title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus [bulk RNA-seq]

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

institute: ETH Zürich

summary: We explore how the tightly regulated molecular response triggered by acute restraint stress becomes altered after repeated restraint exposure. Transcriptomic sampling of the mouse hippocampus at multiple time points revealed that repeated stress leads to widespread habituation, damping stress-induced gene expression of all stress-responsive genes. However, we find no evidence for the emergence of new response profiles or alterations in baseline gene expression. Using single-cell multi-omics, we show that these findings hold true across cell types, and we reveal cell type specific patterns of habituation. Transcriptomic and chromatin accessibility profiles identify two distinct mechanisms that contribute to the observed habituation patterns: an early cAMP-associated mechanism that is related to blunted transcription after chronic stress, and a late corticosterone-dependent mechanism that is linked to a shortened transcriptional response.

overall_design: Restraint stress involves placing the mice in a 50 ml Falcon tube with a large air hole for 1h30. Chronically stressed animals were subjected to daily restraint for 10 or 20 consecutive days (see 'treatment' column) at varying time of day before the final (acute) stress exposure, while handling animals were handled gently (lifting the animals by the tail, simulating the handling method used before restraint stress). Following this treatment, animals were single-housed 24 hours before being subjected once again to the same restraint stress, and the samples were collected at various timepoints (see 'ARS timepoint' column) following stress initiation (time point 0min indicates an absence of acute stress, i.e. homecage animals). All stress exposures were carried out between 10:00 and 17:00 in the animals’ active phase (i.e. reverse light cycle).

first: Rebecca

last: Waag

first: Lukas

last: von Ziegler

first: Johannes

last: Bohacek


title: Hypoxia-induced phase separation of ZHX2 drives 3D chromatin remodeling and cancer metastasis (Hi-C)

status: Public on Mar 18 2025

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

country: China

institute: Wuhan university

summary: Hypoxia and dysregulation of three-dimensional (3D) chromatin architecture can both activate oncogenic transcriptomic profiles, thus contributing to tumor malignancy. But how hypoxia regulates 3D chromatin architecture remains unknown. Here, we find that the transcription factor, zinc fingers and homeoboxes 2 (ZHX2), generates liquid-liquid phase separation (LLPS) under hypoxia, thus promoting its occupancy on chromatin and activating transcription for a cluster of oncogenes, that is enriched by metastatic genes distinct from targets of hypoxia-inducible factor (HIF) and pathologically relevant to breast cancer. Mechanistically, hypoxia induces the LLPS of ZHX2 via a proline-rich intrinsically disordered region (IDR) in the nuclear localization sequence (NLS), thereby enhancing the phosphorylation of ZHX2 at S625 and S628 that incorporates CCCTCbinding factor (CTCF) in condensates to reorganize chromatin looping, consequently resulting in oncogenic super-enhancer formation and breast cancer metastasis. This fundamental mechanism provides significant insight into oncogene activation and suggests a phase separation-based therapeutic strategy for cancer.

overall_design: We conducted Hi-C experiments in T47D cells under normoxia, hypoxia, and hypoxia with ZHX2 knockdown (KD).

first: Zhang

last: Jing

first: Gao

last: Chuan


title: Hypoxia-induced phase separation of ZHX2 drives 3D chromatin remodeling and cancer metastasis

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Hypoxia-induced phase separation of ZHX2 drives 3D chromatin remodeling and cancer metastasis (RNA-Seq)

overall_design:
We conducted RNA-seq experiments in T47D cells under normoxia, hypoxia, and hypoxia with ZHX2 knockdown (KD). Our aim was to identify a specific set of genes that exhibit both hypoxia-inducible characteristics and are positively regulated by ZHX2 under hypoxic conditions. Additionally, we assessed gene expression changes in T47D cells treated with 0.5% and 1% 1,6-hexanediol under hypoxic conditions for 24 hours to detect alterations in gene expression following phase separation disruption.

We conducted RNA-seq experiments in T47D cells under hypoxia to identify a specific set of genes that exhibit both hypoxia-inducible characteristics and are positively regulated by ZHX2 phase separation under hypoxic conditions.

first: Jing

last: Zhang

first: Chuan

last: Gao


title: Hypoxia-induced phase separation of ZHX2 drives 3D chromatin remodeling and cancer metastasis (ChIP-Seq)

overall_design:
We conducted ZHX2, CTCF and H3K27ac ChiP-seq experiments in T47D cells under normoxia, hypoxia, and hypoxia.

We conducted ZHX2-WT, ZHX2-PA-mution Flag-ChIP-seq experiments in T47D cells under normoxia, hypoxia, and hypoxia.


title: CXCL12-CXCR4 signalling axis in cellular senescence

city: Bangalore

first: Suramya

last: Asthana

state: Karnataka

address: Biological Sciences Building, Indian Institute of Science

country: India

institute: Indian Institute of Science

summary: Gene expression analysis in senescent HeLa cells to examine the differential CXCL12-CXCR4 signalling pathways.

overall_design: Non-senescent, Senescent HeLa cells; Control and Stimulated with 200ng/ml CXCL12

first: Deepak

last: Kumar Saini


title: Investigation of the RNMT/RAM RNA interactome in mouse embryonic stem cells [RIP-Seq]

city: Dundee

first: Fiona

last: Haward

address: Life Sciences, Dow St

country: United Kingdom

institute: University of Dundee

summary: Pilot investigation to determine the endogenouse RNA-binding targets of the cap methlytransferase complex RNMT/RAM in mouse ES cells

overall_design: RNMT seCLIP (a single-end adaptation of the eCLIP method) was perfomed in undifferentiated mouse ES cells following the protocol from Van Nostrand et al (2017). After lysis, RNA was digested with an optimised concentration of RnaseI and immunprecipitation carried out using either an antibody for RNMT or an isotype control. A size-matched input control was prepared from each sample.

first: Victoria

middle: H

last: Cowling


title: Lipid Uptake via FATP2 Enhances CAR-T Therapy Resistance in B-cell Acute Lymphoblastic Leukemia

status: Public on Mar 17 2025

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

country: USA

institute: University of Colorado, Denver

summary: This study identifies Fatty Acid Transport Protein 2 (FATP2) as a critical metabolic vulnerability in relapsed/refractory B-ALL. FATP2-mediated free fatty acid uptake by TP53-mutant B-ALL blasts represent a potential leukemia-intrinsic mechanism of CAR-T resistance. Further, targeting FATP2-mediated exogenous lipid uptake represents a novel means of enhancing CD19-directed immunotherapy efficacy.

overall_design: CAR T or Mock T cells were co-cultured with isogenic 697 B-ALL cell lines at 1:16 E:T ratio in lipid-replete media supplementted with 4 U/mL human IL-2 for 72 h. For all CAR-T killing assays, target cells were seeded at a fixed cell surface density of 20,000 target cells (B-ALL) per 0.32 cm2.

first: Matthew

last: Witkowski

first: Tian

last: Liu

first: Julian

last: Grandvallet Contreras

first: Tzu


title: ceRNA network deregulated in ischemic heart failure patients

city: Milan

first: Fabio

last: Martelli

address: Via Olgettina 58

country: Italy

institute: IRCCS Policlinico San Donato

type: Non-coding RNA profiling by high throughput sequencing

summary: Differential expression analyses of mRNA and circRNA were performed in ischemic non end-stage heart failure (HF) left ventricle samples and in healthy controls from individuals not affected from cardiovascular dieseases. The aim of the study was to build an HF regulatory RNA network. Using expression data from HF deregulated microRNAs (Greco et al.,Diabetes 2012 Jun;61(6):1633-41) a total of 1031 circRNA-mirNA-mRNA interactions were identified, and proposed as competing endogenous RNA (ceRNA) network. KEGG pathway enrichment analysis identified among the top enriched categories several relevant pathways such as Ubiquitin mediated proteolysis, apelin signaling pathway, MAPK pathway, Cell cycle, Longevity regulating pathway, FoxO and MTOR signaling pathways.

overall_design: RNA was extracted using TRIzol (Life Technologies, Thermo Fisher Scientific Inc.) from left ventricles tissues collected from 20 heart failure patients and from 20 controls.

first: Simona

last: Greco

first: Anna

middle: S

last: Tascini

first: Jose

last: Garcia Manteiga


title: The role of the cap methyltransferase RNMT in mouse neuron development and neuronal acitvity

summary: The roles of the cap methlytransferase RNMT were investigated in both control neurons and those stimulated using the membrane depolarising agent KCl.

overall_design: Sequencing of rRNA-depleted total RNA isolated from control or KCl-activated primary cortical neurons after 16DIV.


title: RNA-Seq Reveals Enhanced Inflammation and Fibrosis in Alcohol-Induced Liver Injury of Apoe Knockout Mice

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

summary: Alcohol-related liver disease (ALD) involves inflammation, hepatocellular damage, and fibrosis. Apolipoprotein E (Apoe) plays a role in immune regulation and tissue repair, but its function in ALD remains unclear. To explore this, we performed RNA sequencing on liver tissues from wild-type (WT) and Apoe knockout (Apoe KO) mice subjected to a chronic-plus-binge ethanol model. Gene expression analysis revealed distinct clustering between groups and significant alterations in pathways related to neutrophil degranulation, extracellular matrix organization, and collagen formation, indicating heightened inflammation and fibrosis in Apoe KO mice. These findings offer insights into Apoe’s role in ALD and liver repair.

overall_design: Mice subjected to the chronic-plus-binge ethanol-feeding model were fed as described in our previous study. Briefly, 10–12-week-old female mice were acclimated by ad libitum feeding with the Lieber-DeCarli liquid diet (catalog #F1259SP, Bio-Serv) for five days. Following acclimatization, the ethanol-fed groups received a Lieber-DeCarli ethanol diet (catalog #F1258SP, Bio-Serv) containing 5% (v/v) ethanol for 10 days. On day 11, a single dose of ethanol (5 g/kg body weight) was administered via oral gavage in the early morning, and the mice were euthanized nine hours later. Pair-fed control mice were maintained on an isocaloric control diet for 10 days and, on the day of euthanasia, received an oral gavage of isocaloric dextrin-maltose (9 g/kg body weight).

last: GUAN

first: Yang

last: WANG

first: Bin

last: GAO


title: Myeloid FtH deficiency accelerates kidney disease by inducing Snca and ferroptosis

city: Birmingham

first: Yanfeng

last: Zhang

state: AL

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

institute: University of Alabama at Birmingham

summary: This study aimed to investigate impact of myeloid ferritin heavy chain (FtH) deletion on iron trafficking in kidney health and disease. Myeloid FtH deletion (FtHΔ/Δ) led to upregulation of synuclein-α (Snca) as the only iron-binding protein. When exposed to kidney injury, FtHΔ/Δ mice exhibited significantly worse kidney function. Transcriptome analysis identified ferroptosis as a key pathway triggered by FtH deletion. This was confirmed by elevated expression of ferroptosis-related genes, oxidative stress markers, and increased iron deposition in the kidneys. The latter was mediated via reprogramming of macrophages to an iron-recycling phenotype by inducing Spic. Mechanistically, we demonstrate ferrireductase activity of monomeric Snca acts as a catalyst triggering oxidative stress and ferroptosis. Moreover, kidney accumulation of Snca is promoted in kidney diseases marked by heavy leukocyte infiltration in both mice and humans. These findings emphasize role of FtH in regulating iron metabolism and promoting kidney repair by suppressing Snca and Spic.

