated in E18.5 Pax2-cre/+;Trp63(dN-flox/dN-flox) (ΔNp63-cKO) ureters

summary: Evaluation of the transcriptional changes in E18.5 ureters upon loss of ΔNp63 in the ureteric epithelium.

overall_design: Total RNA from dissected ureters of E18.5 ΔNp63-cKO and control embryos was analyzed by microarray analysis.


title: Single cell RNA sequencing (scRNA-seq) of embryonic zebrafish and human aortic endothelial cells following flow modulation

city: Boston

first: Aryan

last: Kaveh

state: MA

address: 60 Fenwood Road

department: Medicine

institute: Brigham and Women's Hospital

summary: The earliest vascular manifestations during atherosclerosis development are incompletely understood. We utilize low density lipoprotein receptor knockout (ldlr-/-) zebrafish and human aortic endothelial cells (HAECs) to discern developmental and flow-dependent features underlying atherosclerosis. ScRNA-seq was used to analyze the transcripitional heterogeneity of endothelial cells from embryonic ldlr-/- zebrafish and HAECs following flow modulation.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: For embryonic Tg(flk:GFP) ldlr-/- zebrafish and wild-type (wt) controls, endothelial cells were isolated using fluorescence-activated cell sorting according to the presence of GFP signal. Non-endothelial cells (all other cell types) were also isolated by the absence of GFP signal. Both GFP+ endothelial cells and GFP- embryonic zebrafish cells were analyzed following blood flow inhibition using scRNA-seq. HAECs were harvested following 48 hours of flow modulation and analyzed using scRNA-seq.

first: Antonio

last: Salazar-Martin

first: Wei

last: Dai

first: Aaron

middle: P

last: Kithcart

first: Emily

last: Pan

first: Ashmita

last: KC

first: Tyler

middle: R

last: Reinoso

first: Franki

last: Vetrano-Olsen

first: Kusumika

last: Saha

first: Manu

last: Beerens

first: Peter

last: Libby

first: Elazer

last: Edelman

first: Calum

last: MacRae


title: Exploring the immune environment of glioblastoma in humanized mouse models

status: Public on Apr 19 2026

city: Birmingham

first: Satoru

last: Osuka

state: Alabama

address: 1720 2nd Ave. South, WTI401

institute: The University of Alabama at Birmingham

summary: Glioblastoma (GBM) is the deadliest primary brain tumor in adults, and progress in therapy development has been hindered by the lack of preclinical models that faithfully recapitulate interactions between human tumor cells and human immune cells, particularly in therapy-resistant disease. To address this limitation, we established a humanized mouse model of GBM using radiation-resistant patient-derived xenografts (PDXs) implanted into immunodeficient mice reconstituted with human hematopoietic stem progenitor cells derived from umbilical cord blood. For single-cell RNA sequencing, peripheral blood (PB), tumor-infiltrating immune cells (TILs), and tumor cells were collected from humanized NOG-EXL mice bearing EGFP-positive JX14P-RT tumors. Tumor cells from the same JX14P-RT model implanted into non-humanized naive NOG-EXL mice were also analyzed for comparison. Single-cell suspensions were prepared from tumor tissues, and CD45-positive immune cells and EGFP-positive tumor cells were isolated by cell sorting. Human CD45-positive cells in peripheral blood were purified separately. The dataset includes three TIL samples from humanized mice, three PB samples from humanized mice, three tumor-cell samples from humanized mice, and two tumor-cell samples from naive mice. Individual samples were labeled with hashtag oligonucleotide antibodies, pooled, and then analyzed separately by compartment as TIL, PB, and tumor groups. Libraries were generated using the 10x Genomics Chromium Single Cell 3' platform and sequenced on an Illumina NovaSeq 6000. The data show infiltration of diverse human immune populations, including T cells, natural killer cells, and myeloid lineage cells, and support the utility of this model for studying the immune microenvironment of recurrent and therapy-resistant GBM.

overall_design: We profiled recurrent GBM cells, tumor-infiltrating immune cells, and paired peripheral blood immune cells from CD34+ hematopoietic stem cell–reconstituted humanized NOG-EXL mice implanted with JX14P-RT tumors. For tumor cell analysis, we analyzed EGFP+ tumor cells from three humanized mice and two naive mice. For immune cell analysis, we analyzed tumor-infiltrating immune cells and paired peripheral blood immune cells from three humanized mice. Single-cell suspensions enriched for CD45+ immune cells or EGFP+ tumor cells by cell sorting were subjected to scRNA-seq using the 10x Genomics single-cell platform. We generated a 10x Genomics Gene Expression library together with a paired Antibody Capture library containing both HTO and ADT features. HTO was used for sample multiplexing, and HTO-to-sample correspondence is provided in the supplementary file HTO_samples.csv. ADT data were included in the integrated dataset. HTO and ADT feature definitions are provided in GBM_feature_reference.csv, TIL_feature_reference.csv, and PB_feature_reference.csv.

first: Jun

last: Takei

first: Ken

last: Furudate

first: Masakazu

last: Kamata


title: Evolutionary diversity of cell-type-specific expression and stress response in Brassicaceae roots

city: Stanford

first: Guannan

last: Wang

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: Environmental stresses trigger distinct responses between stress-sensitive and stress-adapted plants. To explore these stress adaptations at the cellular level, we built root single-cell transcriptome atlases for five biodiverse Brassicaceae species, including two stress-sensitive models (Arabidopsis thaliana and Sisymbrium irio), two extremophytes (Eutrema salsugineum and Schrenkiella parvula), and a polyploid oil crop (Camelina sativa), under control, salt, and ABA treatments. Although these species share similar root anatomy, most Arabidopsis cell type markers were not conserved across species. Cortex cell populations with distinct transcriptomes were spatially segregated among species. Lineage-specific gains in stress responses were more common than losses among cell-type responses across species. The homeologs in the allohexaploid C. sativa showed stress response divergence that was often decoupled from the divergence in their coding sequences and control expression levels. Our dataset provides a foundational root atlas across multiple Brassicaceae species enhanced for user accessibility with a cross species searchable browser and provides an analytical framework for comparative single-cell transcriptomics that can be readily transferred to any multi-species system.

sample_organism:
Arabidopsis thaliana
Sisymbrium irio
Eutrema salsugineum
Camelina sativa
Schrenkiella parvula

overall_design: We built root single-cell transcriptome atlases for five biodiverse Brassicaceae species, including two stress-sensitive models (Arabidopsis thaliana and Sisymbrium irio), two extremophytes (Eutrema salsugineum and Schrenkiella parvula), and a polyploid oil crop (Camelina sativa), under control, salt, and ABA treatments.

first: Guanann

first: Kook

middle: H

last: Ryu

first: Andrea

last: Dinneny

first: Jiyoung

last: Lee

first: Dong-Ha

last: Oh

first: Prashanth

last: Ramachandran

first: Marina

last: Oliva

first: Ryan

last: Lister

first: José

first: John

last: Schiefelbein

first: Maheshi

last: Dassanayake


title: Region- and cell type-specific changes in gene expression in the cerebellum after classical fear conditioning

city: Seoul

first: Jungeun

last: Ji

address: 145 Anam-ro

department: Department of Integrated Biomedical and Life Science

country: South Korea

institute: Korea University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Region- and cell type-specific changes in gene expression in the cerebellum after classical fear conditioning [Spatial Transcriptomics]

summary: The cerebellum has recently been recognized for its role in non-motor functions, including classical fear conditioning. However, the molecular mechanisms underlying non-motor learning and memory remain largely unknown. Here, we investigate the transcriptional changes in the cerebellum associated with auditory fear conditioning. Spatial transcriptomic analysis revealed that in the deep cerebellar nuclei (DCN), an output region of the cerebellum, the expression of immediate early genes increased following fear learning and retrieval, suggesting that DCN may contribute to fear memory processing. As for the cerebellar cortex, robust and region-specific transcriptional changes were observed, with distinct expression patterns emerging across the Purkinje cell layer of vermis region. To further elucidate transcriptional changes in specific DCN cell types involved in fear processing, we performed single-nucleus RNA sequencing and identified prominent gene expression changes in Kit+ inhibitory neurons. Collectively, our findings highlight region- and cell-type-specific molecular adaptations in the cerebellum, providing insights into its contribution to non-motor learning.

overall_design: We performed spatial transcriptomics data analysis using 10X Visium data obtained from coronal mouse cerebellum sections of 3 groups (fear conditioned vs after auditory memory retrieval vs home cage). We performed single-nuclei RNA-sequencing data analysis using data obtained from mouse deep cerebellar nuclei (DCN) of 3 groups (fear conditioned vs after auditory memory retrieval vs home cage).

