title: PANCREATIC DUCTAL ADENOCARCINOMAS RESISTANT TO KRAS INHIBITION ARE DRUGGABLE WITH AN ANTI-MUC1-C ADC

city: Brookline

first: Hiroki

last: Ozawa

address: 450 Brookline

institute: Dana-Farber Cancer Institute

summary: Treatment of pancreatic ductal carcinomas (PDACs) has been advanced by the development of KRAS mutant inhibitors. Despite this progress, PDACs invariably develop resistance to these agents by mechanisms that largely remain unclear. The MUC1 gene, which encodes an oncogenic MUC1-C protein, is upregulated in PDAC KRAS G12D tumors. We report that treatment of PDAC cells with the selective KRAS G12D MRTX1133 inhibitor is associated with induction of MUC1-C expression. We show that KRAS G12D inhibition activates a MUC1-C/NF-B p65 auto-inductive pathway. Our results further demonstrate that MUC1-C drives resistance to MRTX1133 by activating the inflammatory IFN type I and II pathways. Of clinical relevance, targeting MUC1-C genetically and pharmacologically reverses MRTX1133 resistance and is synergistic in combination with MRTX1133 treatment. In leveraging MRTX1133-induced upregulation of MUC1-C expression, an anti-MUC1-C (M1C) antibody-drug conjugate (ADC) is highly effective against MRTX1133-resistant PDAC KRAS G12D cell lines, patient-derived organoids and PDX tumor xenograft models. These findings demonstrate that MUC1-C confers resistance of PDAC KRAS G12D mutant cells to MRTX1133 and identify MUC1-C as a target for M1C ADC treatment of PDAC patients who are refractory to MRTX1133 treatment.

overall_design: RNA Seq in PDAC Cell line with MUC1-C shRNA silencing. We conpared DMSO and DOX treatment cells for differential gene expression analysis. MUC1shRNA (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA)  was inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) . Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).


title: IL-10 Targets IRF1/5 to Suppress IFN and Inflammatory Responses by Epigenetic Mechanisms [RNA-Seq]

status: Public on Apr 11 2025

city: New York

first: Bikash

last: Mishra

state: NY

address: 515 E 71st ST

country: USA

institute: Hospital for Special Surgery

type: Expression profiling by high throughput sequencing

summary: Interleukin-10 (IL-10) is pivotal in suppressing inflammation and innate immune activation, in large part by suppressing induction of genes by potent inflammatory factors such as TLR ligands. Despite decades of research, molecular mechanisms underlying this inhibition have not been resolved. This study utilized an integrated epigenomic analysis of gene transcription, chromatin accessibility, histone modifications and transcription factor binding to investigate IL-10-mediated suppression of LPS and TNF responses in primary human monocytes. Instead of inhibiting core TLR4-activated pathways such as NF-kB, MAPK-AP-1 and TBK1-IRF3 signaling, IL-10 targeted IRF5 an IRF1-mediated amplification loop that is important for IFNB, ISG and inflammatory gene induction in monocytes. This resulted in near-complete suppression of ISGs, and significant inhibition of inflammatory NF-kB target genes, in whose activation IRFs play an amplifying role. Mechanisms of TLR4 and TNFR target gene inhibition included downregulation of chromatin accessibility, de novo enhancer formation, and IRF1-associated H3K27ac activating histone marks. These results describe an underappreciated suppression of IFN responses by IL-10 and provide epigenetic mechanisms by which IL-10 suppresses TLR/TNF-induced gene expression.

overall_design: To investigate regulation of LPS and TNF responses by IL-10 in primary human monocytes. We purified CD14+ monocytes from human buffy coats. Monocytes were cultured overnight at 37°C, 5% CO2 in RPMI-1640 medium supplemented with 10% heat-inactivated defined FBS, penicillin-streptomycin, L-glutamine and 20 ng/ml human M-CSF and treated with indicated stimulation.


title: Albumin treatment transcriptionally reprograms circulating immune cells in patients with acutely decompensated cirrhosis

status: Public on Apr 08 2025

city: Barcelona

first: Ferran

last: Aguilar Parera

state: BARCELONA

address: Avinguda Diagonal 477, 11th floor, EF CLIF

country: Spain

institute: EF-CLIF

summary:
BACKGROUND AND AIMS: The effects of intravenous albumin on lymphocyte perturbations and defective neutrophil anti-microbial functions that characterize patients with acute-on-chronic liver failure (ACLF) are unknown.
METHODS: Forty-nine patients admitted for severe acutely decompensated cirrhosis without ACLF were investigated with the use of whole-blood RNA sequencing (RNA-seq) on admission and after a median period of 15 days once they had developed ACLF. Such patients were selected because they follow a steady systemic inflammation course. Thirty patients had received albumin during the progression to ACLF but not the 19 others. Single-cell RNA-seq (scRNA-seq) in peripheral blood mononuclear cells (PBMCs) exposed ex vivo to albumin or vehicle for 2 hours, and assessment of the anti-microbial capacity of neutrophils exposed ex vivo to albumin were performed in additional patients with acutely decompensated cirrhosis.
RESULTS: Analysis of whole-blood RNA-seq data revealed that patients who had received albumin exhibited specific upregulation of signatures related to B cells, plasma cells and immunoglobulins; CD4 T cells; myeloid cells; mismatch repair, cell cycle and mitosis; and transcription factors such as c-Myc and E2F family members. The use of scRNA-seq to analyze patients' PBMCs exposed ex vivo to albumin showed increases in signatures related to B cells, myeloid cells, and CD4 T cells. Neutrophils exposed ex vivo to albumin exhibited increased chemotactic and degranulation responses, enhanced phagocytosis, and increased pathogen-destroying swarming functions.
CONCLUSIONS: In patients with severe acutely decompensated cirrhosis, albumin rewires transcription in B cells, CD4 T cells and mononuclear myeloid cells, and resets neutrophil anti-microbial functions to normal.

overall_design:
RNA Preparation for Whole-Blood RNA-seq
RNA was isolated from blood stored in Tempus tubes using the Tempus™ Spin RNA Isolation Kit (reference 43802 Applied Biosystems, Foster City, CA). Preparation for RNA-seq is detailed in the Methods section of the Supplementary Appendix. Importantly, using the HUGO Genome Nomenclature Committee, which is a resource for approved human gene nomenclature, we designed a comprehensive protocol that included not only protein-coding genes, but also genes among other gene locus types, such as immunoglobulin genes, and T-cell receptor genes, resulting in a total of 14,615 genes for analysis. Genes brought by sexual chromosomes and mitochondrial DNA were not included in the analysis.

ScRNA-seq in PBMCs
Peripheral venous blood (8 ml) was collected by venipuncture into EDTA-coated sterile pyrogen-free tubes (Becton Dickinson, East Rutherford, NJ) from 9 patients and 4 age-matched healthy subjects. PBMCs were immediately isolated as previously described.27 PBMCs were seeded at a density of 1.5x106 cells/ml and incubated with either albumin (Albutein®, Grifols, Barcelona, Spain) (15 mg/ml) or vehicle (culture medium) for 2 hours at 37ºC in a 5% CO2 incubator. At the end of the culture, cells were rapidly (within 30 min) transferred to ice at the Single Cell Genomics platform from the CNAG. The protocol used for scRNA-seq and analysis of data are detailed in the Methods section of the Supplementary Appendix.

Experiments in Neutrophils
Neutrophils were isolated from peripheral venous blood (20 ml) obtained from 6 patients and 5 age-matched healthy subjects using the Ficoll-Hypaque method or negative depletion (StemCell neutrophil purification kit). Isolated neutrophils were immediately used for different experiments that assessed major anti-microbial functions of neutrophils such as degranulation assay, phagocytosis assay, swarming, and chemotaxis. For more details, see the Methods section in the Supplementary Appendix.

last: Aguilar

first: Joan

last: Clària

first: Juan-José

last: Lozano

first: Laura

last: Jiménez-Gracia

first: Juan

middle: C

last: Nieto

first: Holger

last: Heyn

first: Vicente

last: Arroyo

first: Richard

last: Moreau


title: Transcriptomic profiling of human trophoblast stem cells (hTSCs) and HTR-8/SVneo cells under  normal and MYBL2 knockdown conditions

status: Public on Apr 07 2025

city: Chongqing

first: Zhihong

last: Wu

state: Chongqing

address: No.1 Yixueyuan Rd, Yuzhong District, Chongqing

country: China

institute: Chongqing Medical University

summary: This dataset comprises  the gene expression profiles of human trophoblast stem cells (hTSCs) and HTR-8/SVneo cells under WT and  MYBL2 knockdown conditions. RNA sequencing (RNA-seq) was conducted to examine the effects of MYBL2 depletion on gene expression, with the goal of elucidating its role in trophoblast function, including stemness maintenance, differentiation, and invasion. This dataset offers valuable insights into the molecular mechanisms governed by MYBL2 in trophoblast biology and its potential relevance to pregnancy-related disorders.

overall_design: RNA-seq profiling of MYBL2 knockdown (shMYBL2) and their corresponding control (shNC) in HTR-8/SVneo cells (HTR8) and human trophoblast stem cells (hTSCs).

first: Zhi-Hong

first: Jia-Qi

last: Xu

first: Jing

last: Tang


title: Microenvironmental signals combine to induce non-additive molecular and phenotypic responses in mammary epithelial cells

city: Portland

middle: M

last: Heiser

state: OR

address: 2730 S Moody Ave

department: Biomedical Engineering

institute: Oregon Health and Science University

summary: Cellular phenotypes are dictated not by single signals but by the integration of multiple extracellular cues, a process that remains poorly understood. Here, we systematically dissect how combinations of Oncostatin M, Transforming Growth Factor β1, and Epidermal Growth Factor shape the behavior of MCF10A mammary epithelial cells. Live-cell imaging revealed that ligand combinations drive emergent phenotypes absent in single-ligand contexts, pointing to the induction of novel molecular programs. Transcriptomic profiling uncovered synergistically regulated genes, while partial least-squares regression linked these transcriptional signatures to quantitative imaging-derived phenotypes and validated them across independent datasets. Functional analysis revealed CXCR2 signaling, upregulated through CREB activation, as a key driver of enhanced cell motility under combinatorial ligand treatment. Together, these findings establish a framework for uncovering how extracellular signals converge to modulate gene expression and phenotype, providing new insight into the principles governing complex epithelial cell behaviors.

overall_design: RNA-seq profiling of MCF10A cells treated with EGF, OSM, and TGFB individually and in combination, 24 hours after ligand treatment.

