title: Effect of the overexpression of the NOTCH inhibitor ligand DLL3 in low grade astrocytoma cell line LGG275

city: montpellier

first: Jean-Philippe

last: Hugnot

address: 141 rue de la Cardonille

country: France

institute: Institut de génomique fonctionnelle

summary: Astrocytoma are known to presents a cellular heterogeneity consisting of three identified subpopulation: "astrocyte-like", "oligodendrocyte-like" and "NPC-like" cells. Among these populations, "astrocyte-like" cells show plasticity and can transit to an "oligodendrocyte-like" state. Activation of NOTCH pathways induce an transition into astrocyte-like state. To investigate the effect of NOTCH inhition on cell plasticity, we overexpressed DLL3, the main ligand inhibitor of NOTCH.

overall_design: To investigate the effect of DLL3 overexpression in LGG275 astrocytoma cell lines, we used an lentivirus expressing luciferase (Ctrl) or DLL3 as well as GFP protein. RNA sequencing was realized on cells in presence or absence of growth factors EGF and FGF2.

first: Leonor

last: Garcia


title: Rainbow trout adipose tissue depots (VAT, SAT, IMAT) - mRNAs

status: Public on Jan 13 2026

city: Barcelona

first: Enrique

last: Rosell-Moll

address: Av Diagonal, 643 4º floor

country: Spain

institute: University of Barcelona

type: Expression profiling by high throughput sequencing

summary: The aim of this study was to characterize different adipose tissue depots in rainbow trout (Oncorhynchus mykiss) through the analysis of mRNA and miRNA expression profiles. Mature adipocytes were isolated from visceral (VAT), subcutaneous (SAT), and intramuscular (IMAT) adipose tissues, and RNA sequencing (RNA-seq) was performed. Data were curated, quality-checked, and filtered prior to downstream analyses. This dataset contains the FASTQ files generated in the study. The results will contribute to a better understanding of the molecular differences and similarities among adipose depots in fish reared under standard aquaculture conditions, providing a foundation for improving adiposity control, animal health, fillet yield, and overall product quality.

overall_design: Cell type comparison design. Three adipose tissue depots (VAT, SAT and IMAT) in rainbow trout under standard aquaculture conditions.

first: E

last: Capilla

first: I

last: Navarro

first: D

last: Garcia de la serrana


title: Myelin antigen capture in the CNS by B cells expressing EBV latent membrane protein 1 leads to demyelinating lesion formation [RNA-Seq]

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: The efficacy of B cell depletion therapies, and association with the B lymphotropic Epstein- Barr virus (EBV) implicate B cells in the demyelinating autoimmune disease multiple sclerosis. After observing myelin-reactive B cells in the naïve human repertoire, we studied how such cells behave in the central nervous system. In mice, viral infections induce infiltration of B cells independent of phenotype and specificity into the otherwise lymphocyte-poor brain, and myelin-reactive B cells then capture antigen directly from parenchyma. Trafficking of these antigen-loaded B cells to draining lymph nodes was not observed, and without T cell help, antigen-capturing B cells die rapidly. CD40L signaling or EBV latent membrane protein 1 (LMP1) can override this checkpoint, leading to in situ plasma cell differentiation and antibody-mediated, demyelinating lesion formation. These observations explain the dependency of disease incidence on prior EBV infection, and the increased risk associated with brain infections, and suggest possible treatment strategies.

overall_design: B cells were sorted from mouse brain and lymph node samples and put in culture with human fibroblasts expressing or not their antigen.

first: Julien

last: Roux

first: Nicholas

last: Sanderson

first: Mika

last: Schneider

first: Hyein

last: Kim

first: Tobias

last: Derfuss


title: Transcription factor Etv3 controls the tolerogenic function of dendritic cells

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [CUT&Tag]

city: Cambridge

first: Bongmin

last: Bae

state: MA

address: 16 Divinity Ave

institute: Harvard University

summary: Genomic imprinting is an epigenetic phenomenon in which genes exhibit restricted or biased expression from one allele according to parental origin. Imprinted gene expression plays a crucial role in the development, including the brain. Higher-order chromatin structure has long been associated with gene regulation, particularly in the context of spatial enhancer-promoter interactions. Given the characteristic parental allele-biased expression pattern of imprinted genes, a compelling question is whether the three-dimensional organization of parental genomes plays a role in imprinted gene regulation. Using a capture Hi-C approach, we identifiedparental allele-specific higher-order chromatin structures across multiple imprinted domains in the mouse brain. These allele-specific structural features largely stem from annotated imprinting control regions (ICRs), concomitant with allele-specific binding of CTCF. Detailed analysis suggests that transcriptional start sites (TSS) of active and inactive alleles of imprinted genes form distinct chromatin interactions, differing in degree and/or type. CRISPRi screeningrevealed a distal cis-regulatory element that modulates imprinted expression of the Mest-Copg2locus in neurons, and its regulatory mechanism is tightly associated with allele-specific chromatin interactions. Further investigation revealed that both a cis-acting long non-coding RNA and allele-specific enhancer-promoter architecture modulates Mest-Copg2 imprinted expression. Together, this study highlights the interplay between chromatin structure and regulatory landscapes that modulate allele-specific expression of imprinted genes.

overall_design: CTCF CUT&Tag from primary cortical neurons isolated from F1 E16 embryos, including forward (BxC) and reverse (CxB) crosses. / H3K27ac CUT&Tag from hybrid KRABxCast NPC-derived neurons, treated with scramble (LV-Scrb) or enhancer-targeting (LV-E105) gRNAs. / CTCF CUT&Tag from hybrid mESC, treated with DMSO or DNMTi (GSK-3484862).

first: Amanda

middle: J

last: Whipple


title: Characterization of a diffuse  low and high grade glioma cell line biobank

summary: Diffuse low and high grade glioma are primary brain tumors arising from gllial cells. They are subdivided into three groups: IDH1-mutant oligodendrogliomas, IDH1-mutant astrocytomas and IDH1-Wild Type glioblastomas. Cellular tools to study these tumors remains poors, specially for low grades gliomas. We constituted a biobank of 12 patient-derived cell lines, from IDH1-mutant and wild type gliomas, then charactrized them to test their relevance as in vitro models.

overall_design: To characterized the transcriptomic profile of each cell line, we performed an RNA sequencing after culture the cell in presence or absence of growth factors EGF and FGF2


title: Myelin antigen capture in the CNS by B cells expressing EBV latent membrane protein 1 leads to demyelinating lesion formation


title: Transcription factor Etv3 controls the tolerogenic function of dendritic cells (H3K4me3 CUT&RUN of Etv3 KO GM-DCs)

summary: Dendritic cells (DC) facilitate the maintenance of immunological tolerance in the steady state. We report that transcription factor Etv3 is preferentially expressed in mature DC including tissue-derived migratory DC (migDC), and facilitates their homeostatic maturation and CCR7-dependent migration. Mice with global or DC-specific deletion of Etv3 manifested the expansion of CD25low regulatory T cells (Treg), spontaneous activation of conventional T cells, and multiorgan T cell infiltration. Etv3 deficiency exacerbated TLR7-driven systemic lupus erythematosus (SLE)-like disease, supporting the reported genetic association of human ETV3 with SLE. Etv3-deficient migDC upregulated multiple costimulatory molecules including OX40 ligand (OX40L/TNFSF4), whose blockade partially rescued the Treg abnormalities. These results identify Etv3 as an essential regulator of the tolerogenic function of DC, and implicate it in the regulation of human autoimmunity.

overall_design: CUT&RUN for H3K4me3 was performed on DC enriched from GM-BMDC cultures derived from control (WT) and Etv3-deficient (KO) mice (2 replicates per genotype).

last: Adams

first: Daniel

last: Martinez-Krams

first: Boris

last: Reizis


title: DAXX Directs H3.4-to-H3.3 Histone Replacement During Spermatogenesis [RNA-Seq]

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

institute: University of California, Davis

summary: During spermatogenesis, extensive chromatin remodeling and histone replacement reshape the male germline epigenome. While HIRA is known to mediate transcription-coupled incorporation of histone variant H3.3, we identify DAXX as a key histone chaperone directing genome-wide, transcription-dependent replacement of H3.4 (H3T) with H3.3 on autosomes during male meiosis. Simultaneously, DAXX also directs transcription-independent H3.4-to-H3.3 replacement on the sex chromosomes during meiotic sex chromosome inactivation (MSCI). These distinct, chromosome-specific modes of DAXX-mediated H3.3 deposition are essential for epigenomic integrity in the male germline. Loss of DAXX disrupts this process, leading to widespread transcriptional dysregulation in haploid round spermatids and male infertility.

overall_design: RNA-seq analysis using DAXX-ctrl and DAXX-cKO 4wk FACS sorted pachytene spermatocytes (PS) and round spermatids (RS);CUT&Run analysis on H3.1/H3.2, H3.3, H3t, H3K27ac, and H3K9me3 using DAXX-ctrl and DAXX-cKO 4wk sorted pachytene spermatocytes (PS) and round spermatids (RS).

middle: H

first: Yu-Han

last: Yeh


title: Transcription factor Etv3 controls the tolerogenic function of dendritic cells (CITE-seq of Etv3 KO LN and thymus cDCs)

overall_design: scRNA-seq with "hashtagging" according to the CITE-seq protocol was performed on cDCs from the skin-draining lymph nodes (sdLNs) and thymus of control and ETV3-deficient mice.


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [Bisulfite-seq]

type: Methylation profiling by high throughput sequencing

overall_design: Targeted bisulfite sequencing using Nanopore from hybrid mESC treated with DMSO or DNMTi (GSK-3484862).

first: Katherine

last: Gu


title: Epigenome-wide DNA Methylation Profiling in the Investigation of Treatment and Life-Course Exposures and Adverse Health Outcomes in Survivors of Childhood Cancer from the St. Jude Lifetime Cohort

city: Memphis

first: Zhaoming

last: Wang

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary:
Long-term survivors of childhood cancer experience treatment-related cardiotoxicity among a broad spectrum of chronic health conditions, which may be further aggrevated by suboptimal life-course social/behavioral/environmental exposures. Epigenetic mechanisms, particularly DNA methylation (DNAm), provide a potential link through which these exposures become biologically embedded and subsequently influence long-term health outcomes.
Epigenome-wide association studies (EWAS) identified DNAm signatures associated with both treatment effects as well as life-course exposures. In parallel, DNAm variations were also evaluated in relation to cardiometabolic risk factors, cardiovascular diseases, and other chronic health conditions, revealing individual CpG sites or genes/geomic regions where these CpGs reside linked to clinically relevant phenotypes. Together, these findings support DNAm as a molecular interface connecting diverse exposures to adverse health outcomes.
In addition, epigenetic age acceleration, assessed using DNAm-based aging biomarkers, was observed among survivors exposed to cancer treatments. Epigenetic age acceleration mediated a substantial proportion of the associations between cancer treatment exposures and cardiometabolic risk factors or cardiovascular diseases, supporting accelerated biological aging as a key pathway linking cancer treatment to long-term morbidity. Lifestyle and health behaviors, as well as social vulnerability and psychosocial stress, were also associated with variations in epigenetic age acceleration, highlighting the potential modifiability of aging-related pathways in ameliorating late-effects among childhood cancer survivors.
In conclusion, these findings establish DNAm—captured through EWAS signatures and epigenetic age acceleration—as central molecular mechanisms linking treatment effects and life-course exposures to cardiotoxicity along with other chronic health conditions in childhood cancer survivors. This integrative epigenetic framework supports the use of DNAm-based biomarkers for risk stratification and nominates modifiable pathways as potential intervention targets  to improve long-term survivorship outcomes.

overall_design:
We included childhood cancer survivors and community controls from the St. Jude Lifetime Cohort Study, a retrospective hospital-based cohort with prospective clinical follow-up. DNA methylation profiles were generated using the Illumina Infinium MethylationEPIC BeadChip from blood- or saliva-derived DNA. A subset of participants contributed DNAm profiles at more than one time point.

