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

city: Miami

first: Danny

last: Reinberg

state: FL

address: 1501 NW 10th Avenue (C227)

department: John T. MacDonald Department of Human Genetics

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: 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.

first: Kimberly

last: Lucero


title: CD4+ cells and pediatric obesity-related asthma

status: Public on Mar 21 2025

city: Bronx

first: Deepa

last: Rastogi

address: 3415 Bainbridge Ave

country: USA

institute: Albert Einstein College of Medicine

type: Expression profiling by high throughput sequencing

summary: To investigate the contribution of CD4+ T cells in pediatric obesity-related asthma.

overall_design: Comparison of bulk and single cell RNA-seq footprint of CD4+ T cells in obese children with asthma (B group) to obese children without asthma (C group) and healthy weight children with (A group) or without asthma (D group).

first: David

last: Thompson


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

status: Public on Mar 19 2025

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.


title: Lineage Tracing Reveals Clone-Specific Responses to Doxorubicin in Triple-Negative Breast Cancer

status: Public on Mar 18 2025

city: Austin

first: Daylin

last: Morgan

state: Texas

address: 107 W Dean Keeton St

department: BME

institute: The Univeristy of Texas at Austin

summary: Triple-negative breast cancer, characterized by aggressive growth and high intratumor heterogeneity, presents a significant clinical challenge. Here, we use a lineage-tracing system, ClonMapper, which couples heritable clonal identifying tags with single-cell RNA-sequencing (scRNA-seq), to better elucidate the response to doxorubicin in a model of TNBC. We demonstrate that, while there is a dose-dependent reduction in overall clonal diversity, there is no pre-existing resistance signature among surviving clones. Separately, we found the existence of two transcriptomically distinct clonal subpopulations that remain through the course of treatment. Among clones persisting across multiple samples we identified divergent phenotypes, suggesting a response to treatment independent of clonal identity. Finally, a subset of clones harbor novel changes in expression following treatment. The clone and sample specific responses to treatment identified herein highlight the need for better personalized treatment strategies to overcome tumor heterogeneity.

overall_design: Targeted barcode sequencing of MDA-MB-231 cells with ClonMapper DNA barcode tags selected with doxorubicin treatment.

first: Andrea

middle: L

last: Gardner

first: Amy

last: Brock


title: Structural insights into spliceosome fidelity: DHX35-GPATCH1 mediated rejection of aberrant splicing substrates

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

country: China

institute: Fudan University

summary: The spliceosome, a highly dynamic macromolecular assembly, catalyzes the precise removal of introns from pre-mRNAs. Recent studies have provided comprehensive structural insights in the step-wise assembly, catalytic splicing and final disassembly of the spliceosome. However, the molecular details of how the spliceosome recognizes and rejects suboptimal splicing substrates remained unclear. Here, we show cryo-electron microscopy structures of spliceosomal quality control complexes from a thermophilic eukaryote, Chaetomium thermophilum. The spliceosomes, henceforth termed B*Q, are stalled at a catalytically activated state but prior to the first splicing reaction due to an aberrant 5’ splice site conformation. This is recognized by G-patch protein GPATCH1, which is docked onto PRP8-EN and ‑RH domains and has recruited its cognate DHX35 helicase to its U2 snRNA substrate. In B*Q, DHX35 has dissociated the U2/branch site helix, while the disassembly helicase DHX15 is docked close to its U6 RNA 3’ end substrate. Our work thus provides mechanistic insights into the concerted action of two spliceosomal helicases in maintaining splicing fidelity by priming spliceosomes that are bound to aberrant splice substrates for disassembly.

overall_design: We performed  RNA-seq to investigate the impact of DHX35 or GPATCH1 knock down on splicing fidelity.

first: Qianxing

last: Zhou

first: Jingdong

last: Cheng


title: Genome-wide mapping of H3K9me3 in platinum sensitive and resistant epithelial ovarian cancer cell lines.

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

country: Germany

institute: University Stuttgart

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq for H3K9me3 was performed in A2780 (platinum sensitive) and A2780cis (platinum resistant) cells and in sensitive A2780 cells with shRNA induced knockdown of FLYWCH1.

overall_design: Cells were transduced with control shRNAs and shRNAs targeting FLYWCH1. Treatment with 1 µM cPt was started 7 days after knockdown induction. After completion of the experiment (week 7) cells were sorted for shRNA expressing cells and ChIPseq for H3K9me3 performed.

first: Tabea

last: Fullstone


title: Injectable ECM-mimetic dynamic hydrogels abolish ferroptosis-induced post-discectomy herniation through in-situ delivery of nucleus pulposus progenitor cell-derived exosomes [RNA-Seq]

city: Chongqing

first: Wenkai

last: Wang

state: Chongqing

address: Gaotanyan main street

institute: Army Medical University

summary: The discectomy-induced ferroptosis stress on nucleus pulposus cells (NPCs) is a major cause for postoperative lumbar disc herniation (LDH) recurrence and intervertebral disc degeneration (IDD). Surprisingly, we discovered that nucleus pulposus progenitor cells (NPPCs) could transmit their ferroptosis-resistant phenotype to recipient NPCs through exosome-dependent cell-cell communication while identifying miR-221-3p as the primary anti-ferroptosis effector molecule therein. Based on these findings, we first developed a synthetically-tailored NPPC-derived exosomes with enhanced miR-221-3p expression and NPC uptake capacity through molecular and cellular engineering, which were then integrated into an injectable hydrogel based on extracellular matrix (ECM) analogues. The ECM-mimetic hydrogel (HACS) serves as a biomimetic filler for the post-operative care of herniated discs, which could be facilely injected into the discectomy-established nucleus pulposus (NP) cavity for localized treatment. HACS-mediated in-situ exosome release in the NP cavity enabled marked ferroptosis inhibition in NPCs that not only prevented LDH recurrence but also reversed the IDD symptoms, leading to robust restoration of NP structure and functions. This study offers a promising approach for the treatment of herniated discs with translational potential.

overall_design: RNA sequencing of NPCs following treatment with NPPC-Exo or miR-221-3p overexpressed NPPC-Exo


title: Polymer Model Integrates Imaging and Epigenomics to Elucidate the Role of the Cell’s Microenvironment in Shaping 4D Chromatin Organization [Hi-C]

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

summary: Chromatin epigenetic markers have been recognized to colocalize with phase-separated genomic compartments. While the correlation between 3D organization and epigenetic changes in response to extracellular stimuli has been observed, the causal physical underpinnings of 4D chromatin reorganization with changes in the cell microenvironment remain elusive. To tackle this, we introduce a dynamic, histone epigenetic remodeler-driven polymer model that incorporates next-generation sequencing data to identify active and repressed chromatin regions. The proposed chromatin-chromatin interaction energetics and diffusion-epigenetic reaction driven dynamics predict the formation and maintenance of characteristic heterochromatin-rich domains.  We establish a scaling relation for the sizes of these chromatin domains with modulation of epigenetic reaction rates. Additionally, our model predicts that the epigenetic and accessibility changes occur predominantly at the domain boundaries resulting from the diffusion-reaction balance. These predictions are verified using super-resolution imaging and Hi-C sequencing of hyperacetylated melanoma cells. Subsequent RNA-seq analysis suggests a pivotal role of these epigenetic shifts in driving the cell’s phenotype. Extending our model’s universality, we validate our mesoscale findings against chromatin rearrangement resulting from changes in the microenvironmental substrate stiffness.  Lastly, we evaluate the effect of altering the epigenetic reaction rates in silico and uncover a domain boundary driven cell-type invariant mechanism by which chromatin organization can drive epigenetic memory formation. These findings significantly advance our comprehension of how chromatin dynamics impact both short-term (immediate response) and long-term (memory) cellular behavior.

overall_design: We use Tricostatin A (TSA) as an HDAC inhibitor (Fisher Scientific 14-061). For TSA treatment, the cells were grown to >70% confluence for more than 24 hours before addition of 500 nM TSA along with basal media. These were put back into the incubator and cultured for another 2 hours.  These cells are then used for Hi-C and RNA-seq analyses

first: Vinayak

last: Vinayak

first: Ramin

last: Basir

first: Rosela

last: Golloshi

first: Joshua

last: Toth

first: Lucas

last: Sant’Anna

first: Melike

last: Lakadamyali

middle: P

first: Vivek

middle: B

last: Shenoy


title: Polymer Model Integrates Imaging and Epigenomics to Elucidate the Role of the Cell’s Microenvironment in Shaping 4D Chromatin Organization

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

overall_design: Refer to individual Series


title: Sorafenib-associated translation reprogramming in hepatocellular carcinoma cells

city: Sevilla

first: Alfonso

last: Rodriguez Gil

email: alfrodgil@gmail.com, arg@us.es

state: Sevilla

address: Avda. Manuel Siurot s/n

department: Oncohematology

country: Spain

institute: Instituto de Biomedicina de Sevilla (IBiS)

summary: Sorafenib (Sfb) is a multikinase inhibitor indicated as an oral first-line chemotherapeutic drug for patients with advanced hepatocellular carcinoma (HCC) that has been shown to increase very modestly life expectancy. We have shown that Sfb inhibits protein synthesis at the level of initiation in cancer cells. However, the global snapshot of mRNA translation following Sorafenib-treatment has not been explored so far. In this study, we performed a genome-wide polysome profiling analysis in Sfb-treated HCC cells and demonstrated that, despite global translation repression, a set of different genes remain efficiently translated or are even translationally induced. We reveal that, in response to Sfb inhibition, translation is tuned by established mRNA cis-acting elements and the corresponding protein factors that recognize them, including DAP5 and ARE-binding proteins. At the level of biological processes, Sfb leads to the translational down-regulation of key cellular activities, such as those related to the mitochondrial metabolism and the collagen synthesis, and the translational up-regulation of pathways associated with the adaptation and survival of cells in response to the Sfb-induced stress. Our findings indicate that Sfb induces an adaptive reprogramming of translation and provide valuable information that can facilitate the analysis of other drugs for the development of novel strategies to optimize Sfb therapy.

overall_design: RiboSeq experiment of Sorafenib and Control treated HepG Hepatocascinoma cell line. Samples are divided in Low polysome (F1) and high polysome (F2) fractions. Triplicate experiments.

