title: The hegemonic EWSR1::ETS oncogene overrules core regulatory circuitry mechanisms in Ewing sarcoma [ChIP-seq 2]

first: Olivier

last: Delattre

overall_design:
ChIP-seq (H3K27ac and FLI1) were performed to complete the actual catalog of Ewing sarcoma cell line. We also generate H3K27ac profile after inhibiting the oncogene EWSR1::ETS and in some MSC models. Some transcription factors defined as CRC candidates were also sequenced (IKZF2, POU3F2, SOX6)

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

last: Grossetete

first: Sakina

last: Zaidi

first: Karine

last: Laud-Duval

first: Didier

last: Surdez


title: Unravelling the molecular activation of the reparative cardiac fibroblasts after myocardial infarction

status: Public on Dec 15 2025

city: Thuwal

first: Laura

last: Sudupe

address: King Abdullah University of Science and Technology (KAUST)

country: Saudi Arabia

institute: KAUST

summary: Cardiac fibroblasts have a central role during the ventricular remodeling process associated to different types of cardiac injury. Recent studies have shown that fibroblasts do not respond homogeneously to heart damage, suggesting that the adult myocardium may contain specialized fibroblast subgroups with specific functions. Due to the limited set of bona fide fibroblast markers, a proper characterization of fibroblast population dynamics in response to cardiac damage is still missing. Using single-cell RNA-seq we have identified and characterized a fibroblast subpopulation that emerges in response to myocardial infarction (MI) in a murine model. These activated fibroblasts exhibit a clear pro-fibrotic signature, and localize to the wounded myocardium. Combining epigenomic profiling with functional assays, we unveil important candidate regulators mediating their response to cardiac damage.

overall_design: Time-course of study of cardiac fibroblasts after myocardial infarction. Samples include control, 3 and 5 days after myocardial infarction.

first: Silvia

middle: C

last: Hernandez

first: Marina

last: Ainciburu

first: Nuria

last: Planell

first: Amaia

last: Vilas-Zornoza

first: Maria

last: López-Moreno

first: Sarai

last: Sarvide

first: Luis

last: Díaz-Martínez

first: Jorge

last: Cobos-Figueroa

first: Patxi

last: San Martin-Uriz

first: Emma

last: Muiños-López

first: Gloria

last: Abizanda

first: Purificación

last: Ripalda-Cemboráin

first: Felipe

last: Prosper

first: Adrian

last: Ruiz-Villalba

first: David

last: Gomez-Cabrero


title: Bulk RNA-seq analysis reveals the crucial role of Collagen triplex helix repeat containing-1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction

city: Pamplona

first: Núria

address: Pio XII, 55

country: Spain

institute: CIMA - UNAV

type: Expression profiling by high throughput sequencing

summary: Cardiac fibroblasts have a central role during the ventricular remodeling process associated to different types of cardiac injury. Recent studies have shown that fibroblasts do not respond homogeneously to heart damage, suggesting that the adult myocardium may contain specialized fibroblast subgroups with specific functions. Due to the limited set of bona fide fibroblast markers, a proper characterization of fibroblast population dynamics in response to cardiac damage is still missing. Using single cell RNA-seq we have identified and characterized a fibroblast subpopulation that emerges in response to myocardial infarction (MI) in a murine model. These activated fibroblasts exhibit a clear pro-fibrotic signature, and localize to the wounded myocardium. Combining epigenomic profiling with functional assays, we unveil important candidate regulators mediating their response to cardiac damage.

overall_design: Time-course of study of cardiac fibroblasts after myocardial infarction. Samples include 1, 2, 3, 4, 5 and 6 days after myocardial infarction.

first: Juan

middle: P

last: Romero

first: Elena

last: Iglesias

first: Diego

last: Alignani


title: METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [CRISPR screen_22Rv1]

city: TORONTO

first: Xin

last: Xu

state: Ontario

address: 101 COLLEGE ST EAST TOWER 11-601D

country: Canada

institute: Princess Margaret Cancer Center

summary: In this study, we used a targeted CRISPR/CasRx-METTL3 screen to identify m6A peaks that are critical for prostate and lung cancers.

overall_design: The CRISPR screen employed in our pooled sgRNA library consisted of ~12,045 sgRNAs targeting m6A peaks in prostate cancer and lung cancer patients, with 5 sgRNAs per gene on average. The sgRNAs were designed using the "cas13design". Stable dCasRx-METTL3-expressing 22Rv1 cell line was generated. dCasRx-METTL3-expressing 22Rv1 cell line was infected with the library at an MOI of ~ 0.3 and coverage of 400x. 24h post-infection, cells were selected with blasticidin for 5 days and part of cells were sujected to DNA extraction as day 0. Other cells were cultured in dish for ~16 days (day 16), maintaining 400x coverage prior to our screening assay. Genomic DNA was extracted from replicate samples and sgRNA inserts were amplified by PCR. The input amount of genomic DNA was calculated to achieve 400x coverage of the library and resulting libraries were sequenced on an Illumina HiSeq500.

first: Yujuan

last: Wang

first: Helen

last: Zhu

first: Housheng

middle: H

last: He


title: Immune polarization of type 1 and type 2 mouse eosinophils

city: Scottsdale

first: Elizabeth

middle: A.

last: Jacobsen

state: AZ

address: 13400 E. Shea Blvd.

country: USA

institute: Mayo Clinic

summary: Eosinophils have specific immune phenotypes in type 2 and type 1 environments both in vitro and in translational models of disease in vivo. RNA sequencing was completed on mouse blood eosinophils cultured with cytokines that represent a Th2 (IL-33, IL-4, GM-CSF) or Th1 (TNFα/IFNγ)-associated environment cytokines.

overall_design: Eosinophils were isolated from the blood of IL-5 Tg mice (NJ.1638) and cultured for 18 hrs in different conditions prior to RNA isolation for RNA sequencing. Eosinophils were cultured at 5 million cells per ml in standard RPMI-1640+10% FBS + 1X streptomycin-penacllin-glutamine.  One experiment included duplicates of control eosinophils (CN) has no cytokines added conducted at the same time as eosinophils (E1) were cultured with 15ng/mL IFN-gamma and TNF-alpha. A second experiment included duplicates of IL-5 eosinophils (E0) were cultured with IL-5 10 ng/mL and eosinophils  (E2) were cultured with 10ng/ml of IL-5, GM-CSF, IL-4 and 30ng/mL IL-33.

middle: A


title: Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells [ATAC-seq]

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Inactivation of the von Hippel-Lindau tumor suppressor leads to stabilization of HIF transcription factors and subsequent oncogenic HIF-2 signaling in ccRCC. However, little is known about the transcriptional mechanisms leading to dysregulation of HIF-2α mRNA in renal cancer. Epigenetic analysis of the EPAS1 locus (coding for HIF-2α) using ATAC-seq, ChIP-seq and RNA-seq revealed an oncogenic enhancer that maintains a HIF-dependent feed-forward circuit of HIF-2α regulation in renal tumor cells.

overall_design:
This study consists of ATAC-seq, ChIP-seq, CUT&Tag-seq and RNA-seq samples from primary tubular and primary ccRCC cells as well as genetically modified 786-0 and RCC4 cells.

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Access to unprocessed raw data of primary cells is restricted to protect the privacy and intent of research participants consistent with the informed consent agreements provided by individual research participants.
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first: Johannes

last: Schödel

first: Stephanie

last: Naas


title: METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers

summary:
This SuperSeries is composed of the SubSeries listed below.
GSE242444
GSE242446
GSE255792
GSE255794
GSE312888
GSE312890

overall_design: Refer to individual Serieshttps://submit.ncbi.nlm.nih.gov/geo/submission/update/?acc=GSE242447


title: METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [RNA-Seq_shKD]

summary: To investigate the molecular role of CHD9 in prostate cancer, we knockdown CHD9 gene by two different shRNAs in 22Rv1 cells.

overall_design: Differential gene expression analysis of RNA-seq data for KD control cells and KD CHD9 cells


title: METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [ChIP-Seq]


title: The hegemonic EWSR1::ETS oncogene overrules core regulatory circuitry mechanisms in Ewing sarcoma [RNA-seq]

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: Ewing sarcoma is an aggressive bone tumor of adolescence characterized by a hallmark EWSR1::FLI1 fusion oncogene. This chimeric protein drives tumorigenesis by reshaping transcriptional and epigenetic landscapes. However, how it is transcriptionally regulated and whether additional master transcription factors (MTFs) form a core regulatory circuit (CRC) in Ewing sarcoma remain unclear. Here, using an extensive panel of Ewing sarcoma cell lines and primary tumors, we mapped super-enhancers and identified strong enrichment of GGAA microsatellites, confirming their specificity to Ewing sarcoma as compared to other pediatric cancers and normal tissues. Integrating transcriptomic, epigenetic, 3D chromatin conformation, and dependency data, we predicted a set of MTFs potentially comprising a CRC. However, functional validation demonstrated that these MTFs neither establish auto-regulatory loops nor confer proliferative dependencies typical of CRC s in other pediatric tumors. Instead, EWSR1::FLI1 emerged as an “hegemonic” oncogene, regulating the expression of these MTFs without reciprocal regulation. Knockdown (KD) of EWSR1::FLI1 strongly reduced Ewing sarcoma cell proliferation and shifted H3K27ac profiles toward mesenchymal states, whereas silencing of individual or combined MTFs did not alter cell growth or EWSR1::FLI1 expression. These findings highlight the absence of a classical CRC in Ewing sarcoma and emphasize EWSR1::FLI1 as the dominant oncogene but also as a major vulnerability in this disease.

overall_design: Expression data (RNA-seq) in Ewing sarcoma cell line expressing or not the oncogene EWSR1::ETS

first: Sandrine

last: Grossetete

first: Sakina

last: Zaidi

first: Karine

last: Laud-Duval

first: Didier

last: Surdez


title: Chromatin accessibility profiling of HSPC-derived erythroblast differentiation [ATAC-seq]

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: A prime goal of regenerative medicine is to replace dysfunctional cells in the body. To design protocols for producing target cells in the laboratory, one may need to consider exponentially large combinations of culture components. Here, we tested the potential of iteratively approximating the target phenotype by quantifying the distance between chromatin profiles (ATAC-seq) of differentiating cells in vitro and their in-vivo counterparts. We tested this approach on the well-studied generation of erythroblasts from haematopoietic stem cells, evaluating a fixed number of components over two sequential differentiation rounds (8x8 protocols). We found that the most erythroblast-like cells upon the first round yielded the most erythroblast-like cells at the second round, suggesting that greedy selection by chromatin approximation can be a viable optimisation strategy. Furthermore, by targeting transcriptional regulators linked to chromatin regions that were incompletely reprogrammed even after two rounds of differentiation, we could make a data-driven selection of additions to the protocol that further improved erythropoiesis. In future, our methodology can help craft notoriously difficult cells in vitro, such as B cells.

