title: Convergent DNA Methylation Abnormalities at Enhancers and Bivalent Chromatin in Human Growth Disorders [RNA-seq]

status: Public on Sep 27 2025

city: Irvine

first: Minji

last: Byun

state: CA

address: 829 Health Science Rd, 311

department: Microbiology and Molecular Genetics

institute: University of California Irvine

summary: Overgrowth with Intellectual Disability (OGID) is characterized by generalized overgrowth, including a head circumference and/or height ≥ 2 standard deviations (s.d.) above the mean, accompanied by mild to moderate intellectual disability. Sotos Syndrome, the most common form of OGID, results from loss-of-function (LoF) mutations in NSD1, which encodes a histone methyltransferase. Another major OGID subtype, Tatton-Brown-Rahman syndrome, is caused by LoF mutations in DNMT3A, encoding a de novo DNA methyltransferase. In contrast, gain-of-function (GoF) mutations in DNMT3A cause Heyn-Sproul-Jackson syndrome, characterized by growth restriction and microcephaly. We hypothesize that NSD1 LoF and DNMT3A LoF mutations share a convergent DNA methylation signature that is distinct from the pattern seen in DNMT3A GoF mutations. To test this, we generated human embryonic stem cell lines carrying these growth syndrome-associated mutations in NSD1 and DNMT3A, profiled their DNA methylation patterns using the Illumina EPIC array, and analyzed both shared and unique methylation phenotypes.

overall_design: Ribosomal RNA-depleted RNA from human embryonic stem cells genetically engineered to carry DNMT3A or NSD1 mutations associated with Tatton-Brown-Rahman syndrome, Heyn-Sproul-Jackson syndrome, or Sotos syndrome were subjected to  RNA-seq.

first: Marie

last: Wheeler

first: Yoshiko

last: Takahashi


title: Lithium partially rescues gene expression and enhancer activity from heterozygous knockout of AKAP11 while inducing novel differential changes [RNA-Seq]

status: Public on Sep 29 2025

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

type: Expression profiling by high throughput sequencing

summary: Bipolar disorder (BD) is a complex psychiatric condition usually requiring long-term treatment. Lithium (Li) remains the most effective mood stabilizer for BD, yet it benefits only a subset of patients, and its precise mechanism of action remains elusive. Exome sequencing has identified AKAP11 (A-kinase anchoring protein 11) as a shared risk gene for BD and schizophrenia (SCZ). Given that both the AKAP11-Protein Kinase A (PKA) complex and Li target and inhibit Glycogen Synthase Kinase-3 beta (GSK3β), we hypothesize that Li may partially normalize the transcriptomic and/or epigenomic alterations observed in heterozygous AKAP11-knockout (Het-AKAP11-KO) iPSC-derived neurons. In this study, we employed genome-wide approaches to assess the effects of Li on the transcriptome and epigenome of human iPSC-derived Het-AKAP11-KO neuronal culture. We show that chronic Li treatment in this cellular model upregulates key pathways that were initially downregulated by Het-AKAP11-KO, several of which have also been reported as downregulated in synapses of BD and SCZ post-mortem brain tissues. Moreover, we demonstrated that Li treatment partially rescues certain transcriptomic alterations resulting from Het-AKAP11-KO, bringing them closer to the WT state. We suggest two possible mechanisms underlying these transcriptomic effects: (1) Li modulates histone H3K27ac levels at intergenic and intronic enhancers, influencing enhancer activity and transcription factor binding, and (2) Li enhances GSK3β serine 9 phosphorylation, impacting WNT/β-catenin signaling and downstream transcription. These findings underscore Li's potential as a therapeutic agent for BD and SCZ patients carrying AKAP11 loss-of-function variants or exhibiting similar pathway alterations to those observed in Het-AKAP11-KO models.

overall_design: We utilized our previously generated heterozygous AKAP11-knockout (Het-AKAP11-KO) isogenic clones (three clones, neuronal-glial cultures) and their WT counterparts (three replicates, neuronal-glial cultures) and treated them chronically with lithium (1.5 mM for 11 days). We then performed gene expression profiling on the three AKAP11-KO clones and the three WT replicates, both untreated and lithium-treated, to analyze differential gene expression. Specifically, we aimed to (1) identify differentially expressed genes in AKAP11-KO-Li compared to AKAP11-KO-UNT, (2) detect genes that were differentially expressed in AKAP11-KO-UNT vs. WT-UNT but lost their differential expression in AKAP11-KO-Li vs. WT-UNT, and (3) identify genes that were not differentially expressed in AKAP11-KO-UNT vs. WT-UNT but became differentially expressed in AKAP11-KO-Li vs. WT-UNT.

first: Nargess

last: Farhangdoost

first: Alessia

last: Pietrantonio

first: Yumin

last: Liu

first: Calwing

last: Liao

first: Daniel

last: Rochefort

first: Martin

last: Alda

first: Patrick

middle: A

last: Dion

first: Boris

last: Chaumette

first: Anouar

last: Khayachi

first: Guy

last: Rouleau


title: The Arabidopsis deNADding enzyme DXO1 modulates the plant immunity response.

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary:
The DXO family proteins, highly conserved among eukaryotes, are involved in mRNA 5’-end quality control (5’QC) and also remove non-canonical NAD+ cap from RNA (deNADding). DXO1 protein, the only DXO homolog in Arabidopsis, due to its plant-specific features has a strong deNADding enzymatic activity but no apparent role in 5’ QC. Despite its significant contribution to plant RNA metabolism, a direct role for DXO1 enzymatic activity in the cell has not yet been demonstrated. Notably, all molecular and morphological changes observed so far in dxo1 mutant plants depended on the plant-specific N-terminal domain of the protein. Our investigation into the role of DXO1 in response to biotic stress, specifically its susceptibility to Pseudomonas syringae pv. tomato (Pst) DC3000 infection, unexpectedly revealed the importance of DXO1 enzymatic activity in the plant immune response. We observed that the dxo1-2 knockout mutant and transgenic dxo1-2 lines expressing a DXO1 variant either catalytically inactive (DXO1(E394A/D396A)) or lacking the N-terminal domain (DXO1(deltaN194)) exhibited enhanced resistance to Pst, accompanied by marked changes in the expression of key pathogenesis markers. Also, other markers of plant immunity, such as callose deposition and production of reactive oxygen species, were strongly induced by two pathogen effectors, elf18 and flg22, in the tested mutant lines. These results strongly suggest that both DXO1 features, the N-terminal domain and its catalytic center, contribute to the regulation of plant immunity. In conclusion, this is the first observation revealing the involvement of the DXO1 enzymatic activity in plant physiology.

Founded by National Science Centre Grant, Poland (UMO-2014/13/B/NZ3/00405, UMO-2018/29/B/NZ3/01980, UMO-2021/40/Q/NZ1/00014).

overall_design: Four replicates of Col-0 and dxo1-2 mutant plants were treated with Pseudomonas syringae pv. tomato DC3000 or a mock control, and RNA samples were subjected to 3’RNA-seq.

first: Anna

last: Golisz-Mocydlarz

first: Joanna

last: Kufel


title: A plastic EMP1⁺ to LGR5⁺ cell state conversion as a therapeutic bypass to KRAS-G12D inhibition in metastatic colorectal cancer [SLAM-Seq]

city: Barcelona

first: Adria-Jaume

last: Roura

address: Carrer de Baldiri Reixac, 10

country: Spain

institute: IRB Barcelona

summary: Inhibitors of the oncogene KRAS holds promise for treating metastatic CRC (mCRC). Here we show that the activity of a small molecule RAS inhibitor, RM-044, which covalently binds to the G12D mutation in the active (ON) conformation of RAS, demonstrated strong curative effects in CRC models of early liver metastases, but its therapeutic activity was diminished in the advanced metastatic disease. RM-044-treated metastases underwent a fast transition from a poor-prognosis-associated Emp1⁺ transcriptional cell state to a WNT-driven Lgr5⁺ stem cell-like state that supported tumor growth in the absence of RAS G12D activity. This plastic conversion involved a switch in transcription factor usage, and did not require extensive chromatin remodeling. Enforced conversion of metastatic cells to the Lgr5⁺ state via RAS G12D inhibition, followed by genetic ablation of this population, produced strong therapeutic effects. Overall, these findings demonstrate a central role for oncogenic KRAS in governing cellular plasticity in mCRC.

overall_design: For SLAM-sequencing MTOs were pre-treated 48h post seeding with DMSO or 100nM of RM-044 for 30 min, 4 h, 8 h or 12 h. Newly synthesized RNA was labeled for 120 minutes at a final concentration of 400μM with 4- thiouridine (4sU, Carbosynth). After media removal, MTOs were collected with 1 ml TRIzol (Life Technologies, 15596026) and the lysate was snap frozen.

last: Centonze

first: Adrià-Jaume

first: Meritxell

last: Novillo

first: Cristina

last: Giordano

first: Xavier

last: Hernando

first: Montserrat

last: Llanses

first: Paula

last: Prats

first: Marta

last: Sevillano

first: Mireia

last: Novell

first: Gabriel

last: Pabst

first: Florian

last: Andersch

first: Adrià

last: Cañellas-Socias

first: Chong

last: Zhang

first: Hugh

last: Sparks

first: Chris

last: Dunsby

first: Julien

last: Colombelli

first: Asunción

last: Fernández-Barral

first: Elena

last: Sancho

first: Camille

last: Stephan-Otto Attolini

first: Alberto

last: Muñoz

first: Antonio

last: Barbachano

first: Johannes

last: Zuber

last: Blaj

first: Elsa

last: Quintana

first: Carme

last: Cortina

first: Marc

last: Martí-Renom

first: Eduard

last: Batlle


title: Structural basis of regulated N-glycosylation at the secretory translocon

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

country: USA

institute: Northwestern University

summary: Most human secretory pathway proteins are N-glycosylated by oligosaccharyltransferase complexes as they enter the endoplasmic reticulum. Recent work revealed a substrate-assisted mechanism by which N-glycosylation of the chaperone GRP94 is regulated to control cell surface receptor signaling. Here we report the structure of a GRP94 folding intermediate tethered to a specialized CCDC134-bound translocon. Together with functional analysis, the data reveal how a conserved N-terminal extension in GRP94 inhibits OST-A, and how structural rearrangements within the translocon shield the tethered nascent chain from inappropriate OST-B glycosylation. These interactions depend critically on a hydrophobic CCDC134 groove, which recognizes a non-native conformation of nascent GRP94. These results define a mechanism of regulated N-glycosylation and reveal how the nascent chain customizes translocon subunit composition to facilitate its own biogenesis.

overall_design: Selective ribosome profiling of HEK293 cells expressing near-endogenous levels of 3xFlag-FKBP11 and 3xFlag-CCDC134. Both the solubilized ribosome translocon complexes ("input") and affinity-purified fractions ("IP") were collected for profiling.

first: Melvin

last: Yamsek

first: Qianru

last: Li

first: Yu

last: Wan

first: Robert

middle: J

last: Keenan


title: Human Pluripotent Stem Cell-Derived Alveolar Organoids for Gene-editing and Lung Adenocarcinomas Modeling

city: Xianmen

first: Yuchen

last: Liu

address: Xiangan South Road

country: China

institute: Xianmen University

summary: Human pluripotent stem cell (hPSC)-derived alveolar organoids have emerged as valuable tools for studying lung development, modeling pulmonary diseases, and drug discovery, though their application has been hindered by laborious differentiation protocols and technical complexity. Here, we present an hPSC_x0002_derived alveolar organoid (hALO) system with exceptional long-term expandability (>30 passages), efficient cryopreservation resilience, and streamlined production achieved through earlier 3D culture initiation and elimination of cell sorting requirements. Transcriptomic analysis across passages confirmed hALOs contain alveolar progenitors and AT2 lineages, recapitulating pseudoglandular-to-canalicular development while partially maintaining adult AT2 immune-related functions. The system permits alveolar epithelial differentiation via pharmacological modulation of WNT/YAP signaling or through orthotopic transplantation, while multiplex genetic engineering enables programmable disease modeling and adenocarcinoma pathogenesis studies. These versatile capabilities establish hALOs as a robust dual-phase platform for mechanistic investigation of lung epithelial biology and disease modeling across in vitro and in vivo environments.