first: Laura

last: Contreras

last: Rodríguez-Gil

first: Jordi

last: Muntané

first: Jesús

last: de la Cruz


title: Genome-wide profiling of R-loop by affinity-independent and nuclease-based method [RNA-seq]

city: Guangzhou

first: Ying

middle: liang

last: Sheng

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

summary: R-loop is abundant triplex nucleic strand in organism, but many physiological and pathological functions remain to be fully understood, owing to a lack of robust and high-resolution methods for genome-wide detection. In this study, we develop R-loop identification assisted by nuclease and high-throughput sequencing (RIAN-seq), a method to identify and quantify R-loop stoichiometry at affinity-independent enrichment. We reveal that RIAN-seq has ultrahigh sensitivity, accuracy and reliability for identifying R-loop sites, compared with all existing methods. In addition, RIAN-seq enables capturing previously unidentified clustered R-loop sites with distinct patterns. In sum, we reveal that RIAN-seq can not only quantitatively dissect the R-loop landscape at unprecedented resolution, but also provide an unbiased and convenient method for R-loop biology.

overall_design: Gene expression profiling of overexpressing Flag and RNase H1.


title: Affinity-independent and nuclease-based strategy to profile R-loop genome-wide [HEK293T]

overall_design: R-loop identification assisted by nuclease and high-throughput sequencing (RIAN-seq) in HEK293T cells

first: Yaoyi

last: Li

first: Yingliang

first: Hongjie

last: Yao


title: Differential response of tissue engineered skeletal muscle from rheumatoid arthritis patients and healthy controls

city: Durham

first: George

middle: Alexander

last: Truskey

state: NC

address: 101 Science Drive Room 1427 Room 1427

department: Biomedical Engineering

institute: Duke University

summary: Rheumatoid arthritis (RA) is a chronic inflammatory disease, causing pain, increased mortality, and profound disability rates. RA affects articular joints and multiple organs, including skeletal muscle. Loss of muscle mass is associated with increased disability in RA. We developed an in vitro tissue-engineered human skeletal muscle model (myobundle) to better understand the disease mechanisms driving muscle loss in RA. Myobundles were generated using primary skeletal muscle cells from the vastus lateralis muscle of 5 RA patients and 4 age-matched healthy controls. Compared to controls, RA myobundles were more sensitive to IFN-γ, leading to reduced contractile force. Gene sets enriched in IFN-γ-treated RA myobundles, but not IFN-γ-treated controls, were involved in the response to hypoxia and the unfolded protein response.  We identified PIM1 as a selectively upregulated gene and verified altered protein expression by Western blotting. Tofacitinib restored contractile force and myosin heavy chain protein levels in RA myobundles with IFN-γ-induced dysfunction. Thus, human myobundles can model inflammation of muscle in RA and other diseases.

overall_design: To determine which genes and pathways were most affected in three-diemnsional human myobundles made  with myoblasts from donors with rheumatoid arthritis (RA)  or aged-matched controls  treated with IFN-γ with and without IL-6 for 7 days

middle: A

first: Catherine

middle: E

last: Oliver


title: Base-pair resolution of clustered R-loops and DNA damage susceptible R-loops

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus
Saccharomyces cerevisiae S288C

first: Chao

last: Di


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

first: Danny

last: Reinberg

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

first: Kimberly

last: Lucero


title: Targeted immunotherapy rescues pulmonary fibrosis by reducing activated fibroblasts and regulating alveolar cell profile

first: Jing

last: Yan

address: 800, Dongchuan road

institute: Shanghai Jiaotong University

summary: The single-cell RNA-seq libraries were generated with 10x genomics from mouse lungs. Model mice were  treated with saline (n=2) or  transient CAR-T cells generated by LNP in vivo (n=2) after bleomycin-induced injury. The samples were taken at day28 after surgery and collected as the fresh whole lung tissue.

overall_design: mice were treated with bleomycin or transient CAR-T, and whole lung samples were collected and analyzed with single-cell transcriptomics

first: S

middle: Y

last: Wang

first: Y

last: Huo


title: Thymocytes mRNA profiles of 8 weeks-old p53+/+, p53Y217C/Y217C and p53-/- male mice

city: Paris

first: Boris

last: BARDOT

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Our study represents the first analysis of thymocyte transcriptomes of mice expressing the equivalent of the human p53-Y220C hot-spot oncogenic mutant

overall_design: The experiment was performed in biological replicates on each genotype (p53+/+, p53Y217C/Y217C and p53-/-)

last: Bardot

first: Franck

last: Toledo

first: Marc

last: Gabriel


title: METTL14 promotes intimal hyperplasia through m6A-mediated control of vascular smooth muscle dedifferentiation genes [RNA-seq]

status: Public on Mar 17 2025

city: Sydney

first: Justin

middle: J-L

last: Wong

address: Charles Perkins Centre Lvl4 West, The University of Sydney, Camperdown, NSW, Australia

department: School of Medical Sciences, Faculty of Medicine and Health,

country: Australia

institute: University of Sydney

summary: Vascular smooth muscle cells (VSMCs) possess significant phenotypic plasticity, shifting between a contractile phenotype and a synthetic state for vascular repair/remodelling. Dysregulated VSMC transformation, marked by excessive proliferation and migration, primarily drives intimal hyperplasia. N6-methyladenosine (m6A), the most prevalent RNA modification in eukaryotes, plays a critical role in gene expression regulation; however, its impact on VSMC plasticity is not fully understood. This research investigates the alterations in m6A modification and its regulatory factors during VSMC phenotypic shifts and their influence on intimal hyperplasia. We demonstrate that METTL14, crucial for m6A deposition, significantly promotes VSMC dedifferentiation. METTL14 expression, initially negligible, is elevated in synthetic VSMC cultures, post-injury neointimal VSMCs, and human restenotic arteries. Reducing Mettl14 levels in mouse primary VSMCs decreases pro- synthetic genes, suppressing their proliferation and migration. m6A-RIP-seq profiling shows key VSMC gene networks undergo altered m6A regulation in Mettl14-deficient cells. Mettl14 enhances Klf4 and Serpine1 expression through increased m6A deposition. Local Mettl14 knockdown significantly curbs neointimal formation post-arterial injury, and reducing Mettl14 in hyperplastic arteries halts further neointimal development. We found that Mettl14 is a pivotal regulator of VSMC dedifferentiation, influencing Klf4- and Serpine1- mediated phenotypic conversion. Inhibiting Mettl14 is a viable strategy for preventing restenosis and halting restenotic occlusions

overall_design: mRNA-seq in mouse vascular smooth muscle cells, upon shRNA-induced knockdown of METTL14 (shMettl14) or a negative control shRNA (shCTR). Experiments were performed in duplicate.

first: Grace

last: Chensee

first: Bob

last: Lee

first: Immanuel

last: Green

first: Jessica

last: Tieng

first: Renhua

last: Song

first: Natalia

last: Pinello

first: Quintin

first: David

last: Robinson

first: Mian

first: Mary

last: Kavurma

first: Jun

last: Yu

first: Renjing

last: Liu


title: Estradiol (E2) concentration shapes the chromatin binding landscape of estrogen receptor alpha

city: Aurora

first: Kiran

last: Vinod Paul

institute: University of Colorado-Anschutz medical campus

summary: ER+ Breast cancer cell lines from PDX models

overall_design: MCF7 breast cancer cell lines grown in estrogen withdrawn conditions, induced with +/- estradiol for 1 hour. Samples were ran in triplicates.

first: Amy

last: Han

middle: V

last: Paul

first: Peter

last: Kabos


title: Transcriptome analysis of canine histiocytic sarcoma tumors and cell lines reveals multiple targets for therapy

city: East Lansing

first: Vilma

last: Yuzbasiyan-Gurkan

state: MI

address: 567 Wilson Rd

department: Small Animal Clinical Sciences

institute: Michigan State University

summary: Histiocytic sarcoma (HS) is a highly aggressive malignancy characterized by excessive proliferation of histiocytes in dogs and humans. A subset of dog breeds, including the Bernese mountain dog (BMDs) show a remarkably high prevalence of HS, thus provide opportunities for insight into the molecular pathogenesis of the disease. Previous work by our lab and others has identified somatic driver mutations of HS in the PTPN11 and KRAS genes that activate the MAPK pathway in about 60% of canine HS cases. However, no somatic driver mutations have been identified in the remaining 40%. Here, we report our whole transcriptome analysis of eighteen well-characterized BMD HS tumor tissues, as well as three HS cell lines, allowing us to gain further insight into the molecular basis of HS tumorigenesis. Our analysis reveals significant upregulation of molecular pathways involving the FOXM1, AURKB, PLK1, and E2F genes, providing new information regarding pathways that may be targeted with inhibitors. In addition, we document the expression of multiple checkpoint genes, suggesting the option of treatment with small molecule inhibitors together with checkpoint inhibitors. Further, we show that the transcriptomes of three canine HS cell lines mirror those of canine patient tumors, further highlighting their potential use in drug efficacy studies. Finally, we demonstrate, for the first time, that aurora kinase inhibitors are effective in curtailing growth of HS cells in vitro and show synergism with MAPK inhibition. This study provides the most detailed analysis of the canine HS transcriptome to date, highlighting key pathways in its pathogenesis and suggesting new avenues for both single and combination treatment strategies which may be pertinent to treatment of human HS.

overall_design: RNA-seq profiling of 18 HS tumors samples from BMDs as well as 3 canine HS cell lines to investigate the HS transcriptome and to find significantly affected molecular pathways and gene expression in HS affected dogs.

first: Alexander

middle: I

last: Engleberg

first: Ya-Ting

last: Yang

middle: Z

last: Schall

first: Marilia

last: Takada

first: Tuddow

last: Thaiwong-Nebelung

first: Jacquelyn

middle: M

last: Evans

first: Elaine

last: Ostrander


title: CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [iCLIP2]

first: Danny

last: Reinberg

overall_design: CTCF iCLIP2 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).

first: Kimberly

last: Lucero


title: Lineage Tracing Reveals Clone-Specific Responses to Doxorubicin in Triple-Negative Breast Cancer [scRNA-seq]

first: Daylin

last: Morgan

overall_design: scRNA-sequencing of MDA-MB-231 cells with ClonMapper DNA barcode tags selected with doxorubicin treatment

first: Andrea

last: Gardner

last: Brock


title: GRAMD1B is a novel regulator of lipid homeostasis, autophagic flux, and phosphorylated tau.

city: Columbus

first: Hongjun

last: Fu

state: OH

address: 616 Biomedical Research Tower, 460 W. 12th Ave

department: Department of Neuroscience

institute: The Ohio State University Wexner Medical Center

summary: Lipid dyshomeostasis and tau pathology are found in frontotemporal lobar degeneration (FTLD) and Alzheimer’s disease (AD). However, the relationship between lipid dyshomeostasis and tau pathology and molecular mechanisms underlying this relationship remain unclear. Using single-cell RNA-sequencing, we report that GRAM Domain Containing 1B (GRAMD1B), a nonvesicular cholesterol transporter, is increased in excitatory neurons of human neural organoids from patient-derived induced pluripotent stem cells with the MAPT R406W mutation compared to isogenic controls. Mutant neural organoids also exhibit altered lipid species, increased phosphorylated tau, and decreased neuronal activity. Increased GRAMD1B is also found in human FTLD and AD cases and PS19 tau mice. Phosphorylated tau, free cholesterol, and lipid droplets are also increased in human FTLD and AD cases. Furthermore, GRAMD1B overexpression increases pathological tau and lipid dyshomeostasis, which may be due to blocking of autophagic flux. Our findings suggest GRAMD1B may be a new player in the regulation of autophagic flux, cholesterol transport, and tau pathology in FTLD and AD.

