title: A Single Small-Molecule-Based Human Embryo Model Reveals V-ATPase Requirement in Mammalian Blastocyst Cavitation

city: barcelona

first: aintzane

last: rueda

state: Choose State

address: C/ del Dr. Trueta, 179, 08005 Barcelona

country: Spain

institute: Sequentia Biotech SL.

summary: Human naïve pluripotent stem cells (nPSCs) can be indued by various combinations of signaling factors to genearte blastocyst-like structures known as blastoids. Despite the rapid advances in human blastoid models, their potential to uncover fundamental mechanisms of early development remains limited, leaving key morphogenetic processes poorly understood. Here, we present a simple and robust system in which dimethyl sulfoxide (DMSO) alone induces blastoid formation from human nPSCs. This model faithfully recapitulates pre- and post-implantation features, including amniotic cavity formation, and reveals a previously unrecognized mechanism of trophectoderm (TE) cavitation. Using this system, we identified lysosome-related genes—particularly those encoding subunits of the proton pump V-ATPase—are essential for blastoid cavitation. DMSO treatment upregulates key V-ATPase subunits (ATP6V0A4 and ATP6V1B1), which are also enriched in the TE of human embryos. Inhibition of V-ATPase disrupted lysosomal acidification, blocked intracellular vacuole formation, and impaired blastoid cavitation. Furthermore, both genetic and pharmacological disruption of V-ATPase function significantly impaired cavitation in mouse and human blastocysts. Thus, our simple DMSO model recapitulates key aspects of human blastocyst development and reveals a conserved mechanism involving V-ATPase–mediated lysosomal acidification during early mammalian embryogenesis.

overall_design: Single cell RNA sequencing was performed to profile the cellular composition and transcriptional landscape of day 6 human preimplantation embryo models (blastoids) generated in vitro. Blastoids were collected at day 6 of differentiation, dissociated into single cell suspensions, and processed for single cell transcriptomic analysis using the 10x Genomics Chromium GEM-X platform. Cells were captured in a single library preparation and sequenced to sufficient depth to enable the identification of major preimplantation lineages and associated transcriptional programs. The resulting dataset provides a high-resolution snapshot of lineage specific gene expression at the day 6 preimplantation stage.

first: Arun Pandian

last: Chandrasekaran


title: Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts V

status: Public on Mar 11 2026

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

country: USA

institute: The Jackson Laboratory

type: Expression profiling by high throughput sequencing

summary: Background Genetic variation drives phenotypic diversity and disease susceptibility. Trans-acting genetic variation coordinates genome-wide chromatin changes, yet the molecular mechanisms underlying this regulation remain largely unknown. Here, we use the power of mouse genetics to investigate how genetic variation at trans-acting loci regulates 3D chromatin interactions. Results Genetically variable 3D interactions were identified using HiChIP to map H3K27ac-associated regulatory elements in C57BL/6J (B6) and DBA/2J (D2) embryonic stem cells (ESCs). We identified 4,962 strain-differential interactions (~5% of total interactions), 71% of which overlapped chromatin accessibility quantitative trait loci (caQTL), establishing that chromatin interaction variation is predominantly heritable. These differential interactions showed coordinated changes in chromatin state and gene expression, with stronger interactions associated with increased accessibility and transcription. Notably, loci regulated in trans exhibited a unique chromatin signature where weaker interactions were enriched for H3K9me3-marked heterochromatin. This pattern was 20-fold more enriched at trans-regulated targets compared to cis, implicating heterochromatin in trans-regulation of 3D genome structure. Analysis of F1 hybrids revealed dominant repressive effects, consistent with heterochromatin-mediated trans-regulation. To causally test this mechanism, we generated reciprocal congenic mouse strains carrying a Chr13 trans-QTL region on otherwise inbred genetic backgrounds. Integrated multiomic profiling of congenic ESC lines demonstrated that this single locus coordinates changes in H3K9me3, H3K27ac, chromatin accessibility, and 3D contact frequency at hundreds of distal genomic regions. Remarkably, 73-83% of differential interactions at Chr13 trans-QTL targets changed in the predicted direction, demonstrating that heterochromatin-mediated trans-regulation coordinately regulates hundreds of regulatory loci. Conclusions This work establishes heterochromatin formation as a mechanism by which genetic variation at trans-acting loci coordinates changes across chromatin accessibility, histone modifications, and 3D genome organization, providing a framework for understanding how early developmental chromatin states could generate phenotypic variation while preserving essential developmental programs.

overall_design:
RNA-seq in C57BL/6J, DBA/2J, B6.D2-(rs30079041-rs51756099)/Bakr (QJ), and D2.B6-(rs29224292-rs51756099)/Bakr (XE) mouse embryonic stem cells (3 technical/biological replicates each).
** QJ and XE are congenic strain designations used internally within the lab. For clarity and consistency with standardized nomenclature, QJ samples are referred to as B6-13D2 and XE samples as D2-13B6 throughout the manuscript.


title: Ultrasound-Driven Rochelle Salt-Based Biodegradable Piezoelectric Deviced Promoted Axon Outgrowth After Sciatic Nerve Defect

city: Beijing

first: Haofeng

last: Cheng

state: Beijing

address: No.28 Fuxing Road

country: China

institute: Chinese PLA General Hospital

summary: This study explored Rochelle salt-based biodegradable piezoelectric devices for applications in nerve regeneration and intestinal motility monitoring. Defective rat sciatic nerves were repaired using Rochelle salt-based biodegradable piezoelectric conduits, which were stimulated with transcutaneous ultrasound, leading to enhanced axon growth. High-throughput sequencing was employed to identify significantly altered genes.

overall_design: Six female rats were randomly assigned to two groups. The PLLARS_US group was treated with PLLARS conduits and received ultrasound stimulation, while the PCL group was treated with PCL conduits without ultrasound stimulation.

first: Lan

last: Yin

first: Yu

last: Wang

first: Jun

last: Zhang

first: Fanqi

last: Dai

first: Hui

last: Qi

first: Hongjie

last: Cai

first: Tianqi

last: Su


title: Microglial NUS1 deficiency drives dopaminergic neurodegeneration by activation of the LCN2/SLC22A17 axis-mediated iron transport II

city: Suzhou

first: Lele

last: Liu

state: Jiangsu

address: No. 199, Ren'ai Road

department: college of pharmacy

institute: Soochow University

summary: The mechanisms underlying selective loss of dopaminergic (DAergic) neurons in substantia nigra pars compacta in Parkinson’s disease (PD) remain unclear. The NUS1 gene, encoding NgBR, has recently been identified as a novel PD risk gene. Here, we show that NgBR is highly expressed in microglia, and microglia-specific NgBR deficiency drives progressive PD-like motor deficits and DAergic neurodegeneration via lipocalin-2 (LCN2)/SLC22A17 axis-mediated iron transport. NgBR deficiency in microglia triggers endoplasmic reticulum stress and PERK-ATF4-NUPR1 pathway to selectively upregulate LCN2-mediated iron efflux rather than cytokines. Strikingly, microglia-derived iron-loaded Holo-LCN2 but not iron-free Apo-LCN2 is internalized by SLC22A17, a receptor we identified as specifically highly expressed in DAergic neurons that induces iron overload/ferroptosis. Pharmacological inhibition of the LCN2/SLC22A17 axis or ferroptosis alleviate DAergic neuron loss and PD-like symptoms caused by microglial NgBR deficiency in vitro and in vivo. Our findings establish intercellular iron homeostasis imbalance as a selective pathological driver in PD and highlight the LCN2/SLC22A17 axis for specific therapeutic targeting.

overall_design: RNA-seq profiling of Primary microglia derived from adult Nus1fl/fl mice (Ctrl) and Nus1cKO mice (cKO).

first: Yan

last: Hong

first: Xiying

first: Xiurong

last: Huang

first: Yanni

last: Ma

first: Rui

first: Qian

last: Sun

first: Hongyang

first: Zongbing

last: Hao

first: Chenchen

last: Mu

first: Xiaojun

last: Lu

first: Lifang

last: Hu

first: Jifeng

last: Guo

first: Beisha

last: Tang

first: Guanghui

first: Haigang

last: Ren


title: p300-Mediated Histone H3K18 Lactylation Promotes Mitochondrial ROS Accumulation via Mitophagy Inhibition to Potentiate Dopamine Agonists Efficacy in Prolactinomas [RNA-seq]

city: Wuhan

last: Jiang

address: No. 1095, Jiefang Avenue, Wuhan City, Hubei Province

institute: Department of Neurosurgery, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology

summary: Prolactinomas are the most common functional pituitary adenomas, with dopamine receptor agonists (DAs) as the first-line therapy. However, 10–30% of patients develop DA resistance, and the underlying mechanisms remain incompletely elucidated.Clinical samples were collected to analyze p300 expression. Experiments including immunofluorescence, immunohistochemistry, gene editing, Western blot, co-immunoprecipitation, ChIP-qPCR, RNA/CUT&Tag sequencing, flow cytometry, Seahorse assay, and mass spectrometry were performed to explore the synergistic anti-tumor mechanism of upregulating/activating p300 combined with DAs. DAs downregulated p300 by inhibiting the cAMP-PKA-CREB pathway. Upregulating/activating p300 synergized with DAs to promote mitochondrial ROS elevation and cell apoptosis, which depends on p300’s histone acetyltransferase (HAT) domain mediating histone H3 lysine 18 lactylation (H3K18la). p300-mediated H3K18la significantly promoted intracellular ROS accumulation by upregulating Ndufs7 (promoting mitochondrial ROS production) and Washc1 (inhibiting mitophagy). YF-2, a p300 HAT domain activator, exhibited synergistic anti-tumor activity with DAs.This study reveals the p300-H3K18la- mitophagy-ROS regulatory axis, providing a new target and strategy for treating DA-resistant prolactinomas.

overall_design: AtT-20 cells (transfected with empty vector or OE-p300) were treated with sodium lactate (5 mM) or BRC (10 μM) for 24 h, followed by bulk RNA sequencing

first: Sihan

last: Li

first: Ting

last: Lei

first: Zhuowei


title: Transcriptomic profiling of MCL-1 inhibitor response in lymphoma models in vitro and in vivo

city: Charlottesville

first: Jing

last: Gao

state: VA

address: 21 HOSPITAL DR, OMS BLOG RM 4767

department: Pathology

institute: University of Virginia

summary: This study presents single-cell RNA sequencing (scRNA-seq) profiling of lymphoma models treated with the MCL-1 inhibitor S63845. Human Namalwa lymphoma cellsand mouse Eμ-Myc lymphoma spleen samples were analyzed following vehicle control or S63845 treatment at defined time points to characterize transcriptional responses associated with drug sensitivity, persistence, and resistance.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA sequencing was performed on human Namalwa lymphoma cells and mouse Eμ-Myc lymphoma spleen samples treated with the MCL-1 inhibitor S63845 or vehicle control. Mouse samples include biological replicates of control and treated tumors, while Namalwa cells include parental, short-term treated, and drug-resistant conditions.

first: Xiaohong

last: Zhao

first: Kevin

last: Qiu

first: Jianguo

last: Tao


title: YY1 and ZFP384 CUT&Tag of BV2 cells and microglia after ischemic stroke

city: Yushima, Bunkyo-ku

first: Jun

last: Tsuyama

state: Tokyo

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate YY1 and ZFP384 binding in microglia and the microglial cell line after ischemic stroke, we performed cleavage under targets and tagmentation (CUT&Tag) analysis using anti-YY1 and anti-ZFP384 antibodies.