overall_design: scRNA-seq of pluripotent stem cell-derived alveolar organoids at early (P3), middle (P7) and late (P20) passages

first: Lian

first: Zhili

last: Rong

first: Ying

last: Lin


title: Time-course Transcriptomics Reveals Impact of Treponema pallidum on Microvascular Endothelial Cell Function and Phenotype

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

summary: Syphilis, caused by Treponema pallidum subsp. pallidum, is an urgent global public health threat. Syphilis vaccine development has been impeded by limited understanding of the molecular mechanisms that enable T. pallidum to establish and maintain infection. The vascular endothelium is critical for T. pallidum attachment, dissemination, and host immune response initiation; however, the molecular details of T. pallidum-endothelial interactions are incompletely understood. To enhance understanding, we performed time-course transcriptomic profiling on T. pallidum-exposed brain microvascular endothelial cells. These analyses showed T. pallidum exposure alters pathways related to extracellular matrix, growth factors, integrins, and Rho GTPases. The induced transcriptional response was consistent with endothelial to mesenchymal transition, a key process involved in fetal development and vascular dysfunction. This study provides a comprehensive understanding of the molecular response of endothelial cells to T. pallidum and identifies the host pathways that may cause syphilis disease symptoms, information that could aid syphilis vaccine design.

overall_design: This project aimed to investigate the temporal transcriptomic response of hCMEC/d3 human brain microvascular endothelial cells to T. pallidum. To complete this aim we exposed hCMEC/d3 cells to Treponema pallidum subsp. pallidum at a multiplicity of infection of 30, or a background control lacking the pathogen, and measured the endothelial transcriptional response at 45-minutes, 4-, 12-, and 24-hours post-exposure.

first: Sean

last: Waugh

first: Mara

middle: C

last: Goodyear

first: Alloysius

last: Gomez

first: Akash

last: Ranasinghe

first: Karen

middle: V

last: Lithgow

middle: E

last: Hancock

first: Amy

middle: H

last: Lee

first: Caroline

last: Cameron


title: Immune stromal components impede biological effectiveness of carbon ion therapy in a preclinical model of pancreatic ductal adenocarcinoma.

city: Dallas

first: Todd

last: Aguilera

state: TX

address: 2280 Inwood Rd

department: Molecular radiation biology

institute: UTSouthwestern- Medical Center

summary: Pancreatic ductal adenocarcinoma (PDAC) often invades blood vessels, thrives in hypoxic conditions, and supports an immune microenvironment that is highly resistant to treatment. Carbon ion radiation therapy (CIRT) has potential to benefit patients with PDAC, since oxygen enhancement is not required due to high linear energy transfer (LET) radiation and the spread-out Bragg peak permits sparing of adjacent normal tissues. However, we found that underlying factors impact the response of PDAC to CIRT. Clonal syngeneic KPC pancreatic tumors modeled a treatment-resistant microenvironment and showed limited response to CIRT in vivo. While KPC cell lines exhibited radiobiologic effectiveness (RBE) greater than 3, subcutaneous tumors in the mouse hind leg showed much lower RBEs - 1.3 based on tripling time and 1.7 based on quintupling time - at a LET of 75 keV/μm. Four days after CIRT, we observed widespread transcriptomic changes in the tumor immune microenvironment (TME), including increased infiltration of anti-tumor immune cells, elevated expression of anti-tumor T cell cytokines, MHC class I molecules, and co-stimulatory signals. Fewer immunologic changes were observed following photon irradiation. By seven days after CIRT, tumor-supportive transcriptomic programs - characterized by pro-tumor cytokines, M2 macrophages, and cancer-associated fibroblasts (CAFs) - emerged, promoting resistance and limiting the durability of tumor growth delay. These findings suggest that CIRT may offer a favorable platform compared to conventional photon radiation therapy for combining with immunotherapies.

overall_design: To elucidate the immunological mechanisms underlying treatment resistance in KPC tumors, we conducted single-cell RNA sequencing (scRNAseq) analysis. We injected KPC63 cells SQ in the hind leg of naïve mice and compared three treatment groups: 10 Gy photon RT, combination immunotherapy, or isotype control. TDLNs were harvested, dissociated into single-cell suspensions, and analyzed on day 16 post-irradiation.

first: Katy

middle: L

last: Swancutt

first: Eslam

last: Elghonaimy

first: James

last: Nicholson

first: Laurentiu

middle: M

last: Pop

first: Brock

last: Sishc

first: Elizabeth

last: Alves

first: Cassandra

last: Hamilton

first: Adam

last: Rusek

first: Anthony

last: Davis

first: Raquibul

last: Hannan

first: Michael

middle: D

last: Story


title: Multiomics Analyses Unveil Immune Landscape in Pediatric and Adult Sepsis [scRNA_seq]

status: Public on Sep 28 2025

city: chongqing

first: Ye

last: qian

address: No. 1 Youyi Road, Yuzhong District, Chongqing

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Sepsis is a leading cause of global mortality, characterized by organ dysfunction due to a dysregulated immune response to infection. This study aims to delineate the immune landscape in sepsis through single-cell RNA sequencing (scRNA-seq). A total of 133 samples were analyzed, including PBMCs from healthy adults, adult ICU controls, adult sepsis patients, healthy children, pediatric ICU controls, and pediatric sepsis patients. The scRNA-seq analysis revealed both common and unique immune cell populations across different infection sources and between adults and children. These findings provide insights into the pathophysiology of sepsis and suggest potential targets for personalized therapeutic approaches.

overall_design:
Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples collected from healthy adult controls, adult ICU controls, adult sepsis patients, healthy pediatric controls, pediatric ICU controls, and pediatric sepsis patients. The sepsis patients, both adults and children, were categorized based on infections originating from different anatomical sites, including the abdomen, respiratory tract, urinary tract, skin, and central nervous system (CNS). Single-cell RNA sequencing was performed to analyze immune cell heterogeneity across these groups.

***************************************************************
The raw sequencing have been uploaded to China Genomic Sequence Archive with accession number GSA:HRA008452.
***************************************************************

first: Qian

last: Ye

first: Fang

last: Xu

first: Ju

last: Cao


title: Bulk RNA sequencing reveals the alterations in gene expression levels of myocardial tissues from mice after myocardial infarction

city: Jinan

first: Cheng

last: Congyi

state: Shandong

address: No.44, Wenhua West Road

institute: Qilu Hospital of Shandong University

summary: Gene expression alterations in myocardial tissues following acute myocardial infarction (AMI) are of great significance for studying the pathophysiological mechanisms of this disease. RNA-seq was used to analyse the gene expression levels in myocardial tissues both in a mouse left anterior descending coronary artery (LAD) ligation model at the 4th day after MI and in sham-operated mice.We uncovered the upregulation of several angiogenesis-related genes after MI, which provided a basis for researches on cardiac repair following AMI.

overall_design: 1 experimental condtion; 1 time point; 4 samples in control group and 3 samples in MI group

first: Congyi

last: Cheng

first: Chunlin

last: Wang

first: Weichun

last: Zhu

first: Chungang

last: Zhai

first: Lei

last: Qiao

first: Wenqiang

last: Chen


title: Immune stromal components impede biological effectiveness of carbon ion therapy in a preclinical model of pancreatic ductal adenocarcinoma [bulk RNA-seq]

first: Todd

last: Aguilera

overall_design: To investigate the transcriptomic differences between carbon and photon treated tumor, we collected tumor tissue samples at days 4 and 7 post-treatment, along with control untreated samples for each group at the same time points. We performed bulk RNA-seq to assess the differences in gene expression and identify underlying enriched gene programs.

first: Katy

last: Swancutt

first: Eslam

last: Elghonaimy

first: James

last: Nicholson

first: Laurentiu

last: Pop

first: Brock

last: Sishc

first: Elizabeth

last: Alves


title: Ultra-mild bisulfite outperforms existing methods for 5-methylcytosine detection with low input DNA

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

type: Methylation profiling by high throughput sequencing

summary: Here we present Ultra-Mild Bisulfite Sequencing (UMBS-seq), which minimizes DNA damage and background noise while detecting 5-methylcytosine (5mC) in DNA. When applied to low-input lambda DNA (5 ng-10 pg), UMBS-seq achieved superior library yields, insert sizes, conversion efficiency, and CpG coverages compared to enzymatic alternatives. These results were recapitulated with low-input cell-free DNA (cfDNA) and in combination with targeted capture, highlighting the potential of UMBS-seq for future disease diagnosis.

overall_design: Ultra-Mild Bisulfite Sequencing (UMBS-seq), EM-seq (NEB), and conventional bisulfite sequencing (Zymo Research) were performed using low-input lambda DNA and cell-free DNA ranging from 0.01 ng to 5 ng.

first: Qing

last: Dai

first: Tanner

last: Baldwin

first: Bryan

last: Daniels


title: Maf1 cooperates with progesterone receptors to repress RNA polymerase III transcription of select tRNAs

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Progesterone receptors (PR) can regulate transcription by RNA Polymerase III (Pol III), which transcribes small non-coding RNAs, including all transfer RNAs (tRNAs). Previous work demonstrated that PR associates with the Pol III complex at tRNA genes and that progestins downregulate tRNA transcripts in breast tumor models. To further elucidate the mechanism of PR-mediated regulation of Pol III, we performed ChIP-seq for PR, the Pol III subunit POLR3A, the TFIIIB component Brf1, and the Pol III repressor Maf1 in breast cancer cells with or without progestin treatment. Upon progestin exposure, PR localized to approximately half of POLR3A-occupied tRNA genes, with Maf1 co-recruited to many of these PR-POLR3A sites. While progestin treatment did not significantly alter the number of tRNA genes occupied by Pol III or Brf1, Brf1 occupancy was stabilized, as indicated by increased peak amplitudes. Analysis of nascent tRNA transcription revealed a specific progestin-induced downregulation of approximately one-third of highly expressed tRNA genes. This repression was significantly reduced by Maf1 knockdown, indicating that Maf1 is necessary for PR-mediated tRNA downregulation. Additionally, PR co-immunoprecipitated with Maf1 along with Brf1 and POLR3A. Overall, these findings demonstrate a ligand-dependent PR-mediated repression of tRNA transcription through Maf1.

overall_design: ChIP-seq for progesterone receptor (PR), RNA Polymerase III subunit POLR3A, Maf1, Brf1, and the histone marker H3K27Ac in T47D breast cancer cells with 1h treatment with ethanol vehicle (OH) or the synthetic progestin R5020 (R50).