overall_design: Human iPSC lines were requested from the Tau consortium including iPSC F11362.11C11(WT: CRISPR-Cas9 edited isogenic control), iPSC F11362.11F10 (HET: MAPT R406W/R406R heterozygous), and iPSC GIH-143 (HOM: MAPT R406W/R406W homozygous). Human neural organoids (HNOs) were formed according to previously published protocols. On Day 70 and Day 120, ten healthy HNOs of similar size were selected from each line. Five HNOs were combined to form a technical replicate. Each replicate was gently dissociated following the Single Cell Preparation Guide established by 10x genomics.

first: Diana

last: Acosta

first: Emir

last: Turkes

first: Tae Yeon

last: Kim

first: Nicholas

last: Sweeney

first: Sheeny

last: Vo

first: Ryan

last: Rutherford

first: Dominic

last: Julian

first: Meixia

last: Pan

first: Jacob

last: Marsh

middle: R

last: Argouarch

first: Min

last: Wu

first: Douglas

middle: W

last: Scharre

first: Erica

middle: H

last: Bell

first: Lawrence

middle: S

last: Honig

first: Jean Paul

last: Vonsattel

first: Geidy

last: Serrano

first: Thomas

middle: G

last: Beach

first: Celeste

last: Karch

first: Aimee

last: Kao

first: Mark

last: Hester

first: Xianlin


title: CRISPR-mediated detection of Pneumocystis transcripts in bronchoalveolar, oropharyngeal, and serum specimens for Pneumocystis pneumonia diagnosis

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: Background. Pneumocystis jirovecii pneumonia (PCP) is a leading cause of fungal pneumonia, but its diagnosis primarily relies on invasive bronchoalveolar lavage (BAL) specimens that are difficult to obtain. Oropharyngeal swabs and serum could improve the PCP diagnostic workflow, and we hypothesized that CRISPR could enhance assay sensitivity to allow robust P. jirovecii diagnosis using swabs and serum. Herein we describe the development of an ultrasensitive RT-PCR-coupled CRISPR assay with high active-infection specificity in infant swabs and adult BAL and serum.  Methods. Mouse analyses employed an RT-PCR CRISPR assay to analyze P. murina transcripts in wild-type and Rag2-/- mouse lung RNA, BAL, and serum at 2-, 4-, and 6-weeks post-infection. Human studies used an optimized RT-PCR CRISPR assay to detect P. jirovecii transcripts in infant oropharyngeal swab samples, adult serum, and adult BAL specimens from P. jirovecii-infected and P. jirovecii-non-infected patients.   Results. The P. murina assays sensitively detected Pneumocystis RNA in the serum of infected mice throughout infection. Oropharyngeal swab CRISPR assay results identified infants infected with P. jirovecii with greater sensitivity (96.3% vs. 66.7%) and specificity (100% vs. 90.6%) than RT-qPCR compared to mtLSU standard marker, and CRISPR results achieved higher sensitivity than RT-qPCR results (93.3% vs. 26.7%) in adult serum specimens.  Conclusion. Since swabs are routinely collected in pediatric pneumonia patients, serum is easier to obtain than BAL, and RT-PCR CRISPR results may not detect P. jirovecii colonization, this assay approach could improve pediatric Pneumocystis diagnosis by achieving specificity for active infection and avoiding the requirement for BAL specimens.

sample_organism:
Homo sapiens
Pneumocystis jirovecii RU7

platform_organism:
Homo sapiens
Pneumocystis jirovecii RU7

overall_design: RNA was extracted with the Trizol method from the BAL cells pellets of two patients with Bare Lymphocyte Syndrome who had clinical PCP. Prior to construction of an Illumina total RNA library, DNase treated RNA was quantitated using a Qubit RNA BR assay kit (Thermo Fisher Scientific: Guide MAN0001987 MP10210, Kit #Q10210). Cytoplasmic, mitochondrial, and bacterial rRNA was removed from 2.5 ug of each sample as indicated by the Illumina RiboZero RNA Removal Kit Reference Guide [(Document # 15066012 v02, ScriptSeq Complete Gold (Epidemiology) Kit #BEP1206 (now obsolete)]. Illumina-compatible cDNA libraries were generated according to the instructions of the TruSeq Stranded Total RNA Sample Preparation Guide (Illumina Document #1000000040499v00, Kit #20020596). All libraries were pooled and denatured following the standard normalization method described by the Illumina Denature and Dilute Libraries Guide for the NextSeq System (Illumina Part #15048776), after which denatured libraries were loaded onto an Illumina NextSeq 550. To determine transcript abundance, FASTQ outputs were aligned to the Pneumocystis jirovecii RU7 genome using EdgeR normalization (66)

first: Brady

last: Youngquist

first: Ayanda Trevor

last: Mnguni

first: Dora

last: Pungan

first: Rachel PJ

last: Lai

first: Guixiang

last: Dai

first: Chun Fai

last: Ng

first: Amy

last: Samson

first: Yasmean

last: Abdelgaliel

first: Christopher

middle: J

last: Lyon

first: Bo

last: Ning

first: Shahid

last: Husain

first: Sean

last: Wasserman

middle: K

first: Tony

last: Hu


title: A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (meiosis RNA-Seq)

city: Gif-sur-Yvette

first: Mathieu

last: Rougemaille

address: 1 avenue de la Terrasse

institute: Institute for Integrative Biology of the Cell

summary: Small nucleolar RNAs (snoRNAs) are non-coding transcripts that guide chemical modifications of RNA substrates and contribute to gene expression at the epigenetic and post-transcriptional levels. However, the extent of their regulatory potential and the underlying molecular mechanisms remain poorly understood. Here, we identify a previously unannotated intronic C/D-box snoRNA, termed snR107, hosted in the fission yeast long non-coding RNA (lncRNA) mamRNA and carrying two independent cellular functions. On one hand, snR107 guides site-specific 25S rRNA 2’-O-methylation and promotes pre-rRNA processing/60S subunit biogenesis. On the other hand, snR107 associates with the gametogenic RNA-binding proteins Mmi1 and Mei2, mediating their reciprocal inhibition and restricting meiotic gene expression during sexual differentiation. Both functions require distinct cis-motifs within snR107, including a conserved 2’-O-methylation guiding sequence. Together, our results position snR107 as a dual regulator of rRNA modification and gametogenesis effectors, expanding our vision on the non-canonical functions exerted by snoRNAs in cell fate decisions.

overall_design: To determine the expresion dynamics of meiotic mRNAs during sexual diferentiation in wild type and snR107kloopmut cells, we conducted RNAseq experiments at different time points following induction of synchronized meiosis by adding 3-MB-PP1 to the cultures to chemically inactivate the analogous-sensitive allele of the Pat1 kinase (pat1-L95G).

first: Estelle

last: Leroy

first: Drice

last: Challal

first: Stéphane

last: Pelletier

first: Coralie

last: Goncalves

first: Alexandra

last: Menant

first: Virginie

last: Marchand

first: Yan

last: Jaszczyszyn

first: Erwin

last: van Dijk

first: Delphine

last: Naquin

first: Jessica

last: Andreani

first: Yuri

last: Motorin

first: Benoit

last: Palancade


title: METTL14 promotes intimal hyperplasia through m6A-mediated control of vascular smooth muscle dedifferentiation genes [meRIP-seq]

first: Justin

last: Wong

overall_design: m6A-seq in mouse vascular smooth muscle cells, upon shRNA-induced knockdown of METTL14 (shMettl14) or a negative control shRNA (shCTR). Experiments were performed in duplicate.

first: Grace

last: Chensee

first: Bob

last: Lee

first: Immanuel

last: Green

last: Tieng

first: Renhua

last: Song

first: Natalia

last: Pinello

first: Quintin

first: David

last: Robinson

first: Mian

last: Wang

first: Mary

last: Kavurma

first: Jun

last: Yu

first: Renjing

last: Liu


title: Genome-wide profiling of R-loop by affinity-independent and nuclease-based method [RIAN-seq]

first: Ying

middle: liang

last: Sheng

sample_organism:
Homo sapiens
Saccharomyces cerevisiae S288C

overall_design: R-loop identification assisted by nuclease and high-throughput sequencing (RIAN-seq)


title: WGCNA Analysis and Identification of Key Genes in Tobacco in Response to Different Nitrogen Levels

city: guiyang

first: Wang

middle: xin

last: Zhang

state: guizhousheng

address: Guiyang

department: Tobacco College

institute: Guizhou University

summary:
Background :Nitrogen (N) supply directly impacts growth and quality in flue-cured tobacco. To decipher molecular responses to N gradients, we integrated transcriptomics and weighted gene co-expression network analysis (WGCNA) on leaves from four N treatments: 0 (inherent soil fertility), 60 (low), 105 (standard), and 150 kg/hm² (high).
Results :Phenotypic analysis revealed dose-dependent increases in leaf nitrogen content with higher N application, accompanied by excessive vegetative growth and delayed maturity at 150 kg/hm². Transcriptome sequencing identified 47,216 genes, with differentially expressed genes (DEGs) increasing linearly with N levels (1,458–2,147 DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment highlighted nitrogen metabolism pathways, yielding 14 DEGs (11 in assimilation, 3 in transport). Weighted gene co-expression network analysis (WGCNA) uncovered two modules (lightcyan1 and black) strongly associated with N responses, harboring transcription factors NtERF11 (AP2/ERF), NtWRKY3 (WRKY), and NtSRM1 (MYB). Sub-network analysis within these modules identified five hub genes: NtGLN1-1, two uncharacterized genes, NtDFC , and NtGDSL. NtGDSL may enhance nitrogen use efficiency (NUE) through stress-responsive mechanisms, while NtDFC could integrate N signaling with developmental processes. These findings provide novel insights into N regulatory networks in flue-cured tobacco.
Conclusions :This study reveals the effects of nitrogen application rates on flue-cured tobacco growth and gene expression. By identifying key transcription factors and genes regulating nitrogen metabolism, it provides a theoretical basis for dissecting nitrogen regulatory mechanisms, optimizing fertilization strategies, and improving nitrogen use efficiency in tobacco production.