The data generation was supported by grant awards from the National Cancer Institute at the National Institutes of Health (R01 CA290112 and R01 CA279520 to Dr Wang, U01 CA195547 to Drs Hudson and Ness) and by grant the V-Foundation grant (DT2020-014 to Dr. Wang).


title: DAXX Directs H3.4-to-H3.3 Histone Replacement During Spermatogenesis [Cut & Run]


title: Intestinal Epithelial Tet2 Deficiency Reprograms the Gut Microbiota through Bile Acid Metabolic Alterations

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

summary: Epigenetic mechanisms are increasingly recognized as critical regulators of host-microbiota interactions. Here, we report that intestinal epithelial-specific deletion of Tet2, a key DNA demethylase, leads to structural abnormalities, impaired barrier function, and remarkable reprogramming of the gut microbial community. Mechanistically, Tet2 deficiency significantly downregulated the expression of the apical sodium-dependent bile acid transporter (ASBT/Slc10a2), resulting in altered bile acid homeostasis with specific accumulation of hyocholic acid (HCA) in the intestinal lumen. This metabolic shift created a favorable niche for selective expansion of bile salt hydrolase (BSH)-expressing Lactobacillus species. Furthermore, we identified an age-dependent regulatory role of HCA in shaping microbial composition, promoting Lactobacillus in young mice while enriching Akkermansia in aged animals. Our findings unveil an epigenetic-metabolic-microbial axis centered on Tet2-mediated regulation of bile acid metabolism, providing new insights into how host epigenetic factors shape the gut microbial ecosystem.

overall_design: The gut microbiota is shaped by host-derived factors through mechanisms that remain incompletely understood. This study demonstrates that intestinal epithelial Tet2, an epigenetic modulator, plays a pivotal role in determining gut microbial composition through regulation of bile acid metabolism. Tet2 deficiency downregulates ASBT expression, leading to altered bile acid profiles with accumulation of hyocholic acid (HCA), which in turn selectively enriches BSH-expressing Lactobacillus species. Notably, the effects of HCA on microbial communities are age-dependent. Our work establishes Tet2 as a key epigenetic regulator at the host-microbiota interface and reveals a previously unrecognized connection between DNA demethylation, bile acid transport, and microbial ecology. These findings provide a foundation for developing novel therapeutic strategies targeting the epigenetic-metabolic axis to modulate gut microbiota in diseases associated with microbial dysbiosis.


title: Lymphatic Disruption as a Driver of Lung Transplant Fibrosis

city: Saint Louis

last: Kreisel

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

summary: The consequence of lymphatic disruption during transplantation of solid organs remains unknown. Long-term survival after thoracic organ transplantation is limited by chronic rejection, a poorly understood process involving fibrotic remodeling and functional decline of the graft. Here, we report that transplanted human lungs and hearts with chronic rejection exhibit fibrosis distributed along dysmorphic lymphatics in areas densely concentrated with hyaluronan, an interstitial glycosaminoglycan which depends on lymphatic drainage for clearance. We illustrate similar findings in mouse lung and heart grafts which are accompanied by lymphographic findings of graft lymphedema. We identify interleukin-1-mediated hyaluronan accumulation as a mechanism driving fibrosis that can occur independent of alloimmunity in the setting of lymphatic disruption after lung transplantation and outline three therapeutic interventions with clinical potential.

overall_design: Following syngeneic left lung transplantation of C57BL/6 lungs into C57BL/6 recipients, recipients were treated with an IL-1R1 antagonist versus saline control. Lung grafts were collected at 7 days post-transplant. Two lungs were pooled for submitted samples. Lung tissue was digested, and single-cell suspensions were prepared. Cells were stained using DAPI and CD45. Cells were sorted using a BD FACS Melody cell sorter into CD45+ leukocytes and CD45- stroma. Collected cells were submitted for sequencing.

first: Hailey

middle: M

last: Shepherd

first: Wenjun

last: Li

first: Benjamin

last: Kopecky

first: Yuriko

last: Terada

first: Charles

middle: R

first: Zhiyi

middle: D

last: Lee

first: Katsutaka

last: Mineura

first: Hao

last: Dun

first: Yuhei

last: Yokoyama

first: Brian

middle: W

last: Wong

first: Gokalp

middle: K

last: Kurtoglu

first: Junedh

last: Amrute

first: Davide

last: Scozzi

first: Yun

middle: Z

last: Bai

first: Amit

middle: I

last: Bery

first: Cory

middle: T

last: Bernadt

first: Jon

last: Ritter

first: Steven

middle: L

last: Brody

first: Derek

middle: E

last: Byers

first: Alexander

middle: S

last: Krupnick

first: Ruben

middle: G

last: Nava

first: G

middle: A

last: Patterson

first: Varun

last: Puri

first: Andrew

last: Gelman

first: Kory

last: Lavine

first: Gwendalyn

last: Randolph


title: Transcription factor Etv3 controls the tolerogenic function of dendritic cells (RNA-seq of Etv3 KO Tregs)

first: Eduardo

last: Esteva

overall_design: RNA-seq was performed on regulatory T cells purified from the spleens of control and ETV3-deficient mice (3 replicates per genotype).

first: Nicholas

last: Adams

first: Ai

last: Ra

first: Boris

last: Reizis


title: Explore the molecular profile and properties of quiescent (P27+) and mitotic (P27-) glioma cell in diffuse low grade astrocytoma cell lines LGG275

first: Jean-Philippe

last: Hugnot

summary: Astrocytomas are known to present a cellular heterogeneity consisting of three identified subpopulations: "astrocyte-like", "oligodendrocyte-like" and "NPC-like" cells. It has also been shown that they contain a subpopulations of quiescent, or neural G0 cells, representing more than 90% of the tumor cells. The properties of this cell remain unclear due to the fact that it is difficult to isolate them. We used mVenus/P27 vector expression, constructed by Oki et al (2014), where P27 is fused to mVenus to highlight quiescent cells in LGG275 cell lines, a slow-growing astrocytoma. Then we used this reporter system to sort the mVenus/P27 expressing cells (quiescent) and the negative cells (mitotic) in aims to explore  the properties of these two populations and validate the mVenus/P27 tool.

overall_design: LGG275 cells were infected with a lentivirus containing mVenus/P27 construction, where mVenus is fused to P27. Then, cells were sorted based on their expression of mVenus. mVenus pos cell were P27 pos (quiescent) cells. mVenus neg cells were P27 neg (mitotics) cells.

first: Leonor

last: Garcia


title: Phase II Trial of Ixazomib combined with Gemcitabine and Doxorubicin in Patients with SMARCB1-Deficient Renal Medullary Carcinoma

city: Houston

first: Pavlos

last: Msaouel

state: Texas

address: 1155 Pressler Street, Unit 1374

department: Genitourinary Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: SMARCB1-deficient renal medullary carcinoma (RMC) is an aggressive kidney cancer lacking mechanism-directed therapies. We conducted a single-center, single-arm, phase II study (NCT03587662) testing the oral proteasome inhibitor ixazomib combined with gemcitabine and doxorubicin. Thirty consecutive patients (median age 34.5 years old, 90% Black, 83.3% metastatic at diagnosis) were treated between September 2018 and June 2022. Ixazomib 5.5 mg, gemcitabine 756 mg/m² and doxorubicin 42 mg/m² were given every 2 weeks for up to 13 cycles, followed by ixazomib plus gemcitabine maintenance. Co-primary endpoints were objective response rate (ORR) and 28-week disease-control rate (DCR) versus historical gemcitabine plus doxorubicin controls. Secondary endpoints included progression-free survival (PFS), overall survival (OS) and safety. The posterior ORR was 36% (95% credible interval [CrI], 21–54 %) with a 91.4% probability of exceeding historical doublet therapy. However, the 28-week DCR was 17 % (95% CrI 6–31%), crossing the predefined futility boundary. Median PFS and OS were 3.5 months (95% confidence intervals [CI] 1.9–4.9) and 7.4 months (95% CI 2.1-4.9), respectively. Grade ≥ 3 toxicities were predominantly hematologic (thrombocytopenia 20 %, leukopenia 17%) and manageable. No treatment-related deaths occurred. Single-cell and bulk multi-omics from 11 patients revealed that immune-inflamed tumors enriched for T/NK cells, plasmacytoid and conventional dendritic cells, and S100A8/IL-1ß-skewed monocytes correlated with response, whereas stromal-myeloid niches and proliferative or neuroendocrine-squamous plastic epithelial states were associated with resistance. Resistant lesions upregulated unfolded-protein-response and Hippo pathways. These results pave the way for future biomarker-guided patient selection and rational combination or microenvironment-targeted therapies.

overall_design:
We performed single cell RNA sequencing (scRNAseq) on 15 tissue samples collected from 11 patients with RMC who were enrolled and treated in the trial. Baseline samples were collected from 10 patients (samples from 7 patients coded as “Pre_NR” who did not demonstrate an objective response to trial therapy, and from 3 patients coded as “Pre_R” who showed an objective response to trial therapy), while 3 patients also had samples collected at week 12 of trial therapy (“Post” timepoint), and 2 patients also had samples at the end of treatment (“EOT” timepoint) due to disease progression. Longitudinally collected samples were biopsied from the same organ site in all cases except patient RMC73 who underwent baseline biopsy of a liver metastasis and then in a lung metastasis during trial therapy due to disease response leading to near-resolution of the liver lesions.contributor: Moon Shots Cancer Genomics Laboratory (CGL) contributor: MD Anderson institutional Advanced Genomics Technology Core (AGTC).
***Raw sequencing data (FASTQ files) are not provided due to patient privacy and consent restrictions***

