title: Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [RNA-Seq 4]

city: San Antonio

first: Hui

last: Yan

state: TX

address: 7703 Floyd Curl Dr.

department: MIMG

institute: UTHSCSA

summary: As “effector” cells, B lymphocytes make antibodies.  They also regulate immune functions through ligand-receptor interactions.  The limited understanding of regulatory roles of B cells prompted us to develop a workflow that profiles B cell ligand and receptor expression, maps in silico interactions involving ligands with high “specificity scores”, validates the function of top ligand-receptor interactions, and unveils transcription regulation of specific ligands.  Using this unbiased approach, here we report the regulatory functions of a new subset of murine B cells that express BATF3 as a hallmark transcription factor.  BATF3+ B cells, as generated upon B cell activation by innate TLR and adaptive CD40 and IL-21 receptor signals, lose their effector cell function (making class-switched antibodies) while expressing new ligands, most notably cytokine IL-27 and chemokine CXCL10.  As elicited by viral infection and immunization, IL-27+CXCL10+ B cells target effector B cells through the IL-27 receptor and, together with IFNg, optimize the antibody response and anti-viral immunity.  Also appearing in tumors and retained there through the autocrine CXCL10-CXCR3 interaction, they enhance B cell expression of immune checkpoint PD-L1 and suppress anti-tumor immunity.  Thus, we have identified new regulatory B cells and provided a paradigmatic framework to investigate immune cell communications.

overall_design: Ligand/receptor expression levels were compaired between stimulation conditions.  RNA-seq  samples from 5 different B cell stimulation conditions, namely Nil, LPS, CD154, LPS plus CD154 (LC) and LPS plus CD154 and IL-21 (LC21) were used in analysis.

first: Zhenming


title: Comprehensive analysis of gene expression induced by IFN-γ in the human oral mucosal epithelial cell line HSC-2

status: Public on Aug 31 2025

city: Mizuho

first: Eisuke

last: Domae

state: Gifu

country: Japan

institute: Asahi university

type: Expression profiling by high throughput sequencing

summary: Lipopolysaccharide (LPS) derived from Gram-negative bacteria is recognized by Toll-like receptor 4 (TLR4) on the host cell surface and by inflammatory caspases such as caspase-4 (CASP4) in the cytoplasm. LPS from the periodontal pathogen Porphyromonas gingivalis (PgLPS) is known to be recognized by TLR4, but whether it is sensed in the cytoplasm remains unclear. We investigated the intracellular recognition mechanism of PgLPS using the oral epithelial cell line HSC-2. Transfection of PgLPS alone did not elicit a response in HSC-2 cells; however, when PgLPS was transfected following priming with interferon (IFN)-γ, maturation of IL-18, activation of gasdermin D, and pyroptotic cell death were induced. These responses of HSC-2 cells were unaffected by TLR4 inhibition but were strongly suppressed by CASP4 inhibition. These findings suggest that IFN-γ–inducible genes likely play an auxiliary role in the CASP4-dependent responses of HSC-2 cells induced by PgLPS transfection. To examine the impact of IFN-γ priming on HSC-2 cells, we performed RNA sequencing (RNA-seq). This analysis identified 974 genes whose expression was upregulated by IFN-γ. Among these genes were members of the guanylate-binding protein (GBP) family (GBP1–5, GBP7) as well as CASP5. This analysis provides useful insights into the effects of IFN-γ on oral epithelial cells and into the characterization of IFN-stimulated factors in HSC-2 cells.

overall_design: RNA-seq profiling was conducted after HSC-2 cells were cultured for 18 hours in the presence or absence of IFN-γ (10 ng/mL).

first: Taiki

last: Mori

first: Hideo

last: Kataoka

first: Takeshi

last: Into


title: RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations

status: Public on Aug 28 2025

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

country: USA

institute: Nationwide Children's Hospital

summary: Background RNA-Seq analysis has become a routine task in numerous genomic research labs, driven by the reduced cost of bulk RNA sequencing experiments. These studies generate billions of reads that require easy-to-run, comprehensive, and reproducible analysis. However, many labs rely on in-house scripts, which can be challenging for bench scientist to use and hinder standardization and reproducibility. While existing RNA-Seq pipelines attempt to address these challenges, they often lack a complete end-to-end user interface. Findings To bridge this gap, we developed RNA-SeqEZPZ, an automated pipeline with a user-friendly point-and-click interface, enabling rigorous and reproducible RNA-Seq analysis without requiring programming or bioinformatics expertise. For advanced users, the pipeline can also be executed from the command line, allowing customization of steps to suit specific applications. The innovation of this pipeline lies in the combination of three key features: (1) all software is packaged within a Singularity container, eliminating installation issues, (2) it offers a point-and-click interface from raw FASTQ files through differential expression and pathway analysis, and (3) it includes a Nextflow version, enabling scalability and portability for seamless execution across various platforms including job submission in the cloud and cluster computing. Additionally, RNA-SeqEZPZ generates a thorough statistical report and offers an option for batch adjustment to minimize effects of noise due to technical variations across replicates. Reports can also be reviewed by a bioinformatician to ensure the overall quality of the analysis. Conclusions RNA-SeqEZPZ is a robust, accessible, and scalable solution for comprehensive RNA-Seq analysis, enabling researchers to focus on biological insights rather than computational challenges.

overall_design:
To evaluate the pharmacologic effects of seclidemstat treatment on the transcriptomes of Ewing sarcoma cell line, we treated A673 cell line seclidemstat at IC50 for 48 hours, collected RNA, and performed RNA-seq. We reanalyzed these IC50 samples along with A673 cells treated with either DMSO (GSM8270133, GSM8270134, GSM8270135) or seclidemstat at IC90 for 48 hours (GSM8270136, GSM8270137, GSM8270138). All these samples were analyzed together using RNA-SeqEZPZ pipeline.

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

last: Rask

first: Emily

middle: R

last: Theisen


title: Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [RNA-Seq 3]

overall_design: RNA-seq  samples from 4 different B cell stimulation conditions, namely CD154, CD154 plus IL-27,  CD154 plus IFNg,  and CD154 plus IL-21 were used in analysis.

last: Xu


title: Dietary saturated fatty acids promote lung myeloid cell inflammasome activation and IL-1β-mediated inflammation in mice and humans

status: Public on Aug 27 2025

city: Philadelphia

first: Sam

middle: J

last: McCright

state: PA

address: 3615 Civic Center Blvd.

department: Division of Allergy and Immunology

institute: Children's Hospital of Philadelphia

summary: Resident tissue macrophages and monocytes (RTMs) integrate local and systemic signals to coordinate immune cell function at homeostasis and in response to inflammatory stimuli. Obesity-associated metabolic dysfunction drives the development of RTM populations that contribute to disease states in multiple tissues. However, the contribution of specific dietary components to innate immune cell activation and function, as opposed to the effects of obesity per se, is largely unknown. Herein, we studied the mechanisms by which high fat (HF) diets shape lung RTM phenotype and function in the steady state and influence responses to inflammatory insults. We report that during HF diet feeding, lung RTMs accumulate saturated long chain fatty acids (LCFA), specifically stearic acid (SA), and demonstrate features of NLRP3 inflammasome priming and activation. In vivo, increased dietary SA was sufficient to cause neutrophil-predominant lung inflammation in the steady state and exacerbate a model of innate airway inflammation, while increased dietary oleic acid, the monounsaturated counterpart of SA, was sufficient to reduce inflammasome activation in the steady state and attenuate airway inflammation. Importantly, depletion of IL-1β or pharmacologic inhibition of the endonuclease IRE1⍺ protected against SA-induced exacerbated lung inflammation.  Finally, we identified a population of lung monocytes with hallmarks of HF diet-induced RTM activation that are present in obese humans with asthma. Together, these results identify a class of dietary lipids that regulate lung RTM phenotype and function in the steady state and modulate the severity of inflammation in the lung.

overall_design: Wild type bone marrow derived macrophages were treated with stearic acid (SA) or vehicle (EtOH) for 24 hours.

first: David

middle: A

last: Hill


title: Polymerase theta-mediated end-joining repairs persistent G1-induced DNA breaks in S/G2.

status: Public on Aug 26 2025

city: Stanford

first: Richard

middle: L

last: Frock

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

summary: In homologous recombination deficient cells, polymerase theta (Pol θ)-mediated end-joining (TMEJ) repairs replicative DNA breaks during mitosis through interactions with RHINO and TOPBP1. V(D)J recombination and class switch recombination (CSR) rely on DNA breakage in G1-phase B lymphocytes and repair by non-homologous end-joining (NHEJ). In this study, we assayed CSR in primary B cells deficient in XRCC4, SHLD1, and Pol θ. We found that B cells deficient in both XRCC4 and Pol θ, or SHLD1 and Pol θ, exhibit an increased rate of IgH breaks, while retaining CSR levels similar to those of B cells deficient in XRCC4 or SHLD1. We show that in XRCC4- or SHLD1-deficient B cells, Pol θ promotes the formation of aberrant recombination products characterized by exacerbated double-strand break (DSB) end resection, inversion and microhomology, and that these end-joining events occur independently of RHINO. Furthermore, we find that TMEJ of RAG-generated DSBs is also independent of RHINO and concomitant to S/G2 entry. Based on these results, we propose that in the absence of NHEJ, TMEJ repairs persistent G1-phase DSBs in S/G2, rather than in mitosis.

overall_design: CD19-enriched murine splenic B cells proficient or deficient in Xrcc4 (with CD21-Cre), Polq, Shld1, or in combination were stimulated for IgH class switch reocmbination and subjected to LAM-HTGTS JoinT-seq using Smu bait priming as described in PMIDs: 26308889, 27031497, 34006647.

first: Timea

last: Marton

first: Jinglong

last: Wang

first: Ludovic

last: Deriano


title: Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [RNA-Seq 1]

overall_design: Ligand/receptor expression levels were compaired between stimulation conditions.  Batf3 wildtype or knockout B cells stimulated with LPS plus anti-CD40 and IL-21 (LA21) were used in analysis.


title: Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [RNA-Seq 2]

overall_design: IgD positive, IgD negative GFP (Il27p28) negative, or IgD negative GFP (Il27p28) positive B cells from the spleens of VVWR-infected mice were used in analysis.


title: Proximity-specific ribosome profiling reveals the logic of localized mitochondrial translation

city: Cambridge

first: Jingchuan

last: Luo

state: MA

address: 455 Main Street

institute: Whitehead Institute

summary: Localized translation broadly enables spatiotemporal control of gene expression. Here we present LOCL-TL (LOV-domain-Controlled Ligase for Translation Localization), an optogenetic approach for monitoring translation with codon resolution at any defined subcellular location under physiological conditions. Application of LOCL-TL to mitochondrially-localized translation revealed that ~20% of human nuclear-encoded mitochondrial genes are translated on the outer mitochondrial membrane (OMM). Mitochondrially-translated messages form two classes distinguished by encoded protein length, recruitment mechanism, and cellular function. An evolutionarily ancient mechanism allows nascent chains to drive cotranslational recruitment of long proteins via an unanticipated bipartite targeting signal. Conversely, mRNAs of short proteins, especially eukaryotic origin electron transport chain (ETC) components, are specifically recruited by the OMM protein A-Kinase Anchoring Protein 1 (AKAP1), in a translation-independent manner that depends on mRNA splicing. AKAP1 loss lowers ETC levels. LOCL-TL thus reveals a hierarchical strategy that enables preferential translation of a subset of proteins on the OMM.