first: Kiran

last: Paul

first: Peter

last: Kabos

first: Carol

last: Sartorius


title: Reprogramming of H3K36me2 guides lineage- and locus-specific post-implantation DNA methylation [RNA-Seq]

city: Shanghai

first: Yu

last: Zhang

address: 138 Yi Xue Yuan Road

institute: Fudan university

summary: In mammals, DNA methylation is rapidly re-established after implantation following global erasure in pre-implantation embryos, the regulation of which, however, is not completely understood. Here, by mapping H3K36me2 in pre- and post-implantation mouse embryos, we unravel the dynamic reprogramming of H3K36me2 in mouse early development and its role in post-implantation de novo DNA methylation. Parental H3K36me2 was progressively lost by the 8-cell stage, while de novo H3K36me2 was established at putative enhancers after ZGA mediated by histone acetylation, followed by genome-wide deposition after implantation. H3K36me2 was however excluded from the inactive X chromosome. Catalytic mutation of NSD1, the major H3K36me2 methyltransferase, compromised post-implantation development and DNA methylation re-establishment, with extra-embryonic lineages more severely affected than embryonic lineages. De novo DNA methylation establishment in embryonic lineages partially bypassed H3K36me2/3 through elevated DNMT3B expression. Mechanistically, the PWWP domain of DNMT3A, but not that of DNMT3B, confers strict requirement of H3K36me2/3 for DNA methylation, while DNMT3B is a “leaky” reader of H3K36 methylation. Nevertheless, germline-specific genes, including those contain CpG islands at promoters, still require H3K36me2 to be efficiently methylated and silenced. Amid global remethylation, DNA methylation valleys (DMVs) escape de novo DNA methylation, where PRC1 and H2AK119ub1 antagonize H3K36me2 invasion. Thus, reprogramming of H3K36me2 is required for early embryogenesis and regulates lineage- and locus-specific post-implantation DNA methylation establishment.

overall_design: To investigate the function of H3K36me2 in mouse early development and post-implantaion DNA methylation establishment, we deleted the major methyltransferase, NSD1, in mouse embryos or cell lines, and compare the gene expression in control and Nsd1 KO embryos/cell lines. At least two replicates were involved for each sample.

first: Xukun

last: Lu

first: Lijuan

last: Wang

first: Wei

last: Xie


title: Reprogramming of H3K36me2 guides lineage- and locus-specific post-implantation DNA methylation [methylation]

overall_design: To investigate the function of H3K36me2 in mouse early development and post-implantaion DNA methylation establishment, we deleted the major methyltransferase, NSD1, in mouse embryos or cell lines.  WGBS was used to examine the DNA methylomes in control and Nsd1 KO embryos/cell lines. At least two replicates were involved for each sample.


title: Microproteins Simba1 and Simba2 Activate Wingless Signaling during the Reactivation of Neural Stem Cells in Drosophila

city: Singapore

first: Hongyan

address: 8 College Rd

country: Singapore

institute: Duke-NUS Medical School

summary: The ability of neural stem cells (NSC) to switch between quiescent and proliferative states is fundamental for adult neurogenesis and regeneration. Microproteins or short open reading frame (sORF)-encoded peptides (SEPs), are highly abundant yet largely understudied, and their role in brain development remains unclear. Here, we demonstrate that two microproteins, Simba1 and Simba2 encoded by highly conserved sORFs CG15715 and CG18081, respectively, govern the reactivation of Drosophila quiescent NSCs. Both Simba1 and Simba2 function in NSCs and Blood-Brain-Barrier (BBB) glial cells to promote NSC reactivation. Mechanistically, Simba1 and Simba2 act as transcription factors activating the WNT/Wingless signalling pathway during NSC reactivation. We uncovered a critical role of Wg signalling molecules in promoting NSC reactivation and the translocation of Wingless from BBB glia to NSCs. Moreover, ZNF706, the human ortholog of Simba1/2, is required for WNT signaling activation in human STF3A cells and may also target the WNT signaling pathway in human cancer cells. Our findings reveal a novel role for microproteins in regulating NSC reactivation through Wg signalling. The conserved function of Simba1/2/ZNF706 in activating WNT/Wg signalling in Drosophila and humans suggest that this new regulatory paradigm may be applicable to broader cellular processes and disease conditions.

overall_design: Examination of gene regions targeted by Simba1 or Simba2 in NSCs. Two batches of experiments were conducted. In each batch, one control (UAS-Dam) and two gene-of-interest (UAS-Dam-Simba1 and UAS-Dam-Simba2) were included. UAS contructs were induced under NSC-specific driver, grh-Gal4. Dam-Simba1/2 then bound to DNA and methylated adenines (m6A) at the nearby GATC motifs. By examining the DNA methlyation status through next generation sequencing, Simba1/2 target regions could be identified.

first: Jiaen

last: Lin

first: Lay-Keng

last: Tan

first: Patrick


title: Reprogramming of H3K36me2 guides lineage- and locus-specific post-implantation DNA methylation [ChIP-Seq]

overall_design: To investigate the function of H3K36me2 in mouse early development and post-implantaion DNA methylation establishment, we deleted the major methyltransferase, NSD1, in mouse embryos or cell lines.  STAR ChIP-seq was used to examine H3K36me2, H3K36me3, H2AK119ub1, and H3K27me3 in control and Nsd1 KO embryos/cell lines. At least two replicates were involved for each sample.


title: DNA replication fork speed Acts as A Pacer in Cortical Neurogenesis

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

summary: DNA replication fork speed, which controls the rate of genome duplication, has emerged as a key regulator of cellular plasticity. However, its role in neurogenesis remains unexplored. Mini-chromosome maintenance complex (MCMs)-binding protein (MCMBP) functions as a chaperone for newly synthesized MCMs, increasing chromatin coverage to restrain fork speed. We demonstrate that selective deletion of MCMBP in neural progenitor radial glial cells (RGCs) accelerates fork speed, triggering widespread apoptosis, DNA damage, and micronuclei formation, ultimately activating p53 and causing microcephaly. Unexpectedly, concurrent deletion of Trp53 and Mcmbp further increased fork speed, leading to extensive RGC detachment from the ventricular zone and acquisition of outer-RGC characteristics. Mechanistically, we found that the MCM3 subunit coordinates DNA and centrosome duplication, thereby mediating RGC attachment. Behavioral analysis revealed that disruption of fork speed results in anxiety-like behavior in mice. These findings unveil a previously unrecognized role for replication fork speed in neurogenesis.

overall_design: We sequenced a total of 20 samples of mRNA from E15.5 mouse cerebral cortex.  9 samples were controls (wild type or heterozygote), 6 samples were Emx1-Cre Mcmbp conditional KO, and 5 samples were Emx1-Cre Mcmbp/Trp53 double conditional KO.

first: Jianhong

first: Lei

last: Shi


title: Collagen XXIII (COL23A1): A novel risk factor for eczema herpeticum

city: Hannover

first: Shruti

last: Chopra

state: Lower Saxony

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: Background Eczema herpeticum (EH) is a potentially life-threatening disseminated skin infection caused by herpes simplex virus (HSV) in a subset of atopic dermatitis (AD) patients. The occurrence of EH in a subset of AD patients and its frequent recurrence implies the importance of genetic factors in its pathogenesis. Objective We aimed to identify novel genetic risk factors for EH and to study their impact on HSV-1 infection. Methods Using whole exome sequencing we identified a heterozygous single nucleotide polymorphism (SNP) in the COL23A1 gene (encoding Collagen type XXIII alpha 1 chain or Col23a1) that was associated with EH and validated it by PCR in a larger cohort. We studied the effect of upregulated COL23A1 expression on HSV-1 infection in primary keratinocytes and HaCaT cells and performed bulk RNA sequencing to address the underlying mechanism. Results EH-patient-derived primary keratinocytes carrying this heterozygous SNP rs2973744 had elevated COL23A1 mRNA and protein levels as well as an increased susceptibility to HSV-1. Increasing the Col23a1 levels experimentally enhanced HSV-1 infection in human keratinocytes. COL23A1 overexpression elevated syndecan-1 and nectin-1 levels on the cell surface, which are HSV-1 attachment and entry factors, respectively, and downregulated genes involved in antiviral responses such as IL1R1, IL32, TLR4, IRF1, S100A9, C3, and CFH. Conclusion The SNP rs2973744 enhances Col23a1 expression in ADEH+-derived keratinocytes. Upregulation of Col23a1 promotes HSV-1 infection presumably by upregulating the HSV-1 attachment and entry factors syndecan-1 and nectin-1 on the cell surface and attenuating antiviral responses of keratinocytes.

overall_design:
To investigate the function of COL23A1, we transduced HaCaT cells with control lentiviral particles encoding EGFP and a puromycin resistance cassette or lentiviral particles encoding COL23A1 in addition.
To study the role of COL23A1 overexpression in HSV-1 infection and on the global transcriptome of keratinocytes, we either infected control or COL23A1 overexpressing HaCaT cells with HSV-1 at an MOI of 5 pfu/cell or left them uninfected, and isolated their RNA after 2 hpi and 6 hpi and subjected them to bulk RNA sequencing.

first: Chopra

last: Shruti

first: Traidl

last: Stephan

first: Döhner

last: Katinka

first: Roesner

last: Lennart M.

first: Werfel

last: Thomas


title: Transcriptional profiling of human myeloid cells in healthy donors and oral cavity cancer (OCSCC) patients

status: Public on Sep 26 2025

city: Bethesda

first: Clint

middle: Tanner

last: Allen

state: MD

address: 10 Center Drive, Room 7N240C

department: NIDCD

institute: NIH

summary: This single-cell RNA sequencing (scRNA-seq) dataset profiles human myeloid cells from healthy donors and patients with advanced oral cavity squamous cell carcinoma (OCSCC). scRNA-seq was performed on isolated CD11b⁺ cells from high- and low-density peripheral blood fractions and on isolated CD45⁺ tumor-infiltrating cells from OCSCC patients (n=8), as well as on CD11b⁺ high- and low-density peripheral blood cells from healthy donors (n=5). The dataset enables the characterization of compartment-specific transcriptional states of human myeloid cells and supports investigations into genes and pathways associated with pathologic activation and immune suppression.

overall_design: This study (ClinicalTrials.gov identifier NCT03429036) was approved by the National Institutes of Health Institutional Review Board (IRB). Fresh peripheral blood and tumor samples were collected from 8 patients with newly diagnosed oral cavity squamous cell carcinoma (OCSCC) undergoing standard-of-care surgical procedures. All patients signed IRB-approved informed consent permitting the use of their blood and tumor tissue for research. Peripheral blood samples from 5 healthy donors were also obtained at the National Institutes of Health Clinical Center under informed consent. For single-cell profiling, whole blood was separated into high-density and low-density fractions by Ficoll-based density gradient centrifugation. CD11b⁺ myeloid cells were enriched from both fractions in cancer patients and healthy donors to capture circulating myeloid populations. Tumor specimens were mechanically and enzymatically dissociated into single-cell suspensions, from which CD45⁺ leukocytes were isolated. Enriched suspensions from each compartment (blood high-density CD11b⁺, blood low-density CD11b⁺, and tumor-infiltrating CD45⁺) were immediately processed for scRNA-seq using the 10x Genomics Chromium platform. This design allowed direct comparison of myeloid transcriptional states across circulation and tumor microenvironments in both healthy donors and OCSCC patients.

first: Tian-Gen

last: Chang

middle: T


title: Radiation induced YTHDF2 in dendritic cells impairs antitumor immunity

first: Dapeng

last: Chen

state: Illinois

address: 900 E 57th St

institute: UChicago

summary: We reveal that ionized radiation (IR) induces the expression of m6A reader YTHDF2 in DCs with clinical significance, and the depletion of Ythdf2 in DCs augments the anti-tumor effect of RT. We observed that following IR, SPI-1 promotes the transcription of YTHDF2 in DCs. The IR-induced YTHDF2 in DCs directly targets and degrades m6A-binded Mfng, Aph-1b, and Aph-1c, which are essential for notch activation. YTHDF2 blockades in DCs activates notch signaling to promote the expression of MHC-I family gene Gm8909, thus enhancing cross-priming of CD8+ T cells to afford amplified anti-tumor effect of RT. Pharmacological inhibition of YTHDF2 in DC vaccines contributes to RT efficacy in both local tumor control and distant metastasis suppression. Our findings identify IR-induced YTHDF2 as an immunosuppressor in DCs, reveal the mechanism for regulating anti-tumor immunity, and open a new path for the development of m6A-mRNA targeting therapies.

overall_design: mRNA seq, RIPseq, and m6A-RIP seq profiling of YTHDF2 in tumor-infiltrating or tumor cell-coculturing dendritic cells from  with or without treatment of irradiation

first: Chuan

last: He

first: Hua

last: Liang

first: Ralph

middle: R

last: Weichselbaum


title: MYC inhibition by Omomyc causes DNA damage and overcomes PARPi resistance in breast cancer.

