title: Dynamic Multi-omics Profiling Unveils Bimodal Epigenetic Roles of Chromatin O-GlcNAc modification in Premature Senescence Program [ChIP-seq]

status: Public on May 20 2025

city: Panjin

first: Yubo

last: Liu

address: Dagong Lu

institute: Dalian University of Technology

summary: Cellular senescence, a recognized instigator of tumorigenesis and age-associated disorders, can be precipitated by characteristic alterations in gene expression profiles. However, the underlying mechanisms that precise orchestrate the expression of senescence-related genes are still elusive. Here, we employed a time-series approach using a chemical genomics multi-omics strategy to panoramically investigate the role of O-GlcNAc chromatin-associated proteins (OCPs) throughout the process of oncogene-induced senescence (OIS) in human primary fibroblasts. The progression of OIS is associated with the dynamic accumulation of chromatin O-GlcNAc modification, which facilitates cells commitment to senescence. Through the integration of dynamic analyses of transcriptome and epigenome profiles, we can demonstrate that OCPs experience genomic occupation shifts across diverse epigenetic chromatin states, and display bimodal sequential regulatory activity within the senescence transcriptome. Mechanistically, O-GlcNAc aids in the formation of bimodal epigenetic regulatory complexes (TF-SWI/SNF and NuRD), which dictate the gene expression patterns related to both the senescence-associated secretory phenotype (SASP) and cell cycle arrest. Additionally, we pinpointed O-GlcNAc JUN and GATAD2A as key regulators affecting the phenotypes of OIS in both in vitro and in vivo models of senescence and tumorigenesis. Our findings on the dynamic behavior and chromatin organization principles of O-GlcNAc epigenetic factors provide insights into the senescence process and enable potential therapeutic manipulation of the senescence phenotype.

overall_design: Examination O-GlcNAc protein bound chromatin loci in human primary fibroblasts cells (oncogene induce senescence time D0, D2, D4, D10).Epigenetic modification,include histone modification analysis in human primary fibroblasts cells(oncogene induce senescence time D0, D2, D4, D10).

first: Nana

last: Zhang

first: Jianing


title: Decoding Gene Networks Governing Hypothalamic and Prethalamic Neuron Development

status: Public on May 26 2025

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

country: USA

institute: Johns Hopkins University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Purpose: sc/snRNA-Seq and scATAC-Seq were performed to characterize the developing hypothalamus

overall_design: Cell Dissociation for scRNA-Seq: To prepare samples for scRNA-Seq, tissues were dissociated in Hibernate medium (Hibernate-E Minus Calcium (#HECA500, BrainBits) for embryos or Hibernate-A Minus Calcium (#HACA500, BrainBits) for postnatal stages), supplemented with 2 mg/ml papain (#LS003119, Worthington Biochemical) and 0.5 mM Glutamax. The enzyme mixture was pre-incubated for 15 minutes, then added to tissues for 5 - 30 minutes with 0.1 U/μl RNase inhibitor (N2615, Promega). Toward the end of digestion, 100 μg/ml final DNase I (#, 4716728001, Sigma-Aldrich) was added. Cells were subsequently centrifuged, resuspended in HABG buffer, filtered through a 40 μm cell strainer (BAH136800040-50EA, Sigma-Aldrich), and resuspended in HABG buffer containing RNase inhibitor (0.5 U/μl). Cell viability and counts were assessed with Trypan Blue staining (#15250061, Thermo Fisher Scientific) and a hemocytometer /  Nuclei Preparation for scATAC-Seq:Nuclei for scATAC-Seq were extracted following post-cell dissociation and purified following a 10x Genomics protocol. Nuclei count and yield were verified with Trypan Blue staining and a hemocytometer / Nuclei Preparation for snRNA-Seq:For snRNA-Seq, adult mouse brains were rapidly dissected, and 100 um coronal sections were prepared using a mouse brain matrice. Regions spanning the ZI, TRN, and thalamus were microdissected under a dissection microscope. Nuclei were extracted following a 10x Genomics protocol.

first: Seth

last: Blackshaw


title: Astrocyte-driven suppression of tumor-specific T-cell immunity in glioblastoma

status: Public on May 21 2025

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Glioblastoma (GBM) is the most common and aggressive brain cancer, showing minimal response to available therapies. A highly immunosuppressive tumor microenvironment (TME) contributes to the limited therapeutic response of GBM. Astrocytes are major components of the central nervous system (CNS), with important immunoregulatory roles. However, little is known about the role of astrocytes and their subsets in the immune response to GBM. Using single-cell and bulk RNA sequencing in GBM clinical samples and mouse pre-clinical models, in combination with multiplexed immunofluorescence microscopy, in vivo CRISPR-based cell-specific genetic perturbations, and in vitro mouse and human experimental systems we identified an astrocyte subset that limits tumor-specific immunity by inducing CD8+ and CD4+ T-cell apoptosis via the death receptor ligand TRAIL. Moreover, we identified IL-11 produced by tumor cells as a driver of STAT3-dependent TRAIL expression in GBM-associated astrocytes. pSTAT3+ TRAIL+ astrocytes were co-localized with apoptotic T cells in human GBM samples and were associated with a shorter time to recurrence and overall decreased survival in GBM patients. Conversely, genetic inactivation of the IL-11 receptor or TRAIL in astrocytes extended survival in GBM mouse models and boosted tumor-specific T cells and tumor-associated macrophage responses. Finally, a GBM-targeting oncolytic HSV-1 virus engineered to express a TRAIL-blocking single-chain antibody in the TME extended survival and boosted tumor-specific immunity in GBM pre-clinical models. In summary, we established that IL-11/STAT3-driven astrocytes suppress GBM-specific protective immunity by inducing TRAIL-dependent T-cell apoptosis, and we developed engineered therapeutic viruses to target this novel mechanism of astrocyte-driven tumor immunoevasion.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Sequencing of Different Cell types obtained from TRAIL KD mice and control mice.

first: Camilo

last: Faust Akl

first: Francisco

middle: J

last: Quintana


title: First Generation Tools for the Modeling of Capicua-Family Fusion Oncoprotein-Driven Cancers (April 2023 Dataset)

status: Public on May 13 2025

city: San Francisco

first: Ross

last: Okimoto

address: 513 Parnassus Ave

institute: University of California, San Francisco

summary: The rearrangement of separate genes into neomorphic fusion oncogenes can occur after chromosomal damage and repair, causing cancer. In the case of sarcomas, several tumor types are driven by fusion oncogenes comprised of various partner genes. We study fusions involving capicua (CIC), a developmental transcriptional repressor whose fusion to 3' partner genes including DUX4, NUTM1, and LEUTX drives devastating tumors of the soft tissue, central nervous system, and spine. Here we develop the first tools to investigate previously understudied fusions of CIC and ATXN1 and express them in 293T cells to uncover convergent/divergent biology between various CIC-family fusions depending on what the specific partner genes are.

overall_design: polyA-selected bulk RNAseq of 293T cells transfected with empty vector, HA-CIC::DUX4-, or HA-CIC(ex20)::NUTM1(ex6)-expressing constructs, 48 hours post transfection.

first: Cuyler

last: Luck

first: Kyle

middle: A

last: Jacobs

first: Julia

last: Riad

first: Christopher

middle: D

last: Macaraig

first: Rovingaile Kriska

middle: M

last: Ponce


title: Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [Reporter_CRISPR_screens]

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Developmental genes are controlled by several cis-acting regulatory elements (REs), which in turn respond to multiple trans-acting transcription factors (TFs). Understanding this regulatory complexity has remained a challenge. Here, we combine pooled CRISPR screens with different phenotypic readouts to dissect how a cis-regulatory landscape integrates information from a large number of TFs. We apply our approach to the murine X-inactivation center, which harbors the Xist gene. We identify a large set of Xist-controlling TFs and map their TF-RE wiring at the Xist locus. We show that a transiently expressed group of XX-biased TFs, which includes the X-linked factor ZIC3, control Xist’s promoter-proximal REs. These factors promote initial Xist upregulation in a binary fashion, potentially ensuring female-specific Xist expression. A second set of developmental TFs, which include the epiblast master regulator of the epiblast OTX2, are upregulated slightly later and activate distal REs associated with the lncRNA genes Jpx, Ftx and Xert. We show that this second regulatory axis is required to ensure sufficiently high Xist RNA levels for efficient establishment of X-chromosome inactivation. Our unbiased, systematic approach provides a framework for the comprehensive dissection of regulatory interactions across genomic loci.

overall_design: Reporter CRISPR screens linking Xist-regulating transcription factors (TFs) to Xist-controlling regulatory elements (REs). The CRISPR library targets 119 TF genes with 1270 individual sgRNAs. The assay contains 12 individual CRISPR screens targeting 11 different fluorescent reporter lines (including an RE) and an empty control (noRE). GFP-High (top 10%) and GFP-Low (top 10%) populations were sorted using flow cytometry. Three replicates were collected per screen.

first: Gemma

last: Noviello

first: Eleni

last: Kanata

first: Jonathan

last: Froehlich

first: Melissa

last: Bothe

first: Alexandra

last: Martitz

first: Aybuge

last: Altay

first: Jade

last: Scouarnec

first: Vivi-Yun

last: Feng

first: Heleen

last: Mallie

first: Martin

last: Vingron

first: Edda

middle: G

last: Schulz


title: Hypercapnia induces long-term DNA methylation changes in skeletal muscle.

city: Nutley

first: Andy

last: Madrid

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health

summary: Skeletal muscle dysfunction and elevated CO2 in the blood, or hypercapnia, are both associated with higher mortality in acute and chronic pulmonary diseases. Hypercapnia causes accelerated protein degradation, reduced protein synthesis, and dysfunctional myogenesis. We have recently reported that hypercapnia-induced skeletal myogenic dysfunction persists after resolution of CO2 exposure, suggesting the existence of durable cellular aberrations in previously hypercapnic cells. No data on lingering myofiber atrophy after hypercapnia resolution currently exist. Hypercapnia and age-induced skeletal muscle loss phenotypically overlap, and myogenic progenitor cells from hypercapnic mice elicit senescence-associated transcriptional programs. While aging is characterized by unique DNA methylation and other epigenetic changes, the potential association of hypercapnia and age-related differential methylation have never been investigated. In the present study, we show that hypercapnic mice elicit protracted muscle deterioration even after returning to normocapnia and demonstrate aberrant DNA methylation in comparison to animals never exposed to elevated CO2. We also show that these DNA methylation changes do not overlap with age-induced alterations.

overall_design: RNA sequencing of skeletal muscle tissue from mice exposed to hypercapnic conditions, six months post-hypercapnia, and mice through three aging stages


title: First Generation Tools for the Modeling of Capicua-Family Fusion Oncoprotein-Driven Cancers (February 2025 Dataset)

first: Ross

last: Okimoto

overall_design: polyA-selected bulk RNAseq of 293T cells transfected with empty vector, HA-ATXN1::DUX4, or HA-ATXN1::DUX4 delAXH expressing constructs, 48 hours post transfection.

