title: Dominant negative effects of Weaver syndrome-associated EZH2 variants [RNA-seq]

status: Public on Sep 03 2025

city: Dublin

first: Adrian

middle: P.

last: Bracken

address: The Smurfit Institute, The University of Dublin Trinity College, College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Heterozygous missense mutations in EZH2 cause Weaver syndrome (WS), a developmental disorder characterized by intellectual disability and overgrowth. EZH2 encodes the enzymatic subunit of Polycomb Repressive Complex 2 (PRC2), which mediates mono-, di-, and tri-methylation of histone H3 lysine 27 (H3K27me1/2/3). Most WS-associated EZH2 variants lack functional characterization but are presumed loss of function. However, the lack of early truncating mutations in EZH2 led us to hypothesise a dominant-negative mechanism for WS, which was supported by our structural analysis of all known WS-associated EZH2 variants. We isogenically modelled 10 representative variants in embryonic stem cells and showed they reduce global H3K27me2/3 with concomitant increases in H3K27ac and chromatin decompaction. Notably, the pattern of H3K27me2/3 reductions indicated dominant- negative interference on PRC2 activity, even when WS-variants were expressed at low levels. RNA-seq identified weakly Polycomb-bound genes that lose canonical PRC1 (cPRC1) occupancy and become derepressed, including several phenotypically relevant growth control genes. Comparative analysis of a gain-of-function EZH2 variant causing growth restriction revealed reciprocal chromatin and transcriptional changes compared to WS-associated variants. Taken together, our findings support a model where EZH2 variants associated with opposing developmental growth syndromes affect not only H3K27me3, but also intergenic H3K27me2, chromatin architecture, and cPRC1 recruitment.

overall_design: RNA-seq profiling to assess gene expression in Ezh2fl/∆ heterozygote cells expressing either EZH2-WT, growth restriction-associated EZH2, or one of five WS-associated EZH2 variants in both undifferentiated mESCs and briefly differentiated mESCs by removing 2i/LIF and treating with all-trans retinoicacid (ATRA).

first: Orla

last: Deevy

first: Jingjing

last: Li

first: Eric

last: Conway


title: Dominant negative effects of Weaver syndrome-associated EZH2 variants

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heterozygous missense mutations in EZH2 cause Weaver syndrome (WS), a developmental disorder characterized by intellectual disability and overgrowth. EZH2encodes the enzymatic subunit of Polycomb Repressive Complex 2 (PRC2), which mediates mono-, di-, and tri-methylation of histone H3 lysine 27 (H3K27me1/2/3). Most WS-associated EZH2 variants lack functional characterization but are presumed loss of function. However, the lack of early truncating mutations in EZH2 led us to hypothesise a dominant-negative mechanism for WS, which was supported by our structural analysis of all known WS-associated EZH2 variants. We isogenically modelled 10 representative variants in embryonic stem cells and showed they reduce global H3K27me2/3 with concomitant increases in H3K27ac and chromatin decompaction. Notably, the pattern of H3K27me2/3 reductions indicated dominant-negative interference on PRC2 activity, even when WS-variants were expressed atlow levels. RNA-seq identified weakly Polycomb-bound genes that lose canonical PRC1 (cPRC1) occupancy and become derepressed, including several phenotypically relevant growth control genes. Comparative analysis of a gain-of-function EZH2 variant causing growth restriction revealed reciprocal chromatin and transcriptional changes compared to WS-associated variants. Taken together, our findings support a model where EZH2 variants associated with opposing developmental growth syndromes affect not only H3K27me3, but also intergenic H3K27me2, chromatin architecture, and cPRC1 recruitment.

overall_design: We generated Ezh2 heterozygous knockout mESCs and then exogenously expressed FLAG/HA-tagged human wild-type EZH2 (EZH2-WT) or 5 Weaver syndrome associated EZH2 variants. For comparison, we also expressed growth restriction-associated EZH2-A733T variant. We performed exogenous reference genome-normalised ChIP-seq (ChIP-Rx) for H3K27me2, H3K27me3, H3K27ac, H3K36me2, SUZ12, CBX7, and FLAG in these cell lines.

middle: P


title: KRAS Inhibition Activates an Actionable CD24 “Don’t Eat Me” Signal in Pancreatic Cancer

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

country: USA

institute: M. D. Anderson Cancer Center

summary: KRASG12C inhibitors (G12Ci) have produced encouraging, albeit modest and transient, clinical benefit in pancreatic ductal adenocarcinoma (PDAC). Identifying and targeting resistance mechanisms to G12Ci treatment is therefore crucial. To better understand the function of KRASG12C and possible G12Ci bypass mechanisms, we developed an autochthonous KRASG12C-driven PDAC model. Compared to the classical KRASG12D PDAC model, the G12C model exhibits slower tumor growth, yet similar histopathological and molecular features. Aligned with clinical experience, G12Ci treatment of KRASG12C tumors produced modest impact despite stimulating a ‘hot’ tumor immune microenvironment. Immunoprofiling revealed that CD24, a ‘don’t eat me’ signal, is significantly upregulated on cancer cells upon G12Ci treatment. Blocking CD24 enhanced macrophage phagocytosis of cancer cells and significantly sensitized tumors to G12Ci treatment. Similar findings were observed in KRASG12D-driven PDAC. Together, this study reveals common and distinct oncogenic KRAS allele-specific biology and identifies a clinically actionable adaptive mechanism that may improve the efficacy of oncogenic KRAS inhibitor therapy in PDAC.

overall_design: GeoMx digital spatial profiler (DSP) for RNA profiling in formalin-fixed paraffin-embedded tissue sections from pancreas of 4 genetically engineered mice (2 KRAS G12C mutant and 2 KRAS G12D mutant) at ages of 16 weeks were processed for GeoMX RNA profiling.

first: Yongkun

last: Wei

first: Minghui

last: Liu

first: Er-Yen

last: Yen

first: Jun

last: Yao

first: Zhenzhen

last: Xun

first: Phuoc

middle: T

last: Nguyen

first: Xiaofei

last: Wang

first: Zecheng

last: Yang

first: Abdelrahman

last: Yousef

first: Dean

middle: N

last: Pan

first: Yanqing

last: Jin

first: Ching-Fei

first: Madelaine

middle: S

last: Theardy

first: Jangho

last: Park

first: Yiming

last: Cai

first: Mitsunobu

last: Takeda

first: Matthew

last: Vasquez

first: Elizabeth

first: Yong

last: Zhou

first: Hong

last: Zhao

first: Andrea

last: Viale

first: Huamin

first: Stephanie

last: Watowich

first: Han

last: Liang

first: Dan

first: Ronald

middle: A

last: DePinho

first: Wantong


title: CRISPR-cas cas7 influences the host-pathogen interaction of Porphyromonas gingivalis

city: Gainesville

first: Alejandro

last: Riveros Walker

state: Fl

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

type: Expression profiling by high throughput sequencing

summary: We investigated gene expression using a dual transcriptomic approach to understand if P. gingivalis ∆cas7 responds differently than WT to the intracellular environment of THP-1 cells and if these changes impact host response. Total RNA was extracted from THP-1 cells infected with P.gingivalis WT or Δcas7  for dual-transcriptomics gene expression analyses.

overall_design: Human monocyte/macrophage cell line THP-1 (ATCC, Virginia, USA) were cultured at 37°C in a 5% CO2 incubator in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum, l-glutamine (2 mM), penicillin/streptomycin (100 U/100 μg/ml), HEPES (10 mM), sodium pyruvate (1 mM), glucose (4.5 mg/ml), sodium bicarbonate (1.5 mg/ml), and 2-mercaptoethanol (0.05 mM). For P. gingivalis infection assays, THP-1 cells were adjusted to 5 × 105 cells/ml and were treated with 100 ng/ml phorbol 12-myristate-13-acetate (PMA; Sigma-Aldrich, Missouri, USA) to induce differentiation into a macrophage-like state. These cells were added to each well of 24-well cell culture plates and allowed to differentiate into a macrophage-like state for 48 h. At this point, the cell culture medium was replaced with an antibiotic-free culture medium. P. gingivalis WT and Δcas7 mutant harvested from overnight TSBHK broth culture were washed with RPMI 1640 media, adjusted to an OD600 of 1.0 (approximately 1 × 109 CFU/ml), and added to PMA-activated THP-1 cells at a multiplicity of infection (MOI) of 100, in complete antibiotic-free RPMI-1640 medium. After 2 h of co-culture, the wells were washed with PBS to remove non-attached bacteria and incubated with complete RPMI-1640 media supplemented with gentamicin (300 μg/ml)/metronidazole (200 μg/ml) and incubated for 2h or 6h. Total RNA was extracted from THP-1 cells co-cultured with either P. gingivalis WT, ∆cas7 for 2h or 6h.

first: Nicole

last: de Mello Fiallos

first: Muhammad

last: Irfan

first: Jose

last: Solbiati

middle: R

last: Walker

first: Jorge

last: Frias-Lopez

first: Frank

middle: C

last: Gibson


title: Preventing CpG hypermethylation in oocytes safeguards mouse development [WGBS 4-cell]

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

type: Methylation profiling by high throughput sequencing

summary: Except for regulatory CpG-island sequences, genomes of most mammalian cells are widely DNA-methylated. In oocytes though, DNAme is largely confined to transcribed regions. The mechanisms restricting de novo DNAme in oocytes and the relevance thereof for zygotic genome activation and embryonic development are largely unknown. Here we show that KDM2A and KDM2B, two histone demethylases, prevent genome-wide accumulation of histone H3 lysine 36 di-methylation, thereby impeding DNMT3A-catalyzed DNAme. We demonstrate that aberrant DNAme at CpG-islands inherited from Kdm2a/Kdm2b double mutant oocytes represses gene transcription in two-cell embryos. Aberrant maternal DNAme impairs pre-implantation embryonic development which is suppressed by Dnmt3a deficiency during oogenesis. Hence, KDM2A/KDM2B are essential for confining the oocyte methylome, thereby conferring competence for early embryonic development. Our research implies that the reprogramming capacity eminent to early embryos is insufficient for erasing aberrant DNAme from maternal chromatin, and that early development is vulnerable to gene dosage haplo-insufficiency effects.

overall_design: To study the function of KDM2A and KDM2B in regulating genome-wide DNA methylation in oocytes, we conditionally altered their expression in growing oocytes in several ways. First, by using Zp3-driven CRE recombinase-mediated excision, we removed exons encoding the histone demethylase JmjC domains of Kdm2a or Kdm2b, which fully abrogated expression of either protein. We also generated mice expressing a KDM2B protein lacking its CxxC domain, unable to be recruited to CpG island regions of the mouse genome. To address possible combinatorial roles of both proteins, we generated oocytes conditionally deficient for Kdm2a in combination with either Kdm2b mutation. We profiled genome-wide mCpG methylation in fully grown germinal vesicle oocytes of following genotypes: (1) Kdm2b-deltaCxxC, (2) Kdm2a-KO; Kdm2b-deltaCxxC, (3) Kdm2a-KO; Kdm2b-KO  and (4) controls. To study the impact of Kdm2a-KO and Kdm2b-KO double mutations introduced in oocytes on preimplantation embryo development, we profiled genome-wide CpG methylation in genetically hybrid, morphologically normal four-cell embryos generated by in vitro fertilization using spermatozoa from JF1 strain male mice.