overall_design: 165 ATAC-seq datasets from two round of differentiation with different treatment combinations: 16 from pilot experiment (8 combinations round 1 only) + 135 full experiment (8 combinations round 1; 8x8 combinations round 2) + 15 validation experiment with adapted treatment protocols (+TGFB or IL4);  2-3 replicates per condition, low-quality samples removed

first: Luis

middle: F

last: Montano-Gutierrez

first: Sophie

last: Müller

first: Ana

last: Kutschat

first: Igor

last: Adameyko

first: Davide

last: Seruggia


title: PUF60-Mediated Splicing Is a Key Driver of Triple Negative Breast Cancer

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

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

overall_design: Refer to individual Series


title: Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients

city: Antwerpen

first: Nicolaas

last: Van Renne

address: Universiteitsplein 1

country: Belgium

institute: Laboratory of Experimental Medicine and Pediatrics (LEMP)


title: Cancer cells transfer invasive properties through microRNAs contained in collagen-tracks

status: Public on Dec 14 2025

city: Orsay

first: Kevin

last: MOREAU

address: Rue Henri Becquerel – CS 90030

institute: CNRS

summary: Invasion is a prerequisite for metastasis formation. During tumor development, type I collagen overexpression increases tumor microenvironment stiffness, facilitating cancer cell dissemination. During breast cancer cell migration in 2D and 3D matrices, we observed membrane debris left behind, attached to the collagen fibrils, along the migration path. We named these structures collagen-tracks. Their formation is stimulated by the interaction between the extracellular matrix (ECM) and matrix receptors, such as the discoidin-domain receptor 1 (DDR1). They present a specific nucleic acid and protein contents. When deposited by highly invasive breast cancer cells, internalized collagen-tracks reprogram non-invasive cells into highly pro-metastatic ones by inducing a partial epithelial–mesenchymal transition (EMT) associated with an increase in ECM degradation and cell invasiveness. This cell reprogramming is dependent on specific miRNAs identified in the collagen-tracks. Collagen-tracks thus represent a new form of cell-cell communication important for driving tumor invasion that could be targeted to prevent metastasis.

overall_design: RNA-seq profiling of MCF7 (WT) on collagen and MCF7 with collagen-tracks on collagen after 72H

first: Frederic

last: Saltel

first: Lucile

last: Rouyer

first: Léa

last: Normand

first: Elodie

last: Richard

first: Nathalie

last: Allain

first: Julie

last: Giraud

first: Sylvaine

last: Di-Tommaso

first: Anne-Aurélie

last: Raymond

first: Cyril

last: Dourthe

first: Jean-William

last: Dupuy

first: Kévin

last: Moreau

first: Richard

last: Iggo

last: Dugot-Senant

first: Gaetan

last: MacGrogan

first: Anthony

last: Bouter

first: Sisareuth

last: Tan

first: Alexandre

last: Favereaux

first: Violaine

first: Reini F.

last: Luco

first: Manon

last: Ros


title: NGLY1-dependent conversion of N-glycosylated N to D is essential for transcription of proteasome genes

city: Tokyo

first: Yukiko

last: Yoshida

address: 2-1-6, Kamikitazawa, Setagaya-ku

department: Department of Basic Medical Sciences

country: Japan

institute: Tokyo Motrolopotan Institute of Medical Science

summary: To investigate the sequence editing-specific effects on Nrf1 functions, we utilized glycan-less Nrf1 mutants, 9NA and 9ND, in which all nine of the putative N-glycosylation sites (N-X-S/T; asparagine (N) serine (S), threonine (T), and X is any amino acid except proline) were replaced with alanine (A) and aspartic acid (D), respectively. To comprehensively understand the effects of Nrf1 sequence editing on the transcriptome, microarray analysis was performed on NGLY1-KO HeLa cells stably expressing 9NA and 9ND.

overall_design: Three independent total RNA samples from 20 nM Btz (for 15 h) treated NGLY1-KO HeLa cells without/ with stably expressing 9NA-Nrf1-HA or 9ND-Nrf1-HA were purified.

first: Yasumasa

last: Nishito


title: Transcriptomics in T2-high severe asthmatics treated with biologics: Comparison between anti-IgE, anti-IL-5 and anti-IL-5R-targeted treatments.

status: Public on Dec 13 2025

city: Liège

first: Sara

last: Gerday

address: Av. Hippocrate 1/11

institute: GIGA Research Institute

summary: Background : Biologic therapies have transformed severe asthma management, particularly for T2-high asthma. We aimed to investigate blood proteomics and transcriptomics after biologic treatment. Methods : A prospective study was conducted on 35 patients with severe T2-high asthma treated with mepolizumab (n=9), benralizumab (n=14), or omalizumab (n=12). Evaluations occurred at baseline and after 16 weeks (omalizumab) or 24 weeks (mepolizumab, benralizumab) of treatment. Blood samples were collected. Gene expression was analyzed via Illumina TruSeq RNA Prep, with RNA sequencing on the Illumina NovaSeq-6000 platform. Results : RNA-seq analysis revealed 86 down-regulated genes common to both mepolizumab and benralizumab, primarily associated with eosinophils, basophils, and the purinergic receptor signaling pathway. Additionally, there was evidence of gene regulation involved in antiviral immunity. However, specific gene modulation was observed for benralizumab (114 genes) and mepolizumab (68 genes). Changes following omalizumab treatment were minimal, with only three significantly down-regulated genes. Conclusion : While omalizumab showed minimal quantifiable effects on gene expression, mepolizumab and benralizumab—despite exhibiting distinct profiles—both induced down-regulation of genes related to eosinophil and basophil biology and purinergic signaling pathways, alongside up-regulation of genes involved in innate antiviral immunity.

overall_design: RNA-seq profiling to assess the modifications of blood inflammatory signals and inflammatory cell profile in samples collected at baseline and after 16-24 weeks of treatment in severe asthmatic patients.

first: Florence

last: Schleich

first: Mare

last: Sabbe

first: Catherine

last: Moermans

first: Françoise

last: Guissard

first: Carole

last: Sanchez

first: Severine

last: Kenens

first: Virginie

last: Paulus

first: Monique

last: Henket

first: Fabrice

last: Bureau

first: Christophe

last: Desmet

first: Renaud

last: Louis


title: Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells [RNA-seq]

first: René

last: Krüger

first: Johannes

last: Schödel

first: Stephanie

last: Naas


title: PPSR1 Protein Functions as an Important Regulator to Enhance Plant Growth Performance Under N, P, and K Deficient Stress Conditions

city: Saskatoon

first: Jieyu

last: Chen

state: SK

address: Collaborative Science Research Building, 112 Science Place

department: Department of Biology

institute: University of Saskatchewan

summary: Phosphorus (P) is an essential macronutrient for various biological processes in plant growth. Modern agricultural science has advanced the knowledge of regulatory mechanisms underlying phosphorus starvation responses (PSRs), aiming to develop phosphate-efficient crops with sustainable production under reduced Pi fertilizer application. However, information regarding coordinated shoot and root adaptation in response to combined nutrient stresses is limited. This study investigated the role of Phloem Phosphate Stress Repressed 1 (PPSR1) in modulating PSRs and other nutrient adaptation. The Arabidopsis functional homologue of Cucumis sativus PPSR1 (CsPPSR1), designated AtPPSR1, was identified. AtPPSR1 encodes a glycine-rich domain-containing protein, and its ectopic expression confers enhanced growth performance to plants. Transcriptomic analyses revealed AtPPSR1 as a regulatory mediator of PSRs, photosynthesis and root development. We revealed that AtPPSR1 interacted with PHOSPHATE STARVATION RESPONSE 1 (PHR1) to regulate PHR1-target genes for adaptive root development, in response to Pi-starvation stress. Additionally, AtPPSR1 was discovered as graft-transmissible, and the shoot-borne AtPPSR1 played a role in restoring the root phenotype of the ppsr1 mutant. Physiological analyses revealed that enhanced AtPPSR1 expression enabled resilience to nitrogen (N) and potassium (K)-starvation, as well as to Pi-deficiency. Furthermore, we identified homologues of CsPPSR1 and AtPPSR1 in Brassica napus (canola), which displayed similar expression patterns in response to Pi-starvation stress. Overexpression of PPSR1, identified from Arabidopsis, cucumber and canola, improved growth performance and seed yield in canola under N-, Pi- or K-deficient conditions. These findings provide novel insights into PPSR1-mediated molecular coordination to improve growth performance under mineral nutrient-stresses conditions.

overall_design: Transcriptomics analyses on leaves and roots of Col-0 (WT), ppsr1(KO), and a representative AtPPSR1 overexpression line (OE), which were grown hydroponically for four weeks, and given a Pi-sufficient (200 µM Pi, C200) or Pi-deficient (0 µM Pi, C0) treatment for twenty-four hours.

first: Chuanhezi

last: Quan

first: Yang

last: Zhao

first: Zhangjun

last: Fei

first: Leon

last: Kochian

first: William

last: Lucas

first: Byung-Kook

last: Ham


title: DNA methylation and lncRNA expression control asynchronous DNA replication at imprinted gene domains

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

institute: CNRS/ Université de Paris

type: Genome variation profiling by genome tiling array

summary: Eukaryotic genomes are structured in zones that replicate predominantly early or late.  Besides these genome-wide patterns of replication timing (RT), some genes display asynchronous replication between the two alleles in certain stem cells, brought about by stochastic processes and genetic polymorphisms.  To what extent epigenetic modifications control asynchronous replication remains unclear.  As a paradigm to address this question we explored imprinted chromosomal domains, at which parental DNA methylation imprints mediate parental allele-specific gene expression.  Our genome-wide and locus-specific RT assays in mono-parental and hybrid mouse embryonic stem cells (mESCs) reveal a pronounced replication asynchrony between the parental chromosomes at the Dlk1-Dio3 and Snrpn domains.  This asynchrony is strictly parent-of-origin dependent.  By generating a range of mutant mESC lines, we find that the replication asynchrony at Dlk1-Dio3 is mediated by parental allele-specific methylation at DMRs (Differentially Methylated Regions).  Moreover, lncRNA polycistron expression controls early replication across parts of the domain on the maternal chromosome.  As a result, at these imprinted domains, RT domains become unlinked from 3D chromatin architecture as assayed by Hi-C.  Our combined data highlight how parental DNA methylation imprints and lncRNA expression can locally be used to override intrinsic RT domain organization.

overall_design: nascent-DNA from early S-phase versus nascent-DNA from late S-phase

first: Yui

last: Imaizumi

first: Robert

last: Feil


title: NRF2 upregulation by CDDO-Me protects AC16 human cardiomyocytes against doxorubicin-induced toxicity_3.

status: Public on Dec 12 2025

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

country: United Kingdom

institute: University of Liverool

summary: Sequencing study was performed to elucidate the mechanisms underpinning doxorubicin-induced toxicity in human AC16 cells and the protection afforded by the NRF2 inducer CDDO-Me.

overall_design: AC16 cells were plated and cultured with DMSO (vehicle control), 100 nM CDDO-Me + 100 nM doxorubicin for a total of 72 h. RNA-seq was performed to measure differential transcript expression.