first: Cuyler

last: Luck

first: Kyle

last: Jacobs


title: Dynamic Multi-omics Profiling Unveils Bimodal Epigenetic Roles of Chromatin O-GlcNAc modification in Premature Senescence Program [RNA-seq]

status: Public on May 06 2025

first: Yubo

last: Liu

country: China

overall_design: Gene expression profiling of  human primary fibroblasts cells were performed by RNA-seq(oncogene induce senescence time D0, D2, D4, D6, D8, D10).

first: nana

last: zhang

first: Jianing

last: Zhang


title: Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements

status: Public on May 08 2025

city: Pittsburgh

first: Sarah

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

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

overall_design: Refer to individual Series


title: Dynamic Multi-omics Profiling Unveils Bimodal Epigenetic Roles of Chromatin O-GlcNAc modification in Premature Senescence Program [BiSulfite-seq]

type: Methylation profiling by high throughput sequencing

overall_design: Whole genome DNA methylation(WGBS) analysis in human primary fibroblasts cells(oncogene induce senescence time D0, D2, D4, D10).

first: Nana


title: Heterogeneity of IL-15-expressing mesenchymal stromal cells controls natural killer cell development and immune cell homeostasis

status: Public on May 16 2025

city: Vienna

first: Dietmar

last: Herndler-Brandstetter

address: Borschkegasse 8a

country: Austria

institute: Medical University of Vienna

summary: Bone marrow stromal cells have been shown to not only provide bone tissue structure, but guide hematopoiesis and lymphocyte differentiation. The role of Interleukin 15 (IL-15) expression in BM stromal cells and potential implication on immune cell homeostasis remains unknown. Here, we generated an IL15-IRES-EGFP knockin reporter mouse model to define and study IL15-expressing BM stromal cells.

overall_design: We profiled non-hematopoietic IL-15 expressing bone and bone marrow stromal cells from IL15-IRES-EGFP reporter mice. We enriched stromal and endothelial cells from eight 7 individual IL15-IRES-EGFP mice at the age of 8-12 weeks by FACS (Aqua Zombie- CD45- Ter119- and CD31- IL15-GFP+ for MSCs and CD31+ IL15-GFP+ for endothelial cells) and profiled them by scRNA-seq (10xGenomics, 3' chemistry)

first: Carmen

last: Stecher

first: Romana

last: Bischl

first: Matthias

last: Farlik


title: Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis  [scRNA-Seq]

status: Public on May 11 2025

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

country: United Kingdom

institute: University of Birmingham

summary: recision use of targeted therapies is urgently needed to improve long-term clinical outcomes for children affected by inflammatory arthritis, known as Juvenile Idiopathic Arthritis. Progress has been obstructed by a lack of understanding of the cellular basis of joint inflammation in children, given the difficulties in obtaining and studying synovial tissue itself. To this end, we combine single-cell RNA-sequencing, multiplexed immunofluorescence imaging and spatial transcriptomics to define the cellular and transcriptomic landscape of the synovium in children with Juvenile Idiopathic Arthritis. We identify spatial niches of resident and infiltrating cell populations that correlate with the degree of inflammation, and gene programs associated with arthritis severity. Combined with analyses of synovial fluid and peripheral blood from the same children, we distinguish differences in cellular composition, signalling pathways and transcriptional programs across anatomical compartments. Whilst we identify several pathogenic populations shared with adult-onset arthritis, our analyses highlight increased vascularity of the inflamed developing joint and TGFb-driven stromal subsets that upregulate expression of disease risk-associated genes. Overall, these findings illustrate the need for treatment algorithms informed by a tissue-based classification of arthritis.

overall_design:
To determine the molecular and cellular architecture of the inflamed joint in JIA, nineteen children underwent minimally invasive ultrasound-guided biopsies of the synovium, early in the course of their disease.  Matched peripheral blood and synovial fluid samples were also collected.  All participants were naïve to disease-modifying anti-rheumatic drugs (DMARDs) for the treatment of their arthritis. Participants with four ILAR subtypes of JIA were included, of whom 90% had oligoarticular or Rheumatoid Factor-negative JIA. Biopsy tissue samples were disaggregated and underwent 5’ single-cell RNA-sequencing (scRNA-seq), combined with parallel histopathological assessment of formalin-fixed paraffin-embedded sections, or analysed with spatial profiling technologies (transcriptomics, multiplexed imaging). scRNA-seq was also performed on matched samples of peripheral blood mononuclear cells (PBMC) and synovial fluid mononuclear cells (SFMC), with paired detection of 137 expressed surface proteins.

UPDATE: [Sep-28-2025] The GSE278962_meta_new.tsv file was updated.

first: Chris

middle: B

last: Mahony

middle: P


title: First Generation Tools for the Modeling of Capicua-Family Fusion Oncoprotein-Driven Cancers (May 2024 Dataset)

overall_design: polyA-selected bulk RNAseq of 293T cells transfected with empty vector or one of several CIC-fusion full length/mutant expressing constructs, 48 hours post transfection.

first: Julia

last: Riad

first: Christopher

last: Macaraig

first: Rovingaile Kriska

last: Ponce


title: Atrophin-1 Antisense Oligonucleotide Provides Robust Protection from Pathology in a Fully Humanized DRPLA Model

status: Public on May 05 2025

city: Seattle

first: Robert

last: Bragg

state: Washington

address: 300 9th Ave

institute: University of Washington

summary: Dentatorubral-pallidoluysian atrophy (DRPLA) is a fatal neurodegenerative disease arising from a CAG repeat expansion in the atrophin-1 (ATN1) gene. Because DRPLA, like many repeat expansion disorders (REDs), arises predominantly from toxic gain-of-function mechanisms, we hypothesized that ATN1 knockdown would have therapeutic potential. To test this, we established the first fully-humanized mouse model of a RED, in which one allele of mouse Atn1 is completely replaced by human ATN1, including 112 pure CAG repeats. This novel approach to exploring RED biology provides significant advantages, notably the ability to test sequence-specific therapeutics targeting human sequences, even in introns and untranslated regions of pre-mRNA. We found that our model—the Atn1Q112/+ mouse—recapitulates key features of human DRPLA, including behavioral alterations, reduced brain size and aggregate accumulation. We treated Atn1Q112/+ mice with antisense oligonucleotides (ASOs) targeting mouse Atn1 (to probe for loss of function concerns), human ATN1, or a combination. Treatment with human, but not mouse, ATN1-targeting ASOs provides remarkable protection from a range of disease-related behavioral phenotypes, including aggregation of mutant ATN1 (mATN1), and marked rescue of transcriptional dysregulation in the cerebellum. These results have helped motivate an ongoing human clinical study of ASOs targeting ATN1 for DRPLA.

overall_design: Mice were treated with ASO from 2 days to 9 weeks of age. We sequenced n=5 per genotype (WT or ATN1.Q112/+) treated with Saline, Mo_ASO, or Hu_ASO. Total N=30

first: Velvet

middle: L

last: Smith

first: Bereket

middle: Z

last: Gidi

first: Jeffrey

last: Cantle

first: Aliza

last: Ben-Varon

first: Briana

last: Nobel

first: Silvia

last: Prades

first: Andrea

last: Compton

first: Julie

last: Greenfield

first: Joanna

last: Korecka-Roet

first: Tim

last: Yu

first: Vikram

last: Khurana

first: Holly

last: Kordasiewicz

first: Hien

middle: T

last: Zhao

first: Melissa

last: Barker-Haliski

first: Daniel

last: Child

last: Carroll


title: GCN5-mediated histone H3 Acetylation Orchestrates Gene Expression and Plant Development via H2A.Z

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

institute: Northwest A&F University

summary: H2A.Z is a conserved histone variant that plays essential roles in various DNA-templated processes across eukaryotes. H2A.Z and histone post-translational modifications (PTMs) exert a bidirectional and context-dependent influence on each other. Nevertheless, the functions of the interplay between PTMs and H2A.Z level and the underlying molecular mechanism remain poorly understood. Here, we found that the loss of the histone acetyltransferase GCN5 impedes the overexpression of BSU1 typically observed in nrp1-1 nrp2-2, accompanied by changes in H3 acetylation and H2A.Z levels. Interestingly, the increment in H2A.Z levels typical of nrp1-1 nrp2-2 mutant alleviates the morphological and molecular phenotypes of gcn5. Conversely, H2A.Z-depleted mutants aggravate the phenotype of gcn5. In the gcn5 mutant, the H2A.Z level is globally reduced in the gene bodies, and this reduction is dependent on the histone chaperones NRP1 and NRP2. Additionally, the reduction of H3 acetylation levels caused by GCN5 depletion can be recovered in the nrp1-1 nrp2-2 mutant background, likely due to the over-accumulation of H2A.Z. In conclusion, our genetic, molecular, and genomic findings demonstrate that GCN5-mediated H3 acetylation promotes H2A.Z deposition, H2A.Z over-accumulation recovers the loss of GCN5-mediated H3 acetylation, and this interplay is crucial for regulating gene expression and plant development.

overall_design: ChIP-seq of H3 acetylation and histone H2A.Z in Columbia (WT) and gcn5-7, nrp1-1 nrp2-2, gcn5-7 nrp1-1 nrp2-2 backgrounds.The experimental tissues were collected form 12 day after germination (12DAG) from seedlings cultured on GM medium (1x MS salts, 1% sucrose, pH=5.7).

first: Israel

last: Ausin

first: Yafei

last: Wang

first: Yingpei

last: Su

first: Qin

last: Hu

first: Weiye

last: Qian

first: Min

last: Liu

first: Chao

last: Xu

first: Junjie


title: Enhanced CLIP-Seq (eCLIP-Seq) of endogenous MYC in different cell lines

first: Da

last: Yang

address: 3501 Terrace

department: School of Pharmacy

summary: MYC binds to thousands of gene regulatory elements in the genome such as promoters and enhancers and exerts an amplification effect on the expression of most genes, regardless of the E-box motif existence. In this study, we discovered that MYC is an RNA-binding protein with a high affinity to guanosine-rich RNAs. RNAs binding to MYC enhance its chromatin occupancy. This process helps on MYC-mediated regulation of gene expression. Mechanistically, Lys355, Arg356, and Arg357 in the basic region of MYC are essential for RNA binding. Alanine mutation of these three amino acids abolishes MYC RNA-binding function but causes minimal damage to MYC/MAX DNA-binding capacity. Only loss of MYC RNA-binding function, while maintaining DNA-binding function, significantly decreases MYC chromatin occupancy in vivo. Our study reveals a new dimension to MYC-mediated gene regulation by demonstrating that RNA-binding activity plays an important role in MYC’s function.

overall_design: Enhanced crosslinking and immunoprecipitation followed by sequencing (eCLIP-Seq) of MYC in different cell lines. Two biological replicates were sequenced for each cell line.