first: Ian

last: McLean

first: Sean

last: Gross

first: Jeremy

last: Copperman

first: Daniel

middle: S

last: Derrick

first: Indranil

last: Paul

first: Andrew

last: Emili


title: Tumor associated myeloid cells support CNS invasive murine T-cell acute lymphoblastic leukemia

status: Public on Apr 04 2025

city: Austin

first: Ryan

last: Humphrey

state: Texas

address: 1900 Burton Dr. Apt 157

institute: University of Texas at Austin

summary: Single cell RNA sequencing analysis of leukemia cells (T-ALL) and myeloid cells from the leukemic and healthy murine CNS

overall_design: Myeloid and lymphoid cells were FACS sorted from the CNS of leukemic and healthy mice based on CD11b and CD11c expression

first: Ehrlich

last: Lauren

first: Humphrey

last: Ryan

first: Nam

last: Seohee

first: Wylie

last: Dennis


title: IL-10 Targets IRF1/5 to Suppress IFN and Inflammatory Responses by Epigenetic Mechanisms [ATAC-Seq]

first: Bikash

last: Mishra

type: Genome binding/occupancy profiling by high throughput sequencing


title: Diabetic ischaemic cardiomyopathy: Characterising the left ventricular myocardial molecular profile in advanced human heart failure

city: Panania

first: Benjamin

middle: John

last: Hunter

state: NSW

address: 118 Horsley Rd

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

summary: Ischaemic cardiomyopathy (ICM) is the most common cause of heart failure (HF) and often coexists with diabetes mellitus (DM). Yet, their combined effects are seldom investigated and are poorly understood. Herein, we performed multi-omic analyses of end-stage ICM with DM (ICM-DM) against ICM-No DM, non-ischaemic (dilated) cardiomyopathy with DM (NICM-DM), NICM-No DM, and healthy age-matched donors (AMD). Tissue was sourced from pre-mortem human left ventricular myocardium. Though fatty acid oxidation (FAO) proteins were down-regulated in ICM-DM relative to AMD and other HF, the unique ICM-DM down-regulation of acylcarnitines, perilipin, and ketone body, amino acid, and glucose metabolising proteins indicated FAO may not be entirely impaired. Oxidative phosphorylation appeared reduced in HF but exacerbated in ICM-DM, consistent with purportedly increased oxidative stress. Extracellular matrix proteins including collagens were up-regulated principally in ICM-DM despite the absence of macroscopic scar tissue. These findings were supported histologically and in metabolomic and RNA sequencing analyses.

overall_design: The aim of this study was to perform multi-omics analyses on cryopreserved pre-mortem human left ventricular myocardium to uncover the influence of DM in end-stage HF, and the molecular characteristics of ICM with DM (ICM-DM), thereby creating a comprehensive molecular resource of diabetes related heart failure.

first: Yunwei

last: Zhang

first: Dylan

last: Harney

first: Holly

last: McEwen

first: YenChin

last: Koay

first: Michael

last: Pan

first: Cassandra

last: Malecki

first: Jasmine

last: Khor

first: Robert

last: Hume

first: Giovanni

last: Guglielmi

first: Alicia

last: Walker

first: Shashwati

last: Dutta

first: Vijay

last: Rajagopal

first: Anthony

last: Don

first: Mark

last: Larance

first: John

middle: F

last: O’Sullivan

first: Jean

last: Yang

last: Lal


title: Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids

status: Public on Apr 02 2025

first: David

middle: William

last: McKellar

address: 101 6th Ave

institute: New York Genome Center

summary: The human heart, originating from the splanchnic mesoderm, is the first functional organ to develop, co-evolving with the foregut endoderm through reciprocal signaling. Previously, cardioid models offered new insights on cardiovascular cell lineages and tissue morphogenesis during heart development, while mesoderm-endoderm crosstalk remain incompletely understood. Here, we integrated micropatterned cardioids, CRISPR-engineered reporter hiPSCs, deep-tissue imaging, and single-cell RNA sequencing (scRNA-seq) to explore synergistic mesoderm-endoderm co-development. scRNA-seq with PHATE trajectory mapping reconstructed lineage bifurcations of mesoderm-heart and endoderm-foregut lineages, identifying key cell types in cardiac and hepatic development. Ligand-receptor interaction analysis highlighted mesodermal cells enriched in non-canonical WNT, NRG, and TGF-β signaling, while endodermal cells exhibited VEGF and Hedgehog activity. We found that micropattern sizes influenced cellular composition, cardioid cavitation, contractile functions, and mesoderm-endoderm signaling crosstalk. The cardioids generated from 600 µm diameter circle patterns showed larger cavity formation resembling early heart chamber formation. Our findings establish micropatterned cardioids as a model for mesoderm-endoderm co-development, enhancing our understanding of heart-foregut synergy during early embryogenesis.

overall_design: GCaMP6f reporter hiPSC cell lines were differentiated into cardiac organoids and cultured upon a micropatterned surface allowing for geometric control of multiple sizes. After successful differentiation into cardioids functioning organoids were imaged with samples collected at multiple time points for scRNA-Seq analysis.

first: Plansky

last: Hoang

middle: W

first: Andrew

last: Kowalczewski

first: Nhu

middle: Y

last: Mai

first: Meng

last: Chai

first: Lance

middle: X

last: Lian

first: Yi

last: Zheng

first: Iwijn

last: De Vlaminck

first: Huaxiao

first: Benjamin

middle: D

last: Cosgrove

first: Zhen

last: Ma


title: A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells

city: Boston

first: Tal

middle: Deborah

last: Scully

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

summary: Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impacting data quality and cell representation. We show that a low-salinity phosphate buffer supplemented with D-mannitol (PBS-M) enables higher-quality scRNA-seq of blood cells from the tunicate Ciona robusta. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. This simple protocol modification could enable or improve scRNA-seq for the majority of marine organisms.

overall_design: Circulating cells were collected from adult Ciona robusta animals, then run directly analyzed with scRNA-seq. One sample was prepared in high-salt buffer (Ca- and Mg-free buffered artificial seawater), then diluted shortly before scRNA-seq encapsulation with water (libarary name Cr_blood_asw). The other sample was prepared in a low-salt, high osmolarity buffer (0.7 M D-mannitol in PBS) (library name Cr_blood_mannitol).

first: Allon

last: Klein


title: SARS-CoV-2 Infection Induces Pro-Fibrotic and Pro-Thrombotic Lipid-Laden Macrophage Expansion in Lungs

status: Public on Apr 03 2025

city: Chapel Hill

first: Victor

last: Garcia

state: North Carolina

address: 120 Mason Farm Rd CB #7042

department: Division of Infectious Diseases

institute: University of North Carolina at Chapel Hill

summary: SARS-CoV-2 is the causative agent of COVID-19 and long COVID, two illnesses characterized by a dysregulated immune response. Macrophages have long been considered a key component of the dysregulated immune response occurring during severe cases of COVID-19 and long COVID. Using humanized mice implanted with human lung tissue, we demonstrate that macrophage replication is induced by SARS-CoV-2 infection which also promotes macrophage enlargement and the formation of lipid laden cells. Notably, we show that enlarged macrophages display a pro-fibrotic and pro-thrombotic phenotype. Even after immune-mediated clearance of replication competent virus, macrophage numbers remained elevated, and lung fibrosis and thrombi formation were still present. Importantly, we also showed that pre-exposure prophylaxis or early treatment with a SARS-CoV-2 antiviral, EIDD-2801, was able to reduce macrophage expansion and prevent COVID-19 mediated lung pathology such as fibrosis by reducing collagen deposition and decreasing smooth muscle actin, a biomarker of fibrosis. Elevated macrophage numbers were observed in a mouse-adapted SARS-CoV-2 model, and enlarged macrophage were elevated in a non-human primate model of SARS-CoV-2 infection, and in cadaveric human lung samples from SARS-CoV-2 infected individuals.  We postulate that SARS-CoV-2 infection induces the production of foam cells which in turn contribute to pathology associated with COVID-19 including thrombi formation.

overall_design: BLT-L were used as an in vivo model to evaluate the infection of lung tissue with the recombinant coronaviruses SARS-CoV, MERS-CoV and SARS-CoV-2, as well as the full-length bat coronaviruses WIV1-CoV and SHC014-CoV12,13,44,45. Viruses were directly injected into the human lung tissue of BLT-L, and lung tissue was collected 2, 6 or 14days after exposure to determine virus titre and/or for analysis by histology, electron microscopy or RNA sequencing.

first: D

last: Battaglia

first: R

last: Baric

first: C

last: Jones

first: A

middle: R

last: Wahl

first: E

middle: P

last: Browne

first: J

middle: V


title: The effect of bcCML leukemia progression on the bone marrow microenvironment

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

summary: Single Cell RNA-Sequencing was performed on CD45-Ter119- cells from leukemic mice at different stages of leukemic progression.

overall_design: Bone and bone marrow from mice transplanted with bcCML leukemia (BCR-ABL and NUP98-HOXA9) were extracted at timepoints 0, 2, 4, 7, 8, 11, and 14 days post transplant. CD45- Ter119- cells were sorted and processed for scRNA-Seq.

last: Rodems

first: Jeevisha

last: Bajaj

first: John

last: Ashton


title: Gene expression profile at single cell level of cells from the murine small intestinal tumors

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cells within murine colonic tumors with genetic mutations.

overall_design: Cells from mouse small intestinal tumors with mutant Braf and mutant P53, with and without Rnf43 deletion, were harvested for analysis with scRNAseq

first: Megan

last: Mills

first: Tamsin

last: Lannagan

first: Owen

last: Sansom


title: SARS-CoV-2 Infection Induces Pro-Fibrotic and Pro-Thrombotic Lipid-Laden Foam Cell Formation

overall_design: Mice with implanted human lung tissue (LOM) were used as an in vivo model to evaluate the infection of lung tissue with the  coronaviruses  SARS-CoV-2. Viruses were directly injected into the human lung tissue of LOM mice, and lung tissue was collected 2, 6 or 14days after exposure to determine virus titre and/or for analysis by histology, electron microscopy or transcriptome characterization use the GeoMx platform. GeoMX sequencing was completed only on day 0, 2, or 6.

first: Diana

first: Ralph

first: Corbin

first: Angela

first: Edward


title: SAM-synthase specific effects on metabolism and mitochondria underlie resistance to heat stress in C. elegans

status: Public on Apr 01 2025

city: Worcester

first: Amy

last: Walker

address: 373 Plantation Street

institute: UMass Medical School

summary: S-adenosylmethionine (SAM), produced by SAM synthases, is critical for various cellular regulatory pathways and the synthesis of diverse metabolites. Studies have often equated the effects of knocking down one synthase with broader SAM-dependent outcomes such as histone methylation or phosphatidylcholine (PC) production. However, many organisms express multiple synthase genes including humans and Caenorhabditis elegans. Evidence in C. elegans, which possesses an expanded family of SAM synthases, suggest that the enzymatic source of SAM impacts its function. For instance, loss of sams-1 leads to enhanced heat shock survival and increased lifespan, whereas reducing sams-4 adversely affects heat stress survival. Here, we reveal that loss of sams-1 exerts age-dependent effects on nuclear-encoded mitochondrial gene expression, mitochondrial metabolites, and mitophagy. Notably, we find that that SAMS-1 exerts synthase-specific effects on PC production. We propose a mechanistic framework wherein the reduced SAM from SAMS-1 acts through PC to impact mitochondrial fission and mitophagy, thereby enhancing survival during heat stress. This study highlights multifaceted roles of SAM across metabolic pathways and synthase-specific SAM functions.

overall_design: Lysis of young adult C. elegans was performed in 0.5% SDS, 5% β-ME, 10 mM EDTA, 10 mM Tris-HCl ph7.4, 0.5 mg/ml Proteinase K, before purification of RNA by TRI-Reagent (Sigma). cDNA was produced with Transcriptor First-strand cDNA kits (Roche), and RT-PCR was performed using Kappa SYBR Green 2X Mastermix. RNA for sequencing was purified using RNAeasy columns (Qiagen). RNA sequencing (including library construction was performed by BGI (Hong Kong). Reads were analyzed through the NextFlow analysis platform (https://github.com/DanHUMassMed/RNA-Seq-Nextflow), using DeSeq2 to identify differentially expressed genes. Gene set enrichment was performed using WormCat (http://www.wormcat.com).