overall_design: Male FtHfl/fl and FtHΔ/Δ mice (8–10 weeks old) were randomly assigned to either the aristolochic acid (AA) injection group or the control (Saline) group. Mice in the AA group received intraperitoneal injections of AA (2 mg/kg body weight; Sigma-Aldrich, A9451) once daily for five consecutive days to induce kidney injury, while control mice received an equal volume of saline as a vehicle control. Mice were harvested at Weeks 6 post-final injection, and CD45⁺ immune cells were sorted from kidneys using flow cytometry and subjected to scRNA-seq using the 10× Genomics platform.

first: Tanima

last: Chatterjee

first: Abolfazl

last: Zarjou


title: Myeloid FtH deficiency accelerates kidney disease by inducing Snca and ferroptosis [Fe treatment WT-KO]

address: 618 Zeigler Research Building, 703 South 19th Street

summary: Following kidney injury, we observed increased iron depsoition in kidneys of myeloid specific FtH deficient (FtHΔ/Δ) mice when compared to wild-type (FtHfl/fl) kidneys. To explore mechanisms coordinating increased iron accumulation in FtHΔ/Δ kidneys, we employed a parenterally induced iron overload model by injecting 10–12-week-old male FtHfl/fl (wild-type) and FtHΔ/Δ (myeloid-specific FtH-deficient) mice with 0.4 mg/g body weight iron dextran via five intraperitoneal injections on consecutive days. Three days after the final injection, kidneys were harvested and sent for bulk RNA sequencing to assess transcriptional changes underlying tissue iron deposition due to FtH deletion in myeloid cells.

overall_design: Total RNA was isolated from kidney of wild-type (FtHfl/fl) n=4 and myeloid specific FtH deficient (FtHΔ/Δ) n=4 mice treated with iron using Trizol. We then perfomed gene expression profilling analysis using RNA -Seq

first: Sarah

middle: E

last: Machado

first: Kellen

last: Cowen

first: Mary

last: Miller


title: Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of adapted respiratory variants

city: Mumbai

first: Amitesh

last: Anand

state: Maharashtra

address: Homi Bhabha Road

department: DBS

institute: TIFR

summary: Respiratory variants of E. coli were evolved in succinate and glycerol as carbon sources, to understand their metabolic flexibility and rewiring to attain energy homeostatis.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Growth of E. coli WT MG1655 and the respiratory variants was performed in their respective evolution media, i.e. minimal media supplemented with succinate (2g/L sodium succinate dibasic) and glycerol (0.2%) as the carbon source. The strains were grown at 37C in two biological replicates for each strain. Total RNA was extracted from the mid-log phase culture for RNA-seq library preparation.


title: RNA-seq gene expression profiling comparing ∆vsrA and ∆scmA∆vsrA Caulobacter crescentus NA1000 cells

city: Lausanne

first: Karolina

last: Bojkowska

address: Unil, Genopode

country: Switzerland

institute: University of Lausanne

summary: The precise biological function of solitary cytosine MTases in bacteria remains mostly elusive. In this study, we dissected the potential influence of the solitary cytosine MTase CCNA_01085 (named ScmA), in the Caulobacter crescentus Alphaproteobacterial model. We constructed a ∆scmA mutant and used it to study the impact of ScmA-dependent methylation on C. crescentus phenotypes, on its fitness and on its transcriptome. These analyses revealed that DNA damaging events often take place in ∆scmA cells. Interestingly, these were shown to be dependent on the presence of the CCNA_2930 Vsr-like repair endonuclease naturally expressed in WT C. crescentus cells (named VsrA). Thus, we hypothesize that DNA damage can be induced by VsrA during DNA repair anomalies. Consequently, scmA+ cells largely outcompete ∆scmA cells during standard growth conditions. Interestingly, the vsrA gene is not genetically linked with the scmA gene on the C. crescentus chromosome despite the functional link that we discovered, revealing an original gene positioning architecture compared to previously characterized systems where Vsr-like repair endonucleases are usually encoded by genes located right next to MTase genes.

overall_design: To investigate the impact of DNA methylation by ScmA (CCNA_01085) not linked to VsrA-induced DNA damage on the transcriptome of Caulobacter crescentus NA1000 strain, we constructed mutant strains deleted for VsrA and both VsrA and ScmA. We then performed gene expression profiling analyses using data obtained from RNA-seq of ∆vsrA/∆scmA∆vsrA cells grown exponentially (OD660=~0.4) in M2G medium.

first: Noémie

last: Matthey

first: Giorgia

last: Wennubst

last: Bokkowska

first: Julien

last: Marquis

first: Justine

last: Collier


title: Mannose enhances anti-PD-1 therapy efficacy in ovarian cancer via modulating gut microbial metabolite [Peritoneum]

city: Shanghai

first: Haiou

last: Liu

address: No.128, Shengyang road, Yangpu distinct, Shanghai, P. R. China.

institute: Fudan University

summary: The gut microbiome plays a critical role in enhancing the effectiveness of immune checkpoint blockade (ICB) therapy. Here, we demonstrate that oral supplementation with the prebiotics mannose slows tumor growth in immunocompetent mice in a manner dependent on the gut microbiota. This effect is associated with an increase in the abundance of Faecalibaculum. Mannose generates an immune-stimulatory tumor microenvironment (TME), characterized by a higher percentage of effector and memory CD8+ T cells, along with a notable immunoreactive gene expression signature. Crucially, mannose modulates the stemness program of CD8+ T cells and promotes the generation of progenitor exhausted CD8+ T cells (Tpex). Mechanistically, mannose enhances the production of the short-chain fatty acids (SCFA) propionate and butyrate by the gut microbiota. Administration of propionate and butyrate suppresses tumor progression and stimulates the expansion and differentiation of Tpex both in vivo and in vitro. Furthermore, mannose works synergistically with PD-1 blockade, resulting in tumor regression and enhanced differentiation of intratumoral Tpex into intermediate exhausted CD8+ T cells (Tex-int) and terminally exhausted CD8+ T cells (Tex-term). We also identified a gene signature related to mannose therapy that correlates with favorable responses to ICB across various cancers. Overall, our findings support the combination of mannose dietary supplementation with anti-PD-1 immunotherapy in treating ovarian cancer and suggest its potential for clinical application.

overall_design: 24 mouse peritoneal metastasis samples treated with or without propionate and butyrate alone or in combination


title: Intestinal helminth skews dendritic cell development to counter the anti-helminth immune response

city: Glasgow

first: Andrew

middle: George

last: Farthing

state: Scotland

address: Institute of Infection, Immunity and Inflammation, 120 University Place, Sir Graeme Davies Building

institute: University of Glasgow

summary: Intestinal dendritic cells (DC) orchestrate the adaptive immune response that balances protection against pathogens and tolerance towards harmless antigens. Yet, it remains largely unknown what molecular mechanisms underly this functional duality. Heligmosomoides polygyrus bakeri (Hpb) is a naturally occurring parasite in mice characterised by unique immune-evasion strategies that counter host protective immunity. Here, we utilised this unique infection environment to study mechanisms by which DC maintain the immune balance. In-depth characterisation of intestinal DC during Hpb infection revealed the emergence of distinct populations of DC that drive protective Th2 responses, versus others with immunoregulatory properties. We also identified that the skewing of intestinal DC towards immunoregulatory functions was due to TGFb signalling via endogenous sources or by Hpb-produced TGFb-mimic molecules. Thus, our results present a mechanistic explanation for Hpb’s ability to modulate the adaptive immune system. Furthermore, these data offer an example of how heterogeneity within the DC compartment can determine the simultaneous generation of both pro- and anti-inflammatory immune responses.

overall_design: Bulk RNA sequencing analysis of FACS-purified CD103- and CD103+ DC2 populations isolated from granuloma and non-granuloma regions at 7 days post infection with Heligmosomoides polygyrus bakeri, as well as naïve, from small intestine lamina propria. Pre-gated as live, singlets, CD3-, B220-, CD19-, CD45+, CD64-, CD11c+, MHCII+. Then two populations of DC2 identified as CD11b+CD103- and CD11b+CD103+. Each sample contains pooled RNA isolated at two individual experiments (4-5 aniamls per each experiment; 8-10 animals in total per each sequenced sample). Each sample contains RNA representative of 80-100k cells.

first: Anna

middle: T

last: Andrusaite

first: Olivia

last: Ridgewell

first: Daisy

last: Lints

last: Ahlback

middle: L

last: Heawood

first: Holly

middle: C

last: Webster

first: Ruby

middle: F

last: White

first: Kyle

last: Cunningham

first: Hiroki

last: Yamaguchi

first: Sarwah

last: Al-Khalidi

first: Molly

last: Peel

first: Annika

last: Frede

middle: G

first: Kieran

middle: P

last: Woolcock

first: Annabelle

middle: N

last: Smith

first: Edward

last: Roberts

first: Allan

middle: M

last: Mowat

first: Richard

last: Maizels

first: Georgia

last: Perona-Wright

first: Simon

middle: W

last: Milling


title: Effects of GPX3-Specific Knockout in Renal Tubular Epithelial Cells on Kidney Gene Expression During the IRI-AKI Process

city: Changsha

first: Jinrong

last: He

address: Tongzipo Road

department: Department of Nephrology

institute: The Third Xiangya Hospital, Central South University

summary: GPX3 is primarily synthesized and secreted by renal tubular epithelial cells and serves as the main source of GPX3 in plasma. A portion of GPX3 adheres to the renal basement membrane, suggesting that GPX3 may also regulate renal cell physiological functions. Our previous work has found that GPX3 expression is downregulated in the renal tubular epithelial cells of mice that have undergone ischemia-reperfusion-induced acute kidney injury, but the specific impact of this downregulation remains unclear. To address this, we constructed mice with specific deletion of GPX3 in renal tubular epithelial cells and subjected them to ischemia-reperfusion modeling. We reported the protective role of native GPX3 in the kidneys under IRI-AKI conditions in mitigating oxidative stress and mitochondrial damage in tubular epithelial cells. The deletion of GPX3 in tubular epithelial cells exacerbated oxidative stress, apoptosis, and mitochondrial dysfunction in IRI-AKI. Renal cortex tissue from control and IRI-modeled mice was used for RNA sequencing. Overall, our data provide an overview of the genetic changes in the kidneys of mice with GPX3 knockout in both non-modeled and IRI-AKI-modeled conditions, laying the groundwork for studying the specific mechanisms by which GPX3 regulates renal function.

overall_design: To investigate the specific mechanisms by which GPX3 affects renal function, we constructed mice with specific knockout of GPX3 in renal tubular epithelial cells and subjected them to a bilateral renal ischemia-reperfusion model, involving 30 minutes of ischemia followed by 48 hours of reperfusion.Subsequently, RNA sequencing and bioinformatics analysis were performed on the renal cortex of four groups of mice.