overall_design: Ribosome profiling data were generated from cell lines engineered with LOCL-TL components. Two replicates were used for each group: 1) ER-LOV-BirA and 2) Mito-LOV-BirA. RNA-seq data were collected from cell lines with LOCL-TL components and LOV-BirA targeted to the mitochondria in replicates. RNA-seq data were also collected from cell lines with perturbations on AKAP1, LARP4, or negative control gRNA.

first: Stuti

last: Khandwala

first: Jingjie

last: Hu

first: Song-Yi

last: Lee

first: Kelsey

last: Hickey

first: Zebulon

middle: G

last: Levine

first: J. Wade

last: Harper

first: Alice

middle: Y

last: Ting

first: Jonathan

middle: S

last: Weissman


title: ATRX promotes transcription initiation of HSV-1 immediate early genes [HEP2 PRO-seq]

city: Ithaca

first: Joel

last: Baines

state: NY

address: Hungerford Hill Rd

department: Baker Institute for Animal Health

institute: Cornell University

summary: Herpes simplex virus 1 (HSV-1) transcribes its genome in a highly coordinated temporal cascade, utilizing the host RNA polymerase II (Pol II). Repression of transcription precedes the cascade's progression in a process requiring viral immediate early (IE) genes, in a phenomenon termed Transient Immediate Early gene Mediated Repression (TIEMR). Given that components of promyelocytic leukaemia nuclear bodies (PML-NBs) are known to rapidly engage incoming HSV-1 genomes, we investigated their potential role in TIEMR regulation. Using siRNA knockdown of PML-NB constituents (PML, DAXX, and ATRX), we unexpectedly observed that ATRX depletion resulted in a significant reduction in nascent viral transcription on viral IE promoters at 1.5 hours post-infection (hpi). ChIP-Seq analysis indicated ATRX is associated with both highly transcriptionally active and transcriptionally restricted regions, indicating that ATRX has diverse functions in the viral genome. We show here that ATRX association with active transcription on IE genes is correlated to the presence of G-quadruplexes (G4s).  Drug stabilization of G4s mimicked the effects of ATRX knockdown, significantly reducing transcription initiation on IE genes. These findings suggest that ATRX promotes transcriptional initiation of HSV-1 IE genes by preventing G4 formation. In sum, our results reveal a previously unrecognized pro-transcriptional role for ATRX early in HSV-1 infection.

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

platform_organism:
Homo sapiens
Human alphaherpesvirus 1

overall_design: Cells were infected with HSV-1F at an MOI of 5 and infection allowed to proceed for 1.5 hpi. Nuclei were extracted and subjected to PRO-Seq.

first: Laura

middle: E

last: Dunn

middle: D


title: CRISPR Screens Identify the ATPase VCP as a Druggable Therapeutic Vulnerability in Cholangiocarcinoma

city: Amsterdam

first: Wu

last: Yang

address: B7, Plesmanlaan 121 1066CX Amsterdam

country: Netherlands

institute: Netherlands Cancer Institute

summary: Cholangiocarcinoma (CCA) remains a lethal malignancy with limited therapeutic options. Through genome-wide CRISPR-Cas9 screening, we identified the ATPase valosin-containing protein (VCP) as a critical dependency in CCA. Compound screens revealed that the VCP inhibitor CB-5339 potently suppresses CCA proliferation in a panel of patient derived organoids by inducing cellular senescence. It is known that senescent cells persist and this can contribute to therapy resistance. To address this, we combined CB-5339 with senolytic agents (ABT-263 and conatumumab), which selectively eliminate senescent CCA cells, achieving enhanced tumor suppression in vitro and in vivo. Clinical analysis showed that VCP overexpression in CCA patients correlates with poor prognosis. Our study unveils a “one-two punch” strategy, targeting VCP-mediated senescence followed by senolytic clearance, offering a promising therapeutic approach for CCA.

overall_design: HuCCT1 and RBE cells were seeded in 6-well plates at 60–70% confluency and treated with 2 μM CB-5339 (MedChemExpress, HY-128724) for 7 days.

first: Siying

first: Rene

last: Bernards

first: Haojie

last: Jin


title: HIV broadly neutralizing antibody precursors induced to the Apex epitope in non-human primates

status: Public on Aug 25 2025

city: La Jolla

first: Shane

last: Crotty

address: 9420 Athena

institute: La Jolla Institute For Immunology

summary: An effective prophylactic HIV vaccine will likely need to induce broadly neutralizing antibodies (bnAbs). BnAbs to the Apex region of the HIV envelope glycoprotein (Env) are promising targets for vaccination due to their relatively low somatic hypermutation compared with other bnAbs. Most Apex bnAbs engage Env using an exceptionally long heavy chain complementarity determining region 3 (HCDR3) containing specific binding motifs, which reduces bnAb precursor frequency and makes priming of rare bnAb precursors a likely limiting step in the path to Apex bnAb induction. We found that adjuvanted protein or mRNA-LNP immunization of rhesus macaques with ApexGT6, an Env trimer engineered to bind Apex bnAb precursors, consistently induced Apex bnAb-related precursors with long HCDR3s bearing bnAb-like sequence motifs. Cryo-electron microscopy revealed that elicited Apex bnAb-related HCDR3s possessed structures combining elements of several prototype Apex bnAbs. These results achieve an important HIV vaccine development milestone in outbred primates.

overall_design: HIV Env Apex-specific B cells from PBMCs and lymph nodes were isolated by fluorescence-activated cell sorting (FACS) and analyzed by scRNA-seq, including VDJ and GEX libraries, using the 10X Genomics platform.

first: Henry

last: Sutton


title: ATRX promotes transcription initiation of HSV-1 immediate early genes [ATRX PRO-seq]

overall_design: siRNA knockdown of ATRX in HEp-2 cells. Compared to a non-targeting siRNA control. Cells were infected with HSV-1F at an MOI of 5 and infection allowed to proceed for 1.5 hpi. Nuclei were extracted and subjected to PRO-Seq.


title: Divergent cytokine and transcriptional signatures control functional T follicular helper cell heterogeneity (RNAseq)

city: Parkville

first: Joanna

last: Groom

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: CD4+ T follicular helper (Tfh) cells support tailored B cell responses against multiple classes of pathogens. To reveal how diverse Tfh phenotypes are established, we profiled Tfh cells in response to viral, helminth and bacterial infection. We identified a core Tfh signature that is distinct from CD4+ T follicular regulatory and effector cells and identified pathogen-specific transcriptional modules that shape Tfh function. Cytokine-transcriptional Tfh programming demonstrated that type I interferon and TGFbeta signaling direct individual Tfh phenotypes to instruct B cell output. Cytokine-directed Tfh transcriptional phenotypes are shared within human germinal centers (GCs), but distinct Tfh phenotypes dominate between donors and following immune challenge or in antibody-mediated disease. Finally, we identified novel cell surface markers that align with distinct Tfh phenotypes. Thus, we provide a comprehensive resource of Tfh diversity in humans and mice, to enable immune monitoring during infection and disease and to inform the development of context-specific vaccines.

overall_design: Paired RNA sequencing of lymph node T cells from mice infected with LCMV, influenza A, Trichuris muris, Heligmosomoides polygyrus or Citrobacter rodentium.

first: Lennard

last: Dalit

first: Chin Wee

last: Tan


title: Systematic Evaluation of crRNA Design Parameters for Optimized Cas13d-Mediated RNA Targeting in Chicken Cells

city: Melbourne

first: Mark

last: Ziemann

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

summary: CRISPR/Cas13 systems are increasingly becoming popular tools for programmable RNA targeting owing to its high-precision and ease at which crRNAs can be designed against mRNA targets of interest, often surpassing the usability of traditional RNA-targeting tools such as RNAi. The RNA-targeting capabilities of CRISPR/Cas13 have been harnessed to correct pathogenic mutations and combat infectious diseases. However, the wider adoption of Cas13 systems relies on the ability to design effective crRNAs that are broadly targetable and resistant to emerging mutants. In this study, we delineated the principles for the development of effective crRNAs by targeting DsRed fluorescence reporter and synthetic influenza mRNA in chicken fibroblast DF1 cells. To systematically determine the optimal design for crRNAs, we designed multiple versions of crRNAs to investigate the minimum length of the crRNA, importance of protospacer flanking sequence, degree of mismatch tolerance, and off target effects. Our data revealed variable knockdown levels between crRNAs, in which a few crRNAs achieved over 95% target knockdown. We showed that crRNAs exhibit a high degree of tolerance to single-nucleotide mismatches, regardless of the position at which the single-nt mismatch was introduced. However, 4-nt mismatches within crRNAs significantly reduced targeting efficacy, and eight nucleotide mismatches completely diminished targeting efficacy. Finally, we compared targeting efficiency of two widely used Cas13d variants (RfxCas13d and HfCas13d) and associated collateral degradation of bystander RNA. Our data extend current understanding of Cas13d-mediated RNA targeting and offer a framework for rational crRNA design to enhance effectiveness in diverse applications, including antiviral strategies.

overall_design: RNA-seq profiling of chicken cells expressing different Cas13d targeting constructs. All cells are overexpressing DsRed. (1) RfxCas13d non-targeting control. (2) RfxCas13d targeting DsRes. (3) HfCas13d  non-targeting control. (4) HfCas13d non targeting.

first: Emily

last: Hann

first: Debolina

last: Majumdar

first: Daniel

last: Layton

first: Mohamed

last: Fareh

first: David

middle: M

last: Cahill

first: Beata

last: Ujvari

first: Karel

last: Schat

first: Arjun

last: Challagulla


title: Divergent cytokine and transcriptional signatures control functional T follicular helper cell heterogeneity (scRNAseq/CITEseq)

overall_design: Paired single cell RNA sequencing (scRNAseq) and surface protein sequencing (CITEseq) analysis of Tfh cells from human adult tonsils samples.


title: ATRX promotes transcription initiation of HSV-1 immediate early genes [ATRX ChIP-seq]

first: Joel

last: Baines

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-Seq for ATRX in HEp-2 cells  infected with HSV-1F at an MOI of 5.