overall_design: CUT&Tag of BV2 microglial cell line with anti-YY1, anti-ZFP384, and IgG control antibodies in mock-transduced and Zfp384-overexpressing conditions; and FACS-sorted microglia with anti-YY1 and IgG control antibodies from sham-operated, post-ischemic day 6, and day 28 (Zfp384flox/flox vs. Cx3cr1-CreER;Zfp384flox/flox) mouse brains.

first: Takashi

last: Shichita


title: p300-Mediated Histone H3K18 Lactylation Promotes Mitochondrial ROS Accumulation via Mitophagy Inhibition to Potentiate Dopamine Agonists Efficacy in Prolactinomas [CUT&Tag]

first: Qian

overall_design: In the AtT-20 cell model, the control group was transfected with an empty vector and treated with bromocriptine(10 μM, 24h)  and the treated group was transfected with OE-p300+bromocriptine. Using an H3K18la-specific antibody, DNA fragments bound to H3K18la modifications in the genome were specifically enriched through steps including cell permeabilization, antibody incubation, pA/G-Tn5 binding, and Mg²⁺-activated transposition. Finally, library construction and sequencing were performed to analyze the differences in genome-wide distribution of H3K18la modifications induced by p300 overexpression.


title: Single-cell and Spatial Transcriptomic Profiling of the Bone Metastatic Microenvironment

city: Houston

first: Li

last: Yang

address: 6565 Fannin Street

department: Department of System Medicine and Bioengineering (SMAB)

institute: METHODIST HOSPITAL RESEARCH INSTITUTE

summary: The goal of this study is to comprehensively characterize the cellular composition, transcriptional programs, and spatial organization of the bone metastatic microenvironment and to assess how therapeutic perturbation influences tumor–microenvironment interactions. A mouse bone metastasis model was established via internal iliac artery injection of Lewis lung carcinoma cells, and metastatic lesions were monitored by in vivo imaging. Single-cell RNA sequencing and 10x Genomics Visium–based spatial transcriptomics were generated from metastatic bone tissues to provide complementary cellular and spatial resolution.

overall_design: Mouse bone metastasis samples were generated using an internal iliac artery (IIA) injection model. Mice were maintained under standard laboratory housing conditions with ad libitum access to food and water. Bone metastases were induced by injection of LLC1 tumor cells, and animals were monitored post-procedure until full recovery. Bone tissues were harvested at defined experimental endpoints for downstream single-cell RNA sequencing and spatial transcriptomics analysis. For the details, please refer to Wang, H. et al. The osteogenic niche promotes early-stage bone colonization of disseminated breast cancer cells. Cancer Cell 27, 193-210 (2015).

first: Stephen

last: Wong

first: Xiang

last: Zhang

first: Jianting

last: Sheng

first: Zhan

last: Xu

first: Ju Young

last: Ahn

first: Yuliang

last: Cao


title: Transcriptomic profiling of MCL-1 inhibitor response and resistance in mantle cell lymphoma cell lines and patient PBMCs

summary: Bulk RNA-seq was performed to characterize transcriptional responses to MCL-1 inhibition and acquired drug resistance. Human mantle cell lymphoma cell lines (HBL-2 and Mino) were profiled under untreated (parental), S63845 treatment (1 µM, 72 h), and MCL-1 inhibitor–resistant conditions. In addition, a patient PBMC sample was profiled under DMSO control (12 h) and S63845 treatment (1 µM, 12 h). Gene-level raw count matrices are provided as processed data.

overall_design: Two MCL cell lines (HBL-2, Mino) were analyzed in three conditions (parental untreated; S63845 1 µM for 72 h; MCL-1 inhibitor–resistant) with three biological replicates per condition. One patient PBMC sample was analyzed under DMSO control (12 h) and S63845 1 µM treatment (12 h).


title: Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Properties [ATAC-seq]

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

summary: Microglia arise from yolk sac progenitors and are thought to persist throughout life with minimal input from adult hematopoiesis. However, whether brain-engrafted monocyte-derived macrophages (MDM) exist at homeostasis and during turnover, and how they function relative to yolk sac-derived microglia (YSM) remain unsettled. Here, we combine lineage tracing, pharmacological microglia depletion, and multi-omics profiling to define the ontogeny, identity, and function of brain parenchymal macrophages. Despite sharing the parenchymal milieu, MDM display transcriptional and epigenetic landscapes distinct from YSM. Fate-mapping reveals that brain-engrafted MDM transiently express CD206, echoing a developmental stage of microglial precursors. MDM engraftment and polarization are modulated by IL-34 and CCR2. Furthermore, parabiosis and skull‑flap transplantation reveal that both blood and skull marrow supply the niche, yielding origin‑biased MDM states. Functionally, MDM engraftment enhanced cuprizone-mediated demyelination. Together, our study defines the origins, molecular features, and context-dependent roles of brain parenchymal macrophages across homeostasis, turnover, and CNS pathology.

overall_design: ATAC-seq was performed using the Omni-ATAC protocol with minor adjustments for low-input sorted cells, as described in Grandi et al. Briefly, 20,000–40,000 FACS-sorted brain parenchymal macrophages were incubated on ice for 3 min in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin). Nuclei were washed (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20), pelleted, and resuspended in a 50-µL transposition reaction containing 2× TD buffer and Tn5 transposase, with the Tn5 volume scaled to cell input (1–2 µL for ~20,000–40,000 cells; Nextera DNA Library Prep Kit, Illumina). Transposition was carried out for 30 min at 37°C with mixing at 1,000 rpm. Tagmented DNA was purified using the DNA Clean & Concentrator-5 Kit (Zymo). Sequencing libraries were generated by PCR using indexed primers; samples were pre-amplified for 3 cycles, and a qPCR-based reaction (NEBNext Library Quant Kit, NEB) was used to determine the number of additional amplification cycles required. Final libraries were purified using a combination of the DNA Clean & Concentrator-5 Kit (Zymo) and AMPure XP beads (1.8× volumes). Libraries were pooled at equimolar ratios to a final concentration of 10 nM and sequenced on an Illumina NovaSeq 6000 by the Genome Technology Access Center at Washington University in St. Louis, targeting ~50 million paired-end reads per sample.

first: Siling

last: Du

first: Feiya

last: Ou

first: Antoine

last: Drieu

first: Eric

first: Yumeng

last: Cheng

first: Steffen

middle: E

last: Storck

first: Tornike

last: Mamuladze

first: Jay

first: Nora

last: Abduljawad

first: Bishan

last: Bhattarai

first: Justin

last: Rustenhoven

first: Niall

last: Mortimer

first: Simone

last: Brioschi

first: Khai

last: Nguyen

first: Patrick

middle: F

last: Rodrigues

first: Igor

last: Smirnov

first: Daniel

last: Gibson

first: J

middle: M

last: White

first: Wandy

last: Beatty

first: David

last: DeNardo

first: Qingyun

first: Michael

last: Meers

first: Claudia

middle: Z

last: Han

last: Sun

first: Florent

last: Ginhoux

first: Marina

last: Cella

first: Marco

last: Colonna


title: Wollemia nobilis small RNA sequencing

city: Cold Spring Harbor

first: W. Richard

last: McCombie

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed small RNA profiling analysis using data obtained from RNA-seq of 3 different tissues: leaf, ovule and pollen

overall_design: small RNA profiling analysis using data obtained from RNA-seq of 3 different tissues in triplicate: leaf, ovule and pollen.

first: Srividya

last: Ramakrishnan

first: Cristiane

last: de Santis Alves Rosa

first: Lais

last: Araujo Coelho

first: Melissa

last: Kramer

first: Sara

last: Goodwin

first: Olivia

last: Mendivil Ramos

first: Gil

last: Eshel

first: Veronica

last: Sondervan

first: Samantha

last: Frangos

first: Cecilia

last: Zumajo-Cardona

first: Katharine

last: Jenike

first: Shujun

last: Ou

first: Xiaojin

last: Wang

first: Yin

last: Peng Lee

first: Stella

last: Loke

first: Maurizio

last: Rossetto

first: Hannah

last: McPherson

first: Sebastiano

last: Nigris

first: Silvia

last: Moschin

first: Damon

middle: P

last: Little

first: Manpreet

middle: S

last: Katari

first: Kranthi

last: Varala

first: Sergios-Orestis

last: Kolokotronis

first: Barbara

middle: A

last: Ambrose

first: Larry

middle: J

last: Croft

first: Gloria

last: Coruzzi

first: Dennis

middle: W

last: Stevenson

middle: C

last: Schatz

first: Robert

last: Martienssen


title: Cortistatin antagonizes Piezo1-STING axis and facilitates mitochondrial homeostasis of keratinocytes by attenuating AGEs accumulation in diabetic ulcers [RNA-Seq IFN1]

city: Jinan

first: Qinghao

last: Yuan

state: Shandong

address: wenhuaxilu 44

institute: Qilu hospital

summary: Diabetic complications frequently arise in mechanically stressed regions, yet the molecular links between biomechanical forces and metabolic dysfunction remain unclear. Here, we demonstrate that mechanical stress induces glucose accumulation and downstream metabolic stress in keratinocytes, leading to mitochondrial injury and inflammation. Mechanistically, Piezo1 activation led to intracellular glucose overload and excessive advanced glycation end-products (AGEs) accumulation, which induced mitochondrial DNA (mtDNA) leakage into the cytosol and subsequently activated the cGAS–STINGsignaling cascade. Keratinocyte-specific Piezo1 deletion markedly reduced AGEs accumulation and preserved mitochondrial integrity, while Stimulator of interferon genes (STING) ablation reproduced similar downstream protective effects. Keratinocyte-specific deletion of the mechanosensor Piezo1 reduces advanced glycation end-products (AGEs) accumulation, preserves mitochondrial integrity, and dampens inflammatory signaling. Further, we show that this injury cascade involves cytosolic leakage of mitochondrial DNA (mtDNA) and activation of the cGAS–STING pathway. Stimulator of interferon genes (STING) ablation recapitulates the protective phenotype, confirming its downstream role. Notably, we identify Cortistatin (CST), an endogenous neuropeptide, as a previously unrecognized inhibitory ligand of Piezo1. CST binding attenuates calcium intake and glucose accumulation under mechanical stress, conferring notable protection in vitro and in diabetic ulcer (DUs) models. These findings uncover a CST–Piezo1–STING regulatory axis that integrates mechanical and metabolic cues to drive keratinocyte dysfunction in diabetes.

overall_design: RNA seq profiling of skin samples of CST-treated mice and Yoda1-treated mice at the end of the diabetic ulcer study

first: qinghao

last: yuan

first: guoli

last: ma

first: wenke

last: zhao

first: ben

last: liu

first: yonggang

last: li

first: jingwei

last: bi


title: Single-nucleus multiome analysis of the adult anthropoid cerebellar cortex across four primate species

city: New Haven

first: Yuting

last: Liu

state: CT

address: 333 Cedar Street

institute: YALE UNIVERSITY

summary: This study generated a single-nucleus multiomic dataset of the adult cerebellar cortex across four anthropoid primate species: Homo sapiens (n=4), Pan troglodytes (n=3), Macaca mulatta (n=4), and Callithrix jacchus (n=4). Paired single-nucleus RNA sequencing and chromatin accessibility profiling were performed using the 10x Genomics Chromium Multiome platform. After quality control, 69,302 nuclei were retained for RNA analysis and 63,491 nuclei for ATAC analysis, with 60,824 nuclei profiled in both modalities. The dataset provides single-nucleus transcriptomic and chromatin accessibility profiles for comparative analysis of cerebellar cell types across primates.

