title: High rate triggers increased atrial release of BMP10, a biomarker for atrial fibrillation and stroke, and BMP10 affects ventricular cardiomyocytes

city: Hamburg

first: Laura

last: Sommerfeld

address: Martinistr. 52

institute: UKE Hamburg

summary:
Background
Bone morphogenetic protein 10 (BMP10) is a ligand of the TGFβ superfamily secreted mainly by atrial cardiomyocytes. Elevated BMP10 blood concentrations predict atrial fibrillation (AF), AF recurrence after ablation and AF-related cardiovascular complications like stroke. The conditions increasing BMP10 secretion and downstream effects of BMP10 in cardiomyocytes are poorly understood. We assessed BMP10 secretion dynamics and BMP10 effects in a human 3D model of atrial and ventricular engineered heart tissue (EHT).
Methods
Cardiomyocytes differentiated from human induced pluripotent stem cells (atrial and ventricular) were cast into a fibrin-matrix to generate EHT. Atrial EHTs were optogenetically paced (3-5 Hz) or maintained at intrinsic beating rate for 24 h up to 15 days. Release of BMP10 and other cardiac biomarkers from EHT were quantified. BMP10 plasma concentrations were compared between 1370 patients in different atrial rhythm at blood draw. Additionally, ventricular EHTs were exposed to BMP10 for 10 days.
Results
Atrial but not ventricular EHT released BMP10 within 48 h of culture. High rate optogenetic pacing increased atrial EHT BMP10 release by ~3-fold after a latency of at least 24 h post pacing initiation. BMP10 plasma concentrations were elevated in patients with documented AF compared to sinus rhythm and even higher in patients with current AF. BMP10 induced upregulation of TGFβ pathway transcripts, increased expression of genes related to AF and heart failure, including PITX2 and NPPB, and increased relative contraction times in ventricular EHTs.
Conclusions
High atrial rates elevate BMP10 expression and release, and higher plasma concentrations of BMP10 are observed in patients with active AF. BMP10 exposure induces transcriptomic changes linked to AF and heart failure in ventricular EHT. These findings support BMP10 as a biomarker and potential mediator of AF-related remodeling and tachycardiomyopathy.

overall_design: Effects of BMP10 on ventricular EHT (vEHT) were assessed by longer-term (10 days) exposure of vEHT to recombinant human BMP10 (rhBMP10, 2926-BP-025, R&D Systems, Minneapolis, USA) dissolved in water containing 0.1% bovine serum albumin and 4 mM HCl (vehicle). RNA was harvested and subjected to RNAseq.

first: Jessica

last: Schrapers

first: Justus

last: Stenzig

first: Larissa

last: Fabritz


title: Single-cell RNA Sequencing Analysis Reveals Cell Landscape and Gene Signatures Associated with Granulomatous Lobular Mastitis

status: Public on Oct 14 2025

city: Beijing

first: Junyue

last: Wang

address: No. 23, Art Museum Back Street, Dongcheng District.

department: Department of Breast

country: China

institute: Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical University

type: Expression profiling by high throughput sequencing

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study granulomatous lobular mastitis (GLM), a chronic inflammatory breast disease characterized by granuloma formation and recurrent abscesses. GLM is considered an immune-mediated disorder, yet its underlying pathogenesis remains poorly defined. This study is the first to perform single-cell transcriptomic profiling of GLM tissue and provides new insights into the cellular landscape and immune dysregulation associated with GLM.

overall_design: Fresh breast tissue samples from 3 patients with granulomatous lobular mastitis (GLM) and 3 healthy controls were surgically obtained.  Single-cell suspensions were prepared and subjected to single-cell RNA sequencing (scRNA-seq) using the 10x Genomics Chromium Single Cell 3′ v3 platform.

first: Yifei

last: Zeng

first: Mengjie

first: Dongxiao

last: Zhang

first: Xulong


title: Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress

city: Gent

first: Koen

last: Deserranno

address: Ottergemsesteenweg 460

department: Department of Pharmaceutics

country: Belgium

institute: Ghent University

summary: In this study, we developed a novel plate-based 10X-compatible (PB10X) scRNA-seq strategy. By leveraging the Smart-seq3xpress (SS3X) principle, PB10X supports single-cell indexed sorting and cDNA generation that is downstream compatible with any commercially available 10X Single Cell 5' library construction kits such as the 10X Single Cell 5' Gene Expression and 5' V(D)J library construction kits. We demonstrated PB10X's performance on Jurkat T lymphoblasts by generating gene expression and V(D)J sequencing libraries, benchmarking it against 10X and SS3X.

overall_design: scRNA-seq;Smart-seq3xpress profiling of Jurkat cells

first: Elise

last: Callens

first: Dieter

last: Deforce

first: Filip

last: Van Nieuwerburgh


title: CHD7 Regulates Cardiac Neural Crest Cell Differentiation Through SOX5-Mediated Self-Activation

city: Augusta

first: Kai

last: Jiao

state: GA

address: 1120 15th Street, Rm. CA4098

department: Center for Biotechnology and Genomic Medicine

country: USA

institute: Augusta University

summary: CHARGE syndrome, primarily caused by CHD7 haploinsufficiency, is a complex developmental disorder frequently associated with congenital heart defects. Our comprehensive single-cell RNA sequencing analysis of cardiac neural crest cells (cNCCs) with Chd7 inactivation reveals impaired myocyte differentiation by cNCCs as a major cellular defect; loss of Chd7 disrupts myogenic transcriptional programs, alters cell fate trajectories, and activates cellular stress responses. These results significantly advance our understanding of the NCC-autonomous role of CHD7 and the mechanisms underlying CHARGE-associated heart defects driven by cNCC dysfunction. We further discovered that CHD7 enhances its own expression through interaction with SOX5 at an upstream, evolutionarily conserved enhancer. Notably, SOX5 overexpression in cultured Chd7-haploinsufficient cNCCs restores Chd7 expression from the intact allele, and rescues myocyte differentiation. These findings uncover a SOX5-mediated Chd7 autoregulatory mechanism and suggest that enhancing the SOX5-CHD7 axis may represent a promising strategy to mitigate cardiovascular defects caused by CHD7 insufficiency.

overall_design: GFP+ cells were isolated by fluorescence-activated cell sorting from the PA3–6 trunk and outflow tract (OFT) regions of control (Wnt1-Cre2; R26 +/mtmg; Chd7 +/+) and mutant (Wnt1-Cre2; R26 +/mtmg; Chd7 loxp/loxp) embryos at E10.5. Cells were pooled from three embryos of the same genotype. Single-cell transcriptome libraries were prepared using the 10x Genomics Chromium Single Cell 3ʹ v3 Reagent Kits, following the manufacturer’s standard protocol.

first: Shun

last: Yan

first: Andrey

last: Bombin

first: Jiao

last: Kai


title: Analgesia through FKBP51 inhibition at disease onset confers lasting relief from sensory and emotional chronic pain symptoms

city: London

first: Sandrine

last: Géranton

address: Medawar Building, Malet Place

department: Cell and Developmental Biology

country: United Kingdom

institute: University College London

summary: Chronic pain affects 20-30% of the population and imposes a significant socio-economic burden as it is often accompanied by substantial emotional comorbidities such as anxiety and depression. Yet, the mechanisms underlying the interactions between the sensory and emotional aspects of chronic pain remain poorly understood. Here, we investigated the role of FKBP51, a regulator of the stress response, in mediating both sensory and emotional symptoms of chronic pain. Inhibition of FKBP51, via genetic deletion or pharmacological blockade, in persistent joint pain reduced fast-onset sensory, functional and activity-related symptoms, as well as late anxio-depressive comorbidities. FKBP51 inhibition after the establishment of the hypersensitive state provided only temporary symptoms relief, while acute inhibition at disease onset protected from the full development of sensory and anxio-depressive symptoms for up to 6 months. Our results also indicated that early pain symptoms could predict the late sensory and emotional outcomes of chronic pain. RNA sequencing of spinal cord tissue revealed that late FKBP51 inhibition transiently altered nociceptive genes associated with mechanical hypersensitivity. In contrast, early inhibition persistently downregulated the Naaa gene, a key regulator of the transition to chronic pain, and reorganized spinal cilia. Our results indicate that early FKBP51 inhibition after injury can persistently reduce chronic pain and prevent the onset of associated emotional comorbidities by modulating critical spinal neurobiological pathways that play pivotal roles in the transition to chronic pain.

overall_design: RNA Sequencing (NextSeq 500, Illumina) of mouse lumbar (L4-l6) spinal cord on day 30 after injection of sodium iodoacetate (MIA; 1 mg) into the knee joint. The aim of the study was to establish the mechanisms conferring anti-allodynia by the FKBP5 inhibitor SAFit2 in the MIA model of osteoarthritis and the influence of time of SAFit2 administration. Early samples were injected with vesicular phospholipid gel (VPG)-SAFit2 on days -3 before MIA and day 4 after MIA whilst late samples were injected on days 20 and 27 after MIA. Matched vehicle injections (VPG) occured at the same time points.

first: Sara

last: Hestehave

first: Roxana

last: Florea

first: Samuel

last: Singleton

first: Alexander

middle: J

last: Fedorec

last: Caxaria

first: Oakley

last: Morgan

first: Katharina

last: Tatjana Kopp

first: Laurence

middle: A

last: Brown

first: Tim

last: Heymann

first: Shafaq

last: Sikandar

first: Felix

last: Hausch

first: Stuart

middle: N

last: Peirson

middle: M


title: ChIP-Seq analysis of DMTF1 in mouse neural stem cells; ChIP-Seq analysis of H2AZ in mouse neural stem cells with or wihtout Dmtf1 knockdown.

status: Public on Oct 15 2025

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neural stem cells (NSCs) contribute to embryonic brain development and adult brain homeostasis via their unique properties of self-renewal and differentiation. The Cyclin D binding Myb‑like transcription factor 1 (DMTF1) is reported to be a tumor supressor gene in cancer cells. However,the role of DMTF1 in NSCs is poorly understood. The aim of this study is to determine the role of Dmtf1 in NSCs and elucidate the underlying mechanism.

overall_design: DMTF1 ChIP-Seq in mNSCs; H2AZ ChIP-Seq in mNSCs without and with treatment shRNAs against mouse Dmtf1.

first: Yajing

last: Liang

middle: V

first: Derrick

middle: S

last: Ong


title: Notch-dependent functional conversion of RUNX factors regulates the initiation of T-lineage program [RNA-seq]

city: Isehara

first: Hiroyuki

last: Hosokawa

address: 143 Shimokasuya

department: Immunology

country: Japan

institute: Tokai Univ

summary: RUNX factors play an essential role in the development of T cell. Dynamic interacting partner switching of RUNX1 induces the redeployment of RUNX1 at the T-lineage commitment checkpoint. Here, we attempted to reveal functional differences in RUNX factors between lymphoid progenitor (LP) and Noth-stimulated the earliest T progenitor stage, phase1. We identified CTCF as a LP-specific RUNX1-interacting partner. Indeed, LP-specific RUNX1 binding genomic sites had significantly enriched CTCF consensus motif and co-occupied with CTCF. After Notch stimulation, Notch1-IC directly interacted with RUNX1 and recruited it to the Notch-regulated T-signature gene loci with the Mediator/p300 transcriptional activation complex. CRISPR/Cas9-mediated stage-specific deletion of RUNX factors and its binding partners revealed that the RUNX1/CTCF complex in LP and the RUNX1/Mediator/p300 complex in phase1 negatively and positively regulate T-signature genes expression, respectively. Our results indicate that the Notch-mediated functional conversion of RUNX factors; re-organization of protein complexes and redeployment of genomic binding sites, has a crucial role in the initiation of T-lineage program.