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

institute: Vall d'Hebron Institute of Oncology

summary: MYC is dysregulated in most human cancers and is a DNA damage response (DDR) modulator capable of both promoting genomic instability and enhancing DNA repair. Here, we show that Omomyc, the first direct MYC inhibitor to pass a Phase 1 trial, shuts down DDR genes in triple-negative breast cancer (TNBC), causing DDR defects and inducing DNA damage. Since DDR-deficient tumours are currently targeted by PARP inhibitors (PARPi), we tested combinations with Omomyc. We show that Omomyc-induced DNA damage is enhanced by PARPi and that the inhibitors cooperate even in models with intrinsic or acquired PARPi resistance, both in vitro and in vivo. Moreover, using patient-derived models and clinical samples, we reveal a role for MYC as a predictor of PARPi resistance. Overall, our research highlights the opportunity of combining MYC inhibition by Omomyc with PARPi in PARPi-resistant TNBC, where MYC transcriptional activity represents a predictive biomarker of resistance to therapy.

overall_design: MDA-MB-231 cells were purchased from ATCC (catalogue no. HTB-26) and were maintained in DMEM/F12 (Life Technologies) with 10% FBS. MDA-MB-231 cells were treated with 30μM Omomyc and vehicle for 120 hours. Total RNA extraction of the cell-line samples was done by Qiagen RNeasy Mini Kit and quality checked by TapeStation. The extracted RNA was purified with oligo(dT) magnetic beads to capture mRNAs, fragmented and subject to a stranded RT proceeding with library preparation protocol from Illumina Stranded mRNA Prep. Library QC included fluorometric quantification (Qubit) and fragment size distribution (TapeStation). The prepared libraries were sequenced with Illumina NovaSeq.

first: Fabio

last: Giuntini

first: Íñigo

last: González-Larreategui

first: Andrea

last: Herencia-Ropero

first: Silvia

last: Casacuberta-Serra

first: Mariano

middle: F

last: Zacarías-Fluck

last: Arnal

first: Flaminia

last: Pedretti

first: Sandra

last: Martínez-Martín

first: Hugo

last: Thabussot

first: Virginia

last: Castillo Cano

first: Judit

last: Grueso

first: Laia

last: Foradada

first: Erika

last: Serrano

first: Sergio

last: López-Estévez

first: Olga

last: Rodriguez

first: Marta

last: Guzman

first: Adela

last: Rodriguez-Hernandez

first: Fara

last: Brasó-Maristany

first: Alba

last: Llop-Guevara

first: Judith

last: Balmaña

first: Lara

last: Nonell

first: Aleix

last: Prat

first: Violeta

last: Serra

first: Marie-Eve

last: Beaulieu

first: Jonathan

last: Whitfield

first: Daniel

last: Massó-Vallés

first: Laura

last: Soucek


title: DNA methylation alterations in acute lymphoblastic leukemia survivors with late neurocognitive deficits: PETALE cohort

city: Montréal

last: Sinnett

state: Québec

address: 3175 Chem. de la Côte-Sainte-Catherine

department: Research Center

institute: CHU Sainte-Justine

type: Methylation profiling by genome tiling array

summary: Many survivors of acute lymphoblastic leukemia (ALL) develop late effects that include lifelong impairments in cognitive function. We examined DNA methylation (DNAm) patterns in healthy blood from two independent cohorts of ALL survivor to 1) identify distinct genome-wide DNAm alterations (signatures) in survivors, and establish long-term epigenetic dysregulation as a common outcome of ALL treatment, and 2) elucidate the role of epigenetics as a biomarker and potential mechanism of neurocognitive deficits in ALL survivors. We identified a signature of 452 CpG sites in the blood of ALL survivors vs. controls, that demonstrated ~99% sensitivity and 85% specificity, irrespective of time elapsed from the end of treatment. Using St. Jude LIFE as a validation cohort, we found that survivors of non-ALL childhood cancers carried a different DNAm signature. Finally, we found 43 distinct CpGs associated with neurocognitive deficits as defined by the neuropsychological test, DIVERGT, that replicated across our two cohorts of ALL survivors. We propose DNAm as a potential biomarker that could predict patients most likely to experience neurocognitive deficits following ALL treatment and inform early interventions.

overall_design: Venous blood samples were collected from ALL survivors participating in the PETALE study, at least five years after the diagnosis of ALL. Genomic DNA was extracted, bisulfite converted and DNA methylation was assayed on the Infinium MethylationEPIC Bead Chip array (GPL21145). Healthy controls described in the associated publication are not included here due to lack of consent for public deposition of data. There are no replications in this submission.

first: Sarah

last: Goodman

first: Darci

last: Butcher

first: Sharon

last: Guger

first: Eric

last: Diehl

first: Jack

last: Brzezinski

first: Brenda

last: Spiegler

first: Brian

last: Nieman

first: Prajkta

last: Kallurkar

first: Aubrée

last: Boulet Craig

first: MajaÂ

last: Krajinovic

first: Julie

last: Laniel

first: Caroline

last: Laverdière

last: Lippé

first: Andrei

last: Turinsky

first: Mary

last: Shago

first: Lisa

last: Strug

first: Shinya

last: Ito

first: Johann

middle: K

last: Hitzler

first: Russell

last: Schachar

first: Rosanna

last: Weksberg


title: RNA-sequencing of Endothelial Cell Lines Expressing TIE2 WT or Mutant TIE2-L914F

city: Cincinnati

first: Sandra

last: Schrenk

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

summary: To investigate the transcriptional effects of venous malformation causative somatic mutation in TIE2 p.L914F mutation on endothelial cells, bulk RNA-sequencing was performed on endothelial cells lines expressing TIE2 wildtype or mutant TIE2-L914F

overall_design: Human umbilical vein endothelial cells (HUVEC) were transduced with TIE2-WT and TIE2-L914F constructs. RNA Sequencing performed and the transcriptional changes in HUVEC cells expressing TIE2-L914F were compared to TIE2-WT HUVEC and non-treated (NT) control HUVEC.

first: Lindsay

last: Bischoff

first: Elisa

last: Boscolo


title: Induction of a metabolic switch from glucose to ketone metabolism programs ketogenic diet-induced therapeutic vulnerability in lung cancer [scRNA-seq]

first: Zhengwei

last: Wu

address: 60 Biopolis St

institute: Genome Institute of Singapore

summary: Tumor-initiating cells (TICs) tend to reside in poorly vascularized regions of tumors and are subjected to nutrient stress. How TICs activate metabolic plasticity for adapting to periods of low nutrient availability, especially during glucose-limiting conditions, has remained unclarified. Here, we discover that lung TICs can induce a metabolic switch from glucose towards ketone utilization specifically during glucose deprivation, whereas bulk, non-TIC cells are unable to do so. Through ex vivo supplementation of ketones or keeping mice on prolonged ketogenic diet, we determine the functional importance of ketones in maintaining the growth and tumor-initiating property of lung TICs. Metabolomics, genomics and metabolic flux tracing studies reveal that ketones feed into ketolysis, fatty acid synthesis and de novo lipogenesis pathways. Surprisingly, ketogenic diet programs the metabolic addiction of TICs towards ketolysis, and this paradoxically induces their therapeutic sensitivity towards the inhibition of the monocarboxylate transporter, MCT1, which imports ketones into cells. Additionally, pharmacological inhibition of fatty acid synthase (FASN) also exerts a more pronounced anti-tumorigenic response in the context of a ketogenic diet. MCT1 function is regulated by the chaperone protein, CD147, and its loss is sufficient to ablate lung TICs under glucose-limiting conditions in vitro and in vivo. Our data reveal a metabolic switch that lung TICs adopt to overcome nutrient stress, and provide the mechanistic bases for how diet manipulation can alter the course of cancer progression or enhance the efficacy of targeted therapy in a context-dependent manner.

overall_design: Tumor-initiating cells xenografts harvested from either mice fed with standard chow or ketogenic diet

first: Zhenxun

last: Wang

first: Seow Qi

last: Ng

first: Jessica Alice

last: Lidster

first: Paul

last: Schwerd-Kleine

first: Zi Jin Cheryl

last: Phua

first: Kai Lay Esther

last: Peh

first: Yin Ying

last: Ho

first: Ju

last: Yuan

first: S

last: Shathishwaran

first: Xun Hui

last: Yeo

first: Ying

last: Zhang

first: Yu Hei Jasper

last: Chiu

first: Li Yieng Eunice

last: Lau

first: Tony Kiat Hon

last: Lim

first: Angela

last: Takano

first: Eng Huat

last: Tan

first: Anders Jacobsen

last: Skanderup

first: Vinay

last: Tergaonkar

first: Weiping

last: Han

first: Ying Swan

first: Daniel Shao Weng

first: Wai Leong

last: Tam


title: Gene signature profiles in lung tissues of wild type mice or Has2 heterozygous deficient mice stimulated with porcine pancreatic elastase

city: Tsukuba

first: Takumi

last: Kiwamoto

address: 1-1-1 Tennoudai

department: Pulmonary Medicine

country: Japan

institute: University of Tsukuba

summary: Chronic obstructive pulmonary disease (COPD) is an inflammatory lung condition primarily caused by prolonged exposure to harmful substances, such as cigarette smoke. Hyaluronic acid synthase 2 (HAS2) synthesizes high-molecular-weight hyaluronic acid (HMW-HA), believed to have anti-inflammatory properties. Previous studies have suggested that HAS2 dysfunction may exacerbate COPD. However, the specific impact of HAS2 on pulmonary emphysema progression remains unclear. In this study, we tested the hypothesis that HAS2 dysfunction worsens airway inflammation and emphysema in mouse COPD model. Has2 heterozygous-deficient (Has2+/-) mice and their wild-type (WT) littermates have been evaluated in a porcine pancreatic elastase (PPE)-induced COPD model. Following PPE administration, Has2+/- mice exhibited a significant increase in total cell and neutrophil counts in BALF samples compared to WT mice. Has2+/- mice demonstrated enhanced emphysema development on histological analyses, with higher values of mean linear intercept relative to wild-type mice. Elastase-stimulated Has2+/- mice also demonstrated increased G-CSF level and TGF-β attenuation in lung. RNA-seq analysis suggested that PPE stimulation promotes HMW-HA synthesis and TGF-β signaling. GO analysis using Has2+/- mice-specific DEGs showed that genes associated with pathways that "negative regulation of transforming growth factor beta receptor signaling pathway" were activated after PPE administration. This study demonstrates that Has2 dysfunction exacerbates neutrophilic airway inflammation and emphysema, underscoring the protective role of HAS2 in a PPE induced emphysema model. The exacerbated response appears to involve G-CSF and TGF-β-related signaling pathways. These findings may contribute to the development of novel therapeutic strategies for COPD management.

overall_design: 27 strand-specific RNA libraries for high-throughput sequencing were prepared (7 from the lungs of the wild type mice treated without PPE, 7 from the lungs of the Has2+/- mice treated without PPE, 7 from the lungs of the wild type mice treated with PPE, and 6 from the lungs of the Has2+/- mice treated with PPE using the Illumina Stranded mRNA Sample Preparation Kit with 500ng of total RNA according to manufacturer’s instructions.