first: James

last: Roberts

first: Mihcael

last: Batie

first: Parveen

last: Sharma


title: Dll4 coordinates endothelial migration and smooth muscle cell recruitment to assemble the umbilical cord and placental vasculature

city: Philadelphia

first: Mark

last: Kahn

state: PA

address: 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

summary: Proper development of the umbilical cord and placental vasculature is essential for embryonic growth and development. While the allantois is known give rise to endothelial cells within the placenta, whether the allantois gives rise to endothelial cells (ECs) in the umbilical cord is highly debated. Furthermore, a lack of genetic tools to study placental vascular development independent of the embryo proper has hindered robust investigation into the primary cause of vascular defects from early studies utilizing global knockouts. In this study, we sought to delineate the contribution of the allantois to the umbilical vessels and utilize a novel mouse genetic tool previously developed by our lab to revisit the role of Notch signaling during formation of the placental vasculature. We show that the allantois has mosaic contribution to the umbilical endothelium with higher contributions closer to the placenta. Loss of Notch signaling through deletion of Dll4 in the allantois causes abnormal vascular development in the umbilical cord and placenta with secondary defects on the heart. Lastly, we identify Unc5b as a novel effector of Dll4 signaling that simultaneously restricts EC migration while promoting chemokine signaling for vascular smooth muscle cell recruitment to arteries. These findings identify a novel genetic tool for investigating placental vascular development and give new insights into the ontogeny and mechanisms of placental and umbilical vascular development.

overall_design: Human umbilical artery endothelial cells were treated with siRNAs targeting DLL4, UNC5B, both DLL4 and UNC5B or scrambled control. Total RNA was extracted and sequenced.

first: Derek

last: Sung

first: Jesse

last: Pace


title: Identification of Novel Regulators of LINE-1 Expression via CRISPR/Cas9 Screening

city: Lexington

first: Liyang

last: Diao

state: MA

address: 36 Ledgelawn Ave

institute: Sprout Informatics

summary: Background Long Interspersed Nuclear Elements-1 (LINE-1, L1) are transposable elements that make up roughly 17% of the human genome. These elements can copy and insert themselves into new genomic locations [1]. Typically, LINE-1 is repressed in healthy tissues but may become activated in various human diseases. LINE-1 expression has been associated with aging [2–4], neurodegenerative disorders [5–7], cancer [8–10], and autoimmune diseases [11,12]. Despite the strong association between LINE-1 expression and disease, the regulatory mechanisms controlling the expression of LINE-1-encoded ORF1p and ORF2p and the link between LINE-1 activity and cancer cell survival remain poorly understood. Gaining insights into these regulatory pathways may help elucidate how LINE-1 contributes to disease pathogenesis.  Results To identify upstream regulators of LINE-1 and genes associated with LINE-1 activity-dependent lethality, we developed a dual-reporter system that simultaneously monitors the protein levels of LINE-1-encoded ORF1p and ORF2p (wild-type or catalytically inactive EN/RT mutant). Using genome-wide CRISPR/Cas9-based screens with this system, we identified candidate genes that may influence LINE-1 regulation at multiple levels, including RNA and protein expression. Alongside known factors such as the HUSH complex, the screens revealed additional genes not previously linked to LINE-1 regulation, suggesting possible new regulatory mechanisms for ORF1p and ORF2p expression. We also identified genes whose loss correlated with reduced viability in a manner dependent on LINE-1 activity. These findings collectively provide a broad resource for exploring cellular factors that may modulate LINE-1 expression and activity.  Conclusion This study provides a resource for investigating the cellular regulation of LINE-1, highlighting distinct candidate factors that may modulate ORF1p and ORF2p expression and influence LINE-1 activity-associated cytotoxicity. While functional validation of these candidate regulators remains necessary, the findings offer a foundation for future studies aimed at experimentally confirming their roles and elucidating the molecular mechanisms underlying LINE-1 regulation and its potential contributions to disease contexts.

overall_design: HCT116-Cas9 cells lacking a reporter, or stably expressing the L1 WT or L1 EN/RT mutant reporters, were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin–streptomycin, and 1 mM L-glutamine at 37 °C in a humidified incubator with 5% CO₂. Cells were harvested at 3 × 10⁶ cells per tube for RNA-seq and submitted to Azenta Life Sciences for downstream RNA isolation, library preparation, and sequencing.

first: Ozgur

last: Oksuz

first: Chong

last: Chu

first: Cedric

last: Arisdakessian

first: Dennis

last: Zaller

first: Kimberly

middle: K

last: Long

first: Heike

last: Keilhack

first: Sarah

last: Knutson


title: NRF2 upregulation by CDDO-Me protects AC16 human cardiomyocytes against doxorubicin-induced toxicity_1.

summary: Elucidation of the mechanisms underpinning doxorubicin-induced toxicity in human AC16 cells and the protection afforded by the NRF2 inducer CDDO-Me.

overall_design: AC16 cells were plated and cultured with DMSO (vehicle control) or 100 nM doxorubicin for 48 h. RNA-seq was performed to measure differential transcript expression.


title: NRF2 upregulation by CDDO-Me protects AC16 human cardiomyocytes against doxorubicin-induced toxicity_2.

overall_design: AC16 cells were plated and cultured with DMSO (vehicle control), 100 nM CDDO-Me for 24 h or 100 nM CDDO for 72 h. RNA-seq was performed to measure differential transcript expression.


title: Transcriptomic profiling of brown adipose tissue in high-fat diet-induced obese mice following Pu-erh tea extract intervention

city: Chongqing

first: Xiujuan

last: Jiang

address: Tiansheng road

country: China

institute: Southwest University

summary: Background: Obesity driven by high-fat diet (HFD) is a global public health concern, and Pu-erh tea extract (PTE) exhibits anti-obesity potential, but its regulatory mechanism on brown adipose tissue (BAT) metabolism remains unclear. Transcriptomic analysis of BAT is critical to reveal PTE-mediated metabolic remodeling. Methods: C57BL/6J mice were divided into HFD (high-fat diet) and HFD+PTE groups. BAT samples were collected after 16-week intervention for RNA sequencing. Results: Transcriptomic data showed 623 differentially expressed genes (DEGs) in HFD+PTE vs HFD groups, mainly enriched in cAMP/Calcium signaling, Biosynthesis of unsaturated fatty acids, and Glycerolipid metabolism pathways. Value: This dataset provides transcriptomic evidence for PTE regulating BAT function, complementing our previously deposited gut microbiota 16S rRNA data, and facilitating research on natural product-mediated metabolic regulation.

overall_design: 1. Study Overview This study aimed to elucidate the transcriptomic alterations in brown adipose tissue (BAT) of high-fat diet (HFD)-induced obese mice following intervention with Pu-erh tea extract (PTE), and to explore the molecular mechanisms underlying PTE-regulated metabolic remodeling of BAT. The transcriptomic data submitted here correspond to BAT samples isolated from 8 mice (4 mice per group), capturing the differential gene expression profiles associated with the anti-obesity effects of PTE.  2. Sample Preparation  Animal Model: Specific pathogen-free (SPF) male C57BL/6J mice (6 weeks old, 17±2 g) were obtained from Shanghai SLAC Laboratory Animal Co., Ltd. All mice were acclimatized for one week under standard conditions (22±2°C, 12-h light/dark cycle) with free access to food and water.  Grouping and Intervention: Mice were randomly assigned to two groups (n=4 per group):  HFD Group: Fed a high-fat diet (60% kcal from fat) for 16 weeks.  HFD+PTE Group: Fed the high-fat diet for 16 weeks with ad libitum access to drinking water supplemented with 0.25% (w/v) PTE. The PTE was prepared from ripened Pu-erh tea (7572, Yunnan TEATEA Group, production year 2006) via sequential hot-water extraction (1:15 and 1:10, w/v), followed by filtration, combination of filtrates, and lyophilization. The resulting extract was stored at -80°C until use.  3. Tissue Collection Following the 16-week intervention and a 12-hour fast, mice were euthanized by CO₂ inhalation. Interscapular brown adipose tissue (BAT) was rapidly dissected, rinsed briefly with ice-cold sterile saline, blotted dry, and immediately snap-frozen in liquid nitrogen. All samples were stored at -80°C until RNA extraction.  4. RNA Extraction and Quality Control Total RNA was extracted from frozen BAT samples using TRIzol® Reagent according to the manufacturer’s instructions. RNA concentration and purity were measured using an ND-2000 spectrophotometer (NanoDrop Technologies). RNA integrity was assessed with a 5300 Bioanalyzer (Agilent Technologies). Only RNA samples meeting stringent quality criteria (OD260/280 ratio of 1.8-2.2, OD260/230 ratio ≥ 2.0, RNA Quality Number (RQN) ≥ 6.5, 28S:18S ribosomal RNA ratio ≥ 1.0, and total mass > 1 μg) were proceeded to library construction.  5. Library Construction, Sequencing, and Data Processing Sequencing libraries were prepared from 1 μg of qualified total RNA using the Illumina® Stranded mRNA Prep, Ligation kit, following the manufacturer’s protocol. This included polyA selection, RNA fragmentation, double-stranded cDNA synthesis, adapter ligation, size selection (~300 bp), and PCR amplification. Library quantification was performed using Qubit 4.0. Pooled libraries were sequenced on an Illumina NovaSeq X Plus platform using a NovaSeq Reagent Kit to generate 150-bp paired-end reads. Raw reads were processed with fastp for quality control and adapter trimming. Clean reads were aligned to the GRCm39 reference genome using HISAT2. Transcript assembly and quantification (in TPM) were performed using StringTie and RSEM, respectively. Differential expression analysis was conducted with DESeq2, with significance thresholds set at |log2FC| ≥ 1 and FDR < 0.05. Alternative splicing events were analyzed using rMATS. Functional enrichment analysis (GO and KEGG) was performed on differentially expressed genes.

first: Jiang

last: Xiujuan

first: Zeng

last: Liang


title: Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells [ATAC-seq]

city: New York

first: Julian

last: Pulecio

state: NY

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: It remains unclear how ESCs rapidly establish enhancer regulatory elements to activate lineage-specific genes at the earliest differentiation stages. Previous studies suggest that some tissue-specific enhancers are pre-marked in ESCs with permissive features that support their competence to induce gene expression in response to the binding of lineage transcription factors (TFs). However, the absence of functional assays to identify chromatin regions with the competence to activate gene expression upon TF binding has impeded to better define any pre-marking features and their role on the transcriptional competence of the chromatin. To address this, we leveraged a CRISPR-activation(a) system to systematically interrogate the presence of chromatin regions able to induce the expression of 5 lineage-specific genes that are inactive in human ESCs (hESCs). Multiple CRISPRa screens discovered 42 regions, which we termed Competent Chromatin Regions (CCRs), that can induce the expression of the 5 lineage genes upon CRISPRa targeting. ChIP seq analyses showed that CCRs do not represent primed or active enhancers, since they are not enriched in H3K4me1 or H3K27ac histone modifications. Instead, CCRs are characterized by the enriched occupancy of OCT4, NANOG and demethylation factors TET1 and QSER1, which prevent DNA hypermethylation. Although CCRs are exclusively found at the topologically associated domains shared with their related genes, we found they do not require an enrichment in pre-established chromatin contacts to exert their function. To assess the extent of our findings, we simulated the earliest stages of lineage differentiation by inducing the expression of the lineage TF FOXA2 in undifferentiated hESCs and we found it preferentially binds to the regions predicted as CCRs. Our results suggest that the factors enriched at CCRs facilitate the binding of lineage TFs and enable ESCs to promptly activate the expression of lineage genes. This study advances our understanding of pluripotency regulation in ESCs by identifying a novel type of regulatory regions that supports their developmental plasticity.