title: 17q21.31 locus regulates Parkinson’s disease relevant pathways through KANSL1 activity

city: London

first: Amy

last: Hicks

address: 30 Guilford Street

institute: UCL

summary: An inversion polymorphism at the 17q21.31 locus defines the H1 and H2 haplotypes, with the former linked to multiple neurodegenerative disorders, including an increased risk of Parkinson’s disease (PD). Although the high linkage disequilibrium at this locus has made it difficult to decipher which gene(s) drive the PD association, there is increasing evidence to support the role of KANSL1 as a risk gene. KANSL1 has been shown to regulate the expression of some PD-associated genes and pathways, likely as part of the histone acetylating non-specific lethal (NSL) complex. Here for the first time, we studied the global effects of 17q21.31 haplotype variation using bulk and single-nuclear RNA-sequencing data from control and PD patient brain. We first analysed differential gene expression across haplotype groups, and then assessed the contribution of KANSL1 by comparing with the results of an siRNA knockdown in neuronal and glial human cell lines. We demonstrated that the PD risk-associated H1 haplotype downregulates autophagy, lysosomal and mitochondrial processes, all of which have already been implicated in PD aetiology. Furthermore, these effects were apparent in both neuronal and glial cell types, and in the case of the latter, appear to be associated with the modulation of innate and adaptive immune responses. Thus, we identify important links between NSL complex activity and PD pathophysiology that can be leveraged for novel therapeutic interventions.

overall_design: Bulk RNA-seq profiling of SH-SY5Y cells and H4 cells treated for three days with either scrambled (SCR), KANSL1-targeting or KAT8-targeting siRNA.

middle: R

first: Benjamin

last: O'Callaghan

first: Jonathan

last: Brenton

first: Melissa

last: Grant-Peters

first: Aine

last: Fairbrother-Browne

first: Guillermo

last: Rocamora Perez

first: Caitlin

middle: A

last: Loh

first: Regina

last: Reynolds

first: Emil

middle: K

last: Gustavsson

first: Kylie

last: Montgomery

first: Maria

last: Tsalenchuk

first: Raquel

last: Real

first: Huw

last: Morris

first: Katie

last: Lunnon

first: Sarah

middle: J

last: Marzi

first: Zane

last: Juanmuktane

first: John

last: Hardy

first: Helene

last: Plun-Favreau

first: Mina

last: Ryten


title: ATRX safeguards cellular identity during C. elegans development

city: St Andrews

first: Helder

last: Ferreira

address: North Haugh

institute: University of St Andrews

summary: ATRX is a member of the SWI/SNF family of ATP-dependent chromatin remodellers. In humans, loss of ATRX function in leads to ATRX syndrome, a neurodevelopmental disorder. ATRX mutation in human cell lines is associated with multiple phenotypes including activation of the alternative lengthening of telomere (ALT) pathway, upregulation of retrotransposons and increased sensitivity to replication stress. However, the principal role of ATRX and the reason why its mutation causes such diverse phenotypes is currently unclear. To address this, we studied the role of ATRX in the model organism Caenorhabditis elegans. We find that loss of XNP-1, the C. elegans homologue of ATRX, recapitulates many human phenotypes. In addition, XNP-1 is required to repress the inappropriate activation of germline genes. Importantly, this germline misexpression correlates with most of the phenotypes observed in xnp-1 animals. Seemingly distinct xnp-1 phenotypes such as developmental abnormalities and telomeric defects are both suppressed by mutation of the germline transcription factor gsox-1. These findings suggest that the majority of XNP-1-dependent phenotypes stem from its role in maintaining proper cellular identity, offering insights into the functions of ATRX in humans.

overall_design: RNA-seq and smallRNA-seq profiling of wildtype (N2) and xnp-1-knockdown in C. elegans embryos and L1 larvae grown at 20°C and of L4 larvae of N2, and xnp-1, gsox-1 and gsox-1;xnp-1 mutant backgrounds grown at 25°C.

first: Janie

last: Olver

first: Mariya

last: Shtumpf

first: Karim

last: Hussain

first: Stephen

last: Methot

first: Peter

last: Sarkies


title: Hypoxia-induced phase separation of ZHX2 drives 3D chromatin remodeling and cancer metastasis (ATAC-Seq)

first: gao

last: chuan

summary: Hypoxia and dysregulation of three-dimensional (3D) chromatin architecture can both activate oncogenic transcriptomic profiles, thus contributing to tumor malignancy. But how hypoxia regulates 3D chromatin architecture remains unknown. Here, we find that the transcription factor, zinc fingers and homeoboxes 2 (ZHX2), generates liquid-liquid phase separation (LLPS) under hypoxia, thus promoting its occupancy on chromatin and activating transcription for a cluster of oncogenes, that is enriched by metastatic genes distinct from targets of hypoxia-inducible factor (HIF) and pathologically relevant to breast cancer. Mechanistically, hypoxia induces the LLPS of ZHX2 via a proline-rich intrinsically disordered region (IDR) in the nuclear localization sequence (NLS), thereby enhancing the phosphorylation of ZHX2 at S625 and S628 that incorporates CCCTCbinding factor (CTCF) in condensates to reorganize chromatin looping, consequently resulting in oncogenic super-enhancer formation and breast cancer metastasis. This fundamental mechanism provides significant insight into oncogene activation and suggests a phase separation-based therapeutic strategy for cancer.

overall_design: We conducted ATAC-seq experiments in T47D cells under normoxia, hypoxia, and hypoxia with ZHX2 knockdown (KD).

first: Jing

last: Zhang

first: Chuan

last: Gao


title: Mannose enhances anti-PD-1 therapy efficacy in ovarian cancer via modulating gut microbial metabolite [CD8]

first: Haiou

last: Liu

overall_design: Seven CD8+ T cells samples isolated from ascites of  mouse models of peritoneal metastasis treated with or without co-treatment with propionate and butyrate.


title: Induction of a transcriptional adaptation response by RNA destabilization events [dst278]

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Transcriptional adaptation (TA) is a cellular process whereby mRNA-destabilizing mutations lead to the transcriptional upregulation of so-called adapting genes.  The nature of the TA-triggering factor(s) remains unclear, namely whether an mRNA-borne premature termination codon (PTC) or the subsequent mRNA degradation process, and/or its products, elicits TA.  Here, we first established two perturbations leading to mRNA destabilization for mouse Actg1: a Cas9-induced mutation that leads to a PTC, and Cas13d-mediated mRNA cleavage.  We find that both perturbations are effective in degrading Actg1 mRNA and upregulating Actg2.  Notably, increased chromatin accessibility at the Actg2 locus was observed only in the Cas9-induced mutant allele but not in the Cas13d-targeted cells, suggesting that chromatin remodeling is not required for Actg2 upregulation.  We further show that ribozyme-mediated Actg1 pre-mRNA cleavage also leads to a robust upregulation of Actg2.  Together, these data highlight the critical role of RNA destabilization events as a trigger for TA.

overall_design: Active (T3H48-aHHR) and inactive (T3H48-iHHR) T3H48-HHR ribozyme was knocked into intron 3 of the Actg1 locus to induce ribozyme-mediated pre-mRNA cleavage.  Stable lines were genotyped and samples were collected for ATAC-Seq.

first: Christopher

last: Dooley

first: Stefan

last: Günther

first: Xie

last: Lihan


title: Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses I

city: New York

first: Alana

last: Mendelsohn

state: NY

address: 3227 Broadway

institute: Columbia University

summary: The basal ganglia control multiple sensorimotor behaviors though anatomically segregated and topographically organized subcircuits with outputs to specific downstream circuits. However, it is unclear how the anatomical organization of basal ganglia output circuits relates to the molecular diversity of cell types. Here, we demonstrate that the major output nucleus of the basal ganglia, the substantia nigra pars reticulata (SNr) is comprised of transcriptomically distinct subclasses that reflect its distinct progenitor lineages. We show that these subclasses are topographically organized within SNr, project to distinct targets in the midbrain and hindbrain, and receive inputs from different striatal subregions. Finally, we show that these mouse subclasses are also identifiable in human SNr neurons, suggesting that the genetic organization of SNr is evolutionarily conserved. These findings provide a unifying logic for how the developmental specification of diverse SNr neurons relates to the anatomical organization of basal ganglia circuits controlling specialized downstream brain regions.

overall_design: SNr neurons were retrogradely labeled by injection of AAVretro-hSyn-H2B-mCherry into six different brain target regions. The SNr was subsequently microdissected and nuclei were isolated. Labeled SNr nuclei were isolated by fluorescence activated nuclear sorting (FANS), sorted into individual wells of 96-well plates and sequenced.

first: Mendelsohn

last: Alana

first: Costa

last: Rui


title: Mannose enhances anti-PD-1 therapy efficacy in ovarian cancer via modulating gut microbial metabolite

overall_design: 6 healthy volunteers were recruited and were given 2g/d powder of mannose (Now) in drinking water per day for 14 days. Stool samples were collected and stored at liquid nitrogen for further 16S rRNA analysis.


title: Age-related reproductive performance and transcriptome profiling of testis in male blue catfish, Ictalurus furcatus

city: Auburn

first: Ian

last: Butts

state: Alabama

address: 203, Swingle Hall

department: School of Fisheries, Aquaculture & Aquatic Sciences

institute: Auburn University

summary: Catfish farming is the largest aquaculture industry in the U.S., where hybrid catfish produced by channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂, represent >50% of the harvest. Typically, older blue catfish (≥5 years) are selected for artificial fertilization. However, observations at our facilities and reports from hatcheries indicate a high degree of variation in reproductive performance among individuals. Thus, it is essential to establish links between paternal age and reproductive success, as it is apparent that advanced paternal age leads to changes in reproductive performance. Since there are no prior studies regarding the changes in testis transcriptome in blue catfish males during aging, we evaluated global gene expression of testis at age 2,4,7 and 9. Significant differential expressed genes and gene ontology of pairwise comparisons between age 2 and each test age are presented and discussed.

overall_design: A total of 16 testis tissue samples from blue catfish males were used in this study, corresponding to ages 2, 4, 7 and 9. Age 2 was considered as the control group. Four testis tissue samples were collected per age group and extracted for RNA-seq.

first: Jason

last: Abernathy

first: Nithin

last: Sankappa

first: Samitha

last: Liyanage

first: Xu

last: Wang


title: Mannose enhances anti-PD-1 therapy efficacy in ovarian cancer via modulating gut microbial metabolite.

summary: The gut microbiome serves as a crucial mediator for improving the efficacy of immune checkpoint blockade (ICB) therapy. Here, we show that oral supplementation with prebiotics (mannose) retarded tumor growth in immunocompetent mice in a gut microbiota dependent manner, correlating with the enrichment of Faecalibaculum. Mannose generates an immune-stimulatory tumor microenvironment (TME) characterized by an increase percentage of effector and memory CD8+T cells, accompanied by a prominent immunoreactivegeneexpressionsignature. Most importantly, mannose modulates the stemness program of CD8+T cells and facilitates the generation of progenitor exhausted CD8+T cells (Tpex). Mechanistically, mannose increases gut microbial production of the short-chain fatty acids (SCFA) propionate and butyrate. Administration of propionate and butyrate suppresses tumor progression and stimulates the expansion and differentiation of Tpex both in vivo and in vitro. Mannose synergized with PD-1 blockade in tumor regression and augmented intratumoral Tpex differentiation into intermediate exhausted CD8+T cells (Tex-int) and terminally exhausted CD8+T cells (Tex-term). Moreover, we identified a mannose-therapy related gene signature associated with favorable responses to ICB in pan-cancer. Overall, our findings support the rationale for combining dietary supplementation of mannose with anti-PD-1 immunotherapy in ovarian cancer, and its clinical translation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor tissues and sorted CD8+T cells from HM1 tumors with the supplementation of mannose or not.

first: Mengdi

last: He

first: Kankan

last: Cao


title: Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses II

overall_design: The SNr was microdissected, nuclei were isolated and sequenced using 10x single-nucleus RNA sequencing.