first: Athena

middle: L

last: Munden

first: Dominique

last: Lui

first: Daniel

last: Higgins

first: Matthew

last: Fanelli

first: Thien-Kim

last: Ngyuen

first: Maria

last: Ericsson

first: Adwait

middle: A

last: Godbole

first: Jessica

middle: B

last: Spinelli

last: Haley

first: Caroline

last: Lewis

last: Promislow

first: Benjamin

last: Harrison

last: Raftery

first: Danijel

last: Djukovic

first: Dana L

last: Miller

middle: K


title: Single cell compendium of the muscle microenvironment in peripheral artery disease reveals capillary endothelial heterogeneity and activation of resident macrophages

city: Schwerzenbach

first: Guillermo

last: Turiel

address: Schorenstrasse 16

department: D-HEST

country: Switzerland

institute: ETH Zurich

summary: Background Peripheral artery disease (PAD) is caused by atherosclerosis and chronic narrowing of lower limb arteries leading to decreased muscle perfusion and oxygenation. Current guidelines for treating PAD include endovascular strategies or bypass surgery but long-term outcomes have been suboptimal. This is likely due to our limited understanding of the contribution of the microvasculature as well as other cell types, in particular macrophages, to PAD skeletal muscle pathophysiology. We used single cell sequencing to investigate cellular and transcriptional heterogeneity of the skeletal muscle microenvironment in PAD. Methods Samples from the medial head of the gastrocnemius muscle of individuals undergoing either lower limb aneurysm surgery (controls) or PAD bypass surgery (PAD) were collected. Samples were either frozen for histological evaluation (control: n=4; PAD: n=6) or were immediately processed for single cell RNA sequencing of mononuclear cells (control: n=4; PAD: n= 4). Bioinformatic tools were used to annotate cell types and their subpopulations, to study transcriptional changes and to analyze cellular interactions. Results We generated a dataset comprised of 106,566 high-quality, deep-sequenced cells that compose the muscle microenvironment. Focusing on endothelial cells (ECs) and macrophages, we confirmed the presence of ATF3/4+ ECs with angiogenic and immune regulatory capacities in human muscle and found that their transcriptional profile profoundly alters during PAD. Also, capillary ECs display features of endothelial to mesenchymal transition. Furthermore, we identified LYVE1hiMHCIIlow resident macrophages as the dominant macrophage population in human muscle, even under a chronic inflammatory condition such as PAD. During PAD, LYVE1hiMHCIIlow macrophages get activated and acquire a more pro-inflammatory profile. Finally, we map strong intercellular communication in the muscle microenvironment, which is significantly altered in PAD. Conclusions The dataset we present here provides a highly valuable resource for gaining deeper insights into the critical roles that cells in the muscle microenvironment may play in PAD skeletal muscle pathology. We propose that targeting the crosstalk between ECs and macrophages could provide novel insights for developing effective treatments against this disease.

overall_design: Endothelial cells from PAD patients were isolated in vitro and incubated with vehicle (DMSO) or celastrol (125 or 250 nM) for 24h. After incubation, RNA was extracted for bulk RNA sequencing. 3 biological replicates (3 different patients) were used. For each patient, 3 different wells were incubated with vehicle or each celastrol dose. Total of 9 samples.

first: Thibaut

last: Desgeorges

first: Evi

last: Masschelein

first: Jing

last: Zhang

first: Stephan

last: Engelberger

first: Katrien

last: DeBock


title: RNA-seq for High and low EPA+DHA group in the F2 population of the C. gigas and C.angulata crosses

status: Public on Apr 06 2025

city: Qingdao

first: Qingyuan

last: Li

address: Haijun road 88

institute: IOCAS

summary: To examine the candidate genes for GWAS at the transcriptional level, we selected 40 individuals each of EPA+DHA extreme phenotypes in the F2 population for mixed-pool transcriptome sequencing

overall_design: In this study, a total of 458 oysters from the F2 population resulting from the crossbreeding of C. angulata and C. gigas were utilized for liquid microarray genotyping. The F1 population were established through the crossbreeding of the 30 female C. angulata from Zhangzhou, Fujian (117°41'35 "E, 23°56'42 "N) and 30 male C. gigas from Jiaonan, Qingdao (119°57'3 "E, 35°43'20 "N), involving 30 or more oysters for both male and female parents. The F2 population was subsequently produced by the mating of the 30 female and 30 male F1 individuals and then cultured in Jiaonan, Qingdao, China. At the age of 11 months, a total of 458 F2 individuals were sampled in situ.Two extreme phenotype groups, H (high EPA+DHA) and L (low EPA+DHA), were selected from the GWAS population for transcriptomic analysis. Each group consisted of a total of 40 oyster individuals, and their total RNA was mixed equally for three technical replicates.


title: A bruton’s tyrosine kinase inhibitor reduces stemness and invasiveness of patient-derived glioblastoma tumorspheres

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

summary: Glioblastoma (GBM), the most prevalent primary brain tumor, remains incurable due to the presence of cancer stem cells (CSC), which can be isolated as tumorspheres (TS) that exhibits classical characteristics of CSCs including stemness and invasiveness. The significantly elevated expression of Bruton’s tyrosine kinase (BTK) in GBM tissues identifies BTK as a potential therapeutic target in GBM. Consequently, ibrutinib, an FDA-approved BTK inhibitor for hematological malignancies, has been repurposed as a candidate for GBM treatment, demonstrating inhibitory effects on proliferation, stemness, and invasiveness of GBM cell lines and TSs. However, its broad-spectrum activity targeting other Tec family kinases and members of the epidermal growth factor receptor (EGFR) family, poses potential life-threatening risks, necessitating the development of more selective alternatives. To address this, BTK selective analogs (SPA1758, SPA1763, SPA8004, SPA8007, SPA8009) were synthesized with the aim of targeting two key characteristics of GBM TSs: stemness and invasiveness. WST and ATP assays identified SPA8007 and SPA8009 as the most effective candidates with superior cytotoxic effects in TSs. Additionally, both SPA8007 and SPA8009 significantly inhibited neurosphere formation and reduced invasiveness in GBM TSs. Furthermore, SPA8007 demonstrated improved survival rates in a GBM xenograft mouse model and reduced the expression of invasiveness markers significantly, as observed in immunohistochemistry (IHC) analysis. These findings highlight SPA8007 as potential novel chemotherapeutic agents with high specificity and efficacy to enhance GBM therapy.

overall_design: RNA-seq of patient-derived GBM TS, treated with BTK inhibitors for 72 hours.

first: Euna

last: Jo

first: Yoojung

last: Oh

first: Seok-Gu

last: Kang


title: Brain region-specific and systemic transcriptomic dysregulation in a human alpha-synuclein overexpressing rat model

city: Saarbrüecken

first: Julia

last: Schulze-Hentrich

address: Campus A2.4

department: Genetics/Epigenetics

country: Germany

institute: Saarland University

summary: Synucleinopathies are age-dependent neurodegenerative diseases characterized by alpha-synuclein accumulation with distinct vulnerabilities across brain regions. Understanding early disease stages is essential to uncover initial molecular changes that might enable earlier diagnosis and causal therapy. Here, we profiled longitudinal and brain region-resolved gene expression changes in a rat model of synucleinopathies overexpressing human SNCA. Transcriptomic analyses on gene and transcript level of striatal, frontocortical, and cerebellar tissue in 5- and 12-month-old transgenic (BAC SNCA) and wild type rats revealed that SNCA overexpression leads to age-dependent transcriptomic changes that largely occur region-specific. In frontal cortex, dysregulation of myelination-associated genes agreed with Parkinson patient data as shown before. In addition, BAC SNCA rats displayed more gene expression changes at younger age, with a common and distinctive dysregulation pattern across all three examined brain regions. We also identified a cross-regional set of differential genes with similar perturbation patterns that were affected by SNCA overload. This set was also partially reflected in the gut transcriptome of the same rat model, suggesting a systemic impact of SNCA overload. Taken together, our findings highlight both brain region-specific vulnerabilities and global molecular perturbations associated with alpha-synuclein biology and provide insights into early transcriptomic changes in synucleinopathies.

overall_design: Gene expression changes were profiled in striatal, frontocortical and, cerebellar tissue of 5- and 12-months-old rats. For each time point, 5 wild-type and 5 transgenic rats, overexpressing human SNCA were analyzed.

first: Vivien

last: Hoof

first: Thomas

last: Hentrich


title: Effect of depletion of LEMD3 on chromatin accessibility of A7r5 vascular smooth muscle cells [Hi-C]

city: Beijing

first: Yunxi

last: Liao

state: Beijing

address: 38 Xueyuan Rd, Haidian District

institute: School of Basic Medical Sciences, Peking University

summary: The contractile phenotype of vascular smooth muscle cells is essential for maintaining vascular homeostasis.In this study, we found that LEMD3, a nuclear membrane protein, may be involved in maintaining the contractile phenotype of vascular smooth muscle cells through a genome-scale CRISPR screen. Mechanistically, we combined RNA-seq with ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) to find out differentially expressed genes and altered chromatin accessibility. By overlapping down-regulated genes and genes located in less accessible chromatin regions, we identified 143 genes including VSMCs contractile genes such as Acta2, Cnn1, Tagln, and key transcription factor Srf, suggesting that LEMD3 maintains VSMCs contractile phenotype by regulating chromatin accessibility.

overall_design: A7r5 cells were transfected with scrambled siRNA or siRNA targeting Lemd3.

first: Wenqiang


title: Effect of depletion of LEMD3 on chromatin accessibility of A7r5 vascular smooth muscle cells [ATAC-seq]


title: Inner Nuclear Membrane Protein LEMD3 Stabilizes 3D Chromatin Architecture and Maintains Vascular Smooth Muscle Cell Identity

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

overall_design: Refer to individual Series


title: Muc1-C Regulates Neat1 Lncrna Expresmuc1-C Is Essential For Establishing And Recalling Inflammatory Memory Of Osimertinib Resistance In Nsclc Cellssion And Paraspeckle Formation In Cancer Stem Cells

city: Brookline

first: Naoki

last: Haratake

address: 44 Washington St. #1001,

institute: Dana-Farber Cancer Institute

summary: MUC1-C is necessary for establishing and recalling resistance of NSCLC cells to osimertinib by driving an inflammatory memory responseThe oncogenic MUC1-C protein functions as a master regulator of NSCLC cell resistance to osimertinib by unclear mechanisms. We report that MUC1-C-mediated regulation of STAT1 and the interferon (IFN) type I/II pathways is necessary for establishing osimertinib resistance. Studies of osimertinib-resistant NSCLC cells selected for growth in the absence of drug further demonstrate that revertant cells are dependent on MUC1-C for recalling resistance to osimertinib. We show that establishing and recalling osimertinib resistance is dependent on activation of the MUC1 gene at (i) a proximal enhancer-like signature 1 (pELS-1) by MUC1-C and STAT1 and (ii) a pELS-2 by MUC1-C, JUN/AP-1 and PBAF. The MUC1 pELS regions function as memory domains for activation of MUC1-C and downstream STAT1 and IFN stimulated genes in conferring osimertinib resistance. Of clinical relevance, we report that the MUC1-C-driven inflammatory responses are induced in patient-derived, osimertinib-resistant MGH170 NSCLC cells with MET amplification. Our results further demonstrate that MGH170 cells are dependent on the MUC1-C-induced inflammatory response for resistance to the osimertinib and combination of osimertinib with the MET inhibitor capmatinib. These findings indicate that MUC1-C is necessary for establishing and recalling resistance of NSCLC cells to osimertinib by driving an inflammatory memory response.