sample_organism:
Callithrix jacchus
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Postmortem posterolateral cerebellar cortex (Crus I and II/lobule VI and VII) was obtained from adult donors representing four primate species. Nuclei were isolated from frozen tissue and processed for paired snRNA-seq and snATAC-seq using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC and Gene Expression platform. Approximately 10,000 nuclei were targeted per sample. Libraries were sequenced on an Illumina HiSeq 4000 system and processed using Cell Ranger ARC (v2.0.1) with species-specific reference genomes. Quality control filtering was applied prior to downstream analysis.

first: Suel-Kee

last: Kim

first: Adriana

last: Cherskov

first: Saejeong

last: Park

first: Mingli

last: Li

first: Menglei

last: Zhang

first: Nenad

last: Sestan


title: RNA-seq analysis for wild-type fibroblasts and patient fibroblasts bearing pathogenic EPG5 mutations

city: London

first: Kritarth

last: Singh

state: England

address: Biosciences Stores, Anatomy Building, Gower street

department: Cell and Developmental Biology

country: United Kingdom

institute: University College London

summary: The aim of this study was to compare RNA-seq profiles of wild-type fibroblasts and patient-derived fibroblasts carrying pathogenic EPG5 mutations. Using an adjusted p-value threshold of < 0.05, we identified 5,303 differentially expressed transcripts in patient fibroblasts harboring a homozygous p.Gln336Arg missense mutation, of which 2,651 were upregulated and 2,652 were downregulated. In patient fibroblasts carrying compound heterozygous truncating mutations (p.Arg299*/p.Pro1827Ala), we identified 6,317 differentially expressed transcripts, including 3,239 upregulated and 3,078 downregulated transcripts, compared with control 1 fibroblasts.

overall_design: Three replicates for each fibroblast line (passage 5): Control 1; Patient 1 (p.Gln336Arg) and Patient 3 (p.Arg299*/Pro1827Ala ). Control fibroblasts sometimes refer to as wild-type.

first: Michael

middle: R

last: Duchen


title: Epithelial Reprogramming and Transition during Pulmonary Bioengineering

first: Micha Sam

middle: Brickman

last: Raredon

state: Connecticut

address: 10th Amistad Street

department: Department of Anesthesiology

institute: Yale University

summary: Recent research has emphasized the critical role of cell state transitions in tissue homeostasis. In lung biology, transitional cells are recognized as a feature of tissue-scale processes during both normal physiology and disease. The precise way that transitional cell states emerge and are regulated remains to be determined. Engineered tissues, built in a laboratory through bioengineering approaches, allow detailed study of cellular states that are not commonly found in native biology, and allow opportunities to directly induce and manipulate cellular transitions. The following study explores and characterizes epithelial cell states that emerge via cellular reprogramming in a tissue engineering context.

overall_design:
Bioengineered rat lungs containing reprogrammed epithelial cells were enzymatically dissociated after 24 hours (BDL1, BDL2, BDL3) and 5 days (LEP_DL1, LEP_DL2, LEP_DL3) in culture and sequenced. Epithelial cells reprogrammed via 2D culture were lifted and sequenced at passage 0 (P0-1, P0-2, P0-3) and passage 3 (P3-1, P3-2, P3-3). Samples of dissociated native rat lung (day 0) used for epithelial reprogramming in 2D culture can be referenced from an existing dataset (GSM9039637, GSM9039638, GSM9039639). These samples were used for analysis over time, for both the epithelial populations reprogrammed in 2D culture, and those reprogrammed in whole-lung constructs. Reprogrammed epithelial cells from both 2D and 3D cultures were also compared to native fetal rat lungs (frl1, frl2, NRL19) from both the pseudoglandular and canalicular stages that were enzymatically dissociated and sequenced.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Satoshi

last: Mizoguchi

first: Vi

last: Lee

first: Hahram

first: Sophie

last: Edelstein

first: Wang

last: Nuoya

first: Maria

last: Tomas Gracia

first: Colten

last: Danelski

first: Connor

last: Haynes

first: Rivero

last: Rachel

first: David

last: Stitelman

first: Tomohiro

last: Obata

first: Allison

last: Greaney

first: Tomoshi

last: Tsuchiya

first: Themis

last: Kyriakides

first: Naftali

last: Kaminski

first: Micha Sam Brickman


title: Transient proliferation by reversible YAP- and mitogen-control of the cyclin D1/p27 ratio

city: New York

first: Tobias

last: Meyer

address: 1300 York Ave

institute: Weill Cornell Medical College

summary: Hippo-YAP signaling orchestrates epithelial tissue repair and is therefore an attractive target in regenerative medicine. A challenge has been to understand how YAP activity is integrated with mitogen signaling and contact inhibition to control a transient proliferative response. Here we show that reduced contact inhibition, increased mitogen signaling, and YAP-TEAD activation converge on increasing the nuclear cyclin D1/p27 protein ratio during early G1 phase, towards a threshold ratio that dictates whether individual cells enter or exit the cell cycle. YAP increases this ratio in concert with inducing mitogen signaling, by increasing EGFR and other receptors that signal primarily through ERK. After a delay, contact inhibition suppresses YAP activity, which gradually downregulates mitogen signaling and the cyclin D1/p27 ratio. Increasing YAP activity by ablating the suppressor Merlin/NF2 reveals a balancing mechanism whereby YAP suppression and contact inhibition of proliferation can be recovered but only at higher local cell density. Thus, critical for regeneration, robust proliferation responses result from the YAP-induced and receptor-mediated prolonged increase in the cyclin D1/p27 ratio, which is reversed by delayed suppression of receptor signaling after contact inhibition of YAP.

overall_design: RNA-seq profiling of G0/G1-arrested 1) wildtype (WT) with 0-6h YAP activation by LATS1/2 inhibition, 2) doxycycline-inducible YAP5SA (constitutively active YAP, 'CAYAP') retinal pigmented epithelial cells (hTERT-immortalized) with 0-36h activation of YAP signaling, and 3) Merlin knockout (Merlin KO) cells. Cells were plated with high density seeding (38,000 cells/well, 96-well plate) and arrested with CDK4/6 inhibitor (1 µM, palbociclib) and preconditioned either in starvation media (0.1% serum) or 1.0% serum for 28 hours. WT cells were then treated DMSO or LATS inhibitor (TRULI, 5 µM) for 0, 3, or 6h in starvation or 1.0% serum media (containing CDK4/6 inhibitor). YAP5SA cells were induced with doxycycline ( µg/mL) for 0, 6, 12, 24, or 36h in starvation or 1.0% serum media (containing CDK4/6 inhibitor). A total of 63 samples containing triplicates were analyzed.

first: Katherine

last: Ferrick

first: Nalin

last: Ratnayeke


title: Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Properties [bulkRNA_isolatedBrainParenchymalMacrophages]

first: Jonathan

last: Kipnis

summary: Microglia arise from yolk sac (YS) progenitors and are thought to persist throughout life with minimal input from adult hematopoiesis. However, whether brain-engrafted monocyte-derived macrophages (MDM) exist at homeostasis and during turnover, and how they function relative to yolk sac-derived microglia (YSM) remain unsettled. Here, we combine lineage tracing, pharmacological microglia depletion, and multi-omics profiling to define the ontogeny, identity, and function of MDM in the mouse brain. Despite sharing the parenchymal milieu, MDM display unique transcriptional and epigenetic landscapes distinct from YSM. Fate-mapping reveals that newly engrafted MDM transiently express CD206, echoing a developmental stage of embryonic microglial precursors. The engraftment and polarization of MDM are modulated by the CSF1R ligand IL 34 and the chemokine receptor CCR2. Furthermore, parabiosis and skull‑flap transplantation reveal that both blood and skull marrow supply the niche via distinct routes, yielding origin‑biased MDM states. Functionally, engraftment of MDM exacerbates cuprizone-mediated demyelination. Together, our study reveals the cellular dynamics of brain parenchymal macrophages at homeostasis and during turnover. We define the core molecular features and heterogeneous origins of MDM and imply their context-dependent roles in CNS pathology.

overall_design: For RNA isolation of sorted cells, brain parenchymal macrophages were purified from PLX5622-treated or IR-BMT-treated mouse brains using FACSAria II (BD Biosciences) as live, negative for Ly6C, Ly6G, CD206, CD44; positive for CD45 and CD11b. From the brain parenchymal macrophage gate, tdTomato+ and tdTomato- macrophages were sorted into different tubes containing cold RLT Plus buffer (from RNeasy Micro Plus Kit, RQiagen) supplied with 2-Mercaptoethanol (Sigma).

first: Siling

last: Du

first: Feiya

last: Ou

first: Antoine

last: Drieu

first: Eric

last: Xu

first: Yumeng

last: Cheng

first: Steffen

last: Storck

first: Tornike

last: Mamuladze

first: Jay

last: Cao

first: Nora

last: Abduljawad

first: Bishan

last: Bhattarai

first: Justin

last: Rustenhoven

first: Niall

last: Mortimer

first: Simone

last: Brioschii

first: Khai

last: Nguyen

first: Patrick

last: Rodrigues

first: Igor

last: Smirnov

first: Daniel

last: Gibson

first: J

last: White

first: Wandy

last: Betty

last: DeNardo

first: Qingyun

last: Li

first: Michael

last: Meers

first: Claudia

last: Han

last: Sun

first: Florent

last: Ginhoux

first: Marina

last: Cella

first: Marco

last: Colonna


title: Intra-tumoral microbiota and host genotype cooperatively shape neutrophil antitumor activity in colorectal cancer

city: Trento

first: Fulvio

last: Chiacchiera

address: Via Sommarive  9

department: Department of Cellular, Computational and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

summary: The role of tumor-associated neutrophils (TANs) infiltrating colorectal cancers is still debated.Here we unravel that TAN recruitment and functions are modulated by intra-tumoralmicrobiota and only defined bacterial species are able to unleash TANs’ antitumor potential.Fusobacterium nucleatum (Fn) promotes production of neutrophil-recruiting chemokines bytumor cells and enhances neutrophil migration more efficiently than Bacteroides fragilis (Bf).Importantly, Fn, but not Bf, triggers neutrophils to release cytotoxic proteins showingtumoricidal activity in vitro and in xenograft models. Mechanistically, these antitumor effectsare elicited upon Fn binding to Siglec-14 expressed by neutrophils but are impaired uponSiglec-14 blockade or loss-of-function polymorphism. Supporting these findings, in humanCRCs, elevated Fn loads, high TANs densities, and expression of wild-type, but notpolymorphic, Siglec-14 allele, correlate with improved patient survival.Our findings identify microbiota composition and host genetic background as criticaldeterminants of TAN functional profiles and offer insights into neutrophil-targetedtherapeutic strategies in CRC.

overall_design: We performed single cell RNA-seq (WTA BD Rhapsody™) of non-stimulated, Fn-stimulated, and  Bf-stimulated neutrophils from Siglec-14 WT or -Null donors (total of 6 samples).

first: Elisa

last: Sorrenti

first: Valeria

last: Governa

first: Giandomenica

last: Iezzi


title: Cortistatin antagonizes Piezo1-STING axis and facilitates mitochondrial homeostasis of keratinocytes by attenuating AGEs accumulation in diabetic ulcers

first: Qinghao

last: Yuan

first: qinghao

last: yuan

first: guoli

last: ma

first: wenke

last: zhao

first: ben

last: liu

first: yonggang

last: li

first: jingwei

last: bi


title: Longitudinal transcriptomic profiling of splenic CD8 T cells in Nr4a1-KO mice during Mtb infection

city: Singapore

first: Amit

last: Singhal

address: 8A Biomedical Grove, Immunos #05-13

department: A*STAR Infectious Diseases Labs (ID Labs)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

summary: We used bulk RNA sequencing (RNA-seq) to study the role of Nr4a1 in splenic CD8 T cells of Mtb-infected mice.