first: Yumiko

middle: K

last: Kawamura

first: Panagiotis

last: Papasaikas

first: Evgeniy

last: Ozonov


title: Transepithelial barrier dysfunction drives microbiota dysbiosis to initiate epithelial clock-driven inflammation [16s]

status: Public on Sep 04 2025

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

summary: A time-series alteration in fecal microbiota was linked to the emergence of intraepithelial bacteria and a unique transcriptome profile in the mouse colon during IBD development.

overall_design: The gut microbiota in fecal and epithelial samples was analyzed in a time-series mode.

first: Yu-Chen

last: Pai

first: Yi-Hsuan

last: Li


title: Tumor-derived RAC1A159V mutation promotes an immunosuppressive tumor microenvironment that represses response to immune checkpoint inhibitor [scRNA-seq]

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Immune checkpoint inhibitors that activate cytotoxic T lymphocytes to kill cancer cells have seen great success in therapies against various tumor types. However, the overall response rate in patients remains unacceptable at ~15%.  RAC1, a member of Rho GTPase family, regulates multiple cellular processes in cancer, including vesicle trafficking, glycolysis, and exocytosis/endocytosis, which may contribute to tumor immune microenvironment modulation. RAC1A159V is a hotspot mutation found in several cancer types including colon cancer and is associated with poor prognosis. In this study, we have generated MC38 RAC1A159V cells by using CRISPR/Cas9 and confirmed that RAC1A159V results in upregulated RAC1 activity and downstream PAK1 and mTOR signaling.  We have found the RAC1A159V tumors grow at a similar rate as RAC1WT tumors in immunodeficient NSG mice but faster than RAC1WT tumors in syngeneic immunoproficient mice, and the RAC1A159V tumors are highly resistant to anti-PD1 treatment. Flow cytometry and scRNA-seq analyses reveal that RAC1A159V cells form “cold” tumors with an immunosuppressive microenvironment and suppressed tumor-immune cell interactions. Mechanistically, we show RAC1A159V upregulates glycosphingolipid biosynthesis to activate mTORC1 signaling in tumor cells, which in turn increases glycolysis, impairs key chemokine production, and decreases IFNGR1 expression of the tumor cells. mTORC1 inhibition re-sensitizes the RAC1A159V tumors to anti-PD1 treatment by reversing effects by RAC1A159V mutation on tumor cell glycolysis, chemokine production, and IFNGR1 expression. Our results demonstrate that RAC1A159V in tumors drives immune evasion via mTOR mediated glycolysis, chemotaxis, and IFN-γ response, and further suggest an approach of combining targeting of RAC1-mTOR signaling with immune checkpoint inhibitors for the treatment of immune-cold RAC1A159V tumors.

overall_design: MC38 tumor cells both wild-type and containing the RAC1A159V mutation were treated with IgG (control) and aPD1 (treatment) and subjected to single cell RNA-seq.

first: Adam

last: Mike

first: Zheng

last: Yi

first: Cai

last: Mingjun


title: Regulation of glucose and glutamine metabolism to overcome cisplatin resistance in intrahepatic cholangiocarcinoma

city: Chuncheon-si, Gangwon-do

first: Jueun

last: Kim

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

summary: Intrahepatic cholangiocarcinoma (ICC) is a bile duct cancer and a rare malignant tumor with a poor prognosis owing to the lack of an early diagnosis and resistance to conventional chemotherapy. A combination of gemcitabine and cisplatin is the typically attempted first-line treatment approach. However, the underlying mechanism of resistance to chemotherapy is poorly understood. We addressed this by studying dynamics in the human ICC SCK cell line. Here, we report that the regulation of glucose and glutamine metabolism was a key factor in overcoming cisplatin resistance in SCK cells. RNA sequencing analysis revealed a high enrichment cell cycle-related gene set score in cisplatin-resistant SCK (SCK-R) cells compared to parental SCK (SCK WT) cells. Cell cycle progression correlates with increased nutrient requirement and cancer proliferation or metastasis. Commonly, cancer cells are dependent upon glucose and glutamine availability for survival and proliferation. Indeed, we observed the increased expression of GLUT (glucose transporter), ASCT2 (glutamine transporter), and cancer progression markers in SCK-R cells. Thus, we inhibited enhanced metabolic reprogramming in SCK-R cells through nutrient starvation. SCK-R cells were sensitized to cisplatin, especially under glucose starvation. Glutaminase-1 (GLS1), which is a mitochondrial enzyme involved in tumorigenesis and progression in cancer cells, was upregulated in SCK-R cells. Targeting GLS1 with the GLS1 inhibitor CB-839 (telaglenastat) effectively reduced the expression of cancer progression markers. Taken together, our study results suggest that a combination of GLUT inhibition, which mimics glucose starvation, and GLS1 inhibition could be a therapeutic strategy to increase the chemosensitivity of ICC.

overall_design: mRNA profiles of SCK WT and SCK-R cells were generated by deep sequencing in duplicate by NovaSeq 6000

first: So Mi

last: Yang

first: Ji-Yeon

last: Lee

first: Jung-Shin

first: Ji Min


title: Tumor-derived RAC1A159V mutation promotes an immunosuppressive tumor microenvironment that represses response to immune checkpoint inhibitor [RNA-Seq]

overall_design: MC38 tumor cells both wild-type and containing the RAC1A159V mutation were treated with IgG (control) and aPD1 (treatment) and subjected to bulk RNA-seq.

first: Yi

last: Zheng

first: Mingjun

last: Cai


title: High-throughput single cell omics using semipermeable capsules

city: Vilnius

first: Denis

last: Baronas

address: Saulėtekio al. 7

country: Lithuania

institute: Vilnius University

summary: Biological systems are inherently complex and heterogeneous. Deciphering this complexity increasingly relies on high-throughput analytical methods and tools that efficiently probe the cellular phenotype and genotype. While recent advancements have enabled various single-cell -omics assays, their broader applications are inherently limited by the challenge of efficiently conducting multi-step biochemical assays while retaining various biological analytes. Extending on our previous work, here we present a versatile technology based on semi-permeable capsules (SPCs), tailored for a variety of high-throughput nucleic acid assays, including digital PCR, genome sequencing, single-cell RNA-sequencing (scRNA-Seq) and FACS-based sorting of individual transcriptomes based on nucleic acid marker of interest. Being biocompatible, the SPCs support single-cell cultivation and clonal expansion over long periods of time – a fundamental limitation of droplet microfluidics systems. Using SPCs we perform scRNA-Seq on white blood cells from patients with hematopoietic disorders and demonstrate that capsule-based sequencing approach (CapSeq) offers superior transcript capture, even for the most challenging cell types. By applying CapSeq on acute myeloid leukemia (AML) samples, we uncover notable changes in transcriptomes of mature granulocytes and monocytes associated with blast and progenitor cell phenotypes. Accurate representation of the entirety of the cellular heterogeneity of clinical samples, driving new insights into the malfunctioning of the innate immune system, and ability to clonally expand individual cells over long period of time, positions SPC technology as customizable, highly sensitive and broadly applicable tool for easy-to-use, scalable single-cell -omics applications.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human blood samples were collected from healthy and sick patients from the Vilnius University Hospital Santaros Klinikos Biobank (Vilnius, Lithuania) with a bioethics committee approval Nr. 2024/4-1583-1039. Samples were collected from a total of 8 AML patients, 8 neutropenia patients, 5 G-CSF stimulated donors, and 4 healthy donors.

first: Simonas

last: Norvaisis

first: Justina

last: Zvirblyte

first: Greta

last: Leonaviciene

first: Vincenta

last: Mikulenaite

first: Karolis

last: Goda

first: Vytautas

last: Kaseta

last: Sablauskas

first: Laimonas

last: Griskevicius

last: Juzenas

first: Linas

last: Mazutis


title: Co-mapping Clonal and Transcriptional Heterogeneity in Somatic Evolution via GoT-Multi.

city: New York

first: Anna

middle: S.

last: Nam

state: New York

address: Weiss Research Building, Floor 11

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

summary: Somatic evolution leads to clonal heterogeneity, which fuels cancer progression and therapy resistance. To decipher the consequences of clonal heterogeneity, we require a method that deconvolutes complex clonal architectures and their downstream transcriptional states. We developed Genotyping of Transcriptomes for multiple targets and sample types (GoT-Multi), a high-throughput, formalin-fixed paraffin-embedded (FFPE) tissue-compatible single-cell multi-omics for co-detection of multiple somatic genotypes and whole transcriptomes. We developed an ensemble-based machine learning pipeline to optimize genotyping. We applied GoT-Multi to frozen or FFPE samples of Richter transformation, a progression of chronic lymphocytic leukemia to therapy-resistant large B cell lymphoma. GoT-Multi detected heterogeneous cancer cell states with genotypic data of 27 mutations, enabling clonal architecture reconstruction linked with their transcriptional programs. Distinct subclonal genotypes, including therapy-resistant mutations, converged on an inflammatory state. Other subclones displayed enhanced proliferation and/or MYC program. Thus, GoT-Multi revealed that distinct genotypic identities may converge on similar transcriptional states to mediate therapy resistance.

overall_design:
Single-cell GoT-Multi (based on transcriptome and genotype profiling from 10x Genomics Fixed RNA Profiling)

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

last: Pak

first: Mirca

last: Saurty-Seerunghen

first: Kellie

last: Wise

first: Tsega-Ab

last: Abera

first: Chhiring

last: Lama

first: Neelang

last: Parghi

first: Ted

last: Kang

first: Xiaotian

last: Sun

first: Qi

last: Gao

first: Liming

last: Bao

first: Mikhail

last: Roshal

first: John

last: Allan

first: Richard

last: Furman

first: Luciano

middle: G

last: Martelotto


title: Dimethyl Fumarate (DMFu) as an anti-angiogenic agent in VEGF-treated human microvascular retinal endothelial cells (HRECs).

city: Baulkham Hills

first: Fergus

middle: Campbell

last: McLellan

state: NSW

address: 13 Delaigh Avenue

department: School of Vision Science

country: Australia

institute: University of New South Wales

summary: Vascular endothelial growth factor (VEGF) is a key driver of retinal and choroidal angiogenesis in wet age-related macular degeneration (nAMD). The present study investigated the impact of dimethyl fumarate (DMFu), a novel nAMD therapeutic candidate, on the transcriptomic profile of VEGF-treated primary human retinal endothelial cells (HRECs). In performing this study, we have described the individual transcriptomic implications of VEGF and DMFu in HRECs and characterised the impact of DMFu treatment on gene expression in VEGF-activated HRECs.

overall_design:
n = 6 replicates of primary human retinal endothelial cells (HRECs) were treated with either no treatment (control), vascular endothelial growth factor (VEGF), dimethyl fumarate or as a combination of VEGF + DMFu (total concentration of 10 ng/ml for each group) for 24 hours. RNA extraction was performed at the same time point for all groups, followed by sequencing.
Gene expression profiling was then performed on each group with reference to the untreated control.
Comparative gene expression profile analysis between VEGF, DMFu and VEGF + DMFu differentially expressed genes was then performed.

first: McLellan

last: Fergus

first: Ng

last: Pei Qin

first: Huang

last: Kelvin

first: Shu

middle: Y

last: Daisy


title: snRNAseq from sciatic nerves from mouse of 2-3, 15-16, and 20-30 months old

city: Freiburg im Breisgau

first: Luis

last: Hortells

address: Albertstraße 25

country: Germany

institute: University of Freiburg

summary: Changes in gene expression during peripheral nerves aging, to the single cell level, are unkown. To explore possible age-related changes during healthy aging of peripheral nerves  we compared snRNAseq of sciatic nerves from young adult (2-3 months old), senior adult (15-16 months old), and aged (20-30 month old mice.