first: Laura

last: Dunn


title: Improving Immunotherapy Responses by Dual Inhibition of Macrophage Migration Inhibitory Factor and PD-1

city: New Haven

first: Edward

last: Doherty

state: CT

address: 300 Cedar street

department: Internal Medicine

institute: Yale School of Medicine

summary: Macrophage migration inhibitory factor (MIF) is an upstream regulatory cytokine that is associated with advanced disease and poor outcomes in multiple cancer types, including melanoma. We investigated whether anti-MIF therapy could enhance the antitumor effects of the immune checkpoint inhibitor anti-PD-1 in two murine tumor models. The therapeutic efficacy of anti-MIF, alone or combined with anti-PD-1, was tested in the YUMMER1.7 melanoma and MC38 colorectal cancer models. Tumor growth and survival were assessed in untreated Mif knockout (KO) and low-expression human MIF allele (CATT5) mice and compared to wild-type (WT) or high-expression MIF allele (CATT7) mice. Tumor-bearing animals underwent cytokine profiling, tumor immunohistochemistry, flow cytometry, and single-cell RNA sequencing (scRNA-seq). We also correlated functional variant MIF alleles with melanoma incidence and progression in patients. Our results showed that combined anti-MIF and anti-PD-1 significantly reduced tumor growth, improved survival, and promoted tumor regression, accompanied by enhanced TH1 cytokine levels, macrophage activation, and increased type 1 conventional dendritic cells (cDCs). scRNA-seq analysis revealed an expansion of intra-tumor Cd74/C1q/Aif1-expressing macrophages, which exhibited an antitumor phenotype, in response to anti-MIF therapy. MIF-KO and CATT5 mice exhibited reduced tumor burdens compared to WT or CATT7 mice alone and in the presence of anti-PD-1. In melanoma patients, the high MIF expression genotype (-173C/C) occurred at higher frequencies compared to healthy controls. These findings highlight that the addition of anti-MIF to anti-PD-1 reduces tumor growth, enhances anti-tumor responses, prolongs survival, and augments key intratumor immune cell populations involved in immune activation against tumors. This approach merits further consideration for clinical trial development.

overall_design: YUMMER1.7 tumors from a separate cohort of mice were harvested and processed to create a single cell suspension. The cell suspension was subjected to fluorescence-activated cell sorting (FACS) for CD45 expression, yielding CD45+ (immune cell) and CD45- (tumor cell) populations. Post-sorting, the cells were recombined to enrich for immune cells using 20% CD45- and 80% CD45+ cells to achieve a final population of 100,000 cells. This enriched cell suspension was processed using the Chromium 5′ Single-Cell Gene Expression system (10X Genomics) to generate scRNA seq libraries following the manufacturer’s protocol.

first: Thuy

middle: T

last: Tran

first: Gabriela

last: Sanchez Zuno

first: Lais

last: Osmani

first: Jasmine

last: Caulfield

first: Caroline

middle: N

last: Valdez

first: Marta

last: Piecychna

first: Lin

last: Leng

first: Michelle

last: Armstrong

first: Seamas

middle: C

last: Donnelly

first: Carlo

middle: B

last: Bifulco

first: Terri

last: Clister

first: Rajan

middle: P

last: Kulkarni

last: Zhang

first: Mario

last: Sznol

first: Lucia

last: Jilaveanu

first: Harriet

last: Kluger

first: Insoo

last: Kang

first: Richard

last: Bucala


title: Gene expression profile at single cell level of lung from TRAF5 knockout mouse with Systemic Lupus Erythematosus-associated Pulmonary Arterial Hypertension (SLE-PAH)

city: Beijing

first: Xiaoyue

last: Deng

address: Shuaifuyuan NO.1, Dongcheng district

country: China

institute: Paking Union Medical College Hospital

summary: Pulmonary arterial hypertension (PAH) is a severe complication that significantly impacts the prognosis of patients with systemic lupus erythematosus (SLE). SLE-PAH has high mortality and morbidity but poorly understood pathogenesis. Our goal is to identify novel susceptibility genes associated with SLE-PAH by performing genetic analyses on large cohorts and validating the functional significance. On the genetic level, Whole Exome Sequencing (WES) and Sanger sequencing were performed on the discovery and validation cohorts to identify susceptibility genes associated with SLE-PAH; At the transcriptional level, the expression of susceptibility gene was examined by RNA-seq and RT-qPCR. TRAF5 knockout mice were compared with control after induction of the previously established SLE-PAH model, and the protective effects of TRAF5 overexpression were evaluated. Single-cell RNA sequencing (scRNA-seq) analyses were conducted on lung tissues to investigate pulmonary cellular population. In vitro interventional studies involving TRAF5 knockdown in pulmonary arterial endothelial cells (PAECs) were performed to further investigate its functions. Supporting data from both the discovery and validation cohorts revealed a total of 7 deleterious variants on TRAF5 in 8 cases of SLE-PAH (n=226), with none found in the health control group (HC, n=934). There was decreased TRAF5 expression at the transcriptional level (n=120) compared to SLE-nonPAH (n=116) and HC (n=20). Mice with TRAF5 knockout exhibited more severe pulmonary hypertension, right ventricular hypertrophy, and early mortality. scRNA-seq analyses of lung tissue in knockout mice revealed significantly decreased TRAF5 expression and increased apoptosis in arterial ECs, with distinct pathways identified. In vitro interventional studies confirmed that TRAF5 deficiency caused dysfunction in PAECs, regulating the BMP/TGF-β pathway. Endothelial-targeted overexpression of TRAF5 attenuated PH in model mice.

overall_design: Single cell RNA sequencing (scRNA-seq) was conducted in Novogene Technology Co., Ltd, China. Lung tissue from WT_PtHx and KO_PtHx mice (n=1, respectively) were harvested. Cell preparation followed by 10x Genomics® Cell Preparation Guide. The cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (NovaSeq), according to the manufacturer’s instructions (Illumina). scRNA-seq library was constructed according to the instruction of the Single Cell 3’ Reagent Kit v3.1 (10x Genomics). Cell Ranger (v6.0.1) was used to process raw sequencing data and generate the count matrix. Next, data were normalized and scaled by NormalizeData and ScaleData function, then integrated into an un-banched matrix. Cell clustering were performed and visualized by Uniform Manifold Approximation and Projection (UMAP) algorithm, and identified the distinct cell types were according to the relative expression levels of canonical markers. The differentially expressed genes (DEGs) between KO_PtHx and WT_PtHx groups in each cell type were identified using wilcoxon rank-sum test with (1) |log2 fold change| > 0.25; (2) adjusted P value < 0.05. R package clusterProfiler (version 3.18.1) was used to perform gene ontology (GO) analysis and GSEA enrichment analysis with the default parameter. Additionally, the gene set scores were calculated by AddModuleScore function in R package Seurat.

first: Tianyi

last: Yuan

first: Junliang

last: Zhao

first: Mengtao

last: Li

first: Xiaofeng

last: Zeng


title: Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Mouse scRNA-seq]

status: Public on Aug 23 2025

first: Benjamin

last: Pham

state: CA

address: 257 Campus Drive

summary: A significant complication of Crohn’s disease (CD) is intestinal fibrosis, which narrows the bowel lumen to cause a stricture. Creeping fat (CF) is the wrapping of mesenteric adipose tissue (MAT) around inflamed and fibrotic bowel, but its role in stricture progression in CD is unclear. In this study, we explore whether CF-derived fibroblasts, the cells primarily responsible for extracellular matrix (ECM) deposition, directly contribute to stricture progression.  By performing scRNA-seq and Visium on pediatric CD strictures, we identified a CF-associated, mechanosensitive, CTHRC1+ fibroblast enriched for YAP/TAZ signaling that localized to the fibrotic CF-bowel wall interface within the stricture. We developed a novel mouse model of intestinal fibrosis that exhibited CF and used lineage tracing to show that Postn+ mouse fibroblasts, analogous to human CTHRC1+ fibroblasts, infiltrate fibrotic bowel and deposit ECM in a YAP/TAZ-dependent manner through scRNA-seq. Our findings identify mesenteric fat as a key source of pro-fibrotic fibroblasts that can be therapeutically targeted to limit intestinal fibrosis.

overall_design: Single cell RNA sequencing of mouse bowel and mesenteric adipose tissue from POD14 colotomy mouse model and sham surgeries

first: Khristian

last: Bauer-Rowe

last: Griffin

first: Alexia

last: Kim


title: Establishment, Characterization, and Tissue Comparison of Canine Pancreatic and Endometrial Organoids, Alongside Patient Matched Organoids

status: Public on Aug 22 2025

city: Ames

first: Christopher

last: Zdyrski

state: Iowa

address: 1800 Christensen Dr, Bms 1072 Vet Med, Bms 1072 Vet Med

institute: Iowa State University

summary: Organoids are 3-dimensional (3D) stem cell-derived cultures that offer a variety of technical advantages compared to traditional 2-dimensional (2D) cell cultures. Although murine models have proved useful in biomedical research, rodent models often fail to adequately mimic human physiology and disease progression, resulting in poor preclinical prediction of therapeutic drug efficacy and toxicity. An interesting alternative is to use the canine model in research, due to its numerous similarities to humans (shared environment, intact immune system, and development of civilization diseases). The use of canine organoids in drug testing and disease modeling has been limited by the number of models as well as the depth of characterization. Here, we report the establishment, maintenance, and molecular characterization of six adult-stem cell-derived canine organoid cell lines from endometrium, pancreas, urinary bladder, kidney, lung, and liver from two genetically related canines. The organoids of the canine endometrium and pancreas have not yet been described in the literature. Furthermore, scRNASeq was utilized on a subset of the organoids to identify organoid specific transcriptomic signatures including lung (SFTPC), pancreas (TFF3), kidney (GJB2), and bladder (UPK1A). In total, six tissues and organoid lines from each donor were characterized, allowing for a unique, multi-organ comparison between these two individuals and identification of specific cell types within the organoids.

overall_design: scRNA-seq profiling of four healthy canine organoid lines.

first: Karin

last: Allenspach

first: Jonathan

last: Mochel


title: Methylene Blue Treatment of Fatal Cerebral Malaria and Identification of Potential Blood Biomarkers

city: Singapore

first: Benoit

last: Malleret

address: 5 Science Drive 2, Level 5, MD4-05-03C

department: Microbiology and Immunology

country: Singapore

institute: National University of Singapore, Yong Loo Lin School of Medicine

summary: Cerebral malaria (CM) is a severe complication caused by Plasmodium falciparum infection, leading to persistent neurological impairments in survivors. To understand the complex mechanisms and investigate advanced diagnostic and treatment strategies targeting human CM, we utilize Plasmodium coatneyi-infected male rhesus macaques, a non-human primate model closely resembling P. falciparum infection in humans. Through differential gene expression analysis, our study demonstrates methylene blue’s efficacy in reversing the detrimental effects of infection on the brainstem. Furthermore, by comparing our brainstem dataset from P. coatneyi-infected Macaca mulatta with two additional transcriptomic datasets (P. coatneyi-infected M. mulatta blood and P. falciparum-infected human blood), we identify nine genes associated with CM severity. Most of these genes are expressed in neutrophils, indicating their potential as blood biomarkers for diagnosing P. falciparum-induced fatal CM. This research highlights the necessity for new CM treatments and reveals promising biomarkers that could improve diagnosis and prognosis in affected individuals.