overall_design: CD8 T cells from infected and uninfected WT and Nur77-KO mice spleen at different time points (uninfected, 2wk, 4wk, and 8wk post infection; n=3 per group) were isolated and analyzed using bulk RNA-seq.

first: Yao

last: Chen


title: Single-cell transcriptomic analysis of lung T cells in Nr4a1-KO mice during Mtb infection

summary: We used single-cell RNA sequencing (scRNA-seq) to study the role of Nr4a1 in lung T cells of Mtb-infected mice.

overall_design: CD90.2 T cells from infected and uninfected WT and Nur77-KO mice lung (n=8) were sorted and analyzed using FLEX scRNA-seq.


title: Elevated Lactate in AML Bone Marrow Contributes to Macrophage Polarization via GPR81 Signaling

city: Rochester

first: Benjamin

last: Frisch

address: 601 Elmwood Ave

institute: University of Rochester School of Medicine and Dentistry

summary: Interactions between acute myeloid leukemia (AML) and the bone marrow microenvironment (BMME) are critical to leukemia progression and chemoresistance. In the solid tumor microenvironment, altered metabolite levels contribute to cancer progression. We performed a metabolomic analysis of AML patient bone marrow serum, revealing increased metabolites compared to age- and sex-matched controls. The most highly elevated metabolite in the AML BMME was lactate. Lactate signaling in solid tumors induces immunosuppressive tumor-associated macrophages and correlates with poor prognosis. This has not yet been studied in the leukemic BMME. Herein, we describe the role of lactate in the polarization of leukemia-associated macrophages (LAMs). Using a murine AML model of blast crisis chronic myelogenous leukemia (bcCML), we characterize the suppressive phenotype of LAMs by surface markers, transcriptomics, and cytokine profiling. Then, mice genetically lacking GPR81, the extracellular lactate receptor, were used to demonstrate GPR81 signaling as a mechanism of both the polarization of LAMs and the direct support of leukemia cells. Furthermore, elevated lactate diminished the function of hematopoietic progenitors and reduced stromal support for normal hematopoiesis. We report microenvironmental lactate as a mechanism of AML-induced immunosuppression and leukemic progression, thus identifying GPR81 signaling as an exciting and novel therapeutic target for treating this devastating disease.

overall_design: Bone marrow macrophages (CD45+/F4/80+/Ly6g-/Ly6c-) sorted by FACS from healthy or Leukemic mice. Leukemic mice were at a late stage of disease following transplantation with bcCML model leukemic cells.

first: Celia

last: Soto

first: Maggie

middle: L

last: Lesch

first: Jennifer

last: Becker

first: Azmeer

last: Sharipol

first: Amal

last: Khan

first: Xenia

last: Schafer

first: Zhewen

last: Li

first: Amanda

last: Streeter

first: Michael

first: Joshua

last: Munger


title: Spatial transcriptomic profiling of human saphenous vein grafts reveals molecular remodeling and smooth muscle cell phenotypic transition during early neointima proliferation

city: Augusta

first: David

last: Kim

state: GA

department: Vascular Biology Center

institute: Augusta University

summary: Vein graft failure is driven by early neointima l proliferation involving vascular smooth muscle cell (VSMC) proliferation, inflammation, and extracellular matrix remodeling. To elucidate the spatial and transcriptional landscape of this process, we performed spatial transcriptomic profiling of ex vivo cultured human saphenous vein segments at baseline (Day 0) and after 7 days in organ culture. Integration of spatial gene expression with histological features revealed distinct zones of VSMC transdifferentiation, inflammatory activation, and extracellular matrix reorganization. This dataset provides a resource for investigating molecular mechanisms underlying early human vein graft adaptation and neointimal proliferation.

overall_design: Spatial transcriptomic analysis was performed on freshly harvested (Day 0) and ex vivo cultured (Day 7) human saphenous veins using the 10x Genomics Visium platform. Sections were collected from three biological replicates per time point and processed for library preparation and sequencing on the Illumina NovaSeq 6000 platform.

first: Vy

last: Ong

first: Jiang

last: Zhou

first: Yang

last: Shi

first: Austin

last: Chang

first: Neal

last: Weintraub


title: Whole transcriptome sequencing of UPEC-infected testis and epididymis (5d) following depletion of CX3CR1+ macrophages

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

summary: A finely tuned immune regulation within the epididymis and testis—balancing tolerance towards sperm with effective defense against infections—is essential for maintaining male fertility. This balance is especially critical in the epididymis, where sperm mature and where it is often disrupted during ascending urogenital infections. While testicular inflammation is typically reversible, the epididymis undergoes irreversible tissue remodeling, particularly in distal regions, whereas proximal regions remain mostly unaffected despite bacterial presence.  We previously identified that each epididymal region has a unique immunological landscape, distinct from that of the testis. Notably, CX3CR1⁺ macrophages are the dominant immune cell type and appear central to maintaining homeostasis and orchestrating immune responses in a region-specific manner.  To assess their functional role, we used a transgenic mouse model to deplete CX3CR1⁺ macrophages under steady-state and infected conditions. Whole-transcriptome analysis following E. coli infection revealed downregulation of genes linked to innate immunity and cytokine regulation, indicating that CX3CR1⁺ macrophages restrain excessive inflammation—particularly in proximal regions.  Combined with histological and cellular phenotyping, our data highlight a key role for CX3CR1⁺ macrophages in preserving epithelial integrity and modulating immune responses during infection.

overall_design: Intraepithelial CX3CR1+ macrophages  were selectively depleted using Cx3cr1CreERT2/+Rosa26iDTR/tdTomato transgenic mice). After Dtx-mediated depletion of CX3CR1+ macrophages, an acute bacterial epididymitis was elicited by intravasal injection of uropathogenic Escherichia coli. Testes, proximal and distal epididymal regions were collected for whole transcriptome analysis 5 days after infection. Mice treated solely with Tamoxifen (for induction of DTR expression under the CX3CR1+ promotor control) without subsequent Dtx treatment served as comparator.

first: Christiane

last: Pleuger

first: Tara

last: Procida-Kowalski

first: Linda

last: Kreyling

first: Andreas

last: Meinhardt


title: Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Properties [bulkRNA_braintissue]

first: Jonathan

last: Kipnis

overall_design: For RNA isolation from brain tissue, the forebrain of NT-, PLX-1x-, IR-BMT- and PLX-3x-treated mice was dissected and snap-frozen on dry ice. Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) following the manufacturer’s protocol with minor modifications.

first: Siling

last: Du

first: Feiya

last: Ou

first: Antoine

last: Drieu

first: Eric

last: Xu

first: Yumeng

last: Cheng

first: Steffen

last: Storck

first: Tornike

last: Mamuladze

first: Jay

last: Cao

first: Nora

last: Abduljawad

first: Bishan

last: Bhattarai

first: Justin

last: Rustenhoven

first: Niall

last: Mortimer

first: Simone

last: Brioschii

first: Khai

last: Nguyen

first: Patrick

last: Rodrigues

first: Igor

last: Smirnov

first: Daniel

last: Gibson

first: J

last: White

first: Wandy

last: Betty

last: DeNardo

first: Qingyun

last: Meers

first: Claudia

last: Han

last: Sun

first: Florent

last: Ginhoux

first: Marina

last: Cella

first: Marco

last: Colonna


title: Single-cell transcriptome profiling of Oryza sativa node I at booting, flowering, and grain filling stages

city: KunMing

first: Hu

last: Li

state: Yunnan

address: Yunnan University

institute: agricultural college

summary: This dataset provides processed snRNA-seq gene expression data in the standard 10x Genomics CellRanger output format, including three core files: barcodes.tsv.gz (with quality-controlled nucleus-specific barcodes, matching expression matrix column order), features.tsv.gz (gene annotations: Ensembl ID, gene symbol, "Gene Expression" type, matching matrix row order), and matrix.mtx.gz (sparse MTX-format raw UMI count matrix, m×n dimensions where m=gene number, n=nucleus number, storing non-zero values as [gene_index][barcode_index][count]). These files together form a complete expression matrix and serve as fundamental input for downstream analysis via tools like Seurat and Scanpy.

overall_design: SnRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) on a Chromium Controller. Nuclei were isolated from node I and resuspended in PBS containing 0.04% BSA. Nuclei from each developmental stage were separately loaded onto the Chromium Next GEM Chip G to generate single-cell gel beads in emulsion (GEMs), according to the manufacturer's instructions. The captured nuclei were subsequently lysed, and the released RNA underwent reverse transcription to produce barcoded, full-length cDNA. Libraries were constructed following the protocol provided by the reagent kit. The quality of the libraries was assessed using the Qubit 4.0 Fluorometer and the Agilent 2100 Bioanalyzer. Sequencing was performed on the Illumina NovaSeq 6000 platform, achieving a sequencing depth of at least 50,000 reads per nucleus, with paired-end 150 bp (PE150) reads.

first: Guijie

last: Lei


title: Gene differences between chemoresistant and chemosensitive variants of the human bladder cancer cell line T24

city: Chongqing

first: Weiyang

last: He

state: chongqing

address: No.1 Youyi Road, Yuzhong District

institute: The First Affiliated Hospital of Chongqing Medical University

summary: The chemoresistant cell line was established using a concentration-gradient increment method. Transcriptome sequencing was performed after stable resistance was achieved to identify differentially expressed genes.

overall_design: The chemoresistant cell line was developed by repeatedly exposing the chemosensitive human bladder cancer cell line T24 to increasing concentrations of the chemotherapeutic drug. This cyclic process of treatment, followed by outgrowth of surviving resistant cells, was continued until a stably resistant cell population was established.

first: Yan

first: Tinghao

last: LI

first: Junlong

last: Zhu

first: Xiaoyu

last: Zhang

first: Linfeng

last: Wu

first: Kunyao

first: Aimin

last: Wang


title: ZM-306416 prevents ovariectomy-induced bone loss by promoting osteoblastogenesis and inhibiting osteoclastogenesis - bone marrow-derived macrophages

city: Guangzhou

first: Shuo

last: Shi

state: Guangdong Province

address: No.1023, South Shatai Road Baiyun District

department: School of Basic Medical Sciences

institute: Southern Medical University

summary: Osteoporosis affects millions of people worldwide, and current medications like bisphosphonates and denosumab are not effective enough in reversing bone loss. Moreover, these treatments have drawbacks, including jaw osteonecrosis and skin eczema. Hence, there is an urgent need for new drugs to treat osteoporosis. Drug library screening was performed by alkaline phosphatase (ALP) staining in osteoblasts to identify potential candidates for osteoporosis. qPCR, Western blot, ALP staining, alizarin red staining, and TRAP staining were conducted to assess the impact of ZM-306416 (ZM) on osteoblast and osteoclast differentiation in vitro. Additionally, RNA sequencing and pathway analysis were carried out to explore molecular mechanisms. Micro-CT scan and immunostaining were used to determine bone phenotypes in vivo. Drug library screening demonstrated that ZM enhances ALP activity in osteoblasts, indicating its potential as a pro-osteogenic agent. ZM exerts dual effects by promoting osteoblast differentiation through the Wnt/β-catenin signaling pathway and simultaneously inhibiting osteoclast differentiation by the NF-κB and MAPK signaling pathways. In an OVX mouse model, ZM effectively prevents bone loss by stimulating osteoblast formation and inhibiting osteoclast development. Our study revealed that ZM has a dual anti-osteoporosis effect by promoting osteoblastogenesis and inhibiting osteoclastogenesis, mediated via activation of Wnt/β-catenin signaling and suppression of NF-κB/MAPK cascades. These findings suggest that ZM could be a promising therapeutic strategy for alleviating osteoporosis.