overall_design:
Cas9-LPs with or without Notch stimulation were transduced with various sgRNAs.
Total RNA was isolated from samples of 3 × 105 cultured cells using a RNeasy Micro Kit (Qiagen).  500 ng of total RNA was subjected to the 3’mRNA library preparation with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (LEXOGEN) according to the manufacturer’s instructions.  After the PCR step, size distribution and yield of the library was determined by the D1000 high sensitivity tape station (Agilent) or Agilent High Sensitivity DNA kit on the bioanalyzer (Agilent).  The pooled libraries were loaded on the Illumina Nextseq500 platform and analyzed by 75bp single read.

first: Yuichi

last: Kama

first: Ken-ichi

last: Hirano

first: Kaori

last: Masuhara

first: Yusuke

last: Endo


title: Interferon Dependent Immune Memory during HSV-1 Neuronal Latency via Increased H3K9me3 and Restriction by ATRX

city: Charlottesville

first: Abigail

last: Whitford

state: Virginia

address: 1340 Jefferson Park Ave, Apt 305

department: Microbiology

institute: University of Virginia

summary: Herpes simplex virus-1 (HSV-1) establishes a latent infection in neurons, periodically reactivating to cause disease. Neuronal conditions, including immune signaling, during initial HSV-1 infection, impact later reactivation. Type I interferon (IFNα) exposure during initial infection results in promyelocytic leukemia nuclear-body (PML-NB) formation and subsequent restriction of reactivation, via mechanisms that were unknown. Here we find that PML-NB formation results in the recruitment of histone chaperones to the viral genome and increased enrichment of the repressive heterochromatin mark, histone H3 lysine 9 tri-methylation (H3K9me3), and its reader, ATRX (alpha-thalassemia/mental retardation, X-linked). ATRX is highly abundant in neurons and prevents reactivation from H3K9me3-bound latent genomes by remaining associated with viral chromatin. Therefore, we demonstrate how immune signaling during initial infection results in an epigenetic memory on HSV-1 genomes and identify ATRX as a neuronal restriction factor against HSV-1 reactivation, elucidating a new potential target for inhibiting HSV-1 reactivation and subsequent human disease.

overall_design: CUT&Tag of H3K9me3 in primary murine neurons latently infected with HSV-1. Neurons were either treated or untreated with Interferon alpha at the time of infection with HSV-1.

middle: L

first: Gaelle

last: Auguste

first: Alison

last: Francois

first: Chris

last: Boutell

first: Clint

last: Miller

first: Sarah

last: Dremel

first: Anna

middle: R

last: Cliffe


title: Protein disulphide isomerases regulate androgen receptor stability and promote prostate cancer cell growth and survival

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: Cancer cells exhibit accelerated protein production to accommodate their high metabolic demands. This elevated protein load creates a dependency on endoplasmic reticulum-resident proteins and chaperones, which are required to maintain proteostasis. In this study, we identify the protein disulfide isomerases (PDIs) PDIA1 and PDIA5, which play a critical role in folding of client proteins in the ER, as important regulators of prostate cancer growth and therapy response. PDIA1 and PDIA5 are upregulated in prostate cancer and induced by the androgen receptor (AR) signalling axis. Genetic or pharmacological targeting of PDIA1/PDIA5 causes mitochondrial dysfunction, growth inhibition and apoptosis of prostate cancer cells in vitro and in vivo. Loss of PDIA1/PDIA5 activity leads to AR ubiquitination and degradation, revealing the existence of a feedback loop between these chaperones and the AR pathway. Mechanistically, PDIA1/PDIA5 regulate AR stability by catalysing disulfide bond formation in AR, an activity that requires cysteines 670 and 845 in AR’s ligand-binding domain. Importantly, targeting PDIAs sensitizes prostate cancer cells to the AR antagonist, enzalutamide. Collectively, this study reveals a novel mechanism governing AR proteostasis in prostate cancer and positions PDIA1/5 as viable therapeutic targets.

overall_design: RNA-seq profiling of LNCaP cells following siRNA-mediated knockdown of PDIA1 or PDIA5 for 48h and 96h

first: Shashikanth

last: Marri

first: Jianling

last: Xie


title: Transcriptomic analysis of flies at different days of starvation

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary:
Purpose: Adaptation to changing environmental conditions is essential for survival. When animals adapt to nutrient shortage, intra-organ responses as well as inter-tissue crosstalk mechanisms need to be mounted to coordinate whole-body energy homeostasis. To address this we collected flies at different day of starvtion for transcriptomic analysis
Methods: snRNA-seq analysis of whole-body flies (without heads) at fed, day2 and day5 of starvation
Results: The data provides information of transcriptome alternations related to adaptation of staravtion, including expression of metabolic genes and organ communications.
Conclusions: Expression of many metabolic genes were changed during staravtion and oenocytes play a role in this adaptation

overall_design: The following genotypes were used: PromE-gal4, Tub-gal80ts

first: Huang

last: Kerui

first: Dibra

last: Indira

first: Chen

last: Weihang

first: Hu

last: Yanhui

first: Perrimon

last: Norbert


title: Single cell landscape of extramedullary AML

first: Livius

last: Penter

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: The immune landscape of extramedullary AML remains largely uncharacterized. Here we performed single cell RNA sequencing on cryopreserved eAML samples to define the immune cell landscape and transcriptional profiles associated with extramedullary tropism.

overall_design: Digestion of tissue biopsies, cryopreservation, thawing, resuspension in PBS with 0.04% BSA followed by 5' scRNA-seq and scTCR-seq using 10x Genomics platform

first: Catherine J.

last: Wu


title: Engineered cardoon calli as novel platform for production of renewable feedstock

city: Milano

first: Raul

last: Pirona

address: Via Alfonso Corti 12

country: Italy

institute: IBBA-CNR

summary: In this study, we investigated transcriptomic changes in two cardoon (Cynara cardunculus L. var. altilis) calli cell cultures lines engineered for production of valuable fatty acids, therefore suitable for large-scale production of biofuel precursors, as alternative to triacylglycerols (TAGs) engineered plants. Namely to gain insight in the molecular effects of genetic transformation, we analyzed the transcriptome of SAD-OE line (overexpressing stearic acid desaturase), and FAD-KD (a fatty acid desaturase RNA interference line, FAD2.2-RNAi) accumulating oleic and linoleic acids, respectively. Differentially expressed genes (DEGs) involved in fatty acid metabolism and streamed pathways such as glycolysis, pyruvate, glycerolipid, and glycerophospholipid metabolism, were enriched in the KEGG analysis in both lines. Above all DEGs, we also monitored by qRT-PCR key regulatory and biosynthetic genes involved in TAG formation and assembly to understand transcriptional behavior during ten days of cellular growth in liquid culture. In addition, we explored how genetic transformation affected sugar metabolism. Consistently, with transcriptional induction of TAG biosynthetic genes, fructan depletion supported their possible usage for TAG formation. Further, confocal microscopy confirmed a high accumulation of oil bodies in both transgenic lines as compared to WT calli. In conclusion, in this study we set up an efficient and stable platform for massive production of vegetable oils in in cardoon cells which, unlike plants, do not encounter growth and metabolic defects.

overall_design: RNA-seq experiments on different transformed calli for stearic acid desaturase overexpression (SAD-OE), and fatty acid desaturase RNAi silencing (FAD-KD). four samples with three biological replicates were sequenced: Empty vector transformed calli, SAD-OE transformed calli, FAD-KD transformed calli, WT non trasformed calli.

first: Elisa

last: Cappetta

first: Monica

last: De Palma

first: Rosa

last: D'alessandro

first: Antonio Luca

last: Langellotti

first: Alfredo

last: Ambrosone

first: Teresa

last: Docimo


title: Glutamine: A Novel Player in Maintaining Skeletal Strength and Body Fitness in Obese Mice

city: Prague

first: Yusuf

middle: Caglar

last: Odabasi

state: Vestec

address: Prumyslova 595

department: BIOCEV

country: Czech Republic

institute: IBT

summary: Glutamine plays a key role in cellular metabolism and tissue homeostasis. In obesity, circulating glutamine levels are decreased, accompanied by impaired bone homeostasis and increased fracture risk. While glutamine supplementation in diet has shown metabolic benefits, the mechanisms behind its effects on bone and fat metabolism are not fully understood. This study investigates whether glutamine supplementation may delay the negative impact of obesity on bone and fat metabolism in mice fed a high-fat diet (HFD). Two-month-long dietary intervention in C57BL/6J male mice showed that glutamine supplementantion reduced body weight gain, fat mass, and white adipose tissue (WAT) weight, along with improved glucose tolerance compared to HFD-fed mice. In peripheral WAT, glutamine supplementation improved WAT funcion, as indicated by decreased adipocyte hypertrophy and inflammatory status. Furthermore, glutamine reduced the obesity-driven hyper-metabolic phenotype in primary adipose-derived mesenchymal stem cells by shifting the cells toward a quiescent metabolic state. In bone, glutamine supplementation improved bone quality and microarchitecture, along with reduced bone marrow adiposity and decreased bone resorption  in glutamine-treated mice compared to HFD-fed mice. These changes were confirmed by decreased adipogenic and increased osteogenic potential of bone marrow stromal cells isolated from glutamine-treated mice. This was further supported by enhanced glutamine turnover, which maintained the stemness of the cells and reduced the inflammatory status induced by obesity, The importance of glutamine metabolism was also confirmed in human stem cells, showing a sex-specific pattern of glutaminolysis. Thus, our findings demonstrate that glutamine supplementation in obesity improves metabolic health and bone integrity at both the organ and cellular levels, highlighting its potential as a therapeutic strategy for preventing obesity-related metabolic and bone diseases.

overall_design: High throughput sequencing expression profiling by high throughput sequencing (Bulk RNA-seq data analysis)

first: Martina

last: Dzubanova

first: Michaela

last: Ferencakova

first: Dung

middle: K

last: Nguyen

first: Kristina

last: Bardova

first: Elena

last: Golovina

first: Heleen

last: Fehervary

first: Andrea

last: Benova

middle: C

first: Radek

last: Sindelka

first: Frantisek

last: Spoutil

first: Jan

last: Prochazka

first: Tomas

last: Cajka

first: Harry

last: van Lenthe

first: Martin

last: Rossmeisl

last: Kopecky

last: Tencerova


title: Notch-dependent functional conversion of RUNX factors regulates the initiation of T-lineage program [ChIP-seq]

first: Hiroyuki

last: Hosokawa

overall_design: Ten million of Cas9-LPs with or without Notch stimulation were fixed with 1 mg/ml disuccinimidyl glutarate (Thermo Scientific) in PBS for 30 min at room temperature followed by an additional 10 min with addition of formaldehyde up to 1 %. The reaction was quenched by addition of 1/10 volume of 0.125 M glycine and the cells were washed with cold PBS. Pelleted nuclei were dissolved in lysis buffer (0.5 % SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl [pH 8.0], and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30 sec sonication followed by 30 sec rest, with high power. Five micrograms of anti-RUNX1 (abcam; ab23980), anti-CTCF (CST; 3418), anti-Med12 (Bethyl; A300-774A), or anti-p300 Abs (CST; 57625) were prebound to Dynabeads anti-rabbit Ig and then added to the diluted chromatin complexes. The samples were incubated overnight at 4 ℃, then washed and eluted overnight at 65 ℃ in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 50 mM NaCl, 1 % SDS, and 50 mg/ml proteinase K). Eluted chromatin fragments were cleaned up using ChIP DNA Clean & Concentrator (Zymo). ChIP-seq libraries were constructed using NEBNext Ultra Ⅱ DNA Library Prep with Sample Purification Beads (E7103S, NEB) and NEBNext Multiplex Oligos for Illumina (E7500S, NEB) and sequenced on Illumina NextSeq500 in single read mode with the read length of 75 nt.