overall_design: The experiment was conducted with the same phosphorus and potassium fertilization levels (phosphorus 105 kg/hm2, potassium 210 kg/hm2), employing four nitrogen fertilizer levels: no nitrogen fertilizer, 0 kg/hm2 (T1); nitrogen deficiency, 60 kg/hm2 (T2); standard application, 105 kg/hm2 (T3); and nitrogen excess, 150 kg/hm2 (T4).The experiment utilized a randomized complete block design with plot size of 66.7 m2, replicated three times.Standard float bed seedling raising method was employed, selecting vigorous tobacco seedlings, transplanted on April 28, 2022.Planting density was 16,492 plants/hm2 with row spacing of 1.10 m and plant spacing of 0.55 m, equivalent to 1100 plants/acre, with protective rows around.Only healthy and uniform four-leaf stage tobacco seedlings free from pests and diseases were selected for transplantation.For T3 treatment, fertilization ratio was N:P2O5= 1:1:2, with nitrogen provided as urea (Red Label, N ≥ 46.2%), phosphorus as calcium superphosphate (Red Star, P2O5 ≥ 16.0%), and potassium as potassium sulfate (Rubobuo, K2O ≥ 52.0%).Potassium fertilizer was applied at 210 kg/hm2, with nitrogen and potassium split between basal (70%) and topdressing (30%) applications. Basal fertilizer was applied before transplanting, and topdressing during the topping stage; all phosphorus fertilizer was used as basal at a rate of 105 kg/hm2.

first: Xinwang

first: Shouhui

last: Pan

first: Dong

last: Chen

first: Yin

last: Huang


title: Polymer Model Integrates Imaging and Epigenomics to Elucidate the Role of the Cell’s Microenvironment in Shaping 4D Chromatin Organization [RNA-Seq]

first: Rachel

middle: Patton

last: McCord

overall_design: We use Tricostatin A (TSA) as an HDAC inhibitor (Fisher Scientific 14-061). For TSA treatment, the cells were grown to >70% confluence for more than 24 hours before addition of 500 nM TSA along with basal media. These were put back into the incubator and cultured for another 2 hours.  These cells are then used for Hi-C and RNA-seq analyses

first: Vinayak

last: Vinayak

first: Ramin

last: Basir

first: Rosela

last: Golloshi

first: Joshua

last: Toth

first: Lucas

last: Sant’Anna

first: Melike

last: Lakadamyali

middle: P

first: Vivek

middle: B

last: Shenoy


title: Bulk RNA-sequencing of human Crohn's disease (CD) enteroids treated with interferon-gamma (IFNγ)

status: Public on Mar 15 2025

city: Seoul

first: Sung Noh

last: Hong

state: South Korea

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

country: South Korea

institute: Samsung Medical Center

summary: To investigate the intestinal epithelial cellular responses to interferon-gamma (IFNγ), bulk RNA sequencing (RNA-seq) was performed on human small intestinal organoids (enteroids, n = 10) with and without IFNγ treatment (100 pg/ml). The enteroids were derived from endoscopic biopsy samples obtained from patients with Crohn's disease (CD).

overall_design:
Expression profiling by high throughput sequencing (n = 20)

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

first: Chansu

last: Lee


title: Affinity-independent and nuclease-based strategy to profile R-loop genome-wide [mESC]

overall_design: R-loop identification assisted by nuclease and high-throughput sequencing (RIAN-seq) in mES cells

first: Yaoyi

last: Li

first: Yingliang

first: Hongjie

last: Yao


title: De novo transcriptome assembly of the plant Helianthemum marifolium for the study of adaptive mechanisms

status: Public on Mar 14 2025

city: Seville

first: Rafael

last: Albaladejo

state: Seville

address: c/Profesor García González 2

department: Biología Vegetal y Ecología

institute: Universidad de Sevilla

summary: The genus Helianthemum, commonly known as rockroses, encompasses 140 species primarily distributed in the Palearctic region, with notable diversification driven by climatic and geological changes. These plants are valuable for studying speciation processes and ecological divergence. The chemical properties of the leaves have also been investigated for containing valuable bioactive compounds with several therapeutic properties. However, the availability of genomic resources for species in this genus are almost entirely lacking. Here, we assembled and annotated the first reference transcriptome of Helianthemum marifolium, a species with wide morphological variability and infraspecific diversity. Illumina paired-end RNA sequences were generated using leaves from 16 individuals, representing the four recognized subspecies, all cultivated in a greenhouse. RNA reads were assembled with Trinity and Oases, and EvidentialGene produced a transcriptome with 122,002 transcripts. The transcriptome showed 59524 hits on the UniProtBK database through BLASTx. This transcriptome will be an invaluable resource for transcriptome-level population studies, conservation genetics of the many endangered species within the genus, and for deepen into the metabolic pathways of leaf-derived compounds.

sample_organism: Helianthemum marifolium subsp. marifolium

sample_organism: Helianthemum marifolium subsp. andalusicum

overall_design: RNA-seq profiling of the four subspecies (andalusicum, marifolium, molle and origanifolium) of the species Helianthemum marifolium (Cistaceae).

first: Andrea

last: Martín-Díaz

first: Clara

last: de Vega

first: Sara

last: Martín-Hernanz

first: Abelardo

last: Aparicio

first: Rafael G.


title: Radiation and anti-PD-L1 synergize by stimulating a stem-like T cell population in the tumor-draining lymph node

city: atlanta

first: zach

last: Buchwald

state: ga

address: 1365 Clifton Rd NE Building C

institute: Winship Cancer Institute of Emory University

overall_design: Refer to individual Series


title: SMART-seq of MG lineages in MNU-injured retinas

city: Daejeon

first: Jin Woo

last: Kim

state: Daejeon

address: 291, Daehak-ro, Yuseong-gu

institute: KAIST

summary: We further investigated injury-induced gene expression changes selectively in MG cell lineages. The tdTom-labeled MG and their descendant cells were isolated via FACS from uninjured or MNU-injured Glast-CreERT;R26tdTom/+ mouse retinas, which were infected with either AAV2-Ctrl Ab or AAV2-alpha Prox1, and mRNA expression patterns of individual cells were analyzed using SMART (Switching Mechanism At the 5' end of RNA Template) sequencing methods. We could identify a lineage flow from resting MG to RPC-like cells via activated MG, along with pseudo-time progression.

overall_design: The samples include Müller glia (MG) and their descendant cells isolated via FACS from the retinas of Glast-CreERT;R26tdTom/+ mice. Experimental conditions include uninjured and methyl-nitrosourea (MNU)-injured retinas, with additional treatment using AAV2-Ctrl Ab or AAV2-alpha Prox1 constructs to modulate Prox1 intake for MGs.

first: Eun Jung

first: Museong

first: Dongeun

first: Hanseul

last: Yang

first: Haeun

last: Jeong


title: Tonic ISG expression promotes efficient induction of IFNL in response to influenza infection

city: urbana

first: christopher

last: brooke

state: IL

address: B103 CLSL, MC-110, 601 South Goodwin Avenue

institute: University of Illinois at Urbana-Champaign

summary: The innate immune response, especially the interferon (IFN) response, plays a critical role in limiting initial dissemination of viruses from the site of infection. While the pathogen-associated molecular patterns (PAMPs) and pattern recognition receptors (PRRs) involved in sensing and inducing the innate immune response during influenza A virus (IAV) infections are well-characterized, the factors that regulate IFNL production in infected cells remain poorly understood. Previous studies have highlighted that most infected cells fail to express either type I or III IFNs in response to stimulus, suggesting a regulatory mechanism that controls the activation of IFNs during infection. To investigate the factors influencing IFNL induction during IAV infection, we performed single-cell RNA sequencing (scRNA-seq) of A549 cells infected with A/Perth/16/2009 and sampled at multiple time points post-infection. Using a novel pseudotime analysis approach tailored for temporal scRNA-seq data, we aim to identify host genes whose tonic expression modulates IFNL production in response to IAV infection.

overall_design: Comparison of host gene expression in Perth09 (H3N2) infected human alveolar epithelial cells at different times post-infection

first: Joel

last: Rivera-Cardona

first: Tarun

last: Mahajan

first: Qi Wen

last: Teo

first: Joseph

last: Lederer

first: Elizabeth

middle: F

last: Rowland

middle: A

last: Thayer

first: Neeha

last: Kakuturu

first: Kyle

last: Heimburger

first: Nicholas

middle: C

last: Wu

first: Sergei

last: Maslov

first: Christopher

last: Brooke


title: A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (direct RNA-Seq)

first: Mathieu

last: Rougemaille

overall_design: To delineate the RNA species produced from the mamRNA-U14 locus in wild type cells, we conducted direct RNA sequencing using Oxford Nanopore Technology (ONT).

first: Estelle

last: Leroy

first: Drice

last: Challal

first: Stéphane

last: Pelletier

first: Coralie

last: Goncalves

first: Alexandra

last: Menant

first: Virginie

last: Marchand

first: Yan

last: Jaszczyszyn

first: Erwin

last: van Dijk

first: Delphine

last: Naquin

first: Jessica

last: Andreani

first: Yuri

last: Motorin

first: Benoit

last: Palancade


title: Radiation and anti-PD-L1 synergize by stimulating a stem-like T cell population in the tumor-draining lymph node [TCR-Seq]

first: zach

last: Buchwald

summary: Radiotherapy (RT) and anti-PD-L1 synergize to enhance local and distant (abscopal) tumor control. However, clinical results in humans have been variable. With the goal of improving clinical outcomes, we investigated the underlying synergistic mechanism focusing on a TCF-1+ PD-1+ CD8+ stem-like T cell subset in the tumor-draining lymph node (TdLN). We found that RT + anti-PD-L1 induces a novel differentiation program in the TdLN stem-like population which leads to their expansion and differentiation into effector cells within the tumor. We also found that optimal synergy between RT + anti-PD-L1 is dependent on the TdLN stem-like T cell population as either blockade of TdLN egress or specific stem-like T cell depletion reduced tumor control. Together, these data demonstrate a multistep stimulation of stem-like T cells following combination therapy which is initiated in the TdLN and completed in the tumor.

overall_design: TCR sequencing was performed on CD8+ PD-1+ CD44+ cells isolated from tumors and lymph nodes

first: Buchwald

last: Zach

first: Shen

last: Yang

first: Connolly

last: Erin


title: RNA-Seq of doxorubicin treated rats and vehicle control

city: Cluj-Napoca

first: Emilia

last: Anca

state: Cluj

address: Clinicilor St. no. 7

country: Romania

institute: Faculty of Biology and Geology, Babes-Bolyai University

summary: Despite significant advancements in the oncologic field, cancer remains a major cause of concern for global health. Doxorubicin is a member of the anthracycline class of chemotherapeutic agents which remains among the most effective treatment available up to date. However, its clinical use is significantly limited by severe cardiotoxic effects. The purpose of this study is to investigate the transcriptomic alterations that occur in a rat model of doxorubicin-induced cardiotoxicity. Our results reveal significant dysregulation of cardiac metabolism and provide insights into the molecular mechanisms underlying cardiac damage produced by this treatment.