first: Jinhee

last: Baek

first: Kyoung-Doo

last: Hwang

first: Seunghwan

last: Choi

first: Junko

last: Kasuya

first: Ted

last: Abel

first: Joon-Yong

last: An

first: Yong-Seok


title: Region- and cell type-specific changes in gene expression in the cerebellum after classical fear conditioning [snRNA-Seq]


title: MiT Fusions, TSC1–TSC2 Divergence, and Stem-like Programs Reveal Distinct Origins and Vulnerabilities in PEComa [Methylation]

status: Public on Apr 18 2026

city: Illkirch

first: Gabriel

last: Malouf

state: Grand Est

address: 1 rue Laurent Fries

country: France

institute: INSTITUT/GENETIQUE/BIOLOGIE MOLEC/CELL

type: Methylation profiling by genome tiling array

summary: Perivascular epithelioid cell neoplasms (PEComas) are ultra-rare mesenchymal tumors lacking a molecular classification to guide therapy. Here we perform comprehensive multi-omic profiling of an unselected PEComa cohort. We identify frequent MITF rearrangements involving actin gene partners (ACTA2, ACTG1 and ACTB). Anatomical stratification reveals cyclin-dependent kinase module mutations in gynecologic tumors, whereas soft tissue, gastrointestinal, and pelvic tumors lacked mTOR pathway alterations but are enriched for TFE3/MITF rearrangements. Transcriptomic analysis defines four subtypes with distinct lineage programs—melanocytic, mesenchymal, or adipogenic—as well as unique mutational patterns and clinical behaviors. Notably, an aggressive stem-like subtype enriched for TP53/RB1 mutations exhibits high proliferation, activation of embryonic and Hedgehog signaling, immune infiltration, and resistance to mTOR inhibitors, but potential responsiveness to immunotherapy. Single-nucleus RNA sequencing reveals intra-tumoral heterogeneity within this subtype, including divergent inflammatory states. Together, these findings establish a molecular classification framework and identify actionable vulnerabilities in PEComa.

overall_design:
DNA methylation profiling was performed on human PEComa tumor samples to characterize epigenetic alterations and to support integrative analysis of subtype-specific transcriptional programs and tumor heterogeneity.

***Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.***

first: Justine

last: Gantzer

first: Xiaofan

last: Lu


title: MiT Fusions, TSC1–TSC2 Divergence, and Stem-like Programs Reveal Distinct Origins and Vulnerabilities in PEComa [RNA-seq]

overall_design:
RNA sequencing was performed on human PEComa tumor samples to define transcriptional programs and support integrative molecular subtyping and characterization of tumor heterogeneity.

***Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.***


title: MiT Fusions, TSC1–TSC2 Divergence, and Stem-like Programs Reveal Distinct Origins and Vulnerabilities in PEComa [scRNA-seq]

overall_design:
Single-nucleus RNA sequencing was performed on selected PEComa tumor samples to characterize cellular heterogeneity and to validate transcriptomic subtype classification at single-cell resolution.

***Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.***


title: Relationship between Mycobacterium tuberculosis response to nitric oxide stress and iron limitation

first: Shumin

last: Tan

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

summary: The purpose of this study was to identify genes that are differentially expressed upon M. tuberculosis exposure to nitric oxide (NO) or iron limitation stresses, either individually or in combination.

overall_design: RNAseq profiling of M. tuberculosis CDC1551 wild type exposed for 4 hours to control, nitric oxide (NO), low iron, or nitric oxide + low iron conditions.

first: Natalia

middle: F

last: Quirk


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [Hi-C]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Estrogen is the primary mitogen for ER+ BC cells. However, most studies prior to this examining the genomic effects of E2-regulated signaling in cell-based assays used supraphysiological levels of hormone. While this has allowed us to understand the extremes of E2 signaling, it has limited our ability to examine cellular functions which operate at lower hormone concentrations. In particular, the genomic actions of ligand-bound ERa through transcriptional enhancer formation and function are not understood at physiological E2 doses. Here, we use an integrated genomic approach with RNA-seq, PRO-seq, ChIP-seq,  ATAC-seq, and HiC to identify gene sets that express preferentially at either picomolar or nanomolar concentrations of E2. Expression of these genes is regulated mainly at the transcriptional level and is associated with distinct enhancer features, including chromatin accessibility and H3K27ac enrichment, as well as differential binding of FOXA1 and GATA3 co-transcription factors. These features are also spatially organized within TAD boundries.

overall_design: HiC of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 10 nM).

first: Kim

last: Hyung Bum

first: Nandu

last: Tulip

first: Kraus

last: W Lee


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [ATAC-seq]

summary: Estrogen is the primary mitogen for ER+ BC cells. However, most studies prior to this examining the genomic effects of E2-regulated signaling in cell-based assays used supraphysiological levels of hormone. While this has allowed us to understand the extremes of E2 signaling, it has limited our ability to examine cellular functions which operate at lower hormone concentrations. In particular, the genomic actions of ligand-bound ERa through transcriptional enhancer formation and function are not understood at physiological E2 doses. Here, we use an integrated genomic approach with RNA-seq, PRO-seq, ChIP-seq, and ATAC-seq to identify gene sets that express preferentially at either picomolar or nanomolar concentrations of E2. Expression of these genes is regulated mainly at the transcriptional level and is associated with distinct enhancer features, including chromatin accessibility and H3K27ac enrichment, as well as differential binding of FOXA1 and GATA3 co-transcription factors.

overall_design: ATAC-seq of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 100 pM, 1 nM, 10 nM).


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [RNA-seq]

overall_design: RNA-seq of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 100 pM, 1 nM, 10 nM).


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [PRO-seq]

overall_design: PRO-seq of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 100 pM, 1 nM, 10 nM).


title: Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity [RNA-Seq]

city: 福建省 / 厦门市 / 翔安区

first: Zifeng

last: Li

address: 福建省厦门市厦门大学翔安校区

institute: Xiamen University

summary: A key challenge in improving T cell-mediated immunotherapies is defining the factors that regulate functional versus exhaustion T cell fates. Through multi-round in vivo CRISPR screens in chronic LCMV Clone 13 infection and transcription factor (TF) benchmarking, we identified KLF2 as a top TF driving CX3CR1⁺ effector-like exhausted cell (Texeff-like) differentiation. Overexpression of KLF2 converted CX3CR1⁻ cells into Texeff-like cells by direct engagement of key loci. Conversely, loss of KLF2 increased inhibitory receptor expression and redirected cells toward terminal exhaustion. However, early after infection, KLF2 deficiency yielded increased CD8+ T cell accumulation and improved viral control. This effect was, in part, mediated by TOX and improved T cell localization with dendritic cells. Additional deletion of PD-1 further enhanced viral control, but induced severe immunopathology. Collectively, these findings identify KLF2 as a central regulator of the Texeff-like program and underscore exhaustion features as checkpoints balancing antiviral immunity and immunopathology.

overall_design: For RNA-seq in vitro, P14 cells were activated and transduced with pMIGII empty vector or pMIGII-Klf2. After in vitro culture for an additional 2.5 days, cells were analyzed by flow cytometry or sorted for RNA-seq library preparation. For RNA-seq of Texeff-like and Texterm, Cas9-expressing P14 cells transduced with sgNTC (GFP⁺) and transferred to Cas9-expressing hosts infected with LCMV Cl13.Donor-derived cells were sort for RNA-seq library preparation at day 7.5. For RNA-seq at day 5.5, Cas9-expressing P14 cells transduced with sgNTC (GFP⁺) or sgKlf2 (GFP⁺) were mixed at a 1:1 ratio with sgNTC-transduced “spike” cells (Ametrine⁺) and transferred to Cas9-expressing hosts infected with LCMV Cl13.Donor-derived cells were sort for RNA-seq library preparation at day 5.5. For another RNA-seq at day 5.5, Cas9-expressing P14 cells were transduced with sgNTC (mCherry⁺), sgKlf2 (GFP⁺), and sgRunx3 (Ametrine⁺). The cells were mixed in a 1:1:1 ratio and transferred into Cas9-expressing hosts infected with LCMV Cl13. At day 5.5, donor-derived cells were sorted for RNA-seq library preparation. The sorted populations included sgNTC (mCherry⁺), sgKlf2 (GFP⁺), sgRunx3 (Ametrine⁺), and sgKlf2 + sgRunx3 (GFP⁺ Ametrine⁺).

first: Shengjun

last: Geng

first: Hongling

last: Huang


title: IFN-γ induction of GBP1 drives aberrant macrophage activation in human skin granulomas