overall_design: Nerves from WT (C57BL/6) mice were mechanically dissociated and viable (DRAQ7+) nuclei were sorted using Fluorescent activated cell sorting based on size.

first: Sebastian

last: Preissl

first: Madelon

last: Hossfeld


title: Injectable plant phosphate coordination compounds-based adhesive hydrogel accelerates osteoporotic fracture healing by restoring bone homeostasis

city: guangzhou

first: Lei

last: Zhou

state: guangdong

address: 63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province

country: China

institute: The Third Affiliated Hospital of Guangzhou Medical University

summary: Osteoporotic fractures are notoriously difficult to heal due to an imbalance between osteoblasts and osteoclasts. Current treatments often have limited efficacy or adverse side effects, highlighting the need for safer, more effective solutions. Here, we developed an injectable plant-derived phosphate coordination compound-based adhesive hydrogel to restore bone homeostasis by integrating magnesium ions (Mg2+)-phytic acid (PA) nanoparticles with aminated gelatin and aldehydated starch. The hydrogel can firmly adhere to irregular bone tissue at the fracture site and achieve achieve Mg-PA degradation in response to the osteoporotic acidic microenvironment, releasing PA and Mg2+, which modulated osteoclast and osteoblast activity, respectively. Impressively, PA inhibits osteoclastogenesis by stimulating monocyte secretion of CCN1, which competitively binds RANKL to disrupt RANKL-RANK signaling. Meanwhile, Mg2+ enhances osteoblast differentiation from bone marrow stem cells. In an ovariectomized rat model, the hydrogel significantly accelerates fracture healing (84.63% improvement over the control groups in flexural strength). This study highlights the potential of PA-based coordination compounds as a novel strategy for osteoporotic fracture treatment.

overall_design: In this study, MgPA-Gel adhesive was used to treat osteoporotic femoral fractures in SD rats. Femoral tissue of 1 cm length around the fracture end of the gel-only group and the MgPA-Gel group was selected for high-throughput mRNA detection, with 3 samples in each group.

first: Zunlei

last: Gong

first: Tianhua

last: Xiao

first: Dan

last: Wu

first: Hui

last: Yu

first: Xudan

last: Xing

first: Yuanxin

last: Li

first: Yu

last: Cai

first: Chuke

last: Chen

first: Jiamin

last: Liu

first: Dongming

last: Duan

first: Daxuan

last: Liang

first: Rui

last: Zhu

first: Zerong

last: Wang

first: Song

first: Guoxin

last: Tan

first: Chengyun

last: Ning

first: Le

first: Zenghui


title: Temporal atlas of renal immune cells in crescentic glomerulonephritis

city: Bonn

first: Junping

last: Yin

state: State

address: Venusberg-Campus, 1

institute: uniklinikum bonn

summary: During glomerulonephritis, the phenotype, proliferation, differentiation and function of infiltrated immune cells are affected by the inflammatory context and changed during the course of glomerulonephritis. To comprehensively and temporally understand these characteristics of infiltrated immune cells, we performed single cell RNA sequencing and single cell TCR sequencing from healthy mice and mice with cresentic glomerulonephritis at day 3, day 7 and day 14.

overall_design: Renal CD45+ immune cells and CD3+ T cells were sorted from mouse kidneys with cGN at different timepoints. Sorted cells were loaded for library preparation by using 10x single cell RNA sequencing and 10x single cell TCR sequencing.

first: Christian

last: Krebs

first: Ulf

last: Panzer

last: Kurts


title: Glycogen synthase kinase-3 is essential for Treg development and homeostasis

city: Oxford

first: Alexander

last: Clarke

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

summary: Study of the effects of inducible deletion of Gsk3a and Gsk3b in Tregs.

overall_design: Foxp3-ERT2-cre-eGFP x Gsk3a/b x tdTomato-Ai9 and Foxp3-ERT2-cre-eGFP x tdTomato-Ai9 mice were treated with tamoxifen, and 14 days later tdTomato+ cells were sorted (n=4 mice per condition), labelled with HTO antibodies, and combined into 2 pools (of 2 WT and 2 KO mice each) for 10x single cell RNA sequencing.

middle: J


title: RNA-seq performed for review

city: ShenZhen

first: Luming

last: Zhang

state: Guangdong

address: 1088 Xueyuan Avenue

department: School of Life Sciences

institute: Southern University of Science and Technology

summary: The transition from maternal to zygotic gene expression during zygotic genome activation (ZGA) is tightly associated with  chromatin accessibility modulated by maternal transcription factors. However, due to technical limitations, it remains elusive how the chromatin regulatory landscape is established in Xenopus tropicalis ZGA, and let alone DNA binding transcription regulators involved in this process. Here, by developing concanavalin A beads-based nucleus capture followed by Tn5-mediated accessible chromatin assay with sequencing (CANTAC-seq), we generated a first genome-wide map of accessible chromatin in X. tropicalis embryos from early blastula to neurula stage. We found that open chromatin landscape is progressively established at cis-regulatory elements during ZGA. Based on the motif analysis and perturbation experiments, we demostrated E2f1, a well-known transcriptional activator, maintains a repressive chromatin environment preceding minor ZGA. Moreover, we identified another maternal factor Otx1 counteracts the inhibitory function of E2f1. Mechanistically, E2f1 and Otx1 co-regulate a set of genes required for zygotic gene transcription and germ layer differentiation before the midblastula transition (MBT) through a seesaw model. Taken together, our data reveals the dynamic chromatin regulatory landscape that accompanies early development and elaborates on the function of a coupled transcriptional repressor-activator regulating zygotic gene transcription in a classical model organism.

overall_design: We performed mRNA-seq to analyze the expression profiles of early Xenopus tropicalis embryos.

first: Wei

first: Huanhuan

last: Cui

first: Zhaoying

last: Shi


title: Additional Over-expression RNA-seq Data for CANTAC-seq analysis reveals the maternal factors E2f1 and Otx1 co-modulate minor zygotic gene transcription by a seesaw model


title: CANTAC-seq analysis reveals the maternal factors E2f1 and Otx1 co-modulate minor zygotic gene transcription by a seesaw model (RNA-Seq)

first: Weizheng


title: CANTAC-seq analysis reveals the maternal factors E2f1 and Otx1 co-modulate minor zygotic gene transcription by a seesaw model (ChIP-Seq)

overall_design: We performed ChIP-seq to analyze the  genome-wide binding of E2f1 and Otx1 in early Xenopus tropicalis embryos.


title: CANTAC-seq analysis reveals the maternal factors E2f1 and Otx1 co-modulate minor zygotic gene transcription by a seesaw model (CANTAC-seq)

sample_organism:
Xenopus tropicalis
Homo sapiens
Mus musculus

overall_design: We developed CANTAC-seq to analyze the chromatin accessibility landscape of early Xenopus tropicalis embryos.


title: Deficiency of Smooth Muscle ADAR1 RNA Editing Exacerbates Vascular Remodeling and Pulmonary Hypertension

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

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

overall_design: Refer to individual Series


title: Deficiency of Smooth Muscle ADAR1 RNA Editing Exacerbates Vascular Remodeling and Pulmonary Hypertension [pul51_RNA-seq]

summary: Adenosine deaminase acting on RNA 1 (ADAR1) catalyzes the conversion of adenosine (A) to inosine (I) in double-stranded RNA (dsRNA), which is critical to prevent auto-inflammatory responses mediated by activation of the type I interferon (IFN) signaling. Here, we define the role of ADAR1-dependent RNA editing in interferon-β(IFNβ) activation and pulmonary artery smooth muscle cell (PASMC) remodeling in pulmonary arterial hypertension (PAH), a devastating disease leading to right heart failure and premature death. Methods: RNA editing levels were analyzed in human pulmonary artery smooth muscle cells (PASMCs) from idiopathic PAH (IPAH) patients versus healthy controls. A conditional transgenic line ADAR1SMC-KO was generated by knocking out ADAR1 selectively in α-smooth muscle actin-positive cells, followed by hypoxic exposure to induce PH. Results: PASMCs from IPAH patients displayed decreased levels of ADAR1 mRNA and protein, accompanied by reduced A-to-I editing compared to healthy PASMCs. ADAR1 knockdown in PASMCs upregulated MDA5, PKR, IFN-β and IFN-Stimulated Genes (ISGs). Compared with controls in vivo, hypoxic ADAR1SMC-KO mice developed severe PH, as evidenced by excessive vascular remodeling in distal arterioles and increased vascular leakage resulting in elevated right ventricular systolic pressure and right ventricular hypertrophy. Mechanistically, IFNβ signaling in ADAR1SMC-KO lungs induced the recruitment of inflammatory cells, including macrophages, which in turn enhanced PASMC proliferation and muscularization. Correspondingly, pharmacological treatment with PKR kinase inhibitor Imoxin decreased IFNβ thus attenuating the hypoxia-induced PH phenotype of ADAR1SMC-KO mice. Conclusions: ADAR1-dependent A-to-I RNA editing tempers IFN signaling in PASMCs. Pathologic reduction of ADAR1 in SMCs increased IFNβ activity, macrophage recruitment, and worsened PH, thus demonstrating a direct detrimental role of vascular innate immune responses in PH. Targeting PKR could be the new therapeutic strategy aimed at treating PAH.

overall_design: Human primary PASMCs were transfected 48 hours with non-targeting control siRNA or siADAR1 and processed for RNA-sequencing

first: Giovanni

last: Maroli

first: Stefan

last: Günther


title: Deficiency of Smooth Muscle ADAR1 RNA Editing Exacerbates Vascular Remodeling and Pulmonary Hypertension [pul43_RNA-seq]

overall_design: Human primary PASMCs were transfected 48 hours with non-targeting control siRNA, siADAR1, siADAR2 or siADAR1+siADAR2 and processed for RNA-sequencing


title: Rejuvenation of mesenchymal stem cells by human peripheral blood lymphocytes

status: Public on Sep 02 2025

city: Zunyi

first: Yi

last: Luo

address: 149 Dalian Road, Huichuan District

institute: Affiliated Hospital of Zunyi Medical University

summary: Here we presented a novel approach to combat cellular senescence and promote cell proliferation by coculturing human MSCs with human peripheral blood lymphocytes (PBLs). In a heterogeneous population of MSCs comprising both aged and nonaged cells, PBL effector cells, rather than their cytokines, exhibited a dual role. They selectively induced apoptosis in aged cells by facilitating p53 SUMOylation and activating the p53-dependent mitochondrial pathway, while simultaneously safeguarding younger cells against senescence and promoting cell proliferation by activating Serpinb2/NF-κB signaling. This resulted in a decrease in aged MSCs and an enrichment of rejuvenated MSCs. This process effectively reversed the senescence phenotype, leading to the remodeling of stemness characteristics and the enhancement of functionality within the MSC population. Furthermore, MSCs rejuvenated by PBLs presented an enhanced therapeutic efficacy and a favorable safety profile.

overall_design: The transcriptome changes of PBLs after hAMSCs treatment were determined by RNA-seq analysis. Sequencing was performed on three independent replicates in the PBL group and the ac_PBL group.