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

first: Yu

last: Kai

first: Msaouel

last: Pavlos

first: Wang

last: Linghua

first: Gao

last: Jianjun


title: Transcription factor Etv3 controls the tolerogenic function of dendritic cells (RNA-seq of Etv3 KO migDC from mixed BM chimeras)

overall_design: RNA-seq was performed on donor- and competitor-derived migratory DCs (migDC) purified from the skin-draining lymph nodes (sdLN) of 2 sets of mixed bone marrow (BM) chimeric mice (CD45.1 competitor mixed with either control (WT) or Etv3-deficient (KO) bone marrow, 2 replicates per set)


title: Ramalin ameliorates Alzheimer's disease pathology by targeting BACE1, HDAC6, and MAPK pathways

city: Suwon

first: Dong-Gyu

last: Jo

address: 2066, Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

summary: The accumulation of β-amyloid (Aβ) and hyperphosphorylated tau, along with neuroinflammation, are key drivers of Alzheimer’s disease (AD) pathology. Here, we identify ramalin, a natural antioxidant, as a promising therapeutic agent that targets multiple pathological mechanisms in AD models. Ramalin reduces BACE1 protein levels, without affecting its transcription, translation, or proteolytic activity. This reduction is mediated through selective inhibition of histone deacetylase 6 (HDAC6), as confirmed by genome-wide drug target screening and HDAC activity assays. Knockdown of HDAC6 resulted in decreases in BACE1 levels, positioning HDAC6 as a mediator of BACE1 regulation. Ramalin exhibits anti-inflammatory effects by downregulating iNOS and the NLRP3 inflammasome. In AD mouse models, ramalin treatment significantly reduced neuroinflammation, Aβ plaque burden, tau hyperphosphorylation and improved cognitive performance. Notably, ramalin reversed Aβ oligomer-induced synaptic transmission impairment and restored synaptic vesicle recycling in hippocampal neurons. Transcriptomic analysis revealed ramalin modulates MAPK signaling pathway, reducing phosphorylation of JNK and ERK, which are implicated in tau pathology. These findings position ramalin as a multi-target therapeutic agent, offering neuroprotection through coordinated modulation of BACE1, tau phosphorylation, and inflammatory pathways. Given these promising results, ramalin represents a potential breakthrough for the treatment of AD by targeting key pathogenic processes at multiple levels.

overall_design: RNA-seq analysis of cortical tissues from 3xTg-AD mice treated with vehicle or ramalin

first: Yongeun

last: Cho

first: Jeongmi

last: Lee

first: Bo Youn

last: Choi

first: Jin-Ho

last: Yun

first: Sukmin

last: Han

first: Seung Hyun

last: Baek

first: Jinsu

last: Park

first: Yoonsuk

first: Hark Kyun

last: Kim

first: Eunae

first: Leon

middle: F

last: Palomera

first: Jeein

last: Lim

first: Yeji

last: Jeon

first: Jeonghyeong

last: Im

first: Ju-Mi

last: Hong

first: Tai Kyoung

first: Sung Hyun

first: Joung Han

last: Yim


title: Structure of the MIWI endoribonuclease bound to pachytene piRNAs from mouse testes

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: Animal germlines express small RNAs called PIWI-interacting RNAs (piRNAs) that guide their associated PIWI endoribonucleases to destroy transposon transcripts, ensuring animal fertility. Mouse MIWI binds millions of sequences called pachytene piRNAs that use partial complementarity to target transposons and cellular mRNAs. Here we report the first cryo-EM structure of the MIWI-pachytene piRNA complex isolated from mouse testes. It shows a positively charged channel where the piRNA is held, with specific recognition of the signature first nucleotide uridine being mediated by amino acids within the MID and PIWI domains. The first six nucleotides of the guide RNA are visible and take up the A-form conformation to facilitate pairing with the target. Importantly, part of the channel accommodating the seed sequence is wider than that for insect PIWI, likely explaining the reported tolerance of MIWI to seed sequence mismatches. The catalytic site in the PIWI endonuclease domain presents an inactive state, with the loop containing one of the catalytic residues (E671) requiring structural re-orientation to adopt the catalytically competent state. Finally, we identify a conserved pre-formed pocket on the PIWI domain that may serve to accommodate a conserved tryptophan from the interacting factor GTSF1. Modelling shows how this interaction with GTSF1 can allosterically enforce reorganization of the catalytic pocket to promote small RNA-guided endoribonuclease activity. Our structure informs how MIWI functions using relaxed target engagement rules and associates with its interacting partner.

overall_design: Long RNA sequencing was used to check the gene and repeat expression in the sorted germ cells from two Strep-Miwi knock-in lines and small RNA sequencing was used to verify the proper piRNA loading of Strep-MIWI. Purified mouse Strep-MIWI was then used to slice the artificial piRNA target RNAs. Two RNA pools were generated: "Perfect" with 15,000 RNA targets perfectly complementary to mouse MIWI-bound piRNAs and "Bulge" with 15,000 RNA molecules with 2-nucleotide mismatch to the piRNA nucleotides 10 and 11, and small RNA sequencing was used to identify the potential MIWI slice products in both RNA pools.

first: Nicole

last: Raad

first: Carmen

last: Rodriguez

first: Radha

last: Pandey

first: Inayathulla

last: Mohammed

first: Emiko

last: Uchikawa

first: Fabienne

last: Burger

first: David

last: Homolka


title: Phosphorylation of Barrier-to-Autointegration Factor (BAF) regulates anchoring of centromeric heterochromatin to the nuclear envelope (NE)

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: In eukaryotes, the spatial segregation of heterochromatin and euchromatin is key for the structural organization and function of the genome. Heterochromatin interacts with the nuclear envelope (NE) and occupies a more peripheral position than euchromatin. However, the mechanisms that govern tethering of heterochromatin to the NE are not fully understood. Here, we report that Barrier-to-Autointegration Factor (BAF), a highly conserved NE-associated protein, interacts with centromeric heterochromatin and regulates its anchoring to the NE in a phosphorylation dependent manner. We show that impaired BAF phosphorylation results in its persistent association with centromeric heterochromatin and reinforced anchoring. We also show that reinforced anchoring of centromeric heterochromatin to the NE has important functional consequences, compromising both NE integrity and heterochromatin coalescence, and disturbing mitosis progression and the assembly of functional centromeres. Altogether, our results suggest that anchoring of centromeric heterochromatin to the NE is a highly dynamic process regulated through BAF phosphorylation, and unveil the deleterious functional consequences of perturbing this dynamics.

overall_design: Torras-Llort, Mònica

first: Carbonell

last: Albert

first: Escudero-Ferruz

last: Paula

first: Serrat

last: Martina

first: Zhang

last: Chong

first: Reina

last: Oscar

first: Medina-Giró

last: Sònia

first: Moreno-Moreno

last: Olga

first: Lipinski

last: Zoltan

first: Fernando

last: Azorín


title: Transcription factor Etv3 controls the tolerogenic function of dendritic cells (Combined snRNA-seq and snATAC-seq of Etv3 KO LN migDCs)

first: Eduardo

last: Esteva

overall_design: Combined snRNA-seq and snATAC-seq was performed on migDCs from the skin-draining lymph nodes (sdLNs) of control and ETV3-deficient mice.

first: Nicholas

last: Adams

first: Boris

last: Reizis


title: IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation (Related accession no. GSE275791) - Spatial transcriptomics dataset

city: Daejeon

first: Jeong Ho

last: Lee

address: Daehak-ro

institute: KAIST

summary: Discovering the cell-of-origin harboring the initial driver mutation provides a fundamental basis for understanding tumor evolution and development of new treatments. For isocitrate dehydrogenase (IDH)-mutant gliomas–the most common malignant primary brain tumors in adults under 50–the cell-of-origin remains poorly understood. Here, using patient brain tissues and genome-edited mice, we identified glial progenitor cells (GPCs), including oligodendrocyte progenitor cells (OPCs), as the glioma-originating cell type harboring the IDH mutation as the initial driver mutation. We conducted comprehensive deep sequencing, including droplet digital PCR and deep panel and amplicon sequencing to 142 tissues from 70 patients (32 IDH-mutant gliomas and 38 IDH-negative controls) comprising tumors, histologically normal peritumoral regions or subventricular zones (SVZs), and blood. Surprisingly, low-level IDH mutation was found in the normal peritumor away from the tumor in 37.9% (11 of 29) of IDH-mutant glioma patients, whereas no IDH mutation was detected in the SVZ. Integrating cell-type–specific mutations analysis, the direction of clonal evolution, spatial transcriptomics from patient brains and a novel IDH-mutant glioma mouse model arising from mutant OPCs, we determined that GPCs, including OPCs, harboring the initial driver mutation are responsible for the development and evolution of IDH-mutant gliomas. In summary, our results demonstrate that GPCs containing the IDH mutation are the cells-of-origin harboring the initial driver mutation in IDH-mutant gliomas.

overall_design: To understand the spatial organization of the mutant cells in normal peritumoral tissues, we performed spatial transcriptomic analysis using the Xenium platform on FFPE section from IDH-mutant glioma samples. The customized Xenium mRNA capture probes detect mutant IDH1 trasncripts, along with canonical cell-type marker probes, at single-cell resolution in a spatially resolved context.

first: Jung Won

last: Park


title: Analysis of gene expression in pancreatic cancer cells induced by  treatment of conditioned medium (CM) from cancer-associated fibroblast cells (CAFs)

city: Tokyo

first: Junjiro

last: Yoshida

address: 3-14-23 Kamiosaki, Shinagawa-ku

country: Japan

institute: Institute of Microbial Chemistry

summary: We hypothesized that CAF-induced malignant phenotypes of pancreatic cancer cells may reveal novel therapeutic targets. To explore this possibility, we first analyzed the phenotypic changes in pancreatic cancer cells treated with CAF-CM.

overall_design: Panc-1, pancreatic cancer cell line, cells were cultured in control medium (DMEM with 1% D-FBS), CM of CAFs, or DMEM with 10% FBS for three consecutive cycles of 3 days culture.


title: Piezo1-dependent activation of stromal cells ignites muscle inflammation in exercise and injury and is associated with inflammaging

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: As the actuator of movement and a key regulator of organismal metabolism, skeletal muscle is a site at which inflammatory responses must be carefully calibrated to counteract imposed stressors while preventing protracted functional impairments. Exercise, injury, and aging are common forms of stress associated with inflammation, particularly in skeletal muscle, yet the specific inducers and sensors driving such inflammation are not fully understood. Multi-pronged assessment of acute and chronic endurance-exercise models allowed us to evidence a role for MmSCs in transducing exercise-induced mechanical stress into local inflammatory responses. We identified the mechanosensitive ion channel Piezo1 as the molecular sensor of such mechanical stress. We also demonstrated that mechanosensing by stromal cells is necessary for appropriately timed inflammatory and myogenic responses to acute muscle injury and is associated with age-related muscle inflammation. Taken together, these findings highlight recognition of altered tissue stiffness by the Piezo1:MmSC pair as a fundamental mechanism of stress-induced immunomodulation in skeletal muscle.