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Granuloma annulare (GA) and cutaneous sarcoidosis (cSAR), non-communicable skin conditions, possess an overlapping immunopathology, in which the aberrant activation of macrophages by IFN-γ constitutes a central driver of disease. Nevertheless, our understanding of the molecular events occurring in pathologically activated GA and cSAR macrophages remains limited. Here, we analyzed published single-cell RNA sequencing data of GA and cSAR and performed in-vitro experiments with primary human cells, allowing us to show that oxidative phosphorylation (OXPHOS) is a dominant metabolic pathway in IFN-γ-activated macrophages. Furthermore, we identify an IFN-γ-induced, OXPHOS-sensitive response network in human GA and cSAR macrophages. Within this network, GBP1 plays a central role in controlling IFN-γ-mediated macrophage activation. Meanwhile, inhibition of OXPHOS and GBP1 both promoted resolution of granulomas and prevented granuloma induction in a human in-vitro granuloma model. Taken together, our study suggests that OXPHOS and GBP1 represent therapeutic strategies for treating cutaneous granulomatous diseases.

overall_design: PBMC were obtained from buffy coats by density gradient centrifugation using Ficoll-Paque Plus (Cytiva, 17-1440-03) or Lymphoprep (STEMCELL Technologies, 07851) and monocytes were separate with CD14+ MACS technology (Miltenyi Biotec, 130-050-201), according to manufacturer´s protocol. To induce differentiation into macrophages, eluted CD14+ cells were cultured in RPMI 1640 medium (Life Technologies, 21875091 or 21875158) supplemented with 10% FBS/FCS (Pan-Biotech, P30-3302 or Thermo Fisher, 10099141), 1% Penicillin/streptomycin (Sigma, P0781 or  GIBCO, 15140-122) and M-CSF 50 ng/ml (Miltenyi Biotec, 130-096-492 or R&D Systems, 216-MC-500) for 5-10 days. Activation of MDM was achieved by a treatment with IFN-γ (BD Biosciences, 554617) or LPS at 1 ng/ml (Invivogen, tlrl-eblps) in complete RPMI with 10mM glucose or 10mM Galactose. PBMC were collected from 6 separate buffy coats.

first: Mario

last: Fabri

first: David

middle: E

last: Sanin


title: Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [ChIP-seq]

overall_design: ERa, H3K27ac, FOXA1, or GATA3 ChIP-seq of MCF-7 cells treated with a range of E2 concentrations (veh., 10 pM, 100 pM, 1 nM, 10 nM).


title: Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity [TCR-Seq]

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

overall_design: CD44+PD-1+ or GP33 tetramer+ cells from GzmbCreKlf2wt or GzmbCreKlf2fl/fl mice were sorted at the indicated time points after LCMV Cl13 infection.


title: Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity [ATAC-seq]

city: 福建省 / 厦门市 / 翔安区

address: 福建省厦门市厦门大学翔安校区

overall_design: For ATAC-seq in vitro, P14 cells were activated and transduced with pMIGII empty vector or pMIGII-Klf2. After in vitro culture for an additional 2.5 days, cells were sorted for ATAC-seq library preparation. For ATAC-seq at day 5.5, Cas9-expressing P14 cells transduced with sgNTC (GFP⁺) or sgKlf2 (GFP⁺) were mixed at a 1:1 ratio with sgNTC-transduced “spike” cells (Ametrine⁺) and transferred to Cas9-expressing hosts infected with LCMV Cl13.Donor-derived cells were sort  for ATAC-seq library preparation at day 5.5.


title: Mediator Subunit MED4 Enforces Metastatic Dormancy in Breast Cancer (ATAC-seq_shMed1)

city: New York

first: Seongyeon

last: Bae

state: NY

institute: Columbia University

summary: Breast cancer metastatic relapse after a latency period, known as metastatic dormancy, involves dormant tumor cells within pre-metastatic niches. Through rigorous genetic screening in mice, we identified the mediator complex subunit 4 gene, Med4, as a novel tumor-cell intrinsic gatekeeper in metastatic reactivation. Med4 downregulation effectively awakened dormant breast cancer cells, prompting reactivation and macroscopic metastatic outgrowth in the lungs. Med4 depletion results in profound changes in nuclear size and three-dimensional (3D) chromatin architecture from compacted to relaxed states in contrast to the known canonical function of the Mediator complex. These changes rewire the expression of extracellular matrix (ECM) proteins, integrins, and signaling components resulting in integrin-mediated mechano-transduction and activation of YAP and MRTF. In parallel, assembly of stress fibers pulls on the nuclear membrane, and thereby contributes to mediating and reinforcing the overall chromatin modifications that occur subsequent to Med4 depletion. MED4 gene deletions were observed in patients with metastatic breast cancer, and reduced MED4 expression correlates with worse prognosis. Our findings unveil a unique function of MED4 and identify an innovative mechanism by which MED4 regulates the epigenetic control of integrin signaling, pivotal in the metastatic reactivation of breast cancer. Additionally, we propose MED4 and related gene signatures as novel biomarkers for stratifying patients prone to recurrence, thus identifying subsets of patients who will benefit from targeting effectors activated by MED4 loss.

overall_design: Bulk ATAC-seq of D2A1-d cells expressing either NTC or Med1 shRNAs.

middle: S

first: Filippo

last: Giancotti


title: Mediator Subunit MED4 Enforces Metastatic Dormancy in Breast Cancer (Histone ChIP-seq_shMed4)

overall_design: Comprehensive chromatin state profiling and analysis of metastatic breast cancer by performing ChIP-sequencing of 5 core histone modifications.


title: Mediator Subunit MED4 Enforces Metastatic Dormancy in Breast Cancer (ATAC-seq_shMed4)

overall_design: Bulk ATAC-seq of D2A1-d cells expressing either NTC or Med4 shRNAs. The sample names have been provided as below.


title: Mediator Subunit MED4 Enforces Metastatic Dormancy in Breast Cancer

overall_design: Refer to individual Series


title: Mediator Subunit MED4 Enforces Metastatic Dormancy in Breast Cancer (RNA-seq_shMed4)

overall_design: Total RNA was isolated from murine breast cancer D2A1-d cells expressing either NTC or Med4 shRNAs and sent to BGI for RNA-seq. The sample name was annotated below.


title: Mediator Subunit MED4 Enforces Metastatic Dormancy in Breast Cancer (RNA-seq_shMed1)

overall_design: Total RNA was isolated from murine breast cancer D2A1-d cells expressing either NTC or Med1 shRNAs and sent to BGI for RNA-seq. The sample name was annotated below.


title: CD8⁺ T-cell exhaustion-like and mitochondrial dysfunction define immune dysregulation in feline chronic gingivostomatitis

status: Public on Apr 17 2026

city: Davis

first: Amir

last: Kol

address: One Shields Ave, Davis, CA 95616, USA

institute: UC Davis

summary: Feline chronic gingivostomatitis (FCGS) is a debilitating oral disease characterized by immune dysregulation and chronic inflammation. We hypothesized that CD8+ T cells from FCGS cats exhibit exhaustion features with suppressed mitochondrial pathways, and that mesenchymal stromal cell (MSC) therapy post-extractions might restore these programs. RNA sequencing was performed on peripheral CD8+ T cells from cats with active FCGS before (disease group, D) and after (treated group, M) clinical remission following full-mouth extractions and MSC therapy, with specific-pathogen-free cats as controls (control group, C). CD8+ T cells from active disease displayed terminal effector differentiation and exhaustion-like signatures, including upregulation of cytotoxic markers (GZMB, GZMK, GZMA), differentiation markers (KLRG1, IL18R1/IL18RAP), and exhaustion-associated genes (EOMES, CD244, TNFSF10, CCR5, PRDM1, RGS16). Gene set enrichment analysis confirmed exhaustion-like CD8+ T-cell phenotype enrichment in active disease, which resolved after treatment. Pathway analysis revealed marked downregulation of mitochondrial respiratory chain components, ATP synthesis, and protein import pathways in active FCGS, with partial post-treatment resolution. Immunofluorescence of draining lymph nodes showed significantly increased CTLA-4+CD3+ T cells in both FCGS groups versus controls, suggesting persistent immunoregulatory signaling despite clinical improvement. These findings identify overlapping T-cell exhaustion and mitochondrial dysfunction-associated transcriptomic signatures in FCGS, supporting therapeutic strategies targeting immune-metabolic pathways.

overall_design: CD8+ T cells were selected from feline peripheral blood. Blood was collected from healthy control cats (n=10), cas with active chronic gingivostomatitis (FCGS, n=8) and cats with FCGS in remission post treatemnt (n=4).

