title: Decoding Functional and Developmental Trajectories of Tissue-Resident Uterine Dendritic Cells Through Integrative Omics

city: Detroit

first: Aditi

last: Singh

state: MI

address: 275 E Hancock St

department: CMMG

institute: Wayne State University

summary: Uterine dendritic cells (uDCs) are critical for endometrial function, yet their origin, molecular characteristics, and specific roles during the pre- and post-implantation periods in the human endometrium remain largely unknown. The complexity of the endometrial environment makes defining the contributions of uDCs subtypes challenging. We hypothesize that distinct uDC subsets carry out specialized functions, and that resident progenitor DCs generate these subtypes.  Employing single-cell RNA sequencing on uterine tissues collected across different menstrual phases and during early pregnancy, we identify several uDCs subtypes, including resident progenitor DCs. CITE-seq was performed on endometrial single-cell suspensions to link surface protein expression with key genes identified by the RNAseq analysis. Our analysis revealed the developmental trajectory of the uDCs along with the distinct functional roles of each uDC subtype, including immune regulation, antigen presentation, and creating a conducive environment for embryo implantation. This study provides a comprehensive characterization of uDCs, serving as a foundational reference for future studies for better understanding female reproductive disorders such as infertility and pregnancy complications.

overall_design:
Endometrial biopsies were collected from healthy patients across 10 distinct stages of the menstrual cycle, determined using a precise cycle tracking method. Single-cell suspensions were prepared, and cells were extracted using fluorescence-activated cell sorting (FACS) to enrich for specific populations. The extracted cells were then sequenced using the MARS-seq (Massively Parallel RNA Single-Cell Sequencing) platform, enabling high-resolution analysis of gene expression profiles across the different phases of the menstrual cycle.

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raw data not provided
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first: Jing

last: Yang

first: Nicholas

last: Adzibolosu

first: Songchen

last: Cai

first: Elana

last: Kauf

first: Lingtao

first: Qiyuan

last: Li

first: Hanjie

first: Alexandra

last: Werner

first: Siddharth

last: Parthasarathy

first: Jiahui

last: Ding

first: Jared

last: Fortier

first: Marta

last: Rodriguez-Garcia

first: Lianghui

last: Diao

first: Gil

last: Mor


title: DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation.

status: Public on Aug 08 2025

city: Mainz

first: Joan

last: Barau

address: 4 Ackermannweg

country: Germany

institute: Institute of Molecular Biology IMB - Mainz

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Zbtb16 determines the fate plasticity of cardiovascular progenitors through IGF2BP3-mediated mRNA stabilization [scRNA-seq]

city: Shanghai

first: Wuchan

last: Wang

address: Tongji University

country: China

institute: Tongji University

summary: Cardiovascular progenitors (CPs) are responsible for generating the diverse cell populations in hearts, exhibiting significant transcriptional heterogeneity. However, the regulation of fate plasticity among heterogeneous CP subpopulations, as well as the intrinsic regulatory factors, remains poorly understood. In this study, we characterized three CP subpopulations derived from pluripotent stem cells and found that the deletion of ZBTB family protein Zbtb16 led to a profound imbalance in the branching transition trajectory of Early-CPs, redirecting them toward CPs committed to endothelial cells and cardiac fibroblasts (EC/CF-CPs) rather than that to cardiomyocytes (CM-CPs). Mechanistic studies revealed that Zbtb16 interacted with the m6A reader IGF2BP3 to post-transcriptionally recognize and stabilize the mRNAs of key genes critical for the CM-CP subpopulation determination. Collectively, our findings established Zbtb16 as a key regulator of fate plasticity of heterogeneous CP subpopulations and revealed the interplay with IGF2BP3 to impact the m6A-modified mRNA stabilization, which provided new insights into the intrinsic connections between CP subpopulation plasticity and cardiovascular multi-lineage fate determination.

overall_design: To investigate the subpopulation regulated by Zbtb16 at CP stage, samples from day 6 of cardiomyocyte differentiation in the D3-Ctrl and Zbtb16-KO groups were collected and analyzed by scRNA-seq.


title: RNA expression of Kras;Setd2 versus Kras mouse lung neoplastic cells

city: Xiamen

first: Hongchen

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang'an Campus

institute: Xiamen University

summary: Setd2 is a histone H3K36 methyltransferase that suppresses lung cancer growth. Here we CRISPR knock out Setd2 in Kras-G12D genetically-engineered mouse models, and perform RNA-seq on FACS-purified neoplastic cells to profile the gene expression changes that result from Setd2 inactivation. Control group samples were transduced with inert sgRNAs. H3K36me3 immunoblot was performed to verify Setd2 knockout status.

overall_design: Kras-LSL-G12D;Rosa26-LSL-tdTomato;H11-LSL-Cas9 mice were transduced with Lenti-sgSetd2/Cre or Lenti-sgInert/Cre control to initiate lung neoplasia. Tumors were allowed to grow for 9-12 months before tdTomato+/CD31-/CD45-/Ter119-/F4/80- neoplastic cells were FACS purified for RNA-seq.

first: Yunhai

last: Luo

first: Monte

middle: M

last: Winslow


title: Mitochondrial NNT Promotes Diastolic Dysfunction in Cardiometabolic HFpEF

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry road

department: Cardiovascular Medicine

country: USA

institute: Stanford University

summary: BACKGROUND: Clinical management of heart failure with preserved ejection fraction (HFpEF) is hindered by a lack of disease-modifying therapies capable of altering its distinct pathophysiology. Despite the widespread implementation of a 2-hit model of cardiometabolic HFpEF to inform precision therapy, which utilizes HFD+L-NAME (ad libitum high-fat diet and 0.5% N[ω]-nitro-L-arginine methyl ester), we observe that C57BL6/J mice exhibit less cardiac diastolic dysfunction in response to HFD+L-NAME. METHODS: Genetic strain-specific single-nucleus transcriptomic analysis identified disease-relevant genes that enrich oxidative metabolic pathways within cardiomyocytes. Because C57BL/6J mice are known to harbor a loss-of-function mutation affecting the inner mitochondrial membrane protein Nnt (nicotinamide nucleotide transhydrogenase), we established an isogenic model of Nnt loss-of-function to determine whether intact NNT is necessary for the pathological cardiac manifestations of HFD+L-NAME. Twelve-week-old mice cross-bred to isolate wild-type (Nnt+/+) or loss-of-function (Nnt−/−) Nnt in the C57BL/6N background were challenged with HFD+L-NAME for 9 weeks (N=6–10). RESULTS: Nnt+/+ mice exhibited impaired ventricular diastolic relaxation and pathological remodeling, as assessed via noninvasive echocardiographic quantification of early diastolic pulse-wave velocity (E) to mitral annular velocity (e′) ratio (E/e′) (42.8 versus 21.5, P=1.2×10−10), E/A (early-to-late mitral inflow velocity ratio) (2.3 versus 1.4, P=4.1×10−2), diastolic stiffness (0.09 versus 0.04 mm Hg/μL, P=5.1×10−3), and myocardial fibrosis (P=2.3×10−2). Liquid chromatography and mass spectroscopy exposed a 40.0% reduction in NAD+ (P=8.4×10−3) and a 38.8% reduction in the ratio of reduced-to-oxidized glutathione (GSH: GSSG, P=2.6×10−2) among Nnt+/+ mice after HFD+L-NAME feeding. Using single-nucleus ligand-receptor analysis, we implicate Fgf1 (fibroblast growth factor 1) as a putative NNT-dependent mediator of cardiomyocyte-to-fibroblast signaling in myocardial fibrosis. CONCLUSIONS: Together, these findings underscore the pivotal role of mitochondrial dysfunction in HFpEF pathogenesis, implicating both NNT and Fgf1 as novel therapeutic targets.

