title: Single-nucleus multiomics of murine gonads reveals gene-regulatory networks underlying sex determination

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

address: 111 TW Alexander Drive

institute: NIEHS/NIH

summary: Sex determination in the mammalian gonad involves coordinated lineage decisions in both germ cells and gonadal supporting cells. To define the regulatory programs driving these processes, we generated a single-nucleus multiomics atlas of murine fetal gonads, integrating chromatin accessibility and gene expression from individual nuclei across sex determination timepoints in both XX and XY gonads. In primordial germ cells (PGCs), joint RNA- and ATAC-seq profiling identified transcriptional states and regulatory elements underlying germ cell sex determination. These data resolved previously uncharacterized PGC subpopulations, revealed that changes in chromatin accessibility often precede transcriptional activation during PGC lineage commitment, and showed that sexual dimorphism in gene expression and chromatin state increases over developmental time. Motif enrichment and gene-regulatory network analyses highlighted distinct cohorts of transcription factors associated with XX and XY germ cell differentiation, including TFAP2C, TCFL5, GATA2, MGA, NR6A1, TBX4, and ZFX in XX PGCs, and forkhead-box and POU6 factors in XY PGCs. The dataset also captured dynamic signaling pathways (WNT, BMP, and RA) and potential cell-cell communication interactions between PGCs and the surrounding somatic niche. In the supporting cell lineage, integrated snRNA- and snATAC-seq analyses revealed how precursor cells diverge to form Sertoli cells in testes and granulosa cells in ovaries. Sex-specific chromatin accessibility in supporting cells emerged shortly after sex determination, accompanied by activation-associated histone marks. Motif analyses identified regulatory networks associated with ovary-enriched transcription factors such as LEF1 and MSX1, which promote granulosa fate by activating key target genes including Foxl2 and Fst (bioRxiv 2025.02.24.639877). Together, this dataset provides a multimodal reference map of the chromatin landscapes, transcriptional programs, and regulatory networks that coordinately govern sex determination of germ cells and supporting cells during murine gonadal development.

overall_design: Single nuclei were extracted from embryonic gonads from E11.5-E13.5 male and female mice. Joint snRNA and snATAC-seq libraries were prepared using the 10x Genomics platform.

first: Adriana

last: Alexander

first: Karina

last: Rodriguez

first: Yu-Ying

last: Chen

first: Ciro

last: Amato

first: Martin

last: Estermann

first: Xin

last: Xu


title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus [snRNA-seq]

status: Public on Mar 18 2025

city: Zürich

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

department: D-HEST Institute for Neuroscience

country: Switzerland

institute: ETH Zürich

type: Expression profiling by high throughput sequencing

summary: We explore how the tightly regulated molecular response triggered by acute restraint stress becomes altered after repeated restraint exposure. Transcriptomic sampling of the mouse hippocampus at multiple time points revealed that repeated stress leads to widespread habituation, damping stress-induced gene expression of all stress-responsive genes. However, we find no evidence for the emergence of new response profiles or alterations in baseline gene expression. Using single-cell multi-omics, we show that these findings hold true across cell types, and we reveal cell type specific patterns of habituation. Transcriptomic and chromatin accessibility profiles identify two distinct mechanisms that contribute to the observed habituation patterns: an early cAMP-associated mechanism that is related to blunted transcription after chronic stress, and a late corticosterone-dependent mechanism that is linked to a shortened transcriptional response.

overall_design: Restraint stress involves placing the mice in a 50 ml Falcon tube with a large air hole for 1h30. Chronically stressed animals were subjected to daily restraint for 10 consecutive days at varying time of day before the final (acute) stress exposure, while handling animals were handled gently (lifting the animals by the tail, simulating the handling method used before restraint stress). Following this treatment, animals were single-housed 24 hours before being subjected once again to the same restraint stress, and the samples were collected at various timepoints (see ‘ARS timepoint’ column) following stress initiation. All stress exposures were carried out between 10:00 and 17:00 in the animals’ active phase (i.e. reverse light cycle).

first: Rebecca

last: Waag

first: Emanuel

last: Sonder

first: Johannes

last: Bohacek


title: Combination of Cas9 and adeno-associated vectors (AAVs) enables efficient in vivo knockdown of precise miRNAs in the rodent brain

status: Public on Mar 19 2025

city: Marseille

first: Eduardo

last: Gascon

address: 27 boulevard Jean Moulin

department: Institut de Neurosciences de la Timone

country: France

institute: Aix-Marseille University, CNRS

summary: Although the advent of Cas9 technology has expanded our ability to precisely edit the genome, manipulating microRNAs in vivo has been shown to be particularly challenging, especially in the brain. Here, we sought to generate novel tools aiming at targeting and efficiently downregulating defined microRNAs species in a cell-specific manner so that their function in discrete neuronal networks could be investigated. Focusing on miR-124, a microRNA highly expressed in the mammalian brain and transcribed from three independent chromosomal loci, we designed and validated different gRNAs directed against this miRNA. In vitro, our Cas9 designs show not only a significant reduction in miR-124 levels but also a functional effect on miR-124 silencing. Similarly, when packed into AAV vectors and injected into the mouse cortex, miR-124-Cas9 vectors strongly downregulate miR-124 levels without affecting the expression of other miRNAs. In parallel, levels of endogenous miR-124 targets exhibit a significant increase supporting the release of its silencing activity. To functionally validate our tools, we provide evidences that deletion of miR-124 in the subventricular zone altered migration of newly generated neurons into the olfactory bulb. Finally, we also showed that our vectors altered the expression of Gria 2, a canonical target of miR-124, and modified the Ca2+ permeability of AMPA receptors. These tools are expected to help elucidating miRNA function in complex experimental settings such as brain networks in vivo.

overall_design: A set of seven animals received an injection of AAV-Cas9-miR-124-g4 and AAV-Cas9-miR-124-empty in each motor cortex. RNA sequencing was preformed on FANS sorted Cas9+ and Cas9- nuclei.

first: David

last: Roura-Martinez

first: Natalia

last: Popa

first: Florence

last: Jaouen

first: Cynthia

last: Rombaut

first: Catherine

last: Lepolard

first: Dipankar

last: Bachar

first: Ana

last: Borges

first: Maxime

last: Villet

first: Sebastien

last: Moreno

first: Helene

last: Marie


title: CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [MicroC]

city: Miami

first: Danny

last: Reinberg

state: FL

address: 1501 NW 10th Avenue (C227)

department: John T. MacDonald Department of Human Genetics

country: USA

institute: Miller School of Medicine and Sylvester Comprehensive Cancer Center

summary: CCCTC-binding factor (CTCF) is essential for chromatin organization, but its role in dynamically shaping chromatin loops during cellular differentiation is not fully understood. We previously demonstrated that CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA-binding region disrupts chromatin loops in mouse embryonic stem cells (ESCs). Using an ESC-to-neural progenitor cell (NPC) differentiation model, we show that the ZF1 RNA-binding region of CTCF is crucial for maintaining cell-type specific chromatin loops. Expression of CTCF-∆ZF1 leads to dysregulation of genes within these disrupted loops, particularly those involved in neuronal development and function. We identified NPC-specific, CTCF-interacting RNAs and chose Podxl and Grb10 for further study. We found that CRISPR-Cas9-mediated truncation of Podxl and Grb10 disrupts chromatin loops in cis, similar to the disruption seen in the NPC-∆ZF1 mutant. Our study underscores the importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity.

overall_design: Micro-C analysis of CTCF-AID2 degron and CTCF rescue wild-type (WT) and ΔZF1 mutant in both embryonic stem cells (ESCs) and neural progenitor cells (NPCs). Micro-C analysis of Podxl and Grb10 RNA truncation mutants in NPCs.

first: Kimberly

last: Lucero


title: NASH LiverModel transcriptome

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Mitochondrial reactive oxygen species (mROS) is central to normal physiology, but their excessive production correlates with the etiology of many human metabolic pathologies. We assessed in human liver biopsies from patients with non-alcoholic liver disease with different grades of liver steatosis and fibrosis the gene expression of ubiquinone genes and we uncover a positive relationship between QH2/Q ratio and the steatosis grade.  progresssion.

overall_design: Transcriptome analysis on liver biopsies from patients at different steatosis stages

first: I

last: Graupera

first: M

last: Coll


title: CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CTCF, Rad21, and Smc3 ChIP-seq analysis of CTCF-AID2 degron and CTCF rescue wild-type (WT) and ΔZF1 mutant in both embryonic stem cells (ESCs) and neural progenitor cells (NPCs). CTCF and Smc3 ChIP-seq analysis of Podxl and Grb10 RNA truncation mutants in NPCs.


title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus [bulk RNA-seq]

first: Pierre-Luc

last: Germain

overall_design: Restraint stress involves placing the mice in a 50 ml Falcon tube with a large air hole for 1h30. Chronically stressed animals were subjected to daily restraint for 10 or 20 consecutive days (see 'treatment' column) at varying time of day before the final (acute) stress exposure, while handling animals were handled gently (lifting the animals by the tail, simulating the handling method used before restraint stress). Following this treatment, animals were single-housed 24 hours before being subjected once again to the same restraint stress, and the samples were collected at various timepoints (see 'ARS timepoint' column) following stress initiation (time point 0min indicates an absence of acute stress, i.e. homecage animals). All stress exposures were carried out between 10:00 and 17:00 in the animals’ active phase (i.e. reverse light cycle).

first: Rebecca

last: Waag

first: Lukas

last: von Ziegler

first: Johannes

last: Bohacek


title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus [snATAC-seq]

first: Emanuel

last: Sonder


title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus

overall_design: Refer to individual Series


title: Single cell and clonal analysis of AL amyloidosis plasma cells and their bone marrow microenvironment

city: Boston

first: Nicolas

middle: Alejandro

last: Gort-Freitas

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

summary: AL amyloidosis is a disorder characterized by expansion of clonal plasma cells in the bone marrow and distant end organ damage mediated by misfolded immunoglobulin free light chains. There are currently limited data regarding the functional characteristics of AL amyloidosis plasma cells and their surrounding bone marrow microenvironment. We performed 5’ single cell RNA sequencing on 9 newly diagnosed, treatment naive AL amyloidosis patients and 8 healthy subjects. We identified generalized suppression of normal bone marrow hematopoiesis with distinct expansion of CD16 monocytes and subsets of CD4+ T cells in AL amyloidosis patients. We detected significant transcriptional changes broadly occurring among immune cells with increased interferon α and γ response and decreased TNF-α signaling. T and B cell receptor profiling revealed no overt clonal expansion of B or T cells in AL amyloidosis patients. However, we noted a disproportionate expansion of a distinct population of non-malignant plasma cells in AL amyloidosis patients. Finally, clonal AL amyloidosis plasma cells were identified based on their unique VDJ rearrangement and they showed increased expression of genes involved in proteostasis and antigen processing when compared to autologous, polyclonal plasma cells. Inter-patient transcriptional heterogeneity was evident, with transcriptional states reflective of common genomic translocations easily identifiable. Overall, this study defines the transcriptional characteristics of AL amyloidosis plasma cells and their surrounding bone marrow microenvironment, identifying transcriptional signatures that serve as candidates in early diagnosis in larger studies, and potential molecular targets for therapy.

overall_design:
Bone marrow aspirates were obtained from patients with newly diagnosed AL amyloidosis seen at our center between 2019 and 2023. Healthy samples were obtained from discarded surgical material of patients undergoing primary, elective total hip arthroplasty. On the day of analysis, samples were rapidly thawed in a 37 degree C water bath, transferred to a 15 ml conical tube and washed in RPMI with 50% fetal bovine serum medium (Gibco). Cells were spinned for 5 minutes at 300 rcf and resuspended in PBS without calcium or magnesium (Gibco) with 0.4% BSA (Miltenyi). Cells were counted and viable cells enriched via Dead Cell Removal MicroBeads (Miltenyi) according to the manufacturer's protocol. Cells were resuspended in PBS with 0.4% BSA prior to viability check and encapsulation. Samples with viability less than 70% were not included in downstream processing. 10X Chromium Next GEM Single Cell 5’ reagent kits and BCR/TCR amplification kits were used for joint transcriptional and immune profiling of bone marrow samples. For the CD138+ samples, a combined profiling of BCR and 5’RNA was performed. For CD138- samples, a combined profiling of BCR, TCR, and 5’RNA was performed. The samples were aggregated into a fewer number of fraction-specific pools (details in associated publication) and loaded at a concentration of 20,000 cells per lane. The resulting libraries were sequenced on Illumina NovaSeq S1.

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

first: Maria

last: Moscvin

first: Benjamin

last: Evans

first: Tianzeng

last: Chen

first: Samuel

last: Boullt

first: Sean

last: Rowell

first: Srinidhi

last: Raghav

first: Antonia

middle: F

first: Jacob

middle: P

last: Laubach

first: Allon

middle: M

last: Klein

first: Giada

last: Bianchi


title: Synergistic Potential of CDK4/6 Inhibitors and ATRA in non-APL AML.

city: Jena

first: Tino

last: Schenk

state: Thüringen

address: Am Klinikum 1

department: KIM II

country: Germany

institute: University Hospital Jena

summary: Background: Acute myeloid leukemia (AML) is a heterogeneous disease characterized by diverse genetic abnormalities. The standard of care remains to be chemotherapy and stem cell transplantation. In acute promyelocytic leukemia (APL), differentiation therapy with all-trans retinoic acid (ATRA) has significantly improved outcomes. Despite this, the success of ATRA has yet to be transferred to non-APL AML. Exploring combinations to enhance the efficacy of ATRA in non-APL AML remains a key focus. Objective: To investigate the therapeutic effect of ATRA in combination with cyclin-dependent kinase 4/6 (CDK4/6) inhibitors in non-APL AML. Methods: Non-APL AML cells and primary patient samples were treated with ATRA and CDK4/6 inhibitors. Key outcomes included differentiation, proliferation, cell viability, and colony-forming capacity. Combination synergy was evaluated, and gene expression analysis identified pathways associated with therapeutic effects. Results: The combination demonstrated dose-dependent effects, enhancing differentiation and reducing proliferation, cell viability, and colony-forming capacity. A synergistic effect was observed across AML cell lines. Gene expression profiling revealed the co-regulation of differentiation-associated genes, unveiling the mechanisms driving therapeutic synergy. Conclusion: Combination of CDK4/6 inhibitors with ATRA shows potential for differentiation-based AML treatment. This approach offers a promising avenue for improved outcomes in non-APL AML.

overall_design: RNA-seq profiling of HL-60 cells 3h following treatment with 500 nM palbociclib, 100 nM ATRA or the combination.

first: Rafał

last: Skopek

first: Setenay

last: Özcan

first: Paulina

last: Chmiel

first: Stephanie

last: Morgner

first: Jacqueline

last: Schuett

first: Faezeh

last: Ghazvini Zadegan

first: Clara

last: Stanko

first: Małgorzata

last: Palusińska

first: Karolina

last: Maślińska-Gromadka

first: Yordan

last: Sbirkov

first: Sven

last: Stengel

first: Martin

last: Fischer

first: Annamaria

last: Brioli

first: Arthur

last: Zelent

first: Lukasz

last: Szymanski


title: A rapid and dynamic role for FMRP in the plasticity of adult neurons

status: Public on Mar 15 2025

city: New York

first: Daniel

last: Guzman Gundermann

state: NY

address: 100 Washington Square E

institute: NYU

summary: Fragile X syndrome (FXS) is a neuro-developmental disorder caused by silencing Fmr1, which encodes the RNA-binding protein FMRP. Although Fmr1 is expressed in adult neurons, it has been challenging to separate acute from chronic effects of loss of Fmr1 in models of FXS. We have used the precision of Drosophila genetics to test if Fmr1 acutely affects adult neuronal plasticity in vivo, focusing on the s-LNv circadian pacemaker neurons that show 24-hour rhythms in structural plasticity. We found that over-expressing Fmr1 for only 4 hours blocks the activity-dependent expansion of s-LNv projections without altering the circadian clock or activity-regulated gene expression. Conversely, reducing Fmr1 expression prevented retraction of s-LNv projections. One FMRP target we identified in s-LNvs is sif, which encodes a Rac1 GEF. Our data indicate that FMRP normally reduces sif mRNA translation at dusk to lower Rac1 activity and acutely regulate neuronal plasticity.

overall_design: To identify the targets of Fmr1 in s-LNvs we expressed ADARcd and Fmr1-ADARcd in the s-LNvs of adult flies. We sorted their LNvs by using the Pdf-RFP transgene and then performed RNA-seq. Genomic DNA was isolated from flies which had the different transgenes to remove the posibility of SNPs being identified as targets.

middle: G

last: Gundermann

first: Seana

last: Lymer

first: Justin

last: Blau


title: A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum

city: Cambridge

first: Jens

middle: Bager

last: Christensen

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Understanding the molecular mechanisms driving lineage decisions and differentiation during development is especially difficult in systems with a diverse progenitor pool, such as the mammalian cerebellum. Here, we used single-cell RNA-sequencing (scRNA-seq) to characterise the developmental trajectories of Nestin-expressing progenitors (NEPs) in the neonatal mouse cerebellum. We identified FOXO1 as a key regulator of NEP-to-inhibitory neuron differentiation, acting directly downstream of ASCL1. Genome occupancy and functional genomic experiments using primary NEPs showed that both ASCL1 and FOXO1 regulate neurogenesis genes during in vitro differentiation, while independently regulating proliferation and survival, respectively. Furthermore, we demonstrate that WNT is a regulator of the transition from an ASCL1+ to FOXO1+ state. Finally, we show that the ASCL1-FOXO1 axis and role of WNT signalling is conserved in primary human NEPs. Through understanding how cerebellar interneurons differentiate, our findings may inform therapeutic strategies for cerebellar disorders such as spinocerebellar ataxia, where cerebellar interneurons are overproduced.

overall_design: Targeted DamID of Dam methylase, FOXO1- and ASCL1-Dam during in vitro differentiation of primary nestin-expressing progenitors.

middle: B

first: Alex

last: Donovan

first: Andrea

middle: H

last: Brand

first: Sumru

last: Bayin


title: Distinct molecular mechanisms of stress habituation in the mouse hippocampus [bulk ATAC-seq]

first: Pierre-Luc

last: Germain

overall_design: Restraint stress involves placing the mice in a 50 ml Falcon tube with a large air hole for 1h30. Chronically stressed animals were subjected to daily restraint for 10 consecutive days at varying time of day before the final (acute) stress exposure, while handling animals were handled gently (lifting the animals by the tail, simulating the handling method used before restraint stress). Following this treatment, animals were single-housed 24 hours before being subjected once again to the same restraint stress, and the samples were collected 45min following stress initiation (time point 0min indicates an absence of acute stress, i.e. homecage animals). All stress exposures were carried out between 10:00 and 17:00 in the animals’ active phase (i.e. reverse light cycle).

first: Rebecca

last: Waag

first: Johannes

last: Bohacek


title: BMP-dependent mobilization of fatty acid metabolism promotes Caenorhabditis elegans survival on a bacterial pathogen

status: Public on Mar 12 2025

city: Flushing

first: Cathy

last: Savage-Dunn

address: 65-30 Kissena Ave

department: Biology

institute: Queens College and the Graduate Center, CUNY

summary: The Bone Morphogenetic Proteins (BMPs) are secreted peptide ligands of the Transforming Growth Factor beta (TGF-β) family, initially identified for their roles in development and differentiation across animal species. They are now increasingly recognized for their roles in physiology and infectious disease. In the nematode Caenorhabditis elegans, the BMP ligand DBL-1 controls fat metabolism and immune response, in addition to its roles in body size regulation and development. DBL-1 regulates classical aspects of innate immunity, including the induction of anti-microbial peptides. We theorized that BMP-dependent regulation of fat metabolism could also promote resilience against microbial pathogens. We found that exposure to a bacterial pathogen alters total fat stores, lipid droplet dynamics, and lipid metabolism gene expression in a BMP-dependent manner. We further showed that fatty acid desaturation plays a major role in survival on a bacterial pathogen, while fatty acid β-oxidation plays a more minor role. We conclude that C. elegans mobilizes fatty acid metabolism in response to pathogen exposure to promote survival. Our investigation provides a framework to study potential metabolic interventions that could support therapeutics that are complementary to antibiotic strategies.

overall_design: RNA-seq profiling of C. elegans wildtype and dbl-1 mutants after 24 hour exposure to either control Escherichia coli bacteria or pathogenic Serratia marcescens

first: Katerina

middle: K

last: Yamamoto


title: Development and Characterization of Chicken Lung Organoids for Future In Vitro Modeling of Avian Influenza Virus-Host Cell Interaction [bulk RNA-seq]

status: Public on Mar 11 2025

city: Ames

first: Christopher

last: Zdyrski

state: Iowa

address: 1800 Christensen Dr, Bms 1072 Vet Med, Bms 1072 Vet Med

institute: Iowa State University

summary: High pathogenicity avian influenza viruses pose a growing threat to poultry, livestock, wildlife, and humans as they undergo accelerated expansion of host and geographical ranges. Since 2020, these viruses have driven a panzootic characterized by extensive viral diversification and spillover into species previously considered to be resistant. There is currently a lack of physiologically relevant in vitro models that can be used to screen the rapidly changing viral landscape. To address this need, we describe the first chicken lung organoids derived from adult stem cells of specific pathogen free White Leghorns. We analyze their gene expression with bulk RNA sequencing, confirm their cellular heterogeneity via single-nuclei RNA sequencing, and provide basic morphological characterization using hematoxylin and eosin (H&E) staining, immunohistochemistry, immunofluorescence, and transmission electron microscopy. The results indicate that the organoids contained several cell types, including non-ciliated columnar, cuboidal, squamous, and mucin-producing cells, representative of different regions of the avian respiratory system. Furthermore, expression of genes relevant to influenza A virus replication appeared to be conserved across different samples. These organoids have the potential to effectively and efficiently model viral infection of the chicken lung, enabling the investigation of viral pathogenesis and evolutionary potential, virus-host interactions, and discovery of targets for antiviral treatments.

overall_design: RNA-seq profiling of three SPF White Leghorn chicken organoids and corresponding tissues.

first: Hannah

last: Nicholson

first: Karin

last: Allenspach

first: Jonathan

last: Mochel

first: Silvia

last: Carnaccini


title: Development and Characterization of Chicken Lung Organoids for Future In Vitro Modeling of Avian Influenza Virus-Host Cell Interaction [scRNA-seq]


title: Targeting eRNA-producing super-enhancers regulates TNFα expression and mitigates chronic inflammation in mice and patient-derived immune cells [CUT&RUN]

city: Seoul

first: Su Min

last: Kim

state: Gangnam-gu

address: Dogok-ro 237

country: South Korea

institute: Severance Hospital

summary: Chronic inflammatory diseases are driven by immune cell dysregulation and overproduction of pro-inflammatory molecules, such as tumor necrosis factor alpha (TNFα). Super-enhancers (SEs) and their enhancer RNAs (eRNAs) are critical gene expression regulators and offer therapeutic potential beyond protein-targeting approaches. We hypothesized that targeting eRNAs could reduce chronic inflammation by modulating TNFα expression. We generated TNF-9 knockout (KO) mice by deleting a Tnfα-regulating enhancer region. These mice exhibited significantly reduced Tnfα levels, improved disease outcomes, and diminished immune cell activation in models of rheumatoid arthritis (RA), psoriasis, and lipopolysaccharide (LPS)-induced sepsis. Integrative epigenomic and transcriptomic analysis identified additional LPS-responsive, eRNA-producing enhancers as therapeutic targets. Antisense oligonucleotide (ASO)-mediated knockdown of TNF-9 eRNA in mouse macrophages demonstrated decreased Tnfα expression and alleviated RA symptoms. Furthermore, ASO-mediated inhibition of the eRNA of the human homolog of TNF-9 similarly reduced TNFα levels. These findings support eRNA-targeted interventions as potential treatment for chronic inflammatory diseases.

overall_design: CUT and RUN seq of BMDM from C57BL/6 mouse with or without LPS 1hr stimulation (with LPS stimulation : LPS, without LPS stimulation : UT). Chromatin profiling was conducted using three antibodies : H3K4me1 (me1), H3K27Ac (ac), and input control (IgG).

first: Minjeong

last: Cho

first: Jiyeon

last: Lee

first: Wonjin

last: Woo

first: Hyo Jin

last: Park

first: Eunji

first: Lark Kyun


title: Targeting eRNA-producing super-enhancers regulates TNFα expression and mitigates chronic inflammation in mice and patient-derived immune cells [RNA B6]

overall_design: RNA seq profiling of BMDM from C57BL/6 mouse with our without LPS 1hr stimulation (with LPS stimulation : LPS, without LPS stimulation : Control).


title: Transcriptome Analyses Reveal Molecular Responses of Three Potato (Solanum tuberosum L.) Cultivars to Cold Stress

city: Xining

first: xiang

last: Li

state: Qinghai

address: No. 251 Ningda Road, Chengbei District

country: China

institute: Qinghai University

summary: Potato (Solanum tuberosum L.), as an important food crop on the Qinghai-Tibet Plateau, is prone to low temperature and frost damage during the seedling stage, causing economic losses for farmers. In this study, transcriptome analyses were conducted on the leaves of Atlantic, KY130 and KY140 potato varieties following exposure to cold stress (CS). The genes StPAL(Soltu.Atl.09_2G005110) and StGAD(Soltu.Atl.11_3G000340), suggesting their involvement in the regulation of cold resistance in potato. “Flavonoid-related metabolism,” “lipid metabolism,” “amino acid metabolism,” “carbohydrate metabolism,” “nucleotide metabolism,” and “energy metabolism” might play an important role in the cold resistance of potato. Our results provided novel insights into the molecular mechanisms underlying cold resistance in potato.

overall_design:
Transcriptome analyses were conducted on the leaves of Atlantic, KY130 and KY140 potato varieties following exposure to cold stress (CS). CK(25℃, 12h) and CS( -4℃, 12h ) rep3

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

first: Zhenzhen

last: Zheng

first: Yun

last: Zhou

first: Shenglong

last: Yang

first: Wang

last: Su

first: Heng

last: Guo

first: Guangji

last: Ye

first: Jiang

last: Wang


title: Valorization of seaweed hydrolysate for production of the high-value reverse antibiotic nybomycin using metabolically engineered Streptomyces explomaris

status: Public on Mar 10 2025

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

institute: Bielefeld University

summary: This study develops a pipeline for high-level production  of the reverse antibiotic nybomycin from three seaweed species: Himanthalia elongata, Palmaria palmata, and Ulva lactuca. Screening Streptomyces strains identified S. explomaris, a marine species, as the best host to express the nybomycin gene cluster. The  accumulated low yields in artificial seawater with brown seaweed hydrolysate. Gene expression analysis revealed downregulation of precursor supply pathways and upregulation of repressors, limiting biosynthesis. Metabolic engineering addressed these bottlenecks, leading to a superior S. explomaris mutant achieving 57 mg/L, a five-fold increase as compared to reported yields. The strain effectively valorized commercial seaweed hydrolysates, highlighting marine feedstocks' potential for antibiotic production.

overall_design: Whole transcriptomes of a nybomycin production strain derived from four time points (early exponential phase (17 h), mid-exponential phase after glucose and mannitol depletion (33 h), stationary phase after galactose and mannose exhaustion (75 h), and late phase (175 h)) and two growth conditions (chemically defined medium using either deionized water or artificial sea water as a base) using 3 biological replicates each.

first: Wei

last: Shua

first: Julian

last: Stegmüller

last: Rückert-Reed

first: Jörn

last: Kalinowski

first: Andriy

last: Luzhetskyy

first: Christoph

last: Wittmann


title: Molecular Mechanisms Limiting the Therapeutic Window of AAV Gene Therapy in Mouse Models of Blue Cone Monochromacy

city: Morgantown

first: Gangqing

last: Hu

state: WV

address: 64 Medical Center Drive

institute: West Virginia University

summary: Blue cone monochromacy (BCM) is an X-linked retinal disorder caused by mutations in the OPN1LW/OPN1MW gene locus, resulting in impaired cone function and structural degeneration. We conducted a comparative analysis of AAV-mediated gene therapy in Opn1lw/Opn1mw double knockout (DKO) and Opn1mwC198R/Opn1sw-/- (C198R) BCM mouse models and evaluated the therapeutic window, efficacy, and longevity. Our results demonstrate that the AAV8-Y733F capsid achieved superior cone rescue compared to AAV5. While both DKO and C198R models showed similar therapeutic windows and rescue longevity, treatment efficacy decreased markedly in older mutant mice. Structural analysis revealed that aged cones in both models displayed degenerative changes, including mislocalized mitochondria and compromised connecting cilia. At the molecular level, we observed reduced AAV-mediated transgene expression in DKO and C198R older cones, which may result from decreased transduction efficiency, decreased circular episome stability, genome-wide transcription/translation downregulation, targeted mRNA/protein degradation, or overall cone degeneration. Notably, the cone-specific promoters for Pde6c and Cngb3 maintained robust activity in degenerating cones. These findings suggest that combining an efficient AAV serotype with an optimized cone promoter could be a viable approach to extend the therapeutic window and enhance treatment longevity for BCM patients.

overall_design: We generated two mouse models, DKO and C198R, for blue cone monochroamy. we compare gene expression changes in cone photoreceptors between C198R, DKO, and wild-type at 1- and 4- months ages. We also looked for cone genes whose expression remained unchangedenchavenunpregulatedges or evern upregulared in 4 mon vs 1 month in DKO and C198R mice.

first: Wen-Tao

last: Deng

first: Emily

last: Sechrest

first: Li

last: Ma


title: Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC)

city: Charlottesville

first: Xiaoqin

last: Wei

state: Virginia

address: 2512 Fontaine Ave

institute: University of Virginia

summary: Peroxisomes are essential but often overlooked metabolic organelles. To explore how macrophage peroxisomes protect the lung, we conducted single-cell RNA sequencing (scRNA-seq) on lungs from both naïve and SARS-CoV-2-infected Pex5^flox/flox (WT) and Cd11c-cre Pex5^flox/flox (KO) mice at 7 days post-infection (d.p.i). scRNA-seq revealed an increased proportion of inflammatory monocytes, neutrophils, and monocyte-derived macrophages (MDMs) in the lungs of infected KO mice, alongside a marked reduction in alveolar type 2 (AT2) cells and alveolar macrophages (AMs) compared to infected WT mice. AMs from KO mice showed elevated expression of genes involved in inflammatory responses, innate immunity, and cellular stress signaling, while genes related to wound healing, cell differentiation, and lipid metabolism were downregulated, compared to AMs from WT mice at 7 d.p.i.

overall_design: Cd11c-cre Pex5^flox/flox or Pex5^flox/flox mice were either uninfected (day 0) or infected with 2000 PFU of SARS-CoV-2 MA30 virus. Lung cells were harvested on day 0 and day 7 post infection. For each time point, cells from three individual mice per genotype were pooled and subjected to single-cell RNA sequencing (scRNA-seq) analysis

first: Jie

last: Sun


title: Targeting eRNA-producing super-enhancers regulates TNFα expression and mitigates chronic inflammation in mice and patient-derived immune cells [RNA-KO]

first: Su Min

last: Kim

overall_design: RNA-seq profiling of BMDM from HSS9 KO mouse (KO) and littermate control mouse (WT), with or without LPS 6hr stimulation (with LPS stimulation : LPS, without LPS stimulation : UT).

first: Minjeong

last: Cho

first: Jiyeon

last: Lee

first: Wonjin

last: Woo

first: Hyo Jin

last: Park

first: Eunji

first: Lark Kyun


title: ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vitro]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Tumor-associated macrophages (TAMs) are major players in regulating the immunosuppressive tumor environment, and their abundance is highly correlated with poor clinical outcomes. Here, we constructed a TAM regulatory network by integrating scRNA-seq data across human solid tumors with a dedicated CRISPR knockout screen. Using a deep generative model capable of learning a local representation for each candidate regulator, we constructed a gene perturbation network that linked individual target genes with prototypical functional modules in TAMs. We identified non-redundant pathways regulating distinct TAM functions, showing modular circuitry. For instance, the complement module is repressed by Stat6, Zeb2, Gpnmb, and Spp1, while the Tgfbr1-Smad2/4 pathway induces this program in TAMs. Importantly, we identified Zeb2 as the master regulator of pro-tumor functions in TAMs, orchestrating the suppression of type I interferon response and antigen presentation alongside the activation of immune suppression programs. Genetic ablation of Zeb2 reprogrammed TAMs identity on chromatin, RNA, and protein levels. In human tumors with high macrophage content, ZEB2 expression was associated with poor prognosis in solid cancers, including lung and bladder. Functional macrophage coculturing assays defined Zeb2 as a critical regulator of TAM immunosuppression activity by inhibiting T cell proliferation and activation. Selective in vivo targeting of Zeb2 in macrophages using a CpGsiRNAZeb2 DNA hybrid reprogrammed TAMs and mobilized systematic anti-tumoral T cell responses, achieving complete tumor clearance as a monotherapy. Overall, our study generated a detailed genetic roadmap of TAM gene circuits and identified ZEB2 as a master switch of TAMs with potential therapeutic implications for macrophage-based immunotherapies.

overall_design:
8 weeks old C57BL/6 mice were sacrificed and bone marrow was isolated and cultured in the presence of human MCSF in C10 medium to generate BMDMs. At day 2, medium was replaced with fresh medium and MCSF . At day 6, cells were treated with murine IL4, TGFb, IL13, IL10, IFNg or left untreated. On day 7 for FACS sorting to SPID-seq scRNA-seq protocol.

UPDATE: [Feb-11-2026] The metadata_invitro_p.txt.gz file was updated to correct an error in the x,y coordinates of UMAP.

first: Fadi

last: Sheban

first: Truong

last: San Phan

first: Ken

last: Xie

first: Florian

last: Ingelfinger

first: Chamutal

last: Gur

first: Yuval

last: Shapir Itai

first: Ronnie

last: Blecher-Gonen

first: Chunsong

last: Yu

first: Roberto

last: Avellino

first: Paulina

last: Chalan

last: Yofe

first: Vladimir

last: Yutkin

first: Pierre

last: Boyeau

first: Can

last: Ergen-Behr

first: Justin

last: Hong

first: Kfir

last: Mazuz

first: Rony

last: Dahan

first: Marcin

last: Kortylewski

first: Nir

last: Yosef

first: Assaf

last: Weiner


title: Increasing MG1-Mediated Death in HIV-Infected Cells with SMAC Mimetics

status: Public on Mar 07 2025

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: It was previously shown that interferon defects in latently HIV infected cells make them permissive to MG1 mediated killing. To increase effectiveness of MG1 therapy, we have combined MG1 with the SMAC mimetic birinapant to increase MG1 mediated killing in latently infected J1.1 cells. Increased cell death was observed compared to either treatment alone and was accompanied by increased caspase-3/7 and caspase-1 expression. However, cell death could not be blocked by the pan-caspase inhibitor ZVAD-fmk or the necroptosis inhibitor necrostatin1-s, alone or in combination, indicating that cell death does not occur via a single pathway. Furthermore, it was shown that SMAC mimetic treatment results in decreased transcription of genes that take part in the immune signalling pathway, which is likely one the ways how SMAC mimetic treament senstizes HIV infected cells to MG1 mediated death.

overall_design: 12 samples of J1.1 cells were analyzed using RNA-seq under 4 conditions containing 3 replicates each; untreated, infected with MG1_eGFP, infected with MG1_eGFP and treated with Birinapant, and treated with Birinipant only.

first: Bengisu

last: Yildirir

first: Jonathan

last: Angel


title: Active DNA demethylation is upstream of rod photoreceptor fate determination and required for retinal development [Bisulfite-Seq]

status: Public on Mar 01 2025

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

type: Methylation profiling by high throughput sequencing

summary: The goal of this study is to investigate the role of TET enzyme-mediated DNA demethylation on retinal development and cell fate specification. We utilized an allelic series of TET enzyme retinal conditional mouse mutants using the Chx10-Cre-GFP transgene, removing the TET enzymes from retinal progenitor cells. We observe that inhibition of DNA demethylation results in abnormal retinal development and a loss of visual function. Immunohistological and genomic profiling (RNA-seq, scRNA-seq, WGBS, and bACE-seq) indicate that rod photoreceptor gene regulatory networks are inhibited when DNA demethylation is lost, indicating that DNA demethylation is required for NRL and NR2E3 expression, resulting in a retina with increased specification of cone photoreceptors.

overall_design: Whole Genome Bisulfite Sequencing (WGBS) to profile methylated cytosines (5mC and 5hmC) and Bisulfite-assisted APOBEC-coupled epigenetic sequencing (bACE-seq) to profile hydroxymethylated cytosines (5hmC) in post-natal day 21 (P21)  mouse retinas from Cre-negative control and Tet1/Tet2/Tet3 conditional mutant animals. Recombination of floxed TET exons was induced in retinal progenitor cells using the Chx10-Cre-GFP transgene. Experiments were performed on RNA-DNA extractions from retinas, performing biological triplicates for each genotype with paired RNA and DNA samples for each biological replicate being used for RNA-seq, WGBS, and bACE-seq analyses.

middle: S

first: Ismael

last: Hernández-Núñez

first: Alaina

last: Urman

first: John

middle: R

last: Edwards


title: A circular RNA overcomes acquired resistance to BET inhibitors by antagonizing IGF2BP2-mediated c-MYC translation in triple-negative breast cancer

city: chengdu

first: PAN

last: YiTong

address: Wangjiang Street

institute: Sichuan University

summary: The bromodomain and extra-terminal domain (BET) proteins are promising therapeutic targets to treat refractory solid tumors including triple-negative breast cancer (TNBC); however, acquired resistance remains a major challenge in the clinic. Therefore, elucidation on the mechanism underlying acquired drug resistance is of practical significance. In this study, we found that abnormally upregulated RNA-binding protein IGF2BP2 acts as crucial contributor to triggering acquired BETi resistance in TNBC by facilitating the translational process of c-myc mRNAs. Considering that IGF2BP2 itself are not ideal drug target for small-molecular compounds, we carried out an RIP-seq experiment and identified circRNA-BISC as a potent IGF2BP2 repressor, which was able to repress both c-MYC translation process and acquired BETi resistance. BISC possesses a typical ‘CAC-linker-XGGX’ motif to specifically bind with IGF2BP2 without interactions with IGF2BP1 and IGF2BP3. The effectiveness and specificity of BISC on IGF2BP2 prompted further evaluation of the BISC-based RNA therapeutics in TNBC. In vitro transcribed and circularized BISC, when combined with OTX-015, achieves impressive tumor remission of the BETi-resistant TNBCs without obvious toxicities. Collectively, our result support BISC as a potent IGF2BP2 repressor and highlight the feasibility of pursuing BISC restoration by circRNA therapeutics to overcome BETi resistance.

overall_design: Both MDA-MB-231 parental cells and acquired BETi resistant cells were probed to RIP-seq using anti-IGF2BP2 mAb or normal rabbit IgG. Enrichment of IGF2BP2-associating circRNAs was measured by deducting the circRNA RPMs in IgG. Delta enrichment of IGF2BP2-associating circRNAs were calculated by minusing enrichment in parental cells from acquired BETi resistant cells. Candidates harboring the minus delta enrichments were considered as circRNAs whose association with IGF2BP2 were decreased upon acquired BETi resistance establishment.

first: Jiawei

last: Guo

first: Yitong

last: Pan


title: Active DNA demethylation is upstream of rod photoreceptor fate determination and required for retinal development [snRNA-seq]

overall_design: PIPseq single nucleus RNA-sequencing to profile gene expression patterns within individual retinal cells in post-natal day 21 (P21) mouse retinas from Cre-negative control and Tet1/Tet2/Tet3 conditional mutant animals. Recombination of floxed TET exons was induced in retinal progenitor cells using the Chx10-Cre-GFP transgene. Experiments were performed on pooled samples (> 4 retinas each) from 2 separate nuclear dissociations for each genotype

first: Philip

last: Ruzycki


title: Transcriptomic disruption and functional hypoactivity in DYT-SGCE MGE-patterned inhibitory neurons

status: Public on Mar 06 2025

city: Cardiff

first: Zongze

last: Li

summary: Myoclonus Dystonia is a Mendelian inherited, childhood-onset dystonic disorder, caused by mutations in the autosomal dominantly inherited SGCE gene, and in which both motor and psychiatric phenotypes are observed. Results from murine and in vivo human studies suggest dystonia is caused by disruption to neuronal networks, and in particular the basal gangliacerebello- thalamo-cortical circuit. Work focused on the cortical component implicates disruption to neuronal excitatory/inhibitory balance as being a key contributor in the observed phenotypes. Our previous work, focused on cortical excitatory glutamatergic neurons, demonstrated a hyperexcitable phenotype and more complex dendritic arborisation in an in vitro model of Myoclonus Dystonia. By contrast, human electrophysiological studies have suggested that it is the loss of inhibitory tone in this region that contributes to the overall hyperkinesis. To explore this further we have evaluated the impact of SGCE mutations on medial ganglionic eminence-derived inhibitory GABAergic neurons using the same patientderived induced pluripotent and gene edited embryonic stem cell lines, comparing each to their isogenic wild-type control. Differentiation towards inhibitory interneurons demonstrated no significant differences in neither early (NKX2.1, FOXG1), nor late stage (GAD67, GABA), developmental markers. Single-cell RNA sequencing additionally confirmed evidence of markers consistent with Medial Ganglionic Eminence-derived GABAergic neurons, and when compared to two publicly available human foetal ganglionic eminence transcriptomic datasets, confirmed that the cells generated resembled those found in vivo. Further analysis of this data demonstrated transcriptomic dysregulation in genes related to axonal organization, synaptic signalling and action potential generation in the SGCEmutation positive neurons. Subsequent characterisation of dendritic morphology found SGCE-mutation positive neurons to have shorter branches, fewer higher order branches and reduced branching complexity, compared to their wild-type controls. Functional analyses using Ca2+ imaging and MEA approaches to examine network activity identified significantly lower calcium responses to GABA and reduced spike and burst frequencies in the SGCEmutation carrying lines, compared to their isogenic controls. Reduced activity was also observed in single-cell patch clamp studies with fewer neurons firing action potential trains, coupled with fewer spontaneous post-synaptic currents, compared to controls. Collectively, this work indicates lower neuronal inhibitory activity and complexity of the dendritic arbor in the context of SGCE mutations, further contributing to the disruption of neuronal excitatory/inhibitory balance in motor circuits and potentially underlying the observed clinical hyperkinetic phenotype. These changes may also represent common characteristics across the wider dystonia spectrum, with potential for future target identification with amenability to therapeutic intervention

overall_design: Medial ganglionic eminence-derived inhibitory GABAergic neurons were differentiated from patient-derived induced pluripotent stem cells carrying SGCE mutation for 80 days and processed with Takara iCell8 for full-length single-cell RNA sequencing.

first: Laura

last: Abram

first: Maria

last: Cruz-Santos

first: Olena

last: Petter

first: Kathryn

last: Peall


title: Active DNA demethylation is upstream of rod photoreceptor fate determination and required for retinal development [RNA-Seq]

overall_design: RNA-sequencing to perform gene expression patterns in post-natal day 21 (P21) mouse retinas from Cre-negative control, Tet1/Tet2/Tet3 triple heterozygous Cre-positive, and Tet1/Tet2/Tet3 conditional mutant animals. Recombination of floxed TET exons was induced in retinal progenitor cells using the Chx10-Cre-GFP transgene. Experiments were performed on RNA-DNA extractions from retinas, performing biological triplicates for each genotype.


title: V-ATPase-dependent induction of selective autophagy

city: Ann Arbor

first: Yuxiang

last: Huang

state: MI

address: 2214 Stone Road

department: MCDB

institute: University of Michigan

summary: The general consensus is that the vacuolar-type H+-translocating ATPase (V-ATPase) is critical for macroautophagy/autophagy. However, there is a fundamental conundrum because follicular lymphoma-associated mutations in the V-ATPase result in lysosomal/vacuolar deacidification but elevated autophagy activity under nutrient-replete conditions and the underlying mechanisms remain mysterious. Here, working in yeast, we show that V-ATPase dysfunction activates a selective autophagy flux termed the "V-ATPase-autophagy axis". By combining transcriptomic and proteomic profiling, along with genome-wide suppressor screening approaches, we found that the V-ATPase-autophagy axis is regulated through a unique mechanism distinct from classical nitrogen starvation-induced autophagy. Tryptophan metabolism negatively regulates the V-ATPase-autophagy axis via two parallel effectors. On the one hand, it activates ribosome biogenesis, thus repressing the translation of the transcription factor Gcn4/ATF4. On the other hand, tryptophan fuels NAD+ de novo biosynthesis to inhibit autophagy. These results provide a clear explanation for the mutational activation of autophagy seen in follicular lymphoma patients.

overall_design: Trpytophan prototrophic and tryptophan auxotrophic yeast SEY6210 cells are cultured in nutrient-rich YPD medium, then treated with/without 3-IAA to induce temporal degradation of VMA2-AID*-9MYC protein.

first: Daniel

last: Klionsky


title: Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read and single-molecule resolution [Nanopore]

status: Public on Mar 05 2025

city: Irvine

first: Annie

last: Trinh

state: CA

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: Faithful epigenetic inheritance across cell divisions is essential to maintaining cell identity and involves numerous epigenetic modifications, whose roles in coordinating chromatin architecture are less understood. Technological approaches to temporally order epigenetic modifications throughout the cell cycle often face limitations in sequence resolution and rely on potentially damaging mitotic labeling or conversion steps. Herein, we present Methylation Pseudotime Analysis Through read-level Heterogeneity (MPATH), a label- and conversion-free method to infer post-replication DNA strand maturity from methylation patterns across single molecules. We use MPATH to temporally order hydroxymethylation throughout mitotic inheritance revealing, for the first time, that CpGs within cis-regulatory elements undergo transitions between methylation states at sub-cell-cycle timescales. When applied to long reads generated by NOMe-seq, MPATH uncovered relationships between nucleosome occupancy and DNA maturity. Finally, extension of MPATH to phased reads reveals allele-specific trends in pseudotime distribution associated with X chromosome inactivation. Our findings suggest that when coupled with multimodal sequencing strategies, MPATH could provide valuable insights into chromatin restoration dynamics.

overall_design:
HUES64 hESCs were subjected to several different experimental conditions prior to DNA extraction for long-read sequencing. In the first experiment, hESCs were treated with 2µg/ml nocodazole for 16h. BrdU pulse-chase experiments were conducted on HUES64 hESCs to investigate DNA methylation patterns during chromatin maturation. For the pulse optimization, cells were subjected to 50 µM BrdU for durations of 10 minutes, 20 minutes, 30 minutes, and 1 hour, followed by genomic DNA collection at 0h (nascent chromatin) and 16h (mature chromatin). Mock controls were included for both 0h and 16h timepoints. Optimized labeling conditions included a 500 µM BrdU pulse (10 minute duration) with 0h and 16h chase points. Unlabeled HUES64 samples were also generated (sequenced to a total of 62x coverage across 2 technical replicates). All long-read data was acquired using ONT sequencing platforms. In a separate sequencing experiment, hESCs were subjected to Repli-ATAC sequencing in order to temporally profile chromatin accessibility across replication-associated timescales.
>>>Raw data in POD5 or FAST5 will be available upon request by the submitter.<<<

first: Navied

last: Akhtar

first: Kwadwo

last: Bonsu

first: Nandor

last: Laszik

first: Asia

last: Mendelevich

first: Tanye

last: Wen

first: Julien

middle: L

last: P Morival

first: Katelyn

last: Diune

first: Mitchell

last: Frazeur

first: Justin

last: Vega

first: Alexander

last: Gimelbrant

first: Elizabeth

last: Read

first: Timothy

last: Downing

first: Kehan

last: Ren


title: Nelfb promotes dWAT formation through RNA Polymerase II-mediated adipogenic gene regulation

city: San Diego

first: Samiksha

last: Mahapatra

address: 9452 Medical Center Dr

institute: University of California San Diego

summary: Deletion of Nelfb in preadipocyte lineages in mice cause failure in dWAT and other fat depot formation, perinatal lethality, and reduced expression of adipogenic genes

overall_design: RNA seq on Day 14 CTL and Nelfb depleted cells

first: George

last: Sen


title: Single-cell RNA sequencing of the kidneys from adult old mouse

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

institute: Seoul National University Hospital

summary: This study aims to investigate the impact of aging on the kidney through the analysis of single-cell RNA sequencing datasets.

overall_design: We prepared scRNA-seq datasets from whole kidneys of male WT mouse (n=1; 22 weeks old)

first: Chaelin

last: Kang

first: Yun

last: Donghwan

first: Han

last: Seung Seok


title: Functional interplay between RND efflux pumps and GacS in Pseudomonas aeruginosa

city: Norman

first: Justyna

middle: Weronika

last: Adamiak

state: OK

address: 101 Stephenson Parkway

department: Chemistry and Biochemistry

institute: University of Oklahoma

summary: Pseudomonas aeruginosa is an opportunistic human pathogen, which is ubiquitous in the environment. The environmental versatility of P. aeruginosa is often attributed to a large arsenal of active efflux pumps, low permeability of the outer membrane and extensive regulatory networks. In this study, we analyzed putative functional interplay between polyspecific drug efflux pumps of Resistance-Nodulation-Division (RND) superfamily of proteins and GacSA two-component regulatory system. RND transporters are the major contributors to antibiotic resistance and survival under various environmental stresses, whereas GacSA is a global regulator and governs critical lifestyles during human colonization. We found that the inactivation of either RND pumps or gacS induces broad, partially overlapping responses in lifestyle, virulence and metabolic programs that are more pronounced during exponential than stationary phase. GacSA and RND efflux pumps induced opposite responses in gene expression of P. aeruginosa, whereas the overexpression of GacS was additive with the deletion of efflux pumps in gene expression and under growth conditions typically associated with human infections such as elevated temperature and iron deprivation. We conclude that RND efflux and GacSA networks partially overlap with each other.

overall_design: RNAseq analysis of the exponential and stationary Pseudomonas aeruginosa PAO1 and its derivatives lacking 6 RND efflux pumps (PΔ6fs; ΔmexAB-oprM ΔmexCD-oprJ ΔmexEF-oprN ΔmexJKL ΔmexXY ΔtriABC) and overexpressing gacS (Δ6gacSfs::LAC-gacS). Samples were analyzed in duplicate.

middle: W

first: Charles

last: Bergen

first: Valentin

middle: V

last: Rybenkov

first: Helen

middle: I

last: Zgurskaya


title: Macrophage peroxisomes guide alveolar regeneration and limit post-acute sequelae of SARS-CoV-2 infection (PASC).

first: Xiaoqin

last: Wei

summary: Peroxisomes are essential but often underappreciated metabolic organelles. In this study, we demonstrate that exuberant interferon signaling reshapes the macrophage peroxisome compartment following severe COVID-19. To uncover the molecular characteristics underlying the protective role of macrophage peroxisomes after viral infection, we isolated RNA from wild-type (WT) and Pex5-deficient alveolar macrophages (AMs) with or without Poly(I:C) treatment in vitro, followed by bulk RNA sequencing. Our analysis revealed enhanced expression of inflammation-associated pathways and innate immune responses in Pex5-deficient AMs. However, these cells also exhibited attenuated activation of tissue development-related pathways and impaired mitochondrial functions, regardless of Poly(I:C) treatment.

overall_design: Total RNA was extracted from in vitro cultured WT and Pex5-deficient AMs, with or without Poly(I:C) treatment for 24 hours, for bulk RNA sequencing. After quality control, only high-quality RNA (Agilent Bioanalyzer RIN > 7.0) was used to generate the RNA-seq library.

first: Jie

last: Sun


title: The Gut-larynx Axis and its Contribution to Laryngeal Immunity

status: Public on Mar 04 2025

city: Madison

first: Yixuan

last: Xie

state: Wisconsin

address: 320 East Wilson Street, 602

department: Department of Biostatistics and Medical Informatics

institute: University of Wisconsin - Madison

summary: The larynx is essential for swallowing, breathing, coughing, and voice production, supported by its unique microbial and immunological environment. Our previous research highlighted the role of resident laryngeal microbiota in shaping local immune responses. With growing interest in the gut-lung axis—the bidirectional communication between gut and respiratory immunity—the potential influence of gut microbiota on laryngeal immunity warrants exploration. We hypothesized that a gut-larynx axis may exist, where both resident laryngeal and gut microbiota contribute to immune modulation in the larynx. To investigate this, we treated conventionally raised, wild-type C57BL/6J mice with an oral antibiotic regimen known to disrupt gut microbiota, comparing them to untreated controls. Following treatment, the gut microbiota was significantly disrupted, while the laryngeal microbiota remained largely unchanged. However, antibiotic-treated mice exhibited marked changes in epithelial and immune cell proportions, as well as fibroblasts. Differential gene expression across cell types highlighted pathways related to epithelial barrier integrity, immune signaling, and bacterial response. Additionally, gut dysbiosis affected gene regulatory networks, with the activity of regulons Etv4(+), Irf3(+), Hltf(+), Mga(+), and Nfil3(+) showing significant changes. Notably, cell-cell communication was also altered, especially in immune-epithelial interactions, with integrin-mediated signaling emerging as a key ligand-receptor pathway in these intercellular communications. These findings suggest that gut and laryngeal microbiota may work synergistically to modulate immune responses in the larynx, underscoring the importance of considering gut-larynx interactions in studies of respiratory immunity.

overall_design: We have two experimental conditions: antibiotics treated mice and untreated control mice. Each moue group has 6 biological replicates (3 males, 3 femles). Each biological replicate was a pool of three male/female mosue larynges.

first: Ran

last: An

first: Elliot

first: John

last: Binns

first: Federico

last: Rey

first: Christina

last: Kendziorski

first: Susan

last: Thibeault


title: Copper-induced stress mechanisms in Erwinia amylovora: a comparative phenotypic and transcriptomic study using copper-sensitive and -tolerant strains

status: Public on Feb 28 2025

city: Prosser

first: Ricardo

last: Delgado Santander

address: 24106 N Bunn Rd

institute: Washington State University

summary: Erwinia amylovora causes fire blight. Copper is widely used for fire blight management but there is limited information on the pathogen’s copper homeostasis mechanisms. Upon identifyingE. amylovora strains with unusually high (EaR2, Ea17) and intermediate (Ea19) copper sensitivity, we characterized them phenotypically to find potential correlations with other traits.The highly copper-sensitive strains EaR2 and Ea17 grew slower, showed increased sensitivity to paraquat and cadmium, and developed a characteristic copper-dependent overproduction of amylovoran and levan, with patterns not observed in strain, Ea273, with regular copper tolerance. Copper sensitivity was also associated with higher copper-shock death rates after copper pre-exposure during growth. RNA-Seq analysis revealed similar responses to copper-shock in EaR2 and Ea273 but very different transcriptomic responses during copper adaptation(prolonged growth with copper). EaR2 responded to copper adaptation with earlier activation ofstress responses, exopolysaccharide biosynthesis pathways, and protein quality control systems, while reducing the expression of genes linked to iron uptake. Ea273 mostly displayed an activation of copper homeostasis-related genes, with a characteristic downregulation of histidine catabolism.

overall_design: RNA-seq profiling of copper shock and copper adaptation responses in Erwinia amylovora strains with regular and hypersensitive copper tolerance

first: Awais

last: Khan

first: Paul

last: Stodghill

first: Srðan

last: Aćimović


title: RNA-seq Analysis of Acute myeloid leukemia (AML) primary samples

city: Jena

first: Faezeh

last: Ghazvini Zadegan

address: Hans-Knoll-Strase 2

department: Department of Hematology/Oncology, Clinic of Internal Medicine II

institute: Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB)

summary: In this study, we examined gene expression in 69 primary samples from patients with Acute Myeloid Leukemia (AML), a complex hematologic malignancy, aiming to uncover potential avenues for novel treatment strategies.

overall_design: Primary human AML samples were isolated from peripheral blood mononuclear cells utilizing StemSep columns (STEMCELL Technologies, Canada). These samples were subsequently cultured in Stemline II Medium (Sigma, Hamburg, Germany) prior to harvesting for gene expression experimentation.


title: Integrative epigenomic profiling of hepatocellular carcinoma uncovers aberrant cis-regulatory changes and potential prognostic indicators [RNA-seq]

city: Hong Kong China

first: Cheuk Yin

last: CHENG

address: The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong

department: Life Science

country: Hong Kong

summary: Hepatocellular carcinoma (HCC) exhibits widespread epigenetic aberrations; however, the underlying transcriptional regulatory landscape remains underexplored. Here, we performed integrated analyses with genome-wide profiles of the transcriptomes, histone modifications and DNA methylation from patient-derived HCC tumors and controls. We identified both global and focal epigenetic alterations including large-scale DNA methylation loss, and dysregulation of cis-regulatory elements (CREs) associated with genes involved in cell cycle control, immune responses, and extracellular matrix organization. Notably, we discovered that transcriptional upregulation of Glypican-3 (GPC3), a diagnostic biomarker and immunotherapeutic target for HCC, was linked to the reactivation of a fetal liver super-enhancer (SE). This SE, in concert with DNA hypomethylation of two CpG islands, modulated GPC3 expression. Global DNA hypomethylation also contributed to transcriptional dysregulation of retrotransposon-derived CREs. Specifically, we observed that patients with high expression of a HERVE-int-driven long non-coding RNA transcript showed poorer disease outcomes and specific molecular signatures associated with better response to immunotherapy. Our results highlight this and other retrotransposons as potential prognostic indicators and a predictive signature for immunotherapy response. Taken together, our findings provide insights into the role of epigenetic dysregulation of CREs and retrotransposons in hepatocarcinogenesis, which could benefit the clinical management of HCC.

overall_design: RNA-seq was conducted for wildtype HepG2 and PLC cells, and HepG2-THE1D and PLC-HERVE-int knockdown cells

first: Clooney

middle: C

last: Cheng

first: MingFung

last: Cheung

first: AhYoung

last: Lee

first: Julie

middle: Y

last: Ang

first: Ignacio

last: Riquelme Medina

first: Grace

last: Lo

first: Qiong

last: Wu

first: Savio

last: Ho-Chit Chow

first: Kevin

last: Yip

first: Alfred

first: Danny

last: Leung


title: Deciphering the role of IRF4 and its interacting proteins in differentiated regulatory and T helper 17 cells

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: The transcription factor interferon regulatory factor 4 (IRF4) is crucial for the differentiation and fate determination of pro-inflammatory Th17 and the functionally opposing group of immunomodulatory regulatory T cells.Despite its central role in Th lineage determination, molecular mechanisms of IRF4-mediated gene expression in fully differentiated Th17/Treg cells are still not fully understood. In the present study, we integrated data derived from affinity-purification and full mass spectrometry-based proteome analysis with chromatin immune precipitation sequencing (ChIP-Seq)to unveil IRF4-driven lineage determination in Treg and Th17 cells.This allowed the characterization of IRF4-steered expression of proteins generally involved in the T cell development as well as subtype-specific differentiation and identification of novel, yet uncharted IRF4 interactors. To out knowlede no other study investigated the molecular mechanisms of IRF4-steered gene expression and IRF4 interactions in an unbiased approach, directly comparing fully differentiated T helper 17 and regulatory T cells.

overall_design: Naive CD4+ T cells from splenocytes of IRF4bio (IRF4-Bio.Rosa26BirA) and control (Rosa26BirA) animals were in vitro differentiated into Th17 and Treg cells. IRF4-Bio.Rosa26BirA mice express a fusion protein of IRF4 with a short BirA-recognition site (Avi-Tag, Driegen et al, 2015, PMID: 16201414) and co-express the enzyme BirA, thereby IRF4 gets in vivo biotinylated. Control animals express only the enzyme BirA and have no biotinylated IRF4. After 3 days of cell differentiation with respective cytokines, the cells were harvested and crosslinked with formaldehyde. After cell lysis and sheering of the chromatin, magnetic streptavidin-coated beads (M280 Dynabeads) were added to the lysate and all IRF4-unbound chromatin fragments were washed away. After these extensive washing steps, only sequence-specific IRF4-bound chromatin fragments are eluted and sent for sequencing. As the target protein IRF4 is in vivo biotinylated, the IRF4bio-ChIP approach makes advantage of the strong non-covalent biotin-streptavidin interaction and does not require any IRF4-specific antibodies.

first: Anna

last: Gabele

first: Maximilan

last: Sprang

first: Tobias

last: Bopp

first: Ute

last: Distler


title: The Therapeutic Potential of mRNA-Mediated Type III Collagen Delivery for Photoaged Skin

city: City

first: Lianhao

last: Song

state: Guangzhou

address: Jinsui road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: Background: Skin aging can be classified into intrinsic and extrinsic types, with photoaging representing a significant form of extrinsic aging. Photoaging is caused by prolonged exposure to ultraviolet (UV) radiation, resulting in cellular damage, collagen degradation, and the development of wrinkles and pigmentation changes; severe cases can even lead to skin cancer. This condition affects individual aesthetics and health and imposes a broader societal burden, including increased healthcare costs and reduced quality of life. Addressing photoaging is critical, as effective treatments can enhance skin health, improve mental well-being, and alleviate the burden on healthcare systems, highlighting the importance of preventive and therapeutic strategies. Objective: This study aimed to develop a novel drug based on human type III collagen mRNA (hCOL3A1 mRNA) and to investigate its role in treating UVB-induced skin photoaging. Methods: We designed and synthesized the complete hCOL3A1 mRNA sequence and encapsulated it in lipid nanoparticles for skin delivery. The expression of the hCOL3A1 mRNA drug in human fibroblasts was examined by in vitro experiments, and its potential therapeutic effects on UVB-induced aging, oxidative stress, and inflammation were evaluated. In addition, we evaluated the efficacy of the hCOL3A1 mRNA drug on UVB-induced skin photoaging by an in vivo model. Results: It was found that the hCOL3A1 mRNA drug was effective in reducing UVB-induced skin photoaging, suggesting that the hCOL3A1 mRNA drug could be used as a therapeutic intervention for UVB-induced photoaging and also providing a novel approach to restore aging skin by increasing endogenous collagen production and reducing oxidative and inflammatory damage Conclusion: hCOL3A1 mRNA-LNP, as a novel protein therapeutic approach, overcomes the limitations of retinoic acid (RA) therapy, provides a simpler and more efficient therapeutic option, and is expected to be a new treatment for skin photoaging.

overall_design: RNA-seq profilling of balb/c-nude mice and UVB irradiation on their dorsal skin every other day for 8 weeks and tissue collection at day 28 ,The UV irradiation protocol started at an initial intensity equivalent to the minimal erythemal dose (MED) of 1 MED (60 mJ/cm²) for the first 2 weeks. The intensity was then gradually increased to 2 MED (120 mJ/cm²) in the third week, 3 MED (180 mJ/cm²) in the fourth week, and maintained at 4 MED (240 mJ/cm²) from the fifth to eighth week of the experiment.

first: Jiamin

last: Zhang

first: Shuqi

last: Chen

first: Zhi

last: Xie


title: Characterization of Arabidopsis thaliana MYB47 and MYB95 transcription factors in response to jasmonic acid in leaves.

city: Krakow

first: Kenji

last: Yamada

state: Malopolska

address: Gronostajowa 7A

department: Malopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

summary: We have found that Arabidopsis thaliana paralogous two MYBs, namely MYB47 and MYB95, regulate TSA1 and BGLU18 expression and ER-body formation in response to jasmonic acid (JA). To comprehensively understand the transcriptional regulation of these MYBs in response to JA, we conducted RNA-seq analysis between JA-treated rosette leaves of wild-type and myb47myb95 knockout mutants, together with myc2myc3myc4 mutant that is defective in master transcriptional regulator of JA signaling pathway. The transcriptome data analysis revealed that MYB47 and MYB95 regulate a subset of JA-responsive genes, including ER-body and defense-related genes.

overall_design: RNA-seq of Arabidopsis leaves of wild type, myb47,95, and myc2,3,4 mutants that were treated with or without methyl jasmonate.

first: Jakub

last: Bizan

first: Arpan Kumar

last: Basak


title: Longitudinal analysis of antigen-specific T cells after Shingrix vaccination

status: Public on Mar 09 2025

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: SHINGRIX vaccination was used to investigate the fate of antigen specific memory CD4+ T cell at both cellular and transcriptional level upon immunization in a one-year longitudinal study. SHINGRIX is a subunit vaccine with glycoprotein E (gE) of varicella zoster virus (VZV) as the immunogen and requires two doses at least 60 days apart for protection against Herpes Zoster in adults over 50 years old. Flow cytometry and single-cell RNA sequencing were used to evaluate cellular and transcriptomic changes of VZV gE epitope-specific CD4+ T cells in a TCR clonotypic fashion pre and post vaccination. Antigen-specific T cells remained at a higher frequency compared to baseline and retained markers of cell activation such as ICOS and PD1 even one year post-vaccination. Persistent TCR clonotypes amongst epitope-specific T-cells were common across different time points within each individual. Antigen-specific memory T cells with a dominant TCR clonotype at baseline remained at a relatively high frequency one year later after two doses of vaccine. In contrast, T cells with TCR clonotypes from naïve antigen specific cells at baseline could not be detected post-vaccination. Differential gene expression analyses of cells with identical TCR clonotypes show that cells post vaccination, including those at one year post vaccination, were distinct from cells at baseline, with upregulation of genes related to T cell differentiation, negative T cell regulation and T cell activation. Thus, in addition to an increase in frequency, committed memory T cells gain additional transcriptional changes upon vaccination that could alter the immune response against cognate immunogens compared to pre-vaccinated quiescent memory T cells.

overall_design: Varicella-Zoster virus  glycoprotein E-specific CD4 T Cells were sorted from blood from 7 patients treated with the Shingrix vaccine in two doses at days 0, 60, 74, and 365. Flow cytometry and single-cell RNA-Seq measured surface protein markers and RNA expression of these cells. TCR sequences were assembled from the RNA-Seq data.

first: Xiaomin

last: Wen

first: Alex

last: Hu

first: Scott

last: Presnell

first: David

last: Koelle

first: William

last: Kwok


title: Effect of depletion of HuR on gene expression in mouse head and neck squamous cell carcinoma (mHNSCC) cells

status: Public on Mar 03 2025

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: RNA-binding protein HuR (Hu Antigen R, alias ELAVl1) is a primary post-transcriptional gene regulatory protein. Its overexpression promotes the progression of multiple cancers, including head and neck squamous cell carcinoma (HNSCC). Although HuR promotes cancer progression, the crosstalk between HuR and immune cells during oral tumorigenesis remains elusive. Here, we investigated the effects of HuR on oral tumors and immune cell functions in vitro and in vivo using a transgenic HuR knockout (KO) mouse model. We observed that CRISPR/Cas9 mediated knockout of HuR in murine oral carcinoma cells failed to form colonies and tumors. The HuR KO cells exhibited reduced tumor volume with high infiltration of CD8+ and fewer CD4+ T cells, demonstrating that HuR may control the immune response during oral cancer progression.  Next, oral epithelial tissue-specific HuR KO failed to form neoplastic growth compared with the control 4NQO-induced tumor mice. The HuR KO mice show decreased Tregs and increased IFNg compared to WT tumor-bearing mice. The transcriptome obtained from RNA-Seq showed that multiple cancer pathways were altered between WT and HuR KO oral cancer cells. The HuR KO group showed significant negative regulation of transcription factors and positive regulation of extracellular matrix and cell adhesion pathways, demonstrating its significance in HNSCC. Specifically, positive regulation of HuR target mRNAs that encode proteins responsible for cancer stem cells associated with cell adhesion was observed and confirmed through mRNA half-life analysis. Finally, HuR inhibitor pyrvinium pamoate reduces the tumor burden through activation of CD8+ and reduction in CD4+ in tumors, demonstrating that anti-tumor functions were associated with HuR KO. Together, the results of this study indicate that HuR-mediated oral carcinogenesis, dependent on immune dysfunction and cell adhesion pathway, suggests that inhibition of HuR may enhance the anti-tumor potential for oral cancer therapeutics.

overall_design: To investigate the cooperative function of HuR in the HNSCC cell lines in which HuR has been knocked out by Crispr/Cas9. We then performed gene expression profiling analysis using data obtained from RNA-seq of control and KO cells with Biological triplicates.

first: Mrinmoyee

last: Majumder

first: Viswanathan

last: Palanisamy


title: Unraveling the mechanism of JPI-547 in human pancreatic cancer cells through transcriptome analysis.

city: Seoul

first: Kyoung-Seok

last: Oh

address: 101 Daehak-ro, Jongno-gu

institute: Seoul National University Cancer Research Institute

summary: This study aimed to elucidate the mechanism underlying the action of the dual PARP/Tankyrase inhibitor JPI-547 through RNA-sequencing. Focusing on human pancreatic cancer cell lines with either homologous recombination repair deficiency or Wnt-addiction, the investigation sought to uncover critical insights into the compound's mode of action.

overall_design: Capan-1 and HPAF-II cells treated with 1µM of olaparib or JPI-547 for 72 h were subjected to bulk RNA-seq.


title: Integrative epigenomic profiling of hepatocellular carcinoma uncovers aberrant cis-regulatory changes and potential prognostic indicators [ChIP-seq]

first: Cheuk Yin

last: CHENG

institute: The Hong Kong University of Science and Technology

overall_design: H3K27ac and H3K4me3 ChIP-seq were conducted for wildtype HepG2 and PLC cells

first: Clooney

last: Cheng

first: MingFung

last: Cheung

first: AhYoung

last: Lee

first: Julie

last: Ang

first: Ignacio

last: Riquelme Medina

first: Grace

last: Lo

first: Qiong

last: Wu

first: Savio

last: Ho-Chit Chow

first: Kevin

last: Yip

first: Alfred

first: Danny

last: Leung


title: Glycation-lowering compounds inhibit ghrelin signaling to reduce food intake, lower insulin resistance, and extend lifespan.

city: Novato

first: Pankaj

last: Kapahi

address: 8001 Redwood Blvd

institute: Buck Institute

summary: Non-enzymatic reactions in glycolysis lead to the accumulation of methylglyoxal (MGO), a reactive precursor to advanced glycation end-products (AGEs), which has been hypothesized to drive obesity and aging-associated pathologies. A combination of nicotinamide, lipoic acid, thiamine, pyridoxamine, and piperine (Gly-Low), was identified to lower glycation by reducing MGO and MGO-derived AGE, MG-H1, in mice. Administration of Gly-Low reduced food consumption, lowered body weight, improved insulin sensitivity, and increased survival in both leptin receptor-deficient (Leprdb) and wild-type C57B6/J mice. Unlike caloric restriction, Gly-Low modulated hypothalamic signaling by upregulating mTOR pathway signaling to inhibit ghrelin-mediated hunger response. Gly-Low also slowed hypothalamic aging and increased survival when administered as a late-life intervention, suggesting its potential benefits in ameliorating age-associated decline by inducing voluntary caloric restriction and reducing glycation.

overall_design: We profiled hypothalamic transcripts from male C57BL/6J mice at three ages under different treatment paradigms: 1) young (4-month-old) male C57BL/6J mice fed a control or glycation-lowering (Gly-Low) diet for 1 week, 2) aged (25-month-old) male C57BL/6J mice fed a control or glycation-lowering (Gly-Low) diet for 5 months and 3) young (3-month-old) male C57BL/6J mice fed a control diet for 1 week. We used differential expression anaysis to assess genes and pathways that change under acute treatment (1 week) in young mice and to assess how genes that change with age (old control vs young control) are influenced by prolonged (5 month) Gly-Low treatment of old mice (old Gly-Low vs old control).

first: Lauren

last: Wimer

first: Kiyomi

last: Kaneshiro

first: Jessica

last: Ramirez

first: Neelanjan

last: Bose

first: Martin

last: Valdearcos

first: Muniesh

last: Shanmugam

first: Dominique

middle: O

last: Farrera

first: Parminder

last: Singh

first: Jennifer

last: Beck

first: Durai

last: Sellegounder

first: Lizbeth

middle: E

last: Najera

first: Lisa

last: Ellerby

first: Soo-Jin

last: Cho

first: John

last: Newman

first: James

last: Galligan

first: Suneil

last: Koliwad


title: Epigenetic priming promotes acquisition of TKI resistance and oncogene amplification in human lung cancer [ChIP-seq 2]

status: Public on Feb 26 2025

city: New Haven

first: Eric

last: Sun

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale University

summary: In mammalian cells, gene copy number is tightly controlled to maintain gene expression and genome stability. However, a near-universal molecular feature across cancer types is oncogene amplification, which promotes cancer progression by dramatically increasing the copy number and expression of tumor-promoting genes. For example, in tyrosine kinase inhibitor (TKI)-resistant lung adenocarcinoma (LUAD), oncogene amplification occurs in over 40% of patients’ tumors. Despite the prevalence of oncogene amplification in TKI-resistant tumors, the mechanisms facilitating oncogene amplification are not fully understood. Here, we find that LUAD tumors exhibit a unique chromatin signature demarcated by strong CTCF and cohesin deposition in drug-naïve tumors, which correlates with the boundaries of oncogene amplicons in TKI-resistant LUAD cells. Throughout the acquisition of TKI resistance, we identified a global chromatin priming effect, marked by a dynamic increase of H3K27Ac, cohesin loading, and inter-TAD interactions, which occurs before the onset of oncogene amplification. Furthermore, we have identified that the protein METTL7A, which was previously reported to localize to the ER and inner nuclear membrane, has a novel chromatin regulatory function in binding to amplified oncogenes and regulating cohesin recruitment and inter-TAD interactions. Surprisingly, we discovered that METTL7A remodels the chromatin landscape prior to any noticeable oncogene copy number gains. Furthermore, while METTL7A depletion has little effect on drug-naïve cells, METTL7A depletion prevents the formation of TKI resistant-clones, highlighting the specific role of METTL7A as cells are acquiring resistance. In summary, we discovered an unexpected mechanism required for the acquisition of TKI resistance regulated by a largely uncharacterized factor, METTL7A. This discovery sheds new light into maintenance of oncogene copy number and paves the way to the development of new therapeutics for preventing TKI resistance in LUAD.

overall_design: ChIP-seq: ChIP-seq was performed against IgG or MYC-tag in Wild-Type or METTL7A-MYC-tag-FLAG expressing cells.

first: Rebecca

middle: M

last: Starble

middle: G

first: Rana

last: Gybli

first: Jonathan

last: Radda

first: Jiuwei

last: Lu

first: Tyler

last: Jensen

first: Ning

first: Shuai

last: Zhao

first: Nitin

last: Roper

first: Gang

last: Wang

first: Jikui

last: Song

first: Katerina

last: Politi

first: Siyuan

first: Andrew

middle: Z

last: Xiao


title: Epigenetic priming promotes acquisition of TKI resistance and oncogene amplification in human lung cancer

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

overall_design: Refer to individual Series


title: Single-cell RNA sequencing reveals T and B cell-related immune features in foot and mouth disease virus-infected mice

city: Lanzhou

first: Jingjing

last: Pei

address: No.1, Xujiaping, Chengguan District, Lanzhou, Gansu Province, P. R. China

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (LVRI, CAAS)

summary: T and B lymphocytes protect against foot and mouth disease virus (FMDV). They are essential for long-term immunity and viral clearance, but their immunological features in FMDV infection remain unknown. Here, we performed single-cell RNA sequencing (scRNA-seq) and conducted integrative analyses to determine cell composition, gene expression, cell-cell communication state, and regulatory network of T and B cells in the spleen of FMDV- and mock-infected mice. Our results revealed variational compositions of immune cells on the subsets level. Additionally, we determined the reshaping of several important pathways in T and B cells, such as the inhibition of antigen-presentation capacity. Finally, the remolding of cell-cell communication and regulatory networks was also characterized during FMDV infection. Overall, our research provides valuable insights and abundant resources for understanding the adaptive immune response in FMD.

overall_design: Three infected and three control spleens of ifnar-/- C57/B6 mice were isolated at 5 days post FMDV or solvet injection and analyzed using scRNAseq.

first: Yang


title: Epigenetic priming promotes acquisition of TKI resistance and oncogene amplification in human lung cancer [RNA-seq]

overall_design: RNA-seq: Osimertinib-resistant cells were derived from parental cells over the course of chronic osimertinib treatment. Time-course experiments with Osimertinib treatment specify how many days of treatment occurred before harvesting for RNA.

middle: B


title: Epigenetic priming promotes acquisition of TKI resistance and oncogene amplification in human lung cancer [ChIP-seq]


title: Joint single-cell profiling of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression (Superb-seq)

status: Public on Feb 25 2025

city: La Jolla

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: A longstanding barrier in genome engineering with CRISPR-Cas9 has been the inability to measure Cas9 edit outcomes at single-cell resolution. Here we present Superb-seq, a new technology for joint measurement of on-target and off-target Cas9 edits and transcriptomes by single-cell RNA sequencing. In contrast to Perturb-seq methods that read each cell’s guide RNA, Superb-seq directly reads Cas9 edits by leveraging T7 in situ transcription. We performed Superb-seq on 9,500 K562 cells, targeting four chromatin remodeler genes with seven guide RNAs. Superb-seq identified 11,891 edit events in 6,230 edited cells at all seven on-target sites and at 36 off-target sites. One notable off-target edit fell within the first intron of the deubiquitinase gene USP9X, which decreased its expression and perturbed the expression of downstream genes. Superb-seq uses off-the-shelf kits, standard equipment, and requires no virus, which will enable CRISPR screens in virus-intolerant cell types and functional characterization of off-target events.

overall_design:
To demonstrate that Cas9 genome edits can be identified through T7 RNA, we performed T7 in situ transcription and bulk RNA-seq on human nuclei containing T7 promoter-labeled edits.
To demonstrate single-cell edit capture and gene expression association, we performed Superb-seq on K562 cells edited at four chromatin remodeler genes (ARID1A, SMARCA4, CHD3, CHD4) with seven guide RNAs, and analyzed two single-cell libraries of 500 and 10,000 cells.

first: Michael

middle: H

last: Lorenzini

first: Brad

last: Balderson


title: Mechanistic Insights into Targeting APLN/APJ for Ameliorating Testosterone and Reproductive Disorders in Type 2 Diabetes (ATAC-seq)

status: Public on Feb 24 2025

city: Guangzhou

first: Ke

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

summary: About 10% of couples of reproductive age worldwide suffer from infertility, with male factors accounting for about 50%, and testosterone is essential for male fertility, but the mechanisms behind the poor sperm quality and abnormally low blood testosterone levels in diabetic patients are unclear. In this study, we found that the peptide Apelin (APLN) significantly inhibited testosterone secretion from Leydig cells (LCs), which in turn led to decreased sperm quality. APLN was found to be localized to leydig cells in the testes of several diabetic mice, and its expression was significantly increased. The addition of APLN to mouse leydig cells decreased testosterone content and decreased the expression of genes related to testosterone synthesis, but the addition of ML221, an APLN receptor inhibitor, significantly increased the expression of testosterone synthesis genes. Injecting ML221 into diabetic mice significantly increased testosterone levels in the blood, increased sperm count as well as enhanced sperm motility and ultimately increased live birth rate of mice after in vitro fertilization. Proteomics revealed that ML221 significantly increased the expression of NR2F2 and further activated the transcription of testosterone synthesis genes. This study will further use mouse and cellular models to completely unravel the specific mechanisms by which APLN inhibits testosterone secretion and elucidate the causes of decreased sperm quality in diabetic patients. This study provides a new clinical target for the development of drugs to improve fertility in diabetic patients.

overall_design: To demonstrate changes in chromatin accessibility under different conditions, we performed ATAC-seq analysis in mouse primary Leydig cells in control and high glucose treatment groups.

first: Xinyan

last: Yang


title: Spatial transcriptomics profiling of endometrial tissue from recurrent implanation failure patients.

city: Liverpool

first: Jamie

last: Soul

address: Crown St

department: ISMIB

institute: University of Liverpool

summary: Spatial transcriptomics allows the identification of disease- and cell-specific molecular signatures that may inform advance the biomarker development and future treatments. This study used the GeoMX platform to identify shared and disease-specific transcriptional signatures in  CD45, CD56, stromal and epithelial cell populations from patients with recurrent implantation failure

overall_design: Paraffin-embedded human endometrial biopsies from recurrent implanation faiure (n=8) and fertile controls (n=8) were sectioned and mounted on slides. Slides were stained with CD56, CD45, and PanCk antibodies to allow identification of cell type enriched regions. ROIs were selected based on marker staining and AOIs were collected from each ROI for RNA purification and transcriptome analysis using Digital Spatial Profiling (DSP) on the NanoString GeoMx platform.

first: Nicola

last: Tempest


title: Epigenetic priming promotes acquisition of TKI resistance and oncogene amplification in human lung cancer [CUT&RUN2]

first: Eric

last: Sun

overall_design: CUT&RUN: CUT&RUN was performed in PC9 wild-type and PC9 METTL7A KO (PC9_M7A_KO) against H2A and TOP2B.

first: Rebecca

last: Starble

first: Rana

last: Gybli

first: Jonathan

first: Jiuwei

first: Tyler

first: Ning


title: CD45+/Col I+ Fibrocytes: Major Source of Collagen in the Fibrotic Lung, but not in Fibroblast Cultures

first: Stefano

last: Berto

summary: The role of cells of the hematopoietic lineage in fibrosis is controversial. Here we evaluate the contribution of Col I+/CD45+ cells (fibrocytes) to lung fibrosis. Systemic bleomycin treatment was used to induce fibrosis in a bone marrow transplant and two transgenic mouse models. Lung cells from these mice were analyzed by flow cytometry, both immediately upon release from the tissue or following growth on tissue-culture plastic. Fibrotic and control human lung tissue were also used. Fibroblasts and fibrocytes derived from a transgenic mouse model were compared in terms of their morphology, growth, and adhesion to fibronectin. Single cell RNAseq was performed with the analysis focusing on CD45-/Col I+ “fibroblasts” and CD45+/Col I+ “fibrocytes” in control and fibrotic mouse lung tissue. Finally, we inhibited fibrosis in mice using a novel, water-soluble version of caveolin scaffolding domain (CSD) called WCSD.

overall_design: In both mouse and human lung tissue, we observed a large increase in fibrocyte number and Col I expression associated with fibrosis. In contrast, fibroblast number is not significantly increased. These results on increased fibrocyte number in fibrotic mouse lung tissue were strongly supported by single cell RNAseq. RNAseq also revealed that myfibroblast markers are associated with a fibrocyte cluster, not with a resident fibroblast cluster. Some investigators claim that fibrocytes are not present among primary fibroblasts. However, we find that fibrocytes are the predominant cell type present in these cultures prior to passage.  Fewer fibrocytes are present after one passage, and almost none after two passages. Like the classic description of fibroblasts, passage 0 fibrocytes are spindle-shaped (i.e. not the fried-egg shape of macrophages). Experiments suggest that fibrocytes are crowded out of cultures during passage because fibroblasts have a larger footprint than fibrocytes, even though fibrocytes bind more efficiently to fibronectin. Finally, we observed that in mice treated with bleomycin and WCSD, there was a large decrease in the number of fibrocytes present, but not in the number of fibroblasts, compared to bleomycin alone. In summary, fibrocytes are the major collagen-producing cell type that is increased in number in association with fibrosis as well as the major source of myofibroblasts.  The common observation that collagen-producing spindle-shaped cells associated with fibrosis are CD45- appears to be an artifact of passage in cell culture.

first: Suganya

last: Subramanian

first: Charles

last: Reese

first: Stanley

last: Hoffman


title: RNA Sequencing Analysis of NCAPD2 Knockdown in Lung Adenocarcinoma Cell Line PC9

city: Fuzhou

first: Yun

last: Wu

state: Fujian

address: 134 Dong Street, Gulou District

institute: Fujian Provincial Hospital

summary: This study investigates the effect of NCAPD2 knockdown on lung adenocarcinoma (LUAD) by performing RNA sequencing on PC9 cell lines. The experiment included three control PC9 cells and three PC9 cells in which NCAPD2 was knocked down using shRNA. This RNA sequencing experiment aims to elucidate the role of NCAPD2 in regulating gene expression associated with tumor proliferation, migration, and survival in LUAD. Analysis of differential gene expression provides insights into the pathways affected by NCAPD2 knockdown, with an emphasis on signaling pathways critical to LUAD progression, such as the PI3K/AKT pathway.

overall_design: The experimental design involved RNA sequencing of the lung adenocarcinoma cell line PC9, with the following groups: (1) three control PC9 cell replicates (shNC) and (2) three PC9 cell replicates with NCAPD2 knockdown (shRNA). Total RNA was extracted from each sample, and the quality was verified before sequencing library preparation. Sequencing was conducted using an Illumina platform to generate high-quality reads for transcriptome analysis. Differential expression analysis was performed to compare gene expression between the control and knockdown groups. The objective was to assess the impact of NCAPD2 knockdown on the transcriptional landscape of PC9 cells and identify affected pathways.

first: Ying

last: Lin


title: Single-nuclei RNA Sequencing Reveals Distinct Transcriptomic Signatures of Rat Dorsal Root Ganglia in a Disc-associated Chronic Low Back Pain Model

status: Public on Feb 22 2025

city: Dallas

first: Theodore

last: Price

state: TX

address: 800 W Campbell Rd

institute: The University of Texas at Dallas

summary: This study presents the first application of comprehensive single-nuclei RNA sequencing (snRNA-seq) of dorsal root ganglion (DRG) neurons in a rat model using Parse technology. Our dataset includes two experimental models: (1) control rats representing both sexes and (2) rats with disc-associated chronic lower back pain, alongside sham-treated animals. By leveraging high-resolution transcriptomic profiling, this study provides novel insights into the molecular landscape of DRG neurons, offering a valuable resource for understanding the cellular mechanisms underlying chronic pain.

overall_design: Nuclei were isolated from  T13-L1 DRGs rat dorsal root ganglion followed by fixation and  barcoding using the parse split seq technology.

first: Ishwarya

last: Sankaranarayanan