title: RNA Pol I activity is required for meiotic chromatin organization and the H3K4me3 gradient essential for oogenesis, independent of ribosome synthesis [ATAC-Seq]

city: Austin

first: Elif

last: Sarinay Cenik

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Oogenesis requires extensive and dynamic chromatin remodeling that primes gene promoters for later transcriptional activation during embryonic development. Here, we uncover a pivotal, non-canonical role for RNA Polymerase I (Pol I) in driving these chromatin state transitions during Caenorhabditis elegans oogenesis. Using the auxin-inducible degron system to selectively deplete either Pol I catalytic subunits or ribosome assembly factors, we disentangle the consequences of impaired nucleolar integrity from reductions in ribosome biogenesis. Strikingly, although disrupting ribosome assembly caused minimal effects on oocyte production, loss of Pol I activity led to widespread changes in chromatin accessibility, a dampening of the distal-proximal H3K4me3 gradient required for oogenesis, reduced synapsis, and elevated ATM/ATR phosphorylation, resulting in fewer but significantly larger oocytes. Despite their promoters becoming more accessible, oogenesis genes did not show large changes in steady-state mRNA, consistent with transcriptional repression prior to fertilization. Instead, Pol I depletion prematurely remodeled oogenic chromatin, through a misdirection of H3K4me3 deposition towards promoters normally primed for zygotic genome activation. These findings reveal an epigenetic gating function for nucleolar integrity in oocyte maturation: Pol I preserves three-dimensional chromatin organization and maintains proper spatiotemporal regulation of histone modifications, independent of ribosome production. Given the evolutionary conservation of nucleolar dynamics and histone modifications during gametogenesis, our work suggests that nucleolar stress, whether from environmental factors, aging, or genetic disorders, could broadly compromise fertility by disrupting oogenic chromatin priming.

overall_design: Chromatin accessibility data from dissected gonads of auxin-inducible degron strains used to deplete an RNA Pol I subunit (RPOA-2) or ribosome assembly chaperone (GRWD-1). L4 stage animals were treated with 1 mM auxin (IAA) or EtOH control for 18 hours before germline dissection and ATAC-seq. Each replicate includes 20 gonads.

first: Raquel

last: Mejia-Trujillo

first: Qiuxia

last: Zhao

first: Ayesha

last: Rahman

first: Trevor

middle: F

last: Freeman


title: Identification of targetable epigenetic vulnerabilities for uveal melanoma

status: Public on Jun 25 2025

city: Miami

first: Stefan

last: Kurtenbach

state: FL

address: 1501 NW 10th Ave

department: Ophthalmology

country: USA

institute: University of Miami

type: Expression profiling by high throughput sequencing

summary: Uveal melanoma (UM) is the most common adult primary intraocular malignancy, with a strong predilection for hepatic metastasis, occurring in approximately 50% of cases. Metastatic UM remains highly resistant to therapy and is almost invariably fatal. The strongest genetic driver of UM metastasis is loss of function of the tumor suppressor BRCA-associated protein 1 (BAP1), which leads to widespread epigenetic dysregulation. To identify novel therapeutic strategies, we investigated whether targeting the epigenome could reveal new vulnerabilities in UM. We performed high-throughput compound screening using a curated epigenetic inhibitor library and identified BET (bromodomain and extra-terminal domain) inhibition as a particularly promising approach. While previous clinical trials with BET inhibitors for UM treatment have failed clinically, we found substantial heterogeneity in the efficacy of different BET inhibitors in UM. Notably, the BET inhibitor mivebresib (ABBV-075) significantly improved survival rates by 50% in a metastatic UM xenograft mouse model and prevented detectable metastases in the bones, spinal cord, and brain. Transcriptomic analysis revealed a strong overlap between BET inhibition and histone deacetylase (HDAC) inhibition-- an approach currently under clinical evaluation for UM treatment. BET and HDAC inhibitors reversed gene expression signatures associated with high metastatic risk and induced a neuron-like phenotype in UM cells. These findings establish BET inhibition as a potent and previously underappreciated vulnerability for metastatic UM.

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 MP38 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: Extracellular Vesicles Derived from Mesenchymal Stromal Cells Reduce Pseudomonas aeruginosa Burden and the Inflammatory Response in Cystic Fibrosis Mouse Lung

status: Public on Jun 30 2025

city: Hanover

first: Sharanya

last: Sarkar

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

type: Non-coding RNA profiling by high throughput sequencing

summary: Chronic lung infections and presistent inflammation are a leading cause of morbidity and mortality in people with cystic fibrosis and therefore there is a need for therapies that can simultaneously eliminate infection and the hyperinflammatory lung environment in CF. Mesenchymal stromal cell-derived extracellular vesicles (MSC EVs) represent a promising solution, offering potent anti-inflammatory, immunomodulatory, and antimicrobial properties while being safe and non-toxic. This study demonstrates the efficacy of MSC EVs in a CF mouse model of acute Pseudomonas aeruginosa lung infection. MSC EVs reduced Pseudomonas burden, immune cell infiltration, and pro-inflammatory cytokine levels in the lungs.

overall_design: MSCs were transfected with either 1) a mimic miRNA (negative control) with no known targets in P. aeruginosa or mice or 2) miRNA let-7b-5p. EVs were isolated from the MSCs and inoculated into the lungs of CF mice with an acute P. aeruginosa infection. These smRNA-seq data are from the MSC EVs and their parent MSCs.

first: Lily

last: Taub

first: Bruce

middle: A

last: Stanton

first: Barnaby

last: Roxanna


title: PAF1 N-terminal extension-generated PAF1c-SKIP-CDKB module regulates plant-specific cell cycle in the plant kingdom

city: Beijing

first: Yan

last: Li

address: Haidian

country: China

institute: Capital Normal University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Through systematic biochemical analyses, we identified a novel protein-protein interaction between PAF1 and SKIP in Chlamydomonas reinhardtii.  To investigate the functional significance of this interaction, we generated targeted mutants using CRISPR-Cas9 genome editing technology.  Phenotypic characterization revealed that both PAF1 and SKIP mutants exhibit coordinated regulation of the cell cycle progression.  To elucidate the molecular mechanism underlying PAF1-SKIP mediated cell cycle regulation, we employed an integrated multi-omics approach.  RNA sequencing (RNA-seq) analysis was performed to identify differentially expressed genes, while chromatin immunoprecipitation sequencing (ChIP-seq) was utilized to map the genomic loci directly bound by the PAF1-SKIP protein complex.  This comprehensive strategy enabled us to delineate the transcriptional network governed by the PAF1-SKIP regulatory module.

overall_design:
The Chip experiment was conducted using three materials: CrWT, CrPAF1-HA, and CrSKIP-HA. Chlamydomonas cells were cultured and harvested, then cross-linked with 1% formaldehyde. After terminating the cross-linking with Gly, the cells were sonicated in lysis buffer, followed by immunoprecipitation (IP) using HA antibody. The resulting products were subjected to DNA recovery and subsequent Chip-seq sequencing analysis.

***Please note that processed data files have been updated on Mar 16, 2026***

first: Renshen

last: Yuan


title: Mechanobiological proximal tubular defects in ARC syndrome: A VPS33B CRISPR knockout study

status: Public on Jun 23 2025

city: London

first: Maria

last: Caluianu

address: Gower Street

country: United Kingdom

institute: University College London

summary: ARC syndrome (arthrogryposis-renal dysfunction-cholestasis) is a rare autosomal recessive multisystem disorder affecting the kidneys. The disease is caused by mutations in either VPS33B or VIPAS39. ARC syndrome is currently incurable, with patients rarely surviving beyond their first year of life. The renal component of this disorder is characterised by proximal tubular dysfunction. Here, a proximal tubular cell line, RPTEC-TERT1, was CRISPR-edited to knock out (KO) VPS33B expression. Characterisation of VPS33B-KO cells was performed using brightfield imaging, immunostaining, RNA sequencing, and cell detachment assays. The VPS33B-KO RPTEC-TERT1 cells demonstrated a 'peeling' phenotype and altered cell adhesion. This, along with altered transcription of genes associated with cell adhesion, suggests that VPS33B KO results in cell-matrix attachment defects. These findings provide the first insights into the cause of proximal tubular dysfunction in ARC syndrome.

overall_design: RNA-seq profiling of control RPTEC-TERT1 (with wild-type VPS33B) cells and two VPS33B-knockout RPTEC-TERT1 clones (KO1 and KO2)

first: Kimberley

last: Owen


title: RNA Pol I activity is required for meiotic chromatin organization and the H3K4me3 gradient essential for oogenesis, independent of ribosome synthesis [RNA-seq]

status: Public on Jun 24 2025

state: TX

overall_design:
Gene expression data from dissected gonads of auxin-inducible degron strains used to deplete an RNA Pol I subunit (RPOA-2) or ribosome assembly chaperone (GRWD-1). L4 stage animals were treated with 1 mM auxin (IAA) or EtOH control for 18 hours before germline dissection and RNA-seq. Each replicate includes 20 gonads.
Gene expression data from dissected gonads of auxin-inducible degron strains used to deplete a ribosome assembly chaperone (TSR-2). L4 stage animals were treated with 1 mM auxin (IAA) or EtOH control for 18 hours before germline dissection and RNA-seq. Each replicate includes 20 gonads.


title: Elementary 3D organization of active and silenced E. coli genome (MicroC)

city: New York

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.

overall_design: Using the Micro-C technique, we generated contact maps of the E. coli genome at a resolution up to 10 bp. We analyzed wild-type E. coli cells, cells subjected to heat shock, cells treated with different antibiotics and drugs (rifampicin, bleomycin, novobiocin, ciprofloxacin, netropsin), as well as different knockout strains (deltaHNS, deltaStpA, deltaHNSdeltaStpA, deltaFis, deltaMukBEF). We performed gene expression profiling analysis using data obtained from Red-C and RNA-seq. We also performed Hi-C analysis of wild-type E.coli cells.

first: Alexey

last: Gavrilov


title: BMP, MEK and WNT modulation with NGN2 expression for rapid generation of hiPSC-derived neurons amenable to regional patterning [bulk RNA-seq]

status: Public on Jun 19 2025

city: Ludwigshafen

first: Peter

last: Reinhardt

address: Knollstrasse

country: Germany

institute: AbbVie Deutschland GmbH & Co. KG

summary: hiPSC are a promising tool for studying neurological diseases and developing therapies for neurodegenerative diseases. Differentiation of hiPSC into neurons can be achieved by dual SMAD inhibition (dSMADi) or induced NGN2 overexpression (“iNGN2”). Starting directly from hiPSC, iNGN2 shortens the time to a neuronal stage but leads to neurons partially resembling peripheral or posterior fates while dSMADi more faithfully recapitulates forebrain development. To modify the iNGN2 paradigm, we applied an accelerated induction paradigm that is dependent on inhibition of BMP, MEK and WNT pathways (“BMWi”), to commit hiPSC into a rostral neuroectoderm fate before iNGN2. The resulting neurons showed strong expression of telencephalic and cortical markers, with decreased levels of peripheral and posterior marker genes compared to iNGN2 alone. The resulting cortical neurons are suitable for a tau aggregation assay. Furthermore, we could demonstrate that during BMWi treatment, the cells are amenable to additional regional patterning cues. This allowed the generation of neurons from different regions of the CNS and PNS, which will significantly facilitate in vitro modeling of a range of neurodevelopmental and neurodegenerative disorders.