overall_design: To investigate the potential of acute exercise (AEX/exe) and exercise training (EXT) to modulate muscle mesenchymal stromal cells (MmSCs), 1000 MmSCs were cytofluorometrically sorted (PDGFRa+Sca1+CD31-CD45-DAPI-) from hindlimb muscles of 8 to 10-week old AEX and EXT mice, as well as from sedentary (SED) controls. MmSCs were sorted directly into TCL buffer for subsequent RNA isolation, library construction, and population-level RNA-seq. To determine whether mechanical stress was sufficient to induce an inflammatory reaction, MmSCs were cytofluorometrically sorted and briefly cultured in the presence of the Piezo1-specific agonist, Yoda1 (25uM), or vehicle prior to lysis in TCL buffer, library construction and population-level RNA-seq. For loss-of-function experiments, Pdgfra-Cre.Piezo1f/f (mutant) and Pdgfra-Cre.Piezo1+/+ (WT) mice were injured by intramuscular injection of cardiotoxin (CTX), and tibialis anterior (TA) muscles were dissected and homogenized in TRIzol for RNA isolation, library construction and whole-tissue RNA-seq on days 1, 3 and 7 of recovery. Hearts from a separate cohort of Piezo1 mutant and WT littermates were also dissected 3 days after CTX injury to skeletal muscles (perfused), and RNA was extracted and used for library construction as before. Whole-tissue RNA-seq was also performed on Qd muscles, hearts (perfused), and liver specimens (perfused) from separate cohorts of uninjured, SED mutant and WT littermates. MmSCs were sorted from hindlimb muscles of mutant and WT mice on day 1 after AEX (versus SED controls) or on day 1 after cardiotoxin (CTX)-induced injury. Sorting and sequencing was the same as for AEX and EXT experiments described above.

first: Paul

last: Langston

first: Diane

last: Mathis


title: ROR1-PI3K/AKT signaling drives adaptive resistance to cell cycle blockade in TP53 mutated ovarian cancer

city: Oulu

first: Daniela

last: Ungureanu

address: Aapistie 5A

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

summary: We developed long-term resistant (lt-res, several months) pre-clinical models to adavosertib (ADA) and paclitaxel (PTX). We identified distinct transcriptomic and morphological changes in the ovarian cancer lt-res models. ADA resistance involves signaling pathway alterations that allow cells to maintain unchecked proliferation, while PTX resistance primarily stems from structural changes within the cell, affecting microtubules and drug efflux. Upregulation of receptor tyrosine kinases, such as ROR1, was observed in both ROR1-positive ADA and PTX lt-res models. Targeting ROR1 with zilovertamab-vedotin, a monoclonal antibody-drug conjugate, resulted in enhanced cytotoxicity, demonstrating a new approach against recurrent drug-resistant ovarian cancer.

overall_design: Single-cell RNA-sequencing profiling of untreated parental and short-term, intermediate-resistant and long-term resistant ovarian cancer cell lines. Resistant cell lines were established by gradual increase of PTX or ADA concentrations.

first: Frida

last: Rantanen

first: Alice

last: Dini

first: Harlan

last: Barker


title: Systemic comparison  of dCas9-based DNA methylation editing systems for specificity and stability [RNAseq_secondRun]

city: Solna

first: Maria

last: Needhamsen

address: Solnavagen 1

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Manipulating epigenetic layers during transcriptional regulation poses significant challenges, yet advancements in dCas-based systems offer promising avenues for targeted manipulation. DNA methylation, a widely studied epigenetic mechanism in mammals, has benefited from recent methodological developments enabling comprehensive profiling across various tissues and conditions. While traditional methods for altering methylation levels lacked specificity and often induced pleiotropic effects, the advent of CRISPR technology has revolutionized this landscape, offering precise manipulation of methylation levels at specific loci. However, despite their advantages, these techniques have limitations, underscoring the need for thorough characterization of existing tools and the development of novel approaches. This study aimed to comprehensively compare the on-target/off-target effects of several available epimodifier systems and explore the potential of a multimerization strategy for epimodifier domains. Through our investigations, we provide insights into the methylation-mediated control of human gene expression and the utility of dCas9-based methylation editors.

overall_design: Experimental design: HEK293T cells were transfected with plasmids encoding gRNA (BACH2-g8 or NTC) and dCas9-epimodifier-EGFP (3A, 3A3L, 3A3A, 3A-KRAB, mut3A, M.SssI, SunTag) or CRISPRoff (co-transfected with a gRNA-encoding plasmid). Successfully transfected cells were sorted based on GFP or BFP signal 3 days post-transfection (p.t.) using fluorescent activated cell sorting (FACS), GFP/BFP positive cells were cultured and harvested at days 3, 7, 14, 21, and 30 post transfection for methylation (EPIC, TMS and Pyrosequencing) and expression (Total RNAseq, mRNAseq and qPCR) analyses. Please check for more details under the “Samples” section and the “Treatment” column.

first: Majid

last: Pahlevan Kakhki

first: Fatemeh

last: Rangani

first: Ewoud

last: Ewing

first: Chiara

last: Starvaggi Cucuzza

first: Galina

last: Zheleznyakova

first: Tejaswi

last: Venkata S. Badam

last: Kalomoiri

first: Ruxandra

last: Covacu

first: Ioanna

last: Andreou

first: Lara

last: Kular

first: Maja

last: Jagodic


title: Novel syngeneic cell lines for studying high-risk BRAFV600E-driven colorectal cancer in vivo [RNA-seq_organoids]

city: Freiburg

first: Ariane

last: Lehmann

address: Breisacher Strasse 153

department: IBSM

country: Germany

institute: Medical Center Freiburg

summary: Combining anti-EGFR antibodies with BRAF/MEK/ERK-pathway blockade opened new treatment options for BRAFV600E driven colorectal cancer (CRC). Nevertheless, responses of these poor-prognostic cancers are short-lived and heterogeneous, thereby highlighting the unmet need for novel concepts integrating targeted therapy and immuno-oncology. To this end, an immunocompetent mouse model with reliable disease onset and responding to clinically relevant drugs is essential but unavailable. Here, we generated three cell lines from peritoneal metastases originating from orthotopically transplanted organoids carrying BRAFV600E, Trp53R172H and Apc mutations and characterized their ground state and responses to targeted therapy compounds in detail by RNAseq, WES and various functional assays. Interestingly, these NaJa lines displayed distinct differentiation states and responses to the clinically relevant RAF inhibitors (RAFi) encorafenib and exarafenib, thereby resembling the clinical heterogeneity of BRAFV600E driven CRC. RAFi resistance was overcome by the EGFR-family inhibitor afatinib. RAFi also influenced the expression of the antigen presentation machinery, cytokines and other immunomodulatory factors. Upon re-transplantation into syngeneic mice, all NaJa lines established aggressive tumors with distinct tumor microenvironments correlated with their differentiation states. Thus, the NaJa lines provide a unique tool to study tumor heterogeneity, drug resistance and the interplay between tumor, stroma and immune cells in BRAFV600E driven CRC.

overall_design: Colonic (COL) organoids of 1-2 donor mice per genotype were cultured. Cre recombination was induced with 4-Hydroxytamoxifen (3.5 µM) in duplicates in-vitro for 24 hours. Control organoids were treated with ethanol (EtOH). Isolated mRNA was sequenced on an Illumina HiSeq4000.

first: Jasmin

last: Traichel

last: Metzger

last: Walz

first: Reinhild

last: Feuerstein

first: Nadine

last: Wohlfeil

first: Patrick

first: Lisa

last: Marx

first: Célia

last: Asdih

first: Agnes

last: Lindenthal

first: Alina

last: Seger

first: Jule

last: Schrimpf

first: Luigi

last: Nardella

first: Silke

last: Kowar

first: Ian

last: Frew

first: Sebastian

last: Halbach

first: Rebecca

last: Kesselring

first: Melanie

last: Boerries

first: Ricarda

last: Griffin

first: Tilman

last: Brummer


title: Epigenetic and transcriptomic profiling of cultured mouse retinal progenitor cells

city: Ikoma

first: Kanae

last: Matsuda-Ito

state: 奈良県

address: 8916-5, Takayama-cho

institute: Nara Institute of Science and Techn

summary: Dynamic epigenetic changes guide retinal progenitor cells (RPCs) toward diverse neuronal subtypes and Müller glia during retinal development. However, the epigenetic mechanisms that maintain RPC proliferative and neurogenic potential throughout the final stages of retinal cell genesis remain poorly understood. Here, we integrate RNA sequencing and assay for transposase-accessible chromatin sequencing (ATAC-seq) to investigate how mouse RPC stemness is regulated. Our analysis reveals conserved chromatin accessibility and gene expression profiles in mouse RPCs throughout retinal cell genesis. Notably, the histone methyltransferase Setd8, which catalyzes H4K20 monomethylation, remains persistently expressed in RPCs but is barely detectable in adult Müller glia. Setd8 deletion in developing RPCs reduces proliferation, triggers apoptosis, and disrupts retinal laminar organization and ocular axis length. Additionally, Setd8 deficiency impairs the chromatin accessibility that is normally preserved in RPCs, leading to a partial acquisition of a transcriptomic profile associated with terminally differentiated cells. Our study indicates that Setd8 safeguards mouse RPC identity by maintaining RPC-specific chromatin accessibility, thereby ensuring proper retinal development.

overall_design: We used over 20,000 sorted retinal cells to construct a library for each sample. For library preparation, Nestin-EGFP-positive cells were FACS-isolated from retinas of wild-type Nestin-EGFP mice at E14 and E17, and Nes-Cre-YFP-positive cells were FACS-isolated from the retinas of Setd8 conditional knockout and control mice at P0.

first: Taito

last: Matsuda

first: Haruka

last: Sekiryu


title: Unravel molecular profil of astrocyte-like and oligodendrocyte-like cells in low grade glioma cell line LGG275

city: montpellier

first: Jean-Philippe

last: Hugnot

address: 141 rue de la Cardonille

institute: Institut de génomique fonctionnelle

summary: Astrocytoma are known to presents a cellular heterogeneity consisting of three identified subpopulation: "astrocyte-like", "oligodendrocyte-like" and "NPC-like" cells. Properties of these subpopulation remains unclears, specially due to the fact that no protocol allows isolation of each subpopulation. In these study, we develop a protocol to efficiently sort two populations, "astrocyte-like" and "oligodendrocyte-like" cells, by using 2 astrocyte markers; CD44 and GLAST.

overall_design: After 5 days culture without growth factors, cells were stained with CD44 and GLAST antibodies, then sorted to isolate astrocyte-like CD44+GLAST+ (POS) cells, and oligodendrocyte-like CD44-GLAST- (NEG) cells. RNA extraction of POS, NEG or unsorted (U) cells were performed directly after cell sorting

first: Leonor

last: Garcia


title: Novel syngeneic cell lines for studying high-risk BRAFV600E-driven colorectal cancer in vivo [RNA-seq_NaJa]

first: Ariane

last: Lehmann

overall_design: RNA-seq profiling of the three NaJa cell lines NaJa-D, -F and -G at Day1 or Day5 under encorafenib treatment compared to the correspondent DMSO control.

first: Jasmin

last: Traichel

last: Metzger

first: Maria

last: Walz

first: Reinhild

last: Feuerstein

first: Nadine

last: Wohlfeil

first: Patrick

first: Lisa

last: Marx

first: Célia

last: Asdih


title: Systemic comparison  of dCas9-based DNA methylation editing systems for specificity and stability [EPIC]

last: Needhamsen

overall_design: To investigate the on-target/off-target effects of several available dCas9-based DNA methylation epimodifier systems in HEK293T cells.