overall_design: 6 adult male Wistar rats were divided into two groups. The DOX group (n=3) was treated with weekly tail vein injections of 3.75 mg/kg doxorubicin hydrochloride (European Pharmacopeia Reference Standard, D2975000, Merck), for a total of 4 weeks. The Control group (n=3) received vehicle (0.9% sodium chloride, B.Braun) in the same manner. Heart tissue was collected and immediately placed in RNAlater Solution (Invitrogen), stored at 4°C overnight and then moved at -80°C until RNA isolation according to manufacturer’s instructions. Total RNA was isolated using TRIzol Reagent (Invitrogen) and the RNeasy Mini Kit (QIAGEN) using manufacturer’s instructions.

first: Ovidiu

last: Pavel

last: Licarete

first: Camelia

last: Dobre

first: Corina

last: Rosioru

first: Manuela

last: Banciu


title: BTLA agonist attenuates Th17 inflammation in a mouse model of steroid-resistant asthma

status: Public on Mar 13 2025

city: Los Angeles

first: Christine

last: Quach

state: CA

address: 1450 Biggy St NRT 5509

institute: University of Southern California

summary: Mouse models of steroid-resistant asthma are needed to understand the pathophysiology of the disease in order for effective therapeutics to be developed. The BXD75 mice strain exhibited neutrophilic airway inflammation and steroid resistance. This study investigated the HVEM-BTLA signaling pathway in CD4+ T cells from BXD75 and C57BL/6J (WT) mice exposed to house dust mite (HDM).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD4+ T cells from WT (C57BL/6J) and BXD75 mice

first: Xin

last: Li

first: Stephen

last: Shen

first: Doumet

last: Helou

first: Benjamin

last: Hurrel

first: Pejman

last: Soroosh

first: Omid

last: Akbari


title: Mechanisms underlying the oncogenic and tumour suppressor functions of IER3 [RNA-seq]

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

summary: The IER3 (Immediate Early Response 3) gene exhibits a multifaceted role in cancer biology, acting as both a tumor suppressor and an oncogene depending on the specific cancer type. This duality underscores the complexity of molecular pathways. Despite its significance, there is a dearth of studies dedicated to elucidating the exact mechanisms underlying IER3's involvement in cancer development. Recently, we identified that IER3 functions as an oncogene in cervix, breast, and lung cancer cell lines. In this study, we demonstrate for the first time that IER3 acts as a tumor suppressor in Neuroblastoma.

overall_design: Through RNA sequencing, ChIP sequencing, and functional assays, we identified two critical IER3 target genes.

first: Chandrasekhar

last: Kanduri

first: Meena


title: Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing

city: Changchun

first: Yang

last: Han

address: Xi'an road 5333, Jilin University Heping Campus, Changchun, China

institute: Jilin University

summary: 5-Methylcytosine (m5C) is one of the major post-transcriptional modifications in mRNA and is highly involved in the pathogenesis of various diseases. However, the capacity of existing assays for accurately and comprehensively transcriptome-wide m5C mapping still needs improvement. Here, we developed a deaminase and reader protein assisted RNA methylation analysis, termed DRAM, in which deaminases (APOBEC1 and TadA-8e) are fused with m5C reader proteins (ALYREF and YBX1) to identify the m5C sites through deamination events neighboring the methylation sites. This antibody-free and bisulfite-free approach provided transcriptome-wide editing regions which were highly overlapped with the publicly available BS-seq datasets. Notably, DRAM-seq even discovered a new m5C methylation locus in KAT7, a previously demonstrated key aging regulator. In addition, DRAM system even supports ultra-low input RNA (10ng) and monitor the dynamic accumulation of cellular m5C. We anticipated that the DRAM system could pave the way for uncovering further biological functions of m5C modifications.

overall_design: To comprehensively detect the m5C locus, the readers of m5C (ALYREF and YBX1) were separately fused to the C-terminus of the deaminases (APOBEC1 and TadA-8e), namely DRAM system.DRAM-ABE (mixture of TadA-8e-ALYREF and TadA-8e-YBX1) and DRAM-CBE (mixture of APOBEC1-ALYREF and APOBEC1-YBX1) were then transfected into the human HEK293T cells, respectively. To verify that the detection of DRAM occurs in the presence of m5C, we individually depleted NSUN2 and NSUN6 in HEK293T cells and performed DRAM transfection.Eventually, we performed RNA-seq after DRAM transfection to enable a transcriptome-wide detection of m5C.

first: Jiale

last: Zhou

first: Ding

last: Zhao

first: Jinze

first: Deqiang

last: Kong

first: Xiangrui

first: Renquan

last: Zhang

first: Yuru

last: Liang

first: Xun

last: Gao

first: Yuqiang

last: Qian

first: Di

last: Wang

first: Jiahui

last: Chen

first: Liangxue

last: Lai

first: Zhanjun


title: Obesity hinders the efficacy of adipose-derived stem cells for knee osteoarthritis by reducing the proportion of DPP4+ stem cells

status: Public on Mar 16 2025

city: Shanghai

first: Zhenyu

last: Xu

state: 枫林校区

address: Dongan Road

institute: Shanghai Medical College, Fudan University

summary: Osteoarthritis (OA) is the most prevalent and disabling joint disease, while adipose-derived stem cells (ASCs) have emerged as a promising therapeutic option in pre-clinical studies. However, the therapeutic efficacy of ASCs may be influenced by the source of these cells, especially in obese patients. This study compared the effects of intra-articular injections of ASCs from wild-type (WT) and ob/ob (OB) mice. Behavioral and histological analyses demonstrated that WT-ASCs significantly alleviated OA symptoms, restoring paw withdrawal thresholds and improving gait parameters while reducing cartilage degradation. In contrast, OB-ASCs only partially improved gait and did not significantly affect cartilage degeneration. Single-cell RNA sequencing of stromal vascular fractions from subcutaneous adipose tissue revealed distinct ASC subpopulations, with DPP4+ cells being notably reduced in obese mice. In vitro, OB-ASCs and high-fat-diet (HFD)-ASCs exhibited impaired proliferation and chondrogenesis but HFD-ASCs retained anti-inflammatory properties. Further investigation using fluorescence-activated cell sorting (FACS) isolated DPP4+ and DPP4- ASCs from WT mice, demonstrating that DPP4+ cells had superior chondrogenic potential and reduced OA pain more effectively than DPP4- cells. These findings suggest that obesity impairs the therapeutic potential of ASCs in OA, primarily due to reduced proliferation and chondrogenesis, and highlight DPP4+ ASCs as a promising candidate for cell therapy in OA.

overall_design: To compare the efficacy of adipose-derived stem cells (ASCs) from healthy and obese mice in the context of osteoarthritis. ASCs were obtained through collagenase digestion of subcutaneous adipose tissue from mice and were then subjected to single cell sequencing


title: A bifunctional snoRNA with separable activities in guiding rRNA 2'-O-methylation and scaffolding gametogenic effectors (total and polyA RNA-Seq)

first: Mathieu

last: Rougemaille

overall_design: To investigate the biogenesis and processing of the long non-coding RNA mamRNA, we conducted RNA-seq experiments and compared total, ribodepleted RNA to oligodT-enriched, polyadenylated transcripts.

first: Estelle

last: Leroy

first: Drice

last: Challal

first: Stéphane

last: Pelletier

first: Coralie

last: Goncalves

first: Alexandra

last: Menant

first: Virginie

last: Marchand

first: Yan

last: Jaszczyszyn

first: Erwin

last: van Dijk

first: Delphine

last: Naquin

first: Jessica

last: Andreani

first: Yuri

last: Motorin

first: Benoit

last: Palancade


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

state: NY

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

last: Yamamoto


title: PKM2 regulates osteoclastogenesis by affecting osteoclast precursor cell fusion via down-regulation of OC-STAMP and DC-STAMP

city: Wuhan

first: Jiawei

last: Jiang

state: Hubei

address: No.1095 Jiefang Avenue

department: Orthopedics

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Osteoporosis is a common bone disease that has become a serious public health problem with the aging of population. Osteoclasts are the only cells in body that can resorb bone, whose dysfunction is closely related to osteoporosis. Pyruvate kinase M2 (PKM2) is one of the essential rate-limiting enzymes in the process of glycolysis. This study aimed to elucidate the role of PKM2 in osteoclastogenesis and bone resorption. Bone marrow-derived macrophages (BMMs) were transfected with adenovirus to knock down the expression of PKM2 gene or treated with the PKM2 activators TEPP-46 and DASA-58. Osteoclast formation was detected by TRAP staining, osteoclast-specific gene and protein expression was detected by RT-qPCR and Western blotting, and the effect of DASA-58 on osteoclast gene expression at the transcriptional level was examined by RNA-seq. The results showed that knockdown of PKM2 by adenoviral transfection or treatment with PKM2 activators TEPP-46 and DASA-58 inhibited osteoclast differentiation and suppressed the expression of osteoclast-associated genes in BMMs. Furthermore, PKM2 activators TEPP-46 and DASA-58 could inhibit several signaling pathways in osteoclasts; knockdown of PKM2 or treatment with PKM2 activators TEPP-46 and DASA-58 both affected osteoclast precursor cell fusion by inhibiting the expression of osteoclast stimulatory transmembrane protein (OC-STAMP) and dendritic cell-specific transmembrane protein (DC-STAMP). Therefore, PKM2 is closely related to osteoclast differentiation and formation, and the development of new therapeutic strategies targeting the PKM2 gene in osteoclasts may be feasible for the prevention and treatment of osteoporosis.

overall_design:
BMMs (50×10^4 cells/well) were inoculated in a 6-well plate. The experimental group was treated with DASA-48 and RANKL, and the control group was treated with an equal volume of DMSO. Total RNA was extracted for RNA-seq after three days, with three replicates for each group.