first: Yuichi

last: Kama

first: Ken-ichi

last: Hirano

first: Kaori

last: Masuhara

first: Yusuke

last: Endo


title: Unlocking single cell chromatin accessibility in formalin-fixed paraffin-embedded tissues by scFFPE-ATAC

city: Uppsala

first: Xingqi

last: Chen

address: Husargata

department: Immunology, Genetics and Pathology

country: Sweden

institute: uppsala university

summary: Formalin-fixed paraffin-embedded (FFPE) samples are the gold standard for clinical tissue preservation. However, single-cell chromatin accessibility profiling technology, a powerful tool to understand epigenetic regulation in human disease, is not available for FFPE samples due to extensive DNA damage. To solve this technical challenge, we introduce scFFPE-ATAC by integrating uniquely designed DNA oligos on Tn5 transposase, split-and-pool ligation DNA barcoding, T7 promoter-mediated DNA damage rescue, and in vitro transcription—the first high-throughput single-cell chromatin accessibility assay for FFPE samples. scFFPE-ATAC enables the simultaneous profiling of up to 64 FFPE samples or spatial regions, with 884,736 cell barcodes in a single run. We successfully applied scFFPE-ATAC to clinical FFPE human lymph nodes stored for 8–15 years and identified distinct epigenetic regulators between tumor centers and invasive edge epithelial cells in human lung cancer. Additionally, we analyzed paired primary and relapsed follicular lymphoma (FL), as well as FL transformed into diffuse large B-cell lymphoma, from clinical samples archived for 2–7 years, revealing key epigenetic drivers of tumor progression. Overall, scFFPE-ATAC enables high-throughput, high-sensitivity chromatin accessibility profiling in long-term archived clinical specimens, paving the way for retrospective epigenetic studies and spatial epigenetic analysis. This technology provides a powerful tool for understanding tumor relapse and metastasis, with broad applications in basic research and personalized medicine.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: xingqi

last: chen

first: Ram

last: Yadav

first: Pengwei

last: Xing


title: GDF3 promotes adipose tissue macrophage-mediated inflammation via altered chromatin accessibility during aging

city: Minneapolis

first: Anna

last: Carey

state: Minnesota

address: 312 Church Street SE

department: Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

summary: Age-related susceptibility to sepsis and endotoxemia is poorly defined, although hyperactivation of the immune system and the expansion of the visceral adipose as an immunological reservoir are underlying features. Macrophages from older organisms exhibit substantial changes, including chronic NLRP3 inflammasome activation, genomic remodeling and a dysfunctional, amplified inflammatory response upon new exposure to pathogen. However, the mechanisms by which old macrophages maintain their inflammatory phenotype during endotoxemia remains elusive. We previously identified Gdf3, a TGFβ superfamily cytokine, as a top-regulated gene by age and the NLRP3 inflammasome in adipose tissue macrophages (ATMs). Here, we demonstrate that endotoxemia increases inflammatory (CD11c+) ATMs in a Gdf3-dependent manner in old mice. Lifelong systemic or myeloid-specific deletion of Gdf3 leads to reduced endotoxemia-induced inflammation, with decreased CD11c+ ATMs and inflammatory cytokines, and protection from hypothermia. Moreover, acute blockade of Gdf3 using JQ1, a BRD4 inhibitor, phenocopies old mice with lifelong Gdf3-deficiency. We show that GDF3 promotes the inflammatory phenotype in ATMs by phosphorylating SMAD2/3. Mechanistically, the differential chromatin landscape of ATMs from old mice with or without myeloid-driven Gdf3 indicates that GDF3-SMAD2/3 signaling axis shifts the chromatin accessibility of ATMs towards an inflammatory state during aging. Furthermore, pharmaceutical inhibition of SMAD3 with a specific inhibitor of SMAD3 (SIS3) mimics Gdf3 deletion. SIS3 reduces endotoxemia-mediated inflammation with fewer CD11c+ ATMs and less severe hypothermia in old, but not young mice, as well as reduced mortality. In human adipose tissue, age positively correlates with GDF3 level, while inflammation correlates with pSMAD2/3 level. Overall, these results highlight the importance of GDF3-SMAD2/3 axis in driving inflammation in older organisms and identify this signaling axis as a promising therapeutic target for mitigating endotoxemia-related inflammation in the aged.

overall_design: Old (21-23 months) adipose tissue live CD45+ cells were sorted from GDF3 +/+ (WT) and GDF3 -/- (KO) mice via FACS and submitted for single cell RNA sequencing

first: In Hwa

last: Jang

first: Victor

last: Kruglov

first: Stephanie

last: Cholensky

first: Declan

last: Smith

first: Suxia

last: Bai

first: Timothy

last: Nottoli

first: David

last: Bernlohr

first: Christina D

last: Camell


title: Trimodulin and pneumonia

city: Berlin

first: Peter

last: Pennitz

address: Charitéplatz 1

department: Department of Infectious Diseases, Respiratory Medicine and Critical Care

country: Germany

institute: Charité – Universitätsmedizin Berlin

summary: This RNAseq dataset evaluates gene expression to assess the therapeutic potential of trimodulin in a complex mouse model mimicking critically ill CAP patients infected with S. pneumoniae. In addition, we combined trimodulin with ampicillin to address if trimodulin has further added benefit in addition to reducing bacterial burden.

overall_design: Mice were either infected with S. pneumoniae or sham-infected with PBS as control, 22 h later mice were treated with placebo as control, trimodulin, ampicillin or a combination of both until the 30 hpi analysis time point.

first: Geraldine

last: Nouailles

first: Romina

last: Bischoff

first: Kerstin

last: Linke

first: Alexander

last: Taylor

first: Birgitt

last: Gutbier

first: Cengiz

last: Goekeri

first: Sandra

last: Kunder

first: Anne

last: Voß

first: Theresa

last: Broemel

first: Olivia

last: Kershaw

first: Miha

last: Milek

first: Vadim

last: Farztdinov

first: Michael

last: Mülleder

first: Sabrina

last: Weissmüller

first: Corina

last: Heinz

first: Mayken

last: Visser

first: Fabian

last: Bohlaender

first: Katharina

last: Ahrens

first: Dieter

last: Beule

first: Achim

middle: D

last: Gruber

first: Martin

last: Koenig

last: Witzenrath


title: A direct role for a mitochondrial targeting sequence in triggering a stress response

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

summary: Mitochondrial protein import is required for maintaining organellar function. Perturbations in this process are associated with various physiological and disease conditions. Several stress responses, including the mitoCPR, combat damage caused by mitochondrial protein import stress. However, it remains unknown how this defect is sensed. Here, we reveal that the conserved mitochondrial Hsp70 co-chaperone, Mge1, acts as a stress messenger in budding yeast. During mitochondrial stress, unimported Mge1 entered the nucleus and triggered the transcription of mitoCPR target genes. This was mediated by Mge1’s interaction with the transcription factor Pdr3 on DNA regulatory elements. Mge1’s mitochondrial targeting sequence was both sufficient and essential for mitoCPR induction, demonstrating that in addition to their roles in mitochondrial protein import, targeting sequences can also function as signaling molecules.

overall_design: Experiments was performed using three biological replicates for each of the following six conditions: (1) PSD1 overexpressors, (2) PSD1 overexpressors harboring a PDR3 deletion, (3) overexpressors of the N-terminal 44 amino acids of MGE1, (4) overexpressors of the N-terminal 44 amino acids of MGE1 with a PDR3 deletion, (5) overexpressors of the N-terminal 53 amino acids of MSS116.

first: Hilla

last: Weidberg

first: Zixuan

last: Yuan


title: single cell chromatin accessiblity profiling in formlin fixed paraffin embedded samples

first: Xingqi

last: Chen

summary: We evaluated the performance of ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) on formalin-fixed paraffin-embedded (FFPE) spleen samples from C57BL/6J mice. Nuclei were isolated from FFPE mouse spleen tissue, and ATAC-seq was performed at both the bulk and single-cell levels, with and without reverse crosslinking. The resulting datasets were compared to ATAC-seq and scATAC-seq profiles obtained from fresh spleen samples. Our analysis revealed a markedly reduced library complexity in FFPE-derived samples compared to fresh tissue, across both bulk and single-cell experiments. These findings highlight the technical limitations of applying standard ATAC-seq protocols to FFPE samples. Based on our results, we conclude that conventional ATAC-seq approaches are not well-suited for chromatin accessibility profiling in FFPE-preserved tissues.

overall_design: Nuclei were isolated from snap-frozen FFPE spleen tissues of C57BL/6J mice following the Omni-ATAC-seq protocol. A total of 20,000 to 100,000 DAPI-positive nuclei were counted and collected. The nuclei were pelleted and resuspended in 1 mL of ATAC-Resuspension Buffer (ATAC-RSB) supplemented with 0.1% Tween-20. Transposition was performed using Tn5 transposase. The tagmented DNA was purified under both reverse crosslinking and non-crosslinking conditions, and subsequently PCR-amplified for 8–15 cycles using indexed primers to introduce sample-specific barcodes. For single-cell ATAC-seq, a combinatorial indexing (split-pool) strategy was employed to profile chromatin accessibility in individual nuclei isolated from FFPE mouse spleen samples. Nuclei were first isolated using a modified Omni-ATAC protocol optimized for FFPE tissue. After DAPI staining and counting, the nuclei were subjected to a three-level barcoding scheme. In the first round, transposition was performed using indexed Tn5 transposase. The nuclei were then split across multiple wells and underwent successive rounds of PCR with unique barcoded primers at each step. This split-pool barcoding enabled the unique indexing of individual nuclei. Libraries were pooled, purified under both reverse crosslinking and non-crosslinking conditions, and sequenced to generate single-nucleus ATAC-seq data.

first: Ram

last: Yadav

first: Pengwei

last: Xing


title: Cancer suppresses mitochondrial chaperone activity in macrophages to drive immune evasion

city: Columbus

first: Stanley

last: Huang

state: Ohio

address: 2255 Kenny Road

department: Department of Microbial Infection and Immunity

institute: The Ohio State University

summary: Here we uncover that TNF-receptor associated protein-1 (TRAP1) expression in TAMs is markedly reduced in the TME, a process mediated by the TIM4-AMPK signaling pathway. In addition, TRAP1 deficiency leads to increased activity of mitochondrial electron transport chain complexes and an elevated α-ketoglutarate (α-KG) to succinate ratio. The increase in α-KG facilitate JMJD3-mediated histone demethylation, altering genes expression associated with immunosuppressive activation in macrophages.

overall_design: mRNA of naive or YUMM1.7 tumor-conditioned medium (TCM)-treated bone marrow-derived macrophages isolated from TRAP1 WT, TRAP1 KO, JMJD3 WT or JMJD3 conditional KO mice.