overall_design: RNA-seq profiling was performed on bone marrow-derived macrophages (osteoclast precursor cells, induced for osteoclast differentiation). The cells were cultured in a complete α-MEM medium containing 10% FBS, supplemented with 30 ng/mL M-CSF and 100 ng/mL RANKL (key factors for osteoclast differentiation); those treated without 10 μM ZM served as the control group, and those treated with 10 μM ZM were the intervention group. Both groups were cultured for 2 days before RNA - seq analysis.

first: Jun

last: Chang

first: Junqi

last: Chen

first: Yicheng

first: Deijian

last: Yang

first: Tianyu

first: Wenquan

last: Liang


title: ALS molecular subtypes are a combination of cellular, genetic, and pathological features learned by deep multiomics classifiers (post-mortem cortex)

first: Hemali

last: Phatnani

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Amyotrophic Lateral Sclerosis (ALS) is a complex syndrome with multiple genetic causes and wide variation in disease presentation. Despite this general heterogeneity, several common factors have been identified. For example, nearly all patients show pathological accumulations of phosphorylated TDP-43 protein in affected regions of the motor cortex and spinal cord. Moreover, large patient cohort studies have revealed that most patient samples can be grouped into a small number of ALS subtypes, as defined by their transcriptomic profiles. These ALS molecular subtypes can be grouped by whether postmortem motor cortex samples display signatures of: mitochondrial dysfunction and oxidative stress (ALS-Ox), microglial activation and neuroinflammation (ALS-Glia), or dense TDP-43 pathology and associated transposable element de-silencing (ALS-TE). In this study, we have built a deep layer ALS neural network classifier (DANcer) that has learned to accurately assign patient samples to these ALS subtypes, and which can be run on either bulk or single-cell datasets. Upon applying this classifier to an expanded ALS patient cohort from the NYGC ALS Consortium, we show that ALS Molecular Subtypes are robust across clinical centers, with no new subtypes appearing in a cohort that has quadrupled in size. Signatures from two of these molecular subtypes strongly correlate with disease duration: ALS-TE signatures in cortex and ALS-Glia signatures in spinal cord, revealing molecular correlates of clinical features. Finally, we use single nucleus RNA sequencing to reveal the cell type-specific contributions to ALS subtype, as determined by our single-cell classifier (scDANCer). Single-cell transcriptomes reveal that ALS molecular subtypes are recapitulated in neurons and glia, with both ALS-wide shared alterations in each cell type as well as ALS subtype- specific alterations. In summary, ALS molecular subtypes: (1) are robust across large cohorts of sporadic and familial ALS patient samples, (2) represent a combination of cellular, genetic, and pathological features, and (3) correlate with clinical features of ALS.

overall_design: Expression profiling by high throughput RNA sequencing of ALS patients

first: Maria

middle: H

last: Pedersen

first: Andrew

last: Rice

first: Alexi

last: Runnels


title: Mitochondrial function licenses oocyte fate via TORC1 activation in Drosophila [RNA-Seq]

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

summary: Mitochondrial dysfunction is associated with infertility and primary ovarian insufficiency (POI), yet if and how mitochondrial activity influences oocyte formation has remained unclear. We identify a metabolic check point that links mitochondrial function to oocyte fate. When mitochondrial activity is disrupted, germ cells fail to develop into oocytes. Mitochondria sustain intracellular leucine levels that activate the nutrient-sensing kinase Target of Rapamycin Complex 1 (TORC1), enabling translation of chromatin regulators that silence germ-cell programs and establish oocyte identity. Loss of mitochondrial function depletes leucine, suppresses TORC1 signaling, and arrests oocyte differentiation, whereas removal of the leucine sensor Sestrin restores both TORC1 activity and oocyte development. This metabolic check point ensures that only germ cells with functional mitochondria contribute to the maternal lineage, preserving reproductive fidelity.

overall_design: RNA-seq was performed on duplicates of each genotype: Control: rpS19b-GFP/CyO;nosGAL4, rpS19b-GFP/CyO;nosGAL4>afg3l2 GKD ovaries, and rpS19b-GFP/CyO;nosGAL4>complex v GKD ovaries.

first: Lina

last: Park

first: Anupriya

last: Ramamoorthy

first: Vernon

last: Monteiro

first: Pooja

last: Flora

first: Gulay

middle: B

last: Ulukaya

first: Julia

last: Tang

first: Dan

last: Hasson

first: Daria

last: Siekhaus

first: Deepika

last: Vasudevan

first: Thomas

last: Hurd

first: Prashanth

last: Rangan


title: Benchmarking urinary cell transcriptomes for noninvasive differentiation of BK polyomavirus-associated nephropathy from T cell-mediated rejection

first: Manikkam

last: Suthanthiran

state: New York

address: 1300 York Ave, Rm A569

department: Nephrology and Hypertension

institute: Weill Cornell Medicine

summary: BK polyomavirus-associated nephropathy (BKVN) adversely impacts kidney allograft survival and often mimics acute T cell-mediated rejection (TCMR), confounding diagnosis and management. To address this conundrum, we performed unbiased RNA sequencing of urinary cells matched to biopsies classified as BKVN with intragraft inflammation (BKVN-P), BKVN without inflammation (BKVN-N), TCMR, or no rejection (NR). BKVN-N displayed dominant host DNA replication, cell cycle, and repair programs, while BKVN-P samples exhibited expansive innate immune activation, antigen presentation, chemokine upregulation, and epithelial injury. Both BKVN subtypes shared signatures of T cell exhaustion and mature and tolerogenic dendritic cell activation but differed in immune orientation—Th1 predominance in BKVN-N versus Treg and CD8 enrichment in BKVN-P. Compared to TCMR samples, BKVN-P lacked robust TCR/CD28 signaling and was enriched for viral and innate modules; BKVN-N lacked alloimmune activation. B cell exhaustion characterized BKVN-N, while BKVN-P displayed robust B cell activation with metabolic downregulation. A ratiometric urinary cell biomarker, CXCL10 mRNA/CD3E mRNA, distinguished both BKVN subtypes from TCMR with diagnostic accuracy, replicated by RT-qPCR for clinical translation, and confirmed in an independent cohort. These findings demonstrate the utility of urinary cell transcriptomics for resolving viral injury from alloimmunity, enabling precision diagnostics and targeted immunomodulation in kidney transplantation.

overall_design: RNA-seq profiling of urine specimens matched to kidney allograft biopsies classified as BKVN with BKVN-P and BKVN-N, TCMR, and NR.

first: Mueller

last: Franco B.

first: Li

last: Carol

first: Dadhania

last: Darshana M

first: Seshan

last: Surya V.

first: Salinas

last: Thalia

first: Sharma

last: Vijay K.

first: Xiang

last: Jenny Z.

first: Hirsch

last: Hans H.

first: Muthukumar

last: Thangamani

first: Suthanthiran

last: Mannikkam


title: Cisplatin-based chemoradiation induces delayed systemic tumor-specific T cells expansion in patients with locally advanced head and neck cancer

city: Besançon

first: Olivier

last: Adotévi

state: Franche-Comté

address: 8 rue du Dr JFX Girod

department: Oncology

country: France

institute: Université de Franche-Comté

summary: Cisplatin-based concurrent chemoradiation (CRT) remains the standard therapy for locally advanced head and neck squamous cell carcinoma (LA-HNSCC), yet recurrence rates remain high. Immune checkpoint inhibitors (ICIs) combined with CRT have not improved patient outcomes so far, emphasizing the need to elucidate CRT’s immunological effects. We performed longitudinal, multidimensional immune profiling of peripheral blood lymphocytes from patients with LA-HNSCC at baseline (BSL), one month (CRT-1M), and three months (CRT-3M) after cisplatin-based CRT. CRT induced a transient decline in tumor-specific T cells at CRT-1M, followed by a robust expansion at CRT-3M. Transcriptomic analyses revealed an early shift from B cell–associated to T cell–mediated immune pathways, sustained over time. Genes involved in T-cell activation, polarization, and exhaustion exhibited a biphasic expression pattern, with a delayed increase at CRT-3M, coinciding with the emergence of a proinflammatory cytokine milieu. In parallel, CRT expanded circulating immunosuppressive populations, suggesting a compensatory regulatory response. Integrated immune analyses identified distinct post-CRT signatures, with delayed tumor-reactive T-cell expansion and elevated proinflammatory cytokines correlating with favorable clinical outcomes. These findings reveal dynamic and temporally coordinated systemic immune remodeling following CRT and highlight a delayed activation phase that may represent an optimal window for ICI-based combination strategies in LA-HNSCC.

overall_design: To explore transcriptional factors influencing tumor-specific T cell responses during CRT, bulk RNA-sequencing (RNA-seq) was performed on peripheral blood mononuclear cells (PBMCs) from HNSCC patients undergoing CRT. PBMCs were collected at three time points: before the start of treatment (baseline, BSL), one month after the beginning of CRT (CRT-1M), and three months after the beginning of CRT (CRT-3M). Bulk RNA-seq analysis was performed on the BSL, CRT-1M and CRT-3M PBMC samples from 11 patients.

first: Benoît

last: Lecoester

first: Yaoyao

last: Xie

first: Babacar

last: Ndao

first: Adeline

last: Renaudin

first: Laura

last: Boullerot

first: Marine

last: Malfroy

first: Jihane

last: Boustani

last: Adotevi


title: Disrupting SCD acitivty supresses prostate cancer progression in bone through modulating cellular stress, mTOR signaling and DNA damage

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

summary: The mechanisms supporting progression of metastatic prostate cancer (PCa) in adipocyte-rich bone marrow remain unclear. We hypothesized that Stearoyl-Coenzyme A Desaturase (SCD) promotes PCa survival in bone by modulating stress responses and regulating lipid peroxidation.  We show that SCD-high PCa cells are sensitive to SCD loss, showing smaller spheroids, reduced mTOR signaling, and elevated ER stress. SCD expression is further augmented by adipocytes, and SCD loss induces DNA damage and repair activation only with adipocyte exposure. In vivo, pharmacological SCD inhibition reduces tumor size and increases ER stress and DNA damage in SCD-overexpressing bone tumors. These findings suggest SCD plays a role in redox regulation and DNA repair sensitivity, with therapeutic potential for targeting DNA repair pathways in combination with SCD inhibition.

overall_design: RNA-seq profiling of prostate cancer cells in alone conditions and adipocyte (TW) co-cultures and with or without treatment of SCD inhibitor (CAY10566 at 1 uM) for 48 hours.

first: Alexis

last: Wilson

first: Mackenzie

middle: K

last: Herroon

first: Mecca

last: Shane

first: Garmo

last: Laimar

first: Lindquist

last: Jacob

first: Rajendran

last: Shrila

first: Steve

last: Patrick

first: Podgorski

last: Izabela


title: Glycine max JmjC domain-containing proteins JMJ19/20 exhibit endopeptidase activity and interact with LUXs to mediate flowering time [RNA-seq]