title: RNA-sequence facilitates analyze changes of P3 Pou4f3 mutant mice

city: Nanjing

first: Guoqiang

last: Wan

state: Jiangsu

address: Xuefu Road 12

department: Medical School

institute: Nanjing University

summary: We report application of RNA-seq for transcriptomic analyses of cochlear tissues from wildtype and DFNA15 deafness mouse model Pou4f3(Δ/+) to reveal gene expressions altered by Pou4f3 mutation

overall_design: Cochlear tissues (3 each genotype) were collected from P3 Pou4f3(Δ/+) mice and wildtype littermates and subjected to RNA-seq

first: Sihao

last: Gong


title: RNA-seq gene expression profiling comparing WT (NA1000) and isogenic ∆scmA Caulobacter crescentus cells

first: Karolina

last: Bojkowska

overall_design: To investigate the impact of DNA methylation by ScmA (CCNA_01085) on the transcriptome of Caulobacter crescentus NA1000, we constructed a ∆scmA mutant. We then performed gene expression profiling analyses using data obtained from RNA-seq of WT/∆scmA cells grown exponentially (OD660=~0.4) in M2G medium.

first: Noémie

last: Matthey

first: Giorgia

last: Wennubst

first: Julien

last: Marquis

first: Justine

last: Collier


title: Induction of a transcriptional adaptation response by RNA destabilization events [dst175]

first: Carsten

last: Kuenne

summary: Transcriptional adaptation (TA) is a cellular process whereby mRNA-destabilizing mutations lead to the transcriptional upregulation of so-called adapting genes. The nature of the TA-triggering factor(s) remains unclear. Here, we first generated Cas9-induced mutations in mouse Actg1, including an mRNA-destabilizing allele and an RNA-less allele. We find in the Actg1 mRNA-destabilizing allele, higher levels of Actg2 mRNA as well as increased chromatin accessibility at the Actg2 locus compared with wild-type and the RNA-less allele. Notably, Cas13d experiments show that Actg1 mRNA cleavage, but not Actg1 pre-mRNA cleavage, also triggers Actg2 upregulation; however, this upregulation is not associated with increased chromatin accessibility at the Actg2 locus. Furthermore, time course experiments show that increased Actg2 expression persists even after Actg1 mRNA degradation by Cas13d ceases. Together, our data highlight the importance of cytoplasmic mRNA degradation as a trigger for the TA response and suggest that chromatin remodeling is not necessary for TA.

overall_design: To investigate the role of mRNA degradation during transcriptional adaptation, we used CRISPR-Cas9 to generate three Actg1 knockout alleles in NIH/3T3 cells: Actg1PTC1 with a premature termination codon, Actg1PTC2 with a premature termination codon and Actg1LD with a full locus deletion of the gene. We then performed ATAC-seq to detect the changes in chromatin accessibility in the Actg1PTC 's and Actg1LD mutant cells compared with wildtype cells. Three biological replicates were prepared for each genotype.

first: Lihan

last: Xie

first: Gabrielius

last: Jakutis

first: Christopher

last: Dooley

first: Stefan

last: Guenther

first: Didier

middle: Y

last: Stainier


title: MicroRNA signatures of CD4+ T cell subsets in healthy and multiple sclerosis subjects determined by small RNA-sequencing

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: Diverse CD4+ T cell subsets with specialized functions operate at different phases of the immune response. Among these are naïve, central memory (CM), effector memory (CM), and regulatory (Treg) cells that have been phenotypically and functionally characterized. To expand current knowledge and identify highly subset-selective markers, we have profiled miRNAs using small RNA-sequencing in FACS-sorted CD4+ T cell subsets from healthy subjects and untreated patients with relapsing-remitting multiple sclerosis (RRMS). Genomic clustering and abundance of the miRNAs were also investigated. From the 60 most differentially expressed miRNAs, broad signatures and highly selective core signatures were identified for naïve and memory CD4+ T cells at homeostasis, while miR-146a-5p was strongly upregulated in Treg cells. In line with other studies, a 5-miRNA core signature was identified for naïve cells (miR-125b-5p, miR-99a-5p, miR-365a-3p, miR-365b-3p, miR-193b-3p). Supporting the progressive memory T cell differentiation model, a number of miRNAs were upregulated in CM and EM cells and, notably, at higher level in EM cells. This was particularly the case for a miRNA core of 8 miRNAs from miR-23a~27a~24-2, miR-23b~27b~24-1, miR-221~222 clusters, and miR-22-3p, miR-181c-5p, with highly abundant miR-24-3p. In addition, we detected activation of the large ChrXq27.3 miR-506~514 cluster in EM cells. Interestingly, most of the miRNAs that were enriched in EM cells were shown to negatively regulate cell proliferation and survival. Finally, we found that the miRNA core signatures of naïve and memory CD4+ T cells were conserved in RRMS patients. Only few miRNAs were quantitatively modified, among these, miR-1248 was downregulated and may be a candidate disease marker.

overall_design: We have profiled miRNAs using small RNA-sequencing in FACS-sorted CD4+ T cell subsets from healthy subjects and untreated patients with relapsing-remitting multiple sclerosis (RRMS)

first: Marc

last: Monot

first: Frédérique

last: Michel


title: NAT10 mediates TLR2 to promote podocyte senescence in adriamycin-induced nephropathy

city: Zhengzhou

first: Mingyang

last: Hu

state: Henan

address: jinshui

institute: Department of Nephrology, First Affiliated Hospital of Zhengzhou University

summary: N-acetyltransferase 10 (NAT10) is involved in regulating senescence. However, its role in glomerular diseases remains unclear. Therefore, this study aims to investigate the mechanisms by which NAT10 influences senescence and damage in an adriamycin (ADR)-induced nephropathy model. Senescence (p16 and p21) and DNA damage markers (γ-H2AX (ser139)) were assessed in ADR-induced nephropathy. NAT10 function was demonstrated using Remodelin or small interfering RNA (siRNA) interventions. Transcriptome sequencing was conducted to identify key downstream genes and pathways, while coimmunoprecipitation was performed to evaluate the relationship between NAT10 and toll-like receptor 2 (TLR2) expression. TLR2 overexpression or knockdown further validated its regulatory role in senescence. In ADR-treated mice, the expression levels of P53, P21, P16, γ-H2AX(S139) proteins were elevated, while those of WT-1 and nephrin were reduced. This effect was mitigated by Remodelin and siNAT10 administration. Transcriptome sequencing identified TLR2 as a key downstream gene, and coimmunoprecipitation, along with molecular docking models, confirmed its interaction with NAT10. TLR2 overexpression plasmid or siRNA was employed for recovery experiments. Together, the study findings suggest that NAT10 contributes to podocyte senescence and injury via interaction with TLR2. Further, it demonstrates that NAT10 alleviates ADR-induced podocyte senescence by interacting with TLR2, potentially through a P53-P21-dependent mechanism. Thus NAT10 could serve as a novel therapeutic target for treating podocyte senescence and proteinuric glomerulopathies.

overall_design: Comparative gene expression profiling analysis of RNA-seg data for GROUP:Control, adriamycin, adriamycin+siNAT10

first: Linxiao

last: Lv

first: Yuqi

last: Lei

first: Chen

last: min

first: Sijie

last: Zhou

first: Zhangsuo

last: Liu


title: RNAseq of the cornea of rats that overexpress the human NR3C2 gene coding for mineralocorticoid receptor (hMR)

first: Daniela

last: Rodrigues-Braz

address: 15 rue de l'Ecole de Médecine

institute: Inserm

summary: The aim of this study was to analyse the transcriptional regulation in the cornea of rats that overexpress the human NRC32 gene coding for mineralocorticoid receptor (P1 hMR). Six-month-old male Wild-Type (WT) and transgenic P1 hMR rats were euthanized and the corneas were exised for RNA-sequencing. Total RNA samples were sequenced at the iGenSeq transcriptomic platform of the Brain and Spine Institute (ICM, Paris, France). RNA quality was checked by capillary electrophoresis (Agilent 2100 Bioanalyzer system) and RNA with integrity numbers (RIN) ranging from 7.8 to 8.2 was accepted for library generation. Quality of raw data has been evaluated with FastQC. Illumina DRAGEN bio-IT Platform (v3,8,4) was used to align reads on reference genome rd6 and quantification with genecode vM25 annotation gtf. Library orientation, library composition and coverage along transcripts were checked with Picard tools. differential analysis has been also conducted with edgeR. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR. We identified genes differentially regulated in P1 hMR rats as compared to WT rats.

overall_design: Corneal mRNA profiles of rats that overexpress the human NR3C2 gene coding for mineralocorticoid receptor.

first: Min

last: Zhao

first: Francine

last: Behar-Cohen

first: Justin

last: Guegan


title: Human mast cell interferon responses and survival in the context of Coronavirus and Respiratory Syncytial Virus are enhanced by IL-5

city: Halifax

first: Tobias

last: Karakach

state: NS

address: 5058 College Street

department: Pharmacology

country: Canada

institute: Dalhousie University

summary: Mast cells have been shown to be important sentinel cells in multiple models of viral and bacterial infection. Exacerbations of allergic asthma and asthma deaths are often associated with respiratory viral infections. Elevated levels of type 2 cytokines, especially interleukin 5 (IL-5), are also associated with allergic disease and have been targeted therapeutically. Here, we demonstrate that IL-5 signaling enhances the ability of human mast cells to mount a potent anti-viral response against respiratory viruses. Mast cells derived from umbilical cord-blood, treated with IL-5 and infected with respiratory viruses such as the human Coronavirus OC43 or respiratory syncytial virus (RSV) produced significantly more type I and type III interferons (IFNs) than non-IL-5 treated controls. IL-5 treatment also led to greater expression of IFN stimulated genes and upregulated expression of the pro-survival factor B-cell lymphoma 2 (BCL2) and protected mast cells from apoptosis-induced stress. IL-5 also upregulated expression of Endothelial PAS Domain Protein 1 (EPAS1), demonstrating an important IL-5 driven pro-survival network in mast cells. These resultssuggest an unexpected role for IL-5 signaling in regulating mast cell interferon responses and maintaining mast cell populations during mucosal viral infection.

overall_design: Umbilical cord blood-derived mast cells (CBMCs) from 8 donors were treated them with 10 ng/mL of human IL-5 and 100 ng/mL of human SCF for 24 hours and with 10 ng/mL of human IL-5 and 10 ng/mL human SCF for 18 hours prior to RNA harvest. Gene expression in these samples was compared to that in another set of CBMCs from 8 donors who only received a mock treatment (media).