first: Majid

last: Pahlevan Kakhki

first: Fatemeh

last: Rangani

first: Ewoud

last: Ewing

first: Chiara

last: Starvaggi Cucuzza

first: Galina

last: Zheleznyakova

first: Tejaswi

last: Venkata S Badam

last: Kalomoiri

first: Ruxandra

last: Covacu

first: Ioanna

last: Andreou

first: Lara

last: Kular

first: Maja

last: Jagodic


title: Systemic comparison  of dCas9-based DNA methylation editing systems for specificity and stability [RNAseq_firstRun]

last: Venkata S. Badam


title: H4K16 acylations fine-tune transcriptional response to short-chain acyl-CoA dehydrogenase deficiency (ChIP-seq)

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: We investigated the combined effects of H4K16 acylations in vivo using a mouse model of short-chain acyl-CoA dehydrogenase deficiency (SCADD), which causes metabolic challenges and systemic shifts in acyl-CoA ratios. Our findings indicate that H4K16 acylations modulate transcriptional responses in a concerted manner, providing insights into an adaptive chromatin regulation in response to metabolic stress.

overall_design: H4K16ac, H4K16pr, H4K16bu, H3K9ac ChIP-seq on WT and SCADD male mouse livers in 2 biological replicates.

first: Sandra

last: Nitsch

first: Pablo

last: Ranea-Robles

first: Sander

last: Houten

first: Robert

last: Schneider


title: ADAR1 regulates dsRNA formation in nuclear and mitochondrial transcripts  through editing-dependent and -independent mechanisms

city: New York

first: Hachung

last: Chung

address: 701 W 168th St, HHSC Rm 1506

department: Microbiology & Immunology

institute: Columbia University

summary: Endogenous (self) double-stranded RNAs (dsRNAs) in human cells can activate innate immune responses. ADAR1, an A-to-I editing enzyme of dsRNAs, suppresses aberrant immune activation by self-dsRNAs. However, how ADAR1 influences the cellular dsRNA landscape remains unclear. We show that human ADAR1 downregulates self-dsRNA abundance through editing-dependent and editing-independent mechanisms. We further conducted quantitative dsRNA-sequencing on wild-type and ADAR1-deficient cells. dsRNAs are enriched in protein-coding mRNAs − especially those with repetitive elements and elongated 3’UTRs − and mitochondrial RNAs. ADAR1 loss markedly increased dsRNA quantity but minimally impacted dsRNA identity. ADAR1-regulated dsRNA transcripts consist of nuclear-encoded mRNAs and, unexpectedly, mitochondria-encoded RNAs rarely edited by ADAR1. Accordingly, dsRNAs accumulate to high levels within the mitochondria of ADAR1-deficient cells. Notably, ADAR1 loss sensitizes cells to inflammation under mitochondrial stress (e.g., mitochondrial herniation, X-ray radiation). Hence, we show that dsRNAs regulated by ADAR1 go beyond A-to-I edited transcripts, and that ADAR1 can control mitochondrial-dsRNAs.

overall_design: Double-stranded RNA (dsRNA)-prone transcripts were enriched by immunoprecipitation with the J2 monoclonal antibody (SCICONS), which recognizes dsRNA structures. The enriched RNAs were then converted into a sequencing library, resulting in a dsRNA-seq library. For input control, total RNA was extracted from the cell lysate and converted into a total RNA-seq library. Experiments were performed using WT, ADAR1-E912A KI, and ADAR1 KO Hap1 cells.

first: Heegwon

last: Shin

first: Tyler

last: Dorrity


title: Elevating Pioneer transcription factor Nr5a2 expression promotes the development of mouse somatic cell nuclear transfer embryos

city: Heilongjiang

first: TT

middle: mei

last: Z

address: Health Care Road

institute: Harbin Medical University

summary: Somatic cell nuclear transfer (SCNT) is a valuable tool in regenerative medicine, yet its efficiency remains limited by epigenetic reprogramming barriers. SCNT embryos exhibit aberrant histone modifications, including H3K4me3, H3K9me3, H3K27me3, and H3K9ac, which can be partially corrected by regulating epigenetic enzymes. However, these approaches lack locus specificity and may disrupt normal gene regulation. Additionally, imprinting defects, such as aberrant Xist expression and loss of H3K27me3-dependent imprinting, further impair SCNT development. While targeted gene corrections improve outcomes, their effects are limited due to the extensive dysregulation of genes. Here, we investigated whether the pioneer transcription factor could enhance SCNT efficiency by facilitating an open chromatin state. Our study demonstrates that pioneer transcription factor Nr5a2 overexpression in SCNT embryos improves both zygotic genome activation and the morula-to-blastocyst transition, two major developmental barriers in SCNT, and enhances birth rates. Mechanistically, Nr5a2 recruits P300 to increase H3K27ac at low-expression genes, restoring transcriptional activity and promoting SCNT embryo development.

overall_design: We performed RNA-Seq on 2-cell and morula stage embryos from ICSI, SCNT control, and SCNT Nr5a2-overexpression groups. Additionally, we conducted H3K27ac CUT&Tag sequencing on 2-cell embryos from the same three groups.

first: Yanhua

last: Zhao

first: Meiting

last: Zhang

first: Yan

last: You

first: Jinrong

first: Yuning

last: Ji

first: Lei

last: Lei


title: Single-nucleus chromatin accessibility landscape in mouse preimplantation embryos

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

summary: The initiation of mammalian life begins with fertilization, when terminally committed gametes are reprogrammed into a totipotent state. However, the mechanisms of chromatin reorganization within a single-nucleus during this reprogramming remain shrouded in mystery. Here we developed a single-nucleus assay for transposase-accessible chromatin with high throughput sequencing (snATAC-seq) for preimplantation embryos, and profiling over 3,000 blastomeres from oocyte to blastocyst. We observed dramatic dynamics in chromatin accessibility from the zygote to the 2-cell stage, corresponding to a crucial event in preimplantation development: zygotic genome activation (ZGA). To date, only a handful of transcription factors (TFs) involved in ZGA regulation have been identified. Surprisingly, we discovered 148 significantly enriched ZGA-specific TFs, with nearly all well-studied ZGA regulators including Obox, Nr5a2, Zscan4, and Dux. Notably, accessible chromatin extensively overlaps with transposable elements, particularly B1, which contains numerous binding motifs for TFs associated with ZGA regulation. And a de novo TF family, "AT-rich interactive domain" (ARID), were significantly enriched in both accessible chromatin and B1 in ZGA stages. Taken together, our study offered the first highly sensitive single-nuclear chromatin accessibility maps of mouse preimplantation embryos and provided new insights into the programmatic regulation between cis-elements and trans-regulators in this process.

overall_design: single-nucleus ATAC-seq  were applied on mouse oocytes, pre-implantation embryos, and mESCs.

first: Hui

last: Shi

first: Fangbing

last: Chen

first: Xiaoping

last: Li

first: Yi

last: Yang

first: Xi


title: Systemic comparison  of dCas9-based DNA methylation editing systems for specificity and stability [Bisulfite-Seq (reduced representation)_TMS2]

first: Maria

last: Needhamsen

first: Majid

last: Pahlevan Kakhki

first: Fatemeh

last: Rangani

first: Ewoud

last: Ewing

first: Chiara

last: Starvaggi Cucuzza

first: Galina

last: Zheleznyakova

first: Tejaswi

last: Venkata S. Badam

last: Kalomoiri

first: Ruxandra

last: Covacu

first: Ioanna

last: Andreou

first: Lara

last: Kular

first: Maja

last: Jagodic


title: Myelin antigen capture in the CNS by B cells expressing EBV latent membrane protein 1 leads to demyelinating lesion formation [scRNA-Seq]

city: Basel

first: DBM Bioinformatics

last: Core Facility

address: Hebelstrasse 20

institute: University of Basel

summary: The efficacy of B cell depletion therapies, and association with the B lymphotropic Epstein- Barr virus (EBV) implicate B cells in the demyelinating autoimmune disease multiple sclerosis. After observing myelin-reactive B cells in the naïve human repertoire, we studied how such cells behave in the central nervous system. In mice, viral infections induce infiltration of B cells independent of phenotype and specificity into the otherwise lymphocyte-poor brain, and myelin-reactive B cells then capture antigen directly from parenchyma. Trafficking of these antigen-loaded B cells to draining lymph nodes was not observed, and without T cell help, antigen-capturing B cells die rapidly. CD40L signaling or EBV latent membrane protein 1 (LMP1) can override this checkpoint, leading to in situ plasma cell differentiation and antibody-mediated, demyelinating lesion formation. These observations explain the dependency of disease incidence on prior EBV infection, and the increased risk associated with brain infections, and suggest possible treatment strategies.

overall_design: B cells were sorted from mouse brain and lymph node samples and analyzed by single cell RNA sequencing using the 10X Genomics platform.

first: Julien

last: Roux

first: Nicholas

last: Sanderson

first: Mika

last: Schneider

first: Hyein

last: Kim

first: Tobias

last: Derfuss


title: Expression profiling by high throughput sequencing of Myosin VI

city: Sheffield

first: Chris

last: Toseland

address: Medical School

country: United Kingdom

institute: University of Sheffield

summary: Around 75% of breast cancer patients have estrogen receptor (ER) positive breast cancer. Endocrine-related therapies employed to treat these patients often fail due to resistance. Consequently, new therapeutic targets are needed. Myosin VI (MVI) is increasingly implicated in cancer and has been identified to interact with the ER, and it has roles in the spatial organisation of RNA Polymerase II. In addition, gene and protein expression levels of ER and MVI are correlated across breast cancer tissue samples.

overall_design: Total RNA was extracted from three replicates of WT (scrambled siRNA control) and MYO6  KD by siRNA in MCF7 cells

first: Alia

last: dos Santos

first: Yukti

last: Hari Gupta

first: Christopher


title: NF-κB and STAT3 signaling uniquely stratifies survival in female glioblastoma patients

city: St. Louis

first: Jason

middle: Paul

last: Wong

address: Neuroscience Research Building

department: Pediatrics

institute: Washington University in St. Louis

summary: Sex differences in glioblastoma (GBM) incidence, prognosis, and response to treatment are well established. However, the molecular mechanisms that drive these differences are less well understood. In a pan-cancer study, we previously reported that female patients exhibit a sex bias towards upregulated inflammatory signaling across many cancers. Additionally, upregulated nuclear factor-kappa B (NF-κB) and signal transducer and activator of transcription 3 (STAT3) signaling in GBM is associated with poor survival. Here, we report that only female GBM patients with higher expression of NF-κB- or IL6/JAK/STAT3-related genes have poorer survival compared to females with lower expression, a pattern not seen in male patients. Interestingly this sex difference was only evident in GBM tumors with wild-type epidermal growth factor receptor (EGFR). Using a mouse GBM model, we report that female GBM cells have similar stronger signatures in NF-κB and STAT3 signaling and exhibit a more robust response to manipulation of both pathways. Furthermore, female cells exhibited a stronger relationship between STAT3 activity and its sensitivity towards STAT3 inhibition. These results demonstrate that targeting NF-κB and STAT3 signaling in a sex-informed manner in GBM patients with wild-type EGFR tumors may improve patient response to treatment. Overall, this study highlights the mechanistic and clinical importance of analyzing data that is disaggregated by sex.

overall_design: RNA-sequencing (by BRB-seq) to profile multiple iterations (i.e. dervied from separate litters) of male and female Nf1-/- DNp53 transformed murine astrocytes.