overall_design: RNA Seq in EGFR-mutant NSCLC Cell line with MUC1-C shRNA silencing


title: Effect of depletion of LEMD3 on histone modification H3K27ac of A7r5 vascular smooth muscle cells [ChIP-seq]

summary: The contractile phenotype of vascular smooth muscle cells is essential for maintaining vascular homeostasis.In this study, we found that LEMD3, a nuclear membrane protein, may be involved in maintaining the contractile phenotype of vascular smooth muscle cells through a genome-scale CRISPR screen. To further explore the impact of Lemd3 knockdown on global landscape of H3K27ac and H3K9me3, we performed ChIP-sequencing of scrambled siRNA-transfected and Lemd3 siRNA-transfected rat VSMCs.

first: Sudun

last: Guan


title: Generation of mandibular prominence ectomesenchyme (mdEM) from human induced pluripotent stem cell (iPSC)-derived neural crest cell (NCC) aggregates

status: Public on Mar 31 2025

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

summary: To clarify the changes in cell properties during the differentiation process from iPSCs into mdEM through NCC aggregates, we sampled iPSCs and cell aggregates during the differentiation process and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSCs, NCC aggregates (day 5), and mdEM (day 9).

first: S

last: Motoike

first: M


title: Reannotation of cancer mutations based on expressed RNA transcripts reveals novel functional non-coding mutations in melanoma.

city: Leuven

first: Kim

last: De Keersmaecker

address: ON4 Herestraat 49 - bus 810

department: Oncology

country: Belgium

institute: KUL

summary: The role of synonymous mutations in cancer pathogenesis is currently underexplored. We developed a method to detect significant clusters of synonymous and missense mutations in public cancer genomics data. In melanoma, we show that 22% (11/50) of these mutation clusters are misannotated as coding mutations because the reference transcripts used for their annotation are not expressed. Instead, these mutations are actually non-coding. This, for instance, applies to the mutation clusters targeting known cancer genes kinetochore localized astrin (SPAG5) binding protein (KNSTRN) and BCL2 like 12 (BCL2L12), each affecting 4-5% of melanoma patients. For the latter, we show that these mutations are functional non-coding mutations that target the shared promoter region of the interferon regulatory factor 3 (IRF3) and BCL2L12 genes. This results in downregulation of IRF3, BCL2L12 and tumor protein p53 (TP53) expression in a CRISPR-Cas9 primary melanocyte model and in melanoma patients, in which these mutations are also associated to a worse response to immunotherapy. Finally, we propose a simple automated method to more accurately annotate cancer mutations based on expressed transcripts. This work shows the importance of integrating DNA- and RNA-sequencing data to properly annotate mutations, and identifies a number of previously overlooked and wrongly annotated functional non-coding mutations in melanoma.

overall_design: Long read Nanopore RNA sequencing

first: Daniele

last: Pepe

first: Xander

last: Janssens

first: Kalina

last: Timcheva

first: Grecia

middle: M

last: Marrón-Liñares

first: Benno

last: Verbelen

first: Vasileios

last: Konstantakos

first: Dylan

last: De Groote

first: Jolien

last: De Bie

first: Amber

last: Verhasselt

first: Barbara

last: Dewaele

first: Arne

last: Godderis

first: Charlotte

last: Cools

first: Mireia

last: Franco-Tolsau

first: Jonathan

last: Royaert

first: Jelle

last: Verbeeck

last: Kampen

first: Karthik

last: Subramanian

first: David

last: Cabrerizo Granados

first: Gerben

last: Menschaert


title: Evaluation of the effects of FGF8, Endothelin-1, and BMP4 (FEDB) on induced pluripotent stem cell (iPSC)-derived neural crest cells (NCCs) induced in two-dimensional (2D) conditions

first: Makoto

last: Ikeya

summary: To evaluate the effects of FEDB on NCCs induced in 2D conditions, we sampled 2D cultured cells and cell aggregates during FEDB treatment and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSC-derived NCC aggregates, NCC aggregates treated with FEDB, CD271high+ NCCs sorted from 2D induction protocols (2D NCC CD271high), and 2D NCC CD271high treated with FEDB in 2D culture (2D 271H+FEDB).

first: S

last: Motoike

first: M


title: Induction of osteogenic lineage cells from human induced pluripotent stem cell (iPSC)-derived neural crest cell (NCC) aggregates through mandibular prominence ectomesenchyme (mdEM)

summary: To clarify the changes in cell properties during the differentiation process from iPSC-derived NCC aggregates into osteogenic cells through mdEM, we sampled cell aggregates during the  differentiation and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSC-derived NCC aggregates (day 5), mdEM (day 9), and day 38 clusters.


title: PTEN mutations impair CSF dynamics and cortical networks by dysregulating periventricular neural progenitors

first: Kris

last: Kahle

address: 55 Fruit Street

institute: MGH

summary: Enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles (ventriculomegaly) is a defining feature of congenital hydrocephalus (CH) and an underrecognized concomitant of autism. Here, we show that de novo mutations in the autism risk gene, PTEN, are among the most frequent monogenic causes of CH and primary ventriculomegaly. Mouse Pten-mutant ventriculomegaly results from aqueductal stenosis due to hyperproliferation of periventricular Nkx2.1+ neuroprogenitor cells (NPCs) and increased CSF production from hyperplastic choroid plexus. Pten-mutant ventriculomegalic cortices exhibit network dysfunction from increased activity of Nkx2.1+ NPC-derived inhibitory interneurons. Raptor deletion or post-natal everolimus treatment corrects ventriculomegaly, rescues cortical deficits, and increases survival by antagonizing mTORC1-dependent Nkx2.1+ NPC pathology. Thus, PTEN mutations concurrently alter CSF dynamics and cortical networks by dysregulating Nkx2.1+ NPCs. These results implicate a non-surgical treatment for CH, demonstrate a genetic association of ventriculomegaly and ASD, and help explain neurodevelopmental phenotypes refractory to CSF shunting in select CH patients.

overall_design: Examine the knockout effect of PTEN on choroid plexus, subventricular zone and cortex

first: Kristopher

middle: T

first: Emre

last: Kiziltug

first: Tyrone

last: DeSpanza Jr.


title: A novel regulator of the fungal phosphate starvation response revealed by transcriptional profiling and DNA affinity purification sequencing

city: Ithaca

first: Lori

last: Huberman

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

summary: Cells must accurately sense and respond to nutrients to compete for resources and establish growth. Phosphate is a critical nutrient source necessary for signaling, energy metabolism, and synthesis of nucleic acids, phospholipids, and cellular metabolites. During phosphate limitation, fungi import phosphate from the environment and liberate phosphate from phosphate-containing molecules in the cell. In the model filamentous fungus Neurospora crassa, the phosphate starvation response is regulated by the conserved transcription factor NUC-1. The activity of NUC-1 is repressed by a complex of the cyclin-dependent kinase MDK-1 and the cyclin PREG when phosphate is plentiful. When phosphate is limiting, NUC-1 repression by MDK-1/PREG is relieved by the cyclin-dependent kinase inhibitor NUC-2. We investigated the global response of N. crassa to phosphate starvation. During phosphate starvation, NUC-1 directly activated expression of genes encoding phosphatases, nucleases, and a phosphate transporter and directly repressed genes associated with the ribosome. Additionally, NUC-1 indirectly activated the expression of an uncharacterized transcription factor, which we named nuc-3. NUC-3 directly repressed the expression of genes involved in phosphate acquisition and liberation after an extended period of phosphate starvation. Additionally, NUC-3 directly repressed expression of the cyclin-dependent kinase inhibitor nuc-2. Thus, through the combination of NUC-3 direct repression of genes in the phosphate starvation response and nuc-2, an activator of the phosphate starvation response, NUC-3 serves to act as a brake on the phosphate starvation response after an extended period of phosphate starvation. This braking mechanism could reduce transcription, a phosphate-intensive process, in conditions when phosphate is limiting.

overall_design: mRNA-seq profiling of Neurospora crassa wild type exposed to 7 mM phosphate or phosphate starvation and nuc-1 deletion and nuc-3 deletion strains exposed to phosphate starvation for 4 h or 12 h. Each experiment was performed in biological triplicate.

first: Vincent

last: Wu

last: Kowbel

first: Juna

last: Lee

first: Chris

last: Daum

first: Igor

last: Grigoriev

first: Ronan

middle: C

last: O'Malley

first: N

last: Glass


title: Inhibition of MAFB and PI3K/AKT-signaling reveals a potential therapeutic strategy for multicentric carpotarsal osteolysis-associated nephropathy

city: Tsukuba

first: Akihiro

last: Kuno

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: Multicentric carpotarsal osteolysis (MCTO) is an ultra-rare skeletal dysplasia characterized by aggressive osteolysis and in many patients, progressive renal failure. Previous work identified autosomal dominant missense mutations in the transactivation domain of the transcription factor MAFB as the cause of MCTO. Because the pathological mechanism resulting in MCTO is not clear, we used mice carrying the MCTO mutation (MafbMCTO/MCTO mice) to determine the role of MAFB. Using a cycloheximide chase assay in HEK293T cells, we found that the MCTO mutation resulted in reduced degradation and thus accumulation of recombinant MAFB protein. MafbMCTO/MCTO mice exhibited focal segmental glomerulosclerosis (FSGS) similar to what is observed in MCTO patients. To analyze the effect of the excessive presence of MAFB, we generated heterozygous MafbMCTO/- mice by crossing MafbMCTO/MCTO and Mafb+/- animals. Such MafbMCTO/- mice did not suffer albuminuria and exhibited histologically normal kidney appearance. The finding that MCTO mutation haploinsufficiency rescues animals from nephropathy is consistent with the mutation resulting in excess MAFB as the cause of disease. Next, we performed RNA-seq of the glomeruli from MafbMCTO/MCTO mice. We found marked up-regulation of the PI3K/AKT signaling pathway. Because receptor tyrosine kinases are PI3K/AKT activators, we administered the specific inhibitor imatinib to MafbMCTO/MCTO mice. This resulted in a significant reduction of urinary albumin relative to untreated animals. Taken together, these results suggest that excess MAFB and the activation of PI3K/AKT signaling induce nephropathy in MCTO. MAFB and/or PI3K/AKT signaling may therefore represent new treatment targets in MCTO patients.

overall_design: Glomeruli mRNA profiles of WT and MCTO mice

first: Satoru

last: Takahashi

first: Naoto

last: Morito

first: Toshiaki

last: Usui


title: Time course gene expression pattern during neural crest cell (NCC) differentiation from induced pluripotent stem cells (iPSCs) in three-dimensional (3D) conditions

first: Makoto

last: Ikeya

summary: To clarify the changes in cell properties during the differentiation process from iPSCs into NCC aggregates, we sampled iPSCs and each cell aggregate during the differentiation process and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSCs, cell aggregates at days 1-5, CD271high+ NCCs sorted from day 5 aggregates, and CD271high+ NCCs sorted from two-dimensional (2D) induction protocols.