first: Jasmine

last: Barra

last: Liwski

first: Phoebe

last: Phonchareon

first: Liliana

last: Portales-Cervantes

first: Daniel

last: Gaston

first: Ian

middle: D

last: Haidl

first: Jean

middle: S

last: Marshall


title: IRF1 cooperates with ISGF3 or GAF to form innate immune de novo enhancers

city: Los Angeles

first: Aleksandr

last: Gorin

state: CA

address: 611 Charles E Young Dr E 570C Boyer Hall

institute: UCLA

summary: Macrophages exposed to immune stimuli reprogram their epigenomes to alter their subsequent functions. Endotoxin exposure causes widespread nucleosome remodeling and formation of thousands of de novo enhancers. However, it remains unclear how signal-dependent transcription factors collaborate to remodel the epigenome. Here, we dissected the regulatory logic by which the network of interferon regulatory factors (IRFs) catalyzes the opening of chromatin and the formation of de novo enhancers. We found that endotoxin-activated IRF3 is directly responsible for the induction of few de novo enhancers but is broadly required indirectly through activation of type I interferon-induced ISGF3. However, ISGF3 has limited capacity to initiate enhancer formation by itself – it must cooperate with IRF1, particularly at locations where the chromatin is less accessible. At these locations, IRF1 is required for the initial opening of chromatin, with ISGF3 extending accessibility and promoting the deposition of H3K4me1, marking poised enhancers. Because IRF1 expression must be induced by NFκB, IRF-regulated enhancers require that both branches of the innate immune signaling network, IRF3 and NFκB, are activated.  However, type II interferon, typically produced by T-cells, may also induce IRF1 via the STAT1 homodimer GAF. We show that in this context, IRF1 is also responsible for opening inaccessible chromatin sites that can then be exploited by GAF to form de novo enhancers. Our results reveal how combinatorial logic gates of IRF1-ISGF3 or IRF1-GAF restrict immune epigenomic memory formation to macrophages exposed to pathogen or IFNγ-secreting T cells, but not bystander macrophages exposed only to transient type I interferon.

overall_design: Human monocyte-derived macropahges were generated with MCSF. After 7 days for maturation in MCSF macrophages were left untimulated or stimulated with either LPS 100ng/mL, interferon-gamma 100ng/mL, interferon-beta 10u/mL, or Pam3CSK4 100ng/mL. After 8 hours stimulation cells were isolated and CUT&Tag for mono-mehtylated Lysine 4 on Histone 3 (H3K4me1) was performed.

first: Carolina

last: Chavez

first: Stefanie

last: Brizuela

first: Quen

last: Cheng

first: Alexander

last: Hoffmann


title: Characterizing rhesus fetal gonadal development

first: Jonathan

last: DiRusso

state: California

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

summary: Given the challenges involved in acquiring human fetal tissue for research, non-human primates fill a critical knowledge gap in understanding early developmental progression. Using the 10x Genomics Chromium platform,  we performed single cell RNA-seq on rhesus macaque prenatal gonads at critical stages in embryonic and fetal life. These experiments represent a rare opportunity to analyze primate germline and gonadal somatic cell biology during a developmental window that is almost inaccessible with human tissues.

overall_design: 10x Genomics analyses of n = 3 or 4 biological replicates of rhesus fetal gonads (ovary or testis) collected at 50 - 52, 100 or 130 days of gestation, with 2 technical replicates (A and B) for each sample.

first: Enrique

last: Sosa

first: Sissy

last: Wamaitha

first: Amander

last: Clark


title: Escape from TGF-β-induced senescence promotes aggressive hallmarks in epithelial hepatocellular carcinoma cells

city: Izmir

first: Serif

last: Senturk

address: Dokuz Eylul University - iBG

department: Functional Cancer Genomics Lab

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary: Transforming growth factor-β (TGF-β) signaling and cellular senescence are key hallmarks of hepatocellular carcinoma (HCC) pathogenesis. While provoking senescence-associated growth arrest in epithelial HCC cells, elevated TGF-β activity paradoxically correlates with aggressiveness and poor prognosis in advanced tumors. Whether the transition between these dichotomous functions involves bypassing the senescence barrier during disease progression remains unknown. Exploiting the epithelial HCC cell line Huh7, we demonstrate that chronic TGF-β exposure prompts escape from Smad3-mediated senescence, leading to the development of TGF-β resistance. The resistant state is characterized by restoration of proliferative capacity and acquisition of molecular and functional traits of mesenchymal cells, coinciding with hybrid EMT, increased invasiveness, and metastasis. Mechanistically, resistant cells exhibit defective signaling of Smad molecules, as ectopic activation of the TGF-β/Smad3 axis reinstates TGF-β sensitivity. Gene expression landscape profiling reveals both shared and distinct gene signatures associated with senescent and TGF-β resistant states. Importantly, genetic ablation and molecular studies identify GRM8 (Glutamate Metabotropic Receptor 8) as a critical modulator of the resistance phenomenon, potentially by impairing subcellular spatiotemporal dynamics of Smad activity. Our findings unveil a novel phenomenon wherein epithelial HCC cells may exploit senescence evasion as a mechanism to oppose TGF-β anti-tumor responses and progress towards more aggressive HCC phenotypes.

overall_design: To investigate the gene expression profiles of senescent and resistant states, we established relevant cellular models. To induce cellular senescence, we treated Huh7 cells with 5 ng/mL TGF-β for 3 days. Resistant state was established by chronic TGF-β exposure of Huh7 cells for more than 50 days. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cellular states in three replicates.

first: Gokhan

last: Karakulah


title: Stellate cells are in utero markers of pancreatic disease in cystic fibrosis

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Road

department: Genetics

institute: Case Western Reserve University

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

overall_design: Refer to individual Series


title: Stellate cells are in utero markers of pancreatic disease in cystic fibrosis [scRNA-seq]

summary: Pancreatic fibrosis is an early diagnostic feature of the common inherited disorder cystic fibrosis (CF). Many people with CF (pwCF) are pancreatic insufficient from birth and the replacement of acinar tissue with cystic lesions and fibrosis is a progressive phenotype that may later lead to diabetes. Little is known about the initiating events in the fibrotic process though it may be a sequela of inflammation in the pancreatic ducts resulting from loss of CFTR impairing normal fluid secretion. Here we use the sheep model of CF (CFTR-/-) to examine the evolution of pancreatic disease through gestation. Transcriptomic evidence from bulk RNA-seq showed alterations in the CF pancreas by 65 days of gestation, which are accompanied by marked pathological changes by 80 days gestation. These include a profound fibrotic response, confirmed by immunostaining for COL1A1, αSMA and SPARC, together with acinar destruction. Moreover, using scRNA-seq we identify a unique cell population that is significantly overrepresented in the CF animals at 80- and 120-days gestation, as are activated stellate cells at term. This cellular imbalance likely has a pivotal role in the evolution of CF pancreatic disease and may provide therapeutic opportunities to delay or prevent CF pancreatic destruction.

overall_design: Single cells from sheep (WT and CF) pancreas tissue  were isolated and analyzed using scRNA-seq.

first: Alekh

last: Paranjapye

first: Shih-Hsing

last: Leir

first: Svyatoslav

last: Tkachenko


title: Induction of a transcriptional adaptation response via perturbations at the DNA and RNA levels

first: Carsten

last: Kuenne


title: Identification of the cholesterol-depletion-induced enhancers in HeLa cell using H3K27ac ChIP-seq

status: Public on Mar 16 2025

first: Wei

last: Qi

state: Shanghai

address: B514, L Building

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: The transcription factor SREBP2, plays a specific and non-redundant role in cholesterol metabolism, autophagy of lipid droplets and apoptosis regulation. Under cholesterol-depletion condition, nuclear SREBP2 (nSREBP2) is released after proteolytic cleavage, enters nucleus and activates cholesterogenic genes expression. Here, we report that the nSREBP2 forms discrete nuclear condensates through its N-terminal intrinsically disordered region (IDR) and works together with transcription coactivators BRD4 and p300, partly on super-enhancers, for the transcriptional activation of SREBP2 target genes. The substitution of a critical and conserved phenylalanine (F) to alanine (A) within the IDR abolished the formation of nSREBP2 condensates. Conversely, the condensate formation and efficient transcription activation were rescued by fusion with a phase separation driving FUS-IDR. Knock-in of the F to A substitution in mice compromised the feeding-induced nSREBP2 activity and lowered the cholesterol levels. Furthermore, a SNP of SREBF2 in humans leading to single amino acid change, P183S, showed less nuclear condensate formation and lower transcriptional activity, underscoring the physiological relevance of nSREBP2 condensates. Together, this study reveals that nuclear condensates driven by the N terminal IDR of nSREBP2 facilitate the efficient activation of lipogenic genes and play an important role in cholesterol homeostasis.

overall_design: As a cis-element sequence-specific TF, SREBP2 interacts with transcription coactivators and machineries for gene activation. The histone H3K27ac modification has been used as a marker to define the super-enhancer elements in multiple cells and studies. To investigate if SREBP2 correlates with or contributes to the enhancer or super-enhancer at chromatin level, we performed the H3K27ac ChIP-seq in HeLa cell upon cholesterol-depletion to identify the responsive enhancers and super-enhancers in response to cholesterol-depletion.

first: Mengqiang

last: Xu

first: Shiyou

last: Jiang

first: Chenyang

last: Qin


title: Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis (RNA-seq)

city: Waterloo

first: Benjamin

middle: Jean-Marie

last: Tremblay

state: Ontario

address: 200 University Ave W

department: Department of Biology

institute: University of Waterloo

summary: The tight coordination of sulfur metabolism and growth regulation is predicated upon nutrient availability. Central to this balancing act is the utilization of cysteine (Cys) for the formation of methionine (Met) and S-adenosylmethionine (SAM). Plants that are severely deficient in regenerating Met due to reduced methylthioadenosine (MTA) nucleosidase activity experience numerous developmental abnormalities. Here we assess the developmental, metabolic, and regulatory effects associated with decreased MTA recycling. We show that MTA over-accumulation predominantly occurs  in reproductive tissues and leads to reduced levels of Cys, Met, and SAM, as well as elevated S-adenosylhomocysteine. These disruptions of primary sulfur utilization also lead to the misregulation of energy metabolism and altered cell cycle progression. RNA-seq experiments show a general down-regulation of many developmental and reproductive genes. Targeted metabolite analyses demonstrate clear impacts on the methyl index which are reflected in the results of bisulfite-sequencing experiments including global alterations in CG gene-body methylation levels and decreases of CHG and CHH methylation in transposable elements. Our findings demonstrate the broad impacts of MTA metabolism on plant development, sulfur utilization and the maintenance of the methyl index.

overall_design: RNA-seq of methylthioadenosine nucleosidase-deficient Arabidopsis thaliana (Col-0) mutants using tissue from 14 day-old seedlings and unopened flower buds, with and without spermidine supplementation.

first: Saeer

last: Adeel

first: Maye

last: Saechao

first: Yihan

last: Dong

first: Eric

last: Andrianasolo

first: John

last: Steele

first: Annika

last: Traa

first: Nilanth

last: Yogadasan

first: Ishari

last: Waduwara-Jayabahu

first: Barbara

last: Katzenback

first: Markus

last: Wirtz

first: Rüdiger

last: Hell

last: Moffatt


title: Induction of a transcriptional adaptation response via perturbations at the DNA and RNA levels [dst233]

first: Carsten

last: Kuenne

summary: Transcriptional adaptation (TA) is a cellular process whereby mRNA-destabilizing mutations lead to the transcriptional upregulation of so-called adapting genes.  The nature of the TA-triggering factor(s) remains unclear.  Here, we first generated Cas9-induced mutations in mouse Actg1, including an mRNA-destabilizing allele and an RNA-less allele.  We find in the Actg1 mRNA-destabilizing allele, higher levels of Actg2 mRNA as well as increased chromatin accessibility at the Actg2 locus compared with wild-type and the RNA-less allele.  Notably, Cas13d experiments show that Actg1 mRNA cleavage, but not Actg1 pre-mRNA cleavage, also triggers Actg2 upregulation; however, this upregulation is not associated with increased chromatin accessibility at the Actg2 locus.  Furthermore, time course experiments show that increased Actg2 expression persists even after Actg1 mRNA degradation by Cas13d ceases.  Together, our data highlight the importance of cytoplasmic mRNA degradation as a trigger for the TA response and suggest that chromatin remodeling is not necessary for TA.