first: Haoxin

last: Zhao

first: Yuzhu

last: Wang

first: Wei

last: Cao

first: Yili

last: Ouyang


title: Single-nuclei RNA-seq and ATAC-seq for Human Retina from Diverse Ancestry Backgrounds

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

institute: Stanford University

summary: The Human Retina Cell Atlas (HRCA) integrates data from a wide range of ancestry backgrounds, making it a highly valuable resource for understanding retinal cell types and their molecular profiles. By collecting data from 60 donors with diverse ancestry backgrounds, the atlas enabled the investigation of how ancestry affects gene expression patterns and chromatin accessibility across retinal cell types. The project's findings on gene expression and chromatin openness provide critical insights into how genetic heritage influences retinal function and susceptibility to certain eye conditions. The ancestry-related data can also help identify population-specific variations in retinal biology, potentially paving the way for more personalized diagnosis and treatment of eye disorders across different ethnic groups.

overall_design: snRNA-seq and snATAC-seq of peripheral region of retina tissue, fovea centralis tissue, macula lutea tissue from 59 human donors

first: Rui

first: Jin

last: Li

first: Jun

first: Ignacio

last: Ibarra

first: Xuesen

last: Cheng

first: Malte

last: Luecken

first: Jiaxiong

last: Lu

first: Aboozar

last: Monavarfeshani

first: Wenjun

last: Yan

first: Yiqiao

last: Zheng

first: Zhen

last: Zuo

first: Samantha Lynn

last: Zayas Colborn

first: Berenice Sarahi

last: Cortez

first: Leah

last: Owen

first: Nicholas

last: Tran

first: Karthik

last: Shekhar

first: Joshua

last: Sanes

first: J

middle: T

last: Stout

first: Shiming

first: Yumei

first: Margaret

last: DeAngelis

last: Theis


title: The effects of early systemic neuroinflammation on the brain’s response to further inflammatory insults

city: Shanghai

first: Ping

last: Yang

address: 800 Rd dong chuan

institute: Shanghai Jiao Tong University

summary: To identify how an early life first neuroinflammatory challenge affects response to subsequent challenges.

overall_design: We estabilished a neontal two-hit model: for the first hit, mice were injected subcutaneously at P3 with 5mg/kg lipopolysaccharides (L) or saline (S);for the second hit,  mice received 5mg/kg LPS (L) or saline (S) intraperitoneally. Animals were divided into four groups: SS, SL, LS, LL. Mice were sacrificed at P15, 24 hours after the second hit. RNA was extracted from the hippocampus for sequencing .

first: Xiang

last: Yu

first: Wenhao

last: Zhou


title: Activated Interferon Signaling Suppresses Age-Dependent Liver Cancer

city: La Jolla

first: Kathryn

last: Lande

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

summary: Age is a major risk factor for liver cancer, as is the case for most adult human cancers. However, the underlying mechanisms are not well defined. A better understanding of the role of aging in liver and other cancers can facilitate approaches for risk assessment, early detection and prevention. We hypothesize that age-driven changes render aged liver more sensitive to oncogenic stress and hence tumorigenesis. To investigate how the liver changes with age, we documented the immune profile, transcriptome and epigenome of healthy livers from both young and aged mice, revealing pronounced alterations with aging. Notably, in aged hepatocytes, we identified heightened interferon (IFN) signaling, as well as simultaneous tumor suppressor and oncogene signaling at both bulk and single cell level, suggestive of an aged liver that is poised for neoplasia. To challenge this seemingly poised state, we employed adeno-associated virus (AAV)-mediated expression of a c-Myc oncogene in young and aged mouse liver hepatocytes in vivo. Analysis of aged hepatocytes expressing c-Myc revealed further elevated expression of IFN Stimulated Genes (ISGs). This ISG upregulation was evident in multiple models of oncogenic stress and transformation in older mice and also observed in aged humans with Metabolic dysfunction-Associated Steatohepatitis (MASH). We determined that Stat1 is both necessary and sufficient for the age specific elevated ISG expression in old wild type mice. Remarkably, inhibiting Jak/Stat signaling alongside ectopic c-Myc expression led to high-grade hepatocyte dysplasia and tumor formation, selectively in aged mice. Together, these results suggest that an aged liver is in a state of “precarious balance”, due to concurrent activation of oncogenic and tumor suppressor pathways, but protected against neoplastic progression by IFN-signaling. Age-dependent activation of IFN signaling has been observed in many tissues and recent studies have demonstrated its detrimental consequences on aging, raising the question as to why IFN-signaling is activated during aging. We propose that aged tissues are intrinsically at higher risk of cancer and age-dependent activation of IFN-signaling is an adaptive process to protect from tumorigenesis, but one that also has maladaptive consequences.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3K27Ac in isolated hepatocytes.

first: Aaron P

last: Havas

first: Adarsh

last: Rajesh

last: Evensen

first: Peter D

last: Adams


title: Unraveling and enhancing the dynamics of hepatic bile acid and cholesterol metabolism during ex vivo normothermic machine perfusion; a path to improved liver function through conjugated bile acid infusion

city: Leiden

first: Evita

last: van de Steeg

address: Sylviusweg 71

department: Metabolic Health Research

country: Netherlands

institute: TNO

summary: Summary Ex vivo liver normothermic machine perfusion (NMP) does not fully recapitulate physiological liver function due to the absence of the enterohepatic circulation as only infusion of the bile acid taurocholate (TCA) is applied in most protocols. In this study we characterized the de novo bile acid synthesis and cholesterol homeostasis during liver NMP. We hypothesized that addition of a more diverse pool of (conjugated)bile acids during liver NMP would decrease the metabolic burden of de novo synthesis and thereby improve liver function during NMP. Method First, human and porcine livers were perfused for 360 min at 37°C and perfusate containing TCA (gene expression at t=0min and t=360min was measured by RNAseq). Next, the infusion of different conjugated bile acid mixes was assessed during porcine and human liver perfusion. Perfusate, bile and tissue samples were obtained to study liver viability, functionality, gene expression (qPCR), cholesterol and bile acid levels. Result During human and porcine perfusions with TCA infusion, composition of bile was comparable to literature however, synthesis rates were above physiological average and a decrease over time in cholesterol perfusate levels was observed. Additionally, over time a decreased expression of bile acid synthesis related genes, increased gene expression of cholesterol metabolism related genes and decreased expression in bile acid-dependent uptake and efflux transporters were detected (RNAseq). Upon infusion of a conjugated bile acid mix lower AST and ALT values and stable cholesterol homeostasis was] observed after 720 min of perfusion. Perfused human livers showed appropriate function and good functioning livers showed rapid bile acid clearance from the perfusate into the bile. Conclusion This study reveals new insights that infusion of (un)conjugated bile acids in NMP alleviated the burden of the de novo bile acid synthesis and improved liver function.

sample_organism:
Homo sapiens
Sus scrofa domesticus

platform_organism:
Homo sapiens
Sus scrofa domesticus

overall_design: - Porcine livers of 5 animals were procured, preserved  and perfused for 360 min and  liver samples were taken at t=0min and t=360min for RNAseq analysis.  - Human explanted and discarded livers of 6 adults (1 healthy and 5 types of liver diseases) were perfused for 360 min at 37° and liver samples were taken at t=0min and t=360min for RNAseq analysis.

first: L

last: Stevens

last: Donkers

middle: B

last: Doppenberg

first: M

last: Caspers

last: Dubbeld

first: B

last: Heming

first: N

last: Tramper

middle: E

last: Kleinjan

first: D

last: de Waart

first: R

middle: P

last: Oude Elferink

first: E

first: I

last: Alwayn


title: Pseudomonas aeruginosa clinical isolates can encode functional plastic degrading enzymes that allow survival on plastic and augment biofilm formation

city: Uxbridge

first: Rubén

last: de Dios

state: Middlesex

address: Kingston Lane

department: Life Sciences

institute: Brunel University London

summary: Several environmental bacteria encode plastic-degrading enzymes, a potential evolutionary response to the rapid introduction of plastic across global ecosystems. Given the widespread use of plastic in healthcare, we hypothesised that clinical bacterial isolates may also degrade plastic, rendering plastic-containing medical devices susceptible to degradation and failure and potentially offering these pathogens a carbon source that could be used to persist in the hospital-built environment. Here, we mined the genomes of prevalent pathogens and identified several enzymes in different pathogens with homology to known plastic-degrading enzymes. Synthesising and expressing a potential plastic-degrading enzyme derived from a Pseudomonas aeruginosa wound isolate in a heterologous host, we were able to demonstrate  potent plastic degrading activity. We subsequently found that the original P. aeruginosa clinical isolate could reduce the weight of a medically relevant plastic, polycaprolactone (PCL), by 78% in 7 days, and critically could use it as a sole carbon source to grow. We uncovered a direct link to virulence, demonstrating that encoding a plastic degrading enzyme can significantly enhance biofilm formation and pathogenicity in vivo. We also demonstrate that this augmented biofilm phenotype is conserved in another P. aeruginosa PCL-degrading clinical isolate we identified in a screening. We reveal that the mechanism underpinning this enhanced biofilm formation is the incorporation of the plastic breakdown products into the extracellular matrix, leading to enhanced biofilm levels. The level of PCL degradation we show by a clinical isolate and its ability to promote a key virulence and persistence determinant such as biofilm formation indicates that the integrity of any PCL containing medical device, such as sutures or implants, and the condition of patients receiving such devices could be severely compromised by pathogens with this capacity. Given the central role of plastic in healthcare, this should be considered in the future of medical interventions and practice and hospital designs implementing this material

overall_design: PA-W23 cultures (3 biological replicates per condition) were grown to mid‐exponential phase (OD600 0.6–0.7) in 20 ml Starvation media (10% LB + 90% M9 Minimal Media) supplemented with 0.5 g of PCL beads in the 3 treated samples.

first: Sophie

last: Howard

first: Evgenia

last: Maslova

first: Ronan

last: McCarthy


title: WAGO-4 Localization to Germ Granules Is Important for Its Accurate Small RNA Loading

city: Toronto

first: Julie

last: Claycomb

address: 661 University Ave

institute: University of Toronto

type: Non-coding RNA profiling by high throughput sequencing

summary: Germ granules are liquid-like condensates that regulate small RNA pathways and gene expression, ensuring genome stability and fertility in animals. In C. elegans, several Argonaute proteins, central players of small RNA pathways, localize to germ granules, yet the functional significance of this spatial enrichment remains unclear. Here, we disrupted the localization of WAGO-4 to germ granules by introducing targeted mutations in the FG repeats of Vasa-like GLH proteins. These mutations did not disrupt overall germ granule architecture but significantly reduced WAGO-4 partitioning, leading to its predominant localization in the cytoplasm. Functional analyses revealed that this mislocalization partially compromised WAGO-4 activity, resulting in reduced WAGO-4 binding of small RNAs targeting specific genes, particularly those not co-regulated by CSR-1. This selective effect highlights the importance of WAGO-4’s spatial localization for efficient small RNA loading and gene regulation. Our findings demonstrate that germ granules serve as specialized compartments that fine-tune Argonaute function, emphasizing the role of phase-separated condensates in modulating RNA pathways and gene regulatory networks.