>>>Submitter states that raw data are unavailable due to file loss<<<

first: Cong

last: Cai

first: Song

last: Li

first: Chenghao

last: Gao

first: Hongxu

last: Pu

first: Libo

last: Zhao

first: Jun

last: Xiao


title: Bulk RNA-sequencing of human non-IBD enteroids treated with interferon-gamma (IFNγ)

first: Sung Noh

last: Hong

summary: To investigate the intestinal epithelial cellular responses to interferon-gamma (IFNγ), bulk RNA sequencing (RNA-seq) was performed on human small intestinal organoids (enteroids, n = 6) with and without IFNγ treatment (100 pg/ml). The enteroids were derived from endoscopic biopsy samples obtained from patients without inflammatory bowel disease (IBD).

overall_design:
Expression profiling by high throughput sequencing (n = 12)

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

first: Chansu

last: Lee


title: AAV vectors trigger DNA damage responses and STING-dependent inflammation in human CNS cells

city: Philadelphia

first: Klaudia

last: Kuranda

state: PA

address: 3737 Market St

department: Data Sciences

institute: Spark Therapeutics

summary: Adeno-associated viral (AAV) vector-based gene therapy is gaining foothold as a treatment option for a variety of genetic neurodegenerative diseases. Nonetheless, dose-dependent toxicities and severe adverse events are emerging in recent clinical trials through mechanisms that remain unclear. We have modelled here AAV-mediated neurotoxicity in the context of the human brain taking advantage of human induced pluripotent stem cell-based technologies. Our work uncovers vector-induced cell-intrinsic innate immune mechanisms at the single-cell level that contribute to neurotoxicity in 2D and 3D models of the human central nervous system (CNS). The AAV genome triggered p53-dependent DNA damage responses across CNS cell types followed by induction of IL-1R- and STING-dependent inflammatory responses. In addition, transgene-expression led to MAVS-dependent RNA sensing and activation of type I interferon (IFN) signalling. Cell-intrinsic and paracrine neurotoxicity could be prevented by inhibiting p53 or acting downstream on STING- and IL-1R-mediated activation of inflammatory responses. Activation of DNA damage, type I IFN and CNS inflammation were confirmed in vivo. Together, our work sheds significant light on the cell-autonomous innate immune mechanisms of vector sensing that can contribute to AAV-associated neurotoxicity.

overall_design: Adult male mice were bilaterally injected into the striatum with AAV9-CAG-GFP or vehicle (N=2 mice/group respectively), and mice were sacrificed 28 days post-injection for striatum isolation and assessment of cell type composition and transcriptional changes by single-nuclei RNAseq (snRNAseq)

first: Yulia

last: Dzhashiashvili

first: Emily

last: Fabyanic

first: Xin

last: Huang


title: Expression data from human 3D skin models treated with synthetic pseudo-ceramide for medical containing steroid cream

city: Odawara

first: Masafumi

last: Yokota

state: Kanagawa

address: 5-3-28 Kotobukicho

country: Japan

institute: Kao corporation

summary: Ceramides in the stratum corneum (SC) play an important role in the epidermal barrier function. We focused on these functions and developed a synthetic pseudo-ceramide for medical (SPCM)-containing steroid cream [SPCM (+)]. This cream forms films on the skin surface with multilamellar structures, like the human SC, and exerts anti-inflammatory effects through steroids. However, the preventive effects of this cream on disruption of skin barrier remain unclear. This study aimed to analyze the efficacy of SPCM (+) using human three-dimensional (3D) skin models.

overall_design: In this data set, we included expression data from human 3D skin models treated with or without SPCM (+) under exposure to V8 protease derived from Staphylococcus aureus.


title: Accessing genetically defined cell types in the Superior Colliculus with transgenic mouse lines

city: Charlottesville

first: Yuanming

last: Liu

state: Virginia

address: Gilmer Hall

department: Biology Department

institute: University of Virginia

summary: Molecular identification of Cre+ cells in the sSC of Ntsr1-GN209-Cre mice

overall_design: The sSC was micro-dissected approximately by knife cuts, processed into a single-nuclei suspension, FACS sorted, and prepared for sequencing with 10X Chromium Next GEM 3’ reagent kit v3.1 according to the manufacturer’s protocol

first: Chen

last: Chen

first: Jianhua

last: Cang


title: PI3K-Akt signaling regulates Scx-lineage tenocytes and Tppp3-lineage tendon sheath synovial cells in physiological tendon regeneration

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shituskawa

department: Proteo-Science Center

institute: Ehime University

summary: We identify a PI3K-Akt signaling pathway which is specifically upregulated in neonatal murine injured Achilles tendons. PI3K-Akt signaling inhibition in neonatal murine Achilles tendon rupture model decreases cell proliferation and cell migration to the regenerating tendons in both Scx-lineage intrinsic tenocytes and Tppp3-lineage extrinsic tendon sheath synovial cells. Moreover, PI3K-Akt signaling inhibition decreases stemness and promotes mature tenogenic differentiation in both Scx-lineage and Tppp3-lineage cells. Collectively, PI3K-Akt signaling plays an important role in physiological tendon regeneration.

overall_design: mRNA was extracted from uninjured Achilles tendons and injured Achilles tendons in 7-day old and 6-months-old mice. mRNA profiles were analyzed by deep sequencing using Illumina Miseq.

first: Shingo

last: Komura


title: Mechanisms underlying the oncogenic and tumour suppressor functions of IER3 [ChIP-seq]

first: Santhilal

last: Subhash

first: Chandrasekhar

last: Kanduri

first: Meena


title: Life-long microbiome rejuvenation improves intestinal metabolism and inflammaging in mice [scRNA-seq]

city: Kiel

first: Joana

middle: P.

last: Bernardes

state: SH

address: Am Botanischen Garten 11

department: Systems Immunology

institute: IKMB

summary: Alterations in composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Physiological responses were analyzed by rotarod and a grip strength test, intestinal barrier function by FITC gavage and LAL assay, transcriptional responses by single cell RNA sequencing and microbiome function by 16S profiling and metagenomics. Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB hinting at more stable microbiome communities. Single cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways in enterocytes and TA cells but reduced inflammatory signaling in macrophages. Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including motor coordination, intestinal permeability and immune cell phenotypes.

overall_design: 8-week-old male C57Bl6/J mice (n=60) were subjected to successive 8-week-long cycles consisting of (i) a microbiome depletion for 14 days via antibiotic treatment, (ii) immediate recolonization via fecal microbiota transfer and (iii) 6 weeks of an intermittent phase. Freshly collected fecal pellets of unrelated and untreated male C57Bl6/J mice of the same age (isochronic microbiome transfer, iMB) or 8 weeks of age (young microbiome transfer, yMB) were orally gavaged with suspension to restore the depleted microbiomes. single cell RNA-seq samples were obtained from the intestinal epithelium SI of these mice at the end of the treatment (120w).

first: Felix

last: Sommer

first: Lena

last: Best

first: Nina

first: Jacob

last: Hamm

first: Berith

last: Messner

first: Víctor

last: López-Agudelo

first: Antonella

last: Fazio

first: Georgios

last: Marionos

first: Samer

last: Kadibaldan

first: Go

last: Ito

first: Maren

last: Falk-Paulsen

first: Christoph

last: Kaleta

first: Philip

last: Rosenstiel


title: Two redox-responsive LysR-type transcription factors control the oxidative stress response of Agrobacterium tumefaciens

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätstraße 150, NDEF 06/744

department: Fakultät für Biologie und Biotechnologie

institute: Ruhr Universität Bochum

summary: In the present study we investigate the role of the LysR-type transcriptional regulators LsrB (Atu2186) and OxyR (Atu4641) in the oxidative stress response of Agrobacterium tumefaciens C58 (alias A. fabrum C58). Therein, we used our existing lsrB-deletion (Kraus et al. 2020*) mutant and constructed two additional mutants: An oxyR and a lsrB/oxyR double deletion mutant. Total RNA was isolated from WT and mutant strains grown in LB medium to mid-exponential phase and withdrawn before or after 15 min, 5 mM H2O2 stress. Residual DNA was removed by RNAse-free Dnase. Sequencing was performed done on the Illumina NovaSeq 6000 platform. Our results reveal a central role for both LysR-type transcriptional regulators in the oxidative stress response of Agrobacterium tumefaciens.   Kraus, A., Weskamp, M., Zierles, J., Balzer, M., Busch, R., Eisfeld, J., et al. (2020) Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens. J Bacteriol 202: e00309-20.

overall_design: Illumina RNA sequencing of the transcriptomes of Agrobacterium fabrum C58 wild type; lsrB deletion mutant (∆atu2186); oxyR deletion mutant (∆atu4641); lsrB/oxyR double deletion mutant (∆atu2186∆atu4641) grown in LB medium +/- 5 mM H2O2

first: Janka

last: Schmidt

first: Vivian

last: Brandenburg

first: Hannah

last: Elders

first: Saba

last: Shahzad

first: Sina

last: Schäkermann

first: Ronja

last: Fiedler

first: Lisa

last: Knoke

first: Yvonne

last: Pfänder

first: Pascal

last: Dietze

last: Bille

first: Bela

last: Gärtner

first: Lennart

last: Albin

first: Lars

middle: I

last: Leicher

first: Julia

middle: E

last: Bandow

first: Eckhard

last: Hofmann


title: Life-long microbiome rejuvenation improves intestinal metabolism and inflammaging in mice [bulk RNA-seq]

first: Joana

last: Bernardes

overall_design: 8-week-old male C57Bl6/J mice (n=60) were subjected to successive 8-week-long cycles consisting of (i) a microbiome depletion for 14 days via antibiotic treatment, (ii) immediate recolonization via fecal microbiota transfer and (iii) 6 weeks of an intermittent phase. Freshly collected fecal pellets of unrelated and untreated male C57Bl6/J mice of the same age (isochronic microbiome transfer, iMB) or 8 weeks of age (young microbiome transfer, yMB) were orally gavaged with suspension to restore the depleted microbiomes. Total RNA-seq samples were obtained from the colon of these mice, early in the treatment (40w) and at the end of the treatment (120w-Final).

first: Felix

last: Sommer

first: Lena

last: Best

first: Nina

first: Jacob

last: Hamm

first: Berith

last: Messner

first: Víctor

last: López-Agudelo

first: Antonella

last: Fazio

first: Georgios

last: Marionos

first: Samer

last: Kadibaldan

first: Go

last: Ito

first: Maren

last: Falk-Paulsen

first: Christoph

last: Kaleta

last: Rosenstiel


title: Functional callus organoids reveal distinct cartilage to bone transition mechanisms across donors and a role for biological sex

city: Leuven

first: Ioannis

last: Papantoniou

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: Engineering a cartilage tissue intermediate in vitro that closely mimics the characteristics of the native fracture callus in vivo, ensures a high potency to undergo cartilage-to-bone transition when implanted in vivo. However, there is a lack of critical quality attributes that can be defined in vitro to predict in vivo functionality across donors, which is a significant limitation for the development of autologous tissue engineered implants according to Quality by Design (QbD) principles. In addition, for clinical translation, regulatory bodies require in-process biological data acquisition, preferably noninvasive, to enable closed system manufacturing.  In this study, we produced cartilaginous callus organoids of 10 human donors, both male and female, assembled scaffold-free donor-specific cartilaginous implants. We found two distinct organoid morphologies and transcriptome signatures, with 6 donors (5 male, 1 female) generating hypertrophic cartilage and 4 female donors producing organoids with a fibrocartilage phenotype. This distinction was already detectable early in the differentiation process with differences in proliferation and organoid morphology, leading to differential regulation of gene panels specific for reported periosteal progenitor populations. Further, we compared the secretome of bone-forming and non-bone-forming organoids, identifying a robust panel of 83 proteins that could be measured noninvasively as potency monitoring biomarkers.  These findings provide new insights in donor variability and outlines a quality-driven pathway for the translation of organoid-based tissue engineered implants. The addition of noninvasive quality metrics paves the way towards data-driven closed-system manufacturing of patient-specific living implants.

overall_design: To investigate the requirements for bone formation, periosteum derived cells from 10 donors were chondrogenically cultured as organoids for 21 days and implanted ectopically in nude mice. As negative control, 5 donors were cultured as organoids for 21 days in basal medium.

first: Isaak

last: Decoene


title: Nuclear RNAi Modulates Influenza A Virus Infectivity By Downregulating Type-I Interferon Response

city: Goteborg

first: Davide

last: Angeletti

address: Medicinaregatan 7a

country: Sweden

institute: University of Gothenburg

type: Non-coding RNA profiling by high throughput sequencing

summary: The role of Argonaute (AGO) proteins and the RNA interference (RNAi) machinery in mammalian antiviral response has been debated. Therefore, we set out to investigate how mammalian RNAi impacts influenza A virus (IAV) infection. We demonstrate that IAV infection triggers nuclear accumulation of AGO2, which is directly facilitated by p53 activation. Mechanistically, we show that IAV induces nuclear AGO2 targeting of TRIM71, a proposed AGO2 E3 ligase, and type-I interferon-pathway genes for silencing. Hence, the RNAi machinery is highjacked by the virus to evade the immune system and support viral replication. We demonstrate that the FDA approved drug arsenic trioxide prevents nuclear AGO2:p53 accumulation, thereby increasing interferon response and decreasing viral replication in vitro and in a mouse model in vivo. Our data indicates that targeting the AGO2:p53-mediated silencing of innate immunity may offer a promising strategy to mitigate viral infections.

overall_design: We performed miRNAseq after AGO1-4 IP in cells treated wih PR8 virus in HEK293 cells that were fractionatd into cytoplasmic andn nuclear fraction

first: Hsiang-Chi

last: Huang

first: Iwona

last: Nowak

first: Vivian

last: Lobo

first: Danica

last: Besavilla

first: Karin

last: Schön

first: Jakub

middle: O

last: Westholm

first: Carola

last: Fernandez

first: Angana

last: Patel

first: Clotilde

last: Wiel

first: Volkan

last: Sayin

first: Dimitrios

last: Anastasakis

first: Aishe

last: Sarshad


title: Nuclear Accumulation of YTHDF1 Regulates mRNA Splicing in the DNA Damage Response

city: Hangzhou City

first: Jingyu

last: Hou

state: Zhejiang Province

address: Zhejiang University Student Apartment

institute: Zhejiang University

summary: YTH domain-containing family protein 1 (YTHDF1), a reader of N6-methyladenosine, has been implicated in regulating RNA metabolism in the cytosol. Here we report a role of YTHDF1 within the nucleus in response to genotoxic stress. Upon radiation, YTHDF1 is phosphorylated at serine 182 in an ATR-dependent manner. This phosphorylation inhibits exportin 1-mediated nuclear export of YTHDF1, resulting in its accumulation within the nucleus. Nuclear YTHDF1 enhances the binding capacity of SRSF2 to a group of m6A-modified exons, leading to increased exon inclusion. Specifically, YTHDF1 promotes splicing and expression of DNA repair genes, such as BRCA1 and TP53BP1, thereby mitigating excessive DNA damage. Depletion of YTHDF1 sensitizes cancer cells to radiation treatment. Altogether, our study reveals a crucial role of YTHDF1 in m6A-mediated mRNA splicing in the DNA damage response, proposing it as a potential target for radiation therapy.

overall_design: [dataset 1] 3 samples. m6A-IP-seq of polyA+ RNA samples, including m6A input, m6A-IP in HEK293T cell line and RNA-seq in YTHDF1-KO HEK293T cells after X-ray exposure [dataset 2] 2 samples. RNA-Seq samples of SRSF2-CTL and SRSF2-KD HEK293T cells after X-ray exposure; [dataset 3] 1 samples. Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP-seq) for YTHDF1 in HEK293T cell line after X-ray exposure;[dataset 4] 2 samples.RNA Immunoprecipitation (RIP-seq) for SRSF2 in YTHDF1-WT/KO HEK293T cell line after X-ray exposure;

first: Yunyi

last: Gao

first: Bing

last: Han

first: Sujun

last: Yan

first: Saisai

last: Wei

first: Xiangwei


title: Acoustic modulation of mechanosensitive genes and adipocyte differentiation

city: Kyoto

first: Masahiro

last: Kumeta

address: Yoshidakonoe

department: Graduate School of Biostudies

institute: Kyoto University

summary: Eukaryotic cells are equipped with multiple mechanosensing systems and perceive wide range of mechanical stimuli from the environment. However, cell-level responses against acoustic waves, which transmits feeble but highly frequent physical perturbation, largely remains uninvestigated, especially with regard to audible range of sound. Here we investigate the effect of acoustic stimulation on gene expression profiles of mammalian cultured cells. A direct sound emission system was set up using a vibrational transducer to directly generate acoustic waves in culture medium. A custom-made vibrating plate made of PEEK (poly ether ether ketone) plastic was used as a diaphragm. A set of sound patterns including single-frequency sound and white noise were generated by NCH Tone Generator software. Sound intensity was directly measured by recording it in water using a hydrophone and the pressure level was calculated. C2C12 myoblasts cultured in a plastic dish with approximately 50% confluency were subjected to acoustic stimulation. 440 Hz and 14k Hz single-frequency sine wave sound were selected as representatives of low and high audible frequencies, and white noise was selected as a random noise pattern. 2 and 24 hours after continuous emission of these sound at 100 Pa, total RNA was extracted and subjected to the gene expression profiling analysis by RNA-sequencing technique. Total 42 early- and 145 late-response genes were identified as sound-sensitive genes in 2 and 24 hours stimulation, respectively. Gene annotation analyses revealed that in addition to the known mechanosensitive activities such as fluid shear stress response, cell migration, cell adhesion and blood vessel development, variety of pathways and processes were identified to be affected by acoustic stimulation.

overall_design: C2C12 cells were subjected to acoustic stimulation by a custom-made direct sound emission system using vibrational transducer and a diaphragm. Low frequency (440 Hz), high frequency (14 kHz), and white noise were emitted to the cells at 100 Pa intensity, for 2 and 24 hours.


title: Gene suppression by PRC2 enhances the gene inductions by Aire and the development of mimetic cell populations

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

address: 1-7-22 Suehiro-cho

institute: RIKEN IMS

summary: Aire, a transcriptional regulator whose defect results in the development of autoimmunity, controls the transcriptome in the bulk of medullary thymic epithelial cells (mTECs) including the genes for self-antigens. Mechanisms for this process, however, remained incompletely understood, especially regarding the effects of Aire in each subpopulation in mTECs. Here, we profiled mTECs from EED-cKO (EED conditional knockout mice using Foxn1-Cre, JACKSON LABORATORY #022727 and #018448) and Aire/EED-dKO (Aire EED double knockout mice, PMID: 19015306) by RamDA-seq to evaluate the association between the gene suppression by polycomb repressive complex 2 (PRC2) and the gene induction by Aire. We found that genes are suppressed by PRC2 in an Aire-independent manner in mTEC and the gene suppression by PRC2 paradoxically augments the gene inductions by Aire. Interestingly, PRC2 also suppresses the signature genes for mimetic cell populations and their development was diminished in the absence of EED.

overall_design: deep single-cell RNA-seq analysis of FACS-sorted thymic epithelial cells (TECs, CD45-EpCAM+Ly51-MHCIIhigh) from EED conditional knockout mice (EED-cKO) and Aire/EED double knockout mice (Aire/EED-dKO)

first: Matsumoto

last: Minoru

first: Yoshida

last: Masaki

first: Miyazawa

last: Ryuichiro

first: Morimoto

last: Junko

first: Oya

last: Takeshi

first: Tsuneyama

last: Koichi

last: Mitsuru

last: Hideyuki


title: Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [CUT&Tag]

summary: Aire, a transcriptional regulator whose defect results in the development of autoimmunity, controls the transcriptome in the bulk of medullary thymic epithelial cells (mTECs) including the genes for self-antigens. Mechanisms for this process, however, remained incompletely understood, especially regarding the effects of Aire in each subpopulation in mTECs. Here, we combined single-cell multi-omics (scMulti-seq) technologies by which gene expression and open chromatin were simultaneously profiled from the same cell and deeper single-cell sequencing by RamDA-seq which enabled profiling of the minimum dropout. scMulti-seq effectively demonstrated the subpopulations among mTECs associated with diverse transcription factor activities which are affected by Aire and developmental stages, while RamDA-seq revealed the different modes of gene regulations by Aire in different subpopulations. Aire is not only essential for the development of a specific population in which Aire induces a set of genes in a stochastic manner but also promotes the development of multiple subpopulations in which Aire enhances the expressions of genes in a coordinated manner. The former group of Aire-induced genes was characterized by enhanced H3K27me3 chromatin modifications and Aire seems to unleash these silenced genes by deactivating polycomb repressive complex 2 (PRC2). We also found unique gene signatures for the neonatal stage such as high expression of chemokines and expression of cortical TEC (cTEC)-like genes in TECs, which were Aire-independent. Our approach has illuminated the multilayered transcriptional control in mTECs governing the multiple subpopulations organizing the thymic microenvironment.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) assay followed by NGS for profiling histone modification H3K27me3 in FACS-sorted mouse thymic epithelial cells (mTECs, CD45-EpCAM+Ly51-) from wild-type and Aire knockout (KO) mice.


title: DHODH modulates immune evasion of cancer cells via CDP-Choline dependent phospholipid metabolism

city: Bad Nauheim

first: Lei

last: Gu

state: Hessen

address: Parkstraße 1

department: Epigenetics

institute: Max Planck Institute for Heart and Lung Research

summary: The ability of cancer cells to evade immune destruction is governed by various intrinsic factors including their metabolic state. Here we demonstrate that inactivation of dihydroorotate dehydrogenase (DHODH), a pyrimidine synthesis enzyme, increases cancer cell sensitivity to T cell cytotoxicity through induction of ferroptosis. Lipidomic and metabolomic analyses revealed that DHODH inhibition reduces CDP-choline level and attenuates the synthesis of phosphocholine (PC) via the CDP-choline-dependent Kennedy pathway. To compensate this loss, there was increased synthesis from phosphatidylethanolamine via the phospholipid methylation pathway resulting in increased generation of very long chain polyunsaturated fatty acid-containing PCs. Importantly, inactivation of Dhodh in cancer cells promoted the infiltration of interferong-secreting CD8+ T cells and enhanced the anti-tumor activity of PD-1 blockade in mouse models. Our findings reveal the importance of DHODH in regulating immune evasion through a CDP-choline dependent mechanism and implicate DHODH as a promising target to improve the efficacy of cancer immunotherapies.