overall_design: To investigate cerebral malaria biomarkers, we established P. coatneyi (Hackeri strain) infections in Macaca mulatta. Upon cerebral malaria induction, infected macaques were treated with either 6 mg/kg, 10 mg/kg or 17 mg/kg methylene blue. At study endpoint, the organ tissues (brainstem, thalamus, cerebellum, heart, kidney, and liver) of uninfected group (Pcoat-MB-), infected-untreated group (Pcoat+MB-), and infected-treated group (Pcoat+MB+) were harvested for RNA-seq.

first: Jing Wen

last: Hang

first: Yew Wai

last: Leong

first: Vipin

last: Narang

first: Piyanate

last: Sunyakumthorn

first: Rawiwan

last: Im-Erbsin

first: Shihui

last: Foo

first: Josephine

last: Lum

first: Bernett

last: Lee

first: Arthur

last: Brown

first: Laurent

last: Rénia

first: Gareth

last: Turner

first: Samuel

last: Wassmer

first: Eric

last: Lombardini

first: Bruce

last: Russell

first: Benoît


title: The impact of the Trp53 allelic state on the response to gamma-irradiation in hematopoietic stem and progenitor cells

city: Zurich

first: Jonas

last: Fullin

address: Rämistrasse 100

department: Department  of Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich

summary: We investigated how the Trp53 allelic state influences the response of hematopoietic stem and progenitor cells (HSPCs) to γ-irradiation. We used a transgenic mouse model harboring hematopoietic cell–specific, tamoxifen-inducible Trp53-R245W missense mutations linked to a GFP reporter. In mice with biallelic transgenes, tamoxifen treatment generates three GFP-defined populations: GFP-negative cells (Trp53 wild-type), GFP-low cells (monoallelic Trp53 mutation, due to recombination of only one transgenic allele), and GFP-high cells (biallelic Trp53 mutation). Flow sorting of these populations enables direct comparison of all three allelic states in HSPCs. Using this system, we sought to define the transcriptional responses of HSPCs with different Trp53 genotypes following γ-irradiation.

overall_design: SCL-CreERT; Trp53-fl-R245W-GFP mice were treated with tamoxifen to induce the Trp53 missense mutations. Five weeks later, mice were either treated with 2.5 Gy of gamma-irradiation or left untreated. 12 hours later, bone marrow cells were harvested, stained, and sorted for Lineage-/Sca1+/c-Kit+ (LSK) cells, and further divided into GFP-neg (wt), GFP-low (monoallelic Trp53 mutation) and GFP-high (biallelic Trp53 mutation) populations. RNA was isolated from these cells and subjected to bulk RNA sequencing.


title: Cell-type-specific RNA Pol II activity maps in intact-tissues: gateway to mammalian gene regulatory mechanisms in vivo [CUT&RUN]

first: Tudorita

last: Tumbar

address: 526 Campus Rd

department: Molecular biology and genetics

summary: Accessing ongoing RNA Pol II activity in specific cell types within intact-tissue is critical to reveal regulatory mechanisms of development. We developed PReCIS-seq, a method combining Cre-inducible GFP-tagging of endogenous Pol II with transcriptional run-on and GFP-immunoprecipitation, to map transcriptionally-engaged Pol II genome-wide in targeted cell types of mouse tissues. Applied to keratinocytes within intact-skin, PReCIS-seq demonstrates that transcriptionally activated functions of biological transitions generally employ both Pol II promoter-recruitment and promoter-proximal pause-release mechanisms. We uncover a global Pol II regulatory polarization that modulates cellular safeguarding versus lineage identity genes across embryonic development to adult homeostasis. This polarization is associated with distinct proximal-promoter structures distinguishing high-paused genes with restricted Pol II pause-release from low-paused genes undergoing rapid Pol II firing into productive elongation. PReCIS-seq also identifies active enhancers based on divergent transcription. This approach enables high-resolution, cell-type-specific analysis of Pol II dynamics in intact-tissues across mammalian development, homeostasis, and disease.

overall_design: To confirm motif enrichment and active enhancers, CUT&RUN was performed on newborn mouse skin keratinocytes using BRD4, NRF1, KLF3, and H3K27ac antibodies.

first: Gopal

last: Chovatiya


title: Mapping SET1B Chromatin Interactions with DamID using DamMapper, a Comprehensive Snakemake Workflow

status: Public on Aug 21 2025

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

summary:
Background
DNA adenine methyltransferase identification followed by sequencing (DamID-seq) is a powerful method used to map genome-wide chromatin-protein interactions. However, the bioinformatic analysis of DamID-seq data presents significant challenges due to the inherent complexities of the data and a notable lack of comprehensive software solutions for data-processing and downstream analysis.
Results
To address these challenges, we present a comprehensive bioinformatic workflow for DamID-seq data analysis, DamMapper, using the Snakemake workflow management system. Key features include straightforward processing of multiple biological replicates, visualisation of quality control figures, such as a correlation heatmaps and principal component analysis (PCA) plotting, and robust code quality maintained through continuous integration (CI). Reproducibility is ensured across diverse computational environments, including cloud computing and high-performance computing (HPC) clusters, through the implementation of software environments (Conda) and containerisation (Docker/Apptainer). We validated this workflow using a previously published DamID-seq dataset and Furthermore, we apply it to analyse novel datasets for proteins involved in the hypoxia response, specifically the transcription factor HIF-1α and the histone methyltransferase SET1B. This application reveals a strong concordance between our HIF-1α DamID-seq results and ChIP-seq data, and importantly, provides the first genome-wide DNA binding map for SET1B.
Conclusions
This work provides a validated, reproducible, and feature-rich workflow that overcomes common hurdles in DamID-seq data analysis. By streamlining the processing and ensuring robustness, DamMapper facilitates reliable analysis and enables new biological discoveries, as demonstrated by the characterization of SET1B binding sites. The workflow is available under the MIT license at: https://github.com/niekwit/damid-seq.

overall_design: 24 hours expression of Dam-HIF1a, Dam_SET1B and Dam only in 1% O2 in HeLa cells

first: Bertlin

last: James

first: Wit

last: Niek

first: Hynes-Allen

last: Antony

first: Van den Ameele

last: Jelle

first: Nathan


title: The effect of MDM2 overexpression on the cellular response to etoposide treatment

status: Public on Aug 24 2025

summary: We aimed to study the effect of mutational and non-mutational p53 inactivation on the response of hematopoietic progenitor cells to genotoxic treatment. In order to study this in vitro, we generated HSPC lines by enforced ER-Hoxb8 expression in bone marrow cells derived from transgenic Trp53-fl-R245W-GFP mice (in hetero- or homozygous state). Upon induction of the Trp53-R245W missense mutation, these cells carry mutational mono- or biallelic loss of wild-type p53. In the genetic background of mono- or biallelic Trp53 mutations, we additionally transduced these cells lentivirally with a construct overexpressing murine Mdm2 or a control vector. This leads to non-mutational inactivation of functional p53. Thereby, we aimed to compare the transcriptional response to genotoxic treatment in cells carrying mono- or biallelic Trp53 mutations with or without non-mutational p53 inactivation through Mdm2 overexpression.

overall_design: Hoxb8 cells, immunophenotypically resembling murine granulocyte-macrophage progenitor cells, were induced to carry monoallelic or biallelic Trp53-R245W mutations, each in combination with either an Mdm2 overexpressing or a control vector. These cells were treated with 10 uM etoposide for 3 hours, after which RNA was isolated and subjected to bulk RNA sequencing.


title: Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Visium]

first: Benjamin

last: Pham

overall_design: Spatial transcriptomics of hashed human bowel and mesenteric adipose tissue cells using the 10X Genomics platform.

first: Khristian

last: Bauer-Rowe

first: Michelle

last: Griffin

first: Alexia

last: Kim


title: Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Human scRNA-seq]

overall_design:
Single cell RNA sequencing of hashed human bowel and mesenteric adipose tissue cells using the 10X Genomics platform.

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Submitter states that missing raw files are due to patient privacy concerns.
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title: Transcription Factor 25 Modulates Gametocytogenesis in the Malaria Parasite Plasmodium falciparum [RNA-Seq]

status: Public on Aug 20 2025

city: Changsha

first: Xiaomin

last: Shang

state: Hunan Province

address: 172 Tongzipo Road

department: Department of Parasitology

institute: Central South University

summary: This study elucidates the role of TCF25 as a transcriptional regulator orchestrating sexual conversion in Plasmodium falciparum. Through generation of isogenic tcf25_ko parasite lines, we performed comparative transcriptomic analysis of synchronized ring-stage and schizont-stage parasites (WT vs knockout). Our data demonstrate that tcf25 deletion causes significant dysregulation of both gametocytogenesis-associated genes and antigenic variation gene families. TCF25 directly binds a sexual conversion regulator ap2-g4. These results indicate TCF25 as an essential upstream regulator of malaria parasite sexual development and potential transmission-blocking target.

overall_design: RNA-seq profiling was performed on Plasmodium falciparum at distinct intraerythrocytic stages (ring and schizont).


title: Transcription Factor 25 Modulates Gametocytogenesis in the Malaria Parasite Plasmodium falciparum [ChIP-Seq]

overall_design: ChIP-seq profiling was performed at schizont stage.


title: siPiezo1 or scRNA immortalised MSC cell line (Y201) cultured on soft hydrogels

city: Barcelona

first: Mariana

last: Azevedo Gonzalez Oliva

state: Barcelona

address: Ed. Clúster – Lab EMS1C54, Av. Gregorio Marañon, 6, Rampa 2

country: Spain

institute: IBEC Parc Cientific Barcelona

summary: Mechanosensitive ion channels have emerged as fundamental proteins in sensing extracellular matrix (ECM) mechanics. Among those, Piezo1 has been proposed as a key mechanosensor in cells. However, whether and how Piezo1 senses time-dependent ECM mechanical properties (i.e., viscoelasticity) remains unknown. To address this question, we combined an immortalised mesenchymal stem cell (MSC) line with adjustable Piezo1 expression with soft (0.4 kPa) and stiff (25 kPa) viscoelastic hydrogels with independently tuneable Young’s modulus and stress relaxation. Here, we propose that Piezo1 is an important sensor of stiffness at this range (25kPa) consistent with the molecular clutch model. By performing RNA sequencing (RNA-seq), we identified the transcriptomic phenotype of MSCs response to matrix viscoelasticity and Piezo1 activity, highlighting gene signatures that drive MSCs mechanobiology at this elasticity scale.

overall_design: RNAseq profiling of small interferring RNA (siPiezo1) and scrambled RNA (scRNA) treated immortalised mesenchymal stem cells (Y201) grown on 0.4 kPa elastic (V-) and viscoelastic (V+) Fibronectin coated polyacrylamide hydrogels. Three independent biological replicates cultured in parallel in a single experiment were sequenced.

last: A G Oliva

first: Manuel

last: Salmeron Sanchez


title: The deubiquitinase OTUD7B ameliorates central nervous system autoimmunity by inhibiting degradation of glial fibrillary acidic protein and astrocyte hyperinflammation