first: Kol

last: Amir


title: Mast cells interact directly with colorectal cancer cells to promote epithelial-to-mesenchymal transition

city: Bloomington

first: Heather

last: O'Hagan

state: IN

address: 1001 E 3RD ST

department: School of Medicine

institute: Indiana University

summary: Mast cells (MCs), a type of granulocytic immune cell, can be both pro- and anti-tumorigenic in colorectal cancer (CRC). We hypothesized that these contrasting findings may be in part due to differential interactions of MCs with CRC subtypes. BRAF mutant CRC uniquely contains intestinal secretory cell types. In this study, we demonstrated that MCs are enriched in BRAF mutant CRC, likely because they are recruited by factors released from cancer secretory cells. To investigate the functional consequences of MC-CRC cell interactions, we performed direct coculture experiments. We demonstrated that MCs promote epithelial-to-mesenchymal transition (EMT) in CRC cells in a calcium- and contact-dependent fashion. Furthermore, inhibiting LFA-1 and ICAM1 integrin binding reduced the coculture-induced EMT-related marker expression in CRC cells. The MC-CRC cell interaction facilitates the transfer of biological materials, including mRNA molecules, from MCs to CRC cells. This study is the first to report a contact-dependent, pro-tumorigenic role of MCs in CRC, as well as the transfer of molecules encoded by MCs to CRC cells. These findings enhance our comprehension of cell-cell communication between immune and cancer cells. Furthermore, this work suggests that targeting MC-CRC interactions, particularly through modulating integrin pathways, could offer new therapeutic strategies for aggressive CRC subtypes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HT-29 cells incubated alone or in coculture with LAD2 cells and for LAD2 cells incubated alone or in coculture with HT-29 cells for 12 hours.

first: Rosie

last: Lanzloth


title: BPTF is essential for vaccine-induced germinal center B cell responses

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

summary: Germinal centers (GCs) are microanatomical structures in which antigen-specific B cells undergo proliferation, somatic hypermutation, and affinity-based competition to select high affinity clones that differentiate into memory B cells (MBCs) and plasma cells (PCs). B cell progression through the GC is tightly regulated and the molecular determinants that modulate GC B cell proliferation and survival are still under investigation. Here, we use a conditional deletion mouse model to demonstrate that bromodomain PHD finger transcription factor (BPTF), a subunit of the nucleosome remodeling factor (NURF) chromatin remodeling complex, is required for robust GC B cell responses following vaccination. In GC B cells, Bptf loss induces a stress-like transcriptional profile and a shift towards PC identity-defining transcriptional programing, although this does not lead to accumulation of functional PCs. Rather, we show that BPTF-deficient GC B cells are prone to cell death. Cumulatively, our data demonstrate that BPTF is necessary for GC B cell maintenance and robust antigen-specific B cell responses.

overall_design: RNA-seq profiling of dark zone (DZ) and light zone (LZ) germinal center (GC) B cells of wildtype B6.129P2(Cg)-Ighg1_tm1(cre)Cgn/J mice and floxed Bptf mice following vaccination against SARS-CoV-2 WA1 spike protein.

first: Alexandria

middle: J

last: Sturtz

first: Birk

last: Evavold

first: Zarifeh

last: Rarani

first: Wafaa

last: Alsoussi

middle: Q

first: Hanover

last: Matz

first: Hiromi

last: Muramatsu

first: Wren

last: Simkins

first: Sameer

last: Kumar Malladi

first: Katherine

last: McIntire

first: Jishnu

last: Das

first: Jackson

last: Turner

first: Norbert

last: Pardi

first: Ali

last: Ellebedy


title: Ustekinumab Resistance in Individuals with Ulcerative Colitis is Associated with an Alteration of a Subset of Pro-inflammatory Mucosal Regulatory T cells

city: Bethesda

first: Kristi

last: Briggs

address: 10 Center Drive

institute: NIDDK

summary: Background & Aims: Ustekinumab is a monoclonal antibody therapy targeting interleukin 12 and 23 for the treatment of inflammatory bowel diseases, including ulcerative colitis (UC).  While these pathways remain quite attractive for UC therapy, response to ustekinumab can be variable.  There is an urgent need to better understand the underlying mucosal immune alterations associated with treatment to guide therapy decisions.   This study aims to examine the mucosal immune signatures in individuals with UC with variable treatment response to ustekinumab. Methods: Sigmoid colon tissue from individuals treated with ustekinumab were analyzed using a multi-modal approach.  Single-cell RNA and T cell receptor sequencing was performed on mucosal biopsies.  In a subset of these patents, multiparameter flow cytometry and spatial transcriptomics was also completed on matched pre- and post-treatment tissue samples.  Key findings were also validated on a larger cohort using immunohistochemistry. Results: Ustekinumab significantly altered the frequency and phenotype of mucosal regulatory T cells (Tregs).  Non-responders to ustekinumab had a higher frequency of Tregs that expressed OX40 and GITR, which is associated with decreased suppressive abilities.  In contrast, responders had Tregs with elevated GPR15 and reduced expression of the kinase PIM2, which can alter Treg stability and function.  Additionally, Th17 cells in non-responders demonstrated an enhanced pro-inflammatory gene expression profile. Conclusion: Non-response to ustekinumab in UC is linked to a mucosal immune environment enriched with pro-inflammatory T cell phenotypes and impaired regulatory T cell function. These findings suggest that Tregs are both targets and potential biomarkers of ustekinumab response, with their phenotypic and transcriptional features providing insight into mechanisms of therapeutic resistance.

overall_design: sigmoid colon biopsy tissue analysis of patients with ulcerative colitis on IL12/23 inhibitor


title: Cisplatin resistance in an ovarian cancer model is mediated by the microtubule dynamics regulator TPPP3 which synergizes with tubulin code rewiring

city: East Lansing

first: Sachi

last: Horibata

state: MI

address: 766 Service Rd, Room 2014

institute: Michigan State University

summary: Cisplatin is a mainstay in cancer treatment, but toxicity and resistance limit its potential. Using RNA-seq, we show that ovarian cancer cells undergo broad changes in the microtubule cytoskeleton that correlate with resistance.  Consistent with this, we find that cisplatin directly impacts microtubule dynamics in vitro and in cells. Paclitaxel counteracts cisplatin and increases resistance. By purifying tubulin from cisplatin sensitive resistant and re-sensitized ovarian cancer cells, we demonstrate that resistance acquisition rewires the tubulin code leading to microtubule stabilization. Furthermore, tubulin polymerization promoting protein 3 (TPPP3) contributes to resistance. In vitro, TPPP3 synergizes with tubulin isotypes from resistant cells to yield maximal microtubule stabilization in response to cisplatin. Database analysis shows that patients with low TPPP3 levels have improved therapeutic outcome. Our findings implicate TPPP3 and microtubule dysregulation in cisplatin resistance, independent of effects through DNA damage, and have bearing on the etiology of cisplatin-associated neuropathies and ototoxicity.

overall_design: RNA-seq were performed on cisplatin sensitive (1A9), resistant (1A9CP80), and resensitized (1A9CP80R or 1A9CP80rev) cells.

first: Kishore

last: Mahalingan

first: Ruchi

last: Patel

first: Yu

last: Fan

first: Jordan

middle: M

last: Hotz

first: Adriana

last: Ponton-Almodovar

first: Keith

last: MacRenaris

first: Yan

last: Li

first: Daoud

last: Meerzaman

first: Michael

last: Gottesman

first: Antonina

last: Roll-Mecak


title: Stepwise DNA unwinding gates TnpB genome-editing activity

city: Berkeley

first: Marena

middle: Isabelle

last: Trinidad

address: 2151 Berkeley Way

institute: Innovative Genomics Institute

summary: TnpB is a compact RNA-guided endonuclease and evolutionary ancestor of CRISPR-Cas12 that offers a promising platform for genome engineering. However, the genome-editing activity of TnpBs remains limited and its underlying determinants are poorly understood. Here, we used biochemical and single-molecule assays to examine the DNA-unwinding mechanism of Youngiibacter multivorans TnpB (Ymu1 TnpB). DNA unwinding proceeds through formation of a partially unwound intermediate state to a fully unwound open state. The open state forms inefficiently and collapses readily in the absence of negative supercoiling. An optimized variant, Ymu1-WFR, stabilizes formation of both the intermediate and open states, resulting in enhanced DNA cleavage in vitro and increased genome editing in vivo. These findings identify the physical basis for the observed minimal activities of natural TnpBs, revealing how stabilizing specific unwinding states enables efficient DNA targeting.

overall_design: Small RNA sequencing was performed on purified Ymu1 TnpB RNP complexes expressed in E. coli to characterize reRNA expression from a 200-nt scaffold construct. SHAPE-MaP chemical probing was performed on purified RNP complexes carrying either the 127-nt (wild-type length) or short reRNA scaffold to determine RNA secondary structure and reactivity profiles.