overall_design: 2 biological replicates for each condition (ESC and DE timepoints) and WT and TET1/QSER1 Double-KO (DKO) cells.

first: Danwei

last: Huangfu


title: Gene expression profiling of adult C. elegans in response to heat hormesis regimen

city: Ithaca

first: Siu Sylvia

last: Lee

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

summary: To understand the molecular basis of heat hormesis, we adapted a regimen in which C. elegans that had been cultured at 20°C were exposed to 30°C for 6 hours during early adulthood (referred to as ‘priming’), allowed to recover for 12 hours at 20°C, and then challenged with heat shock (HS) at 35°C. We applied this hormesis regimen to wild-type (N2) or germline-less glp-1(e2144) worms.

overall_design: Gene expression profiling was conducted using 3' mRNA sequencing of Naïve (N) and Primed (P) groups in glp-1(ts) mutants or wild-type (N2) worms at Timepoints 1 (after Priming), 2 (Recovery), 3.3 (upon 3-hour HS), 3.6 (upon 6-hour HS), and NC (negative control-before priming) across the heat hormesis regimen. For the glp-1 mutant, five biological replicates were included for each condition, except for Timepoint 3.6, which had three biological replicates. For N2, there were two biological replicates per condition.

first: Hsin-Yun

last: Chang

first: Siu

middle: S


title: Chromatin accessibility profiling of adult C. elegans in response to heat hormesis regimen

overall_design: Chromatin accessibility profiling was conducted on nuclei isolated from Naïve (N) and Primed (P) groups of glp-1(ts) mutant or wild-type (N2) worms at Timepoints 1 (after Priming), 2 (Recovery), 3.3 (upon 3-hour HS), 3.6 (upon 6-hour HS), and NC (negative control-before priming) across the heat hormesis regimen. For the glp-1 mutant, four biological replicates were included for each condition, except for Timepoint 3.6, which had two biological replicates. For N2, there were two biological replicates per condition.


title: LEFKOTHEA modulates gene expression at the transcriptional and post-transcriptional levels during early light response

city: Athens

first: Anastasios

last: Alatzas

address: IERA ODOS 75

country: Greece

institute: Agricultural University of Athens

summary: Light is the source of energy for photosynthetic organisms such as plants. Due to the great significance of light in the regulation of development, plants possess a sophisticated signaling network that controls light response including a massive gene expression reprogramming as well as post-transcriptional mechanisms such as alternative splicing. LEFKOTHEA is a nucleus-encoded splicing factor found in both the nucleus and chloroplast and its nuclear compartmentalization ensures the early embryonic development in Arabidopsis. LEFKOTHEA gene mutations (lefko1, an EMS mutant allele exhibiting aberrant nuclear partitioning and an albino cotyledon phenotype, and lefko2, a severe allele that results in embryo developmental arrest) have defects in splicing of nuclear and chloroplast genes. Time-series transcriptomic analysis upon light encounter revealed an aberrant response to light in lefko1, characterized by down-regulation of genes involved in photosynthetic apparatus and signal transduction pathways. Further, LEFKOTHEA significantly affects the number and the mode of alternative splicing events during light response. A majority of such events occur on spliceosomal components, light-related transcription factors and genes involved in signal transduction. Altogether, the results indicate that LEFKOTHEA is an active component of early light response signaling, regulating gene expression both transcriptionally and post-transcriptionally.

overall_design: RNAseq profiling of dark-grown Arabidopsis wild-type and lefko1 mutant seedlings upon light encounter in a time-series experiment

first: Despina

last: Samakovli

first: Loukia

last: Roka

first: Konstantinos

last: Panagiotopoulos

first: Gerasimos

last: Daras

first: Dimitra

last: Milioni

first: Stamatis

last: Rigas

first: Kosmas

last: Haralampidis

first: Polydefkis

last: Hatzopoulos


title: DNA methylation and lncRNA expression control asynchronous DNA replication at specific imprinted gene domains [RNA-seq]

city: Gif-sur-Yvette

first: Benoit

last: Moindrot

address: 1, avenue de la terrasse

institute: Institute for Integrative Biology of the Cell

summary: Besides genome-wide patterns of replication timing (RT), some genes display allelic replication asynchrony in stem cells, brought about by stochastic events and genetic polymorphisms. Whether epigenetic modifications control asynchronous replication remains unclear. We explored mammalian imprinted domains, where parental DNA methylation imprints mediate allele-specific gene expression. Our genome-wide and locus-specific assays in mono-parental and hybrid mouse ESCs reveal pronounced RT asynchrony—which is parent-of-origin dependent and lost upon neural differentiation—at the Dlk1-Dio3 and Snrpn domains, which both comprise lncRNA polycistrons.  Generating a range of mutant lines, we find that asynchronous replication at Dlk1-Dio3 is mediated by differential DNA methylation, and that the lncRNA Meg3 controls early replication across parts of the domain on the maternal chromosome.  RT thereby becomes unlinked from 3D chromatin architecture as assayed by Hi-C.  The combined replication timing, DNA methylation, 3D chromatin structure and gene expression data highlight how parental methylation imprints and lncRNA expression control replication and can override RT domain organisation.

overall_design: RNA-seq of mESC cells (BJ1 and JB1 genetic background). Delta-Meg3-C1, Zfp57-/- and Zfp57-/-Meg3pro-/- cell lines were obtained by CRISPR-Cas9 deletion.

first: Yui

last: Imaizumi

first: Pol

last: Arnaud-Romero

first: Jean-Christophe

last: Andrau

first: Robert

last: Feil


title: Proximal ganglionic intestine in Hirschsprung Disease is fibrotic and stiff

city: Charlottesville

first: Lily

middle: S.

last: Cheng

state: VA

address: 409 Lane Rd

department: Surgery

institute: University of Virginia

summary: Hirschsprung disease (HSCR) is a congenital intestinal disorder characterized by the absence of ganglia in the distal intestine. Despite surgical resection of the aganglionic intestine and pull-through surgery, HSCR patients still experience bowel dysfunction, indicating that latent abnormalities may also exist in the proximal ganglionic intestine. To elucidate possible causes of postoperative bowel dysfunction in HSCR, we investigated differences in the proximal ganglionic intestine using an animal model of HSCR (Ednrb-null mice) and validated our findings in tissue from human HSCR patients. We found that the proximal ganglionic colon of HSCR mice exhibited greater stiffness and fibrosis than their wild-type littermates. Similarly, submucosal fibrosis was significantly greater in the proximal ganglionic intestine of HSCR patients than in intestinal tissue from age and site-matched controls. Furthermore, we observed dysregulated expression of extracellular matrix (ECM)-related genes in the proximal ganglionic intestine of HSCR mice compared to controls. We conclude that increased fibrosis, stiffness, and alterations in ECM composition may contribute to persistent dysfunction of the ganglionic intestine in HSCR. These findings add to the growing body of literature that describe abnormalities in the proximal ganglionic intestine of HSCR and suggest that HSCR is not limited to the aganglionic intestine alone.

overall_design: bulk RNA-sequencing of the proximal ganglionic colon from Hirschsprung Disease mouse model (Ednrb -/-) and equivalent segments  from wildtype littermates to investigate differences in the expression levels of extracellular matrix-related genes.

first: Prisca

last: Obidike

first: Britney

last: Hsu

first: Chioma

last: Moneme

first: Oluyinka

middle: O

last: Olutoye

first: Walker

middle: D

last: Short

first: Hui

last: Li

first: Swathi

last: Balaji

first: Yuwen

last: Zhang

first: Sundeep

middle: G

last: Keswani


title: Molecular indicators of hepatocellular carcinoma resistance to Y-90 microspheres revealed through high-throughput screening of cell lines and transcriptomics

city: St. Louis

first: Alexander

last: Zheleznyak

address: 660 S. Euclid

institute: WUSM

summary: Molecular signatures predict prognosis in hepatocellular carcinoma; however, their relevance to Y-90 radioembolization remains unknown. Here, we perform Y-90 microsphere screens in a panel of genetically diverse human HCC cell lines. Ten transcriptomically diverse human HCC cell lines were exposed to 20 MBq of Y-90 glass beads. Normalized AUC values qualified sensitivity. Whole-transcriptome  RNA sequencing at baseline and post-treatment underwent differential expression analysis and gene set enrichment analysis. The response of HCC cell lines to Y-90 was heterogeneous, with SK-Hep1 and SNU-449 being the most resistant and PLC/PRF/5 being the most sensitive.

overall_design: RNA-seq profiling of genetically diverse human HCC cell lines SK-Hep1, Hep-3B, Hep-G2, MHCC-97H, SNU-449, SNU-423, SNU-475, SNU-387, PLC/PRF/5, and SNU-398 before and after treatment with 20 MBq of Y-90.

first: Dhanusha

last: Duraiyan

first: Jessica

last: Silva-Fisher

first: Christopher

last: Malone


title: DNA methylation and lncRNA expression control asynchronous DNA replication at specific imprinted gene domains [Hi-C]

first: Benoit

last: Moindrot

overall_design: Hi-C in monoparental mESC cells (AK2 and PR8 cells).

first: François

last: Charon

first: Daan

last: Noordermeer


title: DNA methylation and lncRNA expression control asynchronous DNA replication at specific imprinted gene domains    [Capture Hi-C]

overall_design: Capture Hi-C in wild-type and mutant mESC cells (BJ and JB genetic background). NPC samples were obtained by in-vitro differentiation of mESCs.