overall_design: small RNA sequencing of immunoprecipitated WAGO-4 complexes and whole worms

first: Stela

last: Jelenic

first: Mathias

last: Renaud

first: Samantha

last: Del Borrello

first: Joseph

last: Gokcezade

first: Janos

last: Bindics

first: Lisa

last: Frasz

first: Philipp

last: Czermak

first: Peter

last: Duchek


title: A cis-regulatory element of the PHYTOCHROME A gene confers the submergence escape capacity for amphibious plants

first: Chuanwei

last: Yang

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

summary: Submergence is a type of abiotic stress that can severely impact the survival of plants and the yield of crops. Plants not only sense the hypoxic conditions during submergence but also exposed to a range of low-light intensities, depending on the submergence depth and turbidity. However, how light availability affects submergence tolerance remains largely unknown. To clarify the functions of light receptor AtPHYA and transcription factor AtEIN3/EIL1 in the transcriptional response to submergence, we conducted RNA-seq analysis on the wild type Col-0, the atphyA-211 mutant, and the atein3eil1 double mutant. Following a 6-hour submergence stress treatment, we identified 7325 differentially expressed genes (DEGs) in the Col-0 seedlings. The expression of 3748 submergence-induced genes was notably reduced in the atein3eil1 double mutant, while it was significantly enhanced in the atphyA-211 mutant. This suggests that AtPHYA exerts a negative regulatory effect on the expression of genes induced by submergence. The absence of AtPHYA leads to an upregulation of these submergence-induced genes, confirming that AtPHYA negatively modulates their expression.

overall_design: Terrestrial-grown plants were either maintained under terrestrial conditions or subjected to submergence for 6 h and leaves tissue was collected. Three replicates were prepared for each condition and each line.


title: The Exon Junction Complex coordinates the co-transcriptional inclusion of blocks of neighboring exons

city: New Haven

first: Alexandra

last: Bergfort

state: CT

address: 333 Cedar Street

department: Molecular Biophysics & Biochemistry

institute: Yale University

summary: The Exon Junction Complex (EJC) has roles in mRNA export and cytoplasmic quality control. Yet EJC is recruited to pre-mRNA by the spliceosome, prior to the second catalytic step of splicing. Because splicing often occurs co-transcriptionally, EJC can be deposited on nascent RNA almost immediately after introns are synthesized and excised, raising the question of whether EJC regulates downstream RNA processing decisions. Here, we show that degron-mediated depletion of EJC component EIF4A3 leads to substantial skipping of neighboring pairs of two or more exons. These exon skipping events occurred on the same molecule of mRNA, detected by long read sequencing, suggesting that “exon blocks” require EJC for inclusion. Introns flanking EJC-dependent exon blocks were longer and spliced after internal introns. Thus, block exons form a larger EJC-marked exon prior to surrounding splicing events. These findings identify a previously unknown nuclear function of EJC that coordinates co-transcriptional inclusion of exon blocks.

overall_design: To investigate a role of EIF4A3 in co-transcriptional splicing, we genereated HEK293T cells with an EIF4A3-SMASh degron tag and an EIF4A3 overexpressing HEK293 Flp-In T-REx cell line. We extracted mRNA and chromatin bound nascent RNA (nRNA) and conducted Illumina  paired end sequencing and PacBio long-read sequencing.

first: Jackson M.

last: Gordon

first: Chuan-Tien

last: Hung

first: Benhur

last: Lee

first: Karla M.

last: Neugebauer

first: Matthew R.

last: Gazzara

first: Yoseph

last: Barash


title: Identification of a novel minor-groove DNA binder that represses mitochondrial genes expression and induces apoptosis in highly aggressive leiomyosarcoma cells

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

institute: University of Udine

summary: The induction of cellular stress is a common strategy in cancer therapy. Leiomyosarcomas (LMS) are aggressive tumors for which there are few effective therapeutic options. Through a combination of in silico and in vitro screens, the compound NSC-260594/XMH95 was identified as a promising molecule that selectively induces apoptosis in aggressive LMS cells. This apoptotic response is associated with the upregulation of the BH3-only genes PMAP1/NOXA, BIK, HRK and BBC3/PUMA. XMH95 binds DNA and possibly the minor groove, similar to Hoechst 33258. Unlike Hoechst, XMH95 is not fluorescent but can be photoactivated by UV irradiation when bound to DNA. Also, unlike Hoechst, XMH95 suppresses mitochondrial gene expression and is a more effective inducer of apoptosis. Apart from suppressing mitochondrial genes, XMH95 has many effects on gene expression that are common to Hoechst. Using an inhibitor of mitochondrial RNA polymerase (POLRMT), we show that XMH95 triggers apoptosis by perturbing both nuclear and mitochondrial transcription. Our results propose a new compound and a novel stress that can trigger apoptosis in aggressive cancer cells by upregulating multiple BH3-only genes.

overall_design: RNA-seq profiling of HUtSMC and SK-UT-1 cells treated with by two double strand DNA binders: Hoechst 33 and NSC26954/XMH95.

first: Eleonora

last: Malavasi

first: Raffaellla

first: Martina

last: Minisini

first: Alessio

last: Bertozzo

first: Claudio

last: Brancolini


title: Genome-wide identification of AphEIN3-targeted genes in A. philoxeroides

summary: Ethylene play a key role in submergence stress. The invasive plant Alternanthera philoxeroides has strong resistance to submergence stress, but the related mechanisms are not clear. We found that the ethylene signaling component AphEIN3 may be involved. To investigate the genome-wide AphEIN3 binding sites, we performed a DNA affinity purification sequencing (DAP-seq) as described by (Bartlett et al., 2017). In two replicates, approximately 22,604 peaks (for 6,831 genes) and 29,912 peaks (for 8,547 genes) were identified as high-confidence AphEIN3 binding peaks. Combined with RNA-seq analysis, we found that submergence can induce AphEIN3 binds to a cluster of elongation genes to regulate theses gene expression.

overall_design:
A DNA affinity purification sequencing (DAP-seq) for transcription factor AphEIN3 in Alternanthera philoxeroides.
To capture the HaloTag fusion proteins, we used magnetic beads containing Halo antibodies (Magne HaloTag Beads, Promega, G728A).

first: Ji


first: In Hwa

last: Jang

address: 100 Church Street SE

summary: SMAD2/3 transcription factors (TFs) have low DNA binding affinity for a specific consensus sequence, allowing them to elicit anti- or pro-inflammatory responses depending on the cellular context. Genes associated with pro-inflammatory processes in immune cells, including myeloid cells, exhibit increased chromatin accessibility with age. We hypothesized that this could affect the transcriptional activity of SMAD2/3 in adipose tissue macrophages (ATMs). To assess chromatin accessibility, ATMs isolated using fluorescence-activated cell sorting (FACS) from young control, old control and old mKO mice were profiled using assay for ATAC-seq.

overall_design: Visceral adipose tissue depots were isolated from mice and digested into stromal vascular fraction and adipocyte fraction (PMID: 33870227).  Then, the stromal vascular fraction was used for fluorescence-activated cell sorting of adipose tissue macrophages: Live CD45+ CD11b+ SiglecF- F4/80+ cells were sorted on a BD FACS Aria II into RPMI with 20% FBS

first: Victor

last: Kruglov

first: Stephanie

middle: H

last: Cholensky

first: Declan

last: Smith

first: Suxia

last: Bai

first: Timothy

last: Nottoli

first: David

last: Bernlohr

first: Christina

last: Camell

first: Anna

last: Carey


title: Addressing the specific roles of histone modifications in transcriptional repression [RRBS]

city: London

first: Aina

middle: Maria

last: Mas

address: Chester Beatty Laboratories, 237 Fulham Rd.

institute: Institute of Cancer Research

type: Methylation profiling by high throughput sequencing

summary: Our understanding of epigenetic processes is based on the hypothesis that individual posttranslational modifications of DNA and histones, or combinations thereof, function to direct unique downstream effects on transcription. Still, histone modifications are broadly categorized as repressive or activating, raising the question of potential functional redundancy. Here, we present an approach for addressing this question by substituting the genome-wide H3K27me3 pattern with other histone modifications. By taking advantage of the modular organization of PRC2, we direct de novo recruitment of H3K9me3 and H3K36me3 to PRC2 target genes in H3K27me3 null mouse embryonic stem cells (mESCs). We show that despite accurate genome-wide re-establishment of H3K36me3 at PRC2 target genes, which leads to significant reduction in H3K4me3 levels, the remaining H3K4me3 prevents H3K36me3 from recruiting sufficient DNA methylation to substitute for H3K27me3-mediated repression. In contrast, we demonstrate that H3K9me3 is more efficient in repressing H3K27me3 regulated genes, however this repression is also contingent on H3K4me3 status. Taken together, these results highlight the unique repressive functions of H3K27me3 and suggest that the functional effects of individual posttranslational modifications are highly dependent on the interplay with the existing chromatin environment.

overall_design: Reduced Representation Bisulfite Sequencing on mESC samples, to identify changes in PRC2 target gene CPG island methylation

first: Lin

last: Hedehus

first: Robin

last: Armstrong

first: Richard

last: Koche

first: Hua

last: Wang

first: Aktan

last: Alpsoy


title: Addressing the specific roles of histone modifications in transcriptional repression [RNA-seq]

overall_design: RNAseq on panel of mESC cell lines, to identify changes en gene expression of PRC2 target genes upon changes of histone modification profiles


title: Single-cell transcriptomic atlas of cystic echinococcosis reveals diversity roles of small extracellular vesicles derived from Echinococcus granulosus during liver infection

city: Chengdu

first: Ruiqi

last: Hua

address: Sichuan, Chengdu, Huimin Road 211

institute: Sichuan Agricultural University

summary: Cystic echinococcosis acts as a public health threat worldwide and causes considerable economic loss. Liver is the main paraistic organ during infection, whereas the the regulatory roles of PSC-sEV for liver cells remains unclear. In this study, we sequenced and analyzed single-cell transcriptomic of liver targeted by PSC -sEV, to illuminate the cross-talk between protoscoleces and host cells.

overall_design: For cystic echinococcosis infection in situ of liver, PSC were injected via portal vein in C57BL/6 mice. Six months after the surgery, another two groups of mice were injected with PSC-sEV or PBS-HAT via the tail vein, respectively. Livers were cut into 0.25 cm3 and transferred into protoplast enzyme solution. After digestion and cell viability check, cells were loaded into single cell instrument (DG1000, Biomarker, China) to produce single-cell GEMs and then sequenced at next generation sequencing platform (BGISEQ-500, BGI, China) after performing cDNA amplification.

first: Guoqing

last: Shao

first: Xiaowei

last: Zhu

first: Guangyou

last: Yang


title: Role of Wnt signalling in the self-renewal and differentiation capacities of primary hepatoblast organoids.