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

summary: Histone demethylases serve essential functions in plant growth and development across various species. However, their roles in Glycine max remain largely unexplored. This study identified GmJMJ19 and GmJMJ20, encoding JmjC domain-containing proteins. They exhibit circadian rhythmic expression patterns and interact with LUX ARRHYTHMO 2 (GmLUX2) both in vitro and in vivo. Although GmJMJ19/20 bind to histones, they lack conventional histone demethylase activity. Rather, GmJMJ19/20 function as endopeptidases that specifically cleave histone H3 peptides at unmethylated lysine 27 residues, in a manner independent of Fe²⁺ and α-ketoglutarate (α-KG), the cofactors required for typical JmjC enzymes. Structural modeling supports the occlusion of the catalytic pocket that prevents access to methylated substrates. The simultaneous knockout of GmJMJ19/20 significantly delays flowering time. Comparative transcriptomic analyses reveal that the GmJM19/20-GmLUX2 module enhances GmFULc expression via independent of the canonical evening complex. Haplotype analysis suggests that GmJMJ19 underwent selection during domestication, potentially contributing to soybean geographical adaptation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 17-day-old leaves of Williams 82, lux1lux2 and gmjmj1920-2

first: Yapeng

last: Han

first: Yingxiang

last: Wang


title: Noncoding SNP rs17728461 modulates lung cancer progression via interchromosomal regulation of RAB27A expression

city: hangzhou

first: Bing

last: guo

state: zhejiang

address: cangqian street No.2318

department: school of Basic Medical Sciences

institute: HZNU

summary: To examine target genes that interact with different alleles of rs17728461 in H155 (G/G、CC) 、A549(G/G、CC、C/G、sg）cells

overall_design: H155 (G/G、CC) 、A549(G/G、CC、C/G、sg） cells were used to performed allele-specific 4C. Hind III and Dpn II were used in the experiments

first: Yan

last: Jin

first: Xiaoling

last: Tian

last: Guo

first: Wenxu

last: Liu


title: Mitochondrial function licenses oocyte fate via TORC1 activation in Drosophila [CUT&Run]

first: BiNGS

last: Core

overall_design: Sequencing of  samples after performing CUT&RUN on mio GKD ovaries, afg3l2 GKD ovaries and WT ovaries for the histone marks: H3k9me3 and H3k27me3

first: Lina

last: Park

first: Anupriya

last: Ramamoorthy

first: Vernon

last: Monteiro

first: Pooja

last: Flora

first: Gulay

last: Ulukaya

first: Julia

last: Tang

first: Dan

last: Hasson

first: Daria

last: Siekhaus

first: Deepika

last: Vasudevan

first: Thomas

last: Hurd

first: Prashanth

last: Rangan


title: Transcriptomic Changes in the Lacrimal Glands of a Sjogren's Disease Animal Model Highlight Key Molecular Mediators and Altered Biological Functions Underpinning Glandular Inflammation and Hypofunction

city: Boston

first: Danny

last: Toribio

state: MA

address: One Kneeland St

department: Basic and Clinical Translational Sciences

institute: Tufts University School of Dental Medicine

summary: Sjogren’s disease (SjD) is a chronic autoimmune condition that targets the lacrimal glands (LGs), resulting in aqueous-deficient dry eye disease (DED). Insufficient or low-grade tear secretion onto the ocular surface affects the normal physiology of the cornea and conjunctiva and can result in ocular surface damage. Herein, we evaluated the transcriptomic profiles of diseased versus healthy LGs to investigate the underlying molecular mechanisms underscoring LG autoimmune inflammation and secretory hypofunction. The number of differentially expressed genes between NOR (diseased animal model/strain) and BALB/c (control strain) mice increased in correlation with the development and progression of dacryoadenitis. The most significantly upregulated pathways were primarily related to immune responses, emphasizing the activation of cellular and cytokine-mediated inflammatory responses. Several cytokines, transcription factors, and toll-like receptors were significantly predicted to drive most of the differential gene expression observed across our datasets. Biological processes involving the migration, recruitment, and activation of lymphocytes, but also lipid metabolism, were most significantly impacted in our disease model. Many of the identified dysregulated genes and affected biological functions were similarly regulated in the differential expression datasets of other transcriptomic based studies of SjD patients and mouse models. Taken together, our data reveals that chronic inflammation induces significant alterations to the LG transcriptome, promoting the recruitment of immune cells into the LG and the overactivation of inflammatory responses that severely impedes normal secretory function. Future studies targeting some of the discovered key dysregulated molecules/pathways could open up potential therapeutic avenues for the treatment of chronic LG inflammation and secretory hypofunction.

overall_design: Bulk RNA-seq profiling of lacrimal glands removed from NOR/LtJ mice (Sjogren's disease mouse model) and sex- and age-matched BALB/c controls (normal, wild-type control for the NOD/NOR strains). Three biological replicates were used for the NOR and BALB/c strains at three different timepoints: 3-weeks of age (pre-disease stage), 8-weeks of age (early disease onset), and 16-weeks of age (intermediately advanced disease stage).

first: Junji

last: Morokuma

first: Albert

last: Tai

first: Driss

last: Zoukhri


title: Single-cell RNA-seq of immune and stromal cells from murine muscle injury and foreign body response to synthetic biomaterial implants

city: Baltimore

first: Jennifer

last: Elisseeff

state: MD

address: 1800 Orleans St

institute: Johns Hopkins

summary: The main objective of this study is to characterize the immune and stromal cell response to tissue injury and the foreign body response (synthetic polycaprolactone PCL implant). We enrich CD45+ immune cells  from injured murine muscles with  fibrotic PCL implants (6 week time point) and perform transcriptomic profile using single-cell RNA-sequencing.

overall_design: PCL particulate was implanted into hindlimb volumetric muscle loss (VML) defects in C57BL/6 wildtype (WT) mice for 6 weeks. CD45+ immune cells and CD45- stromal cells were separated using MACS with CD45 microbeads, then mixed in a 1:1 ratio to enable CD45+ immune cell enrichment. The samples were processed for single-cell RNAseq for transcriptomic profiling.

first: Anna

last: Ruta

first: Joscelyn

last: Mejias

first: Kavita

last: Krishnan

first: Alexandra

last: Rindone

first: Frank

last: Yu

first: Christopher

last: Cherry

first: Michael

last: Patatanian


title: Assessing Senescence in ASC Product and Discovery of Potential Biomarkers

city: København S

first: Tu

last: Hu

address: Oxford Have 73

country: Denmark

institute: True Signal

summary: Adipose-tissue derived stromal cells (ASC) are used in advanced therapy medicinal products due to their regenerative and immunomodulatory properties. Increasing the number of dosages derived from each donor product is essential to reduce variability and improve scalability of cell therapy. However, extended in vitro expansion may induce cellular senescence, potentially compromising therapeutic efficacy. This study aimed to assess the remaining proliferative potential of a cryopreserved ASC product and identify robust transcriptomic biomarkers of senescence.

overall_design: ASC from five donors were cultured post-thaw until replicative senescence or passage 10. Morphology, growth kinetics, and confluence were monitored. Bulk RNA sequencing was performed on samples from passage 1, 3, 6, and final passage.

first: Ellen

last: Johansen

first: Cecilie

last: Hoeeg

first: Rebekka

last: Søndergaard

first: Lisbeth

last: Højgaard

first: Laura

last: Lethager

first: Stine

last: Bangsgaard

first: Jens

last: Kastrup

last: Litman

first: Morten

last: Nørgaard


title: A renal function for Nuclear Factor Of Activated T Cells 5 (NFAT5)

city: Berlin

first: Robert

last: Labes

address: Charitéplatz 1

department: Institute of Translational Physiology

institute: Charité - Universitätsmedizin Berlin

summary: Osmotic stress represents a major challenge to cells, particularly in the kidney, where tonicity gradients are both physiologically relevant and pathologically altered. The transcription factor NFAT5 is a key regulator of the osmoadaptive response, yet its downstream metabolic effectors remain incompletely understood.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MEF cells under control or hyperosmolar conditions with and without NFAT5 knockdown.

last: Faehling


title: Soluble Notch Agonist Enables Human Ameloblast Maturation and Enamel-like Tissue Formation for Tooth Regeneration

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: UW Medicine at South Lake Union, 850 Republican Street

department: Department of Biochemistry

institute: University of Washington

summary: Enamel, the hardest material in the human body, is required to protect the living organ, tooth. However, over 90% of adults have lost or damaged enamel and cannot regenerate the protective structure due to lack of enamel producing cells, ameloblasts. iPSC derived secretory Ameloblasts (isAM) have promise in future regenerative dentistry. Today it is not known why iAM maturation requires intimate contact with the dentin producing cell type, odontoblast. Here we reveal that one of the critical signaling ligands emanating from odontoblasts for ameloblast maturation is Delta, the ligand for Notch receptor. We showed that our designed, soluble Notch agonist can induce iAM organoid maturation in an unprecedented manner, without interactions with odontoblast layer. Notably, soluble Notch agonist induces the iAM maturation to a novel, WDR72 positive mature secretory AM stage (ismAM) in our ameloblast organoid model. When transplanted under the kidney capsule of NOD-SCID mice, these ismAM organoids generated enamel-like calcified material, as confirmed by microCT analysis, marking the first demonstration that Notch-activated iAM organoids can form such tissue in vivo. This novel maturation procedure enabled us to analyze the specific requirements of DLX3 function in ameloblasts, independent of its known function in odontoblasts. We now show that DLX3, the gene associated with Amelogenesis Imperfecta, is required on a cell-autonomous manner in human ameloblasts for the expression of Enamelin, MMP20 and WDR72, a role not previously demonstrated in mouse models.

overall_design: RNA-seq profiling of wildtype induced secretory ameloblast organoids (isAM), C3-DLL4–treated wildtype isAM organoids (ismAM), and C3-DLL4–treated DLX3 knockout isAM organoids (DLX3_KO_ismAM)

first: Anjali

last: Patni

first: Rubul

last: Mout

first: Ammar

last: Alghadeer

first: Rachel

last: Moore

first: Samera

last: Nademi

first: Brandon

last: Ausk

first: Philippe

last: Huber

first: Riya

last: Keshri

first: Mary

last: Regier

last: Cornell

first: Ted

last: Gross

first: Benjamin

last: Freedman

first: George

middle: Q

last: Daley

first: David

last: Baker

first: Julie

last: Mathieu


title: Simplified Molecular Classification of Urothelial Carcinoma via Multi-Omic Profiling: Implications for Precision Therapy

city: Innsbruck

first: Florian

last: Handle

address: Josef-Wilberger-Str. 9a

country: Austria

institute: XPseq Analytics GmbH

summary: Urothelial carcinoma (UC) is a biologically heterogeneous disease and current molecular classification frameworks have limited integration into clinical decision-making. To foster precision oncology in UC, we developed a molecular classification framework of UC applicable to transcriptomic and proteomic data of non-muscle invasive bladder cancers (NMIBC), muscle-invasive bladder cancer (MIBC), and urothelial cancer cell lines. Using a whole-transcriptome self-organized map and regularized semi-supervised clustering ofn 4439 bulk NMIBC and MIBC transcriptomes and proteomes, and 33 UC cell lines, we identified three molecular UC clusters. The clusters had distinct signatures of mRNA, proteins, biological processes, metabolism, and essential driver genes. They also differed in prognosis and machine learning-predicted treatment vulnerabilities. High-risk stroma-rich cluster #1 cancers were predicted to respond to selected cytotoxic drugs, ferroptosis inducers, and PARP inhibitors. For the aggressive, fast proliferating and immune-infiltrated cluster #2 tumors with basal/squamous differentiation, cytotoxic agents and EGFR/ERBB- and MEK/ERK-targeting therapy was proposed. Cluster #3 cancers of predominantly luminal papillary phenotype, with scarce stroma and immune infiltration were enriched with NMIBC and low-risk malignancies. For cluster #3 patients, selected epigenetic drugs or EGFR/FGFR inhibitors may pose an attractive treatment option. This molecular taxonomy holds promise as a practical framework for patient stratification and therapeutic guidance in UC. Our molecular classification scheme may facilitate personalized transcriptome- and proteome-based risk assessment and therapy guidance, and the development of new cancer medication.