title: Post-transcriptional modifications on tRNA fragments confer functional changes to high-density lipoproteins in atherosclerosis

city: Nashville

first: Kasey

last: Vickers

address: 2220 Pierce Ave, PRB 312

institute: VUMC

summary: Epitranscriptomic modifications on RNA play critical roles in stability, processing, and function, partly by influencing interactions with RNA-binding proteins and receptors. The diverse role(s) of post-transcriptional RNA modifications on cell-free small non-coding RNAs (sRNA) remain poorly understood, particularly in disease contexts. Although HDL confer many beneficial properties to health, HDL particles lose these features during atherosclerotic cardiovascular disease (ASCVD). As HDL transport sRNA fragments from classes of RNA known to harbor extensive modifications, we predicted that changes to regulatory modifications on HDL-sRNAs may contribute to HDL functionality changes in ASCVD. To assess HDL-RNA modification levels in ASCVD, total RNA were isolated from HDL of healthy subjects (CAC=0) and those with advanced atherosclerosis, as determined by coronary artery calcium (CAC) scores >21 Agatston units. HDL-RNA were quantified using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and AlkB-facilitated RNA (de)Methylation Sequencing (ARM-seq). LC-MS/MS revealed elevated levels of modified nucleosides in HDL-sRNAs from ASCVD subjects, while ARM-seq detected an enrichment of m1A-modified sRNAs-derived from parent tRNAs (tDR), particularly tDR-ArgACG-1. To assess the impact of disease HDL on immune cells, primary macrophages were treated with HDL isolated from ASCVD (CAC+) and control subjects, and results showed that ASCVD-HDL directly induced expression of genes associated with immune signaling and cell adhesion, including TMEM123, a transmembrane protein linked to immune cell migration, adhesion, and cytoskeletal organization. In addition, recombinant HDL particles loaded with m1A-tDR-ArgACG-1 were found to significantly increase TMEM123 expression in treated primary macrophages. Together, these findings propose a model in which HDL-delivered m1A-HDL-tDRs directly stimulate immune signaling, macrophage activation, and pro-inflammatory sub-phenotypes within the atherosclerotic lesion. This study highlights HDL-associated RNA modifications as previously unrecognized contributors to immune modulation, with direct implications for targeting modified HDL-tDRs as a new approach to therapy for ASCVD.

overall_design: Total RNA sequencing of human monocyte derived macrophages treated with reconstituted HDL (rHDL) complexed with synthetic tRNA fragment that contain a m1A methylation

first: Elizabeth

middle: M

last: Semler

first: Danielle

middle: L

last: Michell


title: DNA methylation and lncRNA expression control asynchronous DNA replication at specific imprinted gene domains [Capture Repli-seq]

overall_design: Capture Repli-seq in mESC cells (BJ1 and JB1 genetic background). NPC samples were obtained by in-vitro differentiation of mESCs. Delta-Meg3-C1, Zfp57-/- and Zfp57-/-Meg3pro-/- cell lines were obtained by CRISPR-Cas9 deletion. Sh-1 cells were obtained in Kota et al., 2014.

first: Yui

last: Imaizumi

first: Robert

last: Feil


title: The hegemonic EWSR1::ETS oncogene overrules core regulatory circuitry mechanisms in Ewing sarcoma.

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'ulm

institute: Institut Curie

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

overall_design: Refer to individual Series


title: snATAC-seq profiling of immune cells in human mucosal tissues

first: Peter

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: We performed single-nucleus ATAC-seq (snATAC-seq) to identify cell type- and tissue-specific transcriptional regulatory programs, including transcription factors and cis-regulatory elements, across multiple immune cell lineages from human jejunum and lung.

overall_design: Immune cells were isolated from fresh jejunum or lung tissue specimens procured from human organ donors. Nuclei were isolated from the cells and profiled with snATAC-seq.

first: Daniel

last: Caron

first: Steven

middle: B

last: Wells

last: Szabo

first: Jennifer

last: Hwu

first: Siddhi

last: Nargund

first: David

last: Chen

first: Donna

last: Farber


title: Single cell profiling of CD11b+ cells from mouse cortex following astrocyte overexpression of mCherry-CAAX or Hevin

city: Durham

first: Cagla

last: Eroglu

state: NC

address: 307 Research Dr

institute: Duke University

summary: Astrocyte derived Hevin regulates formation and maintenance of excitatory thalamocortical synapses in the developing mouse cortex. However, the role of astrocyte secreted factors on other cell types is still understudied. To interrogate the response of microglia to the release of astrocye derived Hevin, astrocytes were virally transduced with AAVs to overexpress Hevin or mCherry-CAAX.

overall_design: P0-P1 mice were intracortically injected with AAVs to overexpress Heivn or mCherry-CAAX under the control of the GfaABC1D promoter to restrict expression to astrocytes. Microglia were then isolated from cortex of these mice at P15 using Magnetic Activated Cell Sorting (MACS) for CD11b+ cells. These CD11b+ cells were then used as input for single cell library preparation using the PIPseq v4.0PLUS kit from FluentBio. Libraries were then sequenced using Illumina NovaSeq 6000.

first: Juan J.

last: Ramirez


title: Daratumumab in systemic lupus erythematosus: a phase 2 trial

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

summary: Antibody-secreting cells (ASCs) play a central role in the pathophysiology of systemic lupus erythematosus (SLE). This single-arm, open-label, phase 2 clinical trial aimed to evaluate the safety and efficacy of the ASC-depleting anti-CD38 monoclonal antibody daratumumab in patients with refractory SLE. The primary endpoint was a significant reduction in serum anti-double-stranded DNA (anti-dsDNA) antibody levels. Ten female patients with active disease and inadequate responses to at least two disease-modifying drugs received eight weekly subcutaneous injections of 1800 mg daratumumab. By week 12, anti-dsDNA antibody levels were significantly reduced (p=0.002), accompanied by rapid and sustained clinical improvements across all patients and organ domains. Adverse events were mild to moderate. Daratumumab treatment depleted circulating ASCs, reduced type I interferon activity, and profoundly modulated T-cell responses. These findings highlight the pivotal role of ASCs in SLE pathogenesis and support daratumumab as a promising therapeutic option for refractory SLE. ClinicalTrials.gov identifier: NCT04810754.

overall_design: This experiment was designed for an in-depth analysis of human T cells, memory B cells from SLE patients receiving the anti-CD38 monoclonal antibody Daratumumab. We sorted memory T cells (CD3+, not double-positive for CCR7/CD45RA) and memory B cells (CD19+CD27+) from the patients at baseline, week 09 and week 36. When multiple samples for analyzed on the same day, hashtag antibodies were used. Single cell transcriptomes and BCR/TCR sequencing of the sorted cells was performed using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit v2 (dual index) and Illumina NextSeq2000 or NextSeq500.

first: Ostendorf

last: Lennard

first: Zernicke

last: Jan

first: Klotsche

last: Jens

first: Kempkens

last: Robin

first: Beenken

last: Anne

first: Pawel

last: Durek

first: Biesen

last: Robert

first: Mir-Farzin

last: Mashreghi

first: Cheng

last: Qingyu

first: Khodadadi

last: Laleh

first: Krönke

last: Gerhard

first: Guerra

last: Gabriela Maria

first: Burmester

last: Gerd-Rüdiger

first: Hiepe

last: Falk

first: Alexander

last: Tobias


title: GSDME-controlled pyroptosis promotes muscle repair by coordinating tissue resident macrophages and fibro-adipogenic progenitors [RNA-seq]

city: shanghai

first: Qi

last: Cao

address: NO.325 Guohe Road

institute: Second Military Medical University

summary: GSDME (Gasdermin E) is a critical protein known for its role in pyroptosis, a form of programmed cell death associated with inflammation. We demonstrated that GSDME as a crucial mediator in muscle repair, particularly in the context of muscle damage induced by cardiotoxin (CTX). Specifically, we found that GSDME-controlled pyroptosis promotes muscle repair by coordinating the activities of tissue-resident macrophages and fibro-adipogenic progenitors (FAPs).

overall_design: To simulate a muscle injury repair model, CTX (cardiotoxin) was injected into the thigh muscles of wild-type (WT) mice. Samples were collected from both the injection group and the control (unloaded) group to assess the effects of the model.To explore the function of the Gsdme, we conducted detailed experiments in both WT and knockout (KO) mice. Gastrocnemius muscles were harvested from WT injection groups and KO injection groups at four different time points: Day 1, Day 4, Day 7, and Day 14 post-injection. Each group included biological triplicates. These samples were then subjected to RNA sequencing (RNA-seq) analysis.

first: Q

first: P

last: Wang


title: Epithelial RXRα activity induced by Westernization of diet instigates enteritis in Crohn’s disease

city: Innsbruck

first: Christina

last: Plattner

address: Innrain 80

department: Institute of Bioinformatics

institute: Medical University of Innsbruck

summary: Westernization of diet, partly characterised by excess of long-chain fatty acids, provides a risk for developing Crohn’s disease (CD), and perturbs the function of specialized intestinal epithelium termed Paneth cells. The lack of a cellular and molecular framework of lipid sensing in intestinal inflammation poses a constraint to understanding detrimental effects of Western diets. Here, we report how Paneth cell sensing of lipid excess in a Western diet is translated into CD-like intestinal inflammation. Small intestinal transcriptional profiling of CD patients from three independent cohorts identified increased activity of the transcription factor retinoid x receptor alpha (RXRα) specifically in intestinal epithelium. Intestinal epithelial RXRα activity was induced by polyunsaturated fatty acid (PUFA) excess in a Western diet in mice with CD-like enteritis. PUFA-induced RXRα activity in Paneth cells governed chronic transmural enteritis by enabling the expression of the interleukin 8 homologue CXCL1. Blockade of PUFA-induced RXRα activity by 9-cis retinoic acid ameliorated CXCL1 production and enteritis, and patients receiving isotretinoin therapy (a precursor for 9-cis retinoic acid) displayed reduced odds of developing CD. Collectively, we identify Paneth cells as gatekeepers of lipid stress that exploit RXRα to sense and translate PUFA excess into enteritis, which could be targeted to prevent or treat CD.

overall_design: Bulk RNA-seq profiling of siGpx4 (n=3) vs siCtrl MODE-K IECs (n=3) stimulated with arachidonic acid (AA) for 8 hours or with the omega-3 PUFA docosahexaenoic acid (DHA), and single-cell RNA-seq profiling of WT (n=3) and Gpx4+/-IEC mice (n=4) fed with a PUFA enriched Western diet for 3 months.

first: Moritz

last: Meyer

first: Felix

last: Grabherr

first: Valentin

last: Marteau

first: Dietmar

last: Rieder

first: Zlatko

last: Trajanoski

first: Timon

middle: E

last: Adolph


title: GSDME-controlled pyroptosis promotes muscle repair by coordinating tissue resident macrophages and fibro-adipogenic progenitors

overall_design:
Prepare mouse gastrocnemius as a single-cell suspension. 10x genomic was used to capture the transcriptomic information of the single cells. All libraries were sequenced by Novaseq on a 150 bp paired-end run.
data colum header nnnnn-1 = GSDME-KO-CTX
data colum header nnnnn-2 = WT-CTX


title: EPOP Restricts PRC2.1 Targeting to Chromatin by Directly Modulating Enzyme Complex Dimerization (RNA-Seq)

city: Dallas

first: Xin

last: Liu

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Polycomb repressive complex 2 (PRC2) mediates developmental gene repression as two classes of holocomplexes, PRC2.1 and PRC2.2.  EPOP is an accessory subunit specific to PRC2.1, which also contains PCL proteins.  Unlike other accessory subunits that collectively facilitate PRC2 targeting, EPOP was implicated in an enigmatic inhibitory role, together with its interactor Elongin BC.  We report an unusual molecular mechanism whereby EPOP regulates PRC2.1 by directly modulating its oligomerization state.  EPOP disrupts the PRC2.1 dimer and weakens its chromatin association, likely by disabling the avidity effect conferred by the dimeric complex.  Congruently, an EPOP mutant specifically defective in PRC2 binding enhances genome-wide enrichments of MTF2 and H3K27me3 in mouse epiblast-like cells (EpiLCs).  Elongin BC is largely dispensable for the EPOP-mediated inhibition of PRC2.1.  EPOP defines a distinct subclass of PRC2.1, which uniquely maintains an epigenetic program by preventing the over-repression of key gene regulators in the continuum of pluripotency and differentiation.

overall_design: Total RNA sequencing (RNA-seq) for mESCs and EpiLCs expressing WT or mutant EPOP.

first: Xiuli

first: Ze

last: Yu

first: Chao

last: Xing


title: Development of antibody-drug conjugates targeting L1CAM to treat metastatic cancer

first: Jin Suk

last: Park

address: 417 East 68th St

institute: MSKCC

summary: Effective treatments for metastatic disease have eluded precision oncology efforts and represent a major unmet need. The L1 cell adhesion molecule (L1CAM) is a transmembrane protein expressed by populations of Metastasis Stem cells (MetSC), that are enriched for the ability to reinitiate and propel metastatic growth and display phenotypic plasticity and resistance to conventional chemotherapies. Notably, L1CAM+ MetSC have been detected in numerous human solid tumor types and in multiple disseminated organ sites. As a selective marker of MetSC, L1CAM is a promising candidate for molecularly targeted drugs aimed at eliminating metastases, yet strategies to date have not achieved clinical success. Here, we develop antibody-drug conjugates to deliver highly toxic PNU-159682 payloads to L1CAM-expressing cells. We report the generation of monoclonal antibodies (mAb) with high binding affinity, specificity and selectivity for the human L1CAM extracellular domain. After further optimization of the L1CAM mAbs, PNU-159682 was conjugated to generate ADC variants with both cleavable and non-cleavable linkers, with an average drug-antibody-ratio (DAR) of four. The three ADCs (Y-004, Y-005 and Y-006) potently killed cells with varying levels of surface L1CAM expression. L1CAM ADCs given as monotherapy resulted in robust tumor growth control and extended survival in mice harboring subcutaneous L1CAM+ xenografts or L1CAM+ lung metastases, with safety analyses indicating a feasible therapeutic window. Our findings provide strong proof-of-concept to extend preclinical development of these novel L1CAM ADCs as therapeutic agents for advanced cancer.

overall_design: LUAD PDX tumoroids were generated, dissociated as single cells, FACS-sorted and submitted for single-cell sequencing.


title: Role of STARD10 in human pancreatic β-cells

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

summary: Purpose: To compare the transcriptome profile between WT and STARD10 KO pancreatic β-like cells at different timepoints

overall_design: Methods: Differentiate WT and STARD10 KO human embryonic stem cells (hESCs) into pancreatic β-like cells which are then used in this study

first: Nur

last: Amirruddin

first: Shawn

last: Hoon


title: Hybrid Endometrial-Derived Hydrogel and Human Endometrial Organoids Synergize for Uterine Regeneration in an Immunocompetent Murine Model

status: Public on Dec 11 2025

city: Badajoz

first: María

last: Gómez Álvarez

state: Badajoz

address: Parque de Cornalvo, 29

institute: IVI Foundation

summary: Study question: Can human endometrial organoids (hEOs) synergize with a hybrid endometrial-derived hydrogel (HG) to regenerate the endometrium in an immunocompetent murine model of Asherman’s Syndrome/Endometrial Atrophy (AS/EA)? Summary answer: The combination of HG+hEOs was biocompatible in an immunocompetent murine model, restored endometrial thickness and glandular structure, reduced fibrosis and ferroptosis, promoted angiogenesis and regenerative immune pathways, but failed to fully restore fertility, likely due to the prolonged retention of the synthetic hydrogel component. Main results and the role of chance: No systemic immune alterations or hematological abnormalities were detected post-treatment, indicating that the combined treatment was compatible and safe in mice. Fourteen days after treatment, HG+hEOs treatment significantly restored endometrial thickness and gland density, reduced collagen deposition and iron accumulation (ferroptosis), and enhanced vascularization compared to the PBS condition (p < 0.05), reaching levels comparable to SHAM controls. RNA sequencing of the murine endometria confirmed restoration of transcriptomic profiles and upregulation of angiogenesis, cell proliferation, and regenerative immune pathways in the HG+hEOs group. However, fertility outcomes (pregnancy rate and embryo number) remained significantly impaired in all conditions, with no statistical improvement over the PBS group. Mice injected with PM confirmed that fertility impairment was linked to the presence of synthetic hydrogel in previously damaged uteri.

overall_design: First, an AS/EA model was established in female C57BL/6 mice via uterine injury using 70° ethanol. After 4 days of endometrial damage, hEOs were co-injected with HG into the uterine horns. Animals (n = 46) were divided into four conditions: SHAM, PBS, HG and HG+hEOs. Two weeks post-injection, a subset of mice (n = 21) was sacrificed for biocompatibility, histological, and transcriptomic analyses. Functional recovery of the endometrium was assessed in the remaining animals (n = 21) through fertility outcome evaluation. In addition, two groups treated with PuraMatrix (PM) alone were also included (n = 12), with (n = 7, PM damaged) or without (n = 5, PM non-damaged) endometrial damage, to address inconsistencies observed in fertility outcomes.


title: Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution

city: South San Francisco

first: Michelle

last: Chen

address: 1 DNA Way

department: Cell & Tissue Genomics

institute: Genentech, Inc.

summary: The intestinal epithelium is often a site of pathology, such as in inflammatory bowel disease (IBD), and its maintenance is highly modulated by interactions with the microenvironment. However, a systematic understanding of how the myriad of niche cues impact distinct epithelial cell types in a diseased context is still lacking. To address this gap, we first benchmarked diverse human colonic organoid injury models against IBD tissue and established a disease-relevant model of epithelial inflammation using TNFɑ, IFNɣ, and IL1β. Using this system, we built a dictionary of epithelial responses to 79 secreted niche factors at single cell resolution via donor-pooled, multiplexed single cell RNA-sequencing (scRNA-seq). The comprehensive nature of our atlas allowed us to map relationships between perturbations, infer the function of less well-characterized ligands, and identify cell type-specific perturbed pathways. Finally, we established the relevance of organoid-derived gene programs by mapping them to single cell and spatial atlases of human IBD tissue. Our resource offers a global view of epithelial responses to microenvironmental cues in a physiologically relevant disease context and generates new hypotheses for signaling factors that may be involved in epithelial homeostasis and repair.

overall_design: Using the low-dose cytomix model, we generated a molecular dictionary of epithelial responses to secreted niche factors in human colon organoids across 3 donors via multiplexed scRNA-seq


title: FABP4, marker of worse prognosis in cardiovascular disease, induces neutrophil’s proatherogenic phenotype which is modulated by semaglutide

city: Santiago de Compostela

first: David

last: Sánchez-López

state: A Coruña

address: Travesía Da Choupana S/n

institute: Institute of Health Research of Santiago de Compostela: Instituto de Investigacion Sanitaria de Santigao de Compostela

summary: Dysfunctional epicardial adiposity is a risk factor for coronary artery disease (CAD). Its genesis is associated with an upregulation of fatty acid binding protein 4 (FABP4) levels, which might exert paracrine inflammatory and atherogenic mechanisms on the cardiovascular system. We aimed to study the prognosis of patients with high systemic FABP4, its association with a neutrophil proatherogenic phenotype, involved mechanisms and its modulation by semaglutide, a glucagon-like peptide-1 receptor agonist (GLP-1ra). Higher plasma FABP4 levels than 50 ng/mL were associated with heart failure (HF) onset during follow-up. In patients with CAD, these levels were associated with pro-inflammatory and pro-atherogenic neutrophil profile markers as MPO, NGAL and CD11b, analysed by real-time PCR. The group of patients with the highest FABP4 levels exhibited higher levels of MMP9, CXCR2, and CD11b in neutrophils. A preclinical model, based on neutrophils and coronary endothelial cells, determined the effects of FABP4 on neutrophils' respiratory burst, by flow cytometry, activity of NF-kB, by western blot checking IkBa phosphorylation, CD11b integrin expression levels and adhesion to coronary endothelial cells. A modulation of the neutrophils' transcriptome, analysed by RNA-seq, and plasma chemokine CCL5 levels suggested changes in leukocyte migration and platelet activation pathways in patients who reduced plasma FABP4 levels after semaglutide treatment. Thus, supraphysiological levels of FABP4 induce pro-inflammatory and proatherogenic mechanisms in neutrophils and coronary endothelial cells. Its modulation by semaglutide could explain its benefits on coronary artery disease (CAD).

overall_design: Neutrophils (isolated by PolymorphPrep) from patients (n=11) with obesity and cardiovascular disease were isolated before and after semaglutide treatment for 6 months.

last: García-Vega

first: J

last: Viñuela

first: Isabel

last: Ferreirós-Vidal

first: Diego

last: Iglesias-Álvarez

first: José

last: Martínez-Cereijo

first: Laura

last: Reija-López

first: Ángel

last: Fernández-González

middle: R

last: González-Juanatey

first: Sonia

last: Eiras


title: CD8 T cells cross-restricted by HLA-B*57 and HLA-E*01 recognize HIV Gag with different functional profiles [dataset 2]

city: Birmingham

first: Kevin

middle: James

last: Maroney

state: Alabama

address: 1001 20th Street S, 1501, Ascend Apartments

institute: University of Alabama at Birmingham

summary: Few non-classical HLA-E restricted HIV-specific epitopes have been described, and even less is known about the functional profile of responding CD8 T cells (CD8s). This study evaluates the functional characteristics of CD8s targeting the Gag epitope (KAFSPEVIPMF or KF11) based on their restriction by either HLA-E (E-CD8s) or HLA-B57 (B57-CD8s). CD8s from 8 people with HIV (PWH) were cocultured with KF11 peptide presented by cell lines expressing HLA-B*57:01, HLA-E*01:01 or E*01:03. CD8s were analyzed through single-cell (sc) RNA and TCR sequencing. Additionally, supernatants were analyzed for soluble proteomics using a Luminex assay. B57-CD8s secreted higher levels of cytotoxic cytokines such as IFNγ, while E-CD8s produced more chemotactic cytokines, including RANTES, CXCL10 (IP-10), and IL27confirmed through scRNAseq. Despite distinct cytokine profiles, TCR clonotypes stimulated by KF11 were cross-restricted by HLA-B*57 and HLA-E*01/03. In vitro T cell reporter assays clearly demonstrated this cross-restriction.  A TRAV5-containing metaclonotype cluster was seen in PWH with lower viral loads. These findings demonstrate that HIV-specific CD8s in PWH exhibit cross HLA-B*57 and HLA-E*01/03 restriction, resulting in functionally distinct immune responses that may contribute to HIV control.

overall_design: CD8+ T cells from 8 people with HIV (PWH), specifically 4 controllers (C), 2 noncontrollers (NC), 1 elite controller (EC), and one noncontroller on antiretroviral therapy (ART+ NC) were used for this assay. Initially, indicated condition cell lines (41A3.CD4, 41A3.CD4.B57, 41A3.CD4.E01, 41A3.CD4.E03) were pulsed with KF11 peptide at 10 ug/mL for 2 hrs at 37°C before peptide was washed off with 1X serum-free media (SFM). CD8+ T cells were then isolated from PBMCs using the StemCell Easy-Sep CD8 Enrichment kit (cat. NC0050243) and coincubated with peptide-pulsed cell lines as indicated for 18 hrs in the presence of α-CD28 and -49d. Cells were then stained with Aqua LIVE/DEAD stain (Thermo Fisher Scientific), anti-CD3-PacBlue, -CD4-AlexaFluor780, -CD8-AlexaFluor700, -CD14/16/19/56-PerCP-Cy5.5 (dump channel, all separate antibodies), -CD69-APC, -CD137-PE, -CD94-PE-Cy7, and -CD107a-FITC. As per gating strategy shown in Figure S1A, single cell lymphocytes were gated on, followed by live cells (Aqua -), CD4/dump -/-, CD8+ CD3-dim, CD69/137+.. Cells which fit this gating strategy and met the criteria of having a CD3-dim activated response to the given HLA pulsed with KF11 significantly (and 3X) higher than 41A3.CD4 also pulsed with KF11 were then sorted into a 96-well plate containing the lysis buffer previously described using the Aria II FACS sorter. scTCR and scRNA-seq was performed as previously described (Bansal et al. 2021).

first: Kevin J.

first: Michael A.

last: Rose

first: Allisa K.

last: Oman

first: Abha

last: Chopra

first: Hua-Shiuan

last: Hsieh

first: Zerufael

last: Derza

first: Rachel

last: Waterworth

first: Mark A.

last: Brockman

first: Spyros A.

last: Kalams

first: Anju

last: Bansal

first: Paul A.

last: Goepfert


title: Fibroblast-like cells in mesothelioma can derive from tumor cells

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

summary: Pleural mesothelioma (PM) is an aggressive cancer that originates from mesothelial cells lining the pleura. To identify the different cell types in mesothelioma and their relationships, we performed single-cell RNAseq analyses of non-malignant pleura biopsies, PM biopsies and PM patient-derived organoids. Gene expression profiles of mesothelial and mesothelioma cells are very similar, suggesting that mesothelioma cells retain most properties of mesothelial cells. Surprisingly, in PM patient-derived organoids mesothelioma cells can acquire a fibroblast-like gene expression profile. Indeed, in most of the original PM biopsies a fraction of cells within the cluster of cancer-associated fibroblasts (CAFs) appear derived from tumor cells, with which they share the same genomic rearrangements. We confirmed by immunohistochemistry, and thus at the protein level, that cancer-derived fibroblast-like cells (CDFs) express smooth muscle actin, as most CAFs do, but have lost the same tumor suppressor proteins as the cognate mesothelioma cells. We propose that mesothelioma cells can become CDFs because they retain the ability of mesothelial cells to differentiate into fibroblasts. CDFs are thus tumor cells with fibroblast-like gene expression associated to tumors, and fulfil the definition of CAFs. CAFs generally support tumor progression, and in most tumors derive from resident fibroblasts or circulating mesenchymal cells. Our finding that a subset of CAFs derive from tumor cells, at least in mesothelioma, challenges current understanding of CAF origin. We suggest that interfering with the mesothelioma-to-CAF transition might offer an avenue to moderate tumor progression and resistance to therapy.

overall_design: Three non-tumoral pleura, five mesothelioma tumor biopsies were extracted from patients and 3 patient-derived-organoids were isolated in culture and analyzed by single-cell RNASeq

first: Eltjona

last: Rapaj

first: Rossanna

last: Mezzapelle

first: Marco

last: Bianchi


title: Functional Role of THRAP3 in Modulating Thyroid Hormone–Mediated Gene Networks in C2C12 Myotubes

city: Nagakute

first: Taku

last: Fukushima

state: Aichi

institute: Aichi Medical University

summary: Thyroid hormone (TH) secreted by the thyroid gland plays essential roles in regulating metabolism, development, and nervous system function. Thyroid hormone receptor-associated protein 3 (THRAP3) is a nuclear coactivator that interacts with the thyroid hormone receptor (TR) and facilitates target gene regulation through the mediator complex. Although this mechanism has been well studied in other tissues, the specific role of THRAP3 in skeletal muscle remains unclear. Here we investigated the function of THRAP3 in skeletal muscle using Thrap3 knockout (KO) C2C12 cells. Loss of THRAP3 significantly suppressed the expression of key myogenic regulatory factors, including Myod1, Mef2c, and myosin heavy chain genes, resulting in impaired myogenic differentiation and muscle diameter. Furthermore, we found that THRAP3 influences triiodothyronine (T3)-induced gene expression, suggesting that it cooperatively modulates thyroid hormone signaling in muscle cells. Taken together, our findings identify THRAP3 as a novel regulator of myogenesis and indicate that it supports T3 activity by coordinating thyroid hormone–responsive gene expression in skeletal muscle.

overall_design: RNA-seq plofiling of Thrap3 Ctrl and knockout C2C12 cells with or without T3 treatment at day 6 of myogenic differentiation.

first: Iori

last: Sakakibara


title: Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [methyl-seq]

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

institute: Institut Pasteur

type: Methylation profiling by high throughput sequencing

summary: A remarkable transition during murine development is the progression from the 1-cell embryo to the 2-cell stage, accompanied by the activation of a specific set of embryonic genes, epigenome reprogramming, and nuclear architecture reorganization. Some of these characteristics are recapitulated in vitro with the spontaneous emergence of 2-cell-like cells from mouse embryonic stem cells, which exhibit a transcriptomic signature resembling the 2-cell stage, including the expression of genes such as Dux, Zscan4, and the repetitive element MERVL, and a more relaxed chromatin state. Here, we show that inter-and intra-chromosomal interactions, driven by Zscan4 chromatin factors, form during this transition and segregate into a distinct genomic compartment (Z compartment). Mechanistically, the formation of Z-DNA, an alternative DNA conformation regulated by polyamine levels, promotes the emergence of totipotent-like cells and the establishment of the Z compartment. This compartment is characterized by a decrease in active histone marks and a reduced expression of genes associated with differentiation and late developmental processes. Overall, these findings suggest that Z-DNA formation may play a dual role, first in activating ZGA genes and later in guiding genome compartmentalization to safeguard the totipotent-like state by restricting the expression of non-ZGA genes within a permissive chromatin environment.

overall_design: Methyl-seq experiments were performed in 2CLCs and ESCs in triplicates.

first: Shireen

last: Shajahan

first: Jack-Christophe

last: Cossec


title: Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [RNA-Seq]

overall_design: RNAseq experiments were performed in ESCs and 2CLCs after different treatments.


title: Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [scRNA-seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell experiments were performed in mouse ESCs or human iPSCs with or without curaxin treatment


title: Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [Hi-C]

overall_design: HiC experiments were performed in ESCs and 2CLCs after different treatments.


title: Discrete and cell-specific hypoxic responses in Arabidopsis roots resolved by single-nuclei transcriptomics

city: Winnipeg

first: Claudio

last: Stasolla

state: MB

address: 66 Dafoe Road

department: Plant Science

institute: University of Manitoba

summary: With the intensification of unpredictable flooding events because of global warming, there is a need to understand how root cells perceive and respond to oxygen deprivation. The use of high-throughput single-nuclei RNA sequencing (snRNA-Seq) allows the examination of gene expression profiles in discrete cell types. Here, root tips segments of Arabidopsis seedlings were subjected to normoxic (21% oxygen) or hypoxic (4% oxygen) treatments for 4h and analyzed by snRNA-Seq. Hypoxia induces a major transcriptome rewiring, most prominent in the meristematic root cells, with the exclusion of the quiescent center (QC), which is vulnerable to low oxygen. Changes in carbon and nitrogen metabolism by low oxygen were centered around increasing demand for carbohydrate to drive substrate phosphorylation via fermentation, reduction of nitrate to sustain energetic processes, and the bypass of the TCA cycle via aminotransferase upregulation. In conclusion, the use of snRNA-Seq provides a high-resolution atlas of gene expression events defining root cell-specific responses to low oxygen.

overall_design: Arabidopsis roots were subjected to 4h of normoxic (21% oxygen) or hypoxic (4% oxygen) conditions. Nuclei were isolated from 1cm root tips and analyzed with snRNA-seq.

first: Robert

last: Hill

first: Sean

last: Robertson

first: Abir

middle: U

last: Igamberdiev

first: Mohammed

last: Mira

first: Olivia

last: Wilkins


title: Differences in mRNA expression in young vs mature adult Drosophila hindguts

first: Jessica

last: Sawyer

address: PO Box 3813

summary: Tissue maintenance in the presence of cell death-promoting insults requires a host of molecular mechanisms. Many studies focus on cell renewal through regeneration, while fewer studies explore mechanisms that promote cell longevity despite cell death stimuli. Here, we reveal that the adult Drosophila hindgut ileum is an excellent model for studying tissue maintenance by long-lived cells. Hindgut ileal enterocytes resist the damaging detergent SDS and upstream caspase signaling by head-involution-defective (hid). This hid-induced death insensitivity arises early in adulthood and is associated with numerous transcriptional changes. We interrogated 82 of these transcriptional changes in a candidate screen for enhancers of hid-induced death in the ileum. Top among our screen hits is an immunoglobulin family cell adhesion gene, CG15312, that maintains the adhesion protein FasIII on cell membranes. In hid-expressing ileal cells, CG15312 loss causes cell death and pyknotic nuclear clustering. We name this conserved gene low on-membrane fas and enhancer of hid (loofah). Our findings reveal a new mechanism linking cell adhesion and cell death resistance in a long-lived cell type. Our work establishes a new model for studying tissue preservation.

overall_design: RNAseq profiling of wildtype young and mature adult Drosophila hindgut cells.

first: Donald

middle: T

last: Fox


title: Activation of IRF3 in cardiomyocytes impairs mitochondrial oxidative function through PGC-1α inhibition and drives heart failure

city: Heidelberg

first: Ashraf

last: Rangrez

address: Im Neuenheimer Feld 410

institute: Heidelberg University Hospital

summary: Heightened sterile inflammation and mitochondrial metabolic dysfunction drives the pathophysiology of heart failure in ischemic cardiomyopathy. Yet, the transcriptional regulators within cardiomyocytes driving crosstalk between inflammation and energy metabolism remain ill-defined. Here we identify elevated Ser396/Ser398 phosphorylation of the type I interferon (IFN) response regulating transcription factor IRF3 in the myocardium of patients and male mice with ischemic cardiomyopathy. Cardiomyocyte-specific IRF3 deficiency attenuates ischemia induced contractile dysfunction. Conversely, IRF3 activation in cardiomyocytes through a phosphomimetic IRF3 mutant represses Ppargc1α expression leading to dysfunctional mitochondrial oxidative phosphorylation, altered metabolic flux in the pentose phosphate pathway/TCA cycle, impaired NAD metabolism and an excessive type I IFN activation, collectively detrimental for cardiac function. Restoring cardiomyocyte-specific Ppargc1α expression in IRF3-overexpressor male mice attenuates contractile dysfunction by augmenting a metabolic shift towards fatty acid oxidation and decreasing inflammatory fibrotic responses. These findings identify IRF3 activation in cardiomyocytes as a transcriptional nexus between cardiac inflammation and metabolic fuel switch contributing to heart failure progression.