first: Xinxin

last: zhu

first: Qingrong

last: le

first: Wenting

last: chen

first: Yan

last: xu

first: Huan

last: yuan

first: Jianhui

last: xiao


title: Rejuvenation of mesenchymal stem cells by human peripheral blood lymphocytes: A dual-mechanism for targeting senescent cell clearance and promoting cell proliferation in a coculture system [RNA-Seq]

overall_design: The transcriptome changes of P10 hAMSCs after PBL treatment were determined by RNA-seq analysis. Sequencing was performed on three independent replicates in the P10 group and the P10+PBL group.


title: Plastic associated endocrine disruptors reduce Nicastrin protein and potentiate inflammation in Hidradenitis Suppurativa skin disease

city: Baltimore

first: Sam

last: Lee

state: MD

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

summary: Hidradenitis Suppurativa (HS) is an inflammatory skin disorder with limited treatments and unclear etiology. While monogenic HS is linked to gamma secretase (GS) mutations, particularly in the Nicastrin (NCSTN) subunit, the pathogenesis of the more common sporadic form remains uncertain, though associated with risk factors such as diets high in ultra-processed foods (UPFs). Consistent with the clinical overlap between sporadic and monogenic HS, we find loss of NCSTN protein in sporadic HS fibroblasts. We hypothesize the rising incidence of sporadic HS and its hormonal associations implicate endocrine-disrupting chemicals (EDCs), especially plastic-associated EDCs (p-EDs) common in UPFs. We detect elevated p-ED adducts in HS skin, persisting in ex vivo cultured fibroblasts. At nanomolar concentrations, p-EDs inhibits NCSTN and primes fibroblasts for inflammation, mimicking NCSTN knockdown. These findings suggest p-ED exposure contributes to HS pathogenesis, highlighting the need to address environmental exposures in HS and other GS-related diseases.

overall_design: RNAseq profiling of scRNA and siNCSTN fibroblasts and keratinocytes. Also included: Gamma secreatase inhibitor treated fibroblasts and pED treated fibroblasts.

first: Kaitlin

last: Williams

first: Luis

last: Garza


title: Genotype-Specific Modulation of Drought Tolerance by Arbuscular Mycorrhizal Symbiosis in Foxtail Millet

first: Wei-Yi

last: Lin

state: Taipei City

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Agronomy

summary: Drought stress is a major environmental factor limiting crop productivity. Arbuscular mycorrhizal fungi (AMF), as beneficial soil microbes, can improve plant growth and stress resilience; however, the effectiveness of this symbiosis is often influenced by the host plant's genetic background. In this study, we investigated the interaction between AM symbiosis and drought tolerance in two foxtail millet (Setaria italica) genotypes with contrasting drought responses: the drought-tolerant ISE42 and the drought-sensitive TT8. Following a 14-day drought treatment, both genotypes exhibited wilting, but only AMF-colonized ISE42 plants recovered upon rewatering. Transcriptomic analysis revealed that AM symbiosis significantly enhanced the expression of genes involved in nitrogen transport, assimilation, lignin metabolism, and cellulose biosynthesis in ISE42, but not in TT8. These molecular changes suggest improved nutrient uptake and cell wall reinforcement as key mechanisms underlying enhanced drought tolerance. Additionally, stress hormone signaling pathways were downregulated in colonized ISE42 roots, indicating possible alleviation of drought-induced stress through AM symbiosis. Our results demonstrate genotype-specific effects of AMF on drought tolerance and highlight the importance of considering host genetic variation in the application of AMF for crop improvement.

overall_design: RNA-seq profiling of drought tolerant and sensitive foxtail millet accessions in response to arbuscular mycorrhizal symbiosis under drought

first: Lin

last: Wei-Yi

first: Chang

last: O-Chi


title: A combined enteric neuron-gastric tumor organoid reveals metabolic vulnerabilities in gastric cancer

city: Hong Kong

first: Alan Siu Lun

last: Wong

address: Laboratory Block, 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: The discrepancy between organoid and immortalized cell line cultures for cancer target discovery remains unclear. Here, our multi-tiered CRISPR screens reveal in vivo-relevant metabolic dependencies and synthetic lethal pairs that can be uncovered with tumor organoids but not cell lines or even 3D spheroids. These screens identify lanosterol synthase and acetyl-CoA carboxylase inhibitors as effective treatments that impede xenografted tumor growth in mice. These lipid metabolic inhibitors exhibit nanomolar IC50 values across diverse human gastric cancer organoids resistant to first-line treatments. Mechanistically, gastric cancer organoids and in vivo tumor exhibit lipid metabolic adaptations not seen in 2D in vitro cultures. Additionally, enteric neurons modulate lipid metabolism in tumor organoids, altering drug sensitivity by up to two orders of magnitude. A neuron-cocultured CRISPR screen further reveals that acetyl-CoA carboxylase expression determines lanosterol synthase inhibitor efficacy. These findings highlight the critical roles of organoid environment and neuronal interaction in cancer lipid reliance.

overall_design: Gene expression profiling analysis of RNA-seq data from patient-derived organoids, 2D cell lines and in vivo tumors.

first: Becky Ka Ching

last: Chan

first: Chu

last: Zhang

first: Chi Him

last: Poon

first: Helen Hoi Ning

last: Yan

first: Suet Yi

last: Leung


title: Single cell expression profiling of brain tumors in mice intracranially injected with 2x105 glioblastoma tumor cells isolated from NTv-a;hUBC-CreERT2;Adar1flox/flox mice and treated with tamoxifen to induce Adar1 deletion, or with vehicle control.

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Glioblastomas are the most frequent and aggressive primary brain tumors. Current treatments invariably fail, a consequence of the pronounced heterogeneity and plasticity of glioblastoma cells, as well as the contribution of an immunosuppressive microenvironment that promotes tumor progression and resistance to therapy. Here, we exploited an innate immunity checkpoint, RNA sensing, to simultaneously target cancer cells and their supporting microenvironment. Using various immunocompetent mouse models of glioblastoma, we found that genetic deletion of Adar1, a key regulator of the RNA sensing pathway, resulted in significantly reduced tumor growth and prolonged survival. Mechanistically, these effects were mediated by two processes: cancer-cell intrinsic responses and reprogramming of the immune microenvironment that fostered a pro-inflammatory, anti-tumoral state via type I interferon signaling. These findings establish proof of concept for the therapeutic potential of targeting ADAR1 in glioblastoma, offering new strategies for the treatment of this aggressive disease.

overall_design: Comparative gene expression profiling of mouse glioblastoma tumor microenvironment upon deletion of Adar1.

first: Ángel

middle: F

last: Álvarez-Prado

first: Johanna

last: Joyce


title: Breast Cancer Remodels Lymphatics in Sentinel Lymph Nodes

city: Turku

first: Diana

last: Lehotina

address: Tykistökatu 6A

country: Finland

institute: University of Turku

summary: Cancer metastasis to sentinel lymph nodes (LNs) is often the first marker of potential disease progression. Although it is recognized that tumor-induced lymphangiogenesis facilitates metastasis into LNs in murine models, tumor-induced alterations in human lymphatic vessels remain obscure. We used single-cell RNA sequencing and high-resolution spatial transcriptomics to profile lymphatic endothelial cell (LEC) subsets in paired metastatic and non-metastatic LNs obtained from patients with treatment-naïve breast cancer. Tumor metastasis decreases immunoregulatory LEC subsets, such as PD-L1+ subcapsular sinus LECs, while inducing an increase in capillary-like CD200+ HEY1+ LECs. Matrix Gla protein (MGP) was the most upregulated gene in metastatic LN LECs, and its expression on LECs was TGF-b and VEGF dependent. Upregulated MGP promotes cancer cell adhesion to LN lymphatics. Thus, breast cancer cell metastasis to LNs remodels LEC subsets in human LNs and escalates MGP expression, potentially facilitating cancer cell dissemination through the lymphatic system.

overall_design: High resolution spatial transcriptomics of paired metastatic and distant human lymph nodes

first: Akira

last: Takeda

first: Sirpa

last: Jalkanen


title: Cancer cell and microenvironmental rewiring by ADAR1 loss impairs glioblastoma tumor growth and extends survival


title: Gene expression profiling of human glioblastoma cell lines treated with 8-Azaadenosine

overall_design: Comparative gene expression profiling of human glioblastoma cell lines treated with 8-Azaadenosine or vehicle.


title: Single-cell exploration of gonadal somatic cell lineage specification during human sex determination

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: Gonad development is an exciting model to study cell fate commitment. A better understanding of sex determination requires the identification of all involved cell types and their dynamic expression programs. Here, we present an atlas of 128,000 single cells from human gonads between 5 and 12 post-conceptional weeks. A focused analysis of somatic cells uncovered a population of bipotential progenitors derived from the coelomic epithelium of both testes and ovaries, which may have the capacity to commit to either a steroidogenic or a supporting fate. Moreover, our analyses suggest that early supporting cells, prior to differentiation into Sertoli or pre-granulosa cells, also give rise to the rete testis/ovarii and that the ovary retains the capacity to feed the supporting cell pool for an extended period of time, directly from the surface epithelium. Finally, the potential involvement of the gonadotropin releasing hormone (GnRH) signaling pathway in regulating testis differentiation was assessed ex vivo.

overall_design:
Testicular mRNA profiles of human male fetal gonads at 5-6 PCW (postconceptional week) (n=10 individuals, 20 testes) exposed to DMSO ± Leuprolide (GnRHR agonist) during 24 hours hanging drop cultures were generated by Bulk RNA Barcoding and sequencing (BRB-seq).

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

first: Aurélie

last: Lardenois

first: Antonio

last: Suglia

first: Bertrand

last: Evrard

first: Antoine

middle: D

last: Rolland


title: Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation

first: Felix

last: Naef

address: EPFL SV IBI

institute: EPFL

summary:
Background
Cells regulate protein synthesis in response to fluctuating nutrient availability through mechanisms that affect both translation initiation and elongation. Branched-chain amino acids, leucine, isoleucine, and valine, are essential nutrients. However, how their depletion affects translation remains largely unclear. Here, we investigate the immediate effects of single, double, and triple branched-chain amino acid deprivation on translational dynamics in NIH3T3 cells using RNA-seq and ribosome profiling.

Results
All starvation conditions increased ribosome dwell times, with pronounced stalling at all valine codons during valine and triple starvation, whereas leucine and isoleucine starvation produced milder, codon-specific effects. Notably, stalling under isoleucine deprivation largely decreased under triple starvation. Positional enrichment of valine codons near the 5′ end and downstream isoleucine codons potentially contributes to these patterns, suggesting a possible elongation bottleneck that influences translational responses under branched-chain amino acid starvation. The presence of multiple valine stalling sites was associated with decreased protein levels. Finally, codon-specific dwell time changes correlated strongly with patterns of tRNA isoacceptor charging.

Conclusions
Together, these findings suggest that differential ribosome stalling under branched-chain amino acid starvation reflects a balance between amino acid supply, tRNA charging dynamics, codon position, and stress-response signaling.

overall_design: NIH3T3 mouse fibroblast cells were grown either in complete medium (control) or in medium lacking specific branched-chain amino acids for 6 hours

first: Lina

last: Worpenberg

first: Cedric

last: Gobet


summary:
Background: Cells regulate protein synthesis in response to fluctuating nutrient availability through mechanisms that affect both translation initiation and elongation. Branched-chain amino acids, leucine, isoleucine, and valine, are essential nutrients. However, how their depletion affects translation remains largely unclear. Here, we investigate the immediate effects of single, double, and triple branched-chain amino acid deprivation on translational dynamics in NIH3T3 cells using RNA-seq and ribosome profiling.