first: S

first: D

last: Kamiya


title: Recapitulation of regional patterning using human induced pluripotent stem cell (iPSC)-derived mandibular prominence ectomesenchyme (mdEM)

summary: To ascertain the induction of developmentally accurate mdEM, we sampled cell aggregates during regional patterning induction and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSC-derived neural crest cell (NCC) aggregates (day 5), mdEM (day 9), distal cap (day 13), proximal-oral domain (day 13), and dental mesenchyme (day 17).

last: Motoike

first: M


title: The 5-methylcytosine DNA glycosylase ROS1 prevents paternal genome hypermethylation in Arabidopsis endosperm

status: Public on Mar 28 2025

city: Cambridge

first: Elizabeth

last: Hemenway

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

type: Methylation profiling by high throughput sequencing

summary: DNA methylation patterning is a consequence of opposing activities of DNA methyltransferases and DNA demethylases. In many species, reproduction is a period of significant epigenome lability. In flowering plants, two distinct female gametes, the egg cell and the central cell, are fertilized, producing the embryo and the endosperm, respectively, of the seed. The endosperm is an unusual tissue, exemplified by triploidy and reduced DNA methylation. In Arabidopsis thaliana, a 5-methylcytosine DNA glycosylase, DME, demethylates regions in the central cell genome, leading to methylation differences between maternally- and paternally-inherited endosperm genomes after fertilization. Expression of DME in the central cell is required for gene imprinting, or parent-of-origin specific gene expression, in endosperm. DME is part of a four member gene family in Arabidopsis that includes ROS1, DML2 and DML3. It is unknown whether any of the other DNA glycosylases are required for endosperm methylation patterning. Using whole-genome methylation profiling, we identify ROS1 target regions in the endosperm. We show that ROS1 prevents hypermethylation of paternally-inherited alleles in the endosperm at regions that lack maternal or paternal-allele methylation in wild-type. Thus, ROS1 promotes epigenetic symmetry between parental genomes in the endosperm by preventing paternal genome hypermethylation. We propose that ROS1 and DME act in a parent-of-origin-specific manner at shared endosperm targets, and consider possible implications for the evolution of imprinting mechanisms.

overall_design: Whole-genome Enzymatic Methyl-Seq (EM-seq) performed on DNA extracted from 3C and 6C endosperm nuclei collected 7 days after pollination (DAP) and 2C/4C leaf nuclei collected from young leaf tissue.

first: Mary

last: Gehring


title: The m6A epitranscriptome of the HepAD38 cell line

city: Fuzhou

first: Kunqi

last: Chen

address: Fujian Medical University

institute: Fujian Medical University

summary: m6A modification appears in HepAD38 cell line

overall_design: To investigate whether m6A modification is involved in evolution, we performed MeRIP-seq on HepAD38 cell line


title: Effect of depletion of LEMD3 on gene expression of A7r5 vascular smooth muscle cells [RNA-seq]

first: Yunxi

last: Liao

first: Wenqiang

last: Li


title: Time series analysis of transcriptomic responses to iron and zinc stress in Sorghum

status: Public on Mar 26 2025

city: Cold Spring Harbor

first: Sunita

last: Kumari

state: New York

address: One Bungtown Road

institute: Cold Spring Harbor Lab

summary: Micronutrient stress impacts growth, biomass production, and grain yield in crops. Multi-omics studies are valuable resources for identifying genes for functional studies for trait improvement such as accumulation of Fe or Zn under deficient or excess conditions for bioenergy or grain agriculture. We conducted transcriptomics and ionomics analyses on Sorghum bicolor BTx623, grown under Fe and Zn limiting and excess conditions over a 21-day time-period. To identify early and late transcriptional response in roots and leaves, 180 RNAseq libraries were sequenced for differential expression and coexpression network analyses. Fe and Zn accumulation was measured using ICP-MS at each time point and a fluorometer was used to estimate chlorophyll content in leaves. Among the four treatments, Fe limiting and Zn excess resulted in the largest phenotypic effects and transcriptional response in roots and leaves.

overall_design: Sorghum seedlings were  grown in a hydroponic growth system for one week and then transplanted into modified Hoagland’s solution for acclimation. After three-week acclimation in hydroponics, seedlings were randomized and transplanted into modified Hoagland’s solutions with different zinc sulphate and ferric sodium  EDTA concentrations for low, medium and high iron and zinc stress treatments. For RNA tissue sampling, leaf and root samples were collected from three individual plants to represent three biological replicates. Root tissues were sampled at 7 time points starting from untreated control and after individual stress treatments on 1hour, 2 days, 4 days, 7 days, 14 days, and 21 days for each low, medium and high iron and zinc stress treatments. Leaf discs were sampled from the young leaf from the same plant at 6 time points starting from untreated control and 2 days, 4 days, 7 days, 14 days, and 21 days after individual stress treatments of iron and zinc stress.

first: Ankita

last: Mishra

first: Aditi

last: Bhat

first: Reena

last: Sharma

first: Janeen

last: Braynen

first: Dimiru

last: Tadesse


title: The expression of regional markers in neural crest cell (NCC) aggregates treated with or without retinoic acid (RA).

summary: To evaluate the anterior-posterior axial identity of the NCC aggregates, we prepared aggregates treated with RA to induce posterior fates as a positive control and compared gene expression patterns among the aggregates.

overall_design: RNA sequencing profiles of 1231A3 iPSCs, day 5 aggregates, CD271high-sorted NCCs from day 5 aggregates, and RA-treated day 5 aggregates.


title: Pioneer transcription factor Runx2 affecting biological function of Schwann Cells via self-inducible reconstruction of super-silencer to remodel chromatin [hitone CUT&Tag]

city: Guangzhou

first: Zhaowei

last: Zhu

address: NO. 58 Zhongshan 2nd Rd, Guangzhou

department: Department of Plastic Surgery

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: The expression of Runx2 in Schwann cells (SCs) increases significantly in the early stage of injury, but its underlying regulating mechanism remained unclear. After up-regulating Runx2 expression in SCs, the proliferation and migration ability of SCs decrease with increased cell apoptosis rate, and no obvious accelaration of axon regeneration rate could be seen when co-cultured with dorsal root ganlia. Through genome-wide mapping of the chromatin landscape, Runx2 displayed features of pioneer transcription factor (pTFs), which could independently action without histone modification, and execute positive feedback up-regulating gene expression of itself. In the meanwhile, it could construct the epigenetic mechanism of silencer to limit interactions of other transcription factors, then finally affect the fate of SCs, expecially SCs’ ability to deal with lipoproteins and form myelin. This study provides noval insight into key function of Runx2 in SCs as pTFs relying on its ability to reorganize the chromatin landscape within SCs, and interfering with the metabolism and synthesis of myelin sheaths by forming super silencers, therefore affecting the regeneration process of peripheral nerves.

overall_design: SCs from neonatal 3-5 day SD rats were isolated and purified. The purified P0 SCs were randomly divided into the Runx2-OE group and EGFP (empty vector) group. SCs were transfected with Runx2-OE or EGFP adenovirus at a concentration of MOI = 200. After 72 hours of incubation in the incubator, the changes in cell morphology were observed under laser confocal microscope. CUT&TAG assay was performed as described previously with modifications.

first: Bo

last: He


title: IL-7-mediated expansion of autologous lymphocytes increases CD8+ T Cell VLA-4 expression and accumulation within glioblastoma

city: Durham

first: Kirit

last: Singh

state: NC

address: Room 215, Sands Building, 303 Research Drive

institute: Duke University

summary: The efficacy of T cell-activating therapies against glioma is limited by an immunosuppressive tumor microenvironment and tumor-induced T cell sequestration. We investigated whether peripherally infused non-antigen specific autologous lymphocytes (ALT) could accumulate in intracranial tumors. We observed that non-specific autologous CD8+ ALT cells can indeed accumulate in this context, despite endogenous T cell sequestration in bone marrow. Rates of intratumoral accumulation were significantly increased when expanding lymphocytes with IL-7 compared to IL-2. Pre-treatment with IL-7 ALT also enhanced the efficacy of multiple tumor-specific and non-tumor-specific T cell-dependent immunotherapies against orthotopic murine and human xenograft gliomas. Mechanistically, we detected increased VLA-4 on mouse and human CD8+ T cells following IL-7 expansion, with increased transcription of genes associated with migratory integrin expression (CD9). We also observed that IL-7 increases S1PR1 transcription in human CD8+ T cells, which we have shown to be protective against tumor-induced T cell sequestration. These observations demonstrate that expansion with IL-7 enhances the capacity of ALT to accumulate within intracranial tumors, and that pre-treatment with IL-7 ALT can boost the efficacy of subsequent T cell-activating therapies against glioma. Our findings will inform the development of future clinical trials where ALT pre-treatment can be combined with T cell-activating therapies.

overall_design:
To evaluate IL-7’s effect on migratory integrin expression, we performed bulk RNA sequencing using  glioblastoma donor hPBMC samples. CD8+ T cells were sorted from naïve (pre-expansion), IL-2-expanded, or IL-7-expanded products.

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Processed individual files are included within this repository per Duke IRB institutional certification requirements.
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first: Kelly

last: Hotchkiss

first: Sarah

last: Cook

first: Pamy

last: Noldner

first: Ying

last: Zhou

first: Eliese

last: Moelker

first: Chelsea

middle: O

last: Railton

first: Emily

middle: E

last: Blandford

first: Bhairavy

middle: J

last: Puviindran

first: Shannon

last: Wallace

first: Pamela

last: Norberg

first: Gary

last: Archer

first: Beth

middle: H

last: Shaz

first: Katayoun

last: Ayasoufi

first: John

last: Sampson

first: Mustafa

last: Khasraw

first: Peter

last: Fecci


title: Pioneer transcription factor Runx2 affecting biological function of Schwann Cells via self-inducible reconstruction of super-silencer to remodel chromatin [TF CUT&Tag]

first: Zhaowei

last: Zhu

first: Bo

last: He


title: Stromal lipid species dictate melanoma metastasis and tropism [MFP_RNA_seq]

city: Manchester

first: Amaya

last: Viros

address: Wilmslow Road

department: Skin Cancer Ageing

institute: Cancer Research UK

summary: Cancer cells adapt to signals in the tumor microenvironment (TME), but the TME cues that impact metastasis and tropism are unknown. We show that stromal lipids from young adipocytes are taken up by melanoma cells, and lipids increase melanoma oxidative phosphorylation (OXPHOS) and oxidative stress, which decreases metastatic burden. In contrast, the aged TME provides fewer lipids, leading to lower OXPHOS and higher metastatic capacity. Young adipocytes transfer phosphatidylcholine (PC) to melanoma cells, where PC upregulates PI3K/AKT and mitochondrial OXPHOS. Melanoma cells with high OXPHOS predominantly seed the lung and brain, but do not colonise the liver, and decreasing oxidative stress with antioxidant supplements shifts tropism from the lung to the liver. In contrast, although the aged stroma has fewer total lipids, it has more ceramides, which activate the S1P/STAT3/IL6 signalling axis to direct melanoma liver tropism. Inhibiting OXPHOS in the young stroma and blocking IL6 receptor in the aged stroma reduces the age-specific patterns of metastasis imposed by stromal lipids.

overall_design: RNA sequencing of c57bl/6j female mammary fat pads of young (8 weeks) and aged (14 months) animals.