first: Sihan

last: Li

first: Zehua


title: innate immune cell memory induced by endogenous and exogenous triggers

city: Oxford

first: Amélie

last: Julé

address: Roosevelt Drive, Headington

institute: Kennedy Institute of Rheumatology (KIR)

summary: Innate memory is a key defence mechanism against infection, enhancing protective immunity and limiting unnecessary collateral tissue damage.  Inflammation triggered by endogenous stimuli that signal cellular stress or tissue injury, must also be tightly controlled to balance robust response to intrinsic danger whilst avoiding catastrophic autoimmunity.  Here, we assess the contribution of innate memory to this balance.  The extracellular matrix protein tenascin-C, a damage-associated, toll-like receptor 4 (TLR4) agonist, reprograms monocyte response to subsequent threat, inducing concomitantly suppressed and enhanced responses to rechallenge.  Comparative analysis of memory evoked by tenascin-C and the pathogenic TLR4 agonist, LPS, revealed both common and distinct gene expression signatures, effects that were controlled transcriptionally, These data highlight how intrinsic and extrinsic innate re-programming exerts control over dysregulated inflammatory networks driving either infectious or chronic ‘sterile’ inflammatory diseases.

overall_design: Primary human monocytes from healthy individuals were stimulated for 24hours with LPS (100 ng/mL) or the FBG domain from tenascin-C (FBG-C). Cells were then washed, rested for 5 days, and restimulated for 4 hours with LPS, FBG-C or POLY-I:C (TRIGGER) on day 6 (7D Protocol), or cells washed and immediately restimulated for 2 hours with LPS or FBG-C (24H Protocol). After restimulation with the TRIGGER cells were lysed and transcriptomic changes analyzed by bulk RNAseq. 5 independent donors were analysed.

first: Anja

last: Schwenzer

first: Kim

last: Midwood

first: Amelie

last: Jule

first: Anna

last: Marzeda

first: Bogdan

middle: S

last: Didov

first: Kieran

last: Woolcock

first: Libby

middle: K

last: Jennings

first: Jean-Baptiste

last: Richard

first: Steve

last: Sansom

first: Adam

last: Cribbs

first: Wyatt

middle: W

last: Yue

first: Carl

last: Goodyear

first: Karim

last: Raza


title: Haploid genome activation exposes genes with a specific chromatin signature for pollen selection

status: Public on May 10 2025

city: wuhan

first: zhu

last: bo

state: beijing

address: shi zi shan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: Here, we obtained datasets of single cell and/or cell type transcriptomes and epigenomes of the rice male germ line isolated at the different developmental stages from hybrid and/or inbred varieties. Analysis of the data pinpoints to a premeiotic set-up of a chromatin state to instruct male germ cell-type specific gene expression during the gametogenesis, reveals that the male haploid genome activation occurs shortly after meiosis, and uncovers a specific chromatin signature for haploid gene expression which has implication in haploid and pollen selection.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Germ cells were obtained by micromanipulation. DNA methylation and transcriptome libraries were constructed by scBS-seq and scRNA-seq techniques. Histone modification library was constructed using CUT&Tag technology.

first: Bo

last: Zhu

first: Feng

last: zhao


title: Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements [TT-seq]

first: Sarah

last: Hainer

summary: Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs) such as promoters and enhancers which drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter element, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and non-coding transcription. Our findings suggest that transcription of paired mRNAs and eRNAs are coordinately co-regulated, while mRNAs and uaRNAs sharing a promoter are independently regulated by remodelers. Our mechanistic studies suggest that while SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcription regulation through maintenance of genomic stability and accurate Integrator complex activity. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.

overall_design:
rRNA depleted Nascent RNA-seq (TT-seq) samples. Wildtype murine embryonic stem cells transfected with an RNAi agent for 48 hours. Twenty nine targets profiled in biological duplicate, and control samples (Atrx, Btaf1, Chd1, Chd1l, Chd2, Chd3, Chd4, Chd5, Chd7, Chd8, Chd9, Ep400, Ercc6, Ercc6l, Hells, Hltf, Ino80, Radb54b, Radb54l, Rad54l2, Shprh, Smarca2, Smarca4, Smarca5, Smarcad1, Smarcal1, Srcap, Ttf2, Zranb3).
Also included are TT-seq for DMSO or dTAG treated (3 hr) for Chd4-dTAG, Chd8-dTAG, or Hltf-dTAG endogenously tagged ES cells.

first: Benjamin

last: Patty

first: Rinku

last: Dhungana


title: Hypothermic machine perfusion alleviates DCD graft liver injury by inducing the expression of KLF2 and promoting macrophage efferocytosis

city: NanChang

first: Qi

last: Xiao

address: Nanchang University, 17 yongwai Zheng jie street, NanChang 33006, Jiangxi, China

institute: Department of Transplantation，The First Affiliated Hospital， Jiangxi Medical College，Nanchang University

summary: This study aims to investigate the protective effects and underlying mechanisms of hypothermic machine perfusion (HMP) on ischemia-reperfusion injury (IRI) in liver grafts from donation after cardiac death (DCD), with a specific focus on the regulation of KLF2 expression and its role in modulating macrophage efferocytosis.

overall_design: A DCD liver grafts model was established to evaluate the protective effects of HMP. KLF2 expression and macrophage efferocytosis were assessed in liver grafts. In vitro, human umbilical vein endothelial cells (HUVECs) were transfected to manipulate KLF2 expression and co-cultured with macrophages in a non-contact system to explore the endothelial–macrophage interaction. The efferocytosis agonist putrescine was administered in vivo to further assess its effect on DCD liver grafts. RNA sequencing (RNA-Seq) was conducted to analyze gene expression changes.

first: Qin

last: Deng


title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels. [CUT&RUN]

status: Public on Apr 28 2025

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

summary: Evolutionary adaptation to diurnal vision in ground squirrels has led to the development of a cone-dominant retina, in stark contrast to the rod-dominant retinas of most mammals. The molecular mechanisms driving this shift remain largely unexplored. Here, we perform single-cell RNA sequencing (scRNA-Seq) and chromatin accessibility profiling (scATAC-Seq) across developmental retinal neurogenesis in the 13-lined ground squirrel (13LGS) to uncover the regulatory basis of this adaptation. We find that 13LGS cone photoreceptors arise not only from early-stage neurogenic progenitors, as seen in rod-dominant species like mice, but also from late-stage neurogenic progenitors. This extended period of cone generation is driven by a heterochronic shift in transcription factor expression, with cone-promoting factors such as Onecut2, Pou2f1, and Zic3 remaining active in late-stage progenitors, while cone-differentiation factors Thrb, Rxrg, and Mef2c are expressed precociously in cone specification. Functional analyses reveal that Zic3 and Mef2c promote cone specification, acting through species-specific regulatory elements that drive their expression in late-stage progenitors. These results demonstrate that evolutionary modifications to gene regulatory networks underlie the development of cone-dominant retinas, providing insight into mechanisms of sensory adaptation and potential strategies for cone photoreceptor regeneration in vision disorders.

sample_organism:
Mus musculus
Ictidomys tridecemlineatus

platform_organism:
Mus musculus
Ictidomys tridecemlineatus

overall_design: Nuclei were isolated from snap-frozen P5 13LGS and P2 mouse retinas for use in CUT&RUN-sequencing. Two biological replicates were assayed for each species, with each 13LGS replicate consisting of a pool of retinas from two individuals, and each mouse replicate consisting of a pool of retinas from 3 individuals.

first: Kurt

last: Weir

first: Sangeetha

last: Kandoi

first: Roujin

last: An

first: Nicole

last: Pannullo

first: Isabella

last: Palazzo

first: Jared A.

last: Tangeman

first: Jun

last: Shi

first: Steven H.

last: DeVries

first: Dana K.

last: Merriman

first: Jiang

last: Qian

first: Seth

last: Blackshaw


title: Defining the mechanisms-of-action of nitrofuranyl piperazines against Mycobacterium abscessus

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

summary: Defining the functions of the small molecule to inhibit M. abscessus growth and comparitive studies examining the mechanisms of action in M. tuberculosis vs. M. abscessus.

sample_organism:
Mycobacterium tuberculosis CDC1551
Mycobacteroides abscessus ATCC 19977

overall_design: Mab cultures were treated in two biological replicates with 10 μM of HC2210 and an equivalent volume of DMSO for 24 hours at T25 standing flasks in 37°C incubator (without 5% CO2). The same is done for Mtb cultures except that 2 μM of HC2210 is used and cultures were incubated in T25 standing flasks at 37°C, 5% CO2 for 24 hours. After treatment, the pellets were harvested, and the bacterial RNA was extracted using the TRIzol-based protocol as previously described(56). Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI). Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.1.5). The sequencing reads were analyzed using the commercially licensed CLC Genomics Suite and are presented in Dataset 3.1 (for Mab) and Dataset 3.2 (for Mtb).

first: Ifeanyichukwu

last: Eke


title: RNA-binding activity plays an important role in MYC function

first: Da

last: Yang


title: RNA-Seq analysis among dps-disrupted mutants in Deinococcus geothermalis

status: Public on Apr 30 2025

city: Seoul

first: Sung-Jae

last: Lee

address: Kyungheedae-ro 26, Dongdaemun-gu

department: Biology

country: South Korea

institute: Kyung Hee University

summary: Transcriptomic analysis was performed in Deinococcus geothermalis wild-type and three mutants including dgeo_0257, dgeo_0281, and double knockout (DK) mutants. dgeo_0281 is a major Dps-coding gene and dgeo_0257 is a novel Dps candidate. Thus, to detecte physiological functions of both Dps-encoded genes, each gene-disrupted mutant and DK mutant was constructed and performed RNA-Seq analysis. This result support better understanding for Dps roles in radiation resistant bacterium through up-regulated and down-regulated genes profile.

overall_design: Experimental strains were cultivated to OD600 of 2.0 as an early exponential growth phase in TGY culture medium. The optical density was nomalized to 1.0 value with 0.9% saline and continuously cultivated for 1 hour present or absent of 50 mM H2O2. Then samples were centrifuged and discarded supernatant. The pellets were applied RNA preperation using manufacturing protocols.

first: Hyun Hee

first: Eunjung

last: Shin

first: Yujin

last: Park


title: Epigenetic library screen reveals novel targets for uveal melanoma

status: Public on Apr 22 2025

city: Miami

first: Stefan

last: Kurtenbach

state: FL

address: 1501 NW 10th Ave

department: Ophthalmology

institute: University of Miami

summary: Uveal melanoma (UM) is the most common primary ocular cancer in adults, which metastasizes mainly to the liver in around half of the cases. The limited potency of current treatment options for metastatic UM necessitates an urgent exploration of novel therapeutic approaches to improve patient prognosis. We conducted a large epigenetic compound library screen with the currently most well characterized, focused epigenetics library available, which consists of 932 potent, cell permeable, medically active, epigenetic-directed small molecule modulators. Our screening identified two new lead compounds, which so-far have been unappreciated for UM. Romidepsin, an HDAC inhibitor with specificity for class I HDACs, was the most efficient compound in-vitro, as well as the BET inhibitor Mivebresib, which showed minimal toxicity on normal cells. RNA sequencing and pathway analysis revealed an upregulation of PRC-associated gene targets induced by HDAC inhibition, while BET inhibition appears to act through retinoic acid related pathways. Mivebresib treatment in a metastatic uveal melanoma mouse model resulted in longer survival times and reduced metastasis to the spinal cord and brain. The results of our drug screen indicate a vulnerability for HDAC and BET inhibition for UM cells. The BET inhibitor Mivebresib may be a promising candidate for future synergistic and clinical trials.