first: Honglue

last: Shi

first: Kamakshi

last: Vohra

first: Zehan

last: Zhou

first: Conner

last: Langeberg

middle: I


title: Mytho/Phaf1 is required to prevent DNA damage and tissue degeneration in Danio rerio

city: Padova

first: Marco

last: Sandri

state: Padova

address: Via Orus 2

department: Biomedical Sciences

country: Italy

institute: University of Padova

summary: Mytho (Macroautophagy and YouTH Optimizer) is a novel FoxO-dependent gene that has been recently identified to control health- and life-span in C. elegans via autophagy regulation. However, the role of this gene in tissue development and function in vertebrates has not yet been established. To address these issues, we generated a zebrafish mytho KO model and observed that mutants exhibited a higher mortality rate than wild-type (WT) siblings during the first month of life and a lower resistance to oxidative stress. Mytho silencing resulted in a decrease of larval locomotor activity and muscle birefringence and caused alteration of adult muscle structure. Autophagy impairment was confirmed in tissues with the highest mytho expression such as brain, muscle and testis. Finally, mutants showed tissue degeneration in pancreas, retina, muscle and a reduction of reproductive capabilities of males and morphological alterations in gonads of both sexes. Importantly, males presented a higher incidence of seminomas, a testicular cancer. The increased susceptibility to cancer is associated with an enhanced DNA fragmentation in sperm cells.  In conclusion, this study highlights the key role of Mytho in maintaining proper tissue function and DNA integrity.

overall_design: RNA was isolated from frozen testicles collected from male zebrafish aged 15 mpf (4 WT and 4 KO, two of which had developed a seminoma), using TRIzol (ThermoFisher Scientific) according to the manufacturer's instruction. RNA quality was assessed using an Agilent 2200 TapeStation System (Agilent Technologies). Sample RIN (RNA integrity number) values ranged from 9.3 to 9.9. Total RNA samples (1 µg) were used for library preparation (Illumina’s TruSeq Stranded mRNA LT Sample Prep Kit with poly A selection). Sequencing was performed using an Illumina NovaSeq 6000 System (150 length, paired-end) platform (Illumina, Inc., San Diego, CA).

first: Tommaso

last: Pagliarusco

first: Anais

last: Franco-Romero

first: Francesca

last: Terrin

first: Filippo

last: Citton

first: Ludovica

last: Carducci

first: Nicola

last: Facchinello

first: Camilla

last: Fontana

first: Marta

last: Giacomazzo

first: Ranieri

last: Verin

first: Maria

middle: B

last: Rasotto

first: Lisa

last: Locatello

first: Luisa

last: Dalla Valle


title: High-resolution spatial transcriptomics of human liver with VisiumHD

city: Toronto

first: Rachel

middle: D

last: Edgar

state: ON

address: 101 College Street

department: Ajmera Transplant Centre

country: Canada

institute: University Health Network

summary: The liver plays a critical role in metabolism and immune function. These crucial functions are diminished in chronic liver diseases, leading to over two million deaths annually worldwide due to liver failure. Single-cell transcriptomics has provided insights into the cellular composition of the liver in health and disease, but is inherently biased due to cell type-specific enrichment and destruction during the single-cell dissociation process. Previous work has highlighted difficulties in capturing specific populations such as cholangiocytes and hepatocytes. Spatial transcriptomics is a promising approach that does not have inherent bias for cell populations and adds important spatial context. Until recently, spatial transcriptomics technologies have only been at a multi-cellular resolution leading to mixed signals from different cell types. The latest spatial transcriptomic technology from 10X Genomics, VisiumHD, enables high-resolution spatial mapping of gene expression in tissue samples, offering a sophisticated platform for exploring the cellular composition of the liver. With a bin width of 2um, it can quantify transcripts at a sub-cellular resolution. Samples from three healthy human liver donors were sequenced and cells were clustered into cell types by integrating spatial transcriptomic data with existing single-cell reference maps. Spatially distinct cell signatures were identified through differential expression analyses and a high-resolution map of the liver was created. This resource provides cell-level and spatially-resolved insights into the cellular and geographical heterogeneity of the liver to serve as a resource for researchers to identify disease-specific spatial signatures and novel therapeutic targets.

overall_design: We applied 10x Genomics Visium HD to liver tissue from three healthy human donors to generate subcellular-resolution spatial transcriptomic profiles. Adjacent sections were imaged and sequenced to identify spatially distinct cell signatures and map the organization of the healthy liver.

first: Faizan

last: Hasan

first: Gary

last: Bader

first: Sonya

last: MacParland


title: Platelet lncRNA LUCAT1 Associates with Risk of Major Adverse Cardiovascular Events

city: New York City

first: Matthew

last: Muller

address: 550 First Avenue

department: Department of Medicine

institute: New York University

summary: CD34+ cell–derived megakaryocytes from four independent donors following treatment with PBS control, IFNα (1000 U/mL), or IFNγ (100 ng/mL). These data define donor-resolved interferon-responsive gene programs in human megakaryocytes under type I versus type II interferon stimulation.

overall_design: Human CD34+-derived megakaryocytes from 4 donors were infected stimulated with IFNα, IFNγ or PBS (vehicle control) for 24 hours.

first: Coen

last: van Solingen

first: Marcin

last: Sowa

first: Tessa

last: Barrett


title: Translocator Protein Deficiency Promotes Splenomegaly with Extramedullary Hematopoiesis after Sepsis

status: Public on Apr 27 2026

city: Minami-ku

first: Kazuya

last: Kikutani

state: Hiroshima

address: 1-2-3 Kasumi

department: Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences

institute: Hiroshima Univeristy

summary: This study investigates the role of translocator protein (TSPO) in splenic immune responses following sepsis using a mouse cecal ligation and puncture (CLP) model. Bulk RNA sequencing of spleen tissue collected 17 days after sham or CLP surgery revealed that TSPO deficiency promotes splenomegaly characterized by red pulp expansion, enhanced erythropoiesis, and reduced immune responses. Gene expression and deconvolution analyses indicated decreased lymphocyte signatures and increased erythroblast and megakaryocyte signatures in TSPO knockout mice. These findings suggest that TSPO plays a critical role in maintaining splenic immune homeostasis after sepsis.

overall_design: Male C57BL/6J wild-type (WT) and TSPO knockout (TSPOKO) mice were subjected to cecal ligation and puncture (CLP) to induce sepsis or sham surgery. Spleen tissues were collected 17 days after surgery. Bulk RNA sequencing was performed on spleen samples from three groups: WT-Sham, WT-CLP, and TSPOKO-CLP (n = 8 per group). Gene expression profiles were analyzed to investigate the effects of TSPO deficiency on post-septic splenic immune responses and hematopoietic remodeling.

first: Hidenori

last: Aizawa

first: Xiao

last: Lyu


title: Developing Midbrain-like Organoid of Gaucher Disease as A Platform for Drug Assessment

city: Cincinnati

first: Stuart

last: Adler

state: OH

address: 3333 Burnet Ave

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

summary: Gaucher disease (GD) is a lysosomal storage disorder caused by GBA1 mutations, leading to defective acid β-glucosidase (GCase) and accumulation of glucosylsphingolipids, causing inflammation and neurodegeneration. We developed midbrain-like organoids (MLOs) from induced pluripotent stem cells (iPSCs) of nGD patients with GBA1L444P/P415R and GBA1L444P/RecNcil mutations to model nGD brain pathogenesis. These nGD MLOs exhibited GCase deficiencies, reduced enzyme activities, lipids accumulation, transcriptomic alterations, and impaired dopaminergic neuron differentiation, mirroring nGD pathology. GBA1 correction mediated by CRISPR/Cas9 restored GCase activity, normalized lipids levels, and rescued dopaminergic neuron function, confirming the causal role of GBA1 mutations during early brain development. Using this novel platform, we further evaluated therapeutic strategies, including SapC-DOPS nanovesicles delivering GCase, AAV9-GBA1 gene therapy, and substrate reduction therapy (SRT) with GZ452, a glucosylceramide synthase (GCS) inhibitor currently under clinical investigation. These treatments either restored GCase activity, and/or reduced lipid accumulation, improved lysosomal function, and partially corrected dysregulated neural development and lysosomal pathways identified by transcriptomic analysis. These findings highlight MLOs as a physiologically relevant platform for studying nGD mechanisms and testing novel therapies, offering insights into potential treatments for this devastating disorder.

overall_design: Midbrain-like organoid (MLO) generated from WT-75.1 (WT) and GD2-1260 (nGD) iPSC cells at week 8 were collected for bulk RNA sequencing. Tree MLOs were pooled as one biological sample and three biological replicates were included for each genotype group.