first: Kengo

last: Nishino

first: Zhenting

last: Wei

first: Masashi

last: Matsuyama

first: Nobuyuki

last: Hizawa


title: Silencing of double stranded RNA sensing is required for early embryonic development

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

summary: The type I interferon (IFN) response is inactive during early mammalian development and becomes functional only after gastrulation. As a result, the totipotent and pluripotent embryonic stages remain susceptible to pathogens, including viruses. Here, we demonstrate that pluripotent mouse embryonic stem cells (mESCs) suppress the RIG-I-like receptor sensing pathway by silencing the expression of the dsRNA sensor MDA5. This silencing is necessary to avoid the recognition of dsRNAs of endogenous origin, which accumulate in mESCs. Reintroducing MDA5 results in recognition of these endogenous dsRNAs and triggers the activation of the IFN response through IRF3. The production of IFN alters the differentiation ability of mESCs, and affects the pluripotency gene expression program, as shown by epigenetic, transcriptomic and proteomic analyses. These findings are conserved in zebrafish, where MDA5 is also expressed at later developmental stages. Similarly, zebrafish lack early-stage IFN activation, and dsRNA-mediated signalling results in developmental defects. Altogether, we conclude that silencing the RIG-I-like receptor pathway during early development is widely conserved and is essential to prevent aberrant immune recognition of endogenous dsRNAs, safeguarding normal development.

overall_design: ATAC-seq profiling of  WT and inducible Mda5 overexpression at 0 hr (- dox) and 24 hr (+dox) in  v6.5 mouse ESC cultured in serum+mlif medium.

first: Jeroen

last: Witteveldt

first: Zicong

last: Liu

first: Ana

last: Ariza-Cosano

first: Christian

last: Ramirez

first: Jessica

last: Walters

first: Pilar

middle: G

last: Marchante

first: Lars

last: Maas

first: Elias

last: Friman

first: Alasdair

last: Ivens

first: Toma

last: Tebaldi

first: Sara

last: Heras

last: Macias


title: Early dissemination and prognostic value of circulating tumor cells in ductal carcinoma in situ

city: Ann Arbor

first: Sunitha

last: Nagrath

state: MI

address: 2800 Plymouth Rd

department: Chemical Engineering

institute: University of Michigan

summary: Widespread mammographic screening has resulted in a substantial increase in women diagnosed with Ductal Carcinoma in Situ (DCIS). To improve patient risk stratification, we investigate the prognostic value of circulating tumor cells (CTCs) as a biomarker for DCIS patients’ biological aggressiveness and as an indicator of early dissemination. Six enriched blood samples and six matching FFPE tissue samples are processed via single cell RNA sequencing.

overall_design: Blood samples are processed via a microfluidic device (the Labyrinth) to enrich CTCs. To meet 10X Genomics' minimum cell number requirement for sequencing, some white blood cells are supplemented into the initial sample. Hence, these data include six CTC enriched blood samples. In conjunction, FFPE tissues acquired from the same six patients are also processed for single cell RNA sequencing.

first: Neha

last: Nagpal


title: The African Swine Fever Virus pH108R Protein Negatively Regulates Innate Immune Response by Inhibiting NF-kappaB Activation.

city: Zhengzhou

first: Enping

address: 100 Kexue Avenue

institute: Zhengzhou university

summary: The NF-κB pathway is an essential signaling cascade in the defence against viral infections, including African swine fever virus (ASFV) infection. ASFV encodes more than 151 proteins via its own transcription machinery and possesses a great capacity to evade or subvert antiviral innate immune responses. Although some of these viral proteins have been reported, many remain unknown. In this study，we find pH108R,  an inner envelope protein of ASFV, can significantly downregulated NF-κB activation induced by IL-1β or TNFα. The overexpression of pH108R suppresses transcription  of several proinflammatory cytokines such as IL-6， IL-8，and TNFα induced by IL-1β or TNFα in HEK293T cells. Consistently, the levels of phosphorylated p65 and IκBα were decreased in pH108R overexpression cells after IL-1β and TNFα stimulation. In addition，Transcriptome sequencing showed that it could significantly down-regulate the expression of TNF-induced immune and inflammatory genes in PK-15 cells. Collectively, our study indicates that ASFV pH108R markedly suppresses NF-κB activation stimulated by IL-1β and TNFα, clarifies the immunosuppressive activity of pH108R and provides a new perspective for analyzing the immune escape of African swine fever.

overall_design: RNA-seq profiling  of pH108R overexpression cells and control cells, treated with TNFα or not.

first: Zehui

last: Li


title: A Ternary-code DNA Methylome Atlas of Mouse Tissues

city: Phialdelphia

first: Wanding

last: Zhou

state: Pennsylvania

address: 3501 Civic Center Blvd, Philadelphia, PA 19104, Colket Translational Research Building, 9300, Colket Translational Research Building

department: Pathology & Lab Medicine

institute: Children's Hospital of Philadelphia

summary: DNA cytosine modifications, including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), are key epigenetic regulators with distinct functions. To better understand the ternary code (C, 5mC, 5hmC) across different tissues and cell types, we used bACE conversion with scalable assays to map these modifications at base resolution in 29 mouse tissues across various ages and sexes. Our atlas revealed complex patterns of 5hmC distribution, shaped by mitotic activity, chromatin states, and interactions with 5mC. Notably, 5hmC complements 5mC in identifying cell types, extending beyond the brain. Each modification, including 5hmC alone, distinguishes tissue types, enabling high-precision classification of epigenetic identity. Additionally, changes in the methylome correlate with gene transcription, with age-related effects varying by tissue type, offering new insights into cytosine modification biology and potential biomarkers.

overall_design: We examined 5mC and 5hmC in 267 tissue samples from 29 tissue types obtained from 32 C75BL/6 mice.

first: SolMoe

last: Lee

first: Zhou

last: Wanding


title: Genetic and Epigenetic Regulation of Pvt1 Monoallelic Expression [Hi-ChIP-seq]

city: Stanford

first: Christy

last: Luong

address: 269 Campus Dr

department: Department of Dermatology

institute: Stanford University School of Medicine

summary: Each gene exists as two copies in the same nucleus of mammalian cells. Although most genes are equivalently controlled on both alleles, Random Monoallelic Expressing (RME) genes stably maintain the expression from only one of two alleles, but the mechanisms and functional consequences of RME remains unclear.  Here we performed allele-specific RNA-seq on over 100 neural progenitor cell (NPC) clonal lines to reveal the extent of RME for genes across clonal lines. Interestingly out of 297 autosomal RME genes, Pvt1, a well-studied oncogenic long non-coding RNA, is monoallelically expressed with a skewed genetic bias towards the Castaneous allele in F1-hybrid NPCs. In the absence of genetic differences, allelic tracking by gene editing reveals Pvt1 undergoes balanced RME that is maintained across somatic cell generations. Monoallelic expression is maintained by a poised Pvt1 promoter with bivalent active histone marks, H3K4me3 and H3K27ac, and silencing histone marks, H3K4me3 and H3K27me3, demonstrating its ability to switch transcriptional states depending on the cellular context. Leveraging our large RNA-seq data set and the genetic skew, we use differential gene expression analysis on clonal lines based on their Pvt1 allelic status to reveal a transcription factor, Tfap2a, with differential binding at the Pvt1 promoter, providing a mechanism for the initiation and allelic choice for RME genes. Additionally, we demonstrate monoallelic Pvt1 expression results in an increase in Pvt1 expression leading to a growth advantage relative to Pvt1 biallelic expressing clonal lines These findings provide an example of how genetic differences can skew a stochastic process which results in an epigenetic phenomenon with a phenotypic consequence in early development.

overall_design: H3K27ac Hi-ChIP-seq of a neuronal progenitor cell (NPC) clonal line differentiated from a male F1-hybrid (129 x Cast) mESC. Library was sequenced using Illumina Hi-Seq (150 x 150bp) and data was analyzed allele-specifically.

first: Katerina

last: Kraft

first: Howard

middle: Y

last: Chang


title: Genetic and Epigenetic Regulation of Pvt1 Monoallelic Expression

overall_design: Bulk RNA-seq of neuronal progenitor cell (NPC) clonal lines differentiated from a male and female F1-hybrid (129 x CAST) mESC.

first: Julia

last: Belk

first: Joanna

last: Wysocka


title: Genetic and Epigenetic Regulation of Pvt1 Monoallelic Expression [ChIP-seq]

summary: Each gene exists as two copies in the same nucleus of mammalian cells. Although most genes are equivalently controlled on both alleles, Random Monoallelic Expressing (RME) genes stably maintain the expression from only one of two alleles, but the mechanisms and functional consequences of RME remains unclear. Here we performed allele-specific RNA-seq on over 100 neural progenitor cell (NPC) clonal lines to reveal the extent of RME for genes across clonal lines. Interestingly out of 297 autosomal RME genes, Pvt1, a well-studied oncogenic long non-coding RNA, is monoallelically expressed with a skewed genetic bias towards the Castaneous allele in F1-hybrid NPCs. In the absence of genetic differences, allelic tracking by gene editing reveals Pvt1 undergoes balanced RME that is maintained across somatic cell generations. Leveraging our large RNA-seq data set and the genetic skew, we use differential gene expression analysis on clonal lines based on their Pvt1 allelic status to reveal a transcription factor, TFAP2a, with differential binding at the Pvt1 promoter, providing a mechanism for the initiation and allelic choice for RME genes. Additionally, we demonstrate monoallelic Pvt1 expression results in an increase in Pvt1 expression leading to a growth advantage relative to Pvt1 biallelic expressing clonal lines These findings provide an example of how genetic differences can skew a stochastic process which results in an epigenetic phenomenon with a phenotypic consequence in early development.

overall_design: Epigentic ChIP-seq of a neuronal progenitor cell (NPC) clonal line differentiated from a male F1-hybrid (129 x Cast) mESC and mouse embryonic cells (mESCs). Library was sequenced using NovaSeq X (150 x 150bp) and data was analyzed allele-specifically.


title: Genetic and Epigenetic Regulation of Pvt1 Monoallelic Expression [Bisulfite-seq]

overall_design: Bisulfite sequencing of a neuronal progenitor cell (NPC) clonal line differentiated from a male F1-hybrid (129 x Cast) mESC.


title: VEGF-C treatment enhances meningeal lymphatic drainage after mild traumatic brain injury and protects against tau pathology, microgliosis and neurodegeneration in a mouse model of tau pathology.

city: Charlottesville

first: John

last: Lukens

state: VA

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

summary: Traumatic brain injury (TBI) increases one’s risk of developing Alzheimer’s disease and tauopathy. Yet, the mechanisms linking TBI to neurodegenerative disease remain poorly defined. Mounting recent evidence indicates that defects in brain lymphatic drainage contribute to multiple neurodegenerative diseases. Here, we investigated whether promoting brain lymphatic drainage recuperation following TBI via treatment with the lymphangiogenic factor VEGFC mitigates the ability of TBI to exacerbate tauopathy. In this study, we show that a single mild TBI leads to worsened neuropathology, brain macrophage activation, and neurodegeneration in the PS19 mouse model of tauopathy. Moreover, we find that viral vector-based delivery of VEGFC into the meningeal compartment 24 hours post-TBI ameliorates tau-mediated neurodegenerative disease pathogenesis. Findings from these studies offer new insights into how TBI leads to the development of tauopathy later in life and suggest that VEGFC-based treatments might offer a therapeutic strategy to limit tauopathy after sustaining a head injury.

overall_design: PS19 mice were subjected to (1) Sham vs. controlled cortical impact (mild TBI, right hemisphere), and were treated with (2) AAV-GFP control vs. AAV-VEGFC. Hippocampi were microdissected from brains, flash-frozen, and nuclear RNA was analyzed via scRNA-sequencing.

first: Ana

last: Royo Marco

first: Maureen

middle: N

last: Cowan


title: Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb

city: Cambridge

first: Alberto

last: Rosello-Diez

address: Physiology building. Downing St.