overall_design: The urothelial carcinoma cell lines UMUC3, 5637 and RT112 were treated with the EGFR inhibitors neratinib (600 nM) and afatinib (4 µM), the MAPK inhibitor trametinib (2 µM) and the FGFR inhibitor erdafitinib (7 µM) for 3 days. The concentration for each drug was selected based on the lowest IC50 value identified in proliferation assays.

first: Nils

last: van Creij

first: Zoran

last: Culig

first: Renate

last: Pichler


title: CyCLoPs: A approach for detecting immune responses with in vivo labeling of cytokine activity

city: Brookline

first: Guangqing

last: Lu

address: 1131 Beacon street, apt 4

institute: HMS

summary: Many studies have centered on delineating cytokine-producing cells, aiming for a comprehensive grasp of upstream signals and critical transcription factors linked to cytokine production. However, it is largely unknown which cell types respond to cytokines. Herein, we developed a reporter system, Cytokine-Cellular-Locating-Platforms (CyCLoPs), that transforms the cytokine and its receptor engagement into a genetically tractable signal. In vitro, CyCLoPs exhibited remarkable specificity, a high signal-to-background ratio, and broad applicability to probe interactions between cytokines and their receptors. In vivo, the IL-17A-CyCLoPs reporter mouse enabled the detection of IL-17A-responsive cells in the ilea, primarily located at the villi rather than the crypt, following colonization by a commensal bacterium. In addition, the IFN-γ-CyCLoPs mouse facilitated the identification of IFN-γ-exposed CD8+ T cells in tumors with reduced effector function. These CD8+ T cells were marked by various cell-surface proteins, such as CD36, CD38, and Leptin receptor, of which expression was dependent on IFN-γ. Thus, our developed CyCLoPs enable visualizing cytokine-induced responses at a single-cell resolution, paving the ways to investigate how cytokines produce distinct immunological outcomes in health and disease.

overall_design: RNA-seq profiles of sorted intestinal epithelial cells, and CD8 T cells isolated from spleen, mesenteric lymph node and tumor of CyCLoPs reporter mice

first: Shanshan

last: Zhang

first: Mengyang

last: Feng

first: Eunha

last: Kim

first: Daniel

last: Cho

first: Gloria

last: Choi

first: Jun

last: Huh


title: Regulation of Sodium/Calcium Homeostasis by BacNav Gene Therapy Rescues Cardiac Dysfunction in Chronic Heart Failure

city: Durham

first: Nenad

last: Bursac

state: NC

address: 101 Science Drive

institute: Duke University

summary: Despite continued progress, therapies to augment contractile function and prevent arrhythmias in patients with heart disease remain limited. Here, we present a two-pronged gene therapy approach whereby simultaneous augmentation of peak Na+ current and Ca2+ transient amplitude in cardiomyocytes (CMs) effectively alleviates pathogenesis of heart failure. Specifically, using in vitro engineered tissue models of neonatal rat CMs, ex vivo adult mouse CMs, and in silico rabbit CMs, we show that expression of prokaryotic Na+ channels (BacNav) dose-dependently enhances Ca2+ transient amplitude and contractility of CMs by modulating the activity of the Na+/Ca2+ exchanger and increasing sarcoplasmic reticulum Ca2+ stores. In vivo, AAV9-mediated BacNav therapy rescues contractile deficit and prevents arrhythmias in a pressure-overload induced model of chronic heart failure in mice. BacNav therapy also confers protective effects on pressure-overload induced dysregulation of the cardiac transcriptome. We further establish the safety of long-term systemic delivery of AAV9-BacNav in mice. Collectively, these studies support the translational promise of BacNav gene delivery as a novel therapy for electrical and contractile dysfunction in heart failure.

overall_design: Bulk RNA-sequencing from C57Bl/6J mouse ventricular tissues to assess BacNav gene therapy in a murine transverse aortic constriction model. Three groups were included: 1) Sham mice injected with PBS 2) TAC mice injected with AAV9-MHCK7-mScarlet 3) TAC mice injected with AAV9-MHCK7-BacNav-mScarlet

first: Tianyu

last: Wu

first: Yongwu

last: Li

first: Robin

last: Perelli

first: Yiu Yan

last: Siu

first: Anna

last: Tornatore

first: Josue

last: Nataren

first: Xixian

last: Jiang

first: Sophia

last: Deluca

first: Donald

last: Bers

first: Craig

last: Henriquez

first: Andrew

last: Landstrom


title: Glycine max JmjC domain-containing proteins JMJ19/20 exhibit endopeptidase activity and interact with LUXs to mediate flowering time [ChIP-seq]

first: Chenjiang

last: You

overall_design: Genomic occupancy of GmLUX2 in soybean leaves at ZT12 in W82 plants

first: Yapeng

last: Han

first: Yingxiang

last: Wang


title: Unraveling the Epigenetic Landscape of Sarcopenic Obesity: Insights into DNA Methylation Mechanisms from a Pilot Study in Older Women

city: Ribeirão Preto

first: Ana

middle: Claudia

last: Rossini Venturini

state: São Paulo

address: Av. Bandeirantes, 3900 - Vila Monte Alegre, Ribeirão Preto - SP,

department: EEFERP

country: Brazil

institute: USP

type: Methylation profiling by genome tiling array

summary: Epigenetic alterations, particularly DNA methylation, are recognized as robust biomarkers of ageing and have been associated with conditions such as obesity and sarcopenia. When these two conditions coexist, the result is sarcopenic obesity (SO), a functional and clinical condition characterized by excess fat mass and reduced muscle mass and function. Although cross-talk between muscle and fat tissue is thought to play a central role in SO pathophysiology, the epigenetic mechanisms involved remain poorly understood. Thus, this study aimed to investigate whole-blood DNA methylation patterns in older women with sarcopenic obesity, obesity, sarcopenia, and normal weight, as well as to explore the associated signaling pathways.

overall_design: 30 older women were classified into four groups: older women with sarcopenic obesity (n=8), obesity (n=8), sarcopenia (n=8) and normal weight (n=6) using body composition analysis, anthropometric measurements, and handgrip strength testing. DNA methylation patterns of whole blood samples were assessed using Illumina Infinium MethylationEPIC BeadChips (850K). Raw data were processed with the SeSAMe package for quality control and normalization.

first: A

last: Rossini-Venturini

first: E

last: Freitas


title: ZM-306416 prevents ovariectomy-induced bone loss by promoting osteoblastogenesis and inhibiting osteoclastogenesis

first: Shuo

last: Shi

address: No.1023, South Shatai Road Baiyun District

institute: Southern Medical University

summary: Osteoporosis affects millions of people worldwide, and current medications like bisphosphonates and denosumab are not effective enough in reversing bone loss. Moreover, these treatments have drawbacks, including jaw osteonecrosis and skin eczema. Hence, there is an urgent need for new drugs to treat osteoporosis. Drug library screening was performed by alkaline phosphatase (ALP) staining in osteoblasts to identify potential candidates for osteoporosis. qPCR, Western blot, ALP staining, alizarin red staining, and TRAP staining were conducted to assess the impact of ZM-306416 (ZM) on osteoblast and osteoclast differentiation in vitro. Additionally, RNA sequencing and pathway analysis were carried out to explore molecular mechanisms. Micro-CT scan and immunostaining were used to determine bone phenotypes in vivo. Drug library screening demonstrated that ZM enhances ALP activity in osteoblasts, indicating its potential as a pro-osteogenic agent. ZM exerts dual effects by promoting osteoblast differentiation through the Wnt/β-catenin signaling pathway and simultaneously inhibiting osteoclast differentiation by the NF-κB and MAPK signaling pathways. In an OVX mouse model, ZM effectively prevents bone loss by stimulating osteoblast formation and inhibiting osteoclast development. Our study revealed that ZM has a dual anti-osteoporosis effect by promoting osteoblastogenesis and inhibiting osteoclastogenesis, mediated via activation of Wnt/β-catenin signaling and suppression of NF-κB/MAPK cascades. These findings suggest that ZM could be a promising therapeutic strategy for alleviating osteoporosis.

overall_design: RNA - seq profiling was performed on primary osteoblasts. The cells were cultured in an osteogenic induction medium; those treated without 10 μM ZM served as the control group, and those treated with 10 μM ZM were the intervention group. Both groups were cultured for 6 days before RNA - seq analysis.

first: Jun

last: Chang

first: Junqi

last: Chen

first: Yicheng

first: Deijian

last: Yang

first: Tianyu

first: Wenquan

last: Liang


title: Bulk RNASeq of Stromal Subsets in Wildtype and GD T cell-deficent Mice in Biomaterial Implant Fibrosis

first: Jennifer

last: Elisseeff

summary: The main objective of this study is to investigate the role of gamma delta (GD) T cells on stromal cell behavior in chronic tissue injury and foreign body response (synthetic polycaprolactone PCL implant). We isolate key stromal cell populations (Fibroblasts and Endothelial Cells) from fibrotic PCL implants of wildtype (WT) and GD-deficient (GDKO) mice using FACS and compare their transcriptomic profile using bulk RNA-sequencing.

overall_design: PCL particulate was implanted into hindlimb volumetric muscle loss defects in C57BL/6 wildtype (WT) and gamma-delta T cell deficient (TCRd-/- or GDKO) mice for 6 weeks. To achieve sufficient cell yields, tissues sourced from 2 independent mice (4 total quads) were pooled together prior to sorting to form a “biological replicate”, resulting in 4 “biological replicates” per experimental group. Stromal cells (LiveCD45-CD31-CD29+) and endothelial cells (LiveCD45-CD31+CD29+) were sorted from the muscle with fibrotic PCL implants and RNA processed for bulk RNAseq.

first: Anna

last: Ruta

first: Kavita

last: Krishnan

first: Joscelyn

last: Mejias


title: Dissection of kinase-dependent and independent functions of RIPK3 in inflammatory disease

city: Suzhou

first: li

middle: jing

last: jing

address: No.100 Chongwen Road

institute: Suzhou institute systems medicine

summary: RIPK3 is a key regulator of necroptosis and inflammation, yet the distinct contributions of its kinase-dependent and -independent functions remain poorly understood. Here, we report the generation and characterization of RIPK3 D143N mutant mice, a novel model that selectively ablates kinase activity without inducing apoptosis or altering protein expression. Unlike previously described RIPK3 mutants (D161N/K51A), the D143N variant fully rescues Casp8-deficient embryonic lethality while effectively blocking necroptosis induced by multiple stimuli. In TNF-a-induced SIRS, we demonstrated that RIPK3's non-kinase activity exacerbates inflammation and tissue damage through JAK-STAT activation. Similarly, the kinase-independent RIPK3 activity promoted influenza-induced pathogenesis. Our findings establish the D143N mutant as a unique tool for dissecting non-catalytic functions of RIPK3, and provide critical insights for targeting RIPK3 for disease treatment.