first: Yi

last: Lin

first: Ying

last: Sun


title: Whole Blood Transcriptomics Differentiates Circulating Gene Expression Between Coronary Artery Disease and Peripheral Artery Disease

summary: Coronary artery disease (CAD) and peripheral artery disease (PAD) are prevalent atherosclerotic disorders that exhibit distinct clinical and pathological presentations. We used whole-blood RNA sequencing to investigate circulating transcriptomic differences between PAD and CAD. Whole-blood RNA sequencing was performed in 71 subjects 40-65 years of age with symptomatic PAD (n=20) or CAD (n=51). Patients with concomitant PAD and CAD were excluded. Differential expression analysis was performed to compare circulating gene expression in patients with PAD and patients with CAD. We identified 106 genes differentially expressed between PAD and CAD (p adj. < 0.1). Pathway analysis identified upregulation of interferon signaling pathways in CAD and upregulation of neutrophil degranulation and toll-like receptor signaling pathways in PAD. Cell type deconvolution revealed greater fractional abundance of T cell subsets in CAD compared to PAD. Patients with PAD had higher neutrophil-lymphocyte ratio that patients with CAD (3.4 vs. 2.3, p=0.01). In conclusion, PAD and CAD have unique circulating transcriptomes characterized by differences in inflammatory gene expression.

overall_design: Whole blood RNA-seq comparison of patients with  PAD and patients with CAD adjusted for demographic variables

first: Richard

last: Ni

first: Kelly

middle: V

last: Ruggles

first: Jeffrey

last: Berger


title: Early Intervention of the PKC-Hippo Signaling Alleviates Post-Traumatic Osteoarthritis

city: Miami

first: xiaomin

last: cai

state: Florida

address: Rosenstiel Medical Science Building 1600 NW, 10th Ave.

institute: University of Miami

summary: Post-traumatic osteoarthritis (PTOA) is a progressive joint disease triggered by mechanical injury and characterized by inflammation and cartilage degradation. The Hippo signaling pathway and its upstream regulator PKCζ have emerged as key modulators of mechano-inflammatory responses in chondrocytes. This study aimed to investigate the dynamic regulation of the PKC-Hippo signaling axis following joint injury and to evaluate the therapeutic potential of targeting this pathway in early PTOA.

overall_design: The study consists of three sets of bulk RNA-seq data. The first set included three groups: sham control, ACL injury treated with vehicle control, and ACL injury treated with a PKC inhibitor. Sham control mice underwent no ACL injury, and tissues were harvested 24 hours after the procedure. Vehicle control mice were subjected to ACL injury and treated with 0.9% saline, with tissues harvested 24 hours post-injury. PKC inhibitor-treated mice were subjected to ACL injury and treated with a PKC inhibitor, with tissues harvested 24 hours post-injury.The second set was designed to examine the early transcriptional response after ACL injury and included three time points: 0 hours, 7 hours, and 72 hours. The 0-hour group consisted of mice without ACL injury. The 7-hour and 72-hour groups consisted of mice harvested at 7 hours or 72 hours after ACL injury, respectively.The third set was designed to compare pharmacological targeting of the PKC-Hippo signaling pathway after ACL injury and included six treatment groups: Vehicle control, PKC inhibitor (PKCi), LATS inhibitor (LATSi), YAP/TAZ inhibitor (Y/Ti), PKC inhibitor + YAP/TAZ inhibitor (PKC+Y/Ti), and LATS inhibitor + YAP/TAZ inhibitor (LATS+Y/Ti). All mice underwent ACL injury and received the indicated inhibitor treatment (or vehicle control) for 24 hours before tissue collection. Each experimental group consisted of three biological replicates.


title: The role of miR-10b-5p/Brain-derived Neurotrophic Factor Axis Deregulation in Poststroke Epileptogenesis

city: Linz

first: Anna

middle: Regina

last: Tröscher

address: Krankenhausstraße 5

department: Center for Medical Research

country: Austria

institute: Johannes Kepler University Linz

type: Non-coding RNA profiling by high throughput sequencing

summary: Objective: Poststroke epilepsy (PSE) is a common complication following stroke, associated with increased mortality, poorer functional outcomes, greater disability, and heightened dementia risk. Currently, no standardized guidelines exist for the primary prevention of PSE, and prophylactic antiseizure medications (ASMs) are not routinely recommended. Management typically begins with ASM initiation after the first unprovoked seizure. Identifying predictive biomarkers is critical for improving post-stroke care and preventing PSE. Materials&Methods: We retrospectively analyzed 25 patients with PSE, ischemic stroke without epilepsy, and epilepsy. Serum-derived miRNA sequencing was conducted to identify differentially expressed miRNAs across the groups. Selected miRNAs were validated by quantitative PCR (qPCR), and target prediction was performed in silico. Brain-derived neurotrophic factor (BDNF), a key regulator of post-stroke recovery and epileptogenesis, was identified as a primary target of miR-10b-5p. BDNF levels were measured using ELISA and correlated with clinical parameters. Results: miRNA profiling revealed significant differences among the groups, with miR-10b-5p expression markedly reduced in PSE patients compared to those with stroke alone. qPCR validation confirmed miR-10b-5p as a potential biomarker distinguishing PSE from stroke. In PSE patients, BDNF concentration correlated with disease duration and latency to first seizure, whereas no such association was observed in stroke or epilepsy groups. Conclusion: Our findings suggest a novel pathophysiological mechanism involving the miR-10b-5p/BDNF axis in PSE development. miR-10b-5p may serve as a promising biomarker for early identification and targeted follow-up of stroke patients at high risk for developing epilepsy.

overall_design: total of 24 samples: 9 epilepsy, 8 PSE, 7 stroke

first: Rainer

last: Dormann

first: Joachim

last: Gruber

first: Mariia

last: Ragozina

first: David

last: Demmel

first: Daniel

last: Wallinger

first: Franziska

last: Ammer-Pickhardt

first: Raimund

last: Helbok

first: Tim

last: von Örtzen


title: Progesterone receptor (PGR)-mediated transcriptional networks in human ovulatory follicles: Identification of SOX9 as a novel PGR-downstream mediator [ChIP-seq]

city: Lexington

first: Hayce

last: Jeon

state: KENTUCKY

address: 800 Rose Street

department: Dept. of OB/GYN

institute: University of Kentucky

summary: Progesterone receptor (PGR) is an essential transcription factor for successful ovulation. Clinically, PGR inhibitors have been used as emergency contraceptives due to their ability to delay or block ovulation. While much of the current understanding of PGR’s function has been derived from animal models, the specific downstream target genes and pathways PGR regulates in human ovulatory follicles remain largely unexplored. In the present study, we utilized a human granulosa cell (hGLC) model that mimics preovulatory hCG-induced increases in PGR expression and progesterone production, combined with a PGR inhibitor (RU486), to identify hCG-induced, PGR-regulated genes in human ovulatory follicles. RNA-Seq and ChIP-Seq analyses revealed numerous genes regulated by PGR in response to human chorionic gonadotropin (hCG) treatment for 12 h, which are involved in diverse biological processes, including metabolism, steroidogenesis, signaling activation, cell cycle regulation, and transcriptional control. By comparing these findings with the existing data from PgrKO mouse models, we also identified both conserved and species-specific PGR-regulated genes. Notably, SOX9 was identified as a human-specific, hCG-induced PGR-target gene in hGLCs. A further characterization study using dominant follicle samples collected before and at different times after ovulatory hCG administration from regularly cycling women demonstrated that SOX9 expression is predominantly induced in the granulosa cells of ovulatory follicles and persists in the developing corpus luteum. Functional studies showed that SOX9 knockdown by siRNA reduced progesterone production and the expression of steroidogenesis-related genes (CYP11A1 and STAR) in hGLCs. In summary, the present finding provides the first comprehensive list of preovulatory PGR-downstream genes in human granulosa cells and unveils SOX9 as a novel human-specific ovulatory transcription factor with potential roles in steroidogenesis. This foundational information not only enhances our understanding of the PGR-regulated ovulatory pathway but also provides a critical resource for developing improved strategies to manage women’s fertility.

overall_design: ChIP-Seq of PGR in cultured human granulosa/lutein cells treated wth or without hCG for 12 h.

first: Yohan

last: Choi

first: Mats

last: Brännström

first: James

middle: W

last: Akin

first: Thomas

last: Curry Jr

first: Misung

last: Jo


title: Progesterone receptor (PGR)-mediated transcriptional networks in human ovulatory follicles: Identification of SOX9 as a novel PGR-downstream mediator [RNA-seq]

overall_design: RNA-Seq profiling of cultured human granulosa/lutein cells treated wthout (Control) or treated with hCG ± RU486 for 12 h.