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

summary: Single-nuclei RNA sequencing of cells dissociated from Hindlimb (femur and tibia, from RZ to PHT Region) from E16.5 embryos to identify how catch up grpwuth happens during injury and to to show transcriptional identities of contributors to chondrocytes in p21-overexpression induced injury  in unilateral models.

overall_design: Pitx2-Cre/Cre; Col2a1-rtTA/+; Col2a1-eCFP/+ females were crossed with TigreDragon-p21/Dragon-p21 males and given Dox (1mg/ml in drinking water with 0.5% sucrose) at E12.5. The knee region (obtained via orthogonal cuts from the hypertrophic region of the distal femur to the hypertrophic region of the proximal tibia in skinned hindlimbs) of E16.5 Left and Right limbs from uCtl and Left-Cart-p21 samples (2 embryos of each genotype) were collected in DMEM with 10% DMSO and 5% calf serum, stored in a MrFrosty (ThermoFisher) at 4ºC for 10 min and then transferred to -80ºC overnight. Tissue lysis and nuclei isolation were done as described by L.G.M. in https://www.protocols.io/view/frankenstein-protocol-for-nuclei-isolation-from-f-5jyl8nx98l2w/v2, in two batches of four samples each (left and right knees from one control and one experimental embryo). Once ~5,000 nuclei per sample were collected, we proceeded with the 10x protocol described in https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry, minimizing the time between nuclei preparation/sorting and chip loading. One chip per batch was used (4 channels in each case, to load left and right samples from one control and one experimental embryo).

first: Xinli

last: Qu

first: Ehsan

last: Razmara

first: Chee

last: H’ng


title: STAT5-activating oncogenes drive Oncostatin M production causing T cell exhaustion and suppressive myeloid cell recruitment [Thy1.2+ splenocytes]

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Understanding the interplay between oncogenic mutations and immune evasion of cancer cells could help to improve cancer immunotherapy in hematological malignancies. We found that the STAT5-activating oncogenes BCR-ABL, JAK2-V617F, and FLT3-ITD induce Oncostatin M (OSM) which acted immunosuppressive. OSM profoundly reprogrammed bone marrow (BM) stromal cells, inducing the secretion of cytokines connected to T cell exhaustion, including IL-6 and MCP-1. OSM overexpressing mice exhibited reduced T cells numbers, more T cell exhaustion and increased lactic acid production by stroma cells. OSM induced expansion of myeloid-derived suppressor cells (MDSCs) thereby promoting immune escape of malignant hematopoietic cells. Osm knockout reduced disease progression and T cell exhaustion in mice with JAK2-V617F-driven polycythemia vera. Consistently, pharmacological inhibition of OSM reduced disease activity and cytokine production. Our study indicates that STAT5-activating oncogenes drive OSM production thereby inducing MDSC recruitment and T cell exhaustion.

overall_design: To investigate the effects of OSM overexpression by transplanted hematopoietic cells on T cells in an in vivo murine model, splenic Thy1.2+ cells were isolated, RNA was extracted and further processed for RNA-sequencing. T cells from animals transplanted with an empty MiG-vector were utilized as controls.

first: Melanie

last: Boerries

first: Michael

last: Rassner

first: Justus

last: Duyster


title: STAT5-activating oncogenes drive Oncostatin M production causing T cell exhaustion and suppressive myeloid cell recruitment

overall_design: To investigate the effects of OSM deficiency in transplanted hematopoietic cells (Osm+/+ vs. Osm-/-) harboring the JAK2V617F mutation on T cells, splenic Thy1.2+ cells were isolated, RNA was extracted and further processed for RNA-sequencing.


summary: Single-cell RNA sequencing of cells dissociated from Hindlimb at E14.5 embryos to identify how catch-up growth happens during injury and to  show transcriptional identities of contributors to chondrocytes in p21-overexpression induced injury model.

overall_design: Female Gli1CreER/CreER mouse was crossed with Col2a1-rtTA; TigreTRE-p21/TRE-p21; R26LSL-tdT/LSL-tdT male. At E12.5, the pregnant mouse was administered doxycycline in water (1 mg/ml with 0.5% sucrose) and food, while Tamoxifen was orally gavaged (120 μg/g) at E13.5. At E14.5, the hindlimb samples (femur and tibia) were carefully dissected. Following, the tissue underwent treatment with Accumax in a rocker at 31°C for 25 minutes and they were gently shaken every 10 min. The supernatant was carefully transferred into a tube and placed on ice for preservation, while the cartilaginous portions were exposed to Collagenase B (5 mg/ml; Sigma) for ~90 min at 37°C in a water bath (and pipetted every 20 min). To stop collagenase activity, we then added 700 µl of cold DMEM+20% FBS for each tube. We then incorporated outer and inner supernatants, and the samples were resuspended in 20 volumes of 1× RBC lysis buffer and incubated for 10 minutes at room temperature on a rocker.  As a final step, the cell suspension was filtered through 40-μm Flowmi® Cell Strainers and cells were stained with DAPI (stock concentration: 0.05 µg/ml) and transferred into Falcon™ Round-Bottom Polypropylene (Fisher Scientific). The tdT+ and tdT- cells were sorted using flow cytometry  and the samples were then multiplexed based on sex and conditions.


title: Induction of a metabolic switch from glucose to ketone metabolism programs ketogenic diet-induced therapeutic vulnerability in lung cancer

first: Zhengwei

last: Wu

summary: To explore metabolic vulnerabilities in lung cancer, relating to ketone metabolism

overall_design:
Next, we performed RNA-sequencing on TS and Adh cells, subjected to glucose limitations to map out common biological processes distinctive to respective cell type and to compare their gene expression profile when glucose is limited
We performed gene expression profiling analysis using data obtained from RNA-seq of both TS and Adh cell lines, with and without glucose limitation.
Treatments:
WT - Wild-type
UL - Glucose-limiting conditions (1.4mM glucose) for 48 hours, HG - Cultured in high glucose (25mM glucose) for 48 hours, ULG - Glucose-limiting conditions (1.4mM glucose) for 48 hours, Early - Low passage of derived cell line.

first: Wai

last: Tam


title: Goblet cell-expressed microprotein FXYD3 determines gut homeostasis by maintaining mucus barrier integrity

status: Public on Sep 25 2025

city: Hangzhou

first: Qingqing

last: Wang

state: Zhejiang

address: 866 Yu Hang Tang Road

department: Institute of Immunology

institute: Zhejiang University

summary: The intestinal mucus layer produced by goblet cells is a critical component of innate immunity. The key host factors and regulatory mechanisms controlling goblet cell function in mucus layer formation remain poorly understood. This study identifies a function for the microprotein FXYD domain-containing transport regulator 3 (FXYD3) in goblet cells in regulating mucus layer formation to maintain intestinal homeostasis. Deficiency of FXYD3 in mouse intestinal epithelial cellsresults in a damaged mucus barrier, leading to microbiota dysbiosis and increased susceptibility to colitis. Mechanistically, FXYD3 interacts with endoplasmic reticulum Ca2+-ATPase SERCA2 to enhances its pump activity. FXYD3 deficiency causes defects in ER Ca2+ homeostasis and mucin glycosylation, impairing mucus layer integrity. Furthermore, metabolites of gut microbiota, propionate and butyrate promoteFXYD3 expression. In ulcerative colitis (UC) patients, FXYD3 expression is significantly downregulated and correlats with disease severity. These findings indicat FXYD3 is a key mediator of  host-microbiota interactions for intestinal health.

overall_design: RNA-seq analysis of wide-type LS174T and FXYD3-deficient LS174T cells (KO)

first: Wenjuan

last: Yang

first: Yue

last: Xue

first: Peishuo

last: Zhu

first: Zhinong

last: Jiang

first: Rukun

last: He

first: Hengrui

last: Tian

first: Tao

first: Peng

last: Xiao

first: Wenwen

last: Lian

first: Qian

last: Cao

first: Yunn-Hwen

last: Gan

first: Lihua

last: Lai


title: Transcriptional profiling of tumor infiltrating neutrophils in a mouse model (MOC1) of oral cavity cancer

first: Clint

last: Allen

summary: Neutrophils are abundant in the tumor microenvironment and frequently acquire immunosuppressive phenotypes, yet the mechanisms driving this transition remain incompletely defined. To investigate the role of the transcription factor Egr1 and MEK signaling in neutrophil-mediated immune suppression, we performed single-cell RNA sequencing (scRNA-seq) of tumor-infiltrating neutrophils isolated from a syngeneic oral cavity cancer model (MOC1) in mice.  This dataset comprises four experimental groups: Egr1 wild-type (WT) vs. Egr1 knockout (KO) and vehicle control vs. trametinib (MEK inhibitor) treatment. Comparative transcriptional profiling revealed that Egr1-deficient neutrophils fail to upregulate key immunosuppressive and pro-inflammatory effectors, including Osm, Ptgs2, and Il1b, in response to the tumor microenvironment. Conversely, trametinib-treated neutrophils displayed reduced expression of hypoxia- and MEK-driven transcriptional programs, including suppression of Osm, Ptgs2, Il1b, and the AP-1 transcription factor Junb.

overall_design: Tumors were harvested and digested into single cell suspensions using the Miltenyi Tumor Dissociation Kit per manufacturer recommendations. Total leukocytes were isolated using 80/40% Percoll centrifugation separation. Neutrophils were then isolated via positive magnetic isolation using Miltenyi anti-Ly6G+ microbeads per manufacturer recommendations. Neutrophils were isolated from three tumor-bearing mice and combined together for one single cell capture for each experimental condition: Egr1 wild-type vs. Egr1 knockout, and vehicle control vs. trametinib treatment. For each group, single-cell suspensions were processed using the 10x Chromium Next GEM Single Cell 3’ v3.1 chemistry to generate scRNA-seq libraries. In total, four libraries were prepared and subsequently pooled for sequencing. Libraries were sequenced on an Illumina NextSeq 2000 P1 flow cell with a non-symmetric run configuration (28 cycles + 90 cycles). Each sample yielded more than 9 million reads, with sequencing quality exceeding Q30 in over 93.9% of barcode bases, 92.2% of read bases, and 95.6% of UMI bases. Demultiplexing was performed allowing one mismatch in barcodes. Alignment and gene quantification were carried out with Cell Ranger v8.0.1 using default parameters. Downstream analysis focused on transcriptional changes in neutrophils associated with Egr1 deficiency and pharmacologic MEK inhibition, enabling interrogation of hypoxia- and Egr1-dependent neutrophil states within the tumor microenvironment.

first: Tian-Gen

last: Chang


title: Spatial transcriptomics for high-grade serous ovarian carcinoma who were treated with Olaparib maintenance therapy

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

summary: Ovarian cancer is one of the leading causes of death among females worldwide. Recently, PARP inhibitors have become widely used for maintenance therapy in ovarian cancer, leading to improvements in patient prognosis. However, resistance to PARP inhibitors is observed in some cases, presenting a clinical challenge. In this study, we investigated the mechanisms of Olaparib resistance using spatial transcriptomics.