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: Primary hepatoblast organoids (HBOs) are grown and passaged in medium that contains both Wnt3a and R-spondin conditioned media (HBO complete medium). It is hypothesised that these molecules that are part of the WNT signalling pathway may be contributing to the HBOs self-renewal properties.

overall_design: To investigate the function of Wnt3a and R-spondin on the self-renewal as well as differentiation capacity of the HBOs the removal of the signalling molecules from the HBO complete medium was tested, separately as well as combined.

first: Ekaterini

last: Zacharis

first: Arash

last: Shahsavari

first: Ludovic

last: Vallier


title: con7 regulates the development of Penicillium oxalicum fungi and the expression of chitinase and cellulolytic genes

status: Public on Oct 13 2025

city: Qingdao 266237

first: Kexuan

last: Ma

state: China

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT) and Con7 destruction strain (con7-A) under conditions of 2% glucose，2% glycerol or 1% bran + 1% microcrystalline cellulose as carbon source. The results of correlation analysis between each sample showed that the gene expression level of con7-A  was significantly different from that of the WT strain. The destruction of con7 significantly affect the expression levels of sporulation process genes and the expression of chitinase and cellulase-encoding genes.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain, con7 destruction mutant strains in 24h in modifeid Mendal’s medium with 2% glucose，2% glycerol or 1% bran + 1% microcrystalline cellulose as carbon sources. Three replicates were included for each samples.

first: Yuqi

last: Qin


title: Comparative analysis of isoproterenol and lipopolysaccharide mediated cytoprotective responses in the heart

city: St. Louis

first: Douglas

last: Mann

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis

summary: This study aimed to compare the mechanisms by which isoproterenol and lipopolysaccharide induce cytoprotection in the heart. We performed bulk RNA sequencing to compare the transcriptomic effects of isoproterenol and lipopolysaccharide on the heart, to examine features that are shared and unique to each treatment.

overall_design: Female 10-wk old wild-type (C57BL/6J) mice were treated with lipopolysaccharide (LPS; 2.5 mg/kg) or isoproterenol (ISO; 300 mg/kg). Mice were then euthanized at baseline (no treatment) and at 1 and 7 days later (n=3-4/group) with hearts collected for bulk RNA sequencing.

first: Kenji Rowel

middle: Q

last: Lim


title: Multi-omics analyses reveal DjTcf4 critical for proper timing of differentiation in planarian regeneration

city: kaifeng

first: Hao

state: Hainan

address: Jinming

institute: Henan University

summary: The blastema is key to forming complete tissues in regenerating Dugesia japonica (D. japonica). However, the dynamic changes in cellular compositions and transcription landscapes in blastema during regeneration are understudied. Here, through genome reannotation, 3D spatial transcriptome construction, scRNA-seq and scATAC-seq analyses of changes in gene expression and chromatin structures, we delineated key transcription factors regulating the developmental trajectories of major cell clusters in the regenerating head. Importantly, we found that the T-cell factor 4 positive (DjTcf4+) cells highly accumulated at wound areas, and its gene network is critical for proper timing of development during regeneration in multiple progenitor cells. Depletion of DjTcf4 and its target genes led to singular eye and/or dull tail phenotypes and delayed regeneration. Taken together, we built multi-omics atlases in D. japonica and revealed noncanonical function of the DjTcf4 network in developmental pattern formation, laying a foundation for studies of regeneration in D. japonica.

overall_design: Examine spital gene expression profiles of head blastema animals by 10X Visium platform.

first: Mengmeng

last: Lu

first: Lei

last: Huang

first: Xiaopeng

last: Zou

first: Hongfei

last: Liu

first: Ya

last: Gao

first: Yanming

first: Yunchao

last: Kan


title: Effect of ATP7A knockdown on gene expression in glioma stem cells

city: PITTSBURGH

first: Fanen

last: Yuan

state: PA

address: 5030 Centra Ave, APT861

institute: University of pittsburgh

summary: Copper-related cell death, cuproptosis, involves accumulation of intracellular copper that triggers mitochondrial lipoylated protein aggregation and destabilization of iron–sulfur cluster proteins. Here, glioblastoma (GBM) stem cells (GSCs) displayed resistance to cuproptosis with circadian variation of intracellular copper levels, unlike differentiated GBM cells (DGCs) or neural stem cells (NSCs). CRISPR screening of copper regulators under concurrent treatment with copper ionophore or clock disruption revealed dependency on ATPase Copper Transporting Alpha (ATP7A). Circadian control of copper homeostasis was mediated by core clock transcription factor, Basic helix-loop-helix ARNT-like protein 1 (BMAL1). In turn, ATP7A promoted tumor cell growth through regulation of fatty acid desaturation. Copper levels negatively fed back onto the circadian clock through SQSTM1 (sequestosome 1/p62)-mediated lysosomal degradation of BMAL1. Targeting cuproptosis and circadian clock or fatty acid desaturation generated synergistic anti-tumor effects. Thus, crosstalk between the circadian rhythm and copper sustains GSCs, reshaping fatty acid metabolism and promoting drug resistance.

overall_design: ATP7A was knockdown by shRNA in GSC387, GSC3565 and GSC738. And then RNA-seq was performed to investigate the effect of ATP7A knockdown on gene expression.

first: Jeremy

middle: N

last: Rich


title: Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis

city: Geelong

first: Laurence

middle: James

last: Croft

state: Victoria

address: 75 Pigdons Road

department: School of Medicine

institute: Deakin University

summary: The serrated neoplasia pathway in an alternate route to colorectal cancer (CRC) development where BRAFV600E is the most common initiating genetic alteration. BRAFV600E-driven tumorigenesisrequires gene expression changes mediated by activation of the ERK MAPK signalling pathway. However, the key effectors of this process are elusive. Here, we identify the ERK-regulated transcription factor Fosl1 one such effector. We show that Fosl1 is dispensable for the initiation ofBRAFV600E-driven serrated neoplasia in mice but promotes progression of the disease by regulatingthe expression of genes involved in inflammation, immunity, cell cycle control, fetal-likeprogramming, and gastric metaplasia. Notably, transgenic Fosl1 expression alone was sufficient to induce tumours with a BRAFV600E-like serrated morphology and transcriptional profile. Thesefindings reveal a mechanism through which oncogenic BRAF-driven ERK signalling reprograms transcription to drive serrated neoplasia.

overall_design: RNA-seq using Illumina paired-ends of polyA transcriptomes comparing mouse normal intestinal epithelium to BRAF mutant and FLAG-Fosl1 transgene tumours and to BRAF mutant with or without Fosl1

first: Zakia

last: Alam

first: Rebecca

last: Nightingale

first: Analia

last: Lesmana

first: Cheng

first: Laura

middle: J

last: Jenkins

first: Mark

middle: F

last: Richardson

first: Larry

first: Ian

middle: Y

last: Luk

first: Camilla

middle: M

last: Reehorst

first: Fiona

last: Chionh

first: Natalia

last: Vukelic

first: Faiza

last: Basheer

first: Eugene

last: Tulchinsky

first: Joshua

last: Badshah

first: Troy

last: Dumenil

first: Latifa

last: Bakiri

first: Erwin

last: Wagner

first: Niall

last: Tebutt

first: Vicki

last: Whitehall

first: John

last: Mariadason

first: Amardeep

last: Dhillon


title: Loss of Brg1 and Pten in pancreatic ductal cells forms intraductal tubulopapillary neoplasm via the YAP/TAZ pathway

city: Kawaracho

first: Kei

last: Iimori

state: Kyoto

department: Gastroenterology

institute: Kyoto University Graduate School of Medicine

summary: Background & Aims Intraductal tubulopapillary neoplasm (ITPN) is a rare, high-grade tumour of the pancreatic duct, characterised by distinct molecular features including frequent alterations in the components of switch/sucrose non-fermenting (SWI/SNF) chromatin remodelling complex and PI3K/AKT pathways. This study aimed to investigate the functional role of BRG1, a key SWI/SNF component, in pancreatic ductal cells, particularly in the context of PI3K/AKT pathway activation. Methods We generated conditional knockout mice by crossing Hnf1b-CreERT2, Brg1flox, and Ptenflox strains. Pancreatic organoids were used for subcutaneous xenografts in NOD/SCID mice. Twelve human ITPN specimens were analysed by immunohistochemistry. Results: In the context of PI3K/AKT pathway activation, Brg1 deletion in pancreatic ductal cells led to the development of ITPN accompanied by invasive carcinoma components. An upregulation of the Yes-associated protein 1/transcriptional coactivator with the PDZ-binding motif (YAP/TAZ) pathway was observed in mutant pancreatic ductal cells. In the xenograft model, pancreatic tumour organoids progressed into invasive pancreatic ductal adenocarcinoma (PDAC) with high TAZ expression, indicating sustained YAP/TAZ pathway activation. Furthermore, administration of verteporfin, a YAP/TAZ pathway inhibitor, reduced tumour formation and partially reversed the dedifferentiation of pancreatic ductal cells. Consistent with the mouse data, analysis of 12 human ITPN specimens showed frequent downregulation of SWI/SNF components, with a significant inverse correlation between BRG1 and TAZ expression. Conclusions: Simultaneous loss of Brg1 and Pten in pancreatic ductal cells results in ITPN formation via the activation of the YAP/TAZ pathway in the mose model. The YAP/TAZ pathway is a key driver of ITPN formation and is a potential therapeutic target for ITPN and ITPN-derived PDAC.

overall_design: RNA-seq profiling of pancreatic ductal cells derived from Hnf1b-CreERT2, Brg1flox, Ptenflox mice and Hnf1b-CreERT2,  Ptenflox mice at day 21 after induction of Tamoxifen-mediated Cre recombination.

first: Akihisa

last: Fukuda


title: Transcriptomic Profiling of siCHRNA5 and siTP53 Perturbations in ER-Positive MCF7 Breast Cancer Cells

city: Ankara

first: Özlen

last: Konu

country: Turkey

institute: Bilkent University

summary: Estrogen receptor (ER)-positive MCF7 breast cancer cells were treated with siRNAs targeting CHRNA5, TP53, or both in combination to investigate TP53-dependent and independent transcriptional responses to CHRNA5 knockdown. Previous studies have shown that CHRNA5 silencing induces cell death via TP53 pathway activation. To further elucidate the molecular mechanisms underlying this effect, we performed RNA sequencing following 72-hour treatments with siCHRNA5, siTP53, and their combination, alongside appropriate siRNA controls. This dataset provides a valuable resource for understanding the role of CHRNA5 in ER-positive breast cancer and its interaction with TP53 signaling, with implications for therapeutic targeting strategies.

overall_design: MCF7 cells were treated with siRNAs targeting CHRNA5, TP53, or both, alongside controls, to investigate TP53-dependent and independent transcriptional responses to CHRNA5 silencing in ER-positive breast cancer using RNA sequencing.

first: Ozlen

first: Ayse

middle: G

last: Keskus


title: Prospective isolation of mouse and human hematopoietic stem cells using PLXDC2

city: Minato

first: Yosuke

last: Tanaka

state: Tokyo

address: Shirokanedai

institute: IMS, The University of Tokyo

summary: Numerous strategies exist to isolate hematopoietic stem cells (HSCs) using complex combinations of markers and flow cytometry. However, robust identification of HSCs using imaging techniques is substantially more challenging which has prompted the recent development of HSC reporter mice. To date, very few molecules used in these reporters have been useful for human HSC identification. Here we report that PLXDC2 is a useful marker for both mouse and human cord blood HSCs. Using a green fluorescent protein (GFP) knock-in at the Plxdc2 locus in mice (hereafter denoted as Plxdc2-GFP), we showed that Plxdc2-GFP is highly expressed in HSCs with 1 in 2.8 Plxdc2-GFP+CD150+ cells giving long-term multi-lineage reconstitution in transplantation. Moreover, we developed a novel human PLXDC2 antibody and showed that human PLXDC2+ HSCs have higher long-term multilineage reconstitution ability compared with PLXDC2- HSCs in a xenograft model. This study identifies PLXDC2 as a highly relevant molecule in HSC identification.