overall_design: RNA-seq analysis of cecum tissues of Ripk3+/+ , Ripk3D143N/D143N and Ripk3-/-  mice at 4 hours post TNFα or PBS change.


title: Single cell RNA-seq of creatine-treated tumor-bearing mice

city: Los Angeles

first: Lili

state: CA

address: 610 Charles E. Young Dr. East, TLSB 3045

institute: UCLA Lili Yang Lab

summary: Tumor-infiltrating immune cells (TIIs) are highly sensitive to metabolic cues. However, the therapeutic potential of targeting TII metabolism remains underexplored. In order to study the in vivo transcriptomal changes in the tumor microevironment upon creatine treatment, we performed scRNA-seq on creatine-treated tumor-bearing mice. Nontreated mice were included as a control.

overall_design: Tumor-infiltrating immune cells from creatine-treated or control B16-OVA tumor-bearing mice were isolated by fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Elliot

last: Kang

first: James

last: Elsten-Brown

first: Yu-Chen

first: Bo

last: Li


title: Macrophage activation and invasion by Porphyromonas gingivalis is modulated by PPAD and accessory fimbriae subunits

city: Krakow

first: Jan

last: Potempa

address: Gołębia 24

department: Microbiology

country: Poland

institute: Jagiellonian University

summary: Background: Porphyromonas gingivalis is a master manipulator of host immune responses in periodontium. Peptidyl arginine deiminase (PPAD), a recently described virulence factor of P. gingivalis, responsible for both host- and bacterium-derived proteins and peptides citrullination,  also plays an important role in hijacking immune responses. While PPAD’s modification of fimbrial subunits (FimCDE) affects TLR2 signaling in fibroblasts, its impact on immune cells remains unclear. Methods: Human monocyte-derived macrophages (MDMs) were stimulated with wild-type or mutant P. gingivalis strains and isolated fimbriae. Inflammatory responses were assessed by measuring cytokine expression and secretion, transcriptional changes using RNA-seq and Pi3K/Akt pathway activation, while bacterial invasion through flow cytometry, fluorescent  microscopy and intracellular survival assay. Results: PPAD-modified fimbriae enhanced MDM proinflammatory responses, such as PGE2- related gene expression as well as cytokines secretion, while fimbriae from accessory subunit mutants failed to induce inflammation. PPAD modification of accessory fimbrial subunits was found to protect P. gingivalis from killing by macrophages. PPAD and accessory fimbriae subunits were involved in complex immune evasion strategies, upregulating genes associated with viral infections or interactions with T cells. Conclusions: These findings highlight the importance of protein citrullination in TLR2-dependent signaling and provide insight on how P. gingivalis subverts host immune responses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDMs that  were infected with  various strains of P. gingivalis ( ATCC 33277 WT and  ATCC 33277-derived mutants of PPAD, FimA, FimC and FimE as well as W83 WT strain) at MOI 20 for 24 h.

first: Aleksandra

last: Wielento

first: Dominika

middle: M

last: Drapała

first: Marina

last: Terekhova

last: Jacuła

first: Maxim

middle: N

last: Artyomov

first: Jakub

last: Kochan

first: Yoshiaki

last: Hasegawa

first: Danuta

last: Mizgalska

first: Juhi

last: Bagaitkar

first: Aleksander

last: Grabiec


title: Single-cell RNA/TCR-seq of T cells from murine muscle injury and foreign body response to synthetic biomaterial implants

first: Jennifer

last: Elisseeff

summary: The main objective of this study is to characterize T cell response to tissue injury and foreign body response (synthetic polycaprolactone PCL implant). We isolate T cells  from injured murine muscles with and without fibrotic PCL implants at various timepoints and perform transcriptomic profile using paired single-cell RNA/TCR-sequencing.

overall_design: PCL particulate was implanted into hindlimb volumetric muscle loss (VML) defects in C57BL/6 wildtype (WT) mice for 1, 6, or 12 weeks. For injury only controls, VML injuries were treated with saline and collected at 1 week. T cells (LiveSSCloCD45+CD3+) were sorted from the muscle with and without fibrotic PCL implants. Sorted T cells were processed for single-cell RNAseq paired with alpha/beta and gamma/delta TCRseq.

first: Anna

last: Ruta

first: Kavita

last: Krishnan

first: Joscelyn

first: Locke

last: Davenport Huyer

first: Christopher

last: Cherry

first: Frank

last: Yu


title: ALDH2/eIF3E Interaction Modulates Protein Translation Critical for Cardiomyocyte Ferroptosis in Acute Myocardial Ischemia Injury

first: Xin

last: Xin

address: 320 Yueyang Road, Shanghai 200031, China

institute: University of Chinese Academy of Sciences (UCAS), Chinese Academy of Sciences (CAS)

summary: BACKGROUND: As an iron-dependent form of regulated cell death caused by lipid peroxidation, ferroptosis has been implicated in ischemic injury, but the underlying mechanisms in acute myocardial infarction (AMI) remain poorly defined. Acetaldehyde dehydrogenase 2 (ALDH2) catalyzes detoxification of lipid aldehydes derived from lipid peroxidation and acetaldehydes from alcohol consumption. The Glu504Lys polymorphism of ALDH2 (rs671, ALDH2*2), affecting around 40% of East Asians, is associated with increased risk of MI. This study aims to investigate the role of ALDH2*2 and ferroptosis in AMI. METHODS: A Chinese cohort of 177 acute heart failure patients with ALDH2 wild type and ALDH2*2 was enrolled. The MI mouse model of left anterior descending (LAD) coronary artery ligation was conducted on wild-type, ALDH2*2, and mice with cardiomyocyte-specific knockdown of eukaryotic translation initiation factor 3 subunit E (eIF3E) by adeno-associated virus. The lipid peroxidation products were measured by mass spectrometry-based lipidomics and metabolomics in human plasma, mouse serum samples, mouse heart tissues, and primary cardiac myocytes. RESULTS: Human ALDH2*2 carriers exhibit more severe heart failure post-AMI with features of ferroptosis in plasma through lipidomic analysis, characterized by increased bioactive lipids and decreased antioxidants, such as Coenzyme Q10 (CoQ10) and tetrahydrobiopterin (BH4). Similar features were observed in MI mouse models of ALDH2*2, whereas ferroptosis inhibition by Fer-1 significantly improved heart functions and reversed ferroptosis markers. Importantly, ALDH2*2 significantly decreased ALDH2 protein levels, while ferroptosis-related markers, including Transferrin receptor (TFRC) and Acyl-CoA synthetase long-chain family member 4 (ACSL4), were notably upregulated in the infarct heart tissues. Mechanistically, ALDH2 physically interacts with the eIF3 complex via the eIF3E factor, which prevents the eIF3E-eIF4G1-mRNA assembly. The ALDH2*2 variant causes ALDH2 deficiency, disrupting its interaction with the eIF3 complex through releasing the bound eIF3E to assemble an eIF3E-eIF4G1-mRNA ternary complex, thereby driving selective translation of mRNAs (e.g., TFRC, ACSL4, and UAP1) containing the GAGGACR (R: represents A/G) motif to promote ferroptosis. Consistently, cardiomyocyte-specific eIF3E knockdown restored ALDH2*2 cardiac function by attenuating ferroptosis in MI. CONCLUSIONS: ALDH2*2 aggravates acute heart failure post-MI through promoting the selective translation of mRNAs containing the GAGGACR motif, thereby driving cardiomyocytes ferroptosis. Targeting ferroptosis represents a potential therapeutic option for mitigating MI injury, especially for ALDH2*2 carriers.  Key Words: ALDH2, myocardial infarction, eIF3E, ferroptosis, protein translation

overall_design: Both shNC and shAldh2 AC16 cells were seeded in 10 cm dishes. Cells were treated with 100 μg/mL cycloheximide (CHX) in medium for 3 to 5 minutes after 1 μM RSL3 treated for 12 hours to induce ferroptosis at 37°C. For Ribo-seq analysis, 1 x 107 cells were rinsed with ice-cold PBS containing 100 μg/mL CHX, pelleted (1000g, 10 minutes, 4°C), and saved at -80°C in nuclease-free tubes. Frozen samples were submitted to APExBIO (Shanghai, China) for RNA seq and Ribo seq library preparation, sequencing, and bioinformatic analysis using two biological replicates following established protocols.

last: Chen


title: Systemic application of IL-4 attenuates secondary local inflammation processes and enhances functional recovery after traumatic spinal cord injury in rats.

city: Heidelberg

first: Alexander

last: Younsi

address: INF 400

department: Neurosurgery

institute: Heidelberg University Hospital

summary: Abstract Background: Traumatic spinal cord injury (SCI) triggers local and systemic inflammation cascades, limiting neuroregeneration and impeding functional recovery. We investigated the systemic effect of immunomodulation with Interleukin-4 (IL-4) on the local immune reaction and regeneration in injured spinal cord tissue, in addition to the systemic cytokine landscape after SCI in rats.  Methodology: After performing a T10 laminectomy, 120 female Wistar rats were randomized to either thoracic clip compression/contusion SCI or sham. SCI animals received intraperitoneal (i.p.) IL-4 or vehicle injections twice daily for up to 7 days post-injury (dpi). Rats underwent a battery of neurobehavioral tests and were sacrificed at 1, 3, 7, 14, and 28 dpi. Transcriptomcis, proteomics and immunohistochemistry (IHC) was used to assess macrophage polarization, cellular neurodegeneration, and astrogliosis of explanted spinal cords. High throughput seromics was applied to measure levels of 18 cytokines in rat serum, which were also compared to SCI patient serum data.  Results: IL-4-treated rats showed a significantly better recovery in the Basso, Beattie, Bresnahan locomotor rating scale score and several Catwalk XT gait analysis parameters at 14 dpi. RNA-Seq and proteomics analyses revealed a significant upregulation in gene ontologies pertaining to improved axonogenisis and tissue repair along with reduced neuronal death and the pro-inflammatory TNFa signaling. This was verified via IHC, showing a higher abundance of IBA1+/ARG1+ and IBA1+/CD206+ M2-macrophages with a lower abundance of IBA1+/iNOS+ M1-macrophages compared to vehicle-treated rats at 3 dpi. Furthermore, post-traumatic cyst size was significantly reduced with IL-4 treatment at 28 dpi. While APC+ oligodendrocytes showed a significantly higher cell count in the IL-4 group, no significant difference was noted in NeuN+ neurons compared to the vehicle-treated group at 28 dpi. Seromics revealed significantly higher levels of pro-inflammatory serum cytokines in vehicle-treated rats compared to sham rats in the acute to subacute post-injury phase (1, 3 and 7 dpi), which were effectively suppressed by IL-4 treatment. Consistent with our rat model, data analysis of SCI patients revealed improved outcome of patients with low serum levels of pro-inflammatory cytokines reduced by IL-4.  Conclusions: Intraperitoneal IL-4 treatment modulated local and systemic inflammation after SCI and improved functional recovery. Transcriptomic and proteomic profiling revealed activation of regenerative and neuroprotective pathways and suppression of pro-inflammatory signaling, supporting the histological and behavioral findings. These results provide mechanistic insight into IL-4’s effects and support its further preclinical evaluation in SCI.

overall_design: RNA-Seq of rat tissue on day 3 after Sham vs Spinal cord injury +  IL-4 vs Spinal cord injury + placebo treatment.

first: Obada

last: Alhalabi

first: Stefan

last: Heene

first: Guoli

last: Zheng

first: Raban

last: Heller

first: Tim

last: Schubert

first: Marcin

last: Luzarowski

first: Xiawei

last: Zha

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