overall_design: To investigate the role of mRNA degradation during transcriptional adaptation, we knocked in CRISPR-Cas13d in NIH/3T3 cells and targeted Actg1 mRNA for degradation by transfecting the cells with Actg1-specific guide RNA. Guide RNA targeting GFP was used as control. Then we performed ATAC-seq to detect the changes in chromatin accessibility in Actg1-targeted cells compared with GFP-targeted cells. Three biological replicates were prepared for each condition.

first: Lihan

last: Xie

first: Gabrielius

last: Jakutis

first: Christopher

last: Dooley

first: Stefan

last: Guenther

first: Didier

last: Stainier


title: Single cell transcriptome of dermal sheath cup cells contributing to efficacy of cell-based therapy for patterned hair loss

city: Yokohama

first: Yumiko

last: Ishimatsu-Tsuji

address: Nishi-ku

country: Japan

institute: Shiseido

summary: Autologous cell-based therapy using dermal sheath cup (DSC) cell is a new approach for male and female pattern hair loss. While its efficacy was recently reported, the mechanism of action remains unclear. Furthermore, the differences in treatment response require clarification. First, we used multivariate analysis to categorize two groups of individuals: patients in which therapy showed high efficacy (HE group) and patients in which therapy showed low efficacy (LE group). Then We analyzed the differences in gene expression between DSC cells from the HE and LE groups by single-cel transcriptome.

overall_design: mRNA profiles of dermal sheath cup cells with high efficacy and low efficacy


title: RNAseq of the peripheral cornea and limboscleral tissues of rats treated with systemic spironolactone in a model of corneal neovascularization

first: Daniela

last: Rodrigues-Braz

summary: The aim of this study was to analyse the transcriptional regulation in the corneal and limbal tissues of rats treated with spironolactone in a model of limbal stem cell deficiency (LSCD). CNV was induced by total corneal de-epithelialization and limbal resection. Rats were injected subcutaneously with spironolactone (25mg/kg/day) diluted in 90% olive oil and 10% DMSO  or vehicle (90% olive oil and 10% DMSO) for 14 days. On day 3 (early inflammatory stage) and day 7 (angiogenic stage), rats were euthanized and the peripheral cornea and the limboscleral tissues were exised for RNA-sequencing. Total RNA samples were sequenced at the iGenSeq transcriptomic platform of the Brain and Spine Institute (ICM, Paris, France). RNA quality was checked by capillary electrophoresis (Agilent 2100 Bioanalyzer system) and RNA with integrity numbers (RIN) ranging from 7.8 to 8.2 was accepted for library generation. Quality of raw data has been evaluated with FastQC. Illumina DRAGEN bio-IT Platform (v3,8,4) was used to align reads on reference genome rd6 and quantification with genecode vM25 annotation gtf. Library orientation, library composition and coverage along transcripts were checked with Picard tools. differential analysis has been also conducted with edgeR. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR. We identified genes differentially regulated by spironolactone vs. vehicle on day 3 and day 7.

overall_design: Corneal and limboscleral mRNA profiles of rats treated with systemic spironolactone in a rat model of limbal stem cell deficiency

first: Min

last: Zhao

first: Francine

last: Behar-Cohen

first: Justin

last: Guegan


title: Effect of photoperiod and seawater tranfer on transcriptome of saccus vasculosus from Atlantic salmon

city: Tromsø

first: Alexander

middle: Christopher

last: West

state: Troms

address: Framstredet 39, Tromsø

department: Arctic Chronobiology and Physiology

country: Norway

institute: Universitetet i Tromsø

summary: Atlantic salmon (Salmo salar) move from fresh- to seawater environments following a seasonally timed preparative transition called smoltification, which takes place under photoperiodic control in the freshwater environment. In masu salmon (Oncorhynchus masou), coordination of photoperiodic sexual maturation is proposed to involve in a fish-specific circumventricular organ, the saccus vasculosus (SV), through its intrinsic opsin-based light sensitivity, thyrotrophin secretion and modulation of deiodinase activity (TSH-DIO cascade). The saccus vasculosus is a highly vascularized structure located on the ventral side of the hypothalamus and its interface between the blood and cerebrospinal fluid also hints at a role in ionic balance of the cerebrospinal fluid (CSF). Both the potential photoperiodic and ionic functions of the SV led us to perform transcriptome analysis of the SV in smoltification in Atlantic salmon. Our data show that SV response to seawater exposure is highly dependent on photoperiodic history and identifies ependymin as a major secretory output of the SV, consistent with a role in control of CSF composition. Conversely, we could not detect crucial elements of the opsin-TSH-DIO cascade suggesting that the photoperiodic history-dependence of the SV to seawater exposure is unlikely to stem from SV-intrinsic responses to photoperiod.

overall_design: RNAseq profiling of saccus vasculosus from Atlantic salmon. Samples were taken from four groups: SPholdFW, SPholdSW, SPLLFW, SPLLSW. SPholdFW and SpholdSW were parr salmon exposed to 16 weeks of short photoperiod conditions. The SPholdFW group were collected from freshwater, the SPholdSW group were exposed to full strength seawater for 24h. The SPLLFW and SPLLSW groups were exposed to 8 weeks short photoperiod conditions and 8 weeks constant light consitions.  The SPLLFW group were collected from freshwater, the SPLLSW group were exposed to full strength seawater for 24h before collection.

first: Shona

last: Wood

first: Marianne

last: Iversen

first: Simen

last: Sandve

first: Even

last: Jørgensen

first: David

last: Hazlerigg


title: Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis (BS-seq)

first: Benjamin

last: Tremblay

type: Methylation profiling by high throughput sequencing

overall_design: BS-seq of methylthioadenosine nucleosidase-deficient Arabidopsis thaliana (Col-0) mutants using tissue from 14 day-old seedlings and unopened flower buds, with and without spermidine supplementation.

first: Saeer

last: Adeel

first: Maye

last: Saechao

first: Yihan

last: Dong

first: Eric

last: Andrianasolo

first: John

last: Steele

first: Annika

last: Traa

first: Nilanth

last: Yogadasan

first: Ishari

last: Waduwara-Jayabahu

first: Barbara

last: Katzenback

first: Markus

last: Wirtz

first: Rüdiger

last: Hell

last: Moffatt


title: SREBP2 ChIP-seq analysis of SREBP2 regulated genes under FBS or cholesterol-depletion condition in HeLa cells

city: Shanghai

first: Wei

last: Qi

overall_design: To investigate the SREBP2 regulated genes, we performed the SREBP2 ChIP-seq in HeLa cells upon cholesterol-depletion to identify the responsive genes in response to cholesterol-depletion.

first: Mengqiang

last: Xu

first: Shiyou

last: Jiang

first: Chenyang

last: Qin


title: Anti-VEGF treatment potentiates ICB responses through a BAFF and IL-12-dependent reprogramming of the TME

city: BETHESDA

first: Cihan

last: Oguz

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

summary: Anti-VEGF treatment has shown clinical activity in combination with checkpoint inhibitor therapy, but the exact mechanism is not known. We show that adding VEGF blockade to the ICB combination of anti-CTLA4 + anti-PD-L1 in cholangiocarcinoma unleashed a therapeutic efficacy driven through a novel multimodal mechanism dependent on BAFF production by T and myeloid cells, leading to a BAFF-dependent proinflammatory B cell response characterized by Germinal center B cell and plasma cell expansion, as well as IL-12 production. Using single cell RNA sequencing (scRNA-Seq) of paired pre- and post-treatment tumor biopsy samples from patients treated with anti-CTLA4, anti-PD-L1 and anti-VEGF, we characterized the treatment-associated immunological changes.

overall_design: We performed single cell RNA sequencing (scRNA-Seq) of liver cancer tumor biopsy samples (pre- and post-treatment) from three patients that contributed a total of seven samples (paired pre- and post- treatment samples from patients 1 and 2, and one pre-treatment and two post-treatment samples from patient 3).

first: Mohamed-Reda

last: Benmebarek

first: Matthias

last: Seifert

last: Ruf

first: Yuta

last: Myojin

first: Kylynda

last: Bauer

first: Patrick

last: Huang

first: Chi

last: Ma

first: Marina

last: Villamor-Payà

first: Francisco

last: Rodriguez-Matos

first: Marlaine

last: Soliman

first: Rajiv

last: Trehan

first: Cecilia

last: Monge

first: Changqing

last: Xie

first: David

middle: E

last: Kleiner

first: Bradford

last: Wood

first: Elliot

middle: B

last: Levy

first: Anuradha

last: Budhu

first: Noemi

last: Kedei

first: Christian

middle: T

last: Mayer

first: Xin

last: Wang

first: Justin

last: Lack

first: William

last: Telford

first: Firouzeh

last: Korangy

first: Tim

last: Greten


title: Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function [CUT&Run]

status: Public on Mar 15 2025

city: Stanford

first: Sai

last: Gourisankar

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

summary: Genes encoding subunits of the BAF (mammalian SWI/SNF) ATP-dependent chromatin remodeling complex are among the those most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not understood. Synaptic activity in neurons is critical for learning and memory and proper neural development. While BAF is required for activity-dependent developmental processes, such as dendritic outgrowth, the immediate molecular consequences of neuronal activity on BAF complexes are unknown. Here we report that neuronal activity induces dramatic remodeling of the subunit composition of BAF complexes within 15 minutes, concurrent with both phosphorylation and dephosphorylation of its subunits. These biochemical effects are a convergent phenomenon downstream of multiple calcium-activated signaling pathways in neurons and fibroblasts and correspond to changes in BAF-dependent chromatin accessibility. Our studies imply that BAF decodes signals at the membrane by altering the combinatorial composition of its subunits.

overall_design: CUTANDRUN: to investigate the targets of the BAF complex in neurons, primary cortical neurons from E16.5 embryonic mice were cultured for 7 days in vitro. Neuronal nuclei were harvested for Brg1 and Smarcc2 CUTANDRUN.

first: Sabin

last: Nettles

first: Wendy

last: Wenderski

first: Joao

last: Paulo

first: Sam

middle: H

last: Kim

first: Kyra

last: Roepke

first: Claire

last: Ellis

first: Hind

last: Abuzaid

first: Steven

last: Gygi

first: Gerald

last: Crabtree


title: Impaired methyl recycling induces substantial shifts in sulfur utilization in Arabidopsis

first: Benjamin

last: Tremblay


title: Transcriptome dynamics in the Arabidopsis male germline during pollen-pistil interactions

city: Lisbon

first: Jörg

middle: Dieter

last: Becker

address: ITQB NOVA Avenida da República

country: Portugal

institute: ITQB

summary: When pollen lands on a receptive stigma, it germinates and extends a tube inside the transmitting tissue of the pistil to deliver the sperm cells for double fertilization. The growth of the pollen tube triggers significant alterations in its gene expression. The extent to which these changes occur in the vegetative cell or extend to the sperm cells transported by the tube is unclear, but important to determine since sperm cells are believed to acquire a competency for fertilization during pollen-pistil interactions. To address these questions, we compared the transcriptomes of Arabidopsis thaliana sperm cells and vegetative nuclei isolated from mature pollen grains with those isolated from in vitro grown pollen tubes. Importantly, we also compared with transcriptomes of sperm cells obtained from pollen tubes grown under semi in vivo conditions where tubes passed through a pistil section. Our data shows that extensive transcriptomic changes occur in sperm cells during pollen tube growth, some of which are elicited only as sperms are carried through the pistil. Their analysis reveals a host of previously unidentified transcripts that may facilitate sperm maturation and gamete fusion. The vegetative cell undergoes even more extensive transcriptomic reprogramming during pollen tube growth, mainly through the upregulation of genes associated with pollen tube growth and vesicle-mediated transport. Interestingly, ATAC-seq data shows that the promoters of genes up-regulated in sperm during pollen tube growth are already accessible in sperm chromatin of mature pollen grains, suggesting pre-configured promoter accessibility. This study's expression data can be further explored here: https://bar.utoronto.ca/eFP-Seq_Browser/.