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: Astrocytes are central to the pathogenesis of multiple sclerosis; however, their regulation by intrinsic post-translational ubiquitination and deubiquitination is unresolved. This study shows that the deubiquitinating enzyme OTUD7B in astrocytes confers protection against murine experimental autoimmune encephalomyelitis, a model of MS, by limiting neuroinflammation. RNA-sequencing of isolated astrocytes and spatial transcriptomics showed that in EAE OTUD7B downregulates the expression of chemokines in astrocytes of inflammatory lesions, which is associated with reduced recruitment of encephalitogenic CD4+ T cells. Furthermore, OTUD7B was essential for GFAP protein expression of astrocytes bordering inflammatory lesions. Mechanistically, OTUD7B (i) restricted TNF-induced chemokine production of astrocytes by sequential K63- and K48-deubiquitination of RIPK1 limiting NF-κB and MAPK activation and (ii) enabled GFAP protein expression by supporting GFAP mRNA expression and preventing its proteasomal degradation through K48-deubiquitination of GFAP. This dual action on TNF signaling and GFAP identifies astrocyte-intrinsic OTUD7B as a central inhibitor of astrocyte-mediated inflammation.

overall_design: Probe-based spatial transcriptomics from spinal cord sections of Otud7bfl/fl and GFAP-Cre Otud7bfl/fl mice at d0 and d15 post immunization with MOG peptide.

first: Kunjan

last: Harit

first: Wenjing

last: Yi

first: Andreas

last: Jeron

first: Jakob

last: Schmidt

first: Ruth

last: Beckervordersandfort-Bonk

first: Izabela

last: Plumbon

first: Artür

last: Manukyan

first: Martina

last: Deckert

first: Thomas

last: Conrad

first: Janine

last: Altmüller

first: Markus

last: Landthaler

first: Helena

last: Radbruch

first: Xu

last: Wang

first: Gopala

last: Nishanth

first: Dirk

last: Schlüter


title: siPiezo1 or scRNA immortalised MSC cell line (Y201) cultured on fibronectin coated glass coverslips

first: Mariana

last: Azevedo Gonzalez Oliva

summary: Mechanosensitive ion channels have emerged as fundamental proteins in sensing extracellular matrix (ECM) mechanics. Among those, Piezo1 has been proposed as a key mechanosensor in cells. However, whether and how Piezo1 senses time-dependent ECM mechanical properties (i.e., viscoelasticity) remains unknown. To address this question, we combined an immortalised mesenchymal stem cell (MSC) line with adjustable Piezo1 expression with soft (400 Pa) and stiff (25 kPa) viscoelastic hydrogels with independently tuneable Young’s modulus and stress relaxation. Here, we propose that Piezo1 is an important sensor of stiffness at this range (25kPa) consistent with the molecular clutch model. By performing RNA sequencing (RNA-seq), we identified the transcriptomic phenotype of MSCs response to matrix viscoelasticity and Piezo1 activity, highlighting gene signatures that drive MSCs mechanobiology at this elasticity scale.

overall_design: RNAseq profiling of small interferring RNA (siPiezo1) and scrambled RNA (scRNA) treated immortalised mesenchymal stem cells (Y201) grown on Fibronectin coated glass coverslips. Three independent biological replicates cultured in parallel in a single experiment were sequenced.

last: A G Oliva

first: Manuel

last: Salmeron Sanchez


title: ATRX promotes transcription initiation of HSV-1 immediate early genes [BRACO-19 PRO-seq]

first: Joel

last: Baines

summary: Herpes simplex virus 1 (HSV-1) transcribes its genome in a highly coordinated temporal cascade, utilizing the host RNA polymerase II (Pol II). Repression of transcription precedes the cascade's progression in a process requiring viral immediate early (IE) genes, in a phenomenon termed Transient Immediate Early gene Mediated Repression (TIEMR). Given that components of promyelocytic leukaemia nuclear bodies (PML-NBs) are known to rapidly engage incoming HSV-1 genomes, we investigated their potential role in TIEMR regulation. Using siRNA knockdown of PML-NB constituents (PML, DAXX, and ATRX), we unexpectedly observed that ATRX depletion resulted in a significant reduction in nascent viral transcription on viral IE promoters at 1.5 hours post-infection (hpi). ChIP-Seq analysis indicated ATRX is associated with both highly transcriptionally active and transcriptionally restricted regions, indicating that ATRX has diverse functions in the viral genome. We show here that ATRX association with active transcription on IE genes is correlated to the presence of G-quadruplexes (G4s).  Drug stabilization of G4s mimicked the effects of ATRX knockdown, significantly reducing transcription initiation on IE genes. These findings suggest that ATRX promotes transcriptional initiation of HSV-1 IE genes by preventing G4 formation. In sum, our results reveal a previously unrecognized pro-transcriptional role for ATRX early in HSV-1 infection.

overall_design: Cells were infected with HSV-1F at an MOI of 5 in the presence of 25µM BRACO-19 or DMSO and infection allowed to proceed for 1.5 hpi. Nuclei were extracted and subjected to PRO-Seq.

first: Laura

last: Dunn


title: Transcriptomic characterization of murine Trp53-mutant acute erytroid leukemias

first: Jonas

last: Fullin

summary: We established a mouse model to study the development of therapy-related myeloid neoplasms (t-MN) arising from TP53-mutant clonal hematopoiesis. Mice carrying conditional Trp53-fl-R245W-GFP alleles, in combination with the inducible hematopoietic-specific Cre driver (SCL-CreERT), allow induction of either monoallelic or biallelic Trp53 missense mutations. To mimic cytotoxic therapies implicated in t-MN pathogenesis, mice were exposed to sublethal γ-irradiation, which promoted the development of hematologic malignancies, including acute erythroid leukemia. We then subjected these leukemias to bulk RNA sequencing to characterize their transcriptomic landscape.

overall_design: We FACS-purified leukemic blasts from mice with mono- or biallelic Trp53-fl-R245W-GFP alleles,  and performed bulk RNA sequencing to define transcriptomic changes associated with malignant transformation. As controls, healthy megakaryocyte-erythroid progenitors (MEPs), immunophenotypically resembling the AML blasts, from mice with biallelic Trp53-fl-R245W-GFP alleles were sorted into GFP negative (Trp53 wild-type), GFP low (monoallelic Trp53  mutation) and GFP high (biallelic Trp53 mutation) populations.


title: siPiezo1 or scRNA immortalised MSC cell line (Y201) cultured on stiff hydrogels

overall_design: RNAseq profiling of small interferring RNA (siPiezo1) and scrambled RNA (scRNA) treated immortalised mesenchymal stem cells (Y201) grown on 25kPa elastic (V-) and viscoelastic (V+) Fibronectin coated polyacrylamide hydrogels. Three independent biological replicates cultured in parallel in a single experiment were sequenced.


title: Histone Variants and H2A Ubiquitination

city: Richmond

first: Hengbin

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

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

overall_design: Refer to individual Series


title: H4K16ac is dispensable for mammalian transcriptional control but necessary for a faithful genome duplication program [EdU-Huseq]

status: Public on Aug 19 2025

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

summary: Histone acetylation has widely been assumed to directly instruct gene activation. Among acetylated residues, H4K16ac is one of the most abundant modifications, conserved across all eukaryotes. Despite its established role in X-chromosome hyperactivation in Drosophila, its function in mammalian cells has remained elusive. Here, we show that in human somatic cells, H4K16ac does not regulate gene expression, but instead controls the spatiotemporal program of genome duplication. By combining a meta-analysis of public datasets and perturbation experiments free of confounding effects, we found that H4K16ac is neither associated with nor required for transcriptional activity. Rather, H4K16ac depletion resulted in premature replication of heterochromatic regions and widespread alterations in replication timing across the genome. These defects were driven by the aberrant activation of cryptic replication origins at long terminal repeats (LTRs)—repetitive elements typically marked by H4K16ac and whose sequence context resembles that of canonical origins in euchromatic regions. Our findings reveal an unexpected role for one of the most prevalent chromatin modifications and uncover a new regulatory mechanism that ensures accurate genome duplication.

overall_design: To unveil H4K16ac impact on replication firing, cells were subjected to EdU-HUseq. Control WT cells (KO for the non-expressed gene TNP2) and MSL3 KO cells (with no H4K16ac left) were compared with two replicates each. Control cells with Myc overexpression were used as positive control of replication alteration induction

first: Marta

last: Milan


title: Myeloid GPSM1 regulates atherosclerosis progression by governing monocyte and macrophage chemotaxis.

city: Shanghai

first: Hong

last: Zhang

address: 600 Yishan Road

department: Shanghai Diabetes Institute

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: The priming of blood monocytes and the infiltration of monocyte-derived macrophages into the vessel walls are the central part of atherosclerosis. However, the mechanisms underlying the processes remain unclear. Here we report that G-protein-signaling modulator 1 (GPSM1) plays a critical role in atherogenesis. We found that GPSM1 expression in lesional macrophages was increased during atherosclerosis development both in mice and human. Myeloid-specific GPSM1 ablation protects mice against atherosclerosis and reduces aortic inflammation, in both Apoe-/- mice and an AAV-PCSK9 injection model. Conversely, myeloid-restricted overexpression of GPSM1 accelerates aortic inflammation and promotes atherosclerosis development in mice. Mechanistically, GPSM1 deficiency suppressed monocyte priming including chemotaxis and adhesion through inhibition of p38/ERK MAPK pathway regulated by cAMP/PKA/KLF4/PMP22 axis, thereby alleviating pro-inflammatory responses within atherosclerotic plaques. Blockade of PMP22 using siRNA-loaded liposomes protected GPSM1 overexpression mice from atherosclerosis. Furthermore, a small-molecule compound inhibiting GPSM1 function could suppress atherosclerosis in vivo. In conclusion, our findings establish that GPSM1 is a novel regulator of atherosclerosis development and targeting GPSM1 might be a promising therapy against atherosclerosis.

overall_design: To understand how GPSM1 affects macrophage chemotaxis, we performed RNA-Seq transcriptomic analysis on GPSM1fl/fl versus GPSM1LKO BMDMs upon CCL2 stimulation.

first: Yuemei

first: Cheng

last: Hu


title: H4K16ac is dispensable for mammalian transcriptional control but necessary for a faithful genome duplication program [REPLIseq]

overall_design: To unveil H4K16ac impact on replication timing, cells were subjected to REPLIseq. Control WT cells (KO for the non-expressed gene TNP2) and MSL3 KO cells (with no H4K16ac left) were compared with two replicates each.


title: Regional and Cell Specific Bioactivity of Injectable ECM Biomaterials in MI through Spatial and Single Nucleus Transcriptomics

first: Karen

last: Christman

address: 2880 Torrey Pines Scenic Drive

department: Shu Chien-Gene Lay Department of Bioengineering

institute: University of California San Diego

summary: Myocardial infarctions (MI) affect 805,000 people per year in the United States. To mitigate the pathological effects of MI, we have developed and investigated pro-reparative decellularized extracellular matrix (ECM) hydrogels. However, no one has ever utilized single cell and spatially resolved transcriptomics to further probe how ECM can elicit pro-repair in an MI model. Thus, we utilize spatial transcriptomics and single nucleus RNA sequencing (snRNAseq) to further delineate the regional and cell-specific bioactivity of decellularized ECM hydrogels. ECM hydrogel subacute treatment induced cardiac resident macrophage preservation, fibroblast activation, increased vasculature development, and a cardiomyocyte development program. Similar findings of cardiomyocyte and vasculature development, alongside fibroblast development was found for chronic treatment. Thus, we depict the pro-reparative nature of decellularized ECM hydrogels on cardiac cell types and elucidate previously undiscovered therapeutic pathways, further demonstrating ECM’s potential as an MI therapy.