last: Virós

first: Shilpa

last: Gurung

first: Fabio

last: Amaral


title: Prolonged airway explant culture enables study of health, disease, and viral pathogenesis

city: Chapel Hill

first: Hong

last: Dang

address: 125 Mason Farm Rd, Cb#7248

institute: University of North Carolina at Chapel Hill

summary: Purpose: To identify cell types and cellular transcriptional profiles in airway explants and precision cut lung slices obtained from non-disease human lung tissue.

overall_design: Methods: Large airway explants (LAE), small airway explants (SAE), and precision cut lung slides (PCLS) obtained from 3 non-disease donor lungs were cryopreserved after 0 (fresh), 2 and 14 days in culture.  Cryopreserved tissues were thawed, enzymatically digested for cell dissociation, and used for scRNA-seq. Single cells were captured using a 10X Chromium controller (10X Genomics) and libraries were prepared following the Single Cell 3’ Reagent Kits v3.1 (Dual Index) User Guide (10X Genomics).

first: Rhianna

last: Lee

first: Kenichi

last: Okuda

first: Jacob

last: Galiger

first: Stephen

last: Schworer

first: Troy

last: Rogers

first: Rodney

last: Gilmore

first: Caitlin

last: Edwards

first: Gillian

last: Crisp

first: Satoko

last: Nakano

first: Anne

last: Cawley

first: Raymond

last: Pickles

first: Samuel

last: Gallant

first: Elisa

last: Crisci

first: Lauraine

last: Rivier

first: James

middle: S

last: Hagood

first: Wanda

last: O'Neal

first: Ralph

last: Baric

first: Barbara

last: Grubb

first: Richard

last: Boucher

first: Scott

last: Randell


title: Interferon gamma suppresses T follicular helper cells and antibody responses upon viral infection

status: Public on Mar 25 2025

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Humoral and cellular immunity upon viral infections usually co-exist; however, sometimes, one of the two responses emerges as dominant and is responsible for most of the antiviral activity. For example, infection with lymphocytic choriomeningitis virus (LCMV) induces very strong cellular responses, but weak and inefficient neutralizing Ab (nAb) responses. Lack of nAb responses is an important issue for complete clearance of LCMV and other similar viruses, which in some instances tend to establish chronic infections. Recent work from our group has shown that this unbalance is observed also at the level of CD4 T cells responses, with subcutaneous LCMV infection leading almost exclusively to TH1 but no TFH differentiation.  Here, we report that LCMV-induced TH1 cells are heterogeneous and comprise a Tcf-1+ subset and a GzmB+ subset. We found that none of the subsets is dependent on the major TH1-polarizing cytokine IL-12. Instead, IFN-gamma (IFN-g) was found to promote the development of GzmB+ cells and to suppress the commitment of the Tcf-1+ population into fully differentiated TFH. As a result, blockade of IFN-g led to a rescue in the TFH population, germinal center B cells and antibody responses. Our results shed light on new mechanisms underlying the inefficient nAbs production in response to non-cytopathic viruses such as LCMV and are promising for the design of new vaccination strategies.

overall_design: scRNA-seq was performed on SMARTA CD4+ T cells which are specific for the MHC-II-restricted GP61-80 epitope of the LCMV glycoprotein. Naïve SMARTA CD4+ T cells were adoptively transferred into WT mice one day prior to s.c. intrafootpad infection with rLCMV and sorted from footpad-draining popliteal LNs (dLNs) five days after infection. To be able to compare transcriptional profiles of TH1 to those of TFH cells, we also sorted total SMARTA CD4+ T cells from dLNs of mice infected with rVSV, a recombinant VSV strain expressing the LCMV WE glycoprotein. Control SMARTA CD4+ T cells were isolated from naïve mice.

first: Eleonora

last: Sala

first: Chiara

last: Laura

first: Eyal

last: David

first: Matteo

last: Iannacone

first: Mirela

last: Kuka


title: Secreted chemokines and transcriptomic analyses reveal diverse inflammatory and degenerative processes in the intervertebral disc of the STZ-HFD mouse model of Type 2 diabetes

city: St Louis

first: Christian

last: Gonzalez

state: MO

address: 450 S Euclid Ave

department: Orthopaedic Surgery

institute: Washington University in St Louis

summary: The chronic inflammation resultant from type 2 diabetes (T2D) is also associated with spinal pathologies, including intervertebral disc (IVD) degeneration and chronic neck and back pain.  Although confounding factors, such as increased weight gain in obesity, studies have shown that even after adjusting age, body mass index, and genetics (e.g. twins), patients with T2D suffer from disproportionately more IVD degeneration and back pain.  We hypothesize that chronic T2D fosters a proinflammatory microenvironment within the IVD that promotes degeneration and disrupts disc homeostasis. To test this hypothesis, we evaluated two commonly used mouse models of T2D – the leptin-receptor deficient mouse (db/db) and the chronic high-fat diet in mice with impaired beta-cell function (STZ-HFD).  STZ-HFD IVDs were more degenerated and showed differential expression of chemokines from the db/db models. Moreover, the RNAseq analysis revealed vast transcriptional dysregulation of many pathways in the STZ-HFD but not in the db/db tissues.  Taken together, the STZ-HFD may better recapitulates the complexities of the chronic inflammatory processes in the IVD during T2D

overall_design: Samples were derived from two cohorts. Cohort 1 is 3 db/db mice and 3 db/+ heterozygous mice as non-diabetic controls. Cohort 2 is 4 Streptozocin-High-Fat-Diet diabetic mice with 4 healthy wild-type C57BL/6J mice as control. Intervertebral discs were extracted, pulverized, and reconstiuted in TRIzol prior to RNA extraction via column extraction in accordance with manufacturer recommendation. RNA in H2O were submitted to the WashU in St Louis GTAC core for Illumina NovaSeq X Plus Analysis.

first: Rachana

last: Vaidya

first: Sade

last: Clayton

first: Simon

last: Tang


title: The epitranscriptome of the MT-4 cell line

first: Kunqi

last: Chen

summary: Epitranscriptomic modifications appear in MT-4 cell line

overall_design: To investigate whether epitranscriptomic modifications is involved in evolution, we performed RIP-seq on MT-4 cell line


title: Stromal lipid species dictate melanoma metastasis and tropism [A375_RNA_seq]

first: Amaya

last: Viros

overall_design: RNA sequencing of A375 cells exposed to serum free (control), old adipocytes secretome (OA) and young adipocyte secretome (YA). All treated for 24 hours.

last: Virós

first: Shilpa

last: Gurung

first: Fabio

last: Amaral


title: Stromal lipid species dictate melanoma metastasis and tropism [MeWo_RNA_seq]

overall_design: RNA sequencing of MeWo cells exposed to serum free (control), old adipocytes secretome (OA) and young adipocyte secretome (YA). All treated for 24 hours.


title: Chromatin activity of IκBα mediates the exit from naïve pluripotency (ChIP-seq Histone marks)

city: Barcelona

first: Anna

last: Bigas

state: Barcelona

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

summary: Inflammatory signals are key in development and cell differentiation but their orchestration with pluripotency and stemness signals is poorly understood. Our previous work identified a chromatin function of IκBα, the NF-κB inhibitor, that is crucial for differentiation in different types of somatic stem cells. Here we demonstrate that deficiency of IκBα imposes a profound chromatin rewiring defect that impacts on DNA methylation, histone post-translational modifications and transcriptional regulation, stabilizing mouse embryonic stem cells (ESCs) in a ground state of pluripotency while preventing them from pluripotency exit and differentiation. By engineering separation-of-function mutants of IκBα with specific binding to either NF-κB or histones, we demonstrate that regulation of pluripotency state by IκBα is independent of NF-kB but requires the chromatin-related IκBα function.

overall_design: We performed ChIP-seq for H3K27me3, H3K9me3, H3K4me3, H3K27ac and H3K4me1 histone marks in mESCs. Per histone mark, three independent biological replicates were tested in two conditions: 3xWT and IκBα 3xKO samples.

first: Luis

middle: G

last: Palma

first: Daniel

last: Álvarez-Villanueva

first: María

last: Maqueda

first: Mercedes

last: Barrero

first: Arnau

last: Iglesias

first: Joan

last: Bertran

first: Damiana

last: Alvarez-Errico

first: Carlos

last: García-Prieto

first: Cecilia

last: Ballaré

first: Virginia

last: Rodríguez-Cortez

first: Clara

last: Bueno

first: August

last: Vidal

first: Alberto

last: Villanueva

first: Pablo

last: Menéndez

first: Luciano

last: di Croce

first: Bernhard

last: Payer

first: Manel

last: Esteller

first: Lluis

last: Espinosa


title: Pioneer transcription factor Runx2 affecting biological function of Schwann Cells via self-inducible reconstruction of super-silencer to remodel chromatin [Smart-seq mRNA]

first: Zhaowei

last: Zhu

overall_design: SCs from neonatal 3-5 day SD rats were isolated and purified. The purified P0 SCs were randomly divided into the Runx2-OE group and EGFP (empty vector) group. SCs were transfected with Runx2-OE or EGFP adenovirus at a concentration of MOI = 200. After 72 hours of incubation in the incubator, the changes in cell morphology were observed under laser confocal microscope. Smart-seq was performed as described previously.

first: Bo

last: He


title: High-Throughput Drug Discovery for a Rare Neurological Disorder: Uncovering a Novel Therapeutic Opportunity for the 19q12 Autism Spectrum Disorder [19q12 neurons baseline data]

status: Public on Mar 24 2025

city: Palo Alto

first: Drishti

last: Guin

state: CA

address: 1804 Embarcadero Rd Ste #201

institute: Transcripta Bio

summary: Discovering new and viable therapies for genetic diseases is a time consuming and cost intensive process. This is even more challenging for rare disorders that affect a small fraction of the population and do not incentivise research and development in the traditional drug discovery lifecycle. There is therefore a need for scalable and efficient solutions for discovering novel therapies for these rare disorders. In this study, we highlight how a high-throughput drug discovery engine was utilized to uncover drugs at scale that normalized the signature for a rare neurological neurodevelopmental disease, 19q12 autism spectrum disorder associated with deficiencies in ZNF536 and TSHZ3. We do this by uncovering and understanding the full 360o view of the biological impact of the drug in a relevant cell line via transcriptomics. This platform, in combination with a statistically viable n-of-1 trial, was able to quickly uncover and utilize a novel therapeutic potential of a previously approved drug for a patient living with from 19q12 autism spectrum disorder.

overall_design: RNA-seq profiling of a 19q12 patient iPSC-derived neurons at 5 timepoints during neuronal differentiation, wildtype neurons treated with Entrectinib at 10 concentrations and whole blood of patient pre- and post-treatment with Entrectinib.

first: Ursula

last: Haditsch

first: Joseph

last: Bellucci

first: Sabine

last: Topka

first: Katherine

last: Dyer

first: Gabriel

last: Rivera Del Toro

first: Michael

last: Blanco

first: Natalie

middle: F

last: Downs

first: Nicole

last: Perfito

first: Christopher

last: Moxham


title: MiR-7a-Klf4 axis as a regulator and therapeutic target of neuroinflammation and ferroptosis in Alzheimer's disease

city: Bengaluru

first: Thimmaiah

last: Govindaraju

state: India

address: Jakkur

department: New Chemistry Unit

country: India

institute: JNCASR

summary: The miRNA expression profiling of annotated miRNA in wild type and APP/PSEN1 Tg mouse brain tissue

overall_design: The total RNA was extracted from cortex and hippocampus of WT and APP/PSEN1 Tg mouse model and subjcetd to miRNA expression profiling of annotated miRNA by Nanostring platform using nCounter Mouse v1 miRNA Panel (NS_M_miR_v1.5) having 599 unique miRNA barcodes for endogenous miRNA.