overall_design: Seeds of a transgenic marker line harbouring MGH3p::MGH3-GFP and ACT11p::H2B-mRFP were sown on soil in short-day conditions (8-h light at 21–23 °C) for 8 weeks and then transferred to long-day conditions (16-h light) to induce flowering. Fresh opened flowers were collected upto 5ml in Falcon tubes and using the previously published protocol, the pollen were cracked. Cracked pollen were then filtered through mesh and sperm cells and vegetative nucleus from mature pollen grain were collected and FACS sorted. The pollen were then germinated on plate or grown semi in vivo for 6h, to collect the sperm cells from the pollen tubes.  Vegetative nuclei were also collected from pollen tubes grown in vitro.

first: Chandra Shekhar

last: Misra

first: António

middle: G

last: Sousa

first: Hasna

last: Khan

first: Asher

last: Pasha

first: Nicholas

last: Provart

first: Michael

last: Borg


title: RNA-seq analysis of WT, SREBP knockout and SREBP2 knockout HeLa cells and liver samples of WT and SREBP2 (F167A) knockin mice

first: Wei

last: Qi

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 1) To investigate the SREBP1- and SREBP2-regulated genes respectively, we estabolished the HeLa cells with either SREBP1 knock-out or SREBP2 knock-out. Then we performed RNA-seq analysis on WT control, SREBP1 and SREBP2 knock-out HeLa cells under FBS or cholesterol-depletion condition. 2) To examine the critical genes/functions regulated by the nuclear condensates of nSREBP2 in vivo, we constructed a SREBP2 (F167A) knockin mice and performed RNA-seq analysis using the liver samples of WT and F167A mice after fast or refeeding conditions.

first: Mengqiang

last: Xu

first: Shiyou

last: Jiang

first: Chenyang

last: Qin


title: Exposure of human cholangiocytes to 1,2-dichloropropane in the presence of macrophages induces base-excision repair-related genes in vitro

city: Tokyo

first: Gaku

last: Ichihara

address: 6-3-1 Niijuku, Katsushika-ku

institute: Tokyo University of Science

summary: 1,2-dichloropropane (1,2-DCP), a synthetic organic solvent, has been implicated in causality of cholangiocarcinoma. 1,2-DCP from Group 3 to Group 1. 1,2-DCP-induced occupational cholangiocarcinoma show a different carcinogenic process compared to common cholangiocarcinoma. However, the mechanism of 1,2-DCP induced carcinogenicity in cholangiocytes remains elusive. We reported previously that exposure of MMNK-1 cholangiocytes co-cultured with THP-1 macrophages, but not monocultured MMNK-1 cholangiocytes to 1,2-DCP induced activation-induced cytidine deaminase (AID) expression, DNA damage and ROS production. The aim of this study was to identify relevant biological processes or target genes expressed in response to 1,2-DCP, using an in vitro system where cholangiocytes are co-cultured with macrophages. The co-cultured cells were exposed to 1,2-DCP at 0, 0.1, and 0.4 mM for 24 hours and the cell lysates, assessed by transcriptome analysis. 1,2-DCP upregulated the expression of base excision repair genes in MMNK-1 cholangiocytes in the co-cultures, whereas it upregulated the expression of cell cycle-related genes in THP-1 macrophages. Activation of the base excision repair pathway might result from the previously observed DNA damage in MMNK-1 cholangiocytes co-cultured with THP-1 macrophages. Cross talk interactions between cholangiocytes and macrophages could explain the observed increase in DNA damage in the cholangiocytes.

overall_design: Transcriptomic profiles of 3 replicates of co-culture of MMNK-1 cholangiocytes and THP-1 macrophages using membrane-seperated transwell system, exposed to 1,2-DCP (0mM, 0.1mM, 0.4mM) for 24 hours.

first: Abigail

last: Ekuban

first: Shigeyuki

last: Shichino

first: Cai

last: Zong

first: Frederick

first: Kazuo

last: Kinoshita

first: Sahoko

first: Kouji

last: Matsushima


title: Stellate cells are in utero markers of pancreatic disease in cystic fibrosis[RNA-seq]

first: Ann

last: Harris

summary: Pancreatic fibrosis is an early diagnostic feature of the common inherited disorder cystic fibrosis (CF). Many people with CF (pwCF) are pancreatic insufficient from birth and the replacement of acinar tissue with cystic lesions and fibrosis is a progressive phenotype that may later lead to diabetes. Little is known about the initiating events in the fibrotic process though it may be a sequela of inflammation in the pancreatic ducts resulting from loss of CFTR impairing normal fluid secretion. Here we use the sheep model of CF (CFTR-/-) to examine the evolution of pancreatic disease through gestation. Transcriptomic evidence from bulk RNA-seq showed alterations in the CF pancreas by 65 days of gestation, which are accompanied by marked pathological changes by 80 days gestation. These include a profound fibrotic response, confirmed by immunostaining for COL1A1, SMA and SPARC, together with acinar destruction. Moreover, using scRNA-seq we identify a unique cell population that is significantly overrepresented in the CF animals at 80- and 120-days gestation, as are activated stellate cells at term. This cellular imbalance likely has a pivotal role in the evolution of CF pancreatic disease and may provide therapeutic opportunities to delay or prevent CF pancreatic destruction.

overall_design: RNA-seq of sheep (ovis aries) tracheal epithelial tissue

first: Shih-Hsing

last: Leir

first: Alekh

last: Paranjapye

first: Jenny

middle: L

last: Kerschner


title: Sin1-mTORC2 Augments Lipid Anabolism of Tumor-associated Macrophages to Limit the Type I Interferon-dependent Anti-tumor Immunity

first: Jingsi

last: Jin

address: 280 South Chongqing Rd.

institute: Shanghai Jiaotong University

summary: The biological consequences and mechanisms of metabolic reprogramming of macrophages in the tumor microenvironment (TME) remain largely elusive. Here we showed, in part by myeloid-specific ablation of Sin1, a key component of mammalian target of rapamycin complex (mTORC) 2, that the Sin1-mTORC2-Akt-sterol regulatory element-binding proteins (SREBPs) signaling was augmented in tumor-associated macrophages (TAMs), leading to excessive lipid synthesis and accumulation, which consequently impaired the STING-dependent type I interferon production and CD8+ T cell mediated anti-tumor immunity. The ability of Sin1 deficiency in TAMs to inhibit lipid synthesis and enhance anti-tumor immunity could be blunted by the accumulation of cholesterol/lipids in TAMs. Furthermore, genetic ablation of Sin1 in TAMs or pharmacologic inhibition of lipid anabolism acted synergistically with immune checkpoint blockade (ICB)-based cancer therapy to control tumor growth. Finally, elevated Sin1-mTORC2-Akt activity and lipid anabolism as well as decreased type I IFN responses were all observed in TAMs from human colon cancers and tightly associated with poor patient survival. Together, our study uncovers a novel role of Sin1-regulated lipid anabolic pathway in TAMs which acts as a metabolic checkpoint for anti-tumor immunity via limiting a STING-dependent type I IFN response.

overall_design: 1. To understand how Sin1 may regulate the anti-tumor activity of TAMs at the molecular level, we isolated WT and Sin1-deficient TAMs from day14 Lewis lung carcinoma (LLC)-bearing Sin1fl/fl (WT) and LysMCre;Sin1fl/fl (cKO) mice to perform RNA-seq. 2. To understand if Sin1 deletion may specifically affect type I IFN signaling in TAMs but not peripheral macrophages,  we compared the transcriptional profile in TAMs with that from splenic macrophages in day14 LLC-bearing WT mice.


title: MYL4 identifies intramural anatomy of Purkinje fibers in human hearts

city: Rochester

first: Atta

last: Behfar

state: MN

address: 200 1st St SW

department: Cardiovascular Diseases

institute: Mayo Clinic

summary: ABSTRACTBACKGROUND: Cardiac Purkinje fibers (PFs) orchestrate myocardial synchrony but in regions of myocardial scarring driver ventricular arrhythmia. It is hypothesized that arrhythmias refractory to ablation may be driven by PFs deep in the scarred myocardium. However, knowledge of human PF anatomy remains reliant on data generated in animal models, obscuring understanding of the substrate underpinning dysrhythmia and pacing strategies. OBJECTIVES: Establish and utilize a human biomarker to delineate PF anatomy in humans. METHODS: RNA-sequencing and differential expression analysis of transcriptomes from human hearts (n=10) revealed 99 genes upregulated in PFs versus ventricular myocardium and endocardium. Whole mount megablock cross sectional analysis was performed with cardiac troponin, MYL4, PAS, Masson’s Trichrome, pro-ANP, and GJA5 colocalization. RESULTS: Comparative transcriptomics from human hearts (n=10) identified Myosin light chain 4 (MYL4) as a promising human PF marker for distinguishing conductive from contractile myocardium. Using PF rich bundle branch and subendocardial regions, MYL4 specificity was validated using canonical PF markers in human (n=3), dog (n=3), goat (n=3), and pig (n=3) hearts. Cross sectional histology of the entire human ventricular myocardium uncovered a deep seeded network of transmurally intercalated, MYL4 positive PFs. This previously unrecognized distribution of the cardiac conduction system accounted for over 60% of human myocardial PF content. CONCLUSIONS: Such significant intramural prevalence exposes limitations associated with treatment approaches based on dogma that PF anatomy is restricted to subendocardium. MYL4 here enabled a comprehensive visualization of human cardiac conduction system, offering an intricate bioanatomical map for heart rhythm management.

overall_design: RNA-seq performed on Cardiac Purkinje fibers, ventricular myocadial, and endocardial transcriptomes isolated from health human donor hearts (n=10).

first: Matthew

last: Hillestad

last: Amontree

first: Ryan

middle: C

last: Mahlberg

first: Monique

last: Bagwell

first: Skylar

last: Rizzo

first: D

last: Arrell

first: Kobra

middle: P

last: Kargaran

first: Ruben

last: Crespo-Diaz

first: Faisal

middle: F

last: Syed

first: Elli

middle: N

last: Jacobson

first: Tyra

last: Witt

first: Paul

last: Stalboerger

first: Andre

last: Terzic

first: Christopher

last: McLeod

middle: V

last: DeSimone

first: Samuel

last: Asirvatham


title: Dbf4-Dependent Kinase Finetunes INO80 Function at Chromosome Replication Origins

city: Planegg

first: Priyanka

last: Bansal

state: Bavaria

address: Großhaderner Str. 9

department: Molecular Biology

institute: Biomedical Center

summary: The highly conserved Dbf4-Dependent Kinase (DDK) plays a pivotal role in the nucleus during S phase, where it directly phosphorylates the replicative helicase, the minichromosome maintenance (MCM) complex. This leads to the initiation of chromosome replication. However, aside from the MCM complex, few other targets have been identified to date, leaving DDK an understudied kinase. Here, we describe a two-pronged mass spectrometry-based approach and define the nuclear DDK-dependent phosphoproteome, which consists of approximately 400 phosphorylation events. Within this network, we found that DDK directly phosphorylates the Arp8 subunit of the multi-subunit chromatin remodeler complex INO80. Arp8 phosphorylation stabilises INO80's intramolecular complex integrity, which finetunes its nucleosome spacing activity at replication origins. This adjustment of origin chromatin architecture stimulates replication and is important for the response to replication stress. Our results represent a significant advance in our understanding of the molecular mechanisms underlying the regulation of replication origins.