overall_design:
Visium spatial transcriptomics was performed on eight patients with high-grade serous ovarian carcinoma.
Abbreviations:  TC, paclitaxel and carboplatin; PLD, pegylated liposomal doxorubicin; NGT, nogitecan; Bev, bevacizumab; CPT-11, irinotecan; CPT-P, irinotecan and cisplatin; NDP, nedaplatin; DTX, docetaxel; GEM, gemcitabine; wPTX, weekly paclitaxel; CBDCA, carboplatin; DC, docetaxel and carboplatin.

first: Hironori

last: Suzuki

first: Yusuke

last: Yamamoto

first: Akira

last: Yokoi


title: Anabolic effects of salbutamol are lost upon removal of muscle contraction

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

institute: TNO

summary:
Highlights:
- Muscle disuse causes atrophy and insulin resistance; salbutamol counteracts both.
- However, salbutamol’s effects are inhibited in immobilized human and mouse limbs.
- RNA-seq reveals blunted signaling effects by salbutamol during immobilization.
Abstract:
Salbutamol’s efficacy depends on muscle contraction.Muscle disuse leads to rapid loss of muscle mass and development of insulin resistance, which may be ameliorated by beta2-agonist administration. Here, we tested the impact of the fast-acting beta2-agonist salbutamol during immobilization. In humans, salbutamol enhanced insulin-stimulated glucose disposal on the whole-body level, but not in immobilized muscle. Salbutamol decreased the efflux of amino acids from the immobilized forearm, indicating increased muscle protein synthesis and/or inhibition of breakdown, but did not affect amino acid net balance. In agreement, in mice salbutamol increased cumulative muscle protein synthesis, but did not result in a net gain of muscle mass upon immobilization, due to an accompanying increase in muscle protein turnover. Molecular analyses revealed immobilization inhibited salbutamol’s effects on muscle-transcriptome. In conclusion, salbutamol can increase muscle mass and glucose uptake, but not effectively in inactive muscle, demonstrating that the mechanism of action and efficacy of beta2-adrenoreceptor signaling is hampered without muscle contraction.

overall_design: RNAseq expression of mouse (16wk old) leg quadriceps muscle, after 2wk of various treatments (15 mice per treatment group): Healthy reference group receiving ad libitum Chow food (Right leg muscle: H.R); Caloric Restriction control group receiving 60% of their normal Chow food intake and an osmotic pump releasing PBS (Left leg muscle: CR.0.L); Caloric Restriction & Salbutamol group receiving 60% of their normal Chow food intake and an osmotic pump releasing 1 mg salbutamol (dissolved in PBS) per kg body weight per day (Left leg muscle: CR.S.L); Caloric Restriction & Immobilisation control group receiving 60% of their normal Chow food intake, unilateral (Right) immobilization and an osmotic pump releasing PBS (Right leg muscle: CRI.0.R); Caloric Restriction & Immobilisation & Salbutamol group receiving 60% of their normal Chow food intake, unilateral (Right) immobilization and an osmotic pump releasing 1 mg salbutamol (dissolved in PBS) per kg body weight per day (Right leg muscle: CR  I.S.R). 0 = no immobilisation or no salbutamol.

first: Jelle

last: de Jong

first: Tom

last: Jameson

first: Rob

last: Andrews

first: Mandy

last: Dunlop

first: Doaa

last: Abdelrahman

first: Andrew

last: Murton

first: Martien

last: Caspers

first: Nicole

last: Worms

first: Anita

last: van Nieuwkoop

first: Nanda

last: Keijzer

first: Qihan

last: Cheng

first: Bruno

last: Guigas

first: Esther

last: van Duijn

first: Wouter

last: Vaes

first: Arie

last: Nieuwenhuizen

first: Jaap

last: Keijer

first: Benjamin

last: Wall

first: Lars

last: Verschuren

first: Francis

last: Stephens

last: van den Hoek

first: Marlou

last: Dirks


title: Transcription factors instruct DNA methylation patterns in plant reproductive tissues [ChIP-Seq]

city: La Jolla

first: Julie

middle: A

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: Plant Molecular and Cellular Biology

institute: Salk Institute for Biological Studies

summary: DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 (CLSY3) targets the RNA-directed DNA methylation (RdDM) machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here, we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLSY3 targets specific to anther or ovule tissues. We designate these factors as REM INSTRUCT METHYLATION (RIMs) and demonstrate that disruption of their DNA binding domains, or the motifs they recognize, blocks RdDM. Furthermore, we demonstrate that mis-expression of RIM12 is sufficient to initiate siRNA production at ovule targets in anthers. These findings reveal a critical role for genetic information in targeting DNA methylation in reproductive tissues, expanding our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

overall_design: 14 ChIP-seq libraries were sequenced.

first: Guanghui

last: Xu

first: Yuhan

last: Chen

first: Laura

last: Martins

first: En

last: Li

first: Fuxi

last: Wang

first: Tulio

last: Magana

first: Junlin

last: Ruan


title: Identification of Ephrin type-B receptor 4 (EphB4) as a critical mediator of tissue fibrosis [snRNA-seq]

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

summary: Pulmonary fibrosis (PF) is a pathology associated with interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF). Fibrosis promotes continual secretion of extracellular matrix (ECM), producing non-functional scar tissue and causing organ failure. This study investigated the tyrosine kinase receptor Ephrin type-B receptor 4 (EphB4) as a mediator of PF. To this end, we generated mice with conditional Col1a2-driven deletion of Ephb4 and used a preclinical mouse model of PF, total and single nuclei RNA (snRNA) sequencing, NanoString, previously published single cell data, computational analysis, and functional assays of mouse and human healthy control and IPF lung fibroblasts. Col1a2-CreERT-driven Ephb4 deletion, or EphB4 inhibition via NVP-BHG712, markedly protected against bleomycin-induced PF. Total RNA-sequencing of fibroblasts isolated from Ephb4-deficient fibrotic mouse lungs exhibited reduced expression of ECM, ER Cargo, and protein trafficking-related genes. NVP-BHG712 reduced expression of these identified genes in mouse lung fibroblasts under fibrotic conditions in vitro. SnRNA sequencing of mouse lungs treated with NVP-BHG712 identified transcriptomic changes of ECM genes in specific fibroblast subpopulations. RNA sequencing, computational, and functional assays using mouse and human IPF fibroblasts identified elastin as a key mediator involved in EphB4 signaling. Combined, our data show that EphB4 is a crucial mediator of PF.

overall_design: Bleomycin (bleo) or PBS instilled mouse lungs were treated with/without EphB4 Inhibitor (NVP-BHG712). Total 12 mouse lungs (n=3 PBS+vehicle, n=3 PBS+ NVP-BHG712, n=3 bleomycin+vehicle and n=3 bleomycin+NVP-BHG712) were subjected to Single-nucleus RNA sequencing by using 10X Genomics Chromium NEXT GEM Single cell 3' Reagent kit and Illumina NextSeq550/NextSeq 2000 sequencer.

first: Brian

last: Wu

first: Starlee

middle: S

last: Lively

first: Shabana

last: Vohra

first: Noah

last: Fine

first: Chiara

last: Pastrello

first: Anca

last: Maglaviceanu

first: Osvaldo

last: Espín-García

first: Evan

last: Pollock-Tahiri

first: Sayaka

last: Nakamura

first: Paramvir

last: Kaur

first: Keemo

last: Delos Santos

first: Jason

last: Rockel

first: Pratibha

last: Potla

first: Himanshi

last: Gupta

first: Poulami

last: Datta

last: Tang

first: Jacob

last: Kwon

first: Akihiro

first: Matthew

middle: B

last: Buechler

first: Rajiv

last: Gandhi

first: Jiangping

first: Boris

last: Hinz

first: Igor

last: Jurisica


title: Origin of the cancer-associated intestinal epigenetic drift

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: Epigenetic alterations, particularly the DNA methylation (DNAm) drift, represent a conserved hallmark of aging across species, influencing biological processes and disease pathogenesis. Recent studies have characterized different DNAm drifts in mammalian aging, and observed, for some of them, a correlation with cell division or organismal lifestyle. However, the molecular mechanisms driving DNAm drifts during aging are still largely unknown. In this study, we identify and characterize a cancer-associated intestine-specific DNAm drift, that initiates in healthy intestinal stem cells with impaired iron homeostasis, propagating through crypt clonality and crypt fission mechanisms to neighboring cells. Experimental evidence using mouse models and intestinal organoids confirms the cell-intrinsic, non-mitotic nature of ACCA drift. Despite the observed heterogeneity at the CpG level confirming the stochastic component of the epigenetic aging, DNAm patterns at the gene level remain consistent, implicating functional relevance to biological processes such as cancer initiation. Mechanistically, ACCA drift is driven by an impaired TET enzyme activity due to dysregulated iron metabolism, linking cellular metabolism to epigenetic alterations. Insights into the interplay between ACCA drift and colorectal cancer (CRC) suggest a mechanistic basis for DNAm changes observed in CRC, potentially explaining the hypermethylation landscape observed in cancerous tissuess. This study enhances our understanding of epigenetic mechanisms in aging and disease, highlighting potential targets for prevention and early-diagnosis of age-related diseases like CRC.

overall_design: We processed around 150 crypts from old mice, analyzed their DNAm level by Pyrosequencing on the 4 gene promoters (Dkk1, Dkk2, Sfrp1 and Sfrp2), calculated the average DNAm level, then we selected the crypts of the top 10% (high 5mC crypts) and the bottom 10% (low 5mC crypts) and performed single-crypt RNAseq.

first: Anna

last: Krepelova

first: Mahdi

first: Francesco

last: Neri


title: ETS1 recruits cBAF to hijack the hematopoietic stem cell MYB enhancer in T-cell leukemia [dataset 1]

first: Mark

middle: Yat-fung

last: Chiang

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

summary: Notch signaling is the most prevalent oncogenic pathway in T-ALL, but clinical trials showed that pan-Notch inhibitors caused dose-limiting toxicities. Thus, we shifted our focus from Notch to ETS1, which is one of the top transcription factors that most frequently co-bind Notch-occupied regulatory elements in the T-ALL context. A top essential ETS1-dependent element was a Notch-bound enhancer at +140kb from MYB that we named the ETS-MYB enhancer (E-Me). Using genetically engineered mouse models and chromatin profiling, we showed that the E-Me selectively promotes self-renewal of hematopoietic stem cells, becomes inactive in committed T cell progenitors; and is reactivated to promote Notch-induced transformation.

overall_design: ATAC-seq analysis of conventional T-ALL cell lines

first: Mullin

last: Carea

first: Ryan

last: Russell

first: Chiang

last: Mark


title: ETS1 recruits cBAF to hijack the hematopoietic stem cell MYB enhancer in T-cell leukemia [dataset 2]

overall_design:
ATAC-seq analysis of conventional T-ALL cell lines
Cells were treated with DMSO (control) or 500nM dTAGV-1 (treated) for 72 hours prior to submission.

first: Carea

last: Mullin

first: Russell

last: Ryan


title: Identification of Ephrin type-B receptor 4 (EphB4) as a critical mediator of tissue fibrosis

first: Mohit

last: Kapoor

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ETS1 recruits cBAF to hijack the hematopoietic stem cell MYB enhancer in T-cell leukemia.