middle: P

first: Lloyd

last: Tripp

first: Robi

last: Mitra

first: Joshua

middle: B

last: Rubin


title: Co-translational determination of quaternary structures in chaperone factories

city: Montpellier cedex 05

first: Séverine

last: Boulon

institute: CNRS

summary: The HSP90/R2TP quaternary chaperone assembles key cellular machines, including the three nuclear RNA polymerases and many non-coding RNPs. Here, we characterized the RNA associated to R2TP and found that it binds many partners co-translationally. Its co-translational interactome further reveals many novel potential clients and identifies clients bound only co-translationally, only post-translationally, or both. For pairs of subunits assembling together and bound co-translationally by R2TP, only a marginal proportion of their mRNAs is co-localized and co-translated. Instead, the HSP90 and R2TP chaperones induce the formation of condensates accumulating client mRNAs and thus favoring co-translational interactions between chaperones and clients. The R2TP then cycles between co- and post-translational steps and this is regulated by ATP: it binds co-translationally in absence of ATP and becomes released from post-translational assembly intermediates by ATP hydrolysis. Assembly of protein complexes is thus initiated early by chaperones and this mechanism, dubbed co-translational chaperone channeling (cha-cha), substitutes for the rarity of co-localized/co-translated mRNAs.

overall_design: RIP-seq analysis of RNA samples following affinity purification of proteins of interest from HCT116 cells, under different drug treatments (puromycin, CB-6644). HCT116 cells lines expressing GFP-tagged protein where constructed via CRISPR/Cas9 edition.

first: Manon

last: Philippe

first: Soha

last: Salloum

first: Jacques

last: Imbert

first: Simon

last: Georges


title: Heritable ER stress impairs mitochondrial metabolism and leads to exhaustion of low-dose irradiated hematopoietic stem cells [ATACseqHSC]

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

institute: cea

summary: How hematopoietic stem cells (HSC) respond to low levels of stress such as exposure to very low doses of radiation currently used in medicine, is largely unknown. Here, we show that 20mGy-irradiated HSC (20mGy-HSC) exhibit, when they proliferate, oxidative stress with increased mitochondrial Reactive Oxygen Species and metabolism together with mitochondrial Ca2+ overload. These mitochondrial defects are due to an immediate and sustained endoplasmic reticulum (ER) stress adapted by proliferative 20mGy-HSC through activation of the eIF2-ATF4 branch of the UPR. The ER stress is heritable and leads, in long-term quiescent 20mGy-HSC, to activation of the IRE1-Xbp1 branch of UPR, which fails to restore ER homeostasis resulting in HSC self-renewal deficiency and exhaustion. Finally, we show that this heritable ER stress leads to a global DNA hypomethylation, partially reverted by early inhibition of ER stress. Our studies illuminate how an adaptive ER stress response can lead to mitochondrial defects and HSC deficiency.

overall_design: ATAC-seq in HSC isolated from bone marrow of mice transplanted with sham or 20mGy-irradiated LSK

first: Federica

last: Ferri

first: Nathalie

last: Gault


title: Heritable ER stress impairs mitochondrial metabolism and leads to exhaustion of low-dose irradiated hematopoietic stem cells [RREMseqHSC]

overall_design: DNA methylation profiling in HSC isolated from bone marrow of mice transplanted with sham or 20mGy-irradiated LSK, pre-treated or not with 4PBA


title: H4K16 acylations fine-tune transcriptional response to short-chain acyl-CoA dehydrogenase deficiency (ATAC-seq)

first: Tamas

last: Schauer

overall_design: ATAC-seq on WT and SCADD male mouse livers in 4 biological replicates.

first: Sandra

last: Nitsch

first: Pablo

last: Ranea-Robles

first: Sander

last: Houten

first: Robert

last: Schneider


title: Regulation of the type I interferon response by chromatin organization (ATAC-seq of IRF8 KO splenic pDCs)

city: New York City

first: Eduardo

last: Esteva

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Antiviral type I interferons (IFN-I) including IFN-β and multiple subtypes of IFN-α are encoded within a single locus. Whereas most cell types produce primarily IFN-β, plasmacytoid dendritic cells (pDCs) respond to viruses by rapidly producing all IFN-I subtypes. We show that during pDC differentiation, the IFN-I locus translocates from the nuclear periphery and undergoes reorganization of topologically associated domains (TADs). Accordingly, IFN-I production by pDCs was strictly dependent on the TAD-organizing cohesin complex. Promoters of Ifna genes in pDCs were poised, which was imparted by the pDC-enriched transcription factor IRF8. Finally, we identified two distal regulatory regions that facilitated the expression of adjacent IFN-I genes. Thus, the IFN-I response is controlled by multilevel chromatin organization of the IFN-I locus, including its unique poised state in pDCs.

overall_design: ATAC-seq was performed on pDCs purified from the spleen of Irf8-/- mice (2 replicates).

first: Nicholas

last: Adams

first: Ai

last: Ra

first: Boris

last: Reizis


title: Systemic comparison  of dCas9-based DNA methylation editing systems for specificity and stability [Bisulfite-Seq (reduced representation)_TMS1]

first: Maria

last: Needhamsen

first: Majid

last: Pahlevan Kakhki

first: Fatemeh

last: Rangani

first: Ewoud

last: Ewing

first: Chiara

last: Starvaggi Cucuzza

first: Galina

last: Zheleznyakova

first: Tejaswi

last: Venkata S. Badam

last: Kalomoiri

first: Ruxandra

last: Covacu

first: Ioanna

last: Andreou

first: Lara

last: Kular

first: Maja

last: Jagodic


title: Lipid metabolism in primary microglia (scRNA-Seq)

city: nanjing

first: guoyong

last: yin

address: hanzhong road 104

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Spinal cord injury (SCI) profoundly affects functional capacity and the immune system plays a crucial role in recovery. In this study, we investigated the effects of SCI on macrophages and microglia in mice. We observed that macrophages infiltrated the spinal cord shortly after injury but decreased over time. Microglial phagocytosis of myelin debris is associated with increased lipid accumulation. Deletion of macrophages or microglia had contrasting effects on recovery: macrophage deletion improved outcomes, whereas microglial deletion worsened them. In addition, PPARG promotes lipid metabolism and recovery, and atorvastatin (a PPARG agonist) effectively reverses altered metabolic processes. These findings highlight the complex roles of macrophages and microglia in SCI, and suggest that targeting PPARG and its agonists could be a promising therapeutic approach.

overall_design: We performed flow sorting on the cells at two time points after spinal cord injury, and isolated four groups of CD45+ and BODIPY-+ cells for single cell sequencing


title: Regulation of the type I interferon response by chromatin organization (RNA-seq of L929 fibroblasts +/- SEV)

last: Esteva

overall_design: RNA-seq was performed on L929 fibroblasts infected with Sendai virus for 4 hours, 8 hours, and 16 hours as well as fibroblasts left uninfected as a control (3 replicates per timepoint).


title: H4K16 acylations fine-tune transcriptional response to short-chain acyl-CoA dehydrogenase deficiency (RNA-seq)

first: Tamas

last: Schauer

overall_design: RNA-seq on WT and SCADD male mouse livers in 3 biological replicates.

first: Sandra

last: Nitsch

first: Pablo

last: Ranea-Robles

first: Sander

last: Houten

first: Robert

last: Schneider


title: Transcriptome-wide profiling of human stromal cells in mouse xenografts during preclinical treatment involving chemotherapy and/or the novel senomorphic agent dihydromyricetin

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Aging is a major risk factor for the vast majority of geriatric conditions, including various malignancies. Although cancer development can be generally attributed to the accumulation of genetic mutations, biological processes associated with aging also hold the potential to regulate cancer progression. Cellular senescence is a cell state characterized by a permanent cell cycle arrest. Senescent cells tend to accumulate with aging, exhibit pro-inflammatory activities (SASP) and promote cancer development. However, as the effect of cellular senescence on cancer progression is heterogeneous and complicated, detailed mechanisms remain to be unraveled. Fortunately, senescent cells can be eliminated by several strategies, a situation that allows to prevent incidence of chronic disorders and prolong healthspan of mammalians. Strategies involving senolytics, which can selectively remove senescent cells by targeting the SCAP, have recently emerged as a prominent and competent solution to ameliorate diverse age-related pathologies. Achieving the goal using synthetic or natural agents (the latter more preferred in clinical settings) would generate a tremendous impact on the quality of life. Here, we test the potential of dihydromyricetin (DMY), a bioactive compound extracted from Salvia miltiorrhiza, in targeting senescent cells through inhibiting the SASP in a preclinical regimen. This study demonstrates the efficacy of DMY in downregulating the SASP expression and reducing the influence of senescent stromal cells in treatment-damaged tumor microenvironment and provides a strong rationale for its future development in anti-aging pipelines.

overall_design:
Examination of the in vivo efficacy of DMY in targeting human senescent stromal cells. Experimental mice xenografted with human stromal cells (PCS27) and prostate cancer epithelial cells (PC3) were administered with vehicle, mitoxantrone (MIT) or MIT/DMY as three independent arms in a 8-week preclinical regimen. Upon completion of treatment, mice were sacrificed and tumors were collected for histological analyses. Stromal cells were isolated from tumor tissues by laser capture microdissection (LCM) and subject to RNA preparation, library construction and high throughput sequencing. This trial was performed beyond previous studies reporting DMY effects in treatment of disorders implicating its anti-inflammatory, antioxidant, anticancer and neuroprotective capacities.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************


title: Regulation of the type I interferon response by chromatin organization (RNA-seq of IFN-I TB2/TB4 DKO FL-BMDC activation)

first: Eduardo

overall_design: RNA-seq was performed on FL-BMDCs from control and IfnΔΤΒ2/ΤΒ4 mice stimulated with CpG-A for 6 hours (2 replicates per genotype).

first: Nicholas

last: Adams

first: Ai

last: Ra

first: Boris

last: Reizis


title: Regulation of the type I interferon response by chromatin organization (ATAC-seq of L929 fibroblasts +/- SEV)

overall_design: ATAC-seq was performed on L929 fibroblasts infected with Sendai virus for 8 hours or left unstimulated as a control (2 replicates per condition).

first: Aleksandra

last: Galitsyna


title: Transcription factor Etv3 controls the tolerogenic function of dendritic cells (RNA-seq of Etv3 KO GM-DCs)

summary: Dendritic cells (DC) facilitate the maintenance of immunological tolerance in the steady state. We report that transcription factor Etv3 is preferentially expressed in mature DC including tissue-derived migratory DC (migDC), and facilitates their homeostatic maturation and CCR7-dependent migration. Mice with global or DC-specific deletion of Etv3 manifested the expansion of CD25low regulatory T cells (Treg), spontaneous activation of conventional T cells, and multiorgan T cell infiltration. Etv3 deficiency exacerbated TLR7-driven systemic lupus erythematosus (SLE)-like disease, supporting the reported genetic association of human ETV3 with SLE. Etv3-deficient migDC upregulated multiple costimulatory molecules including OX40 ligand (OX40L/TNFSF4), whose blockade partially rescued the Treg abnormalities. These results identify Etv3 as an essential regulator of the tolerogenic function of DC, and implicate it in the regulation of human autoimmunity.

overall_design: RNA-seq was performed on DCs purified from GM-CSF and IL-4-driven bone marrow cultures from control (2 replicates) and Etv3-deficient (3 replicates) mice.


title: Regulation of the type I interferon response by chromatin organization (Hi-C of L929 fibroblasts +/- SEV)

overall_design: Hi-C was performed on L929 fibroblasts infected with Sendai virus for 8 hours or left unstimulated as a control (1 replicate per condition).