overall_design: The initial pilot experiment consisted of twenty 12-week-old male mice from the C57BL/6N and C57BL/6J backgrounds that were purchased from 2 vendors (N=5 per diet-genotype)—Janvier and Charles River laboratory—and housed at the Klinisch Experimenteller Bereich mouse facility of Heidelberg University. All cohorts were group-housed (≤4 mice/cage) on a 12:12-hour light-dark cycle from 06:00 to 18:00 at 25±1 °C and constant humidity with either ad libitum access to control laboratory diet (CON, no. 2916; Teklad) and water (CON) or HFD (58.0 kcal% fat, D12492) with water containing L-NAME (0.5 g/L, pH=7.4; Sigma-Aldrich) stored in light-sensitive bottles (HFD+L-NAME), as previously described.

middle: E

first: Johannes

last: Backs


title: The PIK3CA/AKT pathway drives therapy resistance in rhabdomyosarcoma

city: Charlestown

first: David

last: Langenau

state: MA

department: Molecular Pathology

institute: Massachusetts General Hospital

summary: Olaparib and temozolomide (OT) combination therapy is in clinical trial evaluation foradolescent rhabdomyosarcoma (RMS) muscle cancers. Unfortunately, resistance to OT hasbeen reported in other cancers, with no counterstrategies available. Using preclinical mousexenograft experiments, we show that OT is effective at curbing RMS growth, yet a subset oftumors develop resistance that is associated with transcriptomic changes that occur in theabsence of recurrent genomic mutation. Importantly, a majority of resistant RMS modelsupregulate the PIK3CA/AKT pathway, which in turn activates NRF2 transcription factorphosphorylation and subsequent transcriptional expression of multidrug resistance ABCtransport proteins that rapidly efflux drugs from cells. We found that the PIK3CA inhibitoralpelisib re-sensitized resistant tumor cells to OT therapy by suppressing the expression of ABCtransport proteins. Excitingly, RMS use the same PIK3CA/AKT pathway activation to driveresistance to standard-of-care combination therapy vincristine, actinomycin D, andcyclophosphamide (VAC) and the combination of OT + alpelisib effectively killed VAC-resistantRMS. Alpelisib also re-sensitized resistant RMS to chemotherapy in preclinical xenograft mousemodels resulting in reduced tumor burden and extended disease-free survival. Our work definesa common resistance pathway in RMS and has credentialled a new preclinical strategy to killtherapy resistant RMS.

overall_design: Single cells were dissociated by tumor dissociation kit from PDX tumor on NSG mice and analyzed using scRNAseq.

first: Qiqi

last: Yang

first: Qian

last: Qin


title: Single-cell sequencing of colorectal tumors in mice

city: Beijing

first: Xiaowen

last: Qiao

address: No.52 Fucheng Road, Haidian District

institute: Peking University

summary: To explore the underlying mechanism of STK25 in CRC, we performed single-cell transcriptome profiling of the intestinal tumor from STK25 wKO and wile-type mice.We performed dimensional reduction and unsupervised clustering of cells to identify cell groups based on their expression patterns

overall_design: Intestinal tumor from STK25 wKO and wile-type mice were isolated by Fluorescence-activated cell sorting(FACS) according to the presence or absence of mCherry signal and analyzed by using scRNAseq.

first: Xing

last: Pu


title: ATAC-seq of FIL-ASPCs with or without NAC treatment during adipogenic induction

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

summary: To clarify the impact of redox homeostasis regulation on chromatin accessibility in adipogenic stem and precursor cells during adipogenic differentiation, we performed ATAC-seq on FIL-ASPCs treated with or without N-acetylcysteine.

overall_design: Group 1: FIL-ASPCs. Group 2: FIL-ASPCs + NAC

first: Chen

last: Hua

first: Xiaoxi

last: Lin


title: Response of collecting duct cells to hypertonic stress

city: Nashville

first: Juan

middle: Pablo

last: Arroyo

state: TN

address: 1161 21st Ave South MCN C3111

department: Medicine

institute: Vanderbilt University Medical Center

summary: Transcriptional profile of inner medullary collecting duct cells in response to overnight NaCl hypertonic stress

overall_design: To study the transcriptional response of inner medullary collecting duct cells to hypertonic stress, we treated 90% confluent inner medullary collecting duct cells with 100 mmol NaCl for 12 hrs and then extracted RNA for bulq RNA sequencing.

middle: P

first: Joshua

middle: S

last: Carty


title: A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [ZC3H11A_kd_splicing]

city: San Francisco

first: Hani

last: Goodarzi

department: Department of Biochemistry and Biophysics

institute: UCSF

summary: RNA-binding proteins (RBPs) are multifunctional regulators of gene expression with complex and context-dependent mechanisms of action, yet the regulatory grammar that underlies RBP-mediated functions remains underexplored. Here, we performed a multi-omic data integration to systematically decipher the context-specific functions of RBPs. First, we report a compendium of in vivo proximity-dependent biotinylation (BioID) datasets of 50 human RBPs, which we used to generate a large-scale map of RBP protein neighborhoods. In parallel, we took advantage of CRISPR-interference with single-cell RNA-seq read-out (Perturb-seq) to capture rich transcriptomic phenotypes downstream of each RBP knockdown. By combining these physical and functional interaction readouts, along with the ENCODE transcriptome-wide atlas of RBP binding sites from eCLIP assays, we generated an integrated map of functional RBP interactions. This map not only captures well-studied post-transcriptional processes, but also reveals numerous previously unknown RBP-mediated regulatory functions. For a number of these cases, we have validated their predicted context-specific RBP functions using biochemical and genetic approaches. By deciphering these complex modes of functional interactions between RBPs, we have taken the first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar.

overall_design: We obtained transcriptome-wide gene expression measurements for 68 RBPs (representing a variety of regulatory processes) knockdowns using single-cell RNA sequencing and used the resulting high-dimensional data to systematically delineate genetic interactions between RBPs.  Perturb-seq experiment was performed as previously described (Datlinger et al. 2017).