overall_design: To investigate the effects on transcription of treatment with epigenetic compounds of interest on uveal melanoma cells, we subjected human uveal melanoma cell line MP41 to 24 hours of high dose treatment with each drug. Bulk RNA sequencing followed by analysis through BioJupies was performed to determine differential gene expression in treated cells.

first: Yenisehirli

last: Gulum

first: Kurtenbach

last: Stefan


title: Gene Expression Profiling and Epigenetic Alterations in RAW 264.7 Cells Following Treatment with Lipopolysaccharide and Methylcobalamin (MCB) [ATAC-seq]

status: Public on Apr 21 2025

city: Beijing

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

summary: Methylcobalamin (MCB), an active form of Vitamin B12, demonstrates significant anti-inflammatory and neuroprotective properties by modulating pro-inflammatory cytokines such as TNF-α, IL-1β, and IL-6 (Chopra et al., 2013; Scalabrino et al., 2019). This modulation could potentially ameliorate the hyperinflammatory response known as the "cytokine storm" observed in COVID-19 patients, thereby reducing severity and improving clinical outcomes (Tanaka et al., 2020; Scalabrino, 2005). Beyond its immunomodulatory effects, methylcobalamin supports neuronal health, a critical factor given the neurological complications associated with COVID-19 (Scalabrino et al., 2017; Zhu et al., 2021). Although further clinical trials are necessary to confirm its efficacy, methylcobalamin presents a promising adjunctive therapy for managing the inflammatory and neurological symptoms of COVID-19. However, the precise molecular mechanisms underlying MCB's anti-inflammatory effects remain to be fully elucidated. In this study, we aim to investigate the transcriptional and epigenetic mechanisms through which MCB functions as an anti-inflammatory agent.

overall_design:
To explore the transcriptomic and epigenetic mechanisms through which methylcobalamin (MCB) modulates the inflammatory response induced by lipopolysaccharide (LPS) in macrophages, we conducted RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and Cleavage Under Targets and Tagmentation (CUT & Tag) on the RAW 264.7 cell line.
Initially, we conducted a comprehensive gene expression profiling analysis using ATAC-seq data from WT RAW 264.7 cells treated with DMSO, LPS, LPS-MCB, and MCB for 12 hours.
Comparative ATAC-seq analysis of RNA-seq data for DMSO, LPS, LPS-MCB and MCB group.


title: Targeting Glucose Metabolism: Synergistic Strategies to Enhance Apoptosis and Immune Activation in Hepatocellular Carcinoma Treatment

city: Hsinchu City

first: YenNhi

middle: Ngoc

last: Ta

address: No. 101, Sec. 2, Guangfu Rd., East District

department: Institute of Biomedical Engineering

country: Taiwan

institute: National Tsing Hua University

summary: Exploiting the dependency of cancer cells on glycolysis offers a promising avenue to enhance therapeutic strategies for hepatocellular carcinoma (HCC). In our study, we employ glucose oxidase (GOx) as a glucose metabolism modulator to deplete glucose within the tumor microenvironment, initiating reactive oxygen species (ROS)-mediated endoplasmic reticulum (ER) stress and regulating both death receptor and mitochondrial apoptosis pathways, subsequently sensitizing HCC cells to DOX- induced apoptosis. DOX, co-formulated with GOx in nanoparticle (GOx-DOX-NP), not only substantially reduces tumor volume and increases number of apoptotic cells in tumors, but also acts as an immunogenic cell death (ICD) inducer, stimulating anti-tumor immunity. This effect further improves the immunotherapy. In conclusion, our findings underscore the potential of integrating glucose metabolism modulation with apoptosis-based therapies and immunotherapy for more effective liver cancer treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine HCC tumors with or without treatment of GOX-DOX nanoparticles

first: Yunching

last: Chen

first: Yen-Nhi Ngoc


title: Circadian Regulation of Murine Inguinal Adipocytes

city: Hanover

first: Jay

middle: C

last: Dunlap

state: NH

address: 702 Remsen

department: Molecular and Systems Biology

institute: Geisel School of Medicine at Dartmouth

summary:
The focus of this research is in the area of biological clocks. Importance: Metabolic dysregulation is the major preventable risk factor for leading causes of chronic disease-related deaths. More specifically, chronic obesity is correlated with adipocyte hypertrophy and hyperplasia, both of which may be circadianly regulated. All circadian clocks are cell-intrinsic, and circadian oscillators that are tissue-specific control metabolic homeostasis by fine-tuning nutrient utilization; adipose tissue responds to microenvironmental changes in a clock-dependent manner. The objective of this work is to understand how circadian rhythms affect adipocyte biology. To delineate the relationship between the cellular circadian system and adipocyte biology in the absence of organismal cues, circadian output was  characterized by transcriptionally profiling in vitro differentiated adipocytes from inguinal adipose tissue over 3 circadian days with a 2-hour resolution via RNAseq. Goal: Determine what aspects of adipocyte biology and environmental stimuli can be influenced by time-of-day. Impact: Findings from this study will increase our understanding of clock-controlled energy metabolism and adipocyte dysfunction, advancing our understanding of the non-linear association between weight, energy expenditure and risk in chronic disease.
Purpose: The goals of this study are to understand the molecular basis of the biological clock in mammals and the means through which it controls metabolism. PER2::LUC transgenic mice were used as a source of adipocyte stem cells for studies on the role of the clock in adipocyte biology.
Methods: There are two biological replicates. 4 male mice aged 8-12 weeks under 12:12 light-dark cycle and standard chow were used per replicate. The inguinal stromal vascular fraction (SVF) was isolated post-mortem at ZT10*lights on, resting phase, 10am*. Isofluorine anesthesia and cervical dislocation were the method of sacrifice.  Pre-adipocytes were isolated as in (Oeckl 2020, DOI: 10.1016/ j.xpro.2020.100118) with modifications and seeded onto three 35mM plastic bottom tissue culture plates (MatTek) in "base media" (DMEM F/12 + GlutaMAX (Gibco xxxx-018) with penicillin/streptomycin and 10% fetal bovine serum (Gibco: Ref#10437-028). Cells were passaged every 48 hours for a total of 3 passages with a split ratio of 1:2.8. In final passage, cells were seeded into 35mM plastic dishes (MatTek). After confluence, differentiation was induced with  dexamethasone, rosiglitazone and IBMX, biotin, insulin, pantothenate ( "differentiation media"). After 4 days of differentiation, dex, rosi and IBMX were removed from the media ( "maintenance media"). After 4  days in culture, cells were synchronized with 50% FBS, 50% "base media" and 10uM forskolin for 2-2.5hours. Media was switched to "maintenance media" containing 0.01% bright d-luciferin (GoldBio #LUCK-100) in batches of 4 dishes, topped with glass microscopy slides and sealed with vacuum grease before loading into a Lumicycle housed in a 37C, 0%CO2 incubator. Circadian parameters including amplitude were determined using LumiCycle Analysis software (Actimetrics, v.2.44).

overall_design:
In total, 62 samples were analyzed. Two age-matched biological replicates are included. Each time series includes 12 through 72 hours post-synchronization with a 2-hour resolution. Replicate 2 is missing 60h timepoint. Before sequencing, circadian period length was confirmed manually in Excel (mean, +/- SD) as calculated by the Per2::Luc bioluminescence traces using all samples with at least two peaks.

UPDATE [May-02-2025] The Rep1 Samples were removed, the Rep2 Samples were renamed to Rep1, and the Rep3 Samples were renamed to Rep2. The associated data files did not change.

first: Jennifer

last: Worthen

first: Armina-Lyn

last: Frederick

last: Loros

first: Phillip

last: Dumesic


title: Gene Expression Profiling and Epigenetic Alterations in RAW 264.7 Cells Following Treatment with Lipopolysaccharide and Methylcobalamin (MCB) [CUT&Tag]

overall_design:
To explore the transcriptomic and epigenetic mechanisms through which methylcobalamin (MCB) modulates the inflammatory response induced by lipopolysaccharide (LPS) in macrophages, we conducted RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and Cleavage Under Targets and Tagmentation (CUT & Tag) on the RAW 264.7 cell line.
Last, we conducted a comprehensive CUT&Tag data from WT RAW 264.7 cells treated with DMSO, LPS, LPS-MCB, and MCB for 12 hours.
Comparative CUT&Tag analysis for DMSO, LPS, LPS-MCB and MCB group.


title: Single-cell elderly blood-CSF atlas implicates peripherally-influenced neuroinflammatory degeneration in normal pressure hydrocephalus

status: Public on Apr 23 2025

city: Boston

first: Kris

last: Kahle

address: 55 Fruit Street

institute: MGH

summary: Idiopathic normal pressure hydrocephalus (iNPH) is a common, yet enigmatic form of dementia characterized by cerebral ventriculomegaly. In contrast to other types of hydrocephalus, iNPH exhibits normal or even reduced intracranial pressures and infrequent reductions in ventricular size after CSF shunting. Here, we generated the first single-cell RNA sequencing atlas of the peripheral blood and ventricular CSF in elderly iNPH patients totaling 140,207 transcriptomes. Integrated analyses identified a pro-inflammatory signature in peripheral blood and CSF monocytes that was significantly enriched in iNPH subgroups with lower cognitive function. We also identified novel CSF cell populations likely representing the periventricular sloughing of degenerating neuroglial cells. Our findings suggest that immune dysregulation detectable in peripheral blood monocytes contributes to CSF space inflammation, neurodegeneration, and associated cognitive deficits in iNPH. These data shift the paradigm of iNPH from a primary disorder of impaired “brain plumbing” and highlight the potential for non-invasive, immune-based diagnostic and treatment strategies.

overall_design: Investigate the inflammatory features of NPH pathology and their correlation with clinical phenotypes.

first: Kristopher

first: Duy

last: Phan

first: Emre

last: Kiziltug

first: Hao

last: Le


title: The ImmgenT Open-Source project

status: Public on May 14 2025

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

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

Supplementary files current as of 7/8/2025.
v1 - 5/14/2025
v2 - 7/8/2025

overall_design:
The immgen T OpenSource Project is a collaborative effort involving 100 participants across 41 laboratories, working together to create the most comprehensive atlas of T cells in the mouse immune system. Leveraging a common data generation pipeline, the goal is to profile T cells in every body location, capturing their diverse states in response to a broad range of immunological challenges and physiological states (infection, autoimmune, tumor, aging), and how specific gene programs drive this diversity. Profiling was performed at the single-cell level, with multimodal mRNA, surface protein (CITE-seq/TotalSeq, 128 antibody panel), and TCR-VDJ (paired TCRα/TCRβ). Please refer to individual series for a description of each experiment.

UPDATE: [Mar-17-2026] Some processed data files were replaced. See the supplementary file GSE297097_README.txt for details.


title: Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia [scRNA-seq]

status: Public on Apr 11 2025

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

summary: Pediatric cancers are increasingly linked to transformation events before birth, yet how ontogeny influences oncogenesis remains poorly understood. Using a humanized model of NUP98-NSD1-driven pediatric acute myeloid leukemia, particularly aggressive when accompanied by WT1 mutations, we investigated how the developmental stage of hematopoietic stem cells impacts leukemic transformation, disease progression and therapy response. Fetal-derived hematopoietic stem cells readily transform into leukemia, with WT1 mutations enhancing stemness and alter lineage hierarchy, while stem cells from later developmental stages progressively withstand transformation. Single-cell analyses revealed that fetal-origin versus postnatal leukemic stem cells exhibit greater quiescence and metabolic reliance on oxidative phosphorylation. Notably, therapeutic responses markedly differed between fetal- and postnatal-origin leukemias, even when driven by the same oncogenic mutations. In patients, onco-fetal transcriptional programs were associated with worse outcomes. We identified tailored combination therapies that specifically diminished aggressive fetal-origin leukemia, underscoring the need to consider ontogeny in treatment of pediatric cancers.

overall_design: Human CD34+ HSPCs were edited with control, WT1ko, NUP98-NSD1, NUP98-NSD1/WT1ko, and then xenotransplanted into NSG mice. Human CD45+ cells were flow cytometry sorted from primary, secondary, or post-treated xenografts and submitted to scRNA-seq. Additionally, human CD45+ cells were sorted from PDX model and submitted to scRNA-seq.

first: Ke

last: Wang

first: Shayan

last: Saniei

first: Nikita

last: Poddar

first: Subrina

last: Autar

first: Saul

last: Carcamo

first: Meghana

last: Sreenath

first: Jack

middle: H

last: Peplinski

first: Rhonda

middle: E

last: Ries

first: Isabella

last: Martinez

first: Clifford

last: Chao

first: Anna Huo-Chang

last: Mei

first: Noshin

last: Rahman

first: Levan

last: Mekerishvili

first: Miguel

last: Quijada-Álamo

first: Grace

last: Freed

first: Mimi

last: Zhang

first: Katherine

last: Lachman

first: Jing

first: Giang

last: Pham

first: Dan

last: Filipescu

first: Mirela

last: Berisa

first: Tommaso

last: Balestra

first: Julie

middle: R

last: Haines

first: Angelo

last: D’Alessandro

first: Daniel

last: Puleston

first: Emily

last: Bernstein

first: Jerry

last: Chipuk

first: Mark

last: Wunderlich

first: Sarah

last: Tasian

first: Bridget

last: Marcellino

first: Ian

last: Glass

first: Christopher

last: Sturgeon

last: Landau

first: Zhihong

last: Cheng

first: Eirini

last: Papapetrou

first: Franco

last: Izzo

first: Soheil

last: Meshinchi

last: Hasson

first: Elvin

last: Wagenblast


title: Transcriptional profiles are dramatically altered in circulating CD14+ monocytes in Rheumatoid Arthritis [RNA-seq]

status: Public on Apr 10 2025

city: Glasgow

first: Kieran

last: Woolcock

address: Sir Graeme Davies Building, 120 University Place

department: School of Infection & Immunity

institute: University of Glasgow

summary: Peripheral blood samples were collected from healthy controls and rheumatoid arthritis patients (active disease: DAS28 > 2.7), subsequently CD14+ monocytes were isolated using a positive selection kit, RNA was extracted and RNA-Seq was completed.

overall_design: RNA-Seq using the illumina NovaSeq6000 was performed on circulating CD14+ monocytes isolated from 15 healthy controls and 9 rheumatoid arthritis patients.

first: Nila

last: Servaas

first: Maarten

last: van der Kroef

first: John

middle: J

last: Cole

first: Aridaman

last: Pandit

first: Carl

last: Goodyear


title: Epigenome-Wide Association Study of the Interaction between Alzheimer’s disease and Systemic Infection

city: Exeter

first: Katie

last: Lunnon

address: RILD Level 4, Barrack Road

department: Medical Research

institute: University of Exeter Medical School

type: Methylation profiling by genome tiling array

summary: Although most Alzheimer’s disease (AD) cases are sporadic, with no known aetiology, the onset and progression of the disease has been widely linked with inflammation both in the periphery and within the brain. Indeed, many AD sufferers ultimately die with a systemic infection, and infections during life can increase the risk of developing dementia and the rate of cognitive decline in AD patients. However, the mechanistic pathways linking inflammatory processes to AD onset and progression are not known. This study will use an epigenomic approach to elucidate the molecular mechanisms involved in the brain in AD following systemic inflammation. A better understanding of the neurobiological pathways altered in AD during systemic inflammation could ultimately identify new pharmacological targets, potentially improving the lives of millions of AD sufferers worldwide. This work identifies molecular mechanisms that are altered in AD brain during systemic inflammation, which can then be functionally characterised and targeted in in vitro modelling systems.

overall_design: We aimed to profile the genomic DNA methylome of prefrontal cortex brain tissue of Alzheimer’s disease and control patients with and without infection present at the time of death. DNA methylation was analysed in a cohort of 242 samples, including 131 AD patients (n=68 with infection) and 111 control participants (n= 47 with infection); using the Infinium Methylation EPIC array.

first: Lachlan

last: MacBean

first: Adam

last: Smith


title: GRHL and PGR control WNT4 expression in the mammary gland via 3D 2 looping of conserved and species-specific enhancers [T47DS RNA-seq]

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

summary:
This dataset belongs to a study in which we functionally dissect the cis-acting enhancer network and spatiotemporal transcriptional mechanisms that regulate WNT4 expression in the mouse mammary gland and the human breast. As part of these efforts, we identified GRHL as a luminal lineage transcription factor. In follow up work, we studied the interplay between GRHL2 and PGR in the presence and absence of progesterone signaling. This bulk RNAseq dataset allows investigation of the PGR signaling response in human T47DS breast cancer cells in either the presence or absence of GRHL2 gene expression.

The 0, 4 and 24 hours timepoints in T47DS cells were first used and reported in https://doi.org/10.1101/2025.04.11.648333.
The complete dataset, including the GRHL2 knockdown samples, was used and reported in https://doi.org/10.1101/2025.09.01.673508.

overall_design: Bulk RNA sequencing of control (wildtype T47DS) or GRHL2 knockdown (polyclonal shGRHL2) T47DS cells treated with the progesterone analogue R5020 for either 4 or 24 hours.

first: Marleen

last: Aarts

first: Anthonius

last: van Boxtel

first: Renée


title: Single-cell dissection of the genotype-immunophenotype relationship in glioblastoma

status: Public on Apr 20 2025

city: NEW YORK

first: Alexander

last: Tsankov

state: New York

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

summary: We induced de novo brain tumor in immunocompetent genetically engineered mouse models EGFRvIII, Nf1 and PDGFB KO mice of both genders. We isolated brain tumor cells at the end stage in these mice and performed scRNA seq on these cells to compare their functional differences. scRNA demonstrated the distinct Tumor, Myeloid and Lymphoid cell population. PDGFB sample shows the higher proliferation and Wnt5a ligand expression and Nf1 showed the more mesenchymal type.

overall_design: Using immunocompetent de novo mouse models of GBM , we generated tumors in the right-frontal striatumto represent major subtypes of GBM including (Proneural-PDGFB driven), (mesenchymal-NF1 driven) and (classical-EGFRvIII driven). Each tumor subtype contains the relevant driver mutations found in their human counterparts. Brain tumor cells were isolated at the humane endpoint of these mice, and sc-RNA seq was conducted to compare their functional differences.

middle: M

first: Dolores

last: Hambardzumyan

first: Nishant

last: Soni


title: Gene Expression Profiling and Epigenetic Alterations in RAW 264.7 Cells Following Treatment with Lipopolysaccharide and Methylcobalamin (MCB) [RNA-seq]

first: Xuefei

last: Guo

overall_design:
To explore the transcriptomic and epigenetic mechanisms through which methylcobalamin (MCB) modulates the inflammatory response induced by lipopolysaccharide (LPS) in macrophages, we conducted RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and Cleavage Under Targets and Tagmentation (CUT & Tag) on the RAW 264.7 cell line.
Initially, we conducted a comprehensive gene expression profiling analysis using RNA-seq data from WT RAW 264.7 cells treated with DMSO, LPS, LPS-MCB, and MCB for 12 hours.
Comparative gene expression profiling analysis of RNA-seq data for DMSO, LPS, LPS-MCB and MCB group.


title: Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia [ChIP-Seq]

first: BiNGS

last: Core

overall_design: NUP98-NSD1/WT1ko leukemic cells derived from the xenograft model were in vitro cultured and expanded in X-VIVO 10 medium, supplemented with 1% BSA and FLT3L, G-CSF, SCF, TPO and IL-6. Chromatin immunoprecipitation (ChIP) was performed using RPDM16 and H3K27ac antibodies. Following immunoprecipitation, DNA fragments were purified and assessed for quality control. High-quality DNA was used to prepare sequencing libraries, which were subsequently subjected to next-generation sequencing.

first: Ke

last: Wang

first: Shayan

last: Saniei

first: Nikita

last: Poddar

first: Subrina

last: Autar

first: Saul

last: Carcamo

first: Meghana

last: Sreenath

first: Jack

last: Peplinski

first: Rhonda

last: Ries

first: Isabella

middle: G

last: Martinez

first: Clifford

last: Chao

first: Anna Huo-Chang

last: Mei

first: Noshin

last: Rahman

first: Levan

last: Mekerishvili

first: Miguel

last: Quijada-Álamo

first: Grace

last: Freed

first: Mimi

last: Zhang

first: Katherine

last: Lachman

first: Jing

first: Giang

last: Pham

first: Dan

last: Filipescu

first: Mirela

last: Berisa

first: Tommaso

last: Balestra

first: Julie

last: Haines

first: Angelo

last: D’Alessandro

first: Daniel

last: Puleston

first: Emily

last: Bernstein

first: Jerry

last: Chipuk

first: Mark

last: Wunderlich

first: Sarah

last: Tasian

first: Bridget

last: Marcellino

first: Ian

middle: A

last: Glass

first: Christopher

last: Sturgeon

last: Landau

first: Zhihong

last: Cheng

first: Eirini

last: Papapetrou

first: Franco

last: Izzo

first: Soheil

last: Meshinchi

last: Hasson

first: Elvin

last: Wagenblast


title: Time course analysis of gene expression in the liver of a 70% partial hepatectomy mouse model.

city: Fujisawa

first: Yoshinao

last: Oki

state: Kanagawa

address: 1866 Kameino

department: Department of Applied Biological Science

country: Japan

institute: Nihon University College of Bioresource Sciences

summary:
The liver has a remarkable regenerative capacity, allowing it to regain mass through compensatory hypertrophy of the remaining tissue after the surgical removal of 70% of its mass. During this regenerative process, lipid accumulation and proliferation of liver parenchymal cells have been observed; however, the full extent of the underlying regenerative mechanisms remains unclear.
Our study performed a comprehensive gene expression analysis using microarrays on liver samples collected at 0, 0.25, 0.5, 0.75, 1, 1.5, 2, 3, 4, 7, and 14 days following 70% partial hepatectomy in mice.

overall_design: Total RNA was extracted from livers collected from mice at 0, 0.25, 0.5, 0.75, 1, 1.5, 2, 3, 4, 7, and 14 days after 70% partial hepatectomy. Each sample was processed in triplicate as biological replicates. Gene expression profiles were analyzed using microarray experiments with the Affymetrix mouse genome array.

first: Koichiro

last: Kano


title: Response to anti-PD-1 + anti-LAG-3 checkpoint blockade is associated with T regulatory cell functional reprogramming and instability

status: Public on Apr 09 2025

city: Portland

first: venkatesh

last: rajamanickam

state: OR

address: 4805 NE Glisan St, Suite 2N35

institute: Earle A. Chiles Research Institute

summary: We previously identified and validated a pre-treatment peripheral blood biomarker, characterized by a high frequency of LAG-3+ lymphocytes, that predicts resistance in patients receiving anti-PD-1 immune checkpoint blockade. To better understand the mechanism of aPD-1 resistance and select rational therapies to overcome resistance, we identified murine tumor models with a high LAG-3+ lymphocyte frequency (LAG-3hi), which were resistant to aPD-1 therapy, and LAG-3lo murine tumor models that were aPD-1 sensitive, recapitulating the predictive biomarker we previously described in patients. As we hypothesized, LAG-3hi tumor-bearing mice were sensitive to aPD-1+aLAG-3 therapy and the benefit of combination therapy was CD8+ T cell-dependent. Unexpectedly, the benefit of combination therapy was enhanced in LAG-3hi (but not LAG-3lo) mice with depletion of CD4+ T cells. Furthermore, responses to aPD-1+aLAG-3 significantly correlated with T regulatory cell (Treg) phenotypic plasticity in LAG-3hi mice, suggesting a specific role for Tregs in the mechanism of response to this combination. Using Treg fate tracking Foxp3GFP-Cre-ERT2 x ROSAYFP reporter mice we demonstrate that expanded populations of unstable Tregs correlate with response to combination therapy in LAG-3hi mice. Complementing this preclinical data, an increased proportion of unstable Tregs also significantly correlated with higher response rate and improved survival after aPD-1+aLAG-3 therapy in a cohort of patients with metastatic melanoma (n=117). These data indicate that Treg phenotypic plasticity is a key mechanism in aPD-1+aLAG-3 responsiveness, which may represent both a novel biomarker to aid patient selection and a rationale therapeutic target to expand benefit for a subset of PD-1 refractory patients.

overall_design: Subcutaneous implant of CT26 cells, treatment with aPD-1/aLAG-3 (1mg/mL each, IP) on day 7, 10 and 13 post tumor implant. Tumors harvested on day 15 post-tumor implant, prepared for sorting, stained with live/dead, CD45, CD3, CD19, CD11b. Live, CD45+CD3+, CD19-CD11b- cells were sorted and collected for RNA isolation

first: William

last: Redmond


title: Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma [SLAM-seq]

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: The mechanisms underlying tumor cell plasticity driving drug resistance and disease progression remain poorly understood. In Ewing sarcoma (EwS), variations in EWS::FLI1 (EF) activity have been associated with epithelial-mesenchymal plasticity (EMP). Using degron technology, we titrated endogenous EF in an EwS cell line and linked phenotypic states to distinct EF thresholds. Strikingly, modest EF depletion promoted a pro-metastatic phenotype, which was diminished upon near-complete EF loss. Transcriptomic analysis revealed distinct gene clusters with heterogenous response patterns to varying EF dosage. Target genes most sensitive to subtle EF depletion contained GGAA microsatellites in EF-bound enhancers. Furthermore, we identified Krüppel-like zinc-finger transcription factors to be associated with EF-repressed EMP genes. EF rescue after partial depletion for a transient period identified persistently dysregulated genes associated with poor prognosis. This study underscores the therapeutic challenge of insufficient EF inhibition and provides a foundation for exploiting oncoprotein dynamics to uncover therapeutic vulnerabilities in fusion-driven cancers.

overall_design: A673 cells-derived EF-dTAG clone A2.2 was used for SLAM-seq. Various dTAGV-1 concentrations were used as treatment.

first: Veveeyan

last: Suresh

first: Christoph

last: Hafemeister

first: Andri

last: Konstantinou

last: Grissenberger

first: Caterina

last: Sturtzel

first: Florencia

last: Cidre-Aranaz

first: Andrea

last: Wenninger-Weinzierl

first: Martha

last: Zylka

first: Karla

last: Queiroz

first: Dorota

last: Kurek

first: Ana

last: Sastre

first: Javier

last: Alonso

first: Martin

last: Distel

first: Anna

last: Obenauf

first: Thomas

last: Grünewald

first: Heinrich

last: Kovar

first: Valerie

last: Fock


title: Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma [RNA-seq]

first: Florian

last: Halbritter

overall_design: In one part of the experiment, A673 cells in bulk, untagged A673 single cell clones, EF-dTAG clones A2.2 and B3.1 were sequenced without treatment (ssc_experiment). In the other parts, the two EF-dTAG clones were treated with various dTAGV-1 concentrations for various durations with either no ligand washout after treatment, or 7 day washout applied.

last: Suresh

first: Sarah


title: Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia [scATAC-seq]

first: BiNGS

last: Core

overall_design: Human CD34+ HSPCs were edited with control, NUP98-NSD1, NUP98-NSD1/WT1ko, and then xenotransplanted into NSG mice . Human CD45+ cells were flow cytometry sorted from primary or secondary xenografts and submitted to scATAC-seq.

first: Ke

last: Wang

first: Shayan

last: Saniei

first: Nikita

last: Poddar

first: Subrina

last: Autar

first: Saul

last: Carcamo

first: Meghana

last: Sreenath

first: Jack

last: Peplinski

first: Rhonda

last: Ries

first: Isabella

last: Martinez

first: Clifford

last: Chao

first: Anna Huo-Chang

last: Mei

first: Noshin

last: Rahman

first: Levan

last: Mekerishvili

first: Miguel

last: Quijada-Álamo

first: Grace

last: Freed

first: Mimi

last: Zhang

first: Katherine

last: Lachman

first: Jing

first: Giang

last: Pham

first: Dan

last: Filipescu

first: Mirela

last: Berisa

first: Tommaso

last: Balestra

first: Julie

last: Haines

first: Angelo

last: D’Alessandro

first: Daniel

last: Puleston

first: Emily

last: Bernstein

first: Jerry

last: Chipuk

first: Mark

last: Wunderlich

last: Tasian

first: Bridget

last: Marcellino

first: Ian

last: Glass

first: Christopher

last: Sturgeon

last: Landau

first: Zhihong

last: Cheng

first: Eirini

middle: P

last: Papapetrou

first: Franco

last: Izzo

first: Soheil

last: Meshinchi

last: Hasson

first: Elvin

last: Wagenblast


title: Improving genome-scale metabolic model simulations by measuring exchange fluxes during exponential growth phase

status: Public on Apr 07 2025

city: Nijmegen

first: Cyriel

last: Huijer

address: Houtlaan 4

department: Molecular Developmental Biology

institute: Radboud University Nijmegen

summary: With the state-of-the-art techniques currently available, measuring all metabolic reactions in a cell remains impossible. Therefore, systems biology approaches such as genome-scale metabolic models (GEMs) should be used to get a holistic view of metabolism. To reduce the solution space in GEM simulations, models are often constrained with exchange fluxes. However, previous literature that used exchange flux constraints violate the steady-state assumption necessary for GEMs, by inferring the flux from a single metabolomic sample. Here, we present the regression during exponential growth phase (REGP) method, which calculates exchange fluxes only during the log phase, thereby assuring measurements are conducted during metabolic steady-state. The REGP method was tested this method using MCF10A breast epithelial cells. We report that exchange fluxes are generally higher using the REGP method, highlighting the importance of measuring exchange fluxes during steady-state. Even changes in flux direction were observed, which indicates a metabolic shift between the lag phase and the exponential growth phase. While models constrained with previously reported exchange fluxes were infeasible or failed to predict the experimental growth rate, the REGP-constrained GEM accurately predicted the correct growth rate. Flux variability analysis revealed that even with constraints on the exchange of metabolites in central carbon metabolism and amino acid metabolism, these pathways still have intermediate variability in reaction flux. The results of this study suggest that future research should use the REGP method to determine exchange fluxes when these are used as constraints for GEMs, this will provide a better understanding of the complex mechanisms involved in metabolism.

overall_design: MCF10A breast epithelial cells were transduced with the empty vector (EV) using the Retro-X™ Tet-One™ Inducible Expression System (Takara, Cat# 634307) and selected with puromycin. No gene-of-interest was incorporated into the plasmid, resulting in no gene overexpression. Cells were harvested without doxycycline treatment.

first: Xiang

last: Jiao

first: Yun

last: Chen

first: Rosemary

last: Yu


title: Enhancing TREM2 expression activates microglia and modestly mitigates Tau pathology and neurodegeneration

status: Public on Apr 02 2025

city: Jacksonville

last: Zhao

address: 4500 San Pablo Rd S

department: Neuroscience

institute: Mayo Clinic

summary: TREM2, a microglia-specific receptor, is strongly associated with Alzheimer’s disease (AD) risk and modulates microglial responses critical to AD pathogenesis. However, its role in tauopathy and neurodegeneration remains unclear. Here, by using a PS19 tauopathy mouse model with inducible overexpression of human wild-type TREM2 (TREM2-WT) or the R47H variant (TREM2-R47H), we show that TREM2-WT overexpression modestly reduces soluble phosphorylated tau (p-tau) levels and mildly preserves neuronal integrity, whereas TREM2-R47H fails to impact p-tau levels or neurodegeneration. Single-cell RNA sequencing revealed that TREM2-WT enhances disease-associated microglia (DAM) signatures, while TREM2-R47H drives the MHCII+ microglial phenotypes. These findings demonstrate that TREM2-WT confers modest benefits in tauopathy models, whereas TREM2-R47H exhibits reduced functionality. Our study underscores the therapeutic potential of enhancing TREM2 activity to modulate microglial responses and mitigate neurodegeneration in AD.

overall_design: Single-cell RNA sequencing from the cortex of 24 mice. 12 were TREM2-WT and 12 were TEM2-R47H. Among the TREM2-WT group, 6 were control and 6 were tamoxifen-induced. Among the TREM2-R47H group, 6 were control and 6 were tamoxifen-induced.