overall_design: To investigate the effect of the combination of BRQ and anti-PD1 in tumor environment, we isolate the tumor tissue from different treatment mice for gene expression profiling

first: Da

last: Teng

first: Bin

last: Zheng


title: Activated polyreactive B cells are clonally expanded in autoantibody positive and patients with recentonset type 1 diabetes

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

summary: Autoreactive B cells play an important but ill-defined role in autoimmune type 1 diabetes (T1D). To better understand their contribution to disease, we performed single cell gene expression and BCR-seq on pancreatic islet antigen-reactive (IAR) B cells from the peripheral blood of nondiabetic (ND), autoantibody positive prediabetic (AAB), and recent-onset T1D individuals. We found that the frequency of IAR B cells was increased particularly in AAB, but also in T1D compared to ND donors. Additionally, IAR B cells from AAB and T1D donors exhibited differential gene expression in B cell signaling, pro-inflammatory, infection, and antigen processing and presentation pathways compared to ND donors. Strikingly, both AAB and T1D donors demonstrated a significant increase in particular heavy and light chain V gene usages compared to ND, and these B cells were enriched in islet-reactivity.  Shared public clones of IAR B cells were found almost entirely among the AAB and T1D donors. IAR B cells were clonally expanded in the autoimmune donors, particularly the AAB group. Notably, a substantial fraction of IAR B cells in AAB and T1D donors appeared to be polyreactive and was confirmed by production of recombinant monoclonal antibodies. Altogether, these results expand our current understanding of B cells during development of T1D, how autoreactive B cells may become activated, and identify unique BCR repertoire differences that may serve as biomarkers for increased disease risk. These findings could be applied to future therapeutic approaches to prevent or treat T1D, as well as assess response to therapy.

overall_design: This study sought to determine whether differences in the transcriptional phenotype and BCR repertoire of islet antigen reactive B cells exist during development of autoimmunity. We generated uniquely barcoded PE-labeled antigen tetramers for INS, GAD, IA-2, and TET to identify antigen-reactive B cells using scRNA-seq. PBMCs from five ND first-degree relatives, six AAB subjects, and five recent-onset T1D patients were incubated with the various tetramers. Then, PE-binding B cells were sorted and loaded onto the 10X Genomics platform to be analyzed for gene expression and BCR repertoire differences. Recombinant antibodies were generated to confirm antigen-reactivity of some of the identified BCR sequences.

first: Catherine

last: Nicholas

first: Fatima

last: Tensun

first: Spencer

last: Evans

first: Kevin

last: Toole

first: Hali

last: Broncucia

first: Jay

middle: R

last: Hesselberth

first: Peter

last: Gottlieb

middle: L

first: Mia

last: Smith


title: Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [scRNA-Seq and scATAC-Seq]

first: Hideyuki

last: Yoshida

overall_design: single cell multiome ATAC + gene expression analysis of FACS-sorted mouse thymic epithelial cells (TECs, CD45-EpCAM+) from wild-type and Aire knockout (KO) mice

first: Matsumoto

last: Minoru

first: Yoshida

last: Masaki

last: Ryuichiro

last: Junko


title: Navarixin alleviates cardiac remodeling after myocardial infarction by decreasing neutrophil infiltration and the inflammatory response

status: Public on Mar 11 2025

city: Guangzhou

first: Jun

last: Lin

address: 107 Yanjiang West Road, Yuexiu District

department: Cardiovascular Surgery

institute: Sun Yat-sen Memorial Hospital

summary: Introduction: Coronary atherosclerotic heart disease is an important, worldwide burden on human health. Central muscle infarction is the most dangerous condition, has the highest mortality and disability rates, and is gradually becoming more common among young people. After myocardial infarction, neutrophils recruited to the infarcted area promote the myocardial inflammatory response by releasing proinflammatory factors and chemokines and release matrix metalloproteinases and myeloperoxidases that degrade the extracellular matrix and produce reactive oxygen species, resulting in irreversible myocardial damage and thereby promoting ventricular remodeling. Methods: In this study, we constructed a mouse model of myocardial infarction and utilized the CXCR2 receptor inhibitor navarixin (Nav) to reduce neutrophil recruitment after MI. Results: We observed that Nav improved cardiac function, reduced myocardial damage, reduced neutrophil infiltration, reduced inflammatory factor expression and improved cardiac fibrosis in mice. Through transcriptomic analysis, we found that Nav affects signaling pathways such as the innate immune response and the chemokine signaling pathway, thereby decreasing the inflammatory response by reducing neutrophil chemotaxis. Discussion: This study provides new insights for the use of CXCR2 inhibitors as new therapeutic options for myocardial infarction in the future.

overall_design: RNA-seq of the MI and MI+Nav hearts of mice

first: Peikun

last: Hu


title: GA-Camk2a mouse RNAseq data for the manuscript by Rezaei et al: Correction of dysregulated lipid metabolism normalizes gene expression in oligodendrocytes and prolongs lifespan in female poly-GA C9orf72 mouse model

city: Munich

first: Ali

last: Rezaei

address: Feodor-Lynen-Strasse 17

institute: LMU

summary: These sequences support the following paper abstract: "Clinical and genetic research links altered cholesterol metabolism with ALS development and progression, yet pinpointing specific pathomechanisms remain challenging. We investigated how cholesterol dysmetabolism interacts with protein aggregation, demyelination, and neuronal loss in ALS. Bulk RNAseq transcriptomics showed decreased cholesterol biosynthesis and increased cholesterol export in ALS mouse models (GA-Nes, GA-CFP, rNLS8) and patient samples (spinal cord), suggesting an adaptive response to cholesterol overload. Consequently, we assessed the efficacy of the cholesterol-binding drug 2-hydroxypropyl-β-cyclodextrin (CD) in a fast-progressing C9orf72 ALS mouse model with extensive poly-GA expression and myelination deficits. CD treatment normalized cholesteryl ester levels, lowered neurofilament light chain levels, and prolonged lifespan in female but not male GA-Nes mice, without impacting poly-GA aggregates. Single nucleus transcriptomics indicated that CD primarily affected oligodendrocytes, significantly restored myelin gene expression, increased density of myelinated axons, inhibited the disease-associated oligodendrocyte response, and downregulated the lipid-associated genes Plin4 and ApoD. These results suggest that reducing excess free cholesterol in the CNS could be a viable ALS treatment strategy."

overall_design: transgenic and control mice were sacrifiec at the humane endpoint of the transgenic mice (30-40 weeks) and harvested with brain microdissection for RNAseq

first: Katherine

middle: D

last: LaClair

first: Aleksander

last: Janjic

first: Wolfgang

last: Enard

first: Qihui

last: Zhou

first: Dieter

last: Edbauer


title: Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [bulkRNA-seq]

overall_design: Bulk RNA-seq analysis of FACS-sorted mouse thymic epithelial cells (TECs, CD45-EpCAM+Ly51-) from wild-type and knockout (KO) mice

first: Minoru

last: Matsumoto

first: Masaki

first: Ryuichiro

last: Miyazawa

first: Junko

last: Morimoto

first: Takeshi

last: Oya

first: Koichi

last: Tsuneyama

first: Mitsuru


title: AAV vectors trigger neurotoxic DNA damage responses and STING-dependent inflammation in human CNS cells [scRNAseq_dataset2]

city: Milan

first: Monah

last: Abou Alezz

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

summary: Adeno-associated viral (AAV) vector gene therapy is gaining ground as a treatment option for genetic neurodegenerative diseases tha currently have no cure. Nonetheless, significant toxicity and severe adverse events are emerging in recent clinical trials through mechanisms that remain unclear. We have modelled here AAV-mediated neurotoxicity in the context of the human brain taking advantage of human induced pluripotent stem cell-based technologies. We have used single-cell RNA sequencing technologies to interrogate vector-induced cell-intrinsic innate immune mechanisms that could contribute to neurotoxicity in 3D brain sphheroids transduced with AAV vectors at different time-points and harvested at two different time-points.

overall_design: hiPSC-derived brain spheroids containing  neurons, astrocytes and oligodendrocytes were transduced in experimental duplicates with different AAV serotypes and harvested after 2 or 5 days post-transduction for scRNAseq. Duplicates for each condition were pooled for library preparation.

first: Helena

last: Verdera

last: Alezz

first: Ivan

last: Merelli

first: Elisabeth

last: Mangiameli

first: Vasco

last: Meneghini

first: Anna

last: Kajaste-Rudnitski


title: AAV vectors trigger neurotoxic DNA damage responses and STING-dependent inflammation in human CNS cells [RNA-seq]

summary: Adeno-associated viral (AAV) vector gene therapy is gaining ground as a treatment option for genetic neurodegenerative diseases tha currently have no cure. Nonetheless, significant toxicity and severe adverse events are emerging in recent clinical trials through mechanisms that remain unclear. We have modelled here AAV-mediated neurotoxicity in the context of the human brain taking advantage of human induced pluripotent stem cell-based technologies. We have used RNA sequencing technologies to interrogate vector-induced cell-intrinsic innate immune mechanisms that could contribute to neurotoxicity in 2D iPSC-derived cultures of atrocytes and neurons respectively.

overall_design: Astrocytes and neurons were differentiated from healty donor iPSCs. At the end of the respective maturation protocols, cells were transduced with the indicated AAV vector serotype or empty capsid controls for 48 hours, and their transcriptomes were compared to those of untreated (UT) controls.


title: AAV vectors trigger neurotoxic DNA damage responses and STING-dependent inflammation in human CNS cells [scRNAseq_dataset3]

summary: Adeno-associated viral (AAV) vector gene therapy is gaining ground as a treatment option for genetic neurodegenerative diseases tha currently have no cure. Nonetheless, significant toxicity and severe adverse events are emerging in recent clinical trials through mechanisms that remain unclear. We have modelled here AAV-mediated neurotoxicity in the context of the human brain taking advantage of human induced pluripotent stem cell-based technologies. We have used single-cell RNA sequencing technologies to interrogate vector-induced cell-intrinsic innate immune mechanisms that could contribute to neurotoxicity in mixed 2D neuron-glial cultures transduced with AAV vectors at different time-points and harvested at two different time-points.