title: Rapid evolution of mouse saliva through regulatory rewiring and gene expansions

status: Public on Apr 16 2026

city: Buffalo

first: Omer

last: Gokcumen

address: 135 Founders Promenade

department: Biological Sciences

institute: University at Buffalo

summary: Mammalian saliva plays essential roles in digestion, immunity, and host-microbiome interactions, yet its protein composition varies widely across species and sexes. This diversity makes saliva a powerful model to study evolution of gene expression. Here, we compared mouse and human salivary glands at the genomic, transcriptomic, and proteomic levels to understand how saliva composition evolves. We found that evolution of gene expression in mouse salivary glands is driven by rapid gene turnover and sexual dimorphism. In the submandibular and sublingual glands, 68% and 73% of expression from genes encoding secreted proteins derives from lineage-specific genes that lack one-to-one human orthologs. This contrasts the prevailing view that gene expression is largely conserved across tissues and highlights saliva as an unusually dynamic system of molecular evolution. Mouse submandibular gland shows striking sexual dimorphism, with 1537 tissue specific sex-biased genes, five times higher than in the liver, a classic model of sex-biased expression. These genes cluster in regions shaped by recent gene duplication, such as the kallikrein gene cluster, a mouse-specific expansion that accounts for ~16.4% of male-biased submandibular gland expression. Our analyses suggest that this bias arises through regulatory changes that are expanded by gene duplication, including the spread of a testosterone-associated regulatory motif and the expansion of a shared chromatin domain that promotes coordinated gene regulation. Our results describe a novel mechanism through which lineage-specific gene duplication and regulatory rewiring drive rapid, sex-specific evolution of the mammalian saliva.

overall_design: Bulk RNA-seq was performed on salivary glands (parotid, submandibular, and sublingual), pancreas, and liver from male and female mice of two strains. Each strain included 3 males and 3 females, for a total of 12 individuals.

first: Luane

last: Landau

first: Shika

last: Jain

first: Nathan

last: Griffin

first: Achisha

last: Saikia

first: Jill

last: Kramer

first: Sarah

last: Knox

first: Stefan

last: Ruhl


title: Pattern separation memory requires Cerebellin 4-Neogenin 1 signaling at dentate gyrus synapses

city: Palo Alto

first: Xiao

last: Han

state: California

address: 265 Campus Drive

institute: Stanford University

summary: The ability to avoid confusion between similar episodic memories enables organismal survival and fitness. This evolutionarily conserved differentiation process of memories as distinct representations is known as pattern separation. A central role for the entorhinal cortex->dentate gyrus (EC->DG) circuit in pattern separation is well established, but the molecular mechanisms that enable this circuit to mediate pattern separation memory is not known. Here we show the involvement in murine pattern separation memory of a unique transsynaptic protein complex formed by Cerebellin-4, Neogenin-1, and neurexins that is known to be selectively required for long-term plasticity in the EC->DG circuit. In vivo deletion of either presynaptic Cerebellin-4 in the entorhinal cortex or of postsynaptic Neogenin-1 in the dentate gyrus impairs acquisition of pattern separation memory. Thus, we describe a specific memory function for a defined molecular complex at an identified synapse, providing direct support for the hypothesis that synaptic plasticity contributes to the encoding of memory.

overall_design: WT mice (BL/6 background) were divided into three groups: home cage, context exposure, and foot shock. After 90 minutes of behavioural paradigm, each mouse was sacrificed, and the medial entorhinal cortex (MEC), lateral entorhinal cortex (LEC), and hippocampal subregions CA1 and  CA3  were dissected and RNAs were extreacted using TRIzol method. The RNA-seq was performed on IlluminaTruSeq platform.

first: Kif

last: Liakath-Ali

first: Dong

middle: C

last: Südhof


title: Deciphering molecular responses to radiofrequency microneedling in a 3D human skin model: New insights and modulation by aftercare treatment

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstraße 30

institute: Uniklinik RWTH Aachen

summary: Radiofrequency microneedling (RFMN) is an emerging therapeutic approach that enhances skin rejuvenation by delivering targeted thermal injury to the dermal and subdermal layers while sparing the epidermis. However, the molecular mechanisms underlying its biological effects especially in comparison to medical microneedling remain poorly understood. In this study, we aimed to investigate, for the first time, the molecular and histological responses to RFMN using a standardized three-dimensional (3D) human skin model. As a secondary objective, we assessed the modulatory effects of RFMN aftercare treatment with a dexpanthenol-containing ointment.Histological analysis of RFMN-treated 3D skin models showed dermal coagulation zones that disappeared after post-treatment with a dexpanthenol-containing ointment. Transcriptomic profiling 48 hours after RFMN showed an early pro-inflammatory response with upregulated chemokines and cytokines (e.g., CCL7, CXCL2, IL24) and downregulated matrix metalloproteinases and barrier genes, indicating controlled inflammation and skin renewal initiation. Aftercare with the dexpanthenol-containing ointment elicited distinct gene expression changes at 120 hours post-RFMN, including increased expression of cytokines (IL37), matrix metalloproteinases (MMP3, MMP8), and epidermal regeneration markers (LCE1B, VEGFA), consistent with accelerated wound healing, re-epithelialization, and inflammation modulation.In conclusion, this study elucidates the molecular and histological effects of RFMN and highlights the benefits of dexpanthenol-containing topical post-treatment, which may further shorten the already brief downtime. These findings support the optimization of clinical protocols for safer and more effective skin rejuvenation.

overall_design: We investigated the molecular and histological responses to RFMN utilizing a previously established standardized  human 3D skin model composed of primary dermal fibroblasts and epidermal keratinocytes. Histological assessments and transcriptomic analyses employing next-generation sequencing were conducted 48 and 120 hours after RFMN treatment. In addition, the effects of a topical dexpanthenol-containing ointment administered immediately following RFMN on wound healing and gene regulation were evaluated.

first: Yvonne

last: Marquardt

first: Laura

first: Sina

last: Djahed

first: Jens

last: Baron


title: Transcriptome analysis of ureter tissues from wild-type and COL17 knockout mice.

city: Sapporo

first: Takashi

last: Namba

state: Hokkaido

address: Kita 18-Nishi 9, Kita-ku

department: Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine

institute: Hokkaido University

summary: Type XVII collagen (COL17A1) is well-characterized as a critical structural component of the epidermal basement membrane in the skin; however, its presence and function in the urinary tract remain poorly described. We discovered that COL17A1 is also expressed in the urothelium under urological condition. To elucidate the molecular mechanisms underlying early urothelial abnormalities caused by COL17A1 deficiency, we performed transcriptomic profiling (bulk RNA-seq) of ureter tissues from 2-week-old wild-type and Col17a1 knockout mice.

overall_design: To elucidate the molecular mechanisms underlying COL17A1-mediated urothelial homeostasis, bulk RNA-sequencing was performed on ureter tissues isolated from 2-week-old Col17a1 knockout (KO) mice with C57BL/6N background and its wild-type (WT; n = 3 per group) .

first: Amy

last: Suzui

first: Osamu

last: Ichii


title: Aberrant laminin signaling drives melanocyte dedifferentiation and unveils a tractable therapeutic target in vitiligo

city: Osaka

first: fei

last: yang

state: Osaka

address: Abeno Medix 212, 1-2-7, Asahimachi, Abeno-ku

institute: Department of Pigmentation Research and Therapeutics, Graduate School of Medicine, Osaka Metropolitan University

summary: Vitiligo is characterized by progressive loss of melanocytes, but the underlying mechanisms governing melanocyte dysfunction remain incompletely understood. In this study, we aimed to investigate the role of the extracellular matrix microenvironment in regulating melanocyte identity and function.  We performed spatial transcriptomics using the 10x Genomics Visium platform on human skin samples from healthy controls and vitiligo patients. This approach enabled spatially resolved analysis of gene expression changes associated with melanocyte dedifferentiation.  Our analysis revealed that aberrant laminin signaling, particularly involving Laminin-332, is associated with transcriptional reprogramming of melanocytes toward a dedifferentiated state. Spatially resolved gene expression patterns indicated alterations in pathways related to cell adhesion, cytoskeletal organization, and stress responses in vitiligo lesions.  These findings provide insight into how extracellular matrix remodeling contributes to melanocyte dysfunction and identify potential therapeutic targets for restoring melanocyte differentiation in vitiligo.

overall_design: This study includes spatial transcriptomics data generated from human skin samples obtained from vitiligo patients and healthy controls. The experimental design consists of two groups: vitiligo perilesional skin and normal skin.  Each sample represents an independent biological replicate derived from a different individual. The primary variable under investigation is disease state (vitiligo versus healthy control).  Spatial transcriptomic profiling was performed to compare gene expression patterns between these groups and to identify spatially resolved transcriptional changes associated with melanocyte dedifferentiation in vitiligo.

first: Ichiro

last: Katayama

first: Lingli

last: Yang

first: Fei


title: Small Non-Coding RNAs in the Regulatory Network of Wheat Dwarf Virus-Infected Wheat

city: České Budějovice

first: Abdoallah

last: Sharaf

address: Branišovská 31

country: Czech Republic

institute: Biology Centre ASCR, v.v.i.