overall_design: Gene expression profiling of 10x Genomic Chromium single nucleus RNA-Seq or Visium spatial transcriptomics from the left ventricular myocardium ornshort axis sections  on injured Sprague Dawley female rats (225-250 g). Injuries include I/R (35 minutes of ischemia followed by reperfusion).

first: J

last: Mesfin

first: V

middle: K

last: Ninh

first: M

last: Diaz

first: E

last: Wong

first: R

last: Karkanitsa

last: Hunter

first: A

last: Chen

last: Yu

first: B

last: Bridgelal

last: Pham

first: N

last: Taghdiri

first: D

last: Calcagno

first: C

last: Luo

last: Braden

first: Z

last: Fu

first: K

last: King

last: Nguyen


title: Light spectrum modulates stress and defense gene expression in potato (Solanum tuberosum L.) shoot tips during post-cryopreservation recovery

city: Savonlinna

first: Jaanika

last: Edesi

address: Vipusenkuja 5

country: Finland

institute: Natural Resources Institute Finland LUKE

summary: Light intensity and spectral quality are two important factors that affect the cryopreservation success of plant germplasm. In a previous study, we found that LEDs with 90% red and 10% blue (RB) light have a positive effect on potato (Solanum tuberosum L.) shoot tip recovery during post-cryopreservation regeneration. In the present study, transcriptome profiles of non-cryopreserved (-) and cryopreserved (+) potato shoot tips exposed to RB, cool white fluorescent tubes (CW) and full darkness (D) were compared. Results indicated that light spectrum significantly affects transcript numbers in post-cryopreserved samples resulting in 3,284 differentially expressed genes of recovering shoot tips exposed to CW, RB and D. Gene ontology (GO) enrichment analysis revealed that several stress-related terms were more abundant in CW+, whereas morphogenesis-related processes were activated under RB+. Overall, cryopreservation had an extensive effect on gene expression, as 12,017 genes were differentially expressed in non-cryopreserved and cryopreserved shoot tips. Among all cryopreserved samples, enriched GO terms included various defense and stress responses to biotic stimuli and oxidative stress, whereas suppressed responses were mainly related to organ morphogenesis. The present study emphasizes that the optimization of light spectral properties to decrease light-related stress may greatly benefit the cryopreservation efficiency of plant germplasm.

overall_design: Comparison of non-cryopreserved in vitro potato shoot tips to cryopreserved shoot tips during recovery under cool white fluorescent, mixture of red and blue LEDs and complete darkness.

first: Soile

last: Jokipii-Lukkari

first: Heikki

last: Salo

first: Hely

last: Häggman

first: Anna

last: Pirttilä


title: RNA serves as direct thermo and potassium sensors via spliceswitch formed by G-quadruplex in mammals

first: Marco

last: Preussner

address: Takustrasse 6

institute: FU berlin

summary: Mammals maintain their core body temperature in a narrow range, yet how cells sense and respond to small temperature changes at the molecular level remains incompletely understood. Here, we uncover RNA G-quadruplex (rG4) motifs are significantly enriched around splice sites (SSs) of cassette exons repressed at lower temperature. Stabilizing these thermosensing RNA structures masks SSs, reducing exon inclusion. Focusing on cold-induced neuroprotective RBM3, we demonstrate rG4s near SSs of a poison exon become more stable at low temperatures, leading to exon exclusion, thereby elevating RBM3 expression by escaping nonsense-mediated decay. Additionally, increased intracellular potassium with potassium channel blocker also stabilizes rG4s and protects neuronal damage in a subarachnoid hemorrhage mouse model. Our findings unveil a mechanism how mammalian RNAs directly sense temperature and potassium perturbations, integrating them into gene expression programs via spliceswitches. This opens new avenues for treating diseases arising from splicing defect and disorders benefiting from increased RBM3 expression.

overall_design: Two clones of HeLa cells were were incubated for 24-hours at 32, 37 or 40°C. RNA was extracted and analyzed by RNA-Seq.

first: Florian

last: Heyd


title: Recessive TMEM167A variants cause neonatal diabetes, microcephaly and epilepsy syndrome

status: Public on Aug 18 2025

city: Bruxelles

first: Miriam

last: Cnop

address: Route de Lennik 808 CP618

department: Faculté de Medecine

country: Belgium

institute: Université Libre de Bruxelles

summary: Understanding the genetic causes of diseases affecting pancreatic β cells and neurons can give insights into pathways essential for both cell types. Microcephaly, epilepsy and diabetes syndrome (MEDS) is a congenital disorder with two known aetiological genes, IER3IP1 and YIPF5. Both genes encode proteins involved in endoplasmic reticulum (ER) to Golgi trafficking.  We used genome sequencing to identify 6 individuals with MEDS caused by biallelic variants in the novel disease gene, TMEM167A. All had neonatal diabetes (diagnosed <6 months) and severe microcephaly, five also had epilepsy. TMEM167A is highly expressed in developing and adult human pancreas and brain. To gain insights into the mechanisms leading to diabetes, we silenced TMEM167A in EndoC-βH1 cells and knocked-in one patient’s variant, p.Val59Glu, in induced pluripotent stem cells (iPSCs). Both TMEM167A depletion in EndoC-βH1 cells and the p.Val59Glu variant in iPSC-derived β cells sensitized β cells to ER stress. The p.Val59Glu variant impaired proinsulin trafficking to the Golgi and induced iPSC-β cell dysfunction.  The discovery of TMEM167A variants as a new genetic cause of MEDS highlights a critical role of TMEM167A in the ER to Golgi pathway in β cells and neurons.

overall_design: RNA-seq profiling of wildtype and mutant carrying the V59E mutation in TMEM167A  iPSC-derived samples along the differentiation from pancreatic progenitor stage (Day 12 of the differentiation) to maturing β cells (Week 8 of the differentiation)


title: Integral approach to organelle profiling in human iPSC-derived cardiomyocytes enhances in-vitro cardiac-safety classification

status: Public on Aug 15 2025

city: Maastricht

first: Brigitta

middle: Rita

last: Szabo

address: Minderbroedersberg 4-6

department: CARIM

institute: Maastricht University

summary: Efficient preclinical prediction of cardiovascular side effects poses a pivotal challenge for the pharmaceutical industry. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are becoming increasingly important in this field due to inaccessibility of human native cardiac tissue. Functional changes in hiPSC-CMs such as electrophysiological abnormalities, are commonly studied and considered clinically predictive. However, other clinically-relevant safety parameters, such as structural toxicity, are less understood. This study utilized hiPSC-CMs from multiple donors, cultured in serum-free conditions and treated with a library of 17 small molecules with stratified cardiac side effects, to establish an in-vitro drug screening protocol that leverages the power of morphological profiling with established functional readouts. High-content imaging of subcellular organelles, combined with multi-electrode array (MEA) data, was analyzed to identify cardiac safety clusters. Both supervised and unsupervised clustering revealed patterns associated with known clinical side effects. Overall, clustering based on morphological data more accurately reflected clinical classifications than electrophysiology alone. RNA-sequencing was used to support the mechanistic insights derived from morphological profiling, validating the former as a valuable cardiotoxicity tool. Results demonstrate that a combined approach of analyzing morphology, and electrophysiology enhances in-vitro prediction and understanding of drug cardiotoxicity.

overall_design: RNA-seq profiling of compound responses (library of 17 compounds) in healthy control hiPSC-CMs

first: Jeroen

last: Stein

last: Savchenko

first: Thomas

last: Hutschalik

first: Filip

last: Van Nieuwerburgh

first: Tim

last: Meese

first: Georgios

last: Kosmidis

first: Paul

last: Volders

first: Elena

last: Matsa


title: H4K16ac is dispensable for mammalian transcriptional control but necessary for a faithful genome duplication program [RNA-seq]

first: Paola

last: Scaffidi

overall_design: For the study of H4K16ac impact on specific gene programs, the 3 complex-specific subunits of MSL complex were independently deleted using synthetic sgRNAs. The not-expressed TNP2 gene was used as negative control. Three days after transfection, cells were collected, and RNA was extracted using a RNeasy Plus Micro Kit (Qiagen, 74034). 3 replicates per condition were generated. For the study of H4K16ac impact on global levels of transcription, stable KO cells (either MSL3 or not expressed control TNP2) were used. cells were grown for 2 days in two identical replicate plates. Cells in one plate were fixed with 4% paraformaldehyde (PFA, Alfa Aesar, #43368) followed by permeabilization with 0.5% Triton X-100 in PBS and nuclei staining with SYTOX Green Nucleic Acid Stain (Thermo Fisher Scientific, #S7020). Imaging and quantification were performed using an Incucyte S3 Live-Cell Analysis System. Cell counts generated were then used to take the same number of cells (400.000) in all conditions in the other plate. Total RNA extraction was performed using a RNeasy Plus Micro kit (Qiagen, 74034). RNA concentration was checked with the nanodrop. 1ug of RNA was taken from the lowest concentrated sample and same volume was taken for all the other samples. 2 μL (1:100) ERCC Spike-in (Thermo Fisher Scientific, 4456740) was added to each sample. Two replicates per condition were generated.

first: Marta

last: Milan


title: Brain-cervical lymph node crosstalk contributes to brain injury-induced by subarachnoid hemorrhage in mice

status: Public on Aug 14 2025

first: Jinman

last: Chen

address: South of Wanping Road

department: Institute of Spine

institute: Longhua hospital

summary: The neuroinflammation and peripheral immune response following subarachnoid hemorrhage (SAH) aggravates early brain injury and lead to poor prognosis. Cross-talk between brain and cervical lymph nodes (CLNs) plays a crucial role in neuroinflammation and neurological diseases-associated brain injury. However, whether CLNs participate in brain damage and how injured brain activates immune system in SAH remain unclear. Previously, we reported that extravasated erythrocytes are drained into CLNs early following SAH. Here, we demonstrated that the removal of CLNs attenuated neuroinflammation and neurological deficits in 2 mouse models of SAH. Interestingly, we found that extravasated erythrocytes in CLNs following SAH were significantly engulfed by LYVE-1+ lymphatic endothelial cells (LECs) in both mandibular and deep CLNs. Single-cell RNA sequencing of mandibular LNs revealed that the medullary LEC is the primary LEC subset to degrade erythrocytes via lysosome protease cathepsin S. LECs treated by erythrocytes in vitro leaded to increasing the expression of genes related to inflammatory response, chemokines and lysosome protease cathepsin S. Importantly, deficiency of cathepsin S specifically in LECs using transgenic mice or blockage of cathepsin S by its inhibitor reduced SAH-induced brain damage. These results revealed a mechanism of how  extravasated erythrocytes triggers a CLN-mediated inflammatory response and the aggravation of brain injury in SAH, and target this process may become effective therapeutic strategies to alleviate SAH pathology.

overall_design: At 24 hours post SAH ( induced by autologous blood infusion) or sham operation, mandibular lymph nodes were harvest from 20 mice of each group. We performed single-cell RNA sequencing (scRNA-seq) of LECs (CD45-CD31+Podoplanin+) that were isolated from  mandibular LNs.

first: Jie

last: Wang

first: Wenjing

last: Zheng

first: Lianping

last: Xing

first: Yongjun

first: Qianqian

last: Liang


title: Modulating neutrophil phenotype via mesenchymal stromal cell paracrine signals; insights from human and mouse experiments

city: Bucharest

first: Laudy

last: Cherry

state: Sector 5

address: Strada B.P.Hasdeu nr.8, sector 5, Bucuresti

department: Biology

country: Romania

institute: Institute of cellular biology and pathology

type: Non-coding RNA profiling by high throughput sequencing

summary: Neutrophils play a central role in the inflammatory and reparative processes following myocardial infarction (MI), and can switch between pro-inflammatory (N1) and reparatory (N2) states, influencing disease outcomes. Mesenchymal stromal cells (MSC), known for their immunomodulatory effects, may hold the key to controlling neutrophil behaviour. In this study, we explored how MSC influence neutrophil states both in vitro and in vivo in an MI mouse model. We developed a reliable system to study neutrophils by differentiating HL-60 cells into neutrophil-like cells (dHL-60). These cells were polarized into N1 and N2 types, showing distinct protein markers and cytokine signatures. When exposed to MSC, pro-inflammatory N1 cells reduced their production of inflammatory signals (TNFα, MCP-1), while N2 cells increased their reparatory signals (IL-10, TGM2). In mice with MI, MSC reduced the number of neutrophils migrating to damaged heart tissue and altered their transcriptomic signatures. Surprisingly, MSC enhanced inflammatory pathways in heart neutrophils while dampening their ability to support tissue repair. These findings underscore the complex role of MSC in modulating neutrophil responses, demonstrating a nuanced impact on inflammatory and reparative pathways in the cardiac microenvironment. While the results highlight MSC' potential to influence immune cell behaviour, they also reveal context-specific effects that warrant further investigation to fully elucidate their therapeutic implications in cardiovascular disease.

overall_design: Gene expression profiling analysis of RNA-seq data from cardiac and blood neutrophils isolated from C57Bl/6J mice with and without MSC treatment, after induced myocardial infarction. Samples were collected 3 days after LCA ligation.

first: Sinziana

last: Popescu

first: Carmen

last: Neculachi

first: Evelyn

last: Nastase-Rusu

first: Maya

last: Simionescu

last: Butoi

first: Alexandrina

last: Burlacu

first: Mihai

last: Preda


summary:
To  explore the mechanism of how red blood cells activate lymphatic endothelial cells thereby macrophage pro-inflammatory polarization
we performed RNA-seq analysis of lymphatic endothelial cells after they were treated by red blood cells for 24 hours.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lymphatic endothelial cells activated by red blood cells and its control).

first: Jiman


title: Conservation of cis-regulatory codes over half a billion years of evolution

city: Saint Louis

first: Joseph

middle: C.

last: Corbo

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: The identification of homologous cell types across species represents a crucial step in understanding cell type evolution. The retina is particularly amenable to comparative analysis because the basic morphology, connectivity, and function of its six major cell classes have remained largely invariant since the earliest stages of vertebrate evolution. We used comparative single-nucleus chromatin accessibility analysis of lamprey, fish, bird, and mammalian retinas, which began to diverge over half a billion years ago, to demonstrate cross-species conservation of cis-regulatory codes in all six retinal cell classes. In this study, we acquired retinal single-cell gene expression profiling (scRNA-seq) and single-nucleus chromatin accessibility (snATAC-seq) from sea lamprey (Petromyzon marinus), a jawless species. We also acquired long-read sequence data from lamprey retina and single-nucleus chromatin accessibility from chicken (Gallus gallus).

sample_organism:
Petromyzon marinus
Gallus gallus

platform_organism:
Petromyzon marinus
Gallus gallus

overall_design: A publicly available sea lamprey transcriptome assembly was updated using newly generated long-read sequencing data. Subsequently, single nuclei multiome profiles (comprising RNA and ATAC) of the downstream migrant lamprey retina were generated with the updated assembly. Furthermore, a single-nuclei chromatin accessibility profile was generated from the newly hatched (P0) chicken, which serves as a comparison of cis-regulatory features across diverse vertebrate species.


title: Gene profiles of peripheral white blood cells as potential predictors of pregnancy in embryo-recipient heifers

status: Public on Aug 13 2025

city: Jouy-en-Josas

first: Mariam

last: Raliou

address: Allée de Vilvert

department: PHASE

country: France

institute: INRAE

summary: BACKGROUND: The bovine endometrium undergoes cellular, molecular, and functional changes to support embryo survival and development to term. These changes involve a finely coordinated series of events at both local and systemic levels. We postulated that circulating white blood cells (WBCs) may provide valuable biomarkers to predict pregnancy success in heifers when embryo transfer is used sampled from heifers during a preconception cycle and a conception cycle before embryo transfer. WBCs were isolated using PAXgene Blood RNA tubes collected from heifers on Days 7 and 14 of a preconception estrous cycle (PCD7 and PCD14) and, after a rest cycle, on Day 7 of the subsequent estrous cycle (1ETD7) just before embryo transfer. Circulating progesterone and oestradiol-17b were assayed and pregnancy was confirmed by either the delivery of a healthy calf or uterine flushing and conceptus collection on Day 18 post-estrus. Using a custom bovine gene expression microarray representing 19,479 unique transcript, comparison of transcriptomes between heifers classified as non-pregnant or pregnant revealed 1,240, 896 and 1,023 differentially expressed genes (DEGs) at PCD7, PCD14 and 1ETD7 respectively. Our bioinformatics analyses revealed that pregnancy failure after embryo transfer was associated with upstream regulators, biological functions, canonical pathways and gene networks related to inflammation, immunity, apoptosis and cell death regulation, cell proliferation, membrane compounds, lipid metabolism, oxygen transport and ions transport. The heifers classified as non-pregnant showed significant increased transcripts levels of PTGR1 at the three time points (PCD7, PCD14 and 1ETD7), AIF1 at PCD14, FNDC3B, IL15 and SERPINE1 at 1ETD7. Our findings highlight the potential of peripheral WBCs as a non-invasive source of biomarkers for predicting pregnancy outcomes, offering promising insights for improving pregnancy success when reproductive biotechnologies are used in mammalian females.

overall_design: Transcriptional profiling was conducted using a custom 8x60K bovine gene expression microarray, designed based on annotated bovine Ensembl transcripts (http://www.ensembl.org/index.html, genome assembly UMD3.1) represented 19,479 transcripts, previously as described (Raliou, Dembele et al. 2019). RNA labeling was done with total RNA isolated from blood collected from 7 females classified as non-pregnant and 4 pregnant at PCD7 and PCD14. Due to blood sampling issues, at 1ETD7, microarray hybridization was carried out on total RNA from WBCs collected from 5 non-pregnant and 3 pregnant animals (Table 1). RNA labeling followed the Agilent “One-Color Microarray-Based Gene Expression Analysis” protocol (Raliou, Dembele et al. 2019). The microarray data were submitted to the GEO database (accession number GSE185325). Differentially expressed genes (DEGs) were identified using the fold change rank ordering (FCROS) method (Dembele and Kastner 2014) and t-test with the TREAT option of the LIMMA method (Smyth 2004), comparing non-pregnant with pregnant females. p-values were adjusted using the Benjamini & Hochberg method (Benjamini 1995), and a threshold was applied to select significant DEGs.

first: Olivier

last: Sandra


title: Chronic Exposure to a Sublethal Concentration of Methyl-Mercury Early in Life Affects Telomere Dynamics and Genomic Stability in Zebra Finches

city: Bethesda

first: Christian

last: Wake

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Telomeres are essential for chromosomal protection, yet their guanine-rich repeats are sensitive to oxidative damage. ROS-dependent oxidative stress accelerates telomere attrition in vitro, but telomere dysfunction under oxidative conditions in vivo remains unclear. We studied the effects of ROS-inducing agent methyl-mercury (MeHg) on telomere and genome dysfunction in zebra finches (Taeniopygia guttata). Using qPCR, we found that continuous exposure to sublethal MeHg (1.2 ppm in the diet) resulted in longer telomere length than controls by sexual maturity in red blood cells and several other tissues. These findings were accompanied by suppressed bone marrow transcriptomic pathways related to cilia formation and mitotic progression. Further analysis revealed oncogenic and pro-inflammatory signaling reminiscent of tumorigenesis. We also demonstrate that PCNA expression in the lung remains unchanged by MeHg, suggesting telomere maintenance independent of replication. Our results show that chronic sublethal MeHg exposure may lead to replicative immortality of telomeres rather than shortening.

overall_design: To investigate the impact of a sublethal dosage of MeHg (1.2 ppm in food) on the hematopoietic system, we bred zebra finches of varied historical exposure and performed gene expression profiling analyses, alongside gene set enrichment analysis using data obtained from RNA-seq of 4 different developmental time points.

first: Rachel

last: Davis

first: Samuel

last: Mason

first: Giulia

last: Fabozzi

first: William

last: Catalano

first: Chaim

last: Schramm

first: Amy

middle: R

last: Henry

first: Cokie

last: Parker

first: Farida

last: Laboune

first: Casey

last: McLaughlin

first: Jeffrey

last: Kittilson

first: John

last: Swaddle

first: Daniel

last: Cristol

first: Britt

middle: J

last: Heidinger

last: Douek


title: H4K16ac is dispensable for mammalian transcriptional control but necessary for a faithful genome duplication program [ChIP-seq]

first: Paola

last: Scaffidi

overall_design: To unveil H4K16ac genome-wide deposition, we deployed ChIPseq in HME1 cells: pull down was performed with two antibodies (two replicates each) in WT cells (Control KO) and cells lacking the histone mark (MSL3 KO cells). ChIPseq in KO cells retrieves the non-specific signal and can be subtracted to obtain the real H4K16ac occupancy in the genome. As a control for gene-assiciated signal, H3K36me3 ChIPseq was performed in HME1 cells

first: Marta

last: Milan


title: Integrated Methylation and Spatial Transcriptomic Profiling of Metaplastic Breast Cancer to Investigate Intra-tumoral Heterogeneity.

status: Public on Aug 12 2025

city: Brisbane

first: Yufan

last: Feng

state: QLD

address: Building 71/918 RBWH Herston

department: UQ Centre for Clinical Research

institute: The University of Queensland

summary: Metaplastic breast cancer (MpBC) is a rare and aggressive form of breast cancer. Characteristically heterogeneous, MpBC are defined by the presence of various morphological elements, typically biphasic, with epithelial (e.g. non-special type (NST), squamous) and mesenchymal (e.g. spindle, chondroid, osteoid) components. The established clonality of the different components, favours an evolution model encompassing either a multipotent progenitor, or a linear metaplastic conversion. We performed methylation profiling to understand the nature of the different components, and to investigate their origins. The different morphologies demonstrated specific methylation profiles, with inter-patient clustering of common elements, rather than intra-patient clustering of distinct elements. While the malignant squamous components had a methylation profile consistent with normal squamous cells, chondroid regions were more like malignant chondroid tumours e.g. chondrosarcoma; indeed, this corresponds to the good and bad prognosis of squamous and chondroid MpBC phenotypes respectively. Our spatial transcriptomic approach, using 10X Genomics Visium and trajectory analysis evidenced that spindle cells form a transition between the originating carcinoma of non-special type (NST) and pleomorphic regions, with osteoid differentiation likely to be an end-stage fate of the chondroid growth pattern. This data lends itself to the conversion model of lineage differentiation. Considering the gene expression changes in more detail, we have also identified a series of master transcription factors likely to regulate these processes, and which are significantly associated with metaplastic-like features (basal/claudin-low; high grade; triple negative) in clinical data (METABRIC). Together, our study defines the micro-methylome and a spatial transcriptomic profile in MpBC, and identifies potential drivers associated with tumour heterogeneity that supports the conversion model of metaplasia and warrants further functional analysis.

overall_design:
four cases of mixed MpBC were selected for spatial transcriptomics analysis using Visium (10X Genomics). Seven regions of interest (ROIs) were analysed across 3 cases.