overall_design: 100 cells each of PLXDC2⁺ and PLXDC2⁻ human hematopoietic stem cells (CD34⁺CD38⁻CD90⁺CD45RA⁻CD49f⁺), isolated from cord blood-derived CD34⁺ cells, were sorted and subjected to RamDA-seq.

first: Yasushi

last: Kubota


title: Anti-uPAR CAR T cells reverse and prevent aging-associated defects in intestinal regeneration and fitness

city: Cold Spring Harbor

first: Vyom

last: Shah

state: New York

address: 1 bungtown road

department: Beyaz Lab

institute: Cold Spring Harbor Laboratory

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

Intestinal stem cells (ISCs) drive the rapid regeneration of the gut epithelium. However, during aging their regenerative capacity is reduced, possibly through senescence and chronic inflammation, albeit little is known about how aging-associated dysfunction arises in the intestine. We previously identified the urokinase plasminogen activator receptor (uPAR) as a senescence-associated protein in other tissues and developed CAR T cells able to efficiently target it. Harnessing them, here, we identify the accumulation of uPAR-positive cells in the aging gut and uncover their detrimental impact on ISC function in aging. Thus, both therapeutic and prophylactic treatment with anti-uPAR CAR T cells improved barrier function, regenerative capacity, inflammation, and mucosal immune function in aged mice. Overall, these findings reveal the deleterious role of uPAR-positive cells on intestinal aging in vivo and provide proof of concept for the potential of targeted immune-based cell therapies to enhance tissue regeneration in aging organisms.

overall_design: Refer to individual Series


title: A Global View of Cell Type Homology and Transcriptomic Divergence in the Mammalian Brain

city: San Francisco

first: Alex

middle: A

last: Pollen

address: 35 Medical Center Way

department: Neurology

institute: UCSF

summary: This study is a high-level comparison of the embryonic brains of Homo sapiens, Macaca mulatta, and Mus musculus using scRNA-seq. This submission includes the novel Macaca mulatta scRNA-seq generated for this study between PCD40 and 100. The supplementary h5ad file contains the meta-atlas including processed data from all 3 species, with annotations from the publication.

overall_design: 10X Genomics Chromium single cell 3’ capture RNA-sequencing of macaque embryos between embryonic day 40 and 100

first: Matthew

last: Schmitz


title: Gene expression of rat liver tissues treated with UTOpiA

city: Suita

last: Yoneyama

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

institute: The University of Osaka

summary: We compared the global transcriptome between normal liver and ACLF liver treated with empty or UTOpiA.

overall_design: Comparative gene expression profiling analysis of RNA-seq for liver tissues of rats treated in different protocols.

first: Hitomi

last: Yamaguchi

first: Takanori

last: Takebe


title: Gene expression of human iPSC-derived hepatocyte-like cells treated with insulin and dihydrotestosterone

summary: We compared the global transcriptome of human iPSC-derived hepatocyte-like cells (HLC), which have homozygousTM6SF2 E167K, cultured in different conditions: control, insulin, dihydrotestosterone, and insulin plus dihydrotestosterone.

first: Asei

last: Hirai


title: HIV-Induced Sialoglycans on Infected Cells Promote Immune Evasion from Myeloid Cell-Mediated Killing

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Sialic acid-containing glycans (sialoglycans) on pathological cells interact with Siglecs, glyco-immune checkpoint receptors expressed on myeloid cells such as monocytes and neutrophils. This interaction suppresses the cytotoxic functions of these immune cells. We show that HIV infection reprograms the glycosylation machinery of infected cells to increase the expression of specific sialoglycan ligands for Siglecs-3, -7, and -9. These ligands engage Siglecs on myeloid cells, impairing their ability to target HIV-infected cells. Selective disruption of these interactions using 10-1074-Sia, an HIV-specific antibody conjugated to sialidase—an enzyme that removes sialic acids—significantly enhances monocyte- and neutrophil-mediated killing of HIV-infected cells in autologous assays. Treatment with 10-1074-Sia in humanized mice infected with HIV reduces viral load and decreases inflammation. These findings reveal a novel immune evasion mechanism exploited by HIV to evade myeloid cell immune surveillance and highlight the potential of targeting sialoglycan-Siglec interactions to improve immune clearance of HIV-infected cells.

overall_design: RNAseq profilling of non-activated primary CD4 T cells infected with HIV-DH12 virus

first: Shalini

last: Singh

first: Mohamed

last: Abdel-Mohsen


title: Q373fs variant of RBM20 affects splicing of cardiac genes that are causative for sudden death; Human sudden death case and animal experiment

city: Nishinomiya

first: Takuma

last: Yamamoto

address: 1-1 Mukogawa-Cho

institute: Hyogo Medical University

summary: RBM20 is one of the genes predisposing to dilated cardiomyopathy (DCM). Variants in the RS domain and the RNA-recognition motif have been well studied, but the pathogenicity of variants outside the hotspot remains unknown. A human patient with the Q373fs-RBM20 variant without a typical DCM phenotype was identified in sudden death cohorts. In the mouse experiments, RNA seq analysis revealed that Q374fs-Rbm20 mice showed some different splicing patterns in such as Ttn, Ldb3, Camk2d,Obscn, and Ryr2. The expressions of Casq1, Mybpc2, and Myot were also upregulated in Q374fs-Rbm20 mice. The pathway analysis indicated the involvement of some of the 1770 differentially expressed genes in Cytoplasmic ribosomal proteins Calcium regulation in cardiac cells and Striated muscle contraction. Cardiac dysfunction such as cardiac dilation and extended duration of QRS and QTc were observed by ultrasound echocardiography and Electro-cardiogram. The Q373fs-RBM20 (Q374fs-Rbm20) variant changes gene splicing and affects gene expression of sarcomere structural genes and Ca handling genes and presented cardiac dysfunction, suggesting that Q373fs-RBM20 human patient may cause arrhythmogenic sudden death.

overall_design: Using the CRISPR/Cas system, we generated KI mice harboring the c.1121_1122delAG (p. Q374Rfs) variant in the mouse Rbm20 gene, which corresponded to human c.1118_1119delAG (p. Q373Rfs).


title: Oxidative stress sensing by the translation elongation machinery promotes production of detoxifying selenoproteins

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: The special amino acid selenocysteine plays an essential role in metazoan redox biology and is incorporated into nascent protein chains through the recoding of a UGA termination codon. Using GPX1 and GPX4, two selenoenzymes that protect cells from oxidative stress, as fluorescent reporters we carried out the first genome-wide knockout screen to identify regulators of selenocysteine decoding.

overall_design: Two independent clones for each cell line, GPX1, GPX4 and GPX4M, were used for the screen and 1.4x10^8 cells were infected with the Brunello pooled lentiviral CRISPR library (Addgene #73179) in the presence of 5 μg/ml polybrene at a multiplicity of infection between 0.3 to 0.5. Two days after transduction, the cells were selected in medium containing 1 μg/ml puromycin. After 8 days puromycin concentration was lowered to 0.5 μg/ml. After 10 days of selection the top and bottom 0.75% eGFP populations were sorted on a FACS Melody (BD Biosciences). gDNA from sorted pools was isolated by phenol-chloroform extraction. gDNA from 6x10^7 unsorted cells, was isolated with the Masterpure DNA isolation kit (Lucigen). Sequencing libraries were generated from the isolated gDNA through two sequential PCR reactions using the Herculase II DNA polymerase (Agilent). After 18 rounds of initial PCR amplification, 5% of the reaction product was used for a second round of PCR (10cycles) with primers that introduced Illumina sequencing adapters and barcodes. The final PCR products were purified using AMPure XP beads (Beckman Coulter). Libraries were sequenced on a NextSeq2000 (Illumina) with 100bp single-end reads at an average sequencing depth of ~2.2x10^7 reads per sample. sgRNAs sequences were extracted from fastq files through an in-house Galaxy script and normalized reads counts were calculated.

first: Frederick

last: Rehfeld

first: Claire

last: Lundstrom

first: He

last: Zhang


title: Identification of major transcription factor regulating gene signautures associated with jakyakgamcho-tang in PC12 cells

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

summary: Neuropathic pain (NP) is a chronic condition caused by complex molecular mechanisms. Due to the challenges in NP treatment, it is crucial to develop novel targeting strategies that can help elucidate its molecular mechanisms. Jakyakgamcho-tang (JGT) has significant therapeutic potential; however, its precise mechanism of action remains unclear. In this study, we systematically investigated the key transcription factors and mechanisms of action of water/ethanol extract of JGT (WJGT/EJGT) and their compounds using transcriptome analysis. We identified key transcription factor involved in NP pathogenesis by profiling transcriptome and histone ChIP-seq from NP model. We analyzed gene expression changes in PC12 cells treated with JGT extract to determine its key mechanisms and transcriptional regulators. To further validation the novel mechanisms and targets of JGT and its key compounds, we conducted in vitro experiments. The PDGFRB pathway was significantly downregulated by JGT extracts, with Fos identified as a key transcription factor regulating JGT-induced target gene expression. Furthermore, we identified key compounds among seven compounds that were regulated by the PDGFRB pathway and Fos expression. Notably, the targets modulated by JGT extracts and its key compounds were associated with inflammation. Our findings suggest that targeting the PDGFRB pathway and its key transcription factor, Fos, is a potential therapeutic strategy for NP. This study provides novel insights into the mechanism and transcriptional regulator underlying JGT and its key compounds in NP treatment.

overall_design: Total whole transcritome profiles treated with water extract of Jakyakgamcho-tang (JGT) and  ethanol extract of JGT in PC12 cell.


title: MicroRNA miR-196a controls neural crest patterning by repressing immature neural ectoderm programs in Xenopus embryos.

city: Norwich

first: Alice

last: Godden

state: Not applicable

address: School of Biological Sciences, University of East Anglia, Norwich Research Park

institute: University of East Anglia

summary: Neural crest (NC) cells form a multipotent stem cell population specified during neurulation, which undergoes an epithelial-to-mesenchymal transition (EMT) and migrate extensively in the developing embryo, to generate numerous tissues and cell types including the craniofacial skeleton, the peripheral nervous system and pigment cells. The genetic and molecular details of neural crest specification are governed by a complex, yet still partially understood gene regulatory network (NC-GRN). In particular, the precise function of microRNAs in this network remains poorly known. MicroRNAs are short non-coding 20-22 nucleotides long RNAs which control gene expression through post-transcriptional repression. Since miRNA-196a is expressed in the developing neural and neural crest cells of Xenopus laevis embryos we here investigated miR-196a function in the NC-GRN, by knocking-down its expression using antisense morpholinos. Depletion of miR-196a revealed major neural crest and craniofacial phenotypes. These defects were preceded by the perturbed expression of key neural, neural border and neural crest markers such as sox2/3, zic1/3, pax3, sox10 and snail2. Using RNA sequencing of individual neural border and neural crest explants, we have identified a signature of genes up- and down-regulated by miR-196a and validate these with rescue experiments using a miR mimic. We show that Sox10, a predicted target of miR-196a, is lost following morpholino knockdown and rescued upon miR 196a mimic expression. Our study identifies miR-196a as a key actor of early patterning in the dorsal ectoderm, balancing the extent of immature neural plate progenitors with neural crest and placode specification, while also promoting neuron differentiation within the neural plate.

overall_design: RNA-seq profiling of morpholino knockdown of miR-196a in Xenopus laevis neural crest tissue with accompanying control and mismatch morpholino injections. These were conducted on wild-type embryos that were injected at 4-cell stage into right dorsal blastomere and grown to NF stage 14 and 17 before total RNA extraction and RNA-sequencing.