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (Hi-C of SMC3 KO FL-BMDCs)

summary: The cohesin protein complex extrudes chromatin between CTCF binding sites and organizes it into topologically associated domains (TADs), yet the biological implications of this regulatory mechanism are poorly understood. We show that the cohesin subunit Smc3 is required for the postmitotic differentiation and function of antigen-presenting dendritic cells (DCs). In particular, Smc3 deletion impaired antigen cross-presentation and IL-12 secretion by type 1 conventional DCs (cDC1s), thereby crippling antimicrobial and antitumor immune responses. The chromatin profile of DCs was shaped by the interplay of cohesin and the cDC1-specifying transcription factor IRF8. Conversely, optimal expression of IRF8 itself required CTCF/cohesin-binding elements demarcating the Irf8 gene. Cohesin-mediated chromatin remodeling facilitated chromatin priming at activation-inducible genes; accordingly, deletion of CTCF/cohesin-binding sites flanking the Il12b gene reduced basal and activation-induced IL-12 production by cDC1s. Our data reveal an essential role for cohesin-mediated chromatin regulation in the differentiation and function of a key immune cell type.

overall_design: Hi-C was performed on cDCs and pDCs purified from 4-OHT-treated FL-BMDC cultures from Rosa26CreER/+ or Rosa26CreER/+ Smc3fl/fl mice (2 replicates per cell type and genotype).


title: Regulation of the type I interferon response by chromatin organization (RNA-seq of SMC3 KO pDC activation)

overall_design: RNA-seq was performed on pDCs purified from 4-OHT-treated FL-BMDC cultures from R26CreER/+ or R26CreER/+ Smc3fl/fl mice and stimulated with CpG-A for 6 or 24 hours or left unstimulated as a control for 6 hours (3 replicates per genotype and stimulation condition).


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (Hi-C of HoxB8-FL differentiation)

overall_design: Hi-C was performed on undifferentiated HoxB8-FL progenitors, differentiated cDCs and pDCs, as well as differentiated pDCs stimulated with CpG-A for 6 hours (2 replicates per cell type).


title: Lipid metabolism in primary microglia

overall_design: We extracted primary microglia and treated them with myelin, atorvastatin, and virus


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RAD21 and CTCF ChIP-seq of Hoxb8-FL differentiation)

overall_design: ChIP-seq for RAD21 and CTCF were performed on undifferentiated HoxB8-FL progenitors, differentiated cDCs and pDCs (1 replicates per cell type).


title: Transcriptomic characterization of human microglial cells upon therapy-induced senescence and treatment by a natural flavonoid dihydromyricetin

summary: The central mechanisms underlying development of central nervous system (CNS) diseases remain unclear, limiting the development of effective therapeutic strategies. Cellular senescence, a biological phenomenon observed in cultured fibroblasts in vitro, has been reported to be a crucial intrinsic mechanism that influences homeostasis of the brain microenvironment and contributes to the onset and progression of CNS pathologies. Cellular senescence has been observed in disease models established in vitro and in vivo, and in bodily fluids or tissues from patients with CNS diseases. These findings raise senescent cells as a potential target for preventing, delaying and treating CNS diseases. Emerging therapies that target senescent cells have shown promising therapeutic effects in preclinical and clinical studies on aging and age-related diseases. Such innovative therapies can potentially avoid brain cell loss and functional changes, thus improving the prognosis of CNS disorders and providing alternative treatments for CNS patients. Microglia, a group of unique myeloid cells residing in mammalian brain parenchyma, represent the first line of immune defense within the central nervous system (CNS). In addition to their immune functions, microglial cells are actively implicated in other cerebral processes including regulation of synaptic architecture and neurogenesis. However, chronic microglial activation is usually detrimental, and is considered a pathogenic mechanism shared by several neurological disorders. To date, the expression pattern of senescent human microglial cells and their susceptibility to senolytic agents remain underexplored. The human microglial clone 3 cell line, HMC3, was established in 1995, through SV40-dependent immortalization of human embryonic microglial cells. In this study, we treated these cells with a chemotherapeutic agent bleomycin (BLEO), which induces therapy-induced senescence (TIS). We established the expression landscape of senescent microglial cells to characterize their senescence-associated expression pattern. Further, we treated senescent microglial cells with dihydromyricetin (DMY), a natural flavonoid that exhibits senolytic activity against certain types of stromal cells, and investigated their overall transcriptomic expression changes. The senotherapeutic effect of DMY can be partially reflected by the genome-wide expression of senescent microglial cells, which are abundant in the brain and can serve as a novel target for treatment of chronic neurodegenerative diseases.

overall_design: High-throughput RNA-seq examination of genome-wide transcriptional alterations of human microglial cells (HMC3) that underwent senescence-inducing treatment by the chemotherapeutic agent bleomycin.


title: Transcriptome analysis of HSPC at 6 days of culture of non- or 20mGy-irradiated LT-HSC

first: federica

last: ferri

summary: Mouse LT-HSC cells were obtained by cytometry sorting, irradiated or not with 20mGy using a GSRD1 (cesium source) and cultured for 6 days in stem cell maintenance medium. HSPCs from these cultures were sorted and RNA extracted for transcriptomic analysis.

overall_design: we assesed the differentially expressed genes in sorted HSPC at 6 days of culture of non- or 20mGy irradiated LT-HSC

first: Nathalie

last: Gault

first: Daniel

last: Lewandowski


title: IDH-mutant glioma arises from glial progenitor cells harboring the initial driver mutation

city: Daejeon

first: Jeong Ho

last: Lee

address: Daehak-ro

institute: KAIST

summary: Discovering the cell-of-origin with the initial driver mutation provides fundamental basis for understanding tumor evolution and developing new treatments. In isocitrate dehydrogenase (IDH)-mutant gliomas, the most common malignant primary brain tumors in young adult under 50, its cell-of-origin remains poorly understood. Here, we used patient brain tissues and genome edited mice to identify glial progenitor cells (GPCs) including oligodendrocyte progenitor cells (OPCs) as the cell-of-origin harboring the IDH mutation as the initial driver mutation. We conducted comprehensive deep sequencing, including droplet digital PCR and deep panel and amplicon sequencing on 128 tissues from 62 patient (29 IDH-mutant gliomas and 33 IDH-negative controls), comprising tumors, normal cortex, or normal subventricular zone (SVZ), and blood. Surprisingly, we found low-level IDH mutation in the normal cortex away from the tumor, in 38.5% (10 of 26) of IDH-mutant glioma patients, while no IDH mutation was detected in the normal SVZ. Furthermore, through the analysis of cell-type-specific mutations, the direction of clonal evolution, and the single-cell transcriptome from patient brains as well as novel mouse model of IDH-mutant glioma arising from mutation-carrying OPCs, we determined that GPCs including OPCs with the initial driver mutation are responsible for the development and evolution to IDH-mutant gliomas. In summary, our results demonstrate that GPCs containing the IDH mutation are the cells-of-origin harboring the initial driver mutation in IDH-mutant gliomas.

overall_design: To determine whether our mouse IDH-mutant glioma model accurately represents human IDH-mutant glioma at the single-cell transcriptome level, we performed single-cell RNA sequencing (scRNA-seq) in four OPC-ITAN mice (26-38 weeks old) and one control mouse (20 weeks old)

first: Jung

last: Park

first: Jiehoon

last: Kwak

first: Jeong

middle: H


title: Ischemia reperfusion injury (IRI) following syngeneic lung transplantation

city: Saint Louis

last: Kreisel

state: Missouri

address: 660 S Euclid Ave

department: Surgery

institute: Washington University

summary: Ischemia reperfusion injury (IRI) continues to be an important factor contributing to long-term outcomes after transplantation. Here, utilizing a murine model of orthotopic left lung transplantation, we collected single cell RNA sequencing data from naive lungs and syngeneic lung grafts at various time points up to 30 days.

overall_design: We performed syngeneic orthotopic murine left lung transplants from CD45.2+ C57BL/6J to CD45.1+ C57BL/6J mice with 60 minutes of cold ischemia at 4˚C then 45 minutes of warm ischemia at 28˚C. Lung grafts were collected at various time points after reperfusion including 2 hours (WT2H), 3 days (WT3D), 7 days (WT7D), and 30 days (WT30D). Additionally, we collected single cell suspensions from naïve C57BL/6J left lungs (CTRL). For each sample (CTRL, WT2H, WT3D, WT7D, WT30D), we pooled cells from two lungs and sorted recipient CD45.1+ cells, donor CD45.2+ cells, and stromal CD45.1- cells. We then performed single-cell RNA sequencing on these samples.

first: Hailey

middle: M

last: Shepherd

first: Wenjun

last: Li

first: Yuriko

last: Terada


title: Molecular signatures of altered energy metabolism and circadian rhythm perturbations in a model of synucleinopathy

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

summary: A pathological role of alpha-synuclein (AS) aggregation in the nervous system is a recognized feature in Parkinson disease (PD) and related neurodegenerative conditions termed synucleinopathies. In order to characterize the cellular response in CNS to incipient and advanced AS aggregation, we applied spatial transcriptomics on brain sections derived from a mouse model at prodromal and symptomatic stages of pathology. Our spatially-resolved data point to unique perturbations in brain energy metabolism during the progression of AS pathology, such that there is an initial phase of hypermetabolism in disease-affected regions, which is followed by a profound decline leading to the symptomatic phase. This latter stage was also associated with drastic reduction in mRNA translation machinery, neuroinflammation and aberrant expression of molecular drivers controlling circadian rhythms. Collectively, these data offer novel opportunities in knowledge translation for mechanism-based drug discovery and potentially inform on biological markers reflecting disease progression in PD and related diseases.

overall_design: Transgenic M83 mice overexpressing human mutant A53T AS (Prnp-SNCA*A53T) were bilaterally injected with pre-fibrillar aggregates of murine AS. Control animals were injected with phosphate-buffered saline (PBS, n=2) as control. Brains were collected at Early-stage pathology (Day 45, n=3) and Symptomatic stage (Day 75, n=3)

first: Asad

last: Jan


title: Regulation of the type I interferon response by chromatin organization (ATAC-seq of KO HoxB8-FL cells)

first: Eduardo

last: Esteva

overall_design: ATAC-seq was performed on purified pDCs (or bulk DCs for Irf8Δ) differentiated from HoxB8-FL progenitors transfected with sgRNAs targeting either Ifnar1, Irf7, Spib, Irf8 or a non-targeting sgRNA as a control (2 replicates per genotype).


title: Single-cell RNA sequencing of T cells from the spleen and spinal cord

first: guoyong

last: yin

summary: The number variations and specific roles of regulatory T (Treg) cells within spinal cord injury (SCI) remain elusive. To further investigate T cell community chages post-SCI, we conducted the first single-cell RNA  sequencing targeting the T cell populations within the injured spinal cord and spleen.

overall_design: T cells were sorted from the spinal cord and spleen using flow cytometry 14 days post-SCI to perform single-cell RNA sequencing

first: Tao

last: Qin

last: Jiang

first: Zihan

last: Zhou

first: Yuanzhen

last: Zhang


title: Regulation of the type I interferon response by chromatin organization (ATAC-seq of HoxB8-FL pDC activation)

overall_design: ATAC-seq was performed on purified HoxB8-FL pDCs stimulated with CpG-A for 6 hours and 24 hours, as well as unstimulated pDCs at the same timepoints as a control (2 replicates per stimulation condition and timepoint).

first: N

last: Adams

first: I

last: Tiniakou

first: E

first: A

last: Khodadadi-Jamayran

first: B

last: Reizis


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RNA-seq of SMC3 KO FL-BMDC differentiation and activation)

overall_design: RNA-seq was performed on cDC1s, cDC2s and pDCs purified from 4-OHT-treated FL-BMDC cultures from Rosa26CreER/+ or Rosa26CreER/+ Smc3fl/fl mice as well as cDC1s and cDC2s from FL-BMDC cultures stimulated with CpG-A and CpG-B for 6 hours (3 replicates per genotype and cell type without stimulation, 2 replicates with stimulation).


title: Bidirectional regulation of social memory by two distinct types of GABAergic neurons in the lateral septum

city: ChongQing

first: Mingrui

last: Xu

address: Xinqiao

institute: Second Affiliated Hospital of Army Medical University

summary: Humans and animals memorize and recognize familiar conspecifics during social interactions, known associal memory. While the hippocampus is crucial for social memory, the dynamic regulation social memory, particularly the negative regulation, remains unclear. Here, we identified two molecularly distinct subpopulations of GABAergic neurons in the mouse lateral septum(LS) expressing somatostatin(SST) and calbindin1(CB), respectively, with complementary distribution patterns. Activation of SST+ neurons enhances social memory acquisition, whereas activation of CB+ neurons inhibits it. Optogenetic manipulation of SST+ neurons regulates theta rhythm oscillations, correlating with their impact on social memory. SST+-dLS neurons and CB+-vLS neurons preferentially receive stronger excitatory inputs from the dorsal (vCA1d) and ventral(vCA1v) parts of vCA1, respectively. The vCA1d→SST+-dLS→lateral hypothalamic area (LHA) circuit positively regulates social memory acquisition, whereas thevCA1v→CB+-vLS→anterior hypothalamic nucleus (AHN) pathway negatively regulates it. This study uncovers two parallel subcortical neural circuits underpinning the dynamic regulation of social memory.

overall_design: The lateral septum tissue of male C57BL/6 mice at 2-month old were taken for single cell RNA-seq

first: Li

first: Mengbing

last: Huang

first: Chao-Liang

last: Ye

first: Zhiwei

last: Tang

first: Yuan

last: Wang

first: Ting

first: Shu

last: Luo

first: Rui

last: Ji

first: Chang

last: Yu

first: Hongyan

first: Peng

last: Cao

first: Qing-Feng

last: Wu

first: Man


title: RNA-seq analysis of EpCAM-GFP and GFP overexpression in FLO-1 esophageal adenocarcinoma

city: Kuala Lumpur

first: M. Aiman

last: Mohtar

state: (select)

address: UKM Medical Molecular Biology Institute (UMBI)

country: Malaysia

institute: Universiti Kebangsaan Malaysia

summary: EpCAM is one of the highly expressed marker in esophageal adenocarcinoma as identidied in several multi-OMICS platform. We utilize FLO-1 cells which are lacking in EpCAM expresssion and use overexpression strategy to elucidate the function of EpCAM in this cells. Recombinant EpCAM-GFP or GFP only was trasnfected in FLO-1 cells, and the stable cells after antibiotic selection were isolated and expanded. The cells were then subjected to mRNA sequencing.

overall_design: The stable FLO-1 cells overexpressing EpCAM-GFP or GFP were subjected to RNA-seq analysis

first: M

last: Aiman Mohtar


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RNA-seq of IRF8 KO HoxB8-FL DCs)

first: Eduardo

last: Esteva

overall_design: RNA-seq was performed on bulk DCs differentiated from either control or Irf8-mutant HoxB8-FL progenitors (3 replicates per genotype).

first: N

first: E

first: B


title: Receptor Tyrosine Kinases phosphorylate RNA polymerase II at signal-responsive genes [RNA-seq]

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

summary: Receptor Tyrosine Kinases phosphorylate RNA polymerase II and associate with distinct set of signal-responsive genes at different genomic loci.

overall_design: Examination of the targets of EGFR after EGF stimulation, with or without treatment with Erlotinib.

first: Preeti

last: Dabas

first: Beisi

first: Aseem

last: Ansari


title: A Surveillance Pathway Senses Leaked Mitochondrial DNA to Activate UPRmt and Promote Longevity

status: Public on Jan 12 2026

city: 杭州

first: hongyun

last: tang

state: 浙江省 — Zhejiang Sheng

address: 墩余路600号

department: School of Life Sciences

institute: Westlake University

summary: The mitochondrial unfolded protein response (UPRmt) is a critical mechanism for restoring cellular homeostasis and promoting longevity upon mitochondrial stress. However, the mechanisms that sense specific mitochondrial damage-associated signals and activate UPRmt remain largely unknown. Through a genome-wide RNAi screen in Caenorhabditis elegans, we identified the AT-hook protein LIN-15B as a mitochondrial stress sensor that detects leaked mitochondrial DNA (mtDNA) to activate UPRmt. We show that LIN-15B contains a mitochondrial targeting sequence (MTS) and a C-terminal domain with nuclear localization capability. Upon mitochondrial stress, LIN-15B accumulates on the outer mitochondrial membrane (OMM) and utilizes its C-terminal AT-hook domains to directly bind leaked mtDNA, with a preference for the AT-rich D-loop region. This interaction is required for the nuclear translocation of LIN-15B, which occurs independently of the canonical protein import sensor ATFS-1. Nuclear LIN-15B then activates a broad transcriptional program encompassing core UPRmt targets and a unique set of DNA repair genes. This surveillance pathway is critical for preserving mitochondrial network integrity and supporting organismal longevity. Our findings define a mitochondrial surveillance pathway in which LIN-15B senses displaced mtDNA, triggering a protective transcriptional response that promotes longevity, thus revealing a principle of cellular homeostasis monitoring via the detection of displaced self components.

overall_design: RNA-seq profiling of wild-type N2, lin-15B(jef48), and atfs-1(gk3094) C. elegans at the L4 stage treated with EV or cco-1 RNAi to induce mitochondrial stress.

first: Yung

first: Hongyun


title: Argonautes and small RNAs associated with nematode programmed DNA elimination

city: Knoxville

first: Maxim

last: Zagoskin

address: 1311 Cumberland Avenue

department: BCMB

institute: University of Tennessee Knoxville

summary: Programmed DNA elimination (PDE) selectively removes DNA in pre-somatic cells to form the somatic genome during development. Our understanding of PDE mechanisms is mainly based on studies in the single-cell ciliates, where small RNAs and transposases are involved. In contrast, the mechanisms of metazoan PDE remain largely unknown. In the parasitic nematode Ascaris, PDE removes and remodels all germline chromosome ends and partitions fused germline chromosomes into somatic chromosomes, resulting in dramatic karyotype changes. To examine the possible involvement of small RNAs in Ascaris PDE, we identified two Argonautes, AsWAGO-2 and AsWAGO-3, associated with retained or eliminated chromosome regions, respectively, during PDE mitoses. AsWAGO-3 siRNAs target primarily genes. However, a subset of AsWAGO-3 siRNAs targets repeats in regions eliminated from the middle of chromosomes that originated from the fusion of the ends of ancestral chromosomes. In contrast, AsWAGO-2 and its associated siRNAs are enriched and transiently present on retained chromosomes during elimination mitoses. Overall, our data established a link between WAGOs/siRNAs and Ascaris PDE, demonstrating the flexibility of small RNA pathways that selectively distinguish retained and eliminated DNA. We suggest that small RNAs targeting the interior of select chromosomes may be a response to the fusions of germline chromosomes.

overall_design: DuoRIP-seq was performed in Ascaris suum embryos during programmed DNA elimination (PDE) to profile Argonaute-associated small RNAs and their corresponding target RNA fragments. Argonaute immunoprecipitation was carried out for AsWAGO-2 and AsWAGO-3, with related Argonautes used as controls, following subcellular fractionation to enrich for chromatin-associated complexes. Size-enriched RNA libraries capturing both small RNAs (18–30 nt) and protected target RNA fragments (18–150 nt) were prepared and sequenced on an Illumina NovaSeq 6000 platform. Each experimental condition included 2–3 biological replicates. Raw sequencing data have been submitted to the NCBI Sequence Read Archive (submission SUB15919116), and processed expression and annotation files are provided in this GEO submission.

middle: V

first: Yuanyuan

last: Kang


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (RNA-seq of SMC3 KO splenic cDCs)

overall_design: RNA-seq was performed on cDC1s and cDC2s purified from the spleen of CD11cCre/+ (3 replicates for each cDC subset), CD11cCre/+ Smc3fl/fl (3 replicates for each cDC subset), and CD11cCre/+ Smc3fl/- (2 replicates for each cDC subset)

last: Adams

last: Reizis


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (CUT&RUN of FL-BMDCs and HoxB8-FL progenitors)

overall_design: CUT&RUN for H3K4me1, H3K4me3, H3K9me3, H3K27Ac, H3K27me3 were performed on undifferentiated HoxB8-FL progenitors as well as cDC1s, cDC2s and pDCs purified from FL-BMDC cultures (1 replicate per histone mark and cell type)

first: A

last: Khodadadi-Jamayran


title: Neuronal miR-17-5p contributes to interhemispheric cortical connectivity defects induced by prenatal alcohol exposure

city: Marseille Cedex 9

first: Fanny

last: Mann

address: 163 Avenue de Luminy

institute: IBDM

summary: Structural and functional deficits in brain connectivity have been reported in patients with fetal alcohol spectrum disorders (FASD); however, whether and how prenatal alcohol exposure (PAE) affects the axonal development of neurons and disrupts wiring between brain regions is unknown. We developed a mouse model of moderate alcohol exposure during prenatal brain wiring to study the impact of PAE on corpus callosum (CC) development. PAE induced aberrant navigation of interhemispheric CC axons that persisted even after the end of the exposure, causing ectopic termination in the contralateral cortex. We identified neuronal miR-17-5p and its target ephrin type A receptor 4 as mediators of the effect of alcohol on contralateral targeting of CC axons. Alteration of microRNA-mediated regulation of axon guidance signaling by prenatal alcohol exposure may affect interhemispheric cortical connectivity and the associated behavior in FASD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of P0 cortical neurons electroporated with control plasmid (Cont) or miR-17-5P sponge (spg17)

first: Mike

last: Altounian

first: Anaïs

last: Bellon