title: LSD1 Inhibition eliminates HNSCC coordinated by activated Dendritic Cells, IFNg-CXCL9-CXCR3 and MHC-I

city: Boston

first: Lina

last: Kroehling

state: MA

address: 91 E Concord St

institute: Boston Unviersity

summary: Poor infiltration of CD8+ cells and dysregulated MHC-I provide resistance to anti-cancer clinical therapies. This study aimed to uncover mechanisms of lysine-specific demethylase 1 (Kdm1a or LSD1) in antitumor immunity in Head and Neck Squamous cell carcinoma (HNSCC). LSD1 inhibition in syngeneic and chronic tobacco carcinogen-induced HNSCC mice recruited an activated dendritic cell (DCs), CD4+, and CD8+ T cells, enriched IFNγ in T cells, CXCL9 in DCs, and CXCR3 in T cells, evaluated by single cell RNA-seq analysis. Humanized HNSCC mice and TCGA data validate inverse correlation of Kdm1a with markers of DCs, CD8+ T cells, and their activating chemokines. LSD1 knockout or inhibitors in mouse HNSCC and co-culture showed MHC-I upregulation in tumors for efficient antigen presentation. Overall, LSD1 inhibition promoted DCs through IFNγ-CXCL9-CXCR3 axis and MHC-I upregulation in tumors to induce CD8+ T cell medicated antitumor immunity, which has implications for poorly immunogenic and immunotherapy-resistant cancers therapy.

overall_design: C57BL/6J mice were treated with 4-Nitroquinoline 1-oxide (4NQO) for 16 weeks, and at week 20, divided into three groups (n=6) and subjected to different treatments: group 1) vehicle; 2) 4NQO; 3) 4NQO+SP2509. At the time of sacrifice, tongue tumors were cut to prepare single-cell suspensions, followed by scRNA-seq analysis of 8000 cells/mouse (n=2/condition) using a 10X genomics kit according to the manufacturer's recommendations.

first: Amit

last: Chakraborty

first: Rajnikant

last: Raut

first: Stefano

last: Monti

first: Manish

middle: V

last: Bais


title: Variability vs. phenotype: Multimodal analysis of Dravet syndrome brain organoids powered by deep learning

city: L'Hospitalet de Llobregat

first: Sandra

last: Acosta

address: Feixa Llarga

department: Pathology and Experimental Therapeutics

institute: University of Barcelona

summary: Dravet Syndrome (DS) is a developmental epileptic encephalopathy (DEE) driven by pathogenic variants in SCN1A gene. Brain organoids (BO) have emerged as reliable models for neurodevelopmental genetic disorders, reproducing human brain developmental milestones and rising as a promising drug testing tool. Here, we determined the underlaying molecular DS pathophysiology affecting neuronal connectivity, revealing an early onset excitatory-inhibitory imbalance in maturing DS organoids circuitry. However, neuronal circuitry modeling in BO remains hampered by the notorious inter- and intra-organoid variability. Thus, leveraging deep learning (DL), we developed ImPheNet, a predictive tool grounded in BO live imaging datasets, to overcome the limitations of the intrinsic BO variability. ImPheNet accurately classified healthy and DS phenotypes at early onset stages, revealing differences between genotypes and upon antiseizure drug exposure. Altogether, our DL-predictive live imaging strategy, ImPheNet, emerges as a powerful tool to accelerate DEE research and advancing towards treatment discovery in a time- and cost-efficient manner.

overall_design: RNA sequencing data

first: Isabel

last: Turpin


title: Epigenetic regulation of chromosomal instability by EZH2 methyltransferase

city: NY

first: Yang

last: Bai

state: NY

address: 1300 York Ave

department: Cardiothoracic Surgery

institute: Weill Cornell Medicine


title: Egr1 is a sex-specific regulator of neuronal chromatin, synaptic plasticity, and behaviour [RNA-Seq]

city: Bronx

first: Marija

last: Kundakovic

address: 441 E. Fordham Road

department: Biological Sciences

institute: Fordham University

summary: Sex differences are found in brain structure and function across species, and across brain disorders in humans. The major source of brain sex differences is differential secretion of steroid hormones from the gonads across the lifespan. Specifically, ovarian hormones oestrogens and progesterone are known to dynamically change structure and function of the adult female brain, having a major impact on psychiatric risk. However, due to limited molecular studies in female rodents, very little is still known about molecular drivers of female-specific brain and behavioural plasticity. Here we show that overexpressing Egr1, a candidate oestrous cycle-dependent transcription factor, induces sex-specific changes in ventral hippocampal neuronal chromatin, gene expression, and synaptic plasticity, along with hippocampus-dependent behaviours. Importantly, Egr1 overexpression mimics the high-oestrogenic phase of the oestrous cycle, and affects behaviours in ovarian hormone-depleted females but not in males. We demonstrate that Egr1 opens neuronal chromatin directly across the sexes, although with limited genomic overlap. Our study not only reveals the first sex-specific chromatin regulator in the brain, but also provides functional evidence that this sex-specific gene regulation drives neuronal gene expression, synaptic plasticity, and anxiety- and depression-related behaviour. Our study exemplifies an innovative sex-based approach to studying neuronal gene regulation in order to understand sex-specific synaptic and behavioural plasticity and inform novel brain disease treatments.

overall_design: Male and ovariectomized, or intact proestrus female C57BL/6J mice underwent stereotaxic surgery at 7 weeks of age and received either Egr1 overexpression (AAV9-hSYN-Egr1-IRES-eGFP-WPRE3), Egr1 knockdown (AAV9-hSYN-Egr1-shRNA-eGFP-WPRE),  eGFP control (AAV9-hSYN-eGFP-WPRE), or scrambled shRNA control (AAV9-hSYN-scramble-eGFP-WPRE) AAV targeted to the ventral hippocampus to determine the sex-dependent effects of Egr1 overexpresssion or knockdown on the neurons in this brain region. Following 3 weeks of incubation, mice were sacrificed at 10-11 weeks of age and bilateral ventral hippocampi were flash frozen in liquid nitrogen. Nuclei were then extracted from frozen tissue and neuronal nuclei were obtained by FACS using an antibody targeting the neuronal nuclei-specific NeuN protein. Nuclear RNA was extracted from NeuN+ nulcei and RNA-seq libraries were prepared with the KAPA RNA HyperPrep kit. 150 bp, paired-end sequencing was performed in one lane of an S1 flow cell on the NovaSeq 6000 instrument, yielding 60-90 million reads per sample.

first: Devin

last: Rocks

first: Luisa

last: Demarchi

first: Eric

last: Purisic

first: Heining

last: Cham

first: Eduardo

last: Gallo

first: John

last: Greally

first: Masako

last: Suzuki


title: Identification of sex- and inflammation-associated heterogeneity in mouse omentum using single-cell RNA sequencing

city: Shanghai

first: Xueli

last: Zhang

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

summary:
The omentum is a critical intraperitoneal organ essential for peritoneal homeostasis, yet detailed characterization of its cellular composition remains limited by the lack of validated markers. Here, we employed single-cell RNA sequencing to systematically define cellular heterogeneity in naive and activated mouse omentum from both sexes. Our analysis identified previously uncharacterized immune and stromal cell subsets, including three macrophage subtypes with activation-dependent gene expression patterns, implying specialized roles in inflammation and immune regulation. Comparative analysis revealed marked transcriptional differences between omental and peritoneal macrophages, underscoring tissue-specific microenvironments. Additionally, sexually dimorphic gene expression in omental stromal cells correlated with peritoneal macrophage polarization, indicating sex-specific regulatory mechanisms. Critically, macrophages from omentum of female mice with ovarian cancer metastases showed unique gene signatures associated with tumor migration and invasion.
Collectively, we provide the first comprehensive atlas of omental cell populations stratified by sex and activation state, offering novel insights into peritoneal immunity and identifying potential therapeutic targets for inflammatory and metastatic diseases.

overall_design: Single-cell RNA-seq was used to classify the cell heterogeneity in the naive and activated omentum in both male and female mouse.

first: Xue-Li

first: Xin

last: Xing

first: Dong-Xue

last: Li

first: Yi

last: Ding

first: Shu-Yu

last: Xiao

first: Jun-Jie

last: Wang

first: Zhi-Gang

first: Rong

first: Qin

last: Yang

first: Xiao-Cao

last: Miao


title: Identification of Ephrin type-B receptor 4 (EphB4) as a critical mediator of tissue fibrosis [RNA-seq]

first: Mohit

last: Kapoor

overall_design:
Primary human IPF and control donor lung fibroblasts (HLF; from control donor lungs) were treated for 24 h with either 250 nM of the Ephb4 inhibitor NVP-BHG712 or 0.1% DMSO (as with control donors). Total RNA was then extracted, and sequencing libraries were prepared using Illumina's TruSEQ stranded total RNA library preparation kit and sequenced on Illumina's NextSeq550. Differential expression analysis and subsequent pathway analyses were performed.

Following are the groupings for 16 samples:
0.1% DMSO treatment - 4 IPF samples - IPF1C, IPF2C, IPF3C, IPF4C
250 nM NVP-BHG712 treatment - 4 IPF samples - IPF1I, IPF2I, IPF3I, IPF4I

0.1% DMSO treatment - 4 HLF samples - HLF1_Vehicle, HLF2_Vehicle, HLF3_Vehicle, HLF5_Vehicle
250 nM NVP-BHG712 treatment - 4 HLF samples - HLF1_NVP-BHG712, HLF2_NVP-BHG712, HLF3_NVP-BHG712, HLF5_NVP-BHG712

first: Brian

last: Wu

first: Starlee

last: Lively

first: Shabana

last: Vohra

first: Noah

last: Fine

first: Chiara

last: Pastrello

first: Anca

last: Maglaviceanu

first: Osvaldo

last: Espín-García

first: Evan

last: Pollock-Tahiri

first: Sayaka

last: Nakamura

first: Paramvir

last: Kaur

first: Keemo

last: Delos Santos

first: Jason

last: Rockel

first: Pratibha

last: Potla

first: Himanshi

last: Gupta

first: Poulami

last: Datta

first: Laura

last: Tang

first: Jacob

last: Kwon

first: Akihiro

first: Matthew

last: Buechler

first: Rajiv

last: Gandhi

first: Jiangping

first: Boris

last: Hinz

first: Igor

last: Jurisica


first: Mohit

last: Kapoor

overall_design:
Lung fibroblasts were obtained from 17 Ephb4 conditional knockout (Ephb4 f/f; Col1a2-CreERT2) mice treated with either 4-hydroxytamoxifen (1 mg/day for 5 days) or equivalent corn oil (as control) and then subjected to bleomycin-induced lung fibrosis (1.2U/kg) or PBS control. 14 days later, lung fibroblasts were isolated, cultured, and passaged once. Total RNA was then extracted, and sequencing libraries were prepared using Illumina's TruSEQ stranded total RNA library preparation kit and sequenced across two runs of 8 and 9 pooled samples each on Illumina's NextSeq550. Differential expression analysis and subsequent pathway analyses were performed.

Following are the Ephb4 KO sample groupings:
Ephb4 f/f; Col1a2-CreERT2 (corn oil; Ephb4 Control) - 8 samples namely - (4C1233F, 4C1242F, 4C1271M, 4C1272M with bleomycin treatment) and (4C1241M, 4C1154F, 4C1177F, 4C1181F with PBS treatment)

Ephb4 f/f; Col1a2-CreERT2 (4-hydroxytamoxifen; Ephb4 CKO) - 9 samples namely -
(4C1243M, 4C1241F, 4C1164M, 4C1195F with bleomycin treatment) and (4C1231M, 4C1242M, 4C1165M, 4C1172F, 4C1194F with PBS treatment)

first: Brian

last: Wu

first: Starlee

last: Lively

first: Shabana

last: Vohra

first: Noah

last: Fine

first: Chiara

last: Pastrello

first: Anca

first: Osvaldo


title: Whole transcriptome deep sequencing to rat vein graft

first: Qingping

last: Yao

address: Dongchuan Road 800#

institute: Shanghai Jiao Tong University

summary: a rat vein graft model was constructed by the “cuff” technique, and whole transcriptome deep sequencing was applied.

overall_design: Direct comparison of 4 pairs of graft veins and control jugular veins

first: Yingxin

last: Qi