first: Madhu

last: Ramesh


title: Chromatin activity of IκBα mediates the exit from naïve pluripotency (Methylation array)

first: Anna

last: Bigas

summary: Inflammatory signals are key in development and cell differentiation but their orchestration with pluripotency and stemness signals is poorly understood. Our previous work identified a chromatin function of IκBα, the NF-κB inhibitor, that is crucial for differentiation in different types of somatic stem cells. Here we demonstrate that deficiency of IκBα imposes a profound chromatin rewiring  defect that impacts on DNA methylation, histone post-translational modifications and transcriptional regulation, stabilizing mouse embryonic stem cells (ESCs) in a ground state of pluripotency while preventing them from pluripotency exit and differentiation. By engineering separation-of-function mutants of IκBα with specific binding to either NF-κB or histones, we demonstrate that regulation of pluripotency state by IκBα is independent of NF-kB but requires the chromatin-related IκBα function.

overall_design: Bisulphite converted DNA was hybridised to the Illumina Infinium  Mouse Methylation Beadchip (MM285) array in mESCs and one early differentiation stages (EBs 96h). Per timepoint, 3xWT and IκBα 3xKO independent biological replicates were tested resulting in a total of 12 samples.

first: Luis

last: Palma

first: Daniel

last: Álvarez-Villanueva

first: María

last: Maqueda

first: Mercedes

last: Barrero

first: Arnau

last: Iglesias

first: Joan

last: Bertran

first: Damiana

last: Alvarez-Errico

first: Carlos

last: García-Prieto

first: Cecilia

last: Ballaré

first: Virginia

last: Rodríguez-Cortez

first: Clara

last: Bueno

first: August

last: Vidal

first: Alberto

last: Villanueva

first: Pablo

last: Menéndez

first: Luciano

last: di Croce

first: Bernhard

last: Payer


title: Hominoid-specific transposable elements reshaped neural crest migration in craniofacial development

status: Public on Mar 23 2025

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

summary: Craniofacial development is evolutionarily conserved, yet subtle changes in its regulatory network drive species-specific traits. Transposable elements (TEs) contribute to genome evolution, but their role in cranial neural crest cells (CNCCs) remains unclear. Here, we investigate the domestication of hominoid-specific TEs (LTR5Hs and SVAs) as enhancers during human CNCC specification, a process critical for vertebrate craniofacial development. Using human iPSC-derived CNCCs, we identified ~515 hominoid-specific TEs functioning as enhancers, including ~250 human-specific, predominantly LTR5Hs. These elements are enriched for CNCC coordinator motifs, are bound by the CNCC signature factor TWIST1, and their enhancer activity appears largely CNCC-specific. CRISPR-interference targeting ~75% of these active TEs led to widespread transcriptional dysregulation of genes involved in neural crest migration, and two orthogonal functional assays confirmed that CNCC migration is impaired upon TE repression. Finally, genes near human-specific TEs showed higher expression in human CNCCs compared to chimpanzee CNCCs, but TE repression restored gene expression to chimpanzee levels. These findings highlight how young TEs were domesticated to fine-tune CNCC regulatory networks, potentially contributing to lineage-specific craniofacial evolution.

overall_design:
RNA-seq of day 5 NCCs (5-day protocol) with and without gRNAs (2 replicates and 3 replicates respectively)
ChIP-seq of day 5 NCCs (5-day protocol) with and without gRNAs (1 replicate each)
ATAC-seq of day 5 NCCs (5-day protocol) with and without gRNAs (2 replicates each)
ATAC-seq of day 18 NCCs (18-day protocol) with and without gRNAs (2 replicates each)
ChIP-seq (H3k4me3) of day 5 NCCs (5-day protocol) with and without gRNAs (1 replicate each)

first: Laura

last: Deelen

first: Zoe

last: Mitchell

first: Martina

last: Demurtas

first: Beatriz

last: Garcia Del Valle

first: Andria

last: Koulle


title: Elevated brain manganese induces motor disease by up-regulating the kynurenine pathway of tryptophan metabolism

status: Public on Mar 20 2025

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

summary: Elevated brain levels of the essential metals manganese (Mn), copper, or iron induce motor disease. However, mechanisms of metal-induced motor disease are unclear and treatments are lacking. Elucidating the mechanisms of Mn-induced motor disease is particularly important because occupational and environmental Mn overexposure is a global public health problem. To address this, here we combined unbiased transcriptomics and metabolomics with functional studies in a mouse model of human environmental Mn exposure. Transcriptomics unexpectedly revealed that Mn exposure up-regulated expression of metabolic pathways in the brain and liver. Notably, genes in the kynurenine pathway of tryptophan metabolism, which produces neuroactive metabolites that impact neurological function, were up-regulated by Mn. Subsequent unbiased metabolomics revealed that Mn treatment altered kynurenine pathway metabolites in the brain and liver. Functional experiments then demonstrated that pharmacological inhibition of the first and rate-limiting step of the kynurenine pathway fully rescued Mn-induced motor deficits. Finally, elevated Mn directly activates hypoxia-inducible factor (HIF) transcription factors, and additional mechanistic assays identified a role for HIF1, but not HIF2, in regulating expression of hepatic kynurenine pathway genes under physiological or Mn exposure conditions, suggesting that Mn-induced HIF1 activation may contribute to the dysregulation of the kynurenine pathway in Mn toxicity. These findings (1) identify the upregulation of the kynurenine pathway by elevated Mn as a fundamental mechanism of Mn-induced motor deficits; (2) provide a pharmacological approach to treat Mn-induced motor disease; and (3) should broadly advance understanding of the general principles underlying neuromotor deficits caused by metal toxicity.

overall_design: To analyze manganese (Mn) exposure-induced gene expression changes that may influence motor function in an unbiased manner, we performed 3’Tag-seq analyses in brain, liver and small intestine tissue collected from ~2-month old vehicle or Mn-treated (~50mg MnCl2.4H20/kg body weight daily) C57BL/6J mice.

first: Nishant

last: Sharma

first: Steven

last: Hutchens

first: Chunyi

last: Liu

first: Noah

middle: R

last: Haggerty

first: Kerem

last: Gurol

first: Thomas

last: Jursa

first: Donald

last: Smith

first: Dayne

last: Mayfield

first: Somshuvra

last: Mukhopadhyay


title: Chromatin activity of IκBα mediates the exit from naïve pluripotency

last: Bigas

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

overall_design: Refer to individual Series


title: High-Throughput Drug Discovery for a Rare Neurological Disorder: Uncovering a Novel Therapeutic Opportunity for the 19q12 Autism Spectrum Disorder [DRUGseq]

first: Drishti

last: Guin

overall_design: RNA-seq profiling of response of NGN2-derived glutamatergic neurons to Entrectinib at 10 concentrations using DRUG-seq.

first: Ursula

last: Haditsch

first: Joseph

last: Bellucci

first: Sabine

last: Topka

first: Katherine

last: Dyer

first: Gabriel

last: Rivera Del Toro

first: Michael

last: Blanco

first: Natalie

last: Downs

first: Nicole

last: Perfito

first: Christopher

last: Moxham


title: Siglec-1−/FSClow alveolar macrophages exhibit pro-inflammatory phenotypes in chronic obstructive pulmonary disease

city: Sendai

first: Takuya

last: Saito

state: Miyagi

address: 1-1 Seiryomachi, Aobaku

department: Department of Respiratory Medicine

institute: Tohoku University Graduate School of Medicine

summary: Alveolar macrophages (AMs) in patients with chronic obstructive pulmonary disease (COPD) orchestrate persistent inflammation in the airway, however, sub-populations of alveolar macrophages predominantly participating in chronic inflammation have been poorly characterised. We recently reported that Siglec-1 was involved in recognition and engulfment of non-typeable Haemophilus influenzae and that the expression of Siglec-1 on AMs was decreased in COPD lung tissues. Here, based on the expression of Siglec-1 and the intensity of forward scattergram (FSC) using flow cytometry, we identified three subsets present in alveolar macrophages: Siglec-1+/FSChi, Siglec-1−/FSChi, Siglec-1−/FSClow subsets. The Siglec-1−/FSClow subset increased in number in the lungs of COPD subjects. RNA-sequencing revealed that the Siglec-1−/FSClow subset exhibited pro-inflammatory and protease-producing phenotypes compared to other two subsets. Clinically, a decrease in the intensity of Siglec-1 expression in macrophages of induced sputum from COPD subjects was correlated with exacerbation rates in prospective four years. Collectively Siglec-1− AMs showed the pro-inflammatory properties and that their emergence in COPD airways was a risk factor in exacerbation. The Siglec-1−/FSClow subset might serve as “pathogenic macrophages” which could lead to poor clinical outcomes for patients with COPD

overall_design: Examination of monocytes and AMs in control never smoker (CNS), control ex-smoker (CES) and COPD patient

first: Naoya

last: Fujino

first: Yoshinao

last: Ono

first: Mitsuhiro

last: Yamada

first: Hisatoshi

last: Sugiura


title: RNA-seq on FFPE skin samples

status: Public on Mar 21 2025

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: We evaluated the expression profiles on skin samples that are FFPE.

overall_design: Three FFPE skin samples were RNA-seq profiled

first: Johann

last: Gudjonsson

first: Lam

last: Tsoi


title: High-Throughput Drug Discovery for a Rare Neurological Disorder: Uncovering a Novel Therapeutic Opportunity for the 19q12 Autism Spectrum Disorder [post treatment entrectinib patient data]

first: Drishti

last: Guin

overall_design: RNA-seq profiling of whole blood samples from patient (pre- and 3 and 6 months post-treatment with Entrectinib and a sibling.

first: Ursula

last: Haditsch


title: Chromatin activity of IκBα mediates the exit from naïve pluripotency (RNA-Seq)

first: Anna

last: Bigas

overall_design: We performed bulk RNAseq analysis in mESCs and two early differentiation stages (EBs 48h and EBs 96h). Per timepoint, 3xWT and IκBα 3xKO independent biological replicates were tested resulting in a total of 18 samples.

first: Luis

last: Palma

first: Daniel

last: Álvarez-Villanueva

first: María

last: Maqueda

first: Mercedes

last: Barrero

first: Arnau

last: Iglesias

first: Joan

last: Bertran

first: Damiana

last: Alvarez-Errico

first: Carlos

last: García-Prieto

first: Cecilia

last: Ballaré

first: Virginia

last: Rodríguez-Cortez

first: Clara

last: Bueno

first: August

last: Vidal

first: Alberto

last: Villanueva

first: Pablo

last: Menéndez

first: Luciano

last: di Croce

first: Bernhard

last: Payer

first: Manel

last: Esteller

first: Lluis

last: Espinosa


title: Genome-wide tongue epithelia transcriptomic profiles from K14-rtTA;TRE-FLBmi-1 (KrTB), KrTB+Doxycycline (KrTB-D), KrTB+4-nitroquinoline 1-oxide (KrTB-N), and KrTB+Doxycycline+4-nitroquinoline 1-oxide (KrTB-DN).