overall_design: We performed a comparison of short vs. long differentiation (D14, 21 and 28) of BMWi and dSMAD differentiated neurons in different cell lines (hiPSC_1, hiPSC_3, hiPSC_5 and hiPSC_7). Per experiment 3-4 replicates were generated.

first: Carina

last: Habich

first: Astrid

last: Wachter

first: Juergen

last: Korffman

first: Timo

last: Lange


title: Single-nuclei RNA-seq of neural organoids generated from wildtype and FNDC4 KO iPSCs

status: Public on Jun 16 2025

city: Rochester

first: Duan

last: Liu

email: liud25@gmail.com, liu.duan@mayo.edu

state: MN

address: 200 1st ST SW

department: MPET

institute: Mayo Clinic

summary: Large-cohort genome-wide association studies (GWAS) for alcohol use disorder (AUD) risk and drug treatment outcomes have identified significant genetic loci that are splicing quantitative trait loci (sQTLs) for the FNDC4 gene in multiple human brain regions. However, in spite of the fact that FNDC4 is highly expressed in the brain, its function and how it might contribute to AUD pathophysiology remain unknown. In the precent study, we characterized FNDC4 function using CRISPR/cas9 gene editing, the creation of human induced pluripotent stem cell (iPSC)-derived neural organoids and with single-nucleus RNA sequencing (snRNA-seq).

overall_design: Specifically, we generated FNDC4 homozygous knock-out (KO) iPSC lines and differentiated two single-colony KO iPSCs, together with wildtype (WT) iPSCs, to generate forebrain organoids. Those neural organoids were harvested at three time points of differentiation (45, 90, and 150 days) for snRNA-seq using a “split-pool” combinatorial barcoding technology (Parse Bio).

first: Xiujuan

last: Zhu

first: August

last: John

first: Ching Man

last: Wai


title: BMP, MEK and WNT modulation with NGN2 expression for rapid neuron differentiation from hiPSC amenable to regional patterning

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

overall_design: Refer to individual Series


title: BMP, MEK and WNT modulation with NGN2 expression for rapid neuron differentiation from hiPSC amenable to regional patterning [BMWi]

summary: hiPSCs aid in studying neurological diseases and developing therapies. Interventions, such as dual SMAD inhibition or NGN2 overexpression (“iNGN2”), can direct hiPSCs towards neurons. Starting directly from hiPSCs, iNGN2 shortens the time to a neuronal stage but leads to neurons resembling peripheral or posterior fates. We applied an accelerated induction paradigm that is only dependent on inhibition of BMP, MEK and WNT pathways (“BMWi”), to commit iPSCs before to rostral neuroectoderm. The resulting neurons showed strong expression of telencephalic, cortical markers, with decreased levels of peripheral and posterior marker genes compared to iNGN2 alone. The resulting cortical neurons are suitable for a tau aggregation assay. Furthermore, we could demonstrate that during BMWi treatment, the cells are amenable to regional patterning clues. This allowed the generation of neurons from different regions of the CNS and PNS, which will significantly improve existing in vitro models for neurodegenerative disorders.

overall_design: We performed a comparison of iPSCs, iNGN2 and BMWi differentiated neurons at different days of differentiation. Neurons were plated in either NMM+ or NMM- (Neurobasal and B27 with or without retinoids). BMWi cells were replated in NMM- and the medium was changed after 7 days.

first: Christopher

last: Sliwinski


title: Elementary 3D organization of active and silenced E. coli genome


title: Nerve-associated macrophages control adipose homeostasis across lifespan and restrain age-related inflammation

city: New Haven

first: Vishwa

middle: Deep

last: Dixit

state: CT

address: 310 Cedar Street, BML330

department: Pathology

institute: Yale School of Medicine

summary: Age-related inflammation or ‘inflammaging’ is a key mechanism that increases disease burden and may control lifespan. How adipose tissue macrophages (ATMs) control inflammaging is not well understood in part because the molecular identities of niche-specific ATMs are incompletely known. Using intravascular labeling to exclude circulating myeloid cells and subsequent single-cell sequencing with orthogonal validation, we define the diversity and alterations in niche resident ATMs through lifespan. Aging led to depletion of vessel-associated macrophages (VAMs), expansion of lipid-associated macrophages (LAMs), and emergence of a unique subset of CD38+ age-associated macrophages (AAMs) in visceral white adipose tissue (VAT). Interestingly, CD169+CD11c- ATMs are enriched in a subpopulation of nerve-associated macrophages (NAMs) that declines with age. Depletion of CD169+ NAMs in aged mice increases inflammaging and impairs lipolysis suggesting that they are necessary for preventing catecholamine resistance in VAT. These findings reveal specialized ATMs control adipose homeostasis and link inflammation to tissue dysfunction during aging.

overall_design: Stromal vascular fraction (SVF) cells were isolated via enzymatic digestion of visceral white adipose tissue (VAT) from young (2-month) and aged (21-month) WT C57B/6J male and female mice. Adipose tissue macrophages (ATMs) residing in the tissue parenchyma (CD45+CD45.2iv-CD3-CD19-SiglecF-F4/80+CD11b+) were isolated by fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Elsie

last: Gonzalez-Hurtado

first: Claire

last: Leveau

middle: D


title: SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [RNA-Seq]

status: Public on Jun 10 2025

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

summary: Synovial sarcoma (SS) is a rare malignancy, involves a t(X;18) chromosomal translocation that creates a fusion gene SS18-SSX. SS18 is a chromatin remodeling BAF-complexes component, which incorporated in CBAF and GBAF (non-canonical ncBAF). Our previous studies determined that incorporation of the fusion oncoprotein caused degradation of CBAF complexes, emphasizing a critical oncogenic function of GBAF and PBAF in synovial sarcomagenesis.  To determine the SyS dependencies on different subtypes of BAF complexes during tumor development in vivo, we used our SyS mouse model combined with genetic disruption of specific BAF complexes components ARID1A/B or PBRM1. In this study, our fundings suggest that depletion of ARID1A and ARID1B sped tumorigenesis, without significant change in the histomorphology of the developing tumors. Loss of PBRM1 also led to faster tumor growing, but Pbrm1-silenced tumors lacked the full array of SyS histomorphologies observed in wildtype tumors. Overall, Arid1a or Arid1b disruption rendered tumor transcriptomes that clustered within the hSS2 tumor transcriptomes, unlike Pbrm1 disrupted tumors.

overall_design: To explore dependencies of different subtypes of BAF complexes on the synovial sarcomagenesis  in vivo, we used our SyS mouse model cross with conditional knockout mouse targeting either ARID1A, ARID1B or PBRM1. We investigated the tumor development upon disruption of CBAF or PBAF.

first: Jinxiu

first: Kevin

last: Jones


title: SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [ChIP-Seq, Hi-ChIP]

summary: In order to evaluate SS18::SSX distribution across chromatin in synovial sarcoma, we performed ChIP-seq from mouse SyS tumors expressing the human SS18::SSX2 using an antibody specific for the fusion oncoprotein SS18::SS. ChIP-seq was also employed to assess SyS genome profiles of specific chromatin histone marks (H2AK119ub, H3K4me1, H3K4me3, H3K27ac and H3K27me3), and chromatin conformation by HiChIP was evaluated using an antibody against H3K27ac to identify enhancer loops for the purpose of assigning distal regulatory elements to specific genes. Furthermore, we also characterize the distribution of each BAF family subtypes with ChIP-seq ( ARID1A (cBAF), DPF2 (cBAF), PBRM1 (PBAF) and BRD9 (GBAF/non-canonical BAF)). In this study, our fundings suggest that SS18::SSX distributes to proximal and distal regulatory elements bearing ubiquitylated histone 2A and GBAF distributes with the fusion to broad proximal and distal regions; CBAF and PBAF distribute narrowly to active transcriptional start sites.

overall_design: Chromatin immunoprecipitation DNA-sequecning of histone modifications (H2AK119ub, H3K4me1, H3K4me3, H3K27ac and H3K27me3), specific BAF complexes componenants (ARID1A, DPF2, PBRM1, BRD9) and SS18:SSX in mouse SyS tumors expressing the human SS18::SSX2. Chromatin conformation by HiChIP was evaluated using an antibody against H3K27ac to identify enhancer loops for the purpose of assigning distal regulatory elements to specific genes.


title: BMP, MEK and WNT modulation with NGN2 expression for rapid neuron differentiation from hiPSC amenable to regional patterning [BMWi_freeze]

overall_design: We performed a comparison of fresh versus frozen "BMWi" protocol derived neural progenitor cells.


title: RNA sequencing data of mouse caecum tissue following different dietary treatments

status: Public on Jun 06 2025

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: Mice were fed either a semi-synthetic diet ('SSD'), or the same diet supplemented with the fiber inulin ('inulin'). Mice were then infected with Trichuris muris ('Tm').

overall_design: Mice recevied the diets 14 days prior to infection. After infection mice either continued on their pre-assigned diet, or were swtiched to an alternative diet. Mice were killed at either 7 or 11 days post-infection

middle: R


title: Unlocking the aggressive potential of ZNF217 Exon-4 Skipping isoform in breast cancer and its contribution to bone metastasis

status: Public on Jun 15 2025

city: TREVOUX

first: joel

last: lachuer

state: Veuillez sélectionner une région, une état ou une province.

address: 11 allée des acacias

country: France

institute: University Lyon1

summary: Breast cancer remains a major health concern worldwide, with bone metastases presenting a significant threat to patient outcomes. Generation of aberrant splicing variants with oncogenic potential are involved in the development and progression of tumors. this study identifies ZNF217-ΔE4 as a new oncogenic splice variant in breast cancer mediating cell aggressiveness and bone marrow homing, as well as a new indicator of the development of bone metastases. ZNF217-ΔE4 thus represents a novel candidate therapeutic target and a new valuable biomarker in the management of breast cancers, particularly in patients with a higher risk of developing bone metastases

overall_design:
To investigate the role of ZNF217 variant splicing as (ZNF217-deltaE4 variant), HEK293 cells line have been transfected ina  stable manner with vector containing 1) WT ZNF217 gene (called WT group) 2) Vector alone (called CMV group) 3) DeltaE4 ZNF217 variant (called  DE group) 4) G1013 ZNF217 variant (called GLY group)
Transcriptomic analysis by RNA seq  has been realised on 12 samples (3 replicats for each group) (WT1, WT2, WT3); (CMV1,CMV2, CMV3); (DE1, DE2, DE3); (GLY1, GLY2, GLY3)
RNAseq has been performed using DNBseq-G400 from MGI. Libraires have been constructed using the MGIEasy RNA Directional Library Prep Set (MGI). Single read of 100 bases has been realised.
Diffrential expression between groups have been realised using Partek Software with CPM normalisation and DEseq pipeline. Functional analysis was performed with Panther software.

first: Pia

last: Fahmé

first: Lamia

last: Bouazza

first: Martine

last: Croset

first: Farah

last: Ramadan

first: Séverine

last: Croze

first: Mariapia

last: Riso

first: Justin

last: Ferraro

first: Philippe

last: Clézardin

first: Olivier

last: Peyruchaud

first: Joël

last: Lachuer

first: Balázs

last: Győrffy

first: Robert

last: Coleman

first: Pascale

last: Cohen


title: Huangqin Decoction Exerts Antifungal Effects by Interfering with Energy Metabolism of Trichophyton rubrum with Glyoxylate Cycle as a Potential Target

status: Public on Jun 28 2025

city: Nanchang

first: Suqing

last: Yang

address: Nanchang

institute: Jiangxi Provincial People's Hospital (the First Affiliated Hospital of Nanchang Medical College)

summary:
Background: The dermatophyte Trichophyton rubrum (T. rubrum) is a highly specialized filamentous fungus that infects keratinized tissues and is the most common pathogen isolated from human dermatophytosis. The clinical treatment of the infections is challenging due to the prolonged treatment duration, limited efficacy, antifungal resistance and adverse effects of available drugs. Huangqin decoction (HQD) is a classical traditional Chinese medicine (TCM) formula, whose inhibitory efficiency against T. rubrum was disclosed in our previous study. However, the responsible mechanisms are not well understood.
Aim: This study aimed to elucidate the mode of action of Huangqin decoction (HQD) against T. rubrum as a whole by using transcriptome sequencing combined with verification of qRT-PCR and enzymatic activity assays.
Methods: By treating T. rubrum with HQD at minimum inhibitory concentration (MIC), the differentially expressed genes (DEGs) of T. rubrum in response to HQD based on transcriptome profiles were recognized. Gene function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed functions and signaling pathways modulated by the DEGs. The transcriptome results were validated by quantitative real-time PCR (qRT-PCR). The potential targets were further explored using enzymatic activity assays.
Results: At MIC, a total of 338 differentially expressed genes (DEGs) were detected in T. rubrum after HQD exposure compared with the control group (q-value < 0.05), of which 199 genes were significantly up-regulated and 139 genes were down-regulated. Gene function analysis indicated that COG functions of DEGs mainly covered “carbohydrate transport and metabolism” and “energy production and conversion”. The most frequently found GO terms were “metabolic process” and “catalytic activity”. KEGG enrichment analysis revealed that DEGs were predominately enriched in 6 pathways of “valine, leucine and isoleucine degradation”, “indole alkaloid biosynthesis”, “ABC transporters”, “synthesis and degradation of ketone bodies”, “starch and sucrose metabolism”, and “glyoxylate and dicarboxylate metabolism” (q-value < 0.05). Three KEGG pathways were closely related to energy metabolism, which was consistent with the COG and GO results. A subset of eight DEGs by the involvement of the biosynthesis and degradation of cell walls and energy metabolism including amino acid metabolism and the glyoxylate cycle were further confirmed by qRT-PCR and the results verified the transcriptome data. Enzymatic activity assays showed that compared to the control group, activities of citrate synthase (CS), aconitate hydratase (ACO) and isocitrate lyase (ICL) in the glyoxylate cycle were affected by HQD.
Conclusion: The overall evidence suggested that the interference of energy metabolism might contribute to the mode of action of HQD against dermatophyte pathogen T. rubrum, and the glyoxylate cycle may be the potential antifungal target of HQD against the fungi. Our study provides a theoretical basis for the mechanisms of HQD upon T. rubrum infections and offers an important insight regarding the glyoxylate cycle especially enzyme isocitrate lyase as indispensable targets of the herbal formulations.

overall_design: RNA-seq was performed in Trichophyton rubrum  (STRB012) treated with or without HQD to detect the differential genes that HQD may affect.

first: Su-Qing

first: Yi-Can

last: He

first: You-Jin

last: Ge

first: Bao-De

last: Shen

first: Chen-Ying


title: The 5’-end codon bias minimizes fitness costs to facilitate the persistent dissemination of mcr-3 and investigation of novel MCR inhibitors

status: Public on Jun 29 2025

city: Nagoya

first: Yihao

last: Zhang

state: Aichi

address: 65 Tsurumaichō, Showa Ward

department: Graduate School of Medicine

country: Japan

institute: Nagoya University

summary: Background: The rapid evolution and dissemination of mobilized colistin resistance gene (mcr) family has revealed as a severe threat to the global public health. Nevertheless, dramatic reduction in the prevalence of mcr-1, the major member of mcr family, was observed after the withdrawal of colistin in animal fodder in China since 2017, demonstrating that colistin acts as a selective stress to promote the dissemination of mcr-1. As the second largest lineage, mcr-3 was firstly discovered in 2017 and has been identified from numerous sources. However, whether the spreading of mcr-3 is driven by colistin remains unknown.  Methods: To this end, we investigated the global prevalence of mcr-3 from 2005 to 2022 by an up-to-date systematic review, along with a nation-wide epidemiological study to establish the change of mcr-3 prevalence in China before and after 2017. To investigate the fitness cost imposed by MCR-3 upon bacterial host, in vitro and in vivo competitive assays were employed, along with morphological study and fluorescent observation. Moreover, by replacing non-optimal codons with optimal codons, synonymous mutations were introduced into the 5’-coding region of mcr-3 to study mechanisms accounting for the distinct fitness cost conferred by MCR-1 and MCR-3. Furthermore, by combining AlphaFold and molecular dynamics (MD) simulation, we provided a complete characterization on the putative lipid A binding pocket localized at the linker domain of MCR-3. Crucially, inhibitors targeting at the putative binding pocket of MCR-1 or MCR-3 were identified from small molecules library using the pipeline of virtual screening.  Findings: The global prevalence of mcr-3 increased continuously from 2005 to 2022. The average prevalence was 0.18% during 2005-2014 and rapidly increased to 3.41% during 2020-2022. The prevalence of mcr-3 in China increased from 0.79% in 2016 to 5.87% in 2019. We found that the fitness of mcr-3-bearing E. coli and empty plasmid control was comparable but higher than that of mcr-1-positive strain. Although the putative lipid A binding pocket of MCR-3 was similar to that of in MCR-1, mcr-3 occupies remarkable codon bias at the 5’-end of coding region that disrupted the stability of mRNA, further reduced its protein expression in E. coli, resulting in the low fitness burden of bacterial host. Moreover, the 5’-end codon usage frequency appeared as a critical factor related with the evolution of mcr family. Furthermore, based on the similar lipid A binding pocket among MCR family protein, we identified three novel MCR inhibitors targeting at such pocket by screening from small-molecule library, which effectively restored the colistin susceptibility of mcr-bearing E. coli.  Interpretation: For the first time, we found that the prevalence of mcr-3 increased continuously during 2016-2019 in China, demonstrating that the withdrawal of colistin in husbandry failed to prevent the dissemination of mcr-3. Our study evidenced that the 5’-end codon bias appeared as a crucial regulator upon the fitness cost conferred by horizontally transferred genes. Most importantly, the putative lipid A binding pocket verified from current study was a promising target site for designing inhibitors against mcr-positive strains.

overall_design: RNA-seq of E.coli K-12 carrying mcr-1 or mcr-3 resistant gene

first: Lujie

last: Liang

first: Guobao

last: Tian


title: Transcriptome changes in MCF7 cells after treatment with NONO ligands and controls

status: Public on Jun 09 2025

city: La Jolla

first: Garrett

middle: Lee

last: Lindsey

state: CA

address: 10650 N Torrey Pines Rd

department: Chemistry

institute: Scripps Research

summary: RNA-Sequencing to determine transcriptome changes in MCF7 cells after treatment with NONO ligands and controls. NONO knockout (sgNONO) or control (sgControl) cells were treated.

overall_design: sgControl or sgNONO MCF7 cells were treated in biological triplicate with DMSO (0.1%) or (R, R)-GL-373 (20µM) or (S, S)-GL-373 or (R)-SKBG-1(5µM) or (S)-SKBG-1(5µM) for 6 hours

middle: L

first: Benjamin

last: Cravatt


title: EPITHELIAL REMODELING AND MICROBIAL DYSBIOSIS IN THE LOWER RESPIRATORY TRACT OF VITAMIN A-DEFICIENT MOUSE LUNGS

status: Public on Jun 12 2025

city: Newark

first: Kiloni

last: Quiles

state: NJ

address: 205 South Orange Avenue

department: Medicine

institute: Rutgers New Jersey Medical School

summary: The World Health Organization identified vitamin A deficiency (VAD) as a major public health issue in low-income communities and developing countries, while additional studies have shown dietary VAD leads to various lung pathologies. Once believed to be sterile, research now shows that transient microbial communities exist within healthy lungs and are often dysregulated in patients suffering from malnourishment, respiratory infections, and disease. The inability to parse vitamin A-mediated mechanisms from other metabolic mechanisms in humans with pathogenic endotypes, as well as the lack of data investigating how VAD affects the lung microbiome, remains a significant gap in the field. To address this unmet need, we compared molecular, metatranscriptomic, and morphometric data to identify how dietary VAD affects the lung as well as the lung microbiome. Our research shows structural and functional alterations in host-microbe-diet interactions in VAD lungs compared to vitamin A-sufficient (VAS) lungs; these changes are associated with epithelial remodeling, a breakdown in mucociliary clearance, microbial imbalance, and altered microbial colonization patterns after 8 weeks of vitamin A deficient diet. These findings confirm vitamin A is critical for lung homeostasis and provide mechanistic insights that could be valuable for the prevention of respiratory infections and disease.

sample_organism:
Mus musculus
lung metagenome

platform_organism:
Mus musculus
lung metagenome

overall_design: RNAseq (metatranscriptomic) profiling of WT C57B/J6 adult mice maintained on VAS and VAD diets for 3 weeks and 8 weeks. Both host and microbial RNA-seq data was analyzed for epigenetic changes to host and microbial pathways.

first: Feng-Zhi

last: Shao

first: W. Evan

last: Johnson

first: Felicia

last: Chen


title: Nanoplastics dysregulate macrophage function by impairing glutathione metabolism

status: Public on Jun 18 2025

city: Seoul

first: Koung-Min

last: Park

address: 5-26, Sinchon-ro 4-gil

country: South Korea

institute: Yonsei university college of medicine

summary: Micro- and nanoplastics (MNPs) are emerging environmental contaminants increasingly detected in human tissues. However, how MNP-related effector mechanisms that impact the immunological function of macrophages remain elusive. Here, we demonstrated that MNPs disrupt redox homeostasis and induce immune dysfunction in bone marrow-derived macrophages. MNP internalization in macrophages impairs mitochondrial function, inducing excessive and sustained production of reactive oxygen species along with suppressed glutathione metabolism, including the substantial down-regulation of key antioxidant enzymes, such as glutathione peroxidase (GPX) 1, GPX3, and GPX4. These processes cause oxidative imbalance, thereby triggering ferroptosis, compromising cellular integrity, and amplifying inflammatory signaling. Two-photon intravital and three-dimensional imaging in mice confirmed that orally administered MNPs accumulate in multiple organs. Such MNP accumulation exacerbates lung tumor progression, potentially through chronic inflammation and the immune dysregulation of macrophages. These findings reveal a novel mechanism by which MNPs alter innate immunity and promote an inflammatory microenvironment via redox-mediated ferroptosis.

overall_design: Total RNA-seq profiling of mouse bone marrow-derived macrophage and treated or no-treated by polystyrene micro- and nanoplastics.

first: Bora

last: Kim

first: Haerang

last: Lee

first: Young-Min

last: Hyun


title: Effects of transient thermal stress on thyroid cancer cells

status: Public on Jun 13 2025

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

summary: Radiofrequency ablation has been used to treat low-risk thyroid cancer; however, its oncological safety remains unclear. We applied transient sublethal thermal stress to thyroid cancer cells to simulate clinical scenarios in which incomplete radiofrequency ablation leads to residual viable thyroid cancer cells.

overall_design: Thyroid cancer cell lines TPC-1 and B-CPAP were grown in T25 flasks submerged at 37 or 40 degrees Celsius for 20 minutes. Total RNA was extracted and subjected to RNA-seq.


title: SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription [scRNA-Seq]

first: Li

last: Li

summary: In order to profile the transcriptional changes that accompany SyS development along disparate epithelial, mesenchymal, or poorly differentiated trajectories, we performed single cell transcriptome profiling (scRNA-seq) on mouse SyS tumors similar to those profiled epigenomically. The tumors exhibited a variety of histomorphologies, indicated in hematoxylin and eosin tumor sections of tissue immediately adjacent to that submitted for scRNA-seq.

overall_design: we performed single cell RNA-seq for tumors that arose from SS18::SSX2 expression from the Rosa26 locus by TATCre injection in the limbs of mice (hSS2 allele), which exhibited a variety of histomorphologies

first: Jinxiu

first: Kevin

last: Jones


title: The impact of the halogenated phenazine HP-29 on the transcriptome of Streptococcus mutans with or without zinc supplementation

status: Public on Jun 01 2025

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: We sought to identify transcriptomic changes that arise when S. mutans is cultivated in the presence of HP-29 with or without zinc supplementation. Mid-logarithmic broth cultures of Streptococcus mutans UA159 were exposed to 0.025uM HP-29 or to 0.025uM HP-29 and 0.5mM ZnSO4 for 30 minutes.  We compared this transcriptomic data to that of control cultures that were grown in medium (BHI) without exposure to HP-29 or ZnSO4

overall_design: Cultures of S. mutans UA159 were inoculated in BHI and grown to mid-logarithmic phase (OD600 = 0.4), then split into three tubes: 1) BHI control, 2) 0.025uM HP-29, 3) 0.5mM ZnSO4 + 0.025uM HP-29.  These samples were incubated for an additional 30 minutes, then harvested by centrifugation, and then bacterial pellets resuspended in 1 mL RNA Protect Bacterial Reagent (Qiagen).  Total RNA was isolated and prepared for RNA-Seq analysis.

first: Hannah

last: Hosay

first: Robert

middle: W

last: Huigens III

first: Jose

last: Lemos


title: Dual-RNA-seq of Acinetobacter baumannii ABC141 inside endothelial cells EA.hy926

status: Public on Jun 04 2025

city: Dublin

first: Carsten

last: Kroeger

address: Moyne Institute of Preventive Medicine

department: Microbiology

country: Ireland

institute: Trinity College Dublin

summary: Acinetobacter baumannii poses a substantial global health threat, causing severe multi-drug-resistant infections in hospitalized patients. Circulating clinical isolates present remarkable diversity, with a proportion capable of establishing a transient intracellular niche suitable for persistence, multiplication, and spread. Yet, it remains unknown which bacterial factors mediate the formation and maintenance of this niche, especially within non-phagocytic cells, nor what host responses are elicited. This work demonstrates that the invasive A. baumannii ABC141 strain does not secrete ammonia in endothelial cells as previously shown for other A. baumannii strains multiplying within macrophages but resides in an acidic vacuole devoid of active lysosomal degradative enzymes. Using a Dual-RNAseq approach, we mapped the host and bacterial gene expression during the replicative stage of the infection. An atypical hypoxia cell response was observed without significant induction of the HIF1 pathway, with no metabolic shift or disturbance of mitochondria. Surprisingly, ABC141 efficiently grew in hypoxic conditions in culture and within host cells. In addition, we found a bacterial signature reflective of an adaptation to a nutrient-deprived environment. Our work also highlights a differential role for ABC141 secretion systems, with the T1SS assisting intracellular multiplication and the T2SS required for host cell invasion, implicating for the first time the T2SS in the intracellular lifecycle of invasive ABC141 in endothelial cells.

sample_organism:
Acinetobacter baumannii
Homo sapiens

platform_organism:
Acinetobacter baumannii
Homo sapiens

overall_design: Dual-RNA-seq was performed in human cells EA.hy926 infected with Acinetobacter baumannii ABC141 expressing GFP (cells were infected for 24h) to measure bacterial and human gene expression. Human cells were sorted by FACS for infected cells (using GFP to gate infected cells, Sinf) or left unsorted (Inf). Uninfected cells (sorted (SNeg) and un-sorted (Neg)) served as controls. In addition, A. baumannii ABC141 transcriptome was sequenced from the inoculum before infection of human cells (ABC141).

first: Charline

last: Debruyne

first: Landon

last: Hodge

first: Karsten

last: Hokamp

first: Anna

last: Ershova

last: Kröger

first: Suzana

last: Salcedo


title: Using fish models to understand the role of aryl hydrocarbon receptor (AHR)-interacting protein (AIP) in controlling sensitivity and resistance to dioxin-like compounds in vivo

city: Woods Hole

first: Sibel

middle: I

last: Karchner

state: MA

address: 45 Water St

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Humans are exposed to chemicals such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs) that cause toxicity through activation of the aryl hydrocarbon receptor (AHR). There is inter-individual variation in sensitivity to effects of AHR ligands, but it is not fully explained by variation in the human AHR, suggesting that other components of the AHR pathway are involved in controlling sensitivity. A clue to the genetic mechanisms underlying differential sensitivity to AHR agonists has emerged recently from studies of Atlantic killifish (Fundulus heteroclitus) populations with multi-generational exposure to PCBs, TCDD, and PAHs. Genomic studies of these populations identified the AHR chaperone AHR-interacting protein (AIP/Ara9/XAP2) as the strongest candidate resistance gene. However, the precise role of AIP in the mechanism of resistance is unknown. To understand the role of AIP in the toxicity of dioxin-like compounds and how variation in AIP may affect chemical sensitivity, we CRISPR-Cas9 to generate AIP loss-of-function alleles in killifish and zebrafish (Danio rerio). Homozygous mutant killifish and zebrafish die during larval development, while heterozygous mutants develop normally, survive to adulthood, and reproduce normally. Prior to death, homozygous mutant zebrafish exhibit reduced sensitivity to embryotoxic effects of exposure to 3,3',4,4',5-pentachlorobiphenyl (PCB126) and TCDD. Gene expression profiling of control and PCB126-exposed larvae at 3 days post-fertilization reveals some genes differentially expressed between mutant and wild-type larvae, but the induction of AHR-regulated genes is similar in aip-/-, aip-/+, and aip+/+ larvae. Understanding the role of AIP in controlling sensitivity to AHR agonists in fish models may shed light on the factors that determine differential susceptibility of humans to dioxin-like compounds and on the role of AIP in human disease.

overall_design: RNAseq profiling of 3 dpf zebrafish AIP CRISPR knock-out mutants (aipwh239) exposed to PCB126 (10 nM final concentration) or vehicle DMSO. WD: wildtype-DMSO, WP: wildtype-PCB, HED: Heterozygous-DMSO, HEP: Heterozygous-PCB, HOD: Homozygous-DMSO, HOP: Homozygous-PCB. Four biological replicates of each.

first: Neelakanteswar

last: Aluru

first: Diana

last: Franks

first: Chesna

last: Mandl

first: Jared

last: Goldstone

first: Tara

last: Burke

first: Denise

last: Champlin

first: Jane

last: La Du

first: Dante

last: Perone

first: Spencer

last: Stinson

first: Lisa

last: Truong

first: Bryan

last: Clark

first: Diane

last: Nacci

first: Robyn

last: Tanguay

first: Mark

last: Hahn


title: Epicardial Complement C3 Activation in Neonatal Cardiac Regeneration

status: Public on May 31 2025

city: Cambridge

first: Richard

last: Lee

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: The capacity for some neonatal mammals to regenerate damaged myocardium has a known dependency on immune signaling. By utilizing single cell RNA sequencing of the neonatal mouse heart two days following apical resection or a sham thoracotomy right after birth, we identify complement C3 signaling along an epicardial-to-fetal macrophage axis as playing a strong role in post-injury angiogenesis. Specifically, we identify differences in macrophage populations between surgical conditions, with major expansions in pro-angiogenic signaling fetal liver-derived macrophages post-injury. These results suggest a role for primordial macrophage lineages in the early injury response in the neonatal heart, which may in turn promote better recovery or regeneration.

overall_design: Neonatal C57/BL6 mice of mixed-sex littermates underwent surgery at days P0-P1. 4 post-surgery (2 days) hearts per condition (sham and resected) were collected, perfused with PBS, and pooled. Ventricles were minced and 1200μL of dissociation media (RPMI 1640 media (Gibco 1187503), 0.04U/mL Dispase II in DMEM/F-12 (STEMCELL Technologies 07923), 2μg/mL Collagenase D (Roche 11088858001), 32U/mL DNase I (NEB M0303S)) were added. Samples were incubated (30min, 37°C) before deactivating the enzymes with cold 5% FBS in PBS. Samples were filtered through a 40μm cell strainer (Pluriselect 43-10040), centrifuged (300g, 5min, 4°C), resuspended in 2mL ACK lysing buffer (Gibco A10492-01), and incubated (5min, 37°C). Samples were centrifuged, washed (5% FBS in PBS), and recentrifuged. Live cells were enriched through dead cell removal (Miltenyi Biotech 130-090-101) and miniMACS separators. The suspension was washed and pelleted (400g, 5min, 4°C). Pellets were resuspended in 0.04% BSA in PBS at 1000 cells/μL and viability was determined through the LUNA-FL (Logos Biosystems).  Cells were processed using the 10x Genomics Chromium pipeline and sequenced on an Illumina NextSeq 2000. Feature matrices were generated from raw FASTQ files via the Cell Ranger pipeline.

first: Lee

middle: T

last: Richard


title: CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity [scRNA-seq]

city: Boston

first: Robert

last: Fisher

address: 609 Albany St

department: Dermatology

institute: Boston University

summary: Epigenetic macromolecular enzyme complexes tightly regulate gene expression at the chromatin level and have recently been found to colocalize with RNA splicing machinery during active transcription1; however, the precise functional consequences of these interactions are uncertain. Here, we identify unique interactions of the CoREST repressor complex (LSD1-HDAC1-CoREST) with components of the RNA splicing machinery and their functional consequences in tumorigenesis.  Using mass spectrometry, in vivo binding assays, and cryo-EM we find that CoREST complex-splicing factor interactions are direct and perturbed by the CoREST complex selective inhibitor, corin2–5, leading to extensive changes in RNA splicing in melanoma and other malignancies. Moreover, these corin-induced splicing changes are shown to promote global effects on oncogenic and survival-associated splice variants leading to a tumor-suppressive phenotype. Using predictive machine learning models, MHC IP-MS, and ELISpot assays we identify thousands of neopeptides derived from unannotated splice sites which generate corin-induced splice neoantigens that are demonstrated to be immunogenic in vitro. Corin is further shown to reactivate the response to immune checkpoint blockade and promote dramatic expansion of cytotoxic T cells in an immune cold melanoma tumor model, effectively sensitizing them to anti-PD1 immunotherapy. These data position CoREST complex inhibition as a unique therapeutic opportunity in cancer which perturbs oncogenic splicing programs across broad tumor types while also creating tumor-associated neoantigens that enhance the immunogenicity of current therapeutics and may be readily translated to the clinic.

overall_design: 6-10 week-old female C57BL/6 female mice (Jackson Lab) were inoculated with 2.5x105 B16F10 cells. Mice were treated with 200 µg/mice of Corin (HY-111048, MedChemExpress) or 200 µl vehicle control (5% DMSO/PBS) by daily intraperitoneal (i.p.) injections starting from day 6 after the tumor injection. For Anti-PD1 treatment, mice were treated with 150 µg/mice anti-PD1 (clone 29F.1A12, BioLegend, 135248) or isotype control (clone RTK2758, BioLegend, 400566) 3 times/week starting from day 7 post-tumor grafts. 10 mice per treatment group were used. Minced tumor biopsies were incubated with 200uL 20mg/mL collagenase, 200uL 20mg/mL hyaluronidase, and 5uL DNase for 20 minutes to 1 hour with agitation until the tumor fully dissociated. Single-cell suspension was passed through a 100um strainer and washed with 1X PBS by centrifugation. Cells were resuspended in 1ml of freezing media frozen down. Cryopreserved single-suspension tumor samples were thawed and dead cells were removed using the Dead Cell Removal Kit (Miltenyi, 130-090-101) following manufacturer instructions. Live cells from the flow-though were used for CD45+ cell isolation using CD45 mouse MicroBeads (Miltenyi, 130-052-301) following the recommendations. CD45+ cells were counted and resuspended in PBS + 0.04% BSA at 1000 cells/µL for scRNA-seq.

first: Kihyun

last: Park

first: Kwangwoon

first: Katarina

last: Pinjusic

first: Allison

last: Vanasse

first: Christina

middle: S

last: Ennis

first: Scott

last: Ficcaro

first: Jarrod

last: Marto

first: Stephanie

last: Stransky

first: Joseph

last: Duke-Cohan

first: Anupa

last: Geethadevi

first: Eric

last: Raabe

first: Simone

last: Sidoli

first: Derin

middle: B

last: Keskin

first: Chad

last: Hicks

first: Catherine

middle: J

last: Wu

first: Philip

last: Cole

first: Rhoda

middle: M

last: Alani


title: Downregulation of Engulfment and cell motility 1 (Elmo1) induces quiescence and resistance to poly(I:C)-induced apoptosis in endothelial cells

city: CHAPEL HILL

first: Yukako

last: Kayashima

state: NC

address: 710 BRINKHOUS-BULLITT BUILDING CB #7525

department: Pathology Lab Med

institute: University of North Carolina at Chapel Hill

summary: Engulfment and Cell Motility 1 (ELMO1) facilitates activation of Ras-related C3 botulinum toxin substrate 1 (RAC1) through interaction with Dedicator of Cytokinesis (DOCK), a family of guanine nucleotide exchange factors (GEF). ELMO1 plays an important role in acute and chronic inflammation by enhancing immune cell migration, phagocytosis of pathogens and dead cells, and production of reactive oxygen species. Endothelial cells, an integral component of inflammatory responses, also express high levels of ELMO1, although the role of ELMO1 in inflammatory endothelial cells is unclear. We demonstrate that knockdown of ELMO1 in EA.hy926 human umbilical vein endothelial cells (HUVECs) leads to cell quiescence, while protects the cells from Toll-like receptor 3 (TLR3)-induced apoptosis and restores inflammatory responses.

overall_design: RNA-seq profiling of EA.hy926 human umbilical vein endothelial cells treated with transfection reagents-only (Mock), cells transfected with non-targeting siRNA (siNT), and those with ELMO1-targeting siRNA (siELMO1), before (0 h) and after (24 h) the stimulation with poly(I:C)

first: Anshulika

last: Ashvinikumar Deshmukh

first: Nobuyo

last: Maeda


title: FLT3 is genetically essential for ITD-mutated leukemic stem cells but dispensable for human HSCs

city: Toronto

first: Veronique

last: Voisin

state: ON

address: 101 College St, room 8-353

country: Canada

institute: University Health Network

summary: Leukemic stem cells (LSCs) fuel relapse in acute myeloid leukemia (AML), but therapies tailored at eradicating LSCs without harming healthy hematopoietic stem cells (HSCs) are lacking. FLT3 is frequently mutated in AML and associated with relapse; but FLT3 targeting has met with limited clinical success. This raises questions of whether more potent inhibitors would increase  effectiveness but whether toxicity to HSC would become limiting. Here, we tested the consequence of complete FLT3 ablation using CRISPR/Cas9 FLT3 knock-out (FLT3-KO) in human HSCs and LSCs followed by functional xenograft assays to test their ability to regenerate human hematopoiesis and leukemia, respectively.  FLT3-KO in HSCs from human fetal liver, cord blood and adult bone marrow showed no impairment in multilineage hematopoiesis in primary and secondary xenografts. By contrast, FLT3-KO LSCs from 6 of 7  FLT3-ITD mutated AMLs were able to generate short-term engraftment but were completely exhausted by 12 weeks. Thus, FLT3 is essential for LSC long-term propagation. This dependency was unique to FLT3-ITD AML samples as non-FLT3-ITD AML samples generated leukemic grafts upon FLT3-KO. Transcriptomic analysis revealed that FLT3-KO induced downregulation of DNA repair and cell cycle checkpoints, uniquely in FLT3-ITD AML, but not in healthy HSCs or other AMLs. Our research highlights a critical distinction between healthy HSCs and LSCs: whereas healthy hematopoiesis proceeds unperturbed upon FLT3-KO, FLT3-ITD leukemogenesis is impaired through elimination of LSCs. This evidence underscores the necessity for more potent FLT3-targeting and places FLT3 as an ideal therapeutic target to selectively eradicate LSCs, while sparing HSC.

overall_design:
We used three primary patient samples of acute myeloid leukemia (AML) with the internal tandem duplication (ITD) in FLT3 – samples ITD 1, ITD 2 and ITD 3; three primary patient samples of AML without the ITD mutation – samples WT 1, WT 2 and WT 3; and three samples of human umbilical cord blood (CB). AML samples were thawed, and the fraction previously determined (PMID: 27926740) to be enriched in leukemic stem cell activity was sorted: CD34+ population was sorted from all samples, except from WT 3 where the CD45+ CD3- population was sorted. CB samples were thawed and the CD34+CD38- population was sorted. AML samples were cultured for 24-h, while CB cells were cultured for 48-h. Subsequently, FLT3-KO and OR2W5-KO were performed using CRISPR/Cas9 technology through electroporation. After electroporation, cells were cultured for 3 additional days to achieve the maximal reduction on FLT3 expression after FLT3-KO in culture. Subsequently, cells were collected and viably sorted using SYTOX Blue Dead Cell Stain (Thermo Fisher Scientific). A minimum number of 13 x103 live cells was sorted per sample (range 13 to 800 x103). One fifth of the sample was collected for total DNA isolation and subsequent determination of KO percentage mediated by CRISPR/Cas9. The rest of the sample was used for total RNA purification and DNase treatment using the RNeasy Micro kit (Qiagen). RNA integrity was measured using the RNA 6000 Pico kit (Agilent) and the average RNA integrity scores were the following: 8 for AML-ITD samples (6.9-10), 10 for AML-WT samples (9.7-10) and 9.95 for CB samples (9.8-10). To generate RNAseq libraries, total RNA was used as input with SMART-Seq V4 Ultra Low Input RNA kit (Clontech). The cDNA profiles were confirmed on the bioanalyzer using the High Sensitivity 14 DNA kit (Agilent) and next-generation sequencing libraries were made using the Nextera XT DNA Library Preparation kit (Illumina). Sequencing was performed on the NovaSeq 6000 system using 2 x 150 bp paired-ended sequencing to obtain ~50 M reads per sample.
>>>Submitter states that raw data will be submitted to EGA<<<

first: Joana

last: Araújo

first: Elvin

last: Wagenblast

first: Jessica

last: McLeod

first: Olga

last: Gan

first: Liqing

last: Jin

first: Amanda

last: Mitchell

first: Blaise

last: Graton

first: Sarah

last: Cutting

first: Andrea

last: Arruda

first: Monica

last: Doedens

first: Jose-Mario

last: Capo-Chichi

first: Mark

last: Minden

first: Manuel

last: Sobrinho-Simões

first: Perpétua

last: Pinto-do-Ó

last: Lechman

first: John

middle: E

last: Dick


title: Characterization of induced cohesin loop extrusion trajectories in living cells [ChIP-seq]

status: Public on Jun 26 2025

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The cohesin complex shapes chromosomes by DNA loop extrusion, but individual extrusion trajectories were so far unappreciable in vivo. Here, we developed and validated TArgeted Cohesin Loader (TACL), a system enabling the strong activation of anchored loop extrusion from dozens of defined genomic sites in living cells. Studying their individual loop extrusion trajectories revealed that extruding cohesin-STAG2 stops not only at domain boundaries but at all flanking CTCF sites, engaging them in a complex transient looping network that supports intradomain contacts. Cohesin-STAG1 cannot associate with weak CTCF binding sites and fails to similarly support intradomain interactions. NIPBL-MAU2 remains associated with cohesin when stalled at looping CTCF sites, suggesting these factors may also be required for loop stabilization. TACL induces cohesin traffic jams and illegal loops with divergent CTCF sites, demonstrating that stalled cohesin can block extruding cohesin in vivo. Genes exposed to TACL-induced loop extrusion were collectively hindered in transcription and the underlying chromatin altered its accessibility and reduced its H3K27ac marks. Thus, by enabling the study of individual loop extrusion trajectories in vivo, we could assign new functions to players, identify new looping networks and uncover an interplay between loop extrusion, gene transcription and chromatin composition.

overall_design: ChIPseq  of eHAP1 cells carying 27 TetO platforms expressing TetR-MAU2 (TACL) or TetR-mCherry, with and without doxycycline treatment and/or depletion of RAD21, CTCF, PDS5A, WAPL, STAG2  using auxin treatment.

first: Ruiqi

last: Han

first: Yike

last: Huang

first: Michelle

last: Robers

first: Mikhail

last: Magnitov

first: Iwan

last: Vaandrager

first: Amin

last: Allahyar

first: Marjon

last: Verstegen

first: Kexin

last: Zhang

first: Elzo

last: de Wit

first: Wouter

last: de Laat


title: Dynamics of microcompartment formation at the mitosis-to-G1 transition

status: Public on Jun 03 2025

first: Viraat

middle: Yogi

last: Goel

state: Massachusetts

department: Biological Engineering

institute: Massachusetts Institute of Technology (MIT)

summary: As cells exit mitosis and enter G1, mitotic chromosomes decompact and transcription is  reestablished, with prior studies showing that essentially all interphase 3D genome features including A/B-compartments, TADs, and CTCF loops are lost during mitosis. Microcompartments, nested focal interactions between cis-regulatory elements (CREs), can now be resolved using Region Capture Micro-C (RCMC), though the dynamics of their formation remain unknown. We therefore applied Region Capture Micro-C to G1E-ER4 cells across five mitosis-to-G1 stages: prometaphase, ana/telophase, early G1, mid G1, and late G1, along with an asynchronous condition. Five mouse loci ranging from 1-2 Mb in size were selected for capture: Id1, Klf1, Cdt1, Dag1, and Myc. Follow-up RCMC experiments were also performed at these loci in an SMC2 (condensin) degron G1E-ER4 subline, in which cells were arrested in prometaphase and auxin-treated for five tested depletion conditions: 0h, 0.5h, 1h, 4h, and 8h. We find that microcompartments form early in the M-to-G1 transition but weaken as cells enter G1, suggesting that microcompartmentalization is distinct from A/B-compartmentalization and loop extrusion.

overall_design: Region Capture Micro-C was performed in G1E-ER4 cells arrested to different stages of the mitosis-to-G1 transition and varying degrees of condensin depletion

middle: Y

first: Nicholas

middle: G

last: Aboreden

first: James

last: Jusuf

first: Haoyue

first: Luisa

middle: P

last: Mori

first: Leonid

last: Mirny

first: Gerd

last: Blobel

first: Edward

last: Banigan

first: Anders

last: Hansen


title: Hair follicle stem cell fate supports distinct clinical endotypes in Hidradenitis Suppurativa

status: Public on Jun 02 2025

city: Créteil

first: Sophie

last: Hue

address: 1 rue du général Sarrail

institute: Henri Mondor APHP

summary: Hidradenitis suppurativa (HS) is a severe skin disorder affecting 1% of the global population. Its pathogenesis is multifactorial and poorly understood, involving aberrant keratinization and autoinflammation. Whether autoinflammatory events precede or follow hyperkeratotic changes in hair follicle (HF) epithelia is unknown. Using single-cell RNA sequencing (scRNA-Seq), we defined the cellular composition of HF cells, the primary cells involved in HS, and confirmed these findings in the Fol-HYDRA cohort. We identified three main cell families: i) HF matrix lineage enriched for MSX2, ii) non-matrix lineage enriched for KRT14, and iii) immune cells enriched for PTPRC. Unsupervised clustering of HF cells from controls and HS patients revealed significant differences in non-matrix cells, segregating patients into two groups. Group one is enriched in cluster 1 (IBL), while group two is enriched in cluster 0 (mORS), each displaying distinct transcriptomic changes. Gene set enrichment analysis showed IBLs enriched for keratinization genes and mORS for interferon response genes. Trajectory analysis revealed HF stem cells differentiating into either IBL or mORS pathways. Confirmed in 49 HS patients, these pathways correspond to different clinical phenotypes. Our findings provide a novel perspective on HS pathology, identifying two key pathways: one in keratinization and the other in inflammation. These pathways define different endotypes for HS patients, suggesting potential markers for personalized medicine.

overall_design: To investigate the cellular heterogeneity of hair follicles from HS patients compared to heathy donor, we performed single-cell RNA-Sequencing on hair follicles samples from 5 HS patients and 2 healthy donors.

first: Audrey

last: Onfroy

first: Francette

last: Jean-Louis

first: Philippe

last: Lecorvoisier

first: Fanny

last: Coulpier

first: Caroline

last: Boucle

first: Salwa

last: Abid

first: Emilie

last: Sbidian

first: Christina

last: Bergqvist

first: Pierre

last: Wolkenstein

first: Véronique

last: Godot

first: Yves

last: Lévy

first: Piotr

last: Topilko

first: Etienne

last: Audureau

last: Hüe


title: RNA-binding protein Cpeb1 is a marker of healthy adult β cells in mice but is dispensable β cell identity and function

city: Madison

first: Barak

last: Blum

state: Wisconsin

address: 4551 WIMR II, 1111 Highland Ave.

institute: University of Wisconsin-Madison

summary: RNA binding proteins (RBPs) are increasingly being recognized as important regulators of pancreatic β-cells’ identity and function. We identified the poly-A binding RBP, Cpeb1, as a potential new regulator linked to β-cell failure in diabetes based on its enrichment in mature, healthy adult β-cells and its sharp decrease in β-cells in type 1 diabetes (T1D) and type 2 diabetes (T2D). While Cpeb1 is known to regulate an extensive range of biological processes and its involvement in regulating genes involved in insulin signaling and apoptosis in the liver has been reported, Cpeb1 function in β-cells is unknown. Here, we have used two independent genetic models, namely β-cell-specific and whole body Cpeb1 deletions, to assess the role of Cpeb1 in β-cells. We show Cpeb1 function is dispensable for β-cell function and identity. Using bulk RNA sequencing on islets of both models, we also show that Cpeb1 regulates markedly different sets of genes between male and female islets, both at the transcriptional and at the polyadenylation levels.

overall_design: RNA-seq profiling of β cell-specific Cpeb1 knockout primary islets (Cpeb1 βKO: Cpeb1flx/flx; Ins1-Cre) and wildtype control (Cpeb1+/+; Ins1-Cre), and of whole-body knockout of Cpeb1 islets (Cpeb1 KO) and wildtype control.

first: Sutichot

middle: D

last: Nimkulrat

first: Bayley

last: Waters

first: Matthew

last: Wagner

first: Maria

last: Mendoza Niemes

first: Cyrus

last: Sethna

first: Hariharan

last: Jayaraaman


title: Immune-responsive gene-1: The mitochondrial Key to Th17 Cell Pathogenicity in CNS Autoimmunity

status: Public on May 28 2025

city: detroit

first: Shailendra

last: Giri

state: MI

address: 2799 W grand boul

department: Neurology Research

institute: henry ford hospital

summary: Pathogenic Th17 cells play crucial roles in CNS autoimmune diseases such as multiple sclerosis (MS), but their regulation by endogenous mechanisms remains unknown. Through RNA-seq analysis of primary brain glial cells, we identified immuno-responsive gene 1 (Irg1) as one of the highly upregulated gene under inflammatory conditions. Validation in the spinal cord of animals with experimental autoimmune encephalomyelitis (EAE), an MS model, confirmed elevated Irg1 levels in myeloid, CD4, and B cells in the EAE group raising the concern if Irg1 is detrimental or protective. Irg1 knockout (KO) mice exhibited severe EAE disease, increased mononuclear cell infiltration, and increased levels of triple-positive CD4+ T cells expressing IL17a, GM-CSF, and IFNγ. A lack of Irg1 in macrophages elevates Class II expression, promoting the polarization of myelin-primed CD4+ T cells into pathogenic Th17 cells via the NLRP3/IL-1β axis. Adoptive transfer in Rag-1 KO and single-cell RNA sequencing highlighted the crucial role of Irg1 in shaping pathogenic Th17 cells. Moreover, bone marrow chimeras revealed that immune cells lacking Irg1 maintained pathogenic and inflammatory phenotypes, suggesting its protective role in autoimmune diseases, including MS.

overall_design:
For the generation of bone marrow chimeras, host (CD45.1) animals were treated with three doses of busulfan (20 mg/ml), and on the fourth day, the host received an i.v. injection of 10 million BM cells [50:50 mixture of CD45.1 (Wt) and CD45.2 (Irg1 KO)]. Using flow cytometry, we sorted CD45.1+ and CD45.2+ cells from BILs isolated via a Percoll gradient from the brain and spinal cord after EAE induction. BILs were stained with primary antibodies against mouse PerCP-Cy5.5-CD45.1 and BV421-CD45.2 (BioLegend) and sorted on a BD FACSAria™ III. Furthermore, the sorted populations were re-run to check the purity of the sorted cells. Next, we used an automated cell counter (Bio-Rad) to determine the viability of CD45+1+ and CD45.2 cells via trypan blue and found that >98% of the cells were viable. Then, RNA was harvested from the sorted cells and processed for RNA sequencing.
Three mice per group (WT and Irg1 knockout) were pooled for analysis. Experimental autoimmune encephalomyelitis (EAE) was induced using MOG peptide in combination with Pertussis toxin and monitored for 20 days. Following euthanasia, spinal cords were harvested, and single-cell suspensions were prepared using Accumax enzymatic dissociation followed by Percoll gradient purification. A total of approximately 200,000 cells per group were processed using the Fluent pipeline. Two single-cell RNA-seq libraries per group were generated using the Fluent PIPseq T20 3' capture and lysis kit.
The timed pregnant rat was purchased from Charles River Laboratory. The brains of 2–3-day-old female and male pups were used to prepare mixed glial cell cultures. We followed our previously published protocol to prepare primary mixed glial cell cultures (3). After 10 days of culture, the cells were treated with LPS (0.5 µg/ml) + IFN (20 ng/ml) to induce inflammatory conditions in our study. After 8 h of treatment, the cells were processed for RNA isolation and RNA-seq

first: Mohammad

last: Nematullah

first: Mena

last: Fatma

first: Guoli

last: Zhou

first: Bharat

last: Prajapati

first: Faraz

last: Rashid

first: Kameshwar

last: Ayasolla

last: Ahmed

first: Ruicong

last: She

first: Sajad

last: Mir

first: Insha

last: Zahoor

first: Nasrul

last: Hoda

first: Ramandeep

last: Rattan


title: Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease

status: Public on May 30 2025

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

summary: Rapidly progressive glomerulonephritis (RPGN) is the most aggressive group of autoimmune kidney disease with the worst prognosis. Anti-neutrophil cytoplasmic antibody (ANCA) associated vasculitis, anti-glomerular basement membrane (anti-GBM) and lupus nephritis are the most common causes of RPGN and are characterized by the formation of glomerular crescents and infiltration of leukocytes that eventually lead to glomerulosclerosis and kidney failure.    In this work, we used high-resolution spatial transcriptomics of 32 ANCA, 19 lupus nephritis, 6 anti-GBM, and 6 control patients to understand how intercellular signaling between immune and renal tissue cells leads to renal inflammation and glomerular injury. Using 3,218,210 immune and kidney cells, we observed that the biological pathways involved in the sequence of glomerular crescent formation are similar across the diseases. While innate immune cells infiltrated the glomerular compartment relatively early, later increases in adaptive immune cells were largely restricted to the periglomerular regions. These changes in immune cells temporally correlated with increases in glomerular parietal epithelial (PEC) and fibrotic mesangial cells, suggesting disease-relevant functional signaling between these immune and renal cells. Cell communication analysis revealed early disease PDGF signaling from epithelial and mesangial cells to PECs, causing their activation and proliferation. At later stages, TGF-β signaling from macrophages, T cells, epithelial cells, and mesangial cells to PECs triggered the expression of extracellular matrix components resulting in glomerulosclerosis.    Our results highlight a spatio-temporally conserved progression into glomerular crescents and sclerosis for ANCA, lupus nephritis, and anti-GBM disease, which is driven by consecutive PDGF and TGF-β signaling to PECs.

overall_design: 8 slides containing 63 samples (biopsies from 32 ANCA, 19 lupus nephritis, 6 anti-GBM, and healthy tissues from tumor nephrectomies of 6 control patients) were analyzed with Xenium to capture RNA. One additional slide (Sample: 0011186) was used for Xenium + phenocycler run.

first: Zeba

last: Sultana

first: Saskia-Larissa

last: Jauch-Speer

first: Ulf

last: Panzer

first: Stefan

last: Bonn

first: Christian

last: Krebs


title: Using fish models to understand the role of aryl hydrocarbon receptor (AHR)-interacting protein (AIP) in controlling sensitivity and resistance to dioxin-like compounds in vivo 5dpf

first: Sibel

last: Karchner

overall_design: RNAseq profiling of 5 dpf zebrafish AIP CRISPR knock-out mutants (aipwh86) exposed to PCB126 (2 nM final concentration) or vehicle DMSO. WD: wildtype-DMSO, WP: wildtype-PCB, HED: Heterozygous-DMSO, HEP: Heterozygous-PCB, HOD: Homozygous-DMSO, HOP: Homozygous-PCB. Four biological replicates of each.

first: Neelakanteswar

last: Aluru

first: Diana

last: Franks

first: Chesna

last: Mandl

first: Jared

last: Goldstone

first: Tara

last: Burke

first: Denise

last: Champlin

first: Jane

last: La Du

first: Dante

last: Perone

first: Spencer

last: Stinson

first: Lisa

last: Truong

first: Bryan

last: Clark

first: Diane

last: Nacci

first: Robyn

last: Tanguay

first: Mark

last: Hahn


title: Transcriptomic signatures associated with regenerative wound  vs. fibrotic repair outcomes to lens post-cataract surgery wounding

city: Philadelphia

first: Janice

middle: Lynn

last: Walker

state: PA

address: 1020 Locust Street; 571 JAH

department: Pathology and Genomic Medicine

institute: Thomas Jefferson University

summary: RNAseq analysis was used to determine the transcriptomic changes associated with regenerative vs. fibrotic repair to lens injury. Using an ex vivo post-cataract surgery model, we can follow two distinct outcomes to lens injury: 1) A regenerative wound healing response that ensues across the cell-denuded lens capsule basement membrane (BM), culminating in wound closure on Day 3 (D3) post-injury. 2) Induction of fibrosis, which occurs when a wound healing response occurs off the lens capsule, termed the extracapsular zone (ECZ), where transition to a fibrotic phenotype occurs on day 3 post-injury. Here, we report the changes in the transcriptome that occur on D1, D2, and D3 post-injury, a period that covers wound healing across the BM and time points prior to (D1, D2) and after induction of the fibrotic phenotype (D3). Our data provides a molecular map for understanding the gene changes associated with navigating normal and pathological outcomes to lens injury.

overall_design: RNA-seq analysis of regenerative wound vs. fibrotic repair at Day 1, Day 2, and Day 3 post-injury within an ex vivo post-cataract surgery model.

first: J

first: M

last: Basta


title: Natriuretic Peptides Modulate Monocyte-Derived Langerhans Cell Differentiation and Promote a Migratory Phenotype

city: Debrecen

first: Attila

middle: Gábor

last: Szöllősi

address: Egyetem tér 1.

department: Department of Immunology

country: Hungary

institute: University of Debrecen

summary: Introduction: The interaction between the nervous and immune systems is crucial for maintaining homeostasis and can influence disease progression in inflammatory skin diseases, such as atopic dermatitis (AD). Sensory neurons in the skin can secrete neuropeptides that modulate immune cell activity, including Langerhans cells (LCs), the primary antigen-presenting cells in the epidermis. This study investigates the effects of neuropeptides on the differentiation of monocyte-derived LCs (moLCs), specifically the neuropeptides with the most profound effect, i.e. atrial- and B-type natriuretic peptides (ANP and BNP, respectively).

overall_design: Transcriptomic profiling of human monocyte-derived Langerhans cells differenitated in the presence of B-type natriuretic peptide or vehicle control (nuclease-free water).

first: Dorottya

last: Horváth


title: Next Generation Sequencing Facilitates Quantitative Analysis of control and PS micro-/nanoplastics stressed E. faecalis OG1RF , E. faecalis OG1RS , E. coli DH5α and pCF10 plasmid Transcriptomes

city: Shenzhen

first: Yuanyuan

last: Kang

address: No. 6 Pingshan 1st Road, Taoyuan Street, Nanshan District

department: School of Civil and Environmental Engineering

institute: Harbin Institue of Technology

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of E. faecalis OG1RF , E. faecalis OG1RS , E. coli DH5α and plasmid pCF10, and their mRNA response under the exposure of different sizes of Polystyrene (PS), including 20 nm, 120 nm and 1 μm. The concentrations were 0.1, 1, 10 mg/L for every size of PS. The group without adding PS was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these 3 sizes of PS on transcriptional levels can be revealed. Illumina HiSeq PE150 was applied. NEBNextő Ultra II Directional RNA Library Prep Kit for Illumina was used for library construction. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. faecalis OG1RF reference genome (NC_017316.1), E. coli DH5α reference genome (GCF_000982435.1), and plasmid pCF10 reference genome (NC_006827.2) using Bowtie2. RSeQC was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

overall_design: Bacterial mRNA profiles of E. faecalis OG1RF , E. faecalis OG1RS , E. coli DH5α and plasmid pCF10 in response to 0.1 mg/L 20 nm PS, 1 mg/L 20 nm PS, 10 mg/L 20 nm PS, 0.1 mg/L 120 nm PS, 1 mg/L 120 nm PS, 10 mg/L 120 nm PS, 0.1 mg/L 1 μm PS, 0.1 mg/L 1 μm PS, and 10 mg/L 1 μm PS for 2 hours, bacteria and plasmid without adding PS are the control group, in triplicate, using Illumina HiSeq PE150.

first: Shu-Hong

last: Gao

first: Yusheng

last: Pan

first: Tianyao

last: Li

first: Rui

first: Yue

last: Wang

first: Jianhua

last: Guo

first: Jianqiang

last: Su

first: Aijie

first: Zhigang

last: Qiu


title: Gene regulatory programs of NK cells show that NCAM1 (CD56) and KIRs are controlled by genetically polymorphic distal regulatory elements

city: Columbus

first: Patrick

last: Collins

state: Ohio

address: 460 West 12th Avenue, Biomedical Research Tower 770

department: Microbial Infection and Immunity

institute: The Ohio State University

type: Genome binding/occupancy profiling by array

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

overall_design: Refer to individual Series


title: Gene regulatory programs of NK cells show that NCAM1 (CD56) and KIRs are controlled by genetically polymorphic distal regulatory elements [scATAC-seq]

status: Public on May 24 2025

summary: Owing to their immunoprotective properties, natural killer (NK) cells are critical for the innate response to pathogens, as well as a new wave of cancer immunotherapy that harnesses natural cytotoxicity. We sought to understand the genetic and epigenetic drivers behind human specific NK cell receptors, so that we can better understand the underlying cellular function. Here, we present a transcriptomic, proteomic (CITE-seq), and chromatin (single nuclei ATAC-seq and Hi-C) analysis of human peripheral NK cell subsets, uncovering key regulatory programs governing NK cell differentiation. Through integrative multi-omics, we demonstrate that CD56bright versus CD56dim NK cell subsets have differential distal regulatory element (DRE) landscapes, with fewer accessible DREs in the CD56dim NK cells. We combine epigenetic, chromatin looping, and human genetic data to show mechanisms governing the NCAM1 (encoding CD56) and KIR loci. For example, we identify NCAM1 DREs that bind STAT in most NK cells, while identifying a genetic cohort that has motifs for binding repressive BLIMP1 at the DRE and resulting in less CD56 expression.  Together, our findings reveal novel epigenetic and transcriptomic systems for regulation of NK cells cytotoxicity and diversity, deepening our understanding of their function and how transcription factor networks govern CD56bright versus CD56dim phenotypes.

overall_design: Natural killer (NK) cells were isolated from peripheral blood mononuclear cells (PBMCs) using the RosetteSep™ Human NK Cell Enrichment Cocktail (STEMCELL Technologies). ). Following the addition of the cocktail, density gradient centrifugation was performed using Ficoll-Paque to separate enriched NK cells from the remaining blood components. This was performed on three different blood samples. Nuclei were isolated from NK cells and 10x Genomics snATAC-seq protocol was performed

first: Mariam

middle: A

last: Salem

first: Aditi

last: Varkey

first: Matthew

last: Estrada

first: Caprice

last: Eisele

first: Aharon

last: Freud

first: Bethany

middle: L

last: Mundy-Bosse


title: CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity [PRO-seq]

first: Robert

last: Fisher

overall_design: SKMEL5 cells were treated for 24h with 2.5uM corin or DMSO and permeabilized as described. All sample preparation was conducted on ice (4°C). Cells were washed in ice cold 1x PBS and resuspended in wash buffer (10 mM Tris-HCl pH 8.0, 10% glycerol, 250 mM sucrose, 10 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 1mM EGTA, Halt protease inhibitor cocktail (Thermo Scientific), and 4 u/mL RNase inhibitor [SUPERaseIN, Invitrogen]). Then cells (2x10^7) were gently permeabilized in permeabilization buffer (10 mM Tris-HCl pH 8.0, 10% glycerol, 250 mM sucrose, 10 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 0.1% Igepal, protease inhibitors cocktail (Roche), 4 u/mL RNase inhibitor [SUPERaseIN, Invitrogen]) for 5 minutes. Cells were recovered by centrifugation (400 x g for 8 minutes) and the supernatant was carefully removed. Cells were washed with 10 mL of wash buffer and then centrifuged again under the same conditions. Finally, cells were resuspended in 400uL of freeze buffer (50 mM Tris-HCl pH 8.0, 40% glycerol, 5 mM MgCl2, 0.5 mM DTT, 4 u/mL RNase inhibitor [SUPERaseIN, Invitrogen]) and stored at -80°C.

first: Kihyun

last: Park

first: Kwangwoon

last: Lee

first: Katarina

last: Pinjusic

first: Allison

last: Vanasse

first: Christina

last: Ennis

first: Scott

last: Ficcaro

first: Jarrod

last: Marto

first: Stephanie

last: Stransky

first: Joseph

last: Duke-Cohan

first: Anupa

last: Geethadevi

first: Eric

last: Raabe

first: Simone

last: Sidoli

first: Derin

last: Keskin

first: Chad

middle: W

last: Hicks

first: Catherine

last: Wu

first: Philip

last: Cole

first: Rhoda

last: Alani


title: Gene regulatory programs of NK cells show that NCAM1 (CD56) and KIRs are controlled by genetically polymorphic distal regulatory elements [CITE-seq]

status: Public on May 27 2025

first: Patrick

last: Collins

overall_design:
Natural killer (NK) cells were isolated from peripheral blood mononuclear cells (PBMCs) using the RosetteSep™ Human NK Cell Enrichment Cocktail (STEMCELL Technologies). ).  For tonsil NK isolation, Human innate lymphoid cells (ILCs) were enriched from fresh tonsil tissue.

***************************************************************
Submitter states that missing raw files are due to file loss.
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first: Aditi

last: Varkey

first: Matthew

last: Estrada

first: Caprice

last: Eisele

first: Aharon

last: Freud

first: Bethany

last: Mundy-Bosse


title: RNA-seq analysis of MLO-Y4 cells under hypoxic conditions

city: Sendai

first: Kohei

last: Narita

state: Miyagi

address: 4-1 Seiryo-machi, Aoba-ku

department: Dentistry

institute: Tohoku University

summary: To investigate the effects of hypoxia on osteocytes, we cultured MLO-Y4 osteocytic cells under normoxic (20% O₂) and hypoxic (2% O₂) conditions. We then performed gene expression profiling analysis using RNA-seq data obtained from these cells. Differential expression analysis revealed that Lipocalin 2 (LCN2) was one of the most significantly upregulated genes under hypoxic conditions.The dataset provides insights into the transcriptional response of osteocytes to hypoxic stress.

overall_design: RNA-seq profiling of MLO-Y4 osteocytic cells cultured under normoxic (20% O₂) and hypoxic (2% O₂) conditions for 24 hours. Differential gene expression analysis was performed to identify hypoxia-responsive genes in osteocytes.

first: Fumitoshi

last: Ohori

first: Aseel

last: Marahleh

first: Jinghan

last: Ma

first: Jiayi

last: Ren

first: Angyi

last: Lin

first: Ziqiu

last: Fan

first: Kou

last: Murakami

first: Hideki

last: Kitaura


title: CoREST Complex Inhibition Alters RNA Splicing to Promote Neoantigen Expression and Enhance Tumor Immunity [RNA-seq]

first: Robert

last: Fisher

overall_design: Total RNA was extracted from melanoma cell lines treated with corin (2.5uM, 24h) or vehicle control (DMSO) using the Qiagen RNeasy Mini Kit. Samples were quantified using nanodrop and sequenced by Azenta Inc.

first: Kihyun

last: Park

first: Kwangwoon

last: Lee

first: Katarina

last: Pinjusic

first: Allison

last: Vanasse

first: Christina

last: Ennis

first: Scott

last: Ficcaro

first: Jarrod

last: Marto

first: Stephanie

last: Stransky

first: Joseph

last: Duke-Cohan

first: Anupa

last: Geethadevi

first: Eric

last: Raabe

first: Simone

last: Sidoli

first: Derin

last: Keskin

first: Chad

last: Hicks

first: Catherine

last: Wu

first: Philip

last: Cole


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

status: Public on May 21 2025

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

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: scRNAseq was performed in TX1072 SP427 XX CasTuner mESCs with guides targeting the Xist TSS or the Xist-regulating REs 61, 85, 93 and 96 following 4 days of 2i/LIF-withdrawal. Gradual Xist repression was induced via the addition of different dTAG concentrations to the medium (0, 1, 2, 4, 8 and 500 nM). The cells were sequenced with 10x Chromium following a MULTIseq protocol. Sample barcodes for de-convoluting the raw .fastq files, as well as filtered counts with assigned samples are included in the supplementary files. The experiment was conducted  in 2 replicates.

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

last: Schulz


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

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: YAP1-TFE3 mediates endothelial to mesenchymal transition in epithelioid hemangioendothelioma

city: West Lafayette

first: Majid

last: Kazemian

state: IN

address: 201 S. University Steet

department: Biochemistry and Computer Science

institute: Purdue University

summary: Epithelioid Hemangioendothelioma (EHE) is an ultra-rare vascular sarcoma with a high metastatic rate and a lack of reliable prognostic markers. Because of its rarity, EHE is an understudied disease with limited research tools and few effective treatment options. A thorough understanding of the molecular underpinnings that drive EHE tumorigenesis and facilitate metastasis is essential to discovery of druggable targets that could improve patient outcomes. To better understand this EHE biology we generated transgenic endothelial EHE cell models and observed robust transformation of YAP1-TFE3 (YT) expressing cells resulting in a pro-migratory, anti-apoptotic phenotype. We identified endothelial to mesenchymal transition (EndMT) as a contributing process to this transformation as evidenced by the loss of enothelial gene expression and strong increases in EndMT biomarkers Acta2 and Tgm2. To understand the underlying drivers of this process, we utilized mutant versions of YT and pharmacologic inhibitors to determine that the DNA-binding and dimerization bHLH-LZ domain of YT was necessary for EndMT to occur while canonical TEAD activation was dispensable. This project sheds light on molecular mechanisms of EHE which directly contribute to endothelial transformation.

overall_design: To characterize the transcriptional landscape of EHE, transgenic MS1 murine endothelial cell lines were generated to express either YAP1-TFE3 or an RFP control under a doxycycline inducible promoter. RNA was extracted 3 days post-doxycycline induction (1µg/mL). RNA-seq was performed to identify differential gene expression in response to YAP1-TFE3 expression.

first: Jason

last: Hanna

first: Ant

last: Murphy


title: CO2 sensing pathway controls drug resistance and skin tropism in Candida auris

city: Vienna

first: Trinh

last: Phan-Canh

email: phancanht99@univie.ac.at, phancanhtrinh@gmail.com, karl.kuchler@univie.ac.at, karl.kuchler@univie.ac.at

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs Vienna, Campus Vienna Biocenter

country: Austria

institute: Medical University of Vienna

summary: Comparative transcriptomic profiling of Candida auris RCA1 and EFG1 null mutants in comparison to the Wild-Type Strain

overall_design: RNA Sequencing was conducted on clinical isolates of Candida auris, including the wild-type (WT) strains and deletion mutants in RCA1 or EFG1. The cells were cultivated to the exponential phase in YPD at 37°C with agitation at 200rpm. Subsequently, cultures were harvested, and RNA isolation was performed, followed by the preparation of sequencing libraries for three biological replicates. Specifically, for the rca1∆ mutant, sequencing was conducted on two distinct clinical strains labeled as R1 and R2. For the efg1∆ mutant, sequencing analysis was performed on the R1 strain.

first: Karl

last: Kuchler


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

first: Till

last: Schwämmle

overall_design: mRNA-seq in TX1072 XX and XO cells during the first 96 hours of 2i/LIF-withdrawal. Three replicates per timepoint and cell line. Only two replicates are available for XO_36h.


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

overall_design: CUT&Tag for active histone modifications in female mouse embryonic stem cells (mESCs) differentiated for 2 days by 2i/LIF-withdrawal. CRISPRi (dCas9-HDAC4) was used to knockdown the indicated factors. Three replicates per condition are included.

first: Gemma

last: Noviello


title: Analysis of gene expression in TNF transgenic mice

status: Public on May 17 2025

city: Rochester

first: Benjamin

last: Korman

state: NY

address: 601 Elmwood Avenue, Box 695

institute: AIR

summary: Recently, we found that human TNF transgenic (TNF-Tg) mice died by 6-month from cardiopulmonary disease. Histological analysis showed that TNF-Tg mice were characterized by the pulmonary vascular and right ventricular pathology. This pathology closely mimics human connective tissue disease (CTD) associated pulmonary arterial hypertension (PAH). In this study, we aimed to investigate the gene expression in TNF-Tg lung using bulkRNA-seq technology.

overall_design: Lung was harvested from 4-month-old TNF-Tg and WT mice. Total RNA was extracted using QIAGEN Rneasy Plus Kits.

first: Gaochan

last: Wang


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

overall_design: CRISPRi screens targeting transcription factor (TF) genes. Xist-High, -Low and -Negative populations were sorted using flow cytometry following FlowFISH staining for Xist RNA. The TFi library targets 570 TF genes using 11058 sgRNAs. The TFiMini library targets 119 TF genes (FDR <0.2 from the TFi screen) with 1270 individual sgRNAs. Two replicates were collected per screen

first: Eleni

last: Kanata

first: Jonathan

last: Froehlich

first: Melissa

last: Bothe


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

overall_design: scRNAseq was performed in TX1072 XX and TX1072 XX dFtx-Xert -/- mESCs following 4 days of 2i/LIF-withdrawal. The cells were sequenced with 10x Chromium following a MULTIseq protocol. As the libraries were prepared together with an unrelated experiment, the provided FASTQ files were filtered for reads matching assigned cell barcodes (using UMI-tools and seqtk). The setup includes 2 replicates (REP1: 187 WT, 87 DEL cells; REP2 325 WT, 79 DEL cells).

first: Alexandra

last: Martitz

first: Aybuge

last: Altay

first: Jade

last: Scouarnec


title: Changes in Gut, Microbiome, and Cognition after Doxorubicin, Cyclophosphamide, and Paclitaxel Chemotherapy Treatment

status: Public on May 29 2025

city: Little Rock

first: Michael

last: Robeson

state: Arkansas

address: 4301 W. Markham St., Slot 782

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Chemotherapy induced cognitive impairment (CICI), or “chemobrain”, is defined as an impairment in memory, learning, executive function, and attention following chemotherapy treatment. In this study, 12-week-old female C57/BL6 mice were treated with 8 once weekly intraperitoneal injections (IP) of the following chemotherapeutic treatment groups: 1) Doxorubicin (Dox), Cyclophosphamide (CYP), and Paclitaxel (PTX) (AC-T) or 2) saline. At 30 days after the last AC-T or Saline injection, mice underwent the three-chamber sociability test to assess social behavior and social memory. AC-T treated mice spent equal time with both the novel and the stranger mouse, indicating a deficit in social memory. RNA sequencing showed changes in networks associated with neurogenesis, axonal guidance and neurotransmission.

overall_design: Whole brains were harvested and flash frozen in 2-methylbutane. Hippocampal samples were collected from coronal slices using a 0.2mm tissue punch and were sent to the RNA Sequencing Core for processing. There were 6 samples for each treatment group: AC-T and Saline. RNA was extracted from samples using the Zymo Quick-DNA/RNA miniprep Plus Kit (Cat # D7003). mRNA Library was constructed using the Illumina TruSeq Stranded mRNA Library Prep kit (Cat # 20020594). Samples were run on a 200-cycle NextSeq 2000 P2 flow cell. Dragen (v 4.3.6) was used for binary base call conversion and FastQC (v 0.11.9) was used for quality control. Quantification was done using Salmon (v 1.9.0). Fastq files were uploaded into Qiagen Ingenuity Pathway Analysis (IPA) via the RNA-Seq Analysis Portal (https://digitalinsights.qiagen.com/IPA).

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