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

first: Albert

last: Xiong

first: Onkar

last: Mulay

first: Anna

last: Sokolova

first: Peter

last: Simpson

first: Quan

last: Nguyen

first: Sunil

last: Lakhani

last: Reed


title: Peritumoral macrophages recruit eosinophils to promote anti-tumor immune_x000D_responses in breast cancer

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

department: Pathology

institute: NYU Grossman School of Medicine

summary: Breast tumors harbor dynamic tumor microenvironments, with multiple immune cell types often playing opposing roles during tumor progression and/or response to therapy.Tumor-associated macrophages (TAMs) are thought to promote mammary tumorigenesis, whereas the role of mammary tissue macrophages (MTMs) remains incompletely understood. High-dimensional immunostaining of murine mammary tumor progression revealed that MTMs were localized in the peritumoral stroma and associated with eosinophils, which were previously shown to facilitate anti-tumor T cell responses. The depletion of MTMs accelerated tumorigenesis in both spontaneous and orthotopically transplanted mammary tumor models. Upon induction of a productive anti-tumor response via the depletion of regulatory T cells (Tregs), MTMs assumed an alternatively activated state and expressed eotaxins, thereby attracting eosinophils to peritumoral regions. MTMs expressed the receptor for the alarmin IL-33, which induced both MTMactivation and eosinophil recruitment. Thus, MTMs sense IL-33 and recruit eosinophils to facilitate anti-tumor immunity – a mechanism that operates during tumor progression and can be enhanced during productive anti-tumor responses.

overall_design: Two WT mice and two FoxP3-DTR mice were given a two-week DT regimen (500ng/100ul intraperitoneal on days 0, 1, 3, 8, and 14) and tumors were harvested and leukocytes isolated by FACS for CITE-seq.

first: Joseph

last: Saglimbeni

first: Eduardo

last: Esteva

first: Josue

last: Canales

first: Oriana A

last: Perez

last: Eichinger

first: Kamal M

last: Khanna

first: Igor

last: Dolgalev

first: Natalie

last: Klar

first: Sylvia

last: Adams

first: Reizis

last: Boris


title: Evolution of the human autopod skeleton [RNA-seq]

city: Cambridge

first: Terence

last: Capellini

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

summary: We investigate the genetic architecture of autopod development at the regulatory and transcriptomic level.

overall_design: Examination of open chromatin regions (ATAC-seq) and differentially expressed genes (RNA-seq) in the developing autopod skeleton.

first: Alexander

last: Okamoto


title: Epidermal IFN-κ drives cutaneous lupus and systemic immune activation

status: Public on Aug 11 2025

city: Ann Arbor

first: J. Michelle

last: Kahlenberg

state: MI

address: NCRC 20-1841, 2800 Plymouth Rd

department: Department of Internal Medicine – Division of Rheumatology and Department of Dermatology

institute: University of Michigan

summary: Keratinocyte-derived interferon kappa (IFN-κ) is chronically overexpressed in human non-lesional systemic lupus erythematosus (SLE) skin. Recent evidence suggests that epidermal signals instruct the immune system in SLE, but whether epidermal IFN-κ alone is sufficient to drive lupus phenotypes has not been investigated. Here, we show that mice that overexpress Ifnk in the epidermis under the keratin 14 promoter (Ifnk transgenic, TG) on a BALB/c background spontaneously develop cutaneous lupus erythematosus (CLE)-like lesions and systemic immune dysregulation. Lesions show facial predominance, lymphocytic infiltration, and a transcriptional signature reflective of human CLE. Ifnk TG mice exhibit increased immune cell activation and spontaneous signs of systemic autoimmunity with higher anti-dsDNA-antibodies, lymphadenopathy and splenomegaly, but lack signs of renal inflammation. UV exposure enhanced cutaneous inflammation and splenic T cell activation in Ifnk TG mice. Together, we describe a new CLE mouse model that recapitulates features of human CLE and substantiates the role of epidermal IFN-κ as a driver of CLE, photosensitivity and systemic inflammation.

overall_design: Mice: 11595: Ifnk TG and BALB/c WT female and male mice at 12 months were assessed for development of skin lesions. Skin lesions were harvested and stored in RNA later prior to lysis. 11567: To phenotype UV-irradiation-driven immune responses, mice were irradiated for 2 weeks, observed for another two weeks. Inguinal lymph nodes were harvested after the observation period for RNA-bulk sequencing to characterize immune phenotypes in local lymph nodes.

first: Benjamin

last: Klein


title: Integrated Methylation and Spatial Transcriptomic Profiling of Metaplastic Breast Cancer identifies putative master regulators of intratumoral heterogeneity

first: Yufan

last: Feng

type: Methylation profiling by genome tiling array

summary: Metaplastic breast cancer (MpBC) is a rare and aggressive form of breast cancer. Characteristically heterogeneous, MpBC are defined by the presence of various morphological elements, typically biphasic, with epithelial (e.g. non-special type (NST), squamous) and mesenchymal (e.g. spindle, chondroid, osteoid) components. The established clonality of the different components, favours an evolution model encompassing either a multipotent progenitor, or a linear metaplastic conversion. Our study defines the micro-methylome and a spatial transcriptomic profile in MpBC, and identifies potential drivers associated with tumor heterogeneity that supports the conversion model of metaplasia and warrants further functional analysis.

overall_design: This submission includes only methylation arrays. Illumina Human Methylation EPIC BeadChip used for FFPE-origin DNA.

first: Albert

last: Xiong

first: Onkar

last: Mulay

first: Anna

last: Sokolova

first: Malcolm

last: Lim

middle: V

last: Haeringen

first: Natasha

last: McGuire

first: Xavier

last: Luca

first: Peter

last: Simpson

last: Nguyen

last: Lakhani

first: Amy


title: Lung scRNAseq from lung fibroblastic cells from normal chow and high fat diet treated animals

city: Bonn

first: Veronika

last: Lukacs-Kornek

address: Venusberg Campus 1

department: IMMEI

institute: University of Bonn

summary: Fibroblastic stroma was isolated using MACS (negative selection for CD45, CD31 and Epcam)

overall_design: cells were islated from animals fed with normal chow or high fat diet for 16wks

first: Sophia

last: Rottmann


title: H4K16ac is dispensable for mammalian transcriptional control but necessary for a faithful genome duplication program [CUT&Tag]

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

summary: Histone acetylation has widely been assumed to directly instruct gene activation. Among acetylated residues, H4K16ac is one of the most abundant modifications, conserved across all eukaryotes. Despite its established role in X-chromosome hyperactivation in Drosophila, its function in mammalian cells has remained elusive. Here, we show that in human somatic cells, H4K16ac does not regulate gene expression, but instead controls the spatiotemporal program of genome duplication. By combining a meta-analysis of public datasets and perturbation experiments free of confounding effects, we found that H4K16ac is neither associated with nor required for transcriptional activity. Rather, H4K16ac depletion resulted in premature replication of heterochromatic regions and widespread alterations in replication timing across the genome. These defects were driven by the aberrant activation of cryptic replication origins at long terminal repeats (LTRs)—repetitive elements typically marked by H4K16ac and whose sequence context resembles that of canonical origins in euchromatic regions. Our findings reveal an unexpected role for one of the most prevalent chromatin modifications and uncover a new regulatory mechanism that ensures accurate genome duplication.

overall_design: To unveil H4K16ac genome-wide deposition, we deployed CUT&Tag in HME1 cells: pull down was performed with two replicates in WT cells (Control KO) and cells lacking the histone mark (MSL3 KO cells). CUT&Tag in KO cells retrieves the non-specific signal and can be subtracted to obtain the real H4K16ac occupancy in the genome.

first: Manthankumar

last: Patel

first: Pradeepa

last: Madapura


title: Nutrient-driven TOR signaling mediates transcriptional repression by promoting translation to regulate plant growth [ChIP-seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: As is well known, nutrition is essential for plant growth and development. Extensive research has demonstrated that the target of rapamycin (TOR) is a crucial growth regulator, receiving nutritional inputs in eukaryotic cells. Nevertheless, the precise mechanisms by which TOR coordinates nutrient conditions and growth remain elusive in plants. In this study, we identified a novel transcriptional repression complex, TRCG, downstream of the TOR signaling pathway. This complex is responsible for regulating plant growth and the nutritional response. In the presence of favorable nutritional conditions, TOR is activated, leading to the translation of the 5’-terminal oligopyrimidine (5’-TOP) mRNA of TRCG. TRCG directly binds numerous nutrition-responsive genes, particularly those belonging to the ERF family of transcription factors, to repress their transcription. This repression is achieved by influencing the initiation and elongation of RNA polymerase II (Pol II), thereby maintaining growth and development. In the absence of nutritional conditions, TOR activity is inhibited, resulting in the repression of TRCG translation. This, in turn, relieves the repression of nutrient response genes, causing a stagnation of growth and poor nutrient resistance, thus contributing to the survival of the plant. Moreover, we observed a higher histone H3 and H4K5 acetylation level in the TRCG targets. Acetylated chromatin has long been associated with transcriptional activation, suggesting that TRCG could bind to acetylated chromatin to repress transcriptional activation. Our findings elucidate a previously unidentified precise mechanism by which TOR-mediated transcriptional repression occurs through the stimulation of translation, thereby regulating plant growth and the nutritional response.

overall_design: Examination of protein binding levels in transgenic plants; For Pol II 2p and 5p ChIP-seq, examination of Pol II 2p and 5p levels in wild type, drmy1, gtb123.

first: Xin