status: Public on Mar 19 2025

city: New York City

first: Jorge

last: Baquero

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

summary: We developed a transgenic mouse model (truncated K14-rtTA; TRE/Bmi1, KrTB) containing a doxycycline- (dox) controlled, Tet-responsive element system to selectively overexpress BMI1 only in the basal epithelial SCs of the tongue. Here, we used this model to delineate BMI1 actions in tongue epithelia during oral tumorigenesis (as induced by 4-nitroquinoline 1-oxide, 4-NQO). Genome-wide transcriptomics indicated that mRNAs associated with human OSCC, including SOX9, HIF1A, MMP9, INHBB, and MYOF, were further increased by ectopic BMI1 expression in murine tongue epithelia. mRNAs encoding multiple metabolic targets, such as SLC2A1 (GLUT1), PKM, LDHA, and HK2, were also increased upon BMI1 overexpression in 4-NQO-treated tongue epithelia.

overall_design: Examination of genome-wide transcript levels in mouse tongue epithelia samples. 16 samples were analyzed, 4 biological replicates per condition (KrTB vs. KrTB-D and KrTB-N vs. KrTB-DN).

first: Xiao-Han

last: Tang

first: Daniel

last: Galke

first: Theresa

last: Scognamiglio

first: Tuo

last: Zhang

first: Dawson

last: Miller

first: Qiuying

last: Chen

first: Steven

last: Gross

first: Lorraine

last: Gudas


title: Transcript abundance in C. necator grown with piezo-stimulated ZnO

city: Wuhan

first: Pier-Luc

last: Tremblay

state: Hubei

address: 122 Luoshi Road

department: School of Chemistry, Chemical Engineering and Life Science

institute: Wuhan University of Technology

summary: The transcriptome of C. necator H16 grown autotrophically with H2:CO2:O2 in the presence of piezocatalytic ZnO nanosheets under intense tilting agitation at 200 rpm

overall_design: Illumina RNA-seq of total RNA extracted from C. necator H16 grown for 36 hours with H2:CO2:O2 (74:13:13) and 0.8 g/L ZnO nanosheets in nitrogen-limited minimal medium at 30 ℃ under intense tilting agitation at 200 rpm

first: Ziqiu

last: Li

first: Mengying

last: Xu

first: Chun

last: He

first: Yujie

last: Wang

first: Tian


title: CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [iCLIP2]

city: Miami

first: Danny

last: Reinberg

state: FL

address: 1501 NW 10th Avenue (C227)

department: John T. MacDonald Department of Human Genetics

institute: Miller School of Medicine and Sylvester Comprehensive Cancer Center

summary: CCCTC-binding factor (CTCF) is essential for chromatin organization, but its role in dynamically shaping chromatin loops during cellular differentiation is not fully understood. We previously demonstrated that CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA-binding region disrupts chromatin loops in mouse embryonic stem cells (ESCs). Using an ESC-to-neural progenitor cell (NPC) differentiation model, we show that the ZF1 RNA-binding region of CTCF is crucial for maintaining cell-type specific chromatin loops. Expression of CTCF-∆ZF1 leads to dysregulation of genes within these disrupted loops, particularly those involved in neuronal development and function. We identified NPC-specific, CTCF-interacting RNAs and chose Podxl and Grb10 for further study. We found that CRISPR-Cas9-mediated truncation of Podxl and Grb10 disrupts chromatin loops in cis, similar to the disruption seen in the NPC-∆ZF1 mutant. Our study underscores the importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity.

overall_design: CTCF iCLIP2 analysis of CTCF-AID2 degron and CTCF rescue wild-type (WT) and ΔZF1 mutant in both embryonic stem cells (ESCs) and neural progenitor cells (NPCs).

first: Kimberly

last: Lucero


title: Two distinct durable human switched memory B cell populations are induced by vaccination and infection

city: Cambridge

first: Cory

middle: Adam

last: Perugino

address: 600 Main Street

institute: Ragon Institute of MGH, MIT and Harvard

summary: The traditional definition of memory lymphocytes encompasses antigen-experienced, durable subsets that persist in the absence of antigen and are capable of responding to the antigen on subsequent encounters. We examined the relative durability of eight different non-overlapping class-switched human B cell sub-populations (excluding plasmablasts) that together encompass 100% of all human class switched B cells and identified only two long-lived B cell populations that persist after vaccination in the relative absence of their cognate antigen.  In addition to canonical switched memory B cells (SWM) with an IgD- CD27+ CXCR5+ phenotype, a second, non-canonical but distinct memory population of IgD- CD27- CXCR5+ (double negative 1, DN1) B cells is also durable. Beyond surface phenotyping, DN1 memory B cells intriguingly exhibit lower levels of replacement mutations in complementarity determining as well as framework regions of their B cell receptors and have longer CDRH3 sequences relative to canonical SWM B cells. This non-canonical, human memory B cell subset is distinguished by a distinct TP63 driven transcriptional signature that has been linked to extended cell survival and these B cells persist in the circulation at least as long as canonical SWM B cells. Non-canonical human DN1 memory B cells therefore represent a second, distinct, durable, less somatically hypermutated, class-switched human memory B cell subset defined by a unique transcriptomic signature, that likely arises outside germinal centers and may have evolved to preserve immunological breadth.

overall_design: RNA-seq data of 18 samples, comprised of three groups, N, S, and D, representing three types of cells, i.e., "Naive B", "Switched Memory B", and "DN1 B" cells. Each group has 6 biological replicates.

first: Cory A.

first: Hang

last: Liu

first: Jared

last: Feldman

first: Jess

last: Marbourg

first: Thomas V.

last: Guy

first: Anson

last: Hui

first: Nicole

last: Ingram

first: Neha

last: Chaudhary

first: Weiyang

last: Tao

first: Catherine

last: Jacob-Dolan

first: Blake M.

last: Hauser

first: Zayd

last: Mian

first: Anusha

last: Nathan

first: Zezhou

last: Zhou

first: Clarety

last: Kaseke

first: Rhoda

last: Tano-Menka

first: Matthew A.

last: Getz

first: Fernando

last: Senjobe

first: Cristhian

last: Berrios

first: Onosereme

last: Ofoman

first: Zachary

last: Manickas-Hill

first: Duane R.

last: Wesemann

first: Jacob E.

last: Lemieux

first: Marcia B.

last: Goldberg

first: Kerstin

last: Nundel

first: Ann

last: Moormann

last: Marshak-Rothstein

first: John A.

last: Iafrate

first: Gaurav

last: Gaiha

first: Richelle

last: Charles

first: Alejandro B.

last: Balazs

first: Aridaman

last: Pandit

first: Vivek

last: Naranbhai

first: Aaron G.

last: Schmidt

first: Shiv

last: Pillai


title: Genomewide temporal landscape of DNA methylation in pregnant women delivering at term in GARBH-InI cohort

city: Kalyani

first: Arindam

last: Maitra

state: West Bengal

address: PO: NSS

institute: National institute of Biomedical Genomics

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of peripheral blood DNA collected from pregnant individuals throughout three time points (11-14 weeks, 18-20 weeks, 26-28 weeks) across the period of gestation and at term delivery (>37 weeks of gestation). Illumina Infinium EPIC Human DNA methylation Beadchip v1.2.8 was used to obtain DNA methylation profiles across approximately 850k CpGs. Maternal peripheral blood samples were collected in EDTA vacutainers. The goal was to identify temporal DNA methylation changes in maternal peripheral blood during the period of gestation and associate their impact on biological pathways critical for term delivery.

overall_design:
Genome wide DNA methylation profiling of peripheral blood DNA collected from pregnant individuals throughout the period of gestation and at delivery. The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2.8 was used to obtain DNA methylation profiles across approximately 850k CpGs. Maternal peripheral blood samples were collected in EDTA vacutainers.
(contributor) GARBH-Ini Team

first: Jagyashila

last: Das

first: Indranil

last: Bagchi

first: Shekhar

last: Ghosh

first: Nitya

last: Wadhwa

first: Uma

last: Chadramouli Natchu

first: Ramachandran

last: Thiruvengadam

first: Pallavi

last: Kshetrapal

first: Shinjini

last: Bhatnagar

first: Partha

middle: P

last: Majumder


title: Decoding Genome-wide Dysregulation of Translation in eIF2B-mutant Astrocytes: Implications for Vanishing White Matter Disease

city: Tel Aviv

first: Shir

last: Mandelboum

address: chaim levanon

department: Sagol School of Neuroscience

institute: Tel Aviv University

summary: eIF2B is a master regulator of translation initiation and mediator of the integrated stress response (ISR). Partial-loss-of function mutations are associated with eIF2B-leukodystrophy termed Vanishing White Matter Disease (VWMD), a recessive neurodegenerative disorder. Astrocytes, the brain homeostasis keepers, are central to VWMD owing to their hyper-sensitivity to eIF2B activity, as manifested by their phenotypic deficits due to the mutation. Here we used astrocytes isolated from the brains of WT and eIF2B5R132H/R132H mice to assess their transcriptome and translatome responses upon cytokine-mediated activation, an mTOR-driven process critical for brain homeostasis. We found that: (i) a mild eIF2B mutation has the power to disrupt translation regulation programs involving ~30% of the expressed genes; (ii) a common compensatory strategy to overcome the translation regulation failure is manipulation of mRNA abundance; and (iii) dysregulation of functionally related genes can be used to reliably predict deficits of corresponding cellular functions. Specifically, the study illuminates the molecular anomalies responsible for the impaired ribogenesis and mitochondrial respiration of eIF2B-mutant astrocytes. Moreover, it reliably predicts, for the first time, impaired cholesterol biosynthesis in eIF2B-mutant astrocytes. This work demonstrates the strength of combined transcriptome/translatome approach to decipher links between mild expression anomalies and downstream cellular defects associated with VWMD.

overall_design: Three biological repetitions of Eif2b5-R132H-R132H mutant primary astrocytes were treated or not with 20ng/ml TNFα and 0.25ng/ml IL-1β  for 24 hr or 48 hr. A portion of each sample was treated with RNase-I to generate ribosome footprints used for Ribo-seq analysis, while an undigested portion was used for RNA-seq.

first: Liat

last: Lev-Ari

first: Andrea

last: Atzmon

first: Melisa

last: Herrero Boco

first: Naama

last: Brezner

first: Daniel

last: Ben-halevy

first: Orna

last: Elroy-Stein


title: Pattern of variation in DNA methylation during pregnancy among mothers who delivered preterm in the GARBH-Ini cohort

first: Arindam

last: Maitra

summary: Genome wide DNA methylation profiling of peripheral blood DNA collected from pregnant individuals throughout the period of gestation and at delivery. The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2.8 was used to obtain DNA methylation profiles across approximately 850k CpGs. Maternal peripheral blood samples were collected in EDTA vacutainers.

overall_design: Bisulphite converted DNA from the 136 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip v1.2.8

first: Soumi

last: Sarkar

last: Nachu


title: Longitudinal DNA methylation profile of peripheral blood in women delivering preterm informs predictive biomarkers

first: Jagyashila

last: Das

first: Indranil

last: Bagchi

last: Ghosh

last: Chadramouli Nachu

first: GARBH-Ini

last: Team


title: CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [RNA-seq]

first: Danny

last: Reinberg

overall_design: RNA-seq profiling of CTCF-AID2 degron and CTCF rescue wild-type (WT) and ΔZF1 mutant in both embryonic stem cells (ESCs) and neural progenitor cells (NPCs). RNA-seq profiiling of Podxl and Grb10 RNA truncation mutants in NPCs.

first: Kimberly

last: Lucero