Results: All starvation conditions increased ribosome dwell times, with pronounced stalling at all valine codons during valine and triple starvation, whereas leucine and isoleucine starvation produced milder, codon-specific effects. Notably, stalling under isoleucine deprivation largely decreased under triple starvation. Positional enrichment of valine codons near the 5' end and downstream isoleucine codons potentially contributes to these patterns, suggesting a possible elongation bottleneck that influences translational responses under branched-chain amino acid starvation. The presence of multiple valine stalling sites was associated with decreased protein levels. Finally, codon-specific dwell time changes correlated strongly with patterns of tRNA isoacceptor charging.

Conclusions: Together, these findings suggest that differential ribosome stalling under branched-chain amino acid starvation reflects a balance between amino acid supply, tRNA charging dynamics, codon position, and stress-response signaling.

overall_design: NIH3T3 mouse fibroblast cells were grown either in complete medium (control) or in medium lacking specific branched-chain amino acids for 6 hours.


title: CANTAC-seq analysis reveals the maternal factors E2f1 and Otx1 co-modulate minor zygotic gene transcription by a seesaw model

first: Luming

last: Zhang

platform_organism:
Xenopus tropicalis
Homo sapiens
Mus musculus


title: Chd4 remodels chromatin to control retinal cell type specification and lineage termination

city: Ottawa

first: Pierre

last: Mattar

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

summary: During development, neural progenitor cells modify their output over time to produce different types of neurons and glia in chronological sequences. Previous studies have shown that epigenetic processes play a crucial role in regulating neural progenitor potential, but the underlying mechanisms are not well understood. Here, we hypothesized that nucleosome remodelling would regulate the competence transitions of retinal progenitors. We generated retina-specific conditional knockouts (cKOs) in the key nucleosome remodelling enzyme Chd4. Chd4 cKOs overproduced early-born retinal ganglion and amacrine cells. Postnatally, later-born rod photoreceptors were drastically underproduced. Concomitantly, progenitors failed to be exhausted at late phases of development and ultimately overproduced Müller glia. To determine how Chd4 regulates the genome, we used cut&run-seq to reveal Chd4 genome occupancy, and ATAC-seq experiments to visualize nucleosome remodelling. These data revealed that genome accessibility was significantly increased at ∼10,000 regulatory elements and ∼4,000 genes in the Chd4 cKO. Together, these results suggest that Chd4 restricts the genome to repress progenitor identity and promote rod photoreceptor production. Accordingly, multiplexed single-cell transcriptomics demonstrated that deletion of Chd4 led to markedly divergent gene expression profiles. However, despite overproduction of early fates and underproduction of later-born rods, the perinatal transition between early and late progenitor competence was not altered as determined by birthdating experiments and transcriptomic signatures. Taken together, our data suggest that Chd4-dependent chromatin remodelling regulates cell fate specification, and is also required to terminate retinal neurogenesis, but that it does not regulate the progenitor competence windows that restrict early-vs. late-cell-type production.

overall_design: Retinae from control (Chd4 f/+Cre+) and mutant (Chd4 f/f Cre+) P1  mice were dissociated and subjected to a MULTI-seq scRNAseq protocol.

first: Sujay

last: Shah

first: José Alex Lourenço

last: Fernandes

first: Suma

last: Medisetti


title: Plant Mobile Domain protein-DNA motif modules counteract Polycomb silencing to stabilize gene expression

city: Clermont-Ferrand

first: Olivier

last: Mathieu

state: Auvergne

address: 28 Place Henri Dunant

department: UMR 6293 - iGReD

institute: CNRS

summary: In plants and animals, Polycomb group (PcG) proteins are crucial for development, regulating gene expression through H3K27me3 deposition and subsequent gene silencing. While Polycomb silencing target specification is increasingly understood, it remains unclear how certain genes with apparent silencing-attracting features escape this process. Here, we show that the plant mobile domain C (PMD-C) containing proteins MAINTENANCE OF MERISTEMS (MAIN), MAIN-LIKE 1 (MAIL1) and MAIL2 oppose Polycomb silencing at numerous actively transcribed genes in Arabidopsis. Mutations in MAIN, MAIL1 or MAIL2 result in PcG-dependent ectopic H3K27me3 deposition, often associated with transcriptional repression. We show that MAIL1, which functions in concert with MAIN, and MAIL2 target distinct gene sets and associate with chromatin at specific DNA sequence motifs. We demonstrate that the integrity of these motif sequences is essential for promoting expression and antagonizing H3K27me3 deposition. Our results unveil a novel system opposing Polycomb silencing involving PMD-C protein-DNA motif modules, expanding our understanding of eukaryotic gene regulation mechanisms.

overall_design: Expression profiling by high throughput sequencing; epigenome profiling by high throughput sequencing; genome binding/occupancy profiling by high throughput sequencing.

first: Thierry

last: Pélissier

first: Lucas

last: Jarry

first: Margaux

last: Olivier

first: Gabin

last: Dajoux

first: Marie-Noëlle

last: Pouch-Pélissier

first: Charles

last: Courtois

first: Julie

last: Descombin

first: Nathalie

last: Picault

first: Guillaume

last: Moissiard


title: Mutual adaptation of C. albicans and the host in the stably colonized murine tongue tissue

city: Zürich

first: Ricardo

last: Frois-Martins

address: Winterthurerstrasse 260

department: Section of Immunology

institute: University of Zürich - Tierspital

summary: The human commensal fungus C. albicans colonizes the oral mucosa of most healthy individuals. Homeostasis at the fungus-host interface depends strictly on the IL-17 pathway. To understand the mutual adaptations of C. albicans and the host in the oral mucosa and to assess the IL-17-dependence thereof, we employed a mouse model of long-term C. albicans colonization and  transcriptionally profiled the colonized tongue tissue at day 3 and day 19. The antifungal response is strongly induced on day 3 after colonization, with many antimicrobial factors being induced in an IL-17-dependent manner. Due to fungal overgrowth and exacerbated tissue invasion in IL-17-deficient mice, the transcriptome is dominated by a plethora of inflammatory genes such as Il-20 family, Il-17a/f, Il-13 and IFNy, by day 19. Only few fungal transcripts could be reliably be detected, given that the fungal transcripts represent only a small proportion of the entire RNA and without enrichment. They support the notion that C. albicans adopts virulence features in the IL-17-deficient host einvironment with increased expression of hyphae specific genes like HWP1.

sample_organism:
Candida albicans
Mus musculus

platform_organism:
Candida albicans
Mus musculus

overall_design:
Gene expression profiling (RNA-seq) of C.albicans strain 101 grown in YPD broth, and of murine tongues of Il-17rc-/- or Il-17rc+/- mice that were associated with C. albicans strain 101 for 3 days or 19 days.
The samples with low candida concentrations that we sequenced deep to get sufficient candida reads. The raw file linked to the '*_B' sample was used to generate the candida prcessed data file, and the raw file linked to the corresponding *_A sample was used to  generate the mouse processed file.

last: Fróis-Martins

first: Salomé

last: LeibundGut-Landmann

first: Hubert

last: Rehrauer


title: Regulation of the NSL complex by TAF4A is critical for genome stability and quiescence of skeletal muscle stem cells [CnR of NF-YA in WT and Taf4asKO MuSCs]

first: Carsten

last: Kuenne

summary: Acetylation of lamin A/C by the NSL complex, containing MOF and KANSL2, is instrumental for maintaining nuclear architecture and genome stability, but the mechanisms controlling expression of NSL complex components in different cell types are poorly characterized. Here, we describe that TAF4A, primarily known as a subunit of the general transcription factor TFIID, is critical for cell type-specific regulation of Kansl2 in MuSCs. Inactivation of Taf4a in MuSCs reduces expression of Kansl2 and alters post-translational modification of lamin A/C, thereby decreasing the stiffness of MuSC nuclei and disrupting the nuclear architecture. Using CUT&RUN technique, we found that TAF4A together with the heterotrimeric transcription factor NF-Y controls Kansl2 expression. In addition to destabilization of the nuclear architecture, reduced expression of Kansl2 in Taf4a-mutant MuSCs changes expression of numerous genes involved in chromatin regulation. The subsequent loss of heterochromatin and MuSC activation, in combination with pronounced genomic instability, activates MuSCs and impairs MuSC proliferation, which depletes the stem cell pool and abolishes skeletal muscle regeneration. We conclude that TAF4A-NF-Y-dependent transcription regulation safeguards heterochromatin and genome stability of MuSCs via the NSL complex.

overall_design: Genome-wide profiling of NF-YA in wild type  and Taf4asKO muscle stem cells

first: Angelina

middle: M

last: Georgieva

first: Stefan

last: Günther


title: Regulation of the NSL complex by TAF4A is critical for genome stability and quiescence of skeletal muscle stem cells [CnR of KANSL2 in WT MuSCs]

overall_design: Genome-wide profiling of KANSL2 in wild type muscle stem cells


title: Early life injury alters spinal astrocyte development

city: Cincinnati

first: Mark

middle: L

last: Baccei

state: OH

address: 231 Albert Sabin Way

department: Anesthesiology

institute: University of Cincinnati

summary: Neonatal injury alters synaptic transmission and plasticity in the spinal superficial dorsal horn (SDH), resulting in aberrant amplification of ascending nociceptive transmission. Astrocytes orchestrate synapse development and function across the CNS and have been shown to play a critical role in the emergence and maintenance of persistent pain. However, very little is currently known about the postnatal development of spinal astrocytes, nor about how the maturation of SDH astrocytes is impacted by early life injury.  Here, we used a hindpaw incision model of postsurgical pain in postnatal day (P) 3 mice to elucidate the effects of neonatal injury on the maturation of SDH astrocytes. Three-dimensional morphological analysis of individual astrocytes revealed that incision elicits age-dependent changes to astrocyte structure. At P4, spinal astrocytes in incised mice show increased size and complexity compared to naïve controls. This is reversed at P10 and P24, as astrocytes from incised mice are smaller and less ramified compared to their naïve counterparts. Transcriptomic analysis of spinal astrocytes demonstrated that injury-evoked changes to astrocyte gene expression occur acutely. We found 76 differentially expressed genes (DEGs) at P4, many of which are related to cell motility and cytoskeletal organization (Thbs1, Efemp1, Acta1, Acta2, Tpm2, Fgf14) but very few DEGs at P10 and P24. Lastly, we identified that microglial engulfment of astrocytes occurs in the developing dorsal horn, and that this process is altered by neonatal injury in a sex-dependent manner. These data illustrate, for the first time, that neonatal injury alters the postnatal development of spinal astrocytes.

overall_design:
Neonatal mouse pups underwent unilateral hindpaw incision at postnatal day (P)3, or were exposed to isoflurane only as a control. Pups are Aldh1l1-creERT2xSun1-GFP, in which astrocytes are tagged with the nuclear envelope protein Sun1 fused to eGFP (Sun1-GFP).
Ipsilateral dorsal horn L3-L5 was harvested 1, 7, or 21 days after incision, corresponding to ages P4, P10, and P24. Homogenate of intact spinal cord nuclei was prepared from each harvested sample and sorted on the basis of GFP+ fluorescence to selectively isolate spinal dorsal astrocyte nuclei from each sample.
Nuclear RNA was isolated from the sorted astrocytes for each mouse, and differential gene analysis was performed to identify incision-induced transcriptional changes as well as normal developmental changes across the three developmental ages.