overall_design: It was tested whether DDK phosphorylation of INO80 might influence nucleosome positiong at origins of relication. Nucleosome positioning analysis was performed using MNase-seq data obtained remodeling of SGD (salt gradient dialysis) chromatin by INO80 WT and INO80-AA mutant purified protein. Futher, to test if changes in nucleosome positioning is because of DDK dependent phosphorylation, we treated our purified INO80 and INO80-AA protein with Lamda phosphatse, rephosphorylated with DDK and repurified the proteins to perform nucleosome positioing assay. We also tested nucleosome positioning in vivo in WT and ARP8 mutant strain by isolating nuclei. Atleast two biological for each experiment were performed.

first: Shibojyoti

last: Lahiri

first: Chandni

last: Kumar

first: Lorenzo

last: Galanti

first: Erika

last: Chacin

first: Jessica

last: Furtmeier

first: Garp

last: Linder

first: María

middle: A

last: Ortíz-Bazán

first: Marisa

last: Müller

first: Petra

last: Vizjak

first: Tobias

last: Straub

first: Felix

last: Mueller-Planitz

first: Johannes

last: Stigler

first: Andrés

last: Aguilera

first: Belen

last: Gómez-González

first: Boris

last: Pfander

first: Axel

last: Imhof

first: Christoph

last: Kurat


title: Riclin: A novel soluble dietary fiber for promoting gastric health and ameliorating gastric mucosal injury

city: bengbu

first: sun

middle: qi

last: ketizu

address: donghai street 2600

institute: Bengbu Medical University

summary: Focal and diffuse damage to the gastric mucosa contributes to gastric mucosal injury (GMI). Dietary fiber may exert protective effects against GMI; however, its use as a gastrointestinal intervention remains limited. Here, we assessed the potential role of dietary fiber Riclin in GMI. Dietary fiber Riclin exerted a dual effect in enhancing gastric mucosal defense. It modulated microbial-metabolite composition, enhancing biological barriers and reinforcing sustained adhesion to the gastric mucus bicarbonate barrier. Additionally, Riclin enhanced the gastric mucosal immune barrier through the NOD/TLR4/NF-κB pathway. The protective role of Riclin in GMI was revealed by constructing an alcohol-induced murine gastric ulcer model. Our results propose Riclin as a novel dietary fiber with the potential to ameliorate a wide range of gastric disorders characterized by a disrupted gastric mucosal defense and immune dysregulation. In particular, we underscore its potential as a promising dietary fiber for promoting gastric health.

overall_design: To investigate the effect of Riclin on the gastric mucosal defense barrier, 20 mice were randomly selected and divided into a control (saline) and Riclin (20 mg/kg) group with continuous gavage administration for 14 d. On the final day, stools were collected from the mice, rapidly frozen in liquid nitrogen, and transferred to a refrigerator (-80 ℃) until subsequent testing. To assess the prophylactic effect of Riclin on gastric mucosal injury, ethanol-induced gastric mucosal damage was adopted as a pathological model. Mice were randomly divided into six groups (n = 10/group): the control and model groups were administered saline (0.9%); the omeprazole group was administered omeprazole at a dose of 20 mg/kg; and the experimental groups were administered 5, 10, or 20 mg/kg Riclin. All groups were subjected to continuous gavage administration for 14 d, after which the mice were fasted from food for 24 h before a final gavage treatment. One hour later, all mice, excluding the control group, were administered 0.15 mL/10 mg anhydrous ethanol with 3 h of induction.All mice were euthanized via cervical dislocation after anesthesia. Blood samples were collected from the eye socket, and serum samples were obtained. The stomach of each mouse was cut along the greater curvature and removed. Gastric contents were collected and centrifuged at 1,000 g for 10 min. Hydrogen ion concentration in the stomach content was analyzed using a digital pH meter. Subsequently, the mucus of gastric mucosa was obtained by gently scraping it with a glass slide and weighed on a precision analytical balance. The gastric surface was rinsed with ice-based phosphate-buffered saline (PBS), and surface lesions were observed and scored. A portion of the stomach was stored at -80 °C for biochemical analyses, while the other portion was processed for histopathological, immunohistochemical, and immunofluorescence analyses.

last: Li

first: Xiaqing

last: Sun

first: Qiankun

last: Ding

first: Ying

last: Hu

first: Mengzhen

last: Jia

first: Yizhuo

last: Fan

first: Qian


title: Lentinula edodes Cultured Extract Intake at Puberty Mitigates Inflammatory Signals at the Mammary Glands by the Involvement of Epigenetic Mechanisms.

city: ottawa

first: Hamed

last: Yasavoli Sharahi

state: ontario

address: 451 Smyth Rd

institute: university of ottawa

type: Methylation profiling by genome tiling array

summary: Exposure to immune stress or lipopolysaccharide (LPS) during critical developmental stages, particularly puberty, may result in gut microbiome dysbiosis and disturb epigenetic regulation in mammary glands. This disruption can affect gene expression and potentially increase breast cancer susceptibility later in life. While the adverse effects of LPS on intestinal and brain function are documented, its impact on mammary glands is not well understood. An immunocompetent murine model (BALB/c mice) was administered an acute dosage of LPS during the pubertal stage. The study aimed to comprehensively evaluate the enduring effects of LPS exposure, as well as LPS exposure in combination with AHCC (Lentinula Edodes Cultured Extract), on various parameters, including DNA methylation patterns, cytokine profiles, and microRNA expression within the mammary gland during adulthood, at the age of 9 weeks. Analysis was carried out using DNA methylation sequencing, multiplex immunoassays, quantitative PCR, and image processing.Our findings revealed significant and enduring dysregulation in DNA methylation patterns, cytokine levels, and microRNA expression in the mammary glands exposed to LPS during puberty. These dysregulations significantly impacted critical signaling pathways related to mammary gland growth and potential breast cancer development. Notably, we observed hypermethylation of the transcriptional start sites (TSS), promoters, and 5' UTRs of critical genes, including Vav3, Pdgfa, Pdgfc, Jag2, Hras, Ksr1, Il2rb, Il17b, and Il17rb in the LPS group, whereas hypomethylation was evident in the prebiotic+LPS group. The multiplex immunoassays and quantitative PCR confirmed these findings. LPS exposure during puberty causes long-lasting epigenetic and inflammatory alterations in the mammary glands, which could influence breast cancer risk. The use of AHCC as a mitigating factor suggests potential for dietary interventions to prevent or reduce these effects.

overall_design: This study investigates the long-term effects of pubertal exposure to lipopolysaccharide (LPS) and prebiotic supplementation on the gut microbiota and immune system in female BALB/c mice. A total of 36 mice were divided into two dietary intervention groups: the prebiotic group, which received AHCC (2 g/kg BW/day) in drinking water, and the control group, which received regular drinking water. At the onset of puberty, defined by vaginal opening at five weeks of age, half of the mice in each group were intraperitoneally injected with LPS (1.5 mg/kg body weight) to induce inflammation and gut dysbiosis, while the remaining half received sterile PBS as a control. This resulted in four experimental groups, with nine mice per group: control + PBS, control + LPS, prebiotic + PBS, and prebiotic + LPS. The dietary intervention continued for one week after injection, followed by a standard diet until early adulthood. At nine weeks of age, the mice were sacrificed, and mammary gland tissue samples were collected for molecular analysis. DNA methylation profiling was performed using the Infinium™ Mouse Methylation BeadChip (Illumina), cytokine expression was measured using a multiplex Luminex immunoassay, and gene expression analysis was conducted via RT-qPCR for microRNA profiling. The study includes biological replicates (n=9 per group) and was designed to evaluate the impact of LPS exposure and prebiotic supplementation on immune modulation and epigenetic alterations. Control and experimental conditions were carefully structured to enable comparisons of differential methylation, cytokine expression, and miRNA regulation across the treatment groups.

last: Yasavoli-Sharahi

first: Roghayeh

last: Shahbazi

first: Nawal

last: Alsadi

first: Nasim

last: Bondar Sahebi

first: Cyrille

last: Cuenin

first: Vincent

last: Cahais

first: Felicia

last: Fei-Lei Chung

first: Zdenko

last: Herceg

first: Chantal

last: Matar


title: RNA-seq analysis of genes differentially expressed in NCI-H1299 cells with platensimycin (PTM) derivative 6p treatment

city: Changsha

first: danfeng

last: cao

state: Hunan

address: Xiangya International Academy of Translational Medicine, Central South University, No. 172, Tongzipo Road, Yuelu District, Changsha City, Hunan Province

institute: central south university

summary: In order to characterize the global transcriptional effect and evaluate the impact of PTM derivative 6p on non-small cell lung cancer NCI-H1299 cell gene expression. NCI-H1299 cells were treated with vehicle (0.1% DMSO) or 25 μM 6p for 48 h and assessed the gene expression pattern by RNA-Seq. Finally, we show that extensive, coordinated effects of 6p on the transcriptional activity of genes within pathways controlling tumor cell metabolism, proliferation, and survival. Especially, the expression of key genes in de novo lipid synthesis were significantly reduced.

overall_design: NCI-H1299 cells were cultured in 10% serum medium. Six samples obtained from NCI-H1299 cells including vehicle (0.1% DMSO) and 25 μM 6p treatment group were analyzed. Three independent samples were analyzed for each group.

first: Danfeng

last: Cao

first: Jie

last: Yang

first: Yanwen

last: Duan

first: Yong

last: Huang


title: The regulatory mechanisms of SIS3 on bone marrow-derived NK (BM-NK) cells under TGF-β stimulation using RNA sequencing

city: Hong Kong

first: Guang-yu

last: Lian

address: Li Ka Shing Medical Sciences Building, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin

department: Medicine and Therapeutics

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: To explore the underlying mechanisms of SIS3 attenuating TGF-β-induced immunosuppression on NK cells, RNA-sequencing was performed on primary BM-NK cells under TGF-β stimulation with or without SIS3 pre-treatment.

overall_design: BM-NK cells pre-incubated with 10μM SIS3 for 3 hours were stimulated with 5ng/ml TGF-β1 for another 3 hours. Then cells were harvested as Ctrl group (no stimulation nor SIS3 pre-treatment), T group (with TGF-β simulation but no SIS3 pre-treatment) and SIS group (with TGF-β simulation and SIS3 pre-treatment) and subjected for RNA sequencing.

first: Guang-Yu

first: Yingpeng

last: Wan

first: Qing-Ming

last: Wang

first: Thomas

middle: S

last: Mak

first: Jinfeng

last: Zhang

first: Zi-Ying

first: Min

last: Li

first: Xiao-Ru

first: Chun-Sing

last: Lee

first: Xue-Qing

last: Yu

first: Hui-Yao

last: Lan