first: Kai

first: Fuyao

last: Li

first: Shuwen

last: Zhang

first: Tadafumi

first: Yuka

last: Martens

last: zhao


title: Identification of HELLS as a Novel DNA G-quadruplex Helicase

status: Public on Apr 01 2025

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

summary: Guanine quadruplexes (G4s) are unique secondary structures of nucleic acids with functions in many biological processes. Understanding the biological functions of DNA G4s requires the knowledge about their recognitions by cellular proteins. Affinity pull-down coupled with LC-MS/MS analysis was previously employed to identify G4-binding proteins (G4BPs); the approach, however, has limitations in capturing weak and transient interactions, potentially leading to false-positives. Here, we developed a photoclick chemistry-based method, in combination with LC-MS/MS, for uncovering G4BPs. By incorporating a photoactivatable ortho-nitrobenzylamine (o-NBA) moiety into G4 DNA probes and employing UVA irradiation along with stringent washing, we identified 99 proteins enriched with G4 structures derived from the human telomere. We further validated the abilities of one of these proteins, HELLS, in binding and resolving G4 structures both in vitro and in chromatin. Together, we developed a photoclick chemistry-based approach for identifying novel G4BPs. Our work led to the discovery of new G4BPs, and uncovered novel functions of HELLS in recognizing and unwinding G4 structures in vitro and in cells.

overall_design: Genome-wide profiling analysis of G4 structures in shCtrl and shHELLS U2OS cells

first: Zi

last: Gao

first: Xiaomei

last: He


title: HyDrop v2: Scalable atlas construction for training sequence-to-function models

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

summary: Deciphering cis-regulatory logic underlying cell type identity is a fundamental question in biology. Single-cell chromatin accessibility (scATAC-seq) data has enabled training of sequence-to-function deep learning models allowing decoding of enhancer logic and design of synthetic enhancers. Training such models requires large amounts of high-quality training data across species, organs, development, aging, and disease. To facilitate the cost-effective generation of large scATAC-seq atlases for model training, we developed a new version of the open-source microfluidic system HyDrop with increased sensitivity and scale: HyDrop v2. We generated HyDrop-v2 atlases for the mouse cortex and Drosophila embryo development and compared them to atlases generated on commercial platforms. HyDrop-v2 data integrates seamlessly with commercially available chromatin accessibility methods (10x Genomics). Differentially accessible regions and motif enrichment across cell types are equivalent between HyDrop-v2 and 10x atlases. Sequence-to-function models trained on either atlas are comparable as well in terms of enhancer predictions, sequence explainability, and transcription factor footprinting. By offering accessible data generation, enhancer models trained on HyDrop-v2 and mixed atlases can contribute to unraveling cell-type specific regulatory elements in health and disease.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design:
singe-nucleus ATAC profiling of frozen mouse cortex tissue from adult BL/6Jax. The nuclei were dissociated and barcoded with different single-cell platforms and chemistries: 10x v1, 10x v2, HyDrop v1 and HyDrop v2.
single-nucleus ATAC profiling of whole Drosohila melaogaster embryo of developmental stage 17. The embryos were collected at age 16 to 20h old, dechorionated and the nuclei lysed to be processed with different single-cell plattforms: 10x v2 and HyDrop v2.
single-nucleus ATAC profiling of mixed samples (which ones) of cell lines as barnyard. The cells where lysed and barcoding was performed with single-cell platform HyDrop v2.

first: Hannah

last: Dickmänken

first: Marta

last: Wojno

first: Koen

last: Theunis

first: Valerie

last: Christiaens

first: Florian

middle: V

last: De Rop

first: Natalie

last: to be determined

first: Katina

middle: I

last: Spanier

first: Roel

last: Vandepoel

first: Suresh

last: Poovathingal

first: Stein

last: Aerts


title: lncRNA-seq profiling for primary mouse cortical neurons

status: Public on Mar 31 2025

city: Stanford

first: Mengting

last: Han

state: CA

address: 290 Jane Stanford Way  ChEM-H/Neuroscience Building W117

department: Bioengineering

institute: Stanford University

type: Non-coding RNA profiling by high throughput sequencing

summary: To understand the factors influencing gRNA performance for CRISPR-TO system, we performed lncRNA-seq profiling through Novogene Corporation Inc for total RNA extracted from 6 DIV primary mouse cortical neurons dissected from 3 litters of P0 pups of C57BL/6J mice.

overall_design: We performed lncRNA-seq profiling through Novogene Corporation Inc for total RNA extracted from 6 DIV primary mouse cortical neurons dissected from 3 litters of P0 pups of C57BL/6J mice.

first: Jon

last: Bezney

first: Lei

last: Qi


title: roboA and anosmin-1 restrict fate boundaries in planarian stem cells via foxA

city: ITHACA

first: Carolyn

last: Adler

state: NY

address: 930 Campus road

institute: Cornell University

summary: Stem cells integrate extracellular cues with downstream transcriptional responses to channel their differentiation, but the underlying mechanisms responsible remain unclear. Planarians possess distinct organs embedded in a vast pool of pluripotent stem cells that maintain tissue turnover and drive whole-body regeneration. This unique configuration provides an ideal model for exploring how pluripotent stem cells sense tissue boundaries, guiding appropriate differentiation. Here, we use the planarian pharynx to define the cell lineages that originate from stem cells expressing the pioneer transcription factor foxA. The anatomical restriction of pharynx-specific lineages is disrupted by knockdown of the Roundabout receptor roboA, leading to ectopic pharynx neurons (EPNs) emerging in the brain. An RNAi screen for genes that phenocopy roboA identifies the extracellular protein anosmin-1, a gene responsible for Kallmann syndrome, as a potential partner of roboA. Aberrant induction of EPNs in the brain requires foxA, while knockdown of foxA induces head-specific neurons in the pharynx, revealing a latent plasticity in stem cells to adopt alternative fates. Together, we propose that RoboA and Anos1 act as fate-reinforcing genes (FRGs) that suppress inappropriate cell fates, maintaining organ integrity and enabling stem cell plasticity during regeneration.

overall_design: 10X 3'single-cell RNA sequencing from control and foxA(RNAi) planarian cells.

first: Kuang-Tse

last: Wang

first: Yu-Chia

last: Chen

first: Fu-Yu

last: Tsai

first: Catherine

last: Judy


title: Rheumatoid Arthritis circulating CD14+ monocytes are epigenetically primed [ChIP-seq]

first: Kieran

last: Woolcock

summary: Peripheral blood samples were collected from healthy controls and rheumatoid arthritis patients (active disease: DAS28 > 2.7), subsequently CD14+ monocytes were isolated using a positive selection kit, ChIP-Seq was completed for H3K4me3 and H3K27me3.

overall_design: ChIP-Seq using the Illumina NextSeq 500 was performed on circulating CD14+ monocytes isolated from 15 healthy controls and 10 rheumatoid arthritis patients.

first: Nila

last: Servaas

first: Maarten

last: van der Kroef

first: John

last: Cole

first: Aridaman

last: Pandit

first: Carl

last: Goodyear


title: IbinA and IbinB regulate the Toll pathway-mediated immune response in Drosophila melanogaster

city: Tampere

first: Matthew

last: Maasdorp

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

summary: To combat infection, an immune system needs to be promptly activated but tightly controlled to avoid destructive effects on host tissues. IbinA and IbinB are related short peptides with robust expression upon microbial challenge in Drosophila melanogaster. Here, we show that Ibin genes are ubiquitously present in flies of the Drosophila subgenus Sophophora, where they replace a different but probably related gene, Mibin, which is found across a much wider range of cyclorrhaphan flies. Using synthetic peptides, we did not observe any direct bactericidal or bacteriostatic activity for either IbinA or IbinB in vitro. Using mutant Drosophila lines lacking the IbinA gene, IbinB gene, or both, we examined their roles in development and during microbial infections. IbinA is expressed in early pupae, and a lack of IbinA and IbinB leads to temperature-dependent formation of melanized tissue during metamorphosis, frequently around the trachea. IbinA and IbinB have distinct effects on susceptibility to microbial infection. For example, IbinB mutant flies, as well as flies lacking both IbinA and IbinB, had improved survival when challenged with Listeria monocytogenes, an intracellular pathogen, whereas a lack of IbinA alone had no effect. RNA sequencing of wildtype and mutant flies infected with L. monocytogenes showed enhanced Toll target gene expression in flies lacking IbinB, suggesting that IbinB acts as a negative regulator of the Toll pathway. In contrast, IbinA mutants had decreased Toll target gene expression in this context. Correspondingly, IbinB mutant flies had improved and IbinA compromised survival in septic fungal infection, where the Toll pathway has a major role. Our study provides insight into the roles of IbinA and IbinB in regulation of the immune response in Drosophila.

overall_design: 2-5 day old males were infected with Listeria monocytogenes by pricking the flies with a tungsten needle dipped in bacterial solution (OD600=0.07). Samples were collected 36 hours post-infection. As controls, uninfected flies of similar age were collected.

first: Susanna

last: Valanne

first: Laura

last: Vesala

first: Petra

last: Vornanen

first: Elina

last: Haukkavaara

first: Tea

last: Tuomela

first: Aino

last: Malin

first: Tiina

last: Salminen

first: Dan

last: Hultmark

first: Mika

last: Rämet


title: Fingerprint of circulating microRNAs identify acute ischemic stroke patients

status: Public on Mar 28 2025

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

summary:
Aim of the present study is to identify all circulating miRNAs that are modulated in patients with stroke, to select specific miRNAs to be used as disease biomarkers to improve both diagnosis and prognosis.
Background. Stroke is the second-most common cause of death worldwide. The major factor limiting prognosis in patients affected by acute stroke is the very limited therapeutic window, so that most patients are not able receive the most successful treatments because of delays in diagnosis and to differentiate between ischemic and hemorrhagic etiology. Circulating levels of selected microRNAs (miRNAs) were found to be modulated both in animal experimental models and in patients with stroke, opening up new avenues for the identification of more effective and specific biomarkers to identify and risk-stratify stroke patients.  Study aim. Aim of the present study is to identify all circulating miRNAs that are modulated in patients with stroke, to select specific miRNAs to be used as disease biomarkers to improve both diagnosis and prognosis.  Methods. RNA was extracted from plasma samples using a commercial RNA extraction kit and quality of extracted material was assessed using a fluorometric electrophoretic assay (Agilent 4200 TapeStation, Santa Clara, CA, USA). MiRNA profiling was performed using the Affymetrix platform using GeneChip 4.0 (Thermo Fischer Scientific, Waltham, MA, USA). RT-PCR was performed using the Taqman protocol. MiRNA were chosen among those with the most relevant modulation between the groups.  Results. Among the circulating miRNAs that were most down-regulated in stroke patients, we identified miR-3135b (20-fold, p<0.001), associated with vascular calcifications and heart failure; miR-1275 (18-fold, p=0.028), involved in cardiovascular atherosclerotic diseases and a sponge for circMAN2B2 in cancer; miR-4467 (13-fold, p=0.003), modulated in neurodegenerative diseases; and miR-7170 (7-fold, p<0.001).  Among the circulating miRNAs that were most up-regulated in stroke patients, we identified miR-18a (35-fold, p=0.004), associated with stroke in the Framingham Cohort; the platelet-enriched miR-22-5p (24-fold, p=0.004), that is modulated in Huntington Disease; miR-199a (11-fold, p=0.012), a marker of brain microvascular injury and of stroke severity in rats, and miR-106b (10-fold, p=0.009), a regulator of neural stem-cell proliferation/differentiation whose level are modulated in patients with neurodegenerative diseases.  Conclusions. Our results identified several circulating miRNAs that are down- of up-regulated in stroke patients. Among those with the most relevant differential expression, several miRNAs were identified that are known to play a role in the pathophysiology of neurovascular diseases, paving the way to a new class of smart pathophysiology-based biomarkers in stroke.