first: Judy

last: Yoo

first: Elizabeth

last: Serafin

first: Matthew

last: Kofron


title: Regulation of the NSL complex by TAF4A is critical for genome stability and quiescence of skeletal muscle stem cells [CnR of TAF4A in WT MuSCs]

overall_design: Genome-wide profiling of TAF4A in wild type muscle stem cells


title: DBC1 promotes metastatic castration-resistant prostate cancer by enhancing the stability and activity of HSF1 [RNA-seq]

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

institute: Sungkyunkwan University

summary: Heat shock factor 1 (HSF1) is a key stress-protective transcription factor that is exploited by various cancers to promote cancer cell survival, therapy resistance, and metastasis. Metastatic castration-resistant prostate cancer (mCRPC) is the leading cause of cancer-related death in men worldwide, and mCRPC progression is associated with increased dependence on HSF1. However, mechanisms underlying HSF1 stabilization and persistent activation in metastatic malignancies remain unclear. Here we show that the HSF1-driven transcriptional program and its genome occupancy in mCRPC cells are distinct from those of CRPC cells. HSF1 is highly activated and required for the metastatic potential of mCRPC cells. Moreover, we report DBC1 as a critical regulator of HSF1 stability and activity in mCRPC cells. DBC1 is required for genome-wide chromatin occupancy and target gene expression of HSF1. Mechanistically, DBC1 enhances DYRK2/PKA-mediated HSF1 phosphorylation at S320/S326 and inhibits CHIP-mediated HSF1 ubiquitination, thereby stabilizing and activating HSF1. Importantly, DBC1 loss suppresses growth and metastasis of mCRPC cells, and high DBC1 expression correlates with poor outcomes in patients with mCRPC. Our results highlight the critical role of DBC1 as a key HSF1 coregulator in mCRPC progression and provide insights into regulatory mechanisms of HSF1 stability and activity in advanced and metastatic cancers.

overall_design: 22RV1, SM1 (derived from spine-metastasized 22RV1 cells), and their HSF1 or DBC1 knockout counterpart cells (22RV1-H1KO, 22RV1-D1KO, SM1-H1KO, and SM1-D1KO) were used for the analysis. We performed RNA sequencing (RNA-seq) in triplicates to investigate global gene expression changes induced by HSF1 or DBC1 gene knockout.

middle: H

first: Sue

last: Moon


title: Manifold roles of CCR7 chemokine GPCR in human trophoblast differentiation

city: Saint Louis

first: Shuhua

last: Fu

state: MO

address: 4480 Clayton Ave

institute: Washington University in St. Louis

summary: CCR7 chemokine G protein-coupled receptor is expressed in extraembryonic tissues of the early human embryo, including trophectoderm and its derivatives cytotrophoblast (CTB), extravillous trophoblast (EVT), and syncytiotrophoblast (STB). However, its function in placental development remains poorly explored. Here, we generated human embryonic stem cells harboring CCR7 deletions and differentiated them into human trophoblast stem cell (hTSC) and hTSC-derived trophoblast organoids. We found that CCR7 mutant EVTs retained hTSC-like characteristics, exhibited decreased epithelial-to-mesenchymal transition, and reduced cell motility. Additionally, CCL21-CCR7 induced EVT terminal differentiation into endovascular EVT-like cells. Transcriptional profiling in CCR7 KO STBs identified reduced viral defense gene expression related to the protection against maternal-fetal transmission. Investigation of trophoblast organoids using single cell transcriptome profiling showed that CCR7 mutant trophoblast organoids comprised a smaller EVT population, but a larger STB population, compared to wild type organoids, while CellChat analysis indicated altered cell-cell communication including WNT, ACTIVIN, and IFN-I signaling pathways. Mechanistically, we found that CCR7 limited the cell-cell fusion of early STB differentiation by reducing cAMP levels. Together, our studies demonstrate that CCR7 plays multiple roles in cellular decision-making during trophoblast differentiation, promoting EVT differentiation, and limiting cell-cell fusion during early STB differentiation.

overall_design: To understand the CCR7 function in trophoblast differentiation and maturation from naïve to hTSC as well as terminal differentiation of hTSC to EVT and STB, we generated CCR7 KO allele (A10) in the backbone of H9 hESCs and compared the RNA transcriptome of WT vs mutant in each cell types. Naïve H9 vs CCR7 KO (n=2), hTSC H9 vs CCR7 KO (n=4), EVT H9 vs CCR7 KO (n=4), and 3D STB H9 vs CCR7 KO (n=4)

first: Eun-Ja

last: Yoon

first: Mariana

last: Beltcheva

first: Paul

last: Gontarz

first: Bo

last: Zhang

first: Lilianna

last: Solnica-Krezel


title: A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception [RNA-seq]

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

summary: We performed RNA-seq experiments on two KO lines of OsWRKY53. WE also perfomred, wounding, OsPep2 and PSK treatment of KO1 line of WRKY53 followed by RNA-seq analysis. We performed OsPep2 treatment of KO2 lines.

overall_design: We performed RNA-sequencing to check the transcriptional response of WKY53 KO plants to wounding, OsPep2 treatmnet and PSK tretament. For all the sequencing, six-week-old leaves were used. For all the peptide treatment experiments, leaf strips were used.

first: P

middle: V

last: Shivaprasad

first: C

last: Harshith


title: mTORC1-dependent suppression of autophagic activity in somatic cell nuclear transfer mouse embryos

status: Public on Sep 01 2025

city: Tsukuba

first: Inoue

last: Kimiko

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

summary: Activation of autophagy after fertilization is essential for mammalian embryonic development, as it supplies embryos with nutrients and energy. Somatic cell nuclear transfer (SCNT) embryos frequently exhibit developmental arrest, largely because of incomplete genomic reprogramming; however, the role of non-genomic factors remains unclear. Here, we investigated autophagy dynamics in mouse SCNT embryos using immunostaining and live-cell fluorescence imaging. In fertilized embryos, autophagy increased markedly from the late 2-cell stage and peaked at the morula stage. SCNT embryos followed a similar timeline but consistently showed reduced autophagic activity. Notably, the autophagic activity levels varied among SCNT embryos and positively correlated with their developmental potential. Attempts to enhance genomic reprogramming, including the removal of somatic histone methylation, did not restore autophagy. Instead, transcriptome analysis revealed ectopic activation of mTORC1 signaling as a likely cause of impaired autophagy. Consistently, treatment with an mTORC1 inhibitor successfully rescued the autophagic activity in SCNT embryos. These findings identify a persistent autophagy defect during preimplantation development in SCNT embryos and suggest that modulation of non-genomic pathways, such as mTORC1 signaling, could improve SCNT efficiency.

overall_design: Comparative analysis of gene expression in cumulus cells and preimplantation embryos derived from IVF and  SCNT in mouse.

first: Takaki

last: Tatebe

first: Kimiko

last: Inoue


title: Limited activation interdependence, and differing patterns of the in vivo effects, of IKK1 and IKK2 downstream of NIK

city: Rehovot

first: Xun

last: Liang

address: Herzl 234

department: Department of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

summary: The protein kinase NIK controls numerous immune functions by signaling for the processing of NF-kB2 and for the activation of other NF-kB proteins. NIK associates with IKK1 and has been suggested to exert all its effects via IKK1 activation. In this study, we demonstrate that NIK, by binding to IKK1, also associates with IKK2 and NEMO, allowing NIK to dictate the phosphorylation of IKK2 independently of IKK1's enzymatic function. IKK2 activation is also maintained when the phosphorylation of NF-κB2 is compromised by a mutation of NIK that affects its interaction with IKK1 and NF-kB2. Analyzing mice with this mutation reveals the differing dependencies of various effects of NIK on the activation of IKK1 or IKK2 and on the activation of differing NF-kB proteins. These findings indicate that NIK’s signaling mechanisms for the activation of different NF-kB proteins by the two IKKs are not strictly coupled.

overall_design: RNA-seq profiling the TWEAK-induced gene expression in primary mouse dermal fibroblast derived from NIK-KO mice, NIK-X mut mice and their wild-type littermates.

first: David

last: Wallach

first: Noa

last: Wigoda

first: Tianzhen

last: Wang


title: DOT1L-mediated H3K79me2 directs B-cell repertoire establishment, marginal zone development and germinal center function

city: Clayton

first: Kim

last: Good-Jacobson

state: Vitoria

address: 19 Innovation Walk

department: Biochemistry & Molecular Biology

institute: Monash University

summary: DOT1L is an epigenetic regulator that promotes gene expression by methylating lysine 79 on histone H3 and recruits transcription factors to gene targets. DOT1L is also an oncogenic driver in cancers that affect developing lymphocytes, yet how DOT1L activity regulates B-cell maturation remains poorly defined. Here, we use deep-sequencing and conditional knockout models to elucidate gene targets of H3K79me2, and the mechanistic contribution of DOT1L, during key stages of murine B-cell development. In the bone marrow, Dot1l was upregulated in pro B-cells. Deep-sequencing revealed that H3K79me2 accumulated during maturation. The genomic distribution of H3K79me2 peaks indicating that DOT1L regulates transcription and the cell cycle across different stages of B-cell development. As such, DOT1L was found to be essential for pre B-cell expansion, leading to a significant decrease in pre B-cells in the absence of DOT1L and a skewing of the B-cell receptor repertoire to favor proximal VH usage. In addition to the effective generation of a diverse B-cell pool, DOT1L was also required to establish the marginal zone (MZ) B-cell gene expression program. Attenuation of MZ B-cells and a bottlenecking at the pre-MZ B-cell stage in Dot1L-deficient mice correlated to H3K79me2 peaks at key MZ-regulatory genes such as Lfng and Dock10 in developing B cells. In contrast, Dot1l was re-expressed in germinal center (GC) B-cells post-immunization to deposit H3K79me2 at key GC B-cell gene loci during GC differentiation. Together, these data demonstrate a vital role for DOT1L during B cell lymphopoiesis, MZ B-cell generation and GC B-cell biology.

overall_design:
B-cell subsets were sorted from naïve or immunized mice and H3K79me2 ChIP was performed and sequenced. Input and H3K79me2 ChIP files were generated for each sample.
Follicular B cells were sorted and purified from mice bearing a B cell-specific conditional Dot1l deletion (Dot1lf/fMb1Cre/+) and from controls (Mb1Cre/+). BCR sequencing was performed to assess the impact of deleting Dot1l during early B-lymphopoiesis on the VH gene usage in mature B-lymphocytes.

first: Liam

last: Kealy

first: Brendan

middle: E

last: Russ

first: Stephen

last: Turner

first: Elias

last: Hobeika

last: Good- Jacobson


title: DNA methylation contributes to plant acclimation to naturally fluctuating light (RNA-Seq)

city: Birmingham

first: Robyn

last: Emmerson

address: Edgbaston

institute: University of Birmingham

summary: Plants experience dynamic light daily, with light conditions varying on a second-by-second basis. Little is understood about the mechanisms that allow plants to survive such variable conditions. Here, we have exposed Arabidopsis thaliana plants to naturally fluctuating light regimes alongside traditional square light regimes. The response was highly consistent across experiments, leading us to believe there is an epigenetic mechanism involved. We show significant alterations in DNA methylation between fluctuating light acclimated plants, and square light acclimated plants, demonstrating the frequency of fluctuations impacts the plant methylation. This was accompanied by significant changes in gene expression, some of which correlated with altered DNA methylation. Interestingly, several transposable elements which displayed differential methylation were found to be differentially expressed between light regimes. This data suggests DNA methylation may have a role in acclimation to natural light which may directly regulate gene expression and impact transposable element activation.