first: Nicole

last: Ward

first: Meghanne

last: Sittewelle

first: Anne-Helene

last: Monsoro-Burq

first: Grant

last: Wheeler


title: Molecular Features of Aggressive Preinvasive Lesions driven by Combined MYC Activation and PTEN Loss in Mouse Prostate

city: Baltimore

first: Michael

last: Rubenstein

address: 733 N Broadway

institute: Johns Hopkins University School of Medicine

summary: Gain of MYC combined with biallelic PTEN loss strongly predicts prostate cancer mortality. Prior studies have shown that combined MYC overexpression and Pten loss resulted in the development of mouse prostatic intraepithelial neoplastic (PIN) precursor lesions that progress to invasive and metastatic disease (BMPC mice). Yet, single gene alterations in these mice result only in PIN. Herein, we performed transcriptomic profiling of PIN lesions from mouse prostates with MYC overexpression, loss of Pten, and the combination thereof in BMPC mice.

overall_design: Mouse prostates harboring PIN lesions were dissected from mice engineered to have MYC activation alone (MYC PIN, ventral lobes), Pten loss alone(PTENloss PIN, anterior lobes), and the combination thereof (BMPC PIN, anterior lobes), as well as invasive primary adenocarcinomas and metastatic lesions from BMPC mice (BMPC Primary and BMPC Met) and wild-type controls from FVB anterior and ventral prostate lobes (FVB Anterior and FVB Ventral).

first: Apurv

last: Rege

first: Gretchen

last: Hubbard

first: Danielle

last: Cannady

first: Shreya

last: Agarwal

first: Kevin

last: Chen

first: Alex

last: Estrada

first: Carolina

last: Gomes-Alexandre

first: Jessica

middle: L

last: Hicks

first: Tracy

last: Jones

first: Qizhi

last: Zheng

first: Srinivasan

last: Yegnasubramanian

first: Charles

last: Bieberich

first: Angelo

last: De Marzo


title: H2AK119ub dynamics controls hair follicle stem cell quiescence [RNA-Seq 2]

city: Bronx

first: Deyou

state: NY

address: 1301 Morris Park Avenue

department: Department of Genetics

institute: Albert Einstein College of Medicine

summary: The transition of stem cells from a quiescent state to an active state is a finely tuned process that requires the dismantling of the quiescence program and the establishment of a cell cycle-promoting transcriptional landscape. Whether epigenetic processes control stem cell states to promote the regeneration of adult tissues remains elusive. In this study, we show that a repressive histone modification, H2AK119ub, is dynamic between quiescent and active hair follicle stem cells (HFSCs) in the adult murine skin. Ablation of H2AK119ub in HFSCs leads to failure in maintaining quiescence leading to premature activation and an eventual exhaustion of HFSC pool. Transcriptional and chromatin studies revealed that H2AK119ub directly represses a proliferation promoting transcriptional program in the HFSCs to preserve quiescence. Lastly, we identify that the inhibitory FGF signaling produced by the hair follicle niche keratinocytes maintains H2AK119ub in quiescent HFSCs. Together, these findings reveal that a repressive histone mark, H2AK119ub, is under the dynamic regulation of inhibitory niche signaling to prevent the untimely establishment of an activated state to preserve SC function and longevity.

overall_design: Control and PRC1 i2KO mice were induced starting at P50. 15 days after completion of induction treatment, the back skin was collected and the adipose layer from the dorsal side was scraped off using a surgical scalpel. The scraped skin sample was washed with PBS prior to incubation with 0.25% Trypsin/EDTA at 37°C for 1 hour on a rotation plate set at 60 r.p.m. After incubation, the epidermal cells, including the HFSCs, was scraped off from the trypsinized skin into the plate. 25 mLs of E-media was added to the cell suspension and was then sequentially strained through 100μm and 40μm filters. The cell pellet was washed twice with DPBS before proceeding with staining with cell surface markers. The cells were stained with 1:200 PerCP-Cy5.5-Sca1 (Thermo Fisher Scientific, 45-5981-82), 1:200 FITC-α6-integrin (eBioscience, 11-0493-81), 1:100 APC-EpCAM (Biolegend, 324207) and 1:20 Alexa700-CD34 (eBioscience, 56-0341-82) in staining buffer (HBSS + 2% Fetal Bovine Serum) for 30 minutes on ice and then washed twice with DPBS before cell sorting. HFSCs were sorted by gating on EpCAM (+), Sca1(-), α6-integrin(high) and CD34(+).

first: Pooja

last: Flora

first: Meng Yen

last: Li

first: Yudong

last: Zhou

first: Maria

last: Mercédes

first: Xiang Yu

first: Phillip

last: Galbo Jr

first: Elena

last: Ezhkova


title: Addressing the specific roles of histone modifications in transcriptional repression [ChIP-seq and CUT&RUN]

city: London

first: Aina

last: Mas

address: Chester Beatty Laboratories, 237 Fulham Rd.

institute: Institute of Cancer Research

summary: Our understanding of epigenetic processes is based on the hypothesis that individual posttranslational modifications of DNA and histones, or combinations thereof, function to direct unique downstream effects on transcription. Still, histone modifications are broadly categorized as repressive or activating, raising the question of potential functional redundancy. Here, we present an approach for addressing this question by substituting the genome-wide H3K27me3 pattern with other histone modifications. By taking advantage of the modular organization of PRC2, we direct de novo recruitment of H3K9me3 and H3K36me3 to PRC2 target genes in H3K27me3 null mouse embryonic stem cells (mESCs). We show that despite accurate genome-wide re-establishment of H3K36me3 at PRC2 target genes, which leads to significant reduction in H3K4me3 levels, the remaining H3K4me3 prevents H3K36me3 from recruiting sufficient DNA methylation to substitute for H3K27me3-mediated repression. In contrast, we demonstrate that H3K9me3 is more efficient in repressing H3K27me3 regulated genes, however this repression is also contingent on H3K4me3 status. Taken together, these results highlight the unique repressive functions of H3K27me3 and suggest that the functional effects of individual posttranslational modifications are highly dependent on the interplay with the existing chromatin environment.

overall_design: Chromatin Immunoprecipitation (ChIPseq) of PRC2 subunit SUZ12 as well as Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for histone modifications H3K4me3, H3K9me3, H3K27me3, H3K36me3 and H2AK119ub1

first: Lin

last: Hedehus

first: Robin

last: Armstrong

first: Richard

last: Koche

first: Hua

last: Wang

first: Aktan

last: Alpsoy


title: H2AK119ub dynamics controls hair follicle stem cell quiescence [CUT&Seq]

overall_design: C57BL6/J (wild type) mice were acquired from either The Jackson Laboratory or Charles River Laboratories and aged till P56., The back skin was collected and the adipose layer from the dorsal side was scraped off using a surgical scalpel. The scraped skin sample was washed with PBS prior to incubation with 0.25% Trypsin/EDTA at 37°C for 1 hour on a rotation plate set at 60 r.p.m. After incubation, the epidermal cells, including the HFSCs, was scraped off from the trypsinized skin into the plate. 25 mLs of E-media was added to the cell suspension and was then sequentially strained through 100μm and 40μm filters. The cell pellet was washed twice with DPBS before proceeding with staining with cell surface markers. The cells were stained with 1:200 PerCP-Cy5.5-Sca1 (Thermo Fisher Scientific, 45-5981-82), 1:200 FITC-α6-integrin (eBioscience, 11-0493-81), 1:100 APC-EpCAM (Biolegend, 324207) and 1:20 Alexa700-CD34 (eBioscience, 56-0341-82) in staining buffer (HBSS + 2% Fetal Bovine Serum) for 30 minutes on ice and then washed twice with DPBS before cell sorting. HFSCs were sorted by gating on EpCAM (+), Sca1(-), α6-integrin(high) and CD34(+).


title: H2AK119ub dynamics controls hair follicle stem cell quiescence [RNA-Seq 1]

overall_design: Control and PRC1 i2KO mice were induced starting at P50. 10 days after completion of induction treatment, the back skin was collected and the adipose layer from the dorsal side was scraped off using a surgical scalpel. The scraped skin sample was washed with PBS prior to incubation with 0.25% Trypsin/EDTA at 37°C for 1 hour on a rotation plate set at 60 r.p.m. After incubation, the epidermal cells, including the HFSCs, was scraped off from the trypsinized skin into the plate. 25 mLs of E-media was added to the cell suspension and was then sequentially strained through 100μm and 40μm filters. The cell pellet was washed twice with DPBS before proceeding with staining with cell surface markers. The cells were stained with 1:200 PerCP-Cy5.5-Sca1 (Thermo Fisher Scientific, 45-5981-82), 1:200 FITC-α6-integrin (eBioscience, 11-0493-81), 1:100 APC-EpCAM (Biolegend, 324207) and 1:20 Alexa700-CD34 (eBioscience, 56-0341-82) in staining buffer (HBSS + 2% Fetal Bovine Serum) for 30 minutes on ice and then washed twice with DPBS before cell sorting. HFSCs were sorted by gating on EpCAM (+), Sca1(-), α6-integrin(high) and CD34(+).


title: De novo mutations in the MiDAC HDAC complex cause a neurodevelopmental 2 syndrome resulting from increased deacetylase activity [RNA-seq]

city: Leicester

first: John

last: Schwabe

state: Leicestershire

address: Lancaster Road

department: Molecular and Cell Biology

institute: University of Leicester

summary: MIDEAS is a scaffold protein that, together with DNTTIP1, mediates assembly of the 36 MiDAC histone deacetylase complex. Mice lacking MiDAC die before birth suggesting 37 a key developmental function. Here, we report two unrelated individuals, with a 38 multisystem disorder characterized by delayed speech development, joint 39 contractures, dysmorphic features and dysmotility of the gut. Both individuals have the 40 same de novo heterozygous mis-sense variant in MIDEAS (Tyr654Ser). A cryoEM 41 structure of the MiDAC complex reveals that this amino acid is located in a conserved 42 auto-inhibitory loop that covers the active site of the deacetylase enzyme. We suggest 43 that the mutation results in loop displacement leading to elevated deacetylase activity. 44 In support, we observe reciprocal gene expression changes in patient fibroblasts 45 compared with a cell line following rapid MiDAC degradation. Our results establish 46 Mideas as a novel dominant monogenic disease gene and that hyperactivity of the 47 MiDAC complex results in a characteristic multisystem disorder.

overall_design:
RNA seq profiling of HCT 116 cells CRISPR-engineered to express endogenous DNTTIP1 with C-terminal FKBPF36V/FLAG to allow rapid degradation using dTAGv1 over 48h. Mouse embryonic fibroblast (MEF) wildtype and MIDEAS knockout RNA seq samples were reanalysed (samples: GSM4295062, GSM4295063, GSM4295064, GSM4295065, GSM4295066, GSM4295067, GSM4295068, GSM4295069, GSM4295070, GSM4295071) from series GSE144748. Samples were aligned using HISAT2 (v12.3.0) to GRCm39 release 112, sorted and indexed using samtools (v1.17) and count files made using LiBiNorm (v2.5; options -z -r pos -I gene_name -s reverse) with GRCm39 release 112 gene transfer format file. Differential gene expression analysis was performed using DESEQ2 (v1.44.0). Normalised counts are supplied in "reanalysis_samples.xlsx".

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

last: Turnbull

first: Kristupas

last: Sirvydis

middle: W