overall_design: We identified the transcriptomic profile in the left ventricle of CMI3OE mice treated with AAV-PGC-1a or AAV-EGFP for 3 weeks followed by Tamoxifen induction of IRF3-2D gene expression.

first: Manju

last: Kumari

first: Joerg

last: Heeren


title: EPOP Restricts PRC2.1 Targeting to Chromatin by Directly Modulating Enzyme Complex Dimerization (ChIP-Seq)

first: Xin

last: Liu

overall_design: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) for MTF2, JARID2, and H3K27me3 in mouse epiblast-like cells (EpiLCs) containing WT or mutant EPOP.

first: Xiuli

first: Ze

last: Yu

first: Chao

last: Xing


overall_design: To determine the downstream transcriptional changes by IRF3 activation in cardiomyocytes, we performed RNA-seq experiments and identified the transcriptional profile in the left ventricle upon cardiomyocyte-specific activation of IRF3 using IRF3-2D phosphomimic mutant transgene crossed to aMHCMCM.


title: Mammalian ZAP and KHNYN independently restrict CpG-enriched avian viruses

city: Minneapolis

first: Frances

last: Shepherd

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

summary: Zoonotic viruses are an omnipresent threat to global health. Influenza A virus (IAV) transmits between birds, livestock, and humans. Proviral host factors involved in the cross-species interface are well known, less is known about antiviral mechanisms that suppress IAV zoonoses. We observed CpG dinucleotide depletion in human IAV relative to avian IAV. Notably, human ZAP selectively depletes CpG-enriched viral RNAs with its cofactor KHNYN. ZAP is conserved in tetrapods but we uncovered that avian species lack KHNYN. We found that chicken ZAP does not affect IAV (PR8) or CpG enriched IAV. Human ZAP or KHNYN independently restricted CpG enriched IAV by overexpression in chicken cells or knockout in human cells. Additionally, mammalian ZAP-L and KHNYN also independently restricted an avian retrovirus (ROSV). Curiously, platypus KHNYN, the most divergent from eutherian mammals, was also capable of direct restriction of multiple diverse viruses. We suggest that mammalian KHNYN may be a bona fide restriction factor with cell-autonomous activity. Furthermore, we speculate that through repeated contact between avian viruses and mammalian hosts, protein changes may accompany CpG-biased mutations or reassortment to evade mammalian ZAP and KHNYN.

overall_design: RNAseq profiling of chicken DF-1 cells stably expressed human ZAP-L (long isoform of ZAP), ZAP-S (short isoform of ZAP), KHNYN, or dKHNYN (catalytically inactive form). Influenza A strains were either wild-type PR8 or PR8 with elevated CG dinucleotide frequencies.

first: Jordan

last: Becker

first: Clayton

middle: K

last: Mickelson

first: Lauren

last: Pross

first: Autumn

last: Sanders

first: Esther

last: Vogt

first: Chloe

last: Wick

first: Alison

middle: J

last: Barkhymer

first: Stephanie

last: Aron

first: Elizabeth

last: Fay

first: Reuben

last: Harris

first: Ryan

middle: A

last: Langlois


title: CD8 T cells cross-restricted by HLA-B*57 and HLA-E*01 recognize HIV Gag with different functional profiles [dataset 1]

first: Kevin

last: Maroney

overall_design:
CD8+ T cells were isolated from PBMC's of 1 HIV+ controller (C) Ci10004, noncontroller (NC) Ci10076, and ART+ noncontroller (ART+ NC)  Ci10074, or just PBMC's were used. These CD8+ T cells were co-cultured with HLA-null cell line 721.221ΔE transduced with nothing (null), HLA-B*57, E*01:01, or E*01:03, either loaded with no HIV-1 gag KF11 (unstimulated) or loaded with KF11 (stimulated). Alternatively, PBMC's from these same people with HIV (PWH) were unstimulated or stimulated with peptide. This stimulation (co-culture or PBMC) was performed for 18 hours before staining with oligo-tagged antibodies (hashtagging), then CITE-seq and fluorophore-tagged antibody cocktail. An equal number of Activated and unactivated CD8+ T cells in each of these conditions were then sorted into the same tube for each of the 3 PWH (3 tubes of 10 multiplexed conditions each). These were then used for library construction. There were 10 conditions (5 HLA/PBMC conditions - null, E01, E03, B57, PBMC X 2 stimulation conditions (unstimulated, stimulated with KF11)) per PWH, for 30 conditions total. After this, GEX, CITE-seq, and TCR data generated 2 separate sets of files (GEX and CITE-seq were both in GEX_FB)  for each multiplexed of 3 samples. Demultiplexing was performed as described in the manuscript to generate 30 conditions X 3 sample types (but GEX and feature barcoding were demultiplexed to the same GEX_FB file from which CITE-seq and GEX information was obtained) = 60 files. Through the pipeline and based on folder structure, metadata was applied holistically and 30 sets of conditions, each with TCR, GEX, and CITE-seq data were assembled into a single Seurat file at which point downstream analysis was performed. Though CD8 T cells were sorted with high purity, some of the co-cultured cell line was also incorrectly sorted and formed a distinct cluster far from all other clusters which was also used for analysis of the source of Luminex-identified cytokines - thus, the "cell line" column indicates the co-cultured HLA-expressing cell line as well, as this may be relevant for that cluster.
Please note that processed data files generated from both GEX and FB raw files are linked to the correpsonding GEX records.

first: Kevin J.

first: Michael A.

last: Rose

first: Allisa K.

last: Oman

first: Abha

last: Chopra

first: Hua-Shiuan

last: Hsieh

first: Zerufael

last: Derza

first: Rachel

last: Waterworth

first: Mark A.

last: Brockman

first: Spyros A.

last: Kalams

first: Anju

last: Bansal

first: Paul A.

last: Goepfert


title: Rat sperm small RNA following exposure to ethylene glycol monomethyl ether

status: Public on Dec 10 2025

city: Providence

first: Daniel

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-seq analysis was conducted as part of an experiment investigating the effects of ethylene glycol monomethyl ether (EGME), on rat sperm RNA. EGME is a testicular germ cell toxicant that selectively targets spermatocytes. This experiment used an established model in which rats are treated with EGME by daily oral gavage for 5 days, with no additional treatment for 5 weeks, which is the time required for spermatocytes to become mature spermatozoa. The goal of the study was to test which small RNAs in rat sperm are altered following EGME exposure at doses below those that cause testicular histopathology. Testicular histopathology is observed at doses of 100 mg EGME/kg/d and above; this experiment included a dose range of 0 (vehicle), 50, 60, and 75 mg EGME/kg/d.

overall_design: Adult male Fischer rats were treated with 0 (water vehicle), 50, 60, or 75 mg EGME/kg/d in water vehicle, by oral gavage from for five days. Treatment was discontinued, and cauda epidiymal sperm was collected five weeks after cessation of exposure. Each biological replicate consists of total RNA extrated from cauda epidiymal sperm of a single male.

first: Angela

last: Stermer

first: August

last: Guang

first: Yuan

last: Pu


title: Human PSC-derived organoids model sympathetic ganglion development and its functional crosstalk with the heart

city: Shanghai

first: Jinkui

last: Zhu

state: Shanghai

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: The sympathetic ganglia are essential components of the nervous system that regulate various aspects of involuntary body functions. Recapitulating sympathetic ganglion development with three-dimensional (3D) organoids is challenging and has not been achieved. Here, we report a method to differentiate human pluripotent stem cells into 3D neural organoids that resemble peripheral sympathetic ganglia, producing both neurons and glial cells of the ganglia in a self-organized manner. We developed an organoid system to construct functional connections between the sympathetic ganglia and one of their peripheral targets, the heart, by fusing human sympathetic ganglion organoids (hSGOs) and heart-forming organoids. Notably, this system enables the evaluation of signaling controls (i.e., nerve growth factor [NGF] signaling) on human sympathetic-to-cardiac innervation and reveals the reciprocal impacts between the sympathetic and cardiac lineages during their co-development. Our study provides a physiologically relevant platform for understanding the development of human sympathetic ganglia, their crosstalk with peripheral targets, and related diseases.

overall_design: scRNA-seq data profiles of hSGOs and hHFOs generated in this study.

first: Yantong

last: Liu

first: Yangfei

last: Xiang


title: Up-regulation of an epithelial miRNA is associated with immune evasion in progressive bronchial premalignant lesions.

city: Boston

first: Adam

middle: C

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

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

overall_design: Refer to individual Series


title: Up-regulation of an epithelial miRNA is associated with immune evasion in progressive bronchial premalignant lesions [PCGA_miRNA_BR]

summary: Bronchial premalignant lesions (PMLs), precursors of lung squamous cell carcinoma, have distinct molecular subtypes. The proliferative subtype, enriched with bronchial dysplasia, had decreased expression of an antigen processing/presentation gene co-expression module in progressive/persistent versus regressive PMLs, suggesting a functional impact of these genes on immune evasion. Here, we performed miRNA sequencing, miRNA in situ hybridization (ISH), and spatial proteomics of bronchial biopsies from patients at high risk for lung cancer. A miRNA-gene network analysis identified hsa-miR-149-5p as a potential regulator of the antigen presentation gene module. Staining on adjacent biopsy tissue showed that hsa-miR-149-5p was predominantly expressed in the epithelium and up-regulated in progressive/persistent proliferative lesions.  Targets of this miRNA, the transcriptional coactivator of MHC-I gene expression, NLRC5, and the genes it regulates were down-regulated in these lesions. Decreased NLRC5 expression reduced both IFN-gamma induced MHC-I surface expression and CD8 T cell cytotoxicity in lung squamous cancer cells.  In PMLs, basal cells with high levels of NLRC5 were in close spatial proximity to CD8 T cells, suggesting that these cells exhibit increased functional MHC-I gene expression in vivo. These findings indicate a functional role for hsa-miR-149-5p in PML progression/persistence and suggest this axis as a potential therapeutic target for PML immunomodulation.

overall_design: microRNA sequencing (miRNA-seq) was performed in bronchial brushings obtained from patients at high risk of lung cancer.

first: Boting

last: Ning

first: Darren

last: Chiu

first: Jennifer

last: Beane


title: Up-regulation of an epithelial miRNA is associated with immune evasion in progressive bronchial premalignant lesions [PCGA_miRNA_BX]

overall_design: microRNA sequencing (miRNA-seq) was performed in bronchial biopsies obtained from patients at high risk of lung cancer.