overall_design: To investigate whether DNA methylation patterns are impacted by light regime, DNA was extracted from leaf tissue of Arabidopsis thaliana which had been acclimated to one of four growth light regimes for 22 days

middle: A

first: Nicolae

last: Zabet

first: Tracy

last: Lawson


title: DNA methylation contributes to plant acclimation to naturally fluctuating light (WGBS)

middle: R


title: PAX3-FOXO1 drives targetable cell state-dependent metabolic vulnerabilities in rhabdomyosarcoma

city: New York

first: Lydia

last: Finley

state: NY

address: 430 E 67th St

department: Cell Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: PAX3-FOXO1, an oncogenic transcription factor, drives a particularly aggressive subtype of rhabdomyosarcoma (RMS) by enforcing gene expression programs that support malignant cell states. In this study, we show that PAX3-FOXO1+ RMS cells exhibit altered pyrimidine metabolism and increased dependence on enzymes involved in de novo pyrimidine synthesis, including dihydrofolate reductase (DHFR). Consequently, PAX3-FOXO1+ cells display increased sensitivity to inhibition of DHFR by the chemotherapeutic drug methotrexate, and this dependence is rescued by provision of pyrimidine nucleotides. Methotrexate treatment mimics the metabolic and transcriptional impact of PAX3-FOXO1 silencing, reducing expression of genes related to PAX3-FOXO1-driven malignant cell states. Accordingly, methotrexate treatment slows the growth of multiple PAX3-FOXO1+ tumor xenograft models but not their fusion-negative counterparts. Taken together, these data demonstrate that PAX3-FOXO1 induces cell states characterized by altered pyrimidine dependence and nominates methotrexate as an addition to the current therapeutic arsenal for treatment of these malignant pediatric tumors.

overall_design: RNA-sequencing of established rhabdomyosarcoma cell lines treated with vehicle (DMSO) or methotrexate for 48 h. Two PAX3-FOXO1+ cell lines (RH30, RH41) and two fusion-negative cell lines (RD, SMS-CTR) are included.

first: Katrina

middle: I

last: Paras

middle: W


title: Mapping the FOXA1 Interactome in ER+ Breast Cancer Cells using Proximity Labeling Reveals Novel Interactions with the Orphan Nuclear Receptor NR2C2 [RNA-Seq]

city: San Juan

first: Hector

last: Franco

state: Puerto Rico

address: 2nd Floor Centro Medico- Office #275

institute: University of Puerto Rico Comprehensive Cancer Center

summary: FOXA1 is a pioneer transcription factor essential for chromatin accessibility and transcriptional regulation in hormone-driven cancers. In breast cancer, FOXA1 plays a central role in facilitating nuclear receptor binding, reprogramming enhancer landscapes, and promoting transcriptional changes associated with therapy resistance. While FOXA1’s function has been primarily studied in the context of estrogen receptor-α (ER), its broader protein interaction network remains incompletely defined. Here, we systematically map FOXA1-interacting proteins in ER-positive breast cancer cells using proximity-dependent biotin labeling (miniTurbo) combined with quantitative LC-MS/MS proteomics. We engineered MCF-7 cell lines stably expressing miniTurbo-tagged FOXA1 at either the N-terminus or C-terminus to ensure comprehensive coverage of interaction interfaces. This approach recovered known FOXA1 partners, including AR, MLL3, YAP1, and GATA3, and identified 157 previously unreported FOXA1 interactors. Notably, 42 of these novel partners, including NR2C2, were significantly associated with poor relapse-free survival in ER+ breast cancer patients. To demonstrate the utility of this resource, we characterized the FOXA1-NR2C2 interaction in depth. Integrating ChIP-seq and RNA-seq, we show that FOXA1 and NR2C2 co-occupy a subset of genomic regions and drive co-regulated transcriptional programs involved in tumor progression. Our study reveals an expanded FOXA1 interactome and new insights into its functional network in breast cancer, providing candidate proteins for further exploration as biomarkers or therapeutic targets.

overall_design: To comprehensively interrogate the transcriptomic proflie of NR2C2 in ER+ breast cancer cells, we compared MCF-7 and T47D cells treated with 30pmol siRNA against NR2C2 or Scramble (control) for 72 hours. Biological tripilicates of each sample, for a total of 12 samples, were submitted to the Puerto rico OMIC Center (PROMIC). PROMIC performed sequencing using 1ug of RNA per sample, performed the library prep using Illumina Stranded mRNA prep kit and sequenced using Illumina NextSeq 550.

first: Rosemary

middle: N

last: Plagens

first: Shen

last: Li

first: Christine

last: Mills

first: Laura

last: Herring

first: Carla

middle: S

last: Rodriguez Tirado

first: Natalia

last: Maldonado Vazquez

first: Ingrid

last: Montes-Rodriguez

first: Julie

last: Dutil


title: DBC1 promotes metastatic castration-resistant prostate cancer by enhancing the stability and activity of HSF1 [ChIP-seq]

first: Jeong

last: Kim

overall_design: 22RV1, SM1 (derived from spine-metastasized 22RV1 cells), and their HSF1 or DBC1 knockout counterpart cells (22RV1-H1KO, 22RV1-D1KO, SM1-H1KO, and SM1-D1KO) were used for the analysis. We performed chromatin immunoprecipitation sequencing (ChIP-seq) using antibodies for HSF1, DBC1, and H3K27ac.

first: Sue

last: Moon


title: Establishment of human Leber’s hereditary optic neuropathy model using iPSC-derived retinal organoids

city: Gifu

first: Kota

last: Aoshima

state: Gifu

address: 1-25-4 Daigaku-nishi

department: Biofunctional Evaluation

institute: Gifu Pharmaceutical University

summary: Leber’s hereditary optic neuropathy (LHON) is a mitochondrial disease caused by mitochondrial DNA mutations, leading to central vision loss and retinal ganglion cell (RGC) degeneration. Progress in understanding LHON and developing treatments has been limited by the lack of human-like models. In this study, we aimed to establish a human retinal model of LHON using retinal organoids (ROs) from LHON patient-derived induced pluripotent stem cells (LHON-iPSCs). We first confirmed LHON-iPSCs were successfully differentiated into ROs (LHON-ROs). LHON-RO showed a reduction in RGC numbers and the density of neural axons. Additionally, both mitochondrial membrane potential and ATP production were decreased in LHON-RO. Finally, treatment with idebenone, the only approved therapeutic agent for LHON, improved RGC numbers in LHON-RO. This model replicates key clinical features of LHON, including RGC and axonal loss, and demonstrates idebenone’s therapeutic potential. Furthermore, a comprehensive analysis of the LHON-RO model revealed impaired mitophagy, suggesting novel therapeutic targets for LHON. Thus, the LHON-RO model offers a valuable platform for studying LHON pathogenesis and evaluating treatments.

overall_design: RNA-Seq profiling of wildtype and LHON retinal organoid at Day35.

first: Masamitsu

last: Shimazawa

first: Yoshiki

last: Kuse

first: Michinori

last: Funato


title: MBNL loss of function in smooth muscle as a model for myotonic dystrophy gastrointestinal dysmotility

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S. Moody Avenue

institute: OREGON HEALTH & SCIENCE UNIVERSITY

summary: Myotonic dystrophy type 1 (DM1) is the most common adult-onset muscular dystrophy and severely affects multiple organ systems, including the brain, heart, skeletal muscle, and gastrointestinal (GI) tract. Despite 80% of individuals with DM1 experiencing GI dysfunction that affects their daily life, the mechanisms of GI dysmotility in DM1 remain an understudied aspect of the disease. DM1 is caused by a CTG repeat expansion in the DMPK gene that, when expressed as an expanded CUG repeat RNA, sequesters and reduces the activity of the muscleblind-like (MBNL) RNA-binding protein family. We developed a mouse line with conditional, smooth muscle-specific knockout of Mbnl1 and Mbnl2 to model and investigate myogenic mechanisms contributing to GI dysmotility in DM1. Mice with Mbnl knockout exhibited delayed GI transit of small and large bowel in vivo and increased smooth muscle contractile tone of jejunum and colon segments ex vivo. Smooth muscle from jejunum and colon showed no histopathologic changes and contained increased phosphorylation of the 20 kDa myosin light chain (Mlc20), consistent with increased contraction. RNA sequencing of mouse and human DM1 GI samples enriched for smooth muscle revealed conserved misregulated alternative splicing of transcripts associated with the regulation of Mlc20 phosphorylation and smooth muscle contraction. These findings demonstrate that Mbnl KO disrupts the regulation of contraction dynamics and causes GI smooth muscle hyperactivity, suggesting that therapeutics that reduce GI contractile activity may help alleviate DM1 GI symptoms.

overall_design: We performed RNAseq on jejunum and colon smooth muscle from tamoxifen-treated, 4-month-old male conditional double knockout (Myh11-CreERT2 [JAX strain #019079];Mbnl1flox/flox;Mbnl2flox/null), Cre-Control (Myh11-CreERT2;WT) and Flox-Control (Mbnl1flox/flox;Mbnl2flox/null) mice (n=3 per group, total 18 samples). We also sequenced  smooth muscle isolated from DM1 and unaffected control jejunum (n=6 per group, mean/median age for control 52y/55y and affected 49y/57y; three female and three male for each group) and colon (n=7 per group, mean/median age for control 51y/52y and affected 50y/52y, four female and three male for each group) autopsy samples.

first: Janel

last: Peterson

first: Jesus

last: Frias

first: Andrew

last: Miller

first: Krishnakant

middle: G

last: Soni

first: Yi

last: Zhang

first: John

last: Day

first: Geoffrey

last: Preidis

first: Thomas

last: Cooper


title: Regulation of the NSL complex by TAF4A is critical for genome stability and quiescence of skeletal muscle stem cells [CnR of NF-YA in WT MuSCs]

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

overall_design: Genome-wide profiling of NF-YA in wild type muscle stem cells

first: Angelina

last: Georgieva

first: Stefan

last: Günther


title: Tulp3 deficiency results in ciliopathy phenotypes during zebrafish embryogenesis

city: Freiburg

first: Ralf

last: Mertes

address: Breisacher Str.  153

institute: University Medical Center Freiburg

summary: Ciliopathies, caused by defective cilia biogenesis or function, comprise a genetically and clinically diverse group of diseases. Primary cilia play pivotal roles in the regulation of a multitude of signalling pathways during development and tissue homeostasis. Cilia assembly, maintenance and signalling depend on the intraflagellar transport (IFT). Tubby-like protein 3 (TULP3) functions as an adapter protein for the ciliary trafficking of diverse membrane cargos via an interaction with the IFT-A complex. Recently, we and others have shown that individuals carrying pathogenic TULP3 variants suffer from progressive liver, kidney and heart disease. In line with these findings, adult Tulp3 knockout zebrafish displayed liver fibrosis and kidney cyst phenotypes. In the present study, we analysed the functional consequences of Tulp3 deficiency during zebrafish embryogenesis. Tulp3 deficiency resulted in well-known ciliopathy-associated phenotypes including pronephric cysts, otolith deposition defects, body curvature and altered left-right asymmetry. Our analysis of urotensin 2-related peptide (Urp) signaling, which is required for proper spine morphogenesis, revealed reduced expression of urp1 in Tulp3 knockout embryos. We also observed severe scoliosis in a significant number of adult Tulp3 knockout zebrafish. Analysis of ciliogenesis revealed a reduced cilia number and ciliary length in Tulp3 deficient embryos. In addition, Tulp3 deficiency resulted in upregulation of cilia-dependent profibrotic Wnt and Jak/Stat signalling components. Furthermore, we demonstrate that loss of Tulp3 causes upregulation of genes related to liver fibrosis. In conclusion, our data highlights a critical role of Tulp3 in proper cilia formation and function to maintain healthy tissue architecture during zebrafish embryogenesis, and provides further insight into the spectrum of cilia-related phenotypes in adult zebrafish depleted for Tulp3 functions.