summary: Wheat dwarf virus (WDV) is a major constraint to global wheat production, causing severe yield losses and economic disruption. Understanding the molecular basis of wheat–WDV interactions is essential for developing resistant cultivars. Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of gene expression and defence. This study identified ncRNAs involved in wheat responses to WDV, including host lncRNAs, miRNAs, and viral small interfering RNAs (siRNAs) targeting WDV genomic regions. High-throughput sequencing revealed extensive ncRNA reprogramming under WDV infection. A total of 437 differentially expressed lncRNAs (DElncRNAs) and 58 miRNAs (DEmiRNAs) were detected. Resistant genotypes displayed more DElncRNAs (204 in Svitava; 163 in Fengyou 3) than the susceptible Akteur (141). In Akteur, 66.7% of DElncRNAs were downregulated, whereas in Svitava, 56.9% were upregulated. Akteur also exhibited more DEmiRNAs (28) than resistant genotypes (15), with predominant downregulation. A co-expression network analysis revealed 391 significant DElncRNA–mRNA interactions mediated by 16 miRNAs. The lncRNA XLOC_058282 was linked to 298 transcripts in resistant genotypes, suggesting a central role in the host defence. Functional annotation showed enrichment in signalling, metabolic, and defence-related pathways. Small RNA profiling identified 1166 differentially expressed sRNAs targeting WDV, including conserved hotspots and 408 genotype-specific sites in Akteur versus Fengyou 3. Infected plants displayed longer sRNAs, a sense-strand bias, and a 5′ uridine preference, but lacked typical 21–24 nt phasing. These findings highlight the central roles of ncRNAs in orchestrating wheat antiviral defence and provide a molecular framework for breeding virus-resistant wheat.

overall_design: Triticum aestivum miRNA profiles of genotypes associated with resistance against the Wheat dwarf virus were generated

first: Nuc

last: Przemyslaw

first: Jan

last: Ripl

first: Emad

last: Ibrahim

first: Jiban

last: Kumar


title: CRISPRi/a screens to identify modifiers of response to the bi-steric mTORC1 inhibitor RM-006

city: New York

first: Thomas

last: O'Loughlin

address: 1470 Madison Avenue

institute: Icahn School of Medicine

summary: Aberrant activation of the PI3K/AKT/mTOR signaling pathway is a common feature of cancer but, while mTOR kinase represents an attractive drug target, mTOR inhibitors have not seen broad success as single agents. To identify strategies to enhance the utility of mTOR inhibitors we performed forward genetic screens with new bi-steric mTORC1 inhibitors. These screens show that mTORC1 inhibitor-mediated cytostasis leaves cells exquisitely dependent on the lipid peroxide scavenging enzyme GPX4. Mechanistically, using unbiased gene activation screens, we demonstrate that mTORC1-dependent control of ferroptosis occurs, in part, through regulation of SCARB1 expression. Together, our work reaffirms combining mTORC1 with GPX4 inhibition as one of the most promising combinatorial approaches for mTOR-targeted cancer therapies and defines an HDL-dependent ferroptosis suppression system that is regulated by mTORC1 activity.

overall_design: CRISPRi screens in LN229 dCas9-KRAB cells treated with DMSO, 1.56 nM RM-006 or 0.098 nM RM-006 and CRISPRa screens in LN229 dCas9-Suntag cells treated with DMSO, RM-006, RSL3 and RM-006+RSL3 in combination.

middle: A

first: Abolfazl

last: Arab

first: Luke

last: Gilbert


title: Effect of SREBP1 cDNA overexpression on gene expression in LN229 cells

summary: Aberrant activation of the PI3K/AKT/mTOR signaling pathway is a common feature of cancer but, while mTOR kinase represents an attractive drug target, mTOR inhibitors have not seen broad success as single agents. To identify strategies to enhance the utility of mTOR inhibitors we performed forward genetic screens with new bi-steric mTORC1 inhibitors. These screens show that mTORC1 inhibitor-mediated cytostasis leaves cells exquisitely dependent on the lipid peroxide scavenging enzyme GPX4. Mechanistically, using unbiased gene activation screens and RNA-seq, we demonstrate that mTORC1-dependent control of ferroptosis occurs, in part, through regulation of SREBP1 and donwstream impact on SCARB1 expression.

overall_design: RNA-seq profiling of LN229 cells overexpressing GFP or SREBP1 cDNA performed in duplicate


title: Effect of RM-006 treatment on gene expression in LN229 cells

summary: Aberrant activation of the PI3K/AKT/mTOR signaling pathway is a common feature of cancer but, while mTOR kinase represents an attractive drug target, mTOR inhibitors have not seen broad success as single agents. To identify strategies to enhance the utility of mTOR inhibitors we performed forward genetic screens with new bi-steric mTORC1 inhibitors. These screens show that mTORC1 inhibitor-mediated cytostasis leaves cells exquisitely dependent on the lipid peroxide scavenging enzyme GPX4. Mechanistically, using unbiased gene activation screens and RNA-seq, we demonstrate that mTORC1-dependent control of ferroptosis occurs, in part, through regulation of SCARB1 expression.

overall_design: RNA-seq profiling of LN229 cells after treatment with vehicle (DMSO) or 0.098, 0.39, 1.56 nM RM-006 for 72 hours


title: A scalable Tn5-based method for genome-wide DNA methylation profiling in development and disease

city: Geneva

first: Nahuel

last: Simonet

address: 9 chemin des Mines

country: Switzerland

institute: EPFL

summary: DNA methylation is a critical epigenetic modification involved in various diseases, including cancer, and serves as a biomarker for early disease detection. Traditional detection methods, such as bisulfite sequencing, offer base-pair resolution but are costly and require high sequencing depths. We developed CmeCUT&Tag, a novel approach using methylation-binding domain fusion proteins coupled to hyperactive Tn5 transposase that selectively targets methylated DNA regions in both chromatinized and isolated DNA. These fusion proteins insert sequencing adapters into methylated regions, allowing low-depth sequencing for quantitative methylation assessment or bisulfite treatment for base pair resolution. Our approach enables comprehensive genome-wide DNA methylation profiling with minimal sequencing coverage. We demonstrated its efficacy in detecting DNA methylation in human stem cells and organoid systems. The system exhibits a high correlation with traditional bisulfite sequencing. It efficiently identifies CpG islands and DNA methylation dynamics during brain organoid development, highlighting its potential for biomedical applications in disease monitoring and aging research.

overall_design: CmeCUT&Tag, a method enabling selective targeting of methylated DNA regions in both chromatinized samples and isolated genomic DNA. Libraries were generated from the genomic DNA of  human induced pluripotent stem cells (iPSCs, CAU) and brain tumor biopsies. Raw FASTQs avaliable upon request.

first: Hanrong

last: Hu

first: Fides

last: Zenk


title: On-demand GLUT3 expression augments CAR-T cell metabolic fitness and antitumor efficacy whereas preventing toxicity in glioblastoma

city: Tokyo

first: Hiroyoshi

last: Nishikawa

state: Tokyo

address: 5-1-1 Tsukiji, Chuo-ku

department: 3Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC)

institute: National Cancer Center Japan

summary: We show that the dysfunction of CAR-T cells in GBM is attributed to glucose deficiency in the tumor microenvironment (TME) and that on-demand, but not continuous, metabolic replenishment significantly improves the antitumor efficacy of CAR-T cells. The massive consumption of glucose by cancer cells reduces the glucose level in the TME of GBM, consequently impairing CAR-T cells. Adding stable expression of glucose transporter 3 (GLUT3), a high-affinity glucose transporter, to CAR-T cells  restored their cytokine production and killing activity. However, whereas CAR-T cells with stable GLUT3 expression induced tumor reduction in a GBM model, their overactivation led to adverse events and mouse death. On-demand GLUT3-expressing CAR-T cells, in which GLUT3 transcription is driven by the nuclear translocation of nuclear factor of activated T cells (NFAT) by target antigen stimulation, exhibited enhanced metabolic fitness and increased antitumor efficacy, leading to long-lasting tumor control in intracranial human GBM cell xenograft models whereas it prevented adverse events.

overall_design: Sample 1-4: RNA-seq profiling of conventional EGFRvIII-targeting CAR-T cells after 24 hours of culture in 0.5 mM or 10 mM glucose conditions. Sample 5-16: RNA-seq reads were processed using the Genomon RNA-seq pipeline. Adapter sequences and low-quality bases were trimmed prior to alignment. Reads were aligned to the human reference genome (hg38), and gene-level read counts were generated for downstream analysis.

first: Junya

last: Yamaguchi

first: Keisuke

last: Watanabe

first: Akihiro

last: Nakamura