overall_design: We evaluated mirNA expression levels in platelet-depleted plasma samples from treatment group of  patients with the diagnosis of the acute IS based on clinical features according to the World Health Organisation definition and supported by brain imaging (CT or MRI).  Patients with IS were on ASA therapy 24 hours after onset of acute IS. The control group consisted of 35 age- and gender-matched patients on acetylsalicylic acid  (ASA) therapy without history of stroke and/or transient ischemic attack (TIA) with established stable coronary artery disease (CAD) and concomitant cardiovascular risk factors.

first: Ceren

last: Eyileten

first: Aleksandra

last: Gasecka

first: Maria

middle: T

last: Di Martino

first: Joanna

last: Mucha

first: Iwona

last: Kurkowska-Jastrzebska

first: Anna

last: Czlonkowska

first: Marek

last: Postula


title: Menin-MLL complex cooperates with NF-Y to promote HCC survival [CUT&RUN]

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

summary: Identification of new therapeutic targets in hepatocellular carcinoma (HCC) remains critical. Chromatin regulating complexes are frequently mutated or aberrantly expressed in HCC, suggesting dysregulation of chromatin environments is a key feature driving liver cancer. To investigate whether the altered chromatin state in HCC cells could be targeted, we designed and utilized an epigenome-focused CRISPR library that targets all genes involved in chromatin regulation. This focused approach allowed us to test multiple cell lines in both 2D and 3D growth conditions, which revealed striking differences in the essentiality of genes involved in ubiquitination and uncovered multiple chromatin regulators vital for HCC cell survival in 2D but whose loss promoted growth in 3D. We found the core subunits of the menin-MLL1 complex among the strongest essential genes for HCC survival in all screens and thoroughly characterized the mechanism through which menin-MLL1 complex promote HCC cell growth. Inhibition of the menin-MLL1 interaction led to global changes in occupancy of the complex and concomitant decreases in H3K4me3 and gene expression.  We observed that increased chromatin accessibility at sites not bound by menin-MLL1 was associated with the recruitment of the pioneer transcription factor complex NF-Y. A CRISPR/Cas9 screen of chromatin regulators in the presence of the menin-MLL1 inhibitor SNDX-5613 revealed  a synergistic effect on cell death when combining NF-YB loss and menin-MLL1 interaction inhibition. Together, these data show that menin-MLL1 is necessary for HCC cell survival and cooperates with NF-Y to regulate oncogenic gene transcription.

overall_design: CUT&RUN was performed for indicated antibodies following treatment of HLF cells with 5uM SNDX-5613 or DMSO for 24 hours

first: Margarita

last: Dzama


title: Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia [GoT-ChA]

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

summary: Pediatric cancers are increasingly linked to transformation events before birth, yet how ontogeny influences oncogenesis remains poorly understood. Using a humanized model of NUP98-NSD1-driven pediatric acute myeloid leukemia, particularly aggressive when accompanied by WT1 mutations, we investigated how the developmental stage of hematopoietic stem cells impacts leukemic transformation, disease progression and therapy response. Fetal-derived hematopoietic stem cells readily transform into leukemia, with WT1 mutations enhancing stemness and alter lineage hierarchy, while stem cells from later developmental stages progressively withstand transformation. Single-cell analyses revealed that fetal-origin versus postnatal leukemic stem cells exhibit greater quiescence and metabolic reliance on oxidative phosphorylation. Notably, therapeutic responses markedly differed between fetal- and postnatal-origin leukemias, even when driven by the same oncogenic mutations. In patients, onco-fetal transcriptional programs were associated with worse outcomes. We identified tailored combination therapies that specifically diminished aggressive fetal-origin leukemia, underscoring the need to consider ontogeny in treatment of pediatric cancers.

overall_design: Primary FL- and CB-derived CD34+ HSPCs were sorted and cultured in X-VIVO 10 medium supplied with 1% BSA and FLT3L, G-CSF, SCF, TPO and IL-6. After 48h cells were edited with control or NUP98-NSD1/WT1ko, and then cultured and expanded for 4 weeks, then cells were harvested, washed with PBS once and submited for GoT-Cha.

first: Ke

last: Wang

first: Shayan

last: Saniei

first: Nikita

last: Poddar

first: Subrina

last: Autar

first: Saul

last: Carcamo

first: Meghana

last: Sreenath

first: Jack

last: Peplinski

first: Rhonda

last: Ries

first: Isabella

last: Martinez

first: Clifford

last: Chao

first: Anna Huo-Chang

last: Mei

first: Noshin

last: Rahman

first: Levan

last: Mekerishvili

first: Miguel

last: Quijada-Álamo

first: Grace

last: Freed

first: Mimi

last: Zhang

first: Katherine

last: Lachman

first: Jing

first: Giang

last: Pham

last: Filipescu

first: Mirela

last: Berisa

first: Tommaso

last: Balestra

first: Julie

last: Haines

first: Angelo

last: D’Alessandro

first: Daniel

last: Puleston

first: Emily

last: Bernstein

first: Jerry

last: Chipuk

first: Mark

last: Wunderlich

first: Sarah

last: Tasian

first: Bridget

last: Marcellino

first: Ian

last: Glass

first: Christopher

last: Sturgeon

last: Landau

first: Zhihong

last: Cheng

first: Eirini

last: Papapetrou

first: Franco

last: Izzo

first: Soheil

last: Meshinchi

last: Hasson

first: Elvin

last: Wagenblast


title: Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancer

status: Public on Mar 22 2025

city: Bangalore

first: Radhakrishnan

last: Sabarinathan

state: Karnataka

address: GKVK, Kodigehalli

country: India

institute: National Centre for Biological Sciences- Tata Institute of Fundamental Research

summary: CCCTC-binding factor (CTCF) and cohesin play a significant role in the formation of chromatin loops and topologically associating domains (TADs), which influence gene expression and DNA replication. CTCF/cohesin-binding sites (CBSs) present at the loop anchors and TAD boundaries are frequently mutated in cancer; however, the molecular mechanisms underlying this remain unclear. Here, we investigate whether the binding of CTCF/cohesin on DNA imposes constraints on DNA replication, leading to replication stress and genomic instability. Our results reveal that CTCF and cohesin remain cobound to DNA during replication (S phase) in cancer cells (HeLa). Further, examination of replication stress through ChIP-seq of the DNA damage response/repair proteins (MRE11, STN1, FANCD2, γH2AX, RAD51 and ATM) showed high enrichment of these proteins at CBSs (as compared to their immediate flanking regions and control sites) and positively correlated with the binding strength of CTCF/cohesin at CBSs in the S phase. Moreover, analysis of somatic mutations from cancer genomes supports that the enrichment of mutations at CBSs is significantly higher in samples harbouring somatic copy number deletion in MRE11 and STN1 compared to wild-type samples. Together, these results demonstrate that the co-binding of CTCF/cohesin on the DNA during the S phase causes replication stress and DNA strand breaks, and this could lead to genome instability at CBSs observed in cancer.

overall_design: Chromatin Immunoprecipitation (ChIP-seq) for the ATM/ CTCF/ FANCD2/ gH2AX/ H2AX/ MRE11/ RAD21/ RAD51 were performed in Mid S synchronized HeLa cells (2mM Thymidine treatment for 16h followed by 4 h release) with or without DNA damage using 2mM HU (for 3h) or 25uM Etoposide (for 3h). Prolonged (ie, 16h) HU (2mM) treatment was performed in asynchronous HeLa cells

first: Elangoli Ebrahimkutty

last: Faseela


title: Menin-MLL complex cooperates with NF-Y to promote HCC survival [ATAC-seq]

first: Jesse

last: Raab

summary: Identification of new therapeutic targets in liver cancer remains critical. Chromatin regulating complexes are frequently mutated in liver cancer suggesting dysregulation of chromatin environments is a key feature driving liver cancer. We applied a focused CRISPR library targeting all genes involved in chromatin regulation to determine if the altered chromatin state of hepatocellular carcinoma cells could be targeted. The focused approach allowed us to test multiple cell lines in both 2D and 3D growth conditions which revealed striking differences in the essentiality of genes involved in ubiquitination and uncovered multiple chromatin regulators that are essential in 2D but whose loss promotes growth in 3D. We found the menin-MLL complex as among the strongest essential genes in all screens and deeply characterized the mechanism menin-MLL uses to promote hepatocellular carcinoma growth. Inhibition of menin-MLL led to global changes in occupancy of the complex and concomitant decreases in H3K4me3 and gene expression. A surprising increase in chromatin accessibility at sites not bound by menin-MLL was associated with recruitment of the pioneer transcription factor complex NF-Y. A screen of chromatin regulators in the presence of the menin-MLL inhibitor SNDX-5613 revealed a synergy between NF-YB loss and menin-MLL inhibition. Together these data show that menin-MLL is necessary for cell survival in HCC and cooperates with NF-Y to regulate transcription.

overall_design: ATAC-seq for HLF human liver cancer cells treated for 24 hours with DMSO or 5uM SNDX-5613.

first: Margarita

last: Dzama


title: Menin-MLL complex cooperates with NF-Y to promote HCC survival [RNA-seq]

overall_design: RNA-seq on HLF and PLC/PRF/5 liver cancer cell lines following treatment with 5uM menin inhibitor (SNDX-5613) or DMSO or with menin knockout


title: Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma [CUT&RUN]

first: Florian

last: Halbritter

overall_design: A673 cells and EF-dTAG clone A2.2 were used for CUT&RUN profiling with various antibodies (FLI1, H3K27ac, H3K27me3, H3K4me3, IgG). In one experiment the EF-dTAG clone was treated with various dTAGV-1 concentrations.

first: Veveeyan

last: Suresh

first: Christoph

last: Hafemeister

first: Andri

last: Konstantinou

last: Grissenberger

first: Caterina

last: Sturtzel

first: Florencia

last: Cidre-Aranaz

first: Andrea

last: Wenninger-Weinzierl

first: Martha

last: Zylka

first: Karla

last: Queiroz

first: Dorota

last: Kurek

first: Ana

last: Sastre

first: Javier

last: Alonso

first: Martin

last: Distel

first: Anna

last: Obenauf

first: Thomas

last: Grünewald

first: Heinrich

last: Kovar

first: Valerie

last: Fock


title: Menin-MLL complex cooperates with NF-Y to promote HCC survival [CRISPR]

first: Jesse

last: Raab

overall_design: HLF or PLC/PRF/5 cells were infected with lentiviral guide RNA library targeting chromatin regulators (737 genes). gDNA from cells was harvested at an initial time point and again after 28 days grown in 2D or 3D culture conditions. For some samples, either DMSO or SNDX-5613 was added to growth. gRNAs were then sequenced and compared either to the initial time point or to between two endpoint conditions (2D vs 3D ; DMSO vs SNDX-5613)

first: Margarita

last: Dzama