overall_design: RNA-seq profiling of zebrafish control and MZtulp3 embryos at 2dpf

first: Daniel

last: Epting

last: Devane

first: Séverine

last: Kayser

first: Martin

last: Helmstädter

first: Patrick

last: Metzger

first: Melanie

last: Boerries

last: Bergmann

first: Elisabeth

last: Ott


title: Meiotic cohesin RAD21L shapes 3D genome structure and transcription in the male germline [HiC]

city: Cerdanyola del Vallès

first: Laia

last: Marín-Gual

address: Campus UAB

country: Spain

institute: Universitat Autònoma de Barcelona

summary: The unique genome organization that chromosome acquired during meiosis is essential for fertility. Yet, the functional implications of the fine-scale spatial 3D genome folding during this process remain poorly understood. Here, we study the impact of RAD21L depletion, a meiosis-specific cohesin subunit, on the 3D genome architecture and gene expression in the male germ line. Employing fluorescence activated cell sorting, chromosome conformation capture and single cell RNA-seq, we found that the absence of RAD21L impairs chromatin organization during meiosis, leading to pronounced alterations of genome compartmentalization and inter- and intra-chromosomal interactions. This conspicuous genome remodelling also disrupts bouquet formation, resulting in increased telomeric interactions between heterologous chromosomes in primary spermatocytes. Importantly, genome remodelling was accompanied by detectable transcriptional dysregulation in spermatogonia and primary spermatocytes, mainly affecting sex chromosomes. Overall, we demonstrate how cohesin shapes the 3D genome reorganization genome-wide during spermatogenesis and influences its transcriptional landscape.

overall_design: Germ cell populations from RAD21L-deficient mice were isolated by Fluorescence-Activated Cell Sorting. Hi-C of fibroblasts and isolated populations (spermatogonia and primary spermatocytes at leptotene/zygotene) from RAD21L-deficient mice. Single-cell RNA-seq of whole testes from WT and RAD21L-deficient mice

first: Covadonga

last: Vara

first: Raquel

last: Sainz-Urruela

first: Yasmina

last: Cuartero

first: Lucía

last: Álvarez-González

first: Natalia

last: Felipe-Medina

first: Francisca

last: Garcia

first: Elena

last: Llano

first: Marc

last: Marti-Renom

first: Alberto

last: Pendás

first: Aurora

last: Ruiz-Herrera


title: Myocardial disarray drives metabolic inefficiency in human cardiomyocytes

city: Paris

first: Jean-Sébastien

last: Hulot

address: Rue Leblanc

institute: Paris Centre de Recherche Cardiovasculaire

summary: Adult cardiomyocytes are embedded within a highly organized myocardial microenvironment that imposes critical geometric cues essential for the alignment and distribution of organelles and the shaping of their unique, rectangular cellular morphology. Despite the association of cardiomyocyte disarray with human heart disease, the functional consequences of this cellular disorganization remain poorly understood. Here, we leveraged micropatterned substrates to promote structural alignment in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), contrasting the effects of mechanical alignment on mitochondrial form and function with hiPSC-CMs cultured under standard unconstrained conditions. Cardiomyocytes cultured under unconstrained conditions exhibited misaligned sarcomeres and a perinuclear mitochondrial distribution while micropatterned hiPSC-CMs developed linear myofibrils and reconfigured sarcomere and mitochondrial organization, which increased mitochondrial respiration without augmenting mitochondrial mass. Notably, micropatterned hiPSC-CMs exhibited an increased number of mitochondria-associated membranes, as determined by proximity ligation assays and transmission electron microscopy, suggesting enhanced interactions between the sarcoplasmic reticulum and mitochondria. Together, these findings demonstrate that mitochondrial-sarcoplasmic architecture and geometry are critical spatial features that ensure bioenergetic efficiency of cardiomyocytes. This work underscores the importance of cellular organization in cardiomyocyte metabolism and function, providing insights into the pathophysiology of cardiac diseases marked by cellular disarray.

overall_design: RNA-seq profiling of human induced pluripotent stem cells from a healthy male donor and differentiated cardiomyocytes cultured in regular unconstrained or line micropatterned conditions until day 42 post-differentiation.

first: Charlène

last: Jouve

first: Andrea

last: Ruiz-Velasco


title: Meiotic cohesin RAD21L shapes 3D genome structure and transcription in the male germline [scRNA-seq]


title: 4-1BB+ Tregs and inhibitory progenitor exhausted T cells confer resistance to anti-PD-L1 and anti-CTLA-4 combination therapy

first: Junha

last: Cha

address: Yonsei-Ro 50

department: Department of Biotechnology

institute: Yonsei University

summary: Predictors of immune checkpoint inhibitor response in cancer remain elusive. From a previous phase 2 neoadjuvant immunotherapy window-of-opportunity study, we present the single-cell RNA and T cell receptor (TCR) sequencing analysis of 57 pre- and post-treatment tumor biopsies from head and neck cancer patients treated with durvalumab (anti-PD-L1) alone or with tremelimumab (anti-CTLA-4), identifying key cellular and molecular predictors of immune checkpoint inhibitor (ICI) response. Malignant cells and neutrophil senescence promote ICI response. While CXCL13+ exhausted T (Tex) cells enhance response through 4-1BB signaling, anti-CTLA-4 induces 4-1BB+ regulatory T cells (Tregs) restricting ICI efficacy. These opposing roles of 4-1BB in different cellular contexts may explain the limited benefit of combinatorial immunotherapy observed in clinical trials. We identify two subsets of tumor-reactive progenitor Tex (Tpex): ICI-responsive Tpex1 and ICI-resistant Tpex2, a subset characterized by KLRB1 and IL17R. The balance of Tpex1 and Tpex2 associates with ICI response across multiple cancers, offering insights into sustaining response. This study was registered at ClinicalTrials.gov (NCT03737968).

overall_design: 57 HNSCC tumor biopsies, extracted from various tumor primary sites, were sequenced for TCR or GEX at single cell resolution. Samples are either treated with immune checkpoint inhibitor (Durvalumab or Durvalumab and Tremelimumab) or at extracted at baseline (pre-treatment).

first: Chang Gon

last: Kim

first: Gamin


title: Urolithin A abolishes high anxiety and rescues the associated mitochondrial transcriptomic signatures and synaptic function

city: Lausanne

first: Dogukan

middle: Hazar

last: Ulgen

address: EPFL SV BMI Station 19

department: Brain Mind Institute

institute: EPFL

summary: Background Chronic anxiety imposes a major global health burden, yet existing treatments remain inadequate, with limited efficacy or significant side effects. Mitochondrial abnormalities have emerged as key contributors to anxiety-related phenotypes, suggesting that targeting mitochondrial function may offer a novel therapeutic avenue. Urolithin A (UA), a gut microbiota-derived metabolite known to enhance mitochondrial function, has shown neuroprotective effects in preclinical models of aging and neurodegeneration. However, its potential in modulating anxiety and underlying neuronal mechanisms remains unexplored. Methods We examined the effects of UA in two rodent models of heightened anxiety: a natural variation model and a genetically selected high stress-reactivity line. Animals received chronic UA supplementation, and anxiety-like behaviors were assessed across multiple paradigms. Single-nucleus RNA sequencing was performed to identify molecular alterations in nucleus accumbens (NAc) medium spiny neurons (MSNs), incorporating MitoPathway analyses to examine mitochondrion-related transcriptomic signatures. Electrophysiological, immunohistochemical, and morphological analyses were conducted to assess mitochondrial pathways and synaptic function. Results UA selectively reduced anxiety-like behaviors in high-anxiety animals, both males and females, leaving non-anxious controls unaffected. Transcriptomic analyses revealed widespread mitochondrial and synaptic dysregulation in high-anxiety MSNs, with impaired mitophagy emerging as a core feature. UA treatment restored these transcriptomic signatures, normalizing mitophagy-related pathways across all MSN subtypes tightly linked to restored synaptic pathways. These changes translated into structural and functional rescue of MSN dendritic architecture, spine density, and excitatory synaptic transmission. Conclusions These findings identify mitophagy deficits in NAc MSNs as a hallmark of heightened anxiety and highlight UA as a promising mechanism-based intervention.

overall_design: Outbred Wistar rats were classified based on their anxiety profiles using elevated plus maze and open field/novel object tests. Half of the high anxious (HA) group received Urolithin A for two months (HAUA), followed by sacrifice and acquisition of the Nucleus Accumbens punches. Nuclei isolation was performed on the punches, followed by library preparation with Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics)

first: David

last: Mallet

first: Doğukan

last: Ülgen

first: Jocelyn

last: Grosse

first: Olivia

last: Zanoletti

first: Isabelle

last: Guillot de Suduiraut

first: Anna

last: Monzel

first: Davide

last: D’Amico

first: Chris

last: Rinsch

first: Martin

last: Picard

first: Simone

last: Astori

first: Carmen

last: Sandi


title: Differential gene expression in canine prostate cancer vs benign prostate hyperplasia tissue.

city: Wrocław

first: Maciej

last: Zacharski

state: dolnoslaskie

address: Norwida, 31

department: Department of Biochemistry and Molecular Biology

country: Poland

institute: Wroclaw University of Environmental and Life Sciences

summary: Despite its low incidence, the aggressive nature and high metastatic potential of canine prostate cancer (PC) make it a serious problem in veterinary medicine. However, knowledge of the molecular mechanisms and regulatory networks underlying the development and progression of canine PC is still limited.  We used RNAseq to identify diffentially expressed genes between PC (n=2) and benign prostate hyperplasia (BPH, n=3) samples. Based on these results, we chose 26 genes for validation on a larger patient cohorts. We used Nanosting nCounter technology for the comparative analysis of gene expression profiles in PC (n=14) and BPH (n=7) tissue samples. Finally the results for voltage-dependent calcium channel α2δ1 subunit were validated using Western blotting and immunohistochemistry.

overall_design: 3' Quantaseq RNASeq profiling of gene expression for the total RNA extracted from the prostate tissue of 3 dogs with benign prostate hyperplasia and 2 dogs with prostate cancer. Each dog contributed three separate total extractions.

last: Ugorski

first: Przemysław

last: Prządka

first: Stanisław

last: Dzimira

first: Sonja

last: Skevin

first: Iwona

last: Sidorkiewicz

first: Bartłomiej

last: Liszka

first: Piotr

last: Skrzypczak

first: Filip

last: Van Nieuwerburgh

first: Adam

last: Krętowski

first: Alicja

last: Tomaszek