first: Matvei

last: Khoroshkin

first: Andrey

last: Buyan

first: Martin

last: Dodel

first: Albertas

last: Navickas

first: Johnny

last: Yu

first: Fathima

last: Trejo

first: Anthony

last: Doty

first: Rithvik

last: Baratam

first: Shaopu

last: Zhou

first: Tanvi

last: Joshi

first: Kristle

last: Garcia

first: Benedict

last: Choi

first: Sohit

last: Miglani

first: Vishvak

last: Subramanyam

first: Hailey

last: Modi

first: Chris

last: Carpenter

first: Daniel

last: Markett

first: Ivan

middle: V

last: Kulakovskiy

first: M

middle: R

last: Corces

first: Faraz

last: Mardakheh


title: Modification of fat mass through targeting distal enhancer of Ptrf

city: cehngsu

first: zhang

last: songling

state: China

address: wenjianqu

institute: Sichuan Agricultural University, Chengdu 611130, China

summary: We revealed a close positive relationship between Ptrf transcription and adipose mass in mice, and single-nucleus transcriptomics indicated the involment of impariment of adipogenic differentiation, adipocyte metabolism, transportation of multiple nutrients and altered regulatory network in Ptrf knockout-induced decrease of fat mass.

overall_design: We analyzed inguinal white adipose from 6-month-old WT and PTRF KO mice using single-nucleus sequencing.

first: Yu

last: Zhang

first: Keren

last: Long

first: Songling

first: Ziqi

last: Li


title: Effect of FKBP5 inhibitor SAFit2 on fibro-adipose progenitor cells isolated from facial infiltrating lipomatosis

first: Hongrui

last: Chen

summary: Facial infiltrating lipomatosis (FIL) is a congenital disorder characterized by unilateral facial enlargement. Although next-generation sequencing has revealed that the pathogenesis of FIL is associated with phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) mutations, the underlying molecular mechanisms remain undetermined. We found that the adipose tissue in FIL patients demonstrated tissue infiltration accompanied by adipocytes hypertrophy and increased lipid accumulation. All FIL derived fibro-adipose progenitor cells (FIL-FAPs) harboured PIK3CA mutations. Compared to FAPs obtained from normal subcutaneous adipose tissue, FIL-FAPs exhibited a greater capacity for adipogenesis. Suppression of PIK3CA resulted in a reduction in the adipogenic potential of FIL-FAPs. Through single cell sequencing, we find that FIL-FAPs had higher expression of FKBP5. Inhibiting FKBP5 can impair the adipogenic capacity of FIL-FAPs. We also verified that PI3K-AKT pathway regulating FKBP5 expression. To find the downstream target of FKBP5, we performed RNA-seq of FIL-FAPs treated with FKBP5 inhibitor SAFit2 in DMSO or DMSO alone.

overall_design: To explore the gene expression alterations in FIL-ADSCs after SAFit2 treatment, we applied SAFit2 to FIL-FAPs isolated from three different patients. By utilizing RNA sequencing, we compared the gene expression profiles between SAFit2-treated and untreated FIL-FAPs.

first: Bin

last: Sun

first: Chen

last: Hua

first: Xiaoxi

last: Lin


title: Synergizing Translational Repression Versus RNA Degradation by miRNAs during T Cell Activation [RIBOseq]

city: Berkeley

first: Thyago

middle: Leal

last: Calvo

state: California

address: 2151 Berkeley Way

department: IGI

institute: UC Berkeley

summary: T cells, crucial for immune regulation, risk malfunction leading to immune deficiencies or autoimmune diseases. Understanding the molecular cycle of T cell activation is vital for potential therapeutic interventions. Activation remodels the cellular transcriptome and proteome, impacting metabolism and protein synthesis pathways. The human genome encodes microRNAs (miRNAs), regulating hundreds of protein-coding mRNAs through translational repression and mRNA decay. While mRNA degradation is terminal, translational repression is reversible, allowing rapid responses to internal or external cues. In this study, we investigated changes in the miRNA repertoire and their impact on translational repression and mRNA degradation during T cell activation using high-throughput techniques. Our findings reveal that miRNAs induced upon T cell activation clear their targets through multiple pathways, with some following the canonical path of mRNA degradation and others initiating translational repression before mRNA degradation.

overall_design: mRNAseq, Ribosome profiling and smallRNAseq experiments were carried out with non-activated Jurkat cells or Jurkat cells activated for 5 hr and 12 hr with anti-CD3/anti-CD28 antibodies (Tonbo). For activation, flat bottom plates were coated with anti-CD3 antibody at a 10 μg/mL concentration at 4C for at least 12h, and anti-CD28 antibody was added to the cell culture media at a concentration of 5 µg/mL and cells were incubated for the required timepoints. All experiments had 3 biological replicates and control samples were non activated Jurkat cells.

first: Pooja

last: Mukherjee

first: Lucas

last: Ferguson

last: Leal-Calvo

first: Jamie

last: Cate


title: Synergizing Translational Repression Versus RNA Degradation by miRNAs during T Cell Activation [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing


title: Beta-catenin deletion and GSK3b inhibition in B-ALL cells

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

summary: In most cell types, nuclear β-catenin functions as prominent oncogenic driver and pairs with TCF7-family factors for transcriptional activation of MYC. Surprisingly, B-lymphoid malignancies not only lacked expression and activating lesions of β-catenin but critically depended on GSK3b for effective b-catenin degradation. Our interactome studies in B-lymphoid tumors revealed that b-catenin formed repressive complexes with lymphoid-specific Ikaros and Lef1 factors at the expense of TCF7. While Lef1 was critical for nuclear β-catenin translocation, nuclear b-catenin enabled Ikaros-mediated recruitment of nucleosome remodeling and deacetylation (NuRD) complexes for transcriptional repression of MYC.

overall_design: To study gene expression changes induced by β-catenin deletion in B-ALL, BCR-ABL1 transformed Ctnnb1fl/fl cells were transduced with tamoxifen inducible Cre (Cre-ERT2) or control (ERT2) vectors. To induce deletion of β-catenin, cells were treated with 1μM 4-OHT for two days. For studying changes induced by small molecule induced activation of β-catenin, cells were treated with 40nM LY2090314 for 1 day. To assess whether β-catenin deletion reverts the LY2090314-induced transcriptional changes, cells were pre-treated 1μM 4-OHT 1 day before  LY2090314 treatment.

first: Kadriye

last: Nehir Cosgun

first: Markus

last: Müschen


title: GRO-seq profiles in ST2 cell line

city: Kuopio

first: Ana

last: Hernández de Sande

email: anah@uef.fi, ahdesande@gmail.com

state: North-Savo

address: Yliopistonranta 1E

country: Finland

institute: University of Eastern Finland

summary: Nascent transcription was studied using GRO-seq in the stromal bone marrow derived cell line ST2.

overall_design: GRO-seq profiles were generated from ST2 cell line.We follow the adipogenic differentiation protocol established for the 3T3-L1 cell line to induce adipogenesis.  DMSO treated cells were used as controls.

first: Maria

last: Bouvy-Liivrand

first: Merja

last: Heinäniemi

first: Lasse

last: Sinkkonen

first: Minna

middle: U

last: Kaikkonen


title: Single-cell RNA sequencing of ST2 mouse cell line

summary: Single-cell transcription was studied in the stromal bone marrow derived cell line ST2.

overall_design: scRNA-seq profiles were generated from ST2 cell line.

first: Mari

last: Lahnlampi


title: Genome-wide analysis of replication initiation in Tetrahymena [Vegetative growing cells]

city: Bryan

first: GEOFFREY

last: KAPLER

state: TX

address: 4209B Medical Research Education Building II

institute: Texas A&M University

summary: We mapped Tetrahymena macronuclear replication origins on a genome-wide scale using nanopore sequencing. Nanopore sequencing quantifies individual BrdU incorporated replication intermediates on individual DNA molecules.

overall_design: The asynchronous exponentially growing Tetrahymena cells were pulse labeled with 100 µM (or 500 µM) of BrdU for 5 min and chased with 50 µM (or 250 µM) thymidine for 5 min, then added final 1 mM (or 2 mM) of thymidine for 20 min (Hennion et al. 2020).

first: Zhang

last: Linying

first: Dang

last: Hung

first: Pan

last: Simin


title: Transcriptomic Analysis of the Adaptive Response of Staphylococcus aureus during Chronic Phases of periprosthetic joint infection versus Acute Phases

city: Fuzhou

first: Xinyu

last: Fang

address: Chazhong road

institute: The First Affiliated Hospital of Fujian Medical University

summary: To explore the difference in the expression profile of Staphylococcus aureus in chronic periprosthetic joint infection (C_PJI) and acute PJI (A_PJI), we assayed S. aureus isolates from 4 C_PJI and 4 A_PJI by RNA-sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C_PJI and  A_PJI.


title: Zbtb16 determines the fate plasticity of cardiovascular progenitors through IGF2BP3-mediated mRNA stabilization [RIP-Seq]

first: Wuchan

last: Wang

overall_design: To investigate the potential downstream target genes regulated by  the interaction of Zbtb16 and IGF2BP3 at CP stage, samples from day 6 of cardiomyocyte differentiation in the D3-Ctrl and Zbtb16-KO groups were collected. Gene expression levels were quantitated by RNA-seq analysis, and the potential target genes were identified through overlapping with RIP-seq analysis.


title: Oncogenic β-catenin activation

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

overall_design: Refer to individual Series


title: Changes in Ikaros binding and histone-modifications upon oncogenic β-catenin activation [ChIP-Seq]

summary: We find that, in contrast to most cancer types, beta-catenin activation in preB-ALL cells supresses proliferation and leads to cell death. Proteomic analyses indicate that unlike in solid tumors beta-catenin interacts with Ikaros factors (IKZF1 and IKZF3) in pre-B cells. In order to examine the interaction between IKZF1/IKZF3 and beta-catenin we performed ChIPseq to assay chromatin state and TF binding in CTNNB1-GOF and IKZF1/3-LOF conditions.

overall_design: IKZF1, IKZF3, H3K27ac and H3K4me3 ChIP-seq was performed in pre-B cells from Ctnnb1Ex3fl/+ mice transformed with BCR-ABL1 and transfected with either non-targeting or IKZF1 and IKZF3 CRISPR/Cas9-RNP in order to study the effect of beta-catenin activation on IKZF1/3 binding and histone modifications in both IKZF1/3-WT and IKZF1/3-KO conditions.

middle: N

last: Cosgun

last: Muschen


title: Molecular Signatures and Lineage Diversification of Neurogenic and Gliogenic Radial Glia in the Gyrencephalic Ferret Cortex

status: Public on Aug 07 2025

first: TongYe

last: Fu

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: Human exceptional cognition stems from evolutionarily derived cortical adaptations that drive expansive neurogenesis. Deciphering these mechanisms is crucial for understanding mammalian cortical evolution. In this study, we employ the ferret model to comprehensively map molecular profiles and lineage dynamics of cortical radial glia (RGs). By applying scRNA-Seq to ferret and human cortices, we identify conserved regulatory programs underlying cortical neurogenesis and gliogenesis in mammals. Through integrated scRNA-Seq, BrdU pulse-chase labeling, and immunohistochemical approaches, we demonstrate that, similar to their human counterparts, ferret cortical outer radial glia (oRGs), exhibit enhanced ERK and PKA signaling. ERK and PKA act in a mutually reinforcing manner to boost oRG self-renewal and neurogenesis, while inhibiting gliogenesis and prolonging the neurogenic period. Furthermore, we identify regional specialization within cortical gliogenic RGs: YAP/TAZ activation drives ventricular zone truncated radial glia (tRGs) toward ependymal fate in medial cortex, whereas SHH signaling instructs lateral cortical tRGs to generate tripotential intermediate progenitor cells, which serve as a shared source of astrocytes, oligodendrocytes, and olfactory bulb interneurons. Our data support a model in which mammalian cortical neurogenesis, gliogenesis, and evolutionary expansion are co-regulated through an integrated signaling network involving ERK, PKA, YAP/TAZ, and SHH. These findings provide key insights into the molecular and cellular mechanisms driving cortical development and evolution.

overall_design: P3 ferret pups were deeply anesthetized, and their brains were immediately harvested and immersed in ice-cold Hanks' Balanced Salt Solution (Gibco 14175-095). The dorsal cortices were dissected into small pieces and dissociated into a single-cell suspension using the Papain Cell Dissociation Kit, following the manufacturer’s instructions (Miltenyi Biotec, catalog no. 130-092-628). Single-cell RNA sequencing (scRNA-Seq) libraries were prepared using the Chromium droplet-based sequencing platform (10X Genomics), in accordance with the manufacturer’s guidelines (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina HiSeq 4000.

first: Jialin

last: Li

first: Zhengang

last: Yang


title: miRNA expression profiling of mouse colon in chronic colitis and colitis-associated cancer models

city: Guri

first: Jae Gon

last: Lee

address: 153 Gyeongchun-ro

country: South Korea

institute: Hanyang University Guri Hospital

summary: This study aims to investigate alterations in colonic microRNA expression in mouse models of chronic colitis and colitis-associated colorectal cancer. Using the Affymetrix GeneChip miRNA 4.0 Array, miRNA profiles were analyzed from control mice, DSS-induced colitis mice, and AOM/DSS-induced colorectal tumor mice.

overall_design: A total of 20 mouse colon tissue samples were analyzed, including 6 control samples, 7 DSS-treated samples, and 7 AOM/DSS-treated samples. Total RNA was extracted and hybridized to the GeneChip miRNA 4.0 Array (Affymetrix). CEL and CHP files were generated for each sample and used for downstream analysis.

first: Chang

last: Eun


title: Synergizing Translational Repression Versus RNA Degradation by miRNAs during T Cell Activation

first: Thyago

last: Calvo


title: Synergizing Translational Repression Versus RNA Degradation by miRNAs during T Cell Activation [RNAseq]

first: Pooja

last: Mukherjee

first: Lucas

last: Ferguson

last: Leal-Calvo

first: Jamie

last: Cate


title: Structural and functional basis of PU.1-BAF interaction enables targeting of lineage-specific transcription

city: Cambridge

first: Salih

last: Topal

address: 500 Technology Square Suite 700

institute: Foghorn Therapeutics


title: CD40 induces PIR-A+ macrophages to promote chronic rejection of cardiac transplantation [ChIP-seq]

city: Wuhan

first: Shi

last: Chen

state: Hubei

address: 1095 Jiefang Avenue, Qiaokou District, Wuhan

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

summary: To explore whether transcription factor NF-κB2 interacts with the DNA region, NF-κB2 chip-seq studies, both in FGK45-treatment and IgG (Ctrl), were carried out to identify the direct target of NF-κB2.

overall_design: NF-κB2 chip-seq studies, both in FGK45-treated and IgG (Ctrl)-treated bone marrow-derived macrophages.

first: Peixiang

last: Lan


title: TGF-β-induced MIR99AHG synergizes with PTBP1 to trigger an alternative splicing switch of SMARCA1 that promotes invadopodia formation for metastasis in colorectal cancer

city: Xi'an

first: Xiaodi

last: Zhao

address: No.127 Changle West Road

department: Xijing Hospital of Digestive Diseases

institute: Xijing Hospital of Fourth Military Medical University

summary: Alternative splicing (AS) of pre-mRNAs is an essential process that regulates gene expression and functional diversity, yet the underlying regulatory mechanisms that control this process during cancer metastasis are not clear. Here, we uncovered that a long non-coding RNA (lncRNA), MIR99AHG, mediates regulation of AS to alter chromatin remodeler function and promote invadopodia formation in colorectal cancer (CRC). We found that MIR99AHG is highly expressed in metastatic CRC cells and patient tissue samples. In vitro and in vivo assays showed that MIR99AHG potently drove CRC cell motility, invasion, and metastasis. MIR99AHG bound to and stabilized the RNA splicing factor PTBP1, which cooperatively increased cassette exon inclusion of the chromatin remodeling gene SMARCA1. Mechanistically, MIR99AHG acted as an address label for PTBP1 to fine-tune its binding pattern on SMARCA1 pre-mRNA, thereby controlling the skipping-to-inclusion splicing switch of SMARCA1 and favouring the production of a long isoform (SMARCA1-L). Canonical SMARCA1 was found to suppress cell migration and invasiveness by inhibiting invadopodia formation, but SMARCA1-L was functionally inert. Clinical data revealed that MIR99AHG was positively correlated with PTBP1 and SMARCA1-L in human CRC specimens and predicted patient outcome. Furthermore, we showed that the crosstalk with cancer-associated fibroblasts triggers TGF-β/SMAD signalling in CRC cells and activates MIR99AHG expression. Our findings establish a novel mechanism for a lncRNA that interacts with PTBP1 to regulate AS process, providing a potential therapeutic target and predictive biomarker of CRC.

overall_design: We performed whole transcriptome sequencing using CRC cell lines with divergent spontaneous metastatic properties. The biological roles and mechanisms of lncRNA MIR99AHG were characterized with a series of in vitro and in vivo models and molecular analyses.

first: Yuanyuan

last: Lu

first: Ling

first: Xin

first: Danxiu


title: Structural and functional basis of PU.1-BAF interaction enables targeting of lineage-specific transcription [RNA-seq]

summary: Transcription factors (TFs) regulate gene expression by engaging chromatin remodeling complexes, yet the structural principles governing these critical interactions remain poorly defined. Here, we uncover the molecular mechanism by which lineage-specific pioneer transcription factor PU.1 (encoded by SPI1) directly engages the BAF (mSWI/SNF) chromatin remodeling complex. First, using a variety of genomic approaches, we establish that BAF collaborates with PU.1 to regulate transcription in AML cells. Then, using a combination of biochemistry and biophysics, mass spectrometry-based protein footprinting, and crystallography, we map the PU.1-BAF60A interface to a disordered region of PU.1 that adopts a helical conformation upon binding to the YEATS-like domain of BAF60A. Disruption of this functionally critical interface via knockdown abrogates the ability of PU.1 to rescue cell viability. Finally, we conducted a high-throughput screen that yielded small molecules which selectively bind BAF60A and disrupt PU.1 binding. Co-crystal structures reveal distinct compound binding modes that converge on a critical PU.1-BAF60A interaction hotspot. These findings define, for the first time, the structural interface between a pioneer transcription factor and the BAF complex and establish a platform that enables targeting transcription factor-chromatin remodeling complex interactions in cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 cells cells treated with dual SMARCA4/SMARCA2 inhibitor Compound 49 for 24h; MV-4-11 cells treated with dual SMARCA4/SMARCA2 inhibitor FHT-1015 for 24h or shPU.1 for 48h.

first: Asad

last: Taherbhoy


title: CD40 induces PIR-A+ macrophages to promote chronic rejection of cardiac transplantation

summary: To investigate the mechanism PIR-A+ macrophages regulated by CD40 in chronic rejection of cardiac transplantation, we performed gene expression profiling analysis using data obtained from RNA-seq of bone marrow-derived macrophages stimulated with anti-CD40 mAb (FGK45) or IgG (Ctrl) for 24h.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow-derived macrophages stimulated with anti-CD40 mAb (FGK45) or IgG (Ctrl) for 24h.


title: Isoliensinine induces vasorelaxation by regulating Calcium Channel in Hypertension：An in vitro and in vivo approach [vascular tissue]

first: Jun

last: Peng

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to compare the differently expressed genes in abdominal aortaof WKY and SHR with or without isoliensinine treatment. The SHRs (n=10) were randomly divided into 2 groups: SHR, and SHR + isoliensinine (5mg/kg/d) groups (n=5 for each group). WKY rats (n=5) were set as control. Rats in WKY and SHR groups were  intragastrically with double distilled water (dd H2O), while rats in  SHR + isoliensinine (5mg/kg/d) group were intragastrically with 5mg/kg/d of  isoliensinine for 10 weeks.  Then the vascular vessel tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with abdominal aortaof rats in 3 groups: WKY, SHR, SHR + isoliensinine (5mg/kg/d) treated (n=5 for each group) to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Yuting

last: Zhou

first: Dawei

last: Lian

first: Meizhu

last: Wu


title: Eosinophils protect against SARS-CoV-2 following a vaccine breakthrough infection

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Waning immunity and the emergence of immune evasive SARS-CoV-2 variants jeopardize vaccine efficacy and contribute to breakthrough infections. The immune response that promotes vaccine-induced protection against SARS-CoV-2 breakthrough infection remains poorly understood. To model breakthrough infections, we vaccinated mice with a low dose vaccine formulation containing MF59-like adjuvant with prefusion-stabilized SARS-CoV-2 spike protein and challenged with immune evasive B.1.351 variant. Here, we show that eosinophils are required for protection against SARS-CoV-2 during a vaccine breakthrough infection. We found that vaccine breakthrough infection leads to a 2-log reduction in lung viral burden with restricted replication within the large airways as compared to naïve infected mice. Despite reduced antiviral gene expression, infected vaccinated mice show increased immune cell infiltration, characterized by monocytes, interstitial macrophages, and eosinophils, but with reduced activation markers into the lung parenchyma as compared to infected naïve mice. Single cell RNA-seq revealed that viral RNA was highly associated with eosinophils that corresponded to an IFN-γ biased phenotype and expression of antiviral genes including Cystatin B, an inhibitor of cysteine protease involved in SARS-CoV-2 entry via the endosome. Monocytes from infected vaccinated, but not naïve, mice showed high expression for eosinophil chemoattractant Ccl24 (eotaxin-2). Antibody-mediated depletion of eosinophils prior to infection of vaccinated mice resulted in increased virus replication and viral antigen staining deep in the lungs as compared to isotype control infected vaccinated mice. These results demonstrate the importance of eosinophils in vaccine-mediated protection and highlight the need for durable antibody responses that protect against lung infection and inflammation.

overall_design: Two mice in each group were either unvaccinated and mock infected, unvaccinated and infected, or vaccinated and infected using the AddaVax protein subunit vaccine and B.1.351 strain of the SARC-CoV-2 virus

first: Kathryn

last: Moore

first: Stephanie

middle: L

last: Foster

first: Elizabeth

middle: J

last: Elrod

first: Katharine

middle: A

last: Floyd

first: M

last: Williams

first: Meenakshi

last: Kar

first: Jacob

last: Vander Velden

first: Madison

last: Ellis

first: Ansa

last: Malik

first: Bushra

last: Wali

first: Stacey

last: Lapp

first: Amanda

last: Metz

first: Steven

last: Bosinger

first: Robert

last: Seder

first: Rama

last: Amara

last: Kohlmeier

first: Arash

last: Grakoui

first: Mehul

last: Suthar


title: Cross-species comparison reveals therapeutic vulnerabilities halting glioblastoma progression

city: Heidelberg

first: Leo

middle: Carl

last: Förster

state: Deutschland

address: Im Neuenheimer Feld 581

institute: DKFZ

summary: The growth of a tumor is tightly linked to the distribution of its cells along a continuum of activation states. Here, we systematically decode the activation state architecture (ASA) in a glioblastoma (GBM) patient cohort through comparison to adult murine neural stem cells. Modelling of these data forecasts how tumor cells organize to sustain growth and identifies the rate of activation as the main predictor of growth. Accordingly, patients with a higher quiescence fraction exhibit improved outcomes. Further, DNA methylation arrays enable ASA-related patient stratification. Comparison of healthy and malignant gene expression dynamics reveals dysregulation of the Wnt-antagonist SFRP1 at the quiescence to activation transition. SFRP1 overexpression renders GBM quiescent and increases the overall survival of tumor-bearing mice. Surprisingly, it does so through reprogramming the tumor’s stem-like methylome into an astrocyte-like one. Our findings offer a framework for patient stratification with prognostic value, biomarker identification, and therapeutic avenues to halt GBM progression.

overall_design: performed Smart-seq3 scRNAseq of sorted TCF/Lef-H2B::EGFP Wnt-reporter SVZ NSC lineage populations from SVZ and OB to benchmark ptalign performance and investigate healthy lineage Wnt activity dynamics

first: Oguzhan

last: Kaya

middle: C

last: Foerster

first: Ana

last: Martin-Villalba


title: Single Cell Multiomics Across Nine Mammals Reveals Cell Type Specific Regulatory Conservation in the Brain [ATAC-seq]

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Here, we generated a multiomic data from post-mortem cortex tissue across nine mammals and identified candidate CREs (cCREs) in a cell type–specific manner. We developed a multidimensional framework of conservation, integrating sequence, chromatin accessibility, and enhancer–gene linkage. Using massively parallel reporter assays (MPRA) in human neural progenitor cells and neurons, we measured activity of cCREs spanning conserved to human-specific regions. CRISPR interference (CRISPRi) validated conserved enhancer function, including at neurodevelopmental loci like FAM181B. Motif enrichment and chromBPnet revealed transcription factors distinguishing conserved versus recent cCREs. Linkage disequilibrium  score regression showed both conserved and human-specific cCREs were enriched for neuropsychiatric GWAS risk, while neurodegenerative risk was confined to conserved elements. Our findings define functional dimensions of enhancer conservation and demonstrate how regulatory evolution shapes human brain biology and disease susceptibility.

sample_organism:
Felis catus
Equus caballus
Bos taurus
Oryctolagus cuniculus
Rattus norvegicus

overall_design: NeuN+ sorted ATAC-seq from cortex of 5 species

first: Ashlyn

last: Anderson

first: Brianne

last: Rogers

first: Nicholas


title: The PAS domain of the Polarly-Localized Histidine Kinase FlrB in Vibrio cholerae Controls Class III Flagellar Transcription and Contributes to Intestinal Colonization

city: San Antonio

first: Venus

middle: Shawn

last: Stanton

state: Texas

address: One UTSA Circle

department: Molecular Microbiology and Immunology (MMI)

institute: University of Texas, San Antonio

summary: FlrB is a histidine kinase and along with FlrC it represents the two-component system that regulates flagellar transcription within Vibrio cholerae. FlrB autophosphorylates the conserved histidine at amino acid position 135, then transfers the phosphate to the conserved aspartate residue at position 54 in FlrC.  FlrC-P binds promoter regions and activates sigma54-dependent transcription of class III flagellar genes. By mutating the histidine at position 135 to an asparagine (H135N), FlrB is unable to undergo autophosphorylation, prohibiting phosphorylation of FlrC and transcription of FlrC-dependent genes. Mutating the leucine residue at position 36 in the PAS domain of FlrB to a phenylalanine (L36F) results in increased FlrC-dependent transcription. We hypothesize that V. cholerae with the FlrB L36F mutant form produces significantly higher amounts of FlrC-dependent transcripts. Conversely, FlrB H135N mutants will be significantly downregulated for the same genes.

overall_design: Mid-log cultures of V. cholerae O395 strains WT (KKV598), DflrB, FlrB H135N, FlrB L36F, DflaBCDE, DflaBCDE + FlrB L36F, DflaBCDE + FlrB H135N, and DflaBCDE + FlrB L36F H135N underwent Trizol-mediated RNA extraction and RNA-seq analysis. RNA extraction was performed on 3 biological replicates. FlrB is a histidine kinase and member of the two-component flagellar-regulated transcriptional system. By phosphorylating the histidine at amino acid position 135, FlrB is activated, permitting transfer of the phosphate from H135 to aspartate residue D54 on FlrC, which in turn binds with sigma-54 and RNAP to facilitate transcription of class III and class IV flagellar genes. By mutating the histidine at position 135 to an asparagine (H135N), FlrB is unable to undergo autophosphorylation, prohibiting phosphorylation of FlrC and transcription of FlrC-dependent genes. Mutating the leucine residue at position 36 in the PAS domain of FlrB to a phenylalanine (L36F) results in constitutive activation of FlrB and FlrC-dependent transcription. We hypothesize that V. cholerae with the FlrB L36F mutant form produce significantly higher amounts of FlrC-dependent transcripts. Conversely, FlrB H135N mutants will be significantly down-regulated for the same genes.

first: Bradley

last: Himes

first: Adrian

last: Meija-Santana

first: Jesus

last: Romo

first: Jiawei

last: Xing

first: Hong

last: Cai

first: Yufeng

last: Wang

first: Karl

last: Klose


title: Single Cell Multiomics Across Nine Mammals Reveals Cell Type Specific Regulatory Conservation in the Brain [MPRA]

overall_design: MPRA of candidate CREs evaluated in triplicate in HEK293s, NPCs, and Neurons.


title: Loss of tumor cell MHC Class II drives MAPK-inhibitor insensitivity of BRAF-mutant anaplastic thyroid cancers

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Cancer cells present neoantigens dominantly through MHC class I (MHCI) to drive tumor rejection through cytotoxic CD8+ T-cells. There is growing recognition that a subset of tumors express MHC class II (MHCII), causing recognition of antigens by TCRs of CD4+ T-cells that contribute to the anti-tumor response. We find that mouse BrafV600E-driven anaplastic thyroid cancers (ATC) respond markedly to the RAF + MEK inhibitors dabrafenib and trametinib (dab/tram) and that this is associated with upregulation of MhcII in cancer cells and increased CD4+ T-cell infiltration. A subset of recurrent tumors lose MhcII expression due to silencing of Ciita, the master transcriptional regulator of MhcII, despite preserved interferon gamma signal transduction, which can be rescued by EZH2 inhibition. Orthotopically-implanted Ciita-/- and H2-Ab1-/- ATC cells into immune competent mice become unresponsive to the MAPK inhibitors. Moreover, depletion of CD4+, but not CD8+ T-cells, also abrogates response to dab/tram. These findings implicate MHCII-driven CD4+ T cell activation as a key determinant of the response of Braf-mutant ATCs to MAPK inhibition.

overall_design: We performed whole exome sequencing on mouse cell lines generated from thyroid tumors derived from a genetic engineered anaplastic thyroid cancer mouse model (Tpo-Cre/eYFP/BRaf-CA/Trp53fl/fl; termed Braf-CAV600E/p53) and corresponding normal tissue (mouse tail). The mouse cell lines are B34286 cells, which retained IFNγ and trametinib-induced MhcII expression, and two celllines derived from recurrent tumors (B36934 and B36244) which lost MhcII expression in response to IFNγ and trametinib treatment. MhcII expression is regulated by the master transcriptional regulator Ciita, which is dependent on BRG1 (SMARCA4), one of the two mutually exclusive ATPases that serve as catalytic subunits of SWI/SNF chromatin remodeling complexes. Upon IFNγ stimulation BRG1 displaces EZH2 and SUZ12, key components of the Polycomb Repressor Complex 2 (PRC2), from inter-enhancer regions across the Ciita locus. We tested whether non-synonymous mutations in any of the Swi/Snf genes were present in the two MhcII negative recurrent cell lines (B36244 and B36934) or the MhcII responsive recurrent cells B34286.

first: Vera

last: Tiedje

first: Jillian

last: Greenberg

first: Tianyue

last: Qin

first: Soo-Yeon

last: Kim

first: Gnana

last: Krishnarmoorthy

first: Laura

last: Boucai

first: Bin

last: Xu

first: Jena

middle: D

last: French

first: Eric

last: Sherman

first: Alan

last: Ho

first: Elisa

last: de Stanchina

last: Socci

first: Jian

last: Jin

first: Ronald

last: Ghossein

first: Jeffrey

last: Knauf

first: Richard

last: Koche

first: James

last: Fagin


title: Gene expression changes in B-ALL upon oncogenic β-catenin activation [RNA-Seq]

first: Mark

last: Robinson

summary: We find that, in contrast to most cancer types, beta-catenin activation in preB-ALL cells supresses proliferation and leads to cell death. Proteomic analyses indicate that unlike in solid tumors beta-catenin interacts with Ikaros factors (IKZF1 and IKZF3) in pre-B cells. We performed RNA-seq in order to examine changes in expression upon beta-catenin activation in the presence and absence of Ikaros factors.

overall_design: RNA-seq was performed in pre-B cells from Ctnnb1Ex3fl/+ mice transformed with BCR-ABL1 and transfected with either non-targeting or IKZF1 and IKZF3 CRISPR/Cas9-RNP in order to study the effect of beta-catenin activation on gene expression in both IKZF1/3-WT and IKZF1/3-KO conditions.

first: Kadriye

last: Cosgun

middle: E

first: Markus

last: Muschen


title: T cell-intrinsic cGAS-CTCF regulation maintains regulatory T cell development and function [Hi-C]

city: Beijing

first: Hang

middle: Hubert

last: Yin

address: Shuangqing Road 30, Haidian District

department: School of Pharmaceutical Sciences

institute: Tsinghua University

summary: Cyclic GMP-AMP synthase (cGAS) is a cytosolic double-strand DNA (dsDNA) sensor in innate immune cells. A function of cGAS is to detect cytosolic double-stranded DNA and synthesize the cyclic dinucleotide 2'3'-cGAMP. This second messenger binds to and activates the adaptor protein STING, triggering the TBK1-IRF3 signaling pathway. However, the function of cGAS in T cells remain unknown and its role in adaptive immunity is also poorly characterized. Here we show that nuclear cGAS promotes regulatory T cell (Treg) development by cooperating with the genome organizer CTCF through a T cell-intrinsic and synthase function-independent way. Conditional deletion of cGAS using Foxp3Cre-YFP Cgasfl/fl and CD4Cre Cgasfl/fl mice demonstrated that cGAS imprints thymocytes for Treg development before the expression of FOXP3. cGAS also promotes the FOXP3 inheritability and suppressive activity of Treg. At steady state, cGAS is located in the nucleus of Treg, while stimulation of naïve CD4+ T cell with anti-CD3/CD28 antibodies induces transcription of cGAS and its translocation into nucleus. ATAC-sequencing of thymic Treg and Treg precursors revealed that CTCF binding is reduced in mature Treg. Mechanistically, cGAS interacts with CTCF and recruits CTCF to Tnfrsf9 (4-1BB) and Tnfrsf4 (OX40) gene locus to maintain their stable transcription through formation of chromatin loops. Physiologically, in mouse tumor model, Treg specific deletion of cGAS reduced tumor growth. Therefore, we uncovered a T cell-intrinsic role of nuclear cGAS in maintaining Treg development and function by imprinting the genome architecture with CTCF.

overall_design: To investigate chromatin architecture differences between wild-type and cGAS-deficient tTreg

first: Hongpeng

last: Li

first: Yuchen

last: Zhang


title: T cell-intrinsic cGAS-CTCF regulation maintains regulatory T cell development and function [CTCF-CR]

overall_design: To investigate CTCF genome binding profile in wild-type and cGAS-deficient tTreg


title: Interferon-sensitized hematopoietic progenitors dynamically alter organismal immunity

first: Dr. Shruti

last: Naik

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

summary: Inflammation has enduring impacts on organismal immunity. However, the precise mechanisms by which tissue-restricted inflammation conditions systemic responses are poorly understood. Here, we leveraged a highly compartmentalized model of skin inflammation and identified a surprising type I interferon (IFN)-mediated activation of hematopoietic stem/progenitor cells (HSPCs) that results in profound changes to systemic host responses. Post-inflamed mice were protected from atherosclerosis and had worse outcomes following influenza virus infection. This IFN-mediated HSPC modulation was dependent on IFNAR signaling and could be recapitulated with the administration of recombinant IFNα. Importantly, the transfer of post-inflamed HSPCs was sufficient to transmit the immune suppression phenotype. IFN modulation of HSPCs was rooted both in long-term changes in chromatin accessibility and the emergence of an IFN-responsive functional state from multiple progenitor populations. Collectively, our data reveal the profound and enduring effect of transient inflammation and more specifically type I IFN signaling and set the stage for a more nuanced understanding of HSPC functional modulation by peripheral immune signals.

overall_design: 8-week old female, C57BL/6J mice were treated topically with imiquimod (post-inflamed; PI) or petrolium jelly (as control) for 7 days. Mice were then rested for allowed to recover for 23 more days, at which point animals were euthanized and bone marrow harvested. LSK (Lin-/Sca+/Kit+) cells were flow-sorted and ATAc-seq performed.

first: Ikjot

last: Sidhu

first: Aleksandr

last: Prystupa

first: Ada

last: Weinstock

first: Shruti


title: Structural and functional basis of PU.1-BAF interaction enables targeting of lineage-specific transcription [ATAC-seq]

first: Salih

last: Topal

overall_design: Comparative chromatin accessibility profiling analysis of ATAC-seq data for THP-1 cells treated with dual SMARCA4/SMARCA2 inhibitor Compound 49 for 24h and MV-4-11 cells treated with dual SMARCA4/SMARCA2 inhibitor FHT-1015 for 24h

first: Asad

middle: M

last: Taherbhoy


title: Structural and functional basis of PU.1-BAF interaction enables targeting of lineage-specific transcription [ChIP-seq]

overall_design: Comparative genomic binding profiling analysis of ChIP-seq data for PU.1 and H3K27ac in THP-1 treated with Compound 49 for 24h


title: In vitro and in vivo models to predict ADAR RNA editing oligonucleotides potential in human liver tissue

city: Leiden

first: Monica

last: Aguila

address: Zernikedreef 9

country: Netherlands

institute: ProQR Therapeutics

summary: Liver-originated diseases remain a significant global health burden, with limited treatment options available. RNA therapeutics, particularly adenosine deaminase acting on RNA (ADAR)-mediated  editing using editing oligonucleotides (EONs) offer a novel approach to address these unmet medical needs. This study evaluates in vitro and in vivo liver models to predict the therapeutic potential of chemically modified EONs in human liver tissue, using ACTB as target. Multiple liver models, including primary human hepatocytes (PHH), cancer-derived cell lines, and iPSC-derived hepatocytes in both 2D and 3D formats, were characterized for ADAR expression, liver functionality, and RNA editing efficiency. The results show consistent ADAR expression across most models, with 3D models, particularly PHH spheroids and liver microtissues, closely mimicking human liver tissue in gene expression and editing capacity. In vivo, non-human primate liver biopsies showed high levels of ACTB editing, consistent with findings from PHH models. These findings highlight the critical role of preclinical models in EON selection, where multiple factors must be carefully considered. A multimodel assessment utilizing composite scoring to comprehensively assess the key parameters seems to be the approach of choice to maximize translatability across preclinical models and increase the likelihood of success in clinical applications

overall_design: RNA-seq profiling comparison between different hepatic cell lines cultured in vitro for 3 days and human liver tissue


title: Single Cell Multiomics Across Nine Mammals Reveals Cell Type Specific Regulatory Conservation in the Brain [Multiome]

first: J.

last: Cochran

sample_organism:
Danio rerio
Felis catus
Equus caballus
Bos taurus
Oryctolagus cuniculus
Rattus norvegicus

overall_design: snRNA-seq and snATAC-seq generated from cortex tissues from 6 species (10x Epi Multiome)

first: Ashlyn

last: Anderson

first: Brianne

last: Rogers

first: Nicholas


title: T cell-intrinsic cGAS-CTCF regulation maintains regulatory T cell development and function [ATAC-seq]

overall_design: To investigate regulatory function of nuclear cGAS on chromatin accessibility in tTreg and preTreg


title: Glucose-dependent glycosphingolipid biosynthesis fuels CD8+ T cell function and tumor control

city: Grand Rapids

first: Robert

last: Fillinger

state: Michigan

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: Glucose is essential for T cell proliferation and function, yet the metabolic fates of glucose critical for T cell responses in vivo remain poorly defined. Here, we identify glycosphingolipid (GSL) biosynthesis as an essential arm of glucose metabolism that fuels CD8+ T cell expansion and cytotoxic function in vivo. Using stable isotope tracing, we show that CD8+ effector T (Teff) cells in vivo use glucose to synthesize uridine diphosphate-glucose (UDP-Glc), a common precursor for glycogen, glycan, and GSL biosynthesis. Blocking GSL production–by targeting the enzymes UDP-Glc pyrophosphorylase 2 (UGP2) or UDP-Glc ceramide glucosyltransferase (UGCG)–blunts CD8+ T cell expansion and cytotoxic activity without impacting glucose-dependent energy production. Mechanistically, we show that glucose-dependent GSL biosynthesis (via UGCG) maintains lipid integrity at the plasma membrane and is required for lipid raft aggregation following T cell receptor (TCR) stimulation. CD8+ T cells lacking UGCG display poor cytotoxic function and reduced tumor control in vivo. Together, our data highlight GSL biosynthesis as an essential metabolic fate for glucose–independent of energy production–required to maintain membrane lipid homeostasis and CD8+ T cell cytotoxic function in vivo.

overall_design: RNA-seq profiling of control (NTC) and UGCG-deficient (sgUgcg) CD8+ OT-I T cells purified from spleens of Listeria (Lm-OVA)-infected mice at day 7 post-infection. 3-4 biological replicates were included per genotype (4 mice for NTC and 3 mice for sgUgcg).

first: Joseph

last: Longo

first: Russell

middle: G

last: Jones


title: Acquisition of neural crest promoted thyroid evolution from chordate endostyle

city: Pasadena

first: Jan

last: Stundl

address: 1200E California Blvd

department: BBE

institute: California Institute of Technology

summary: The endostyle is an endodermal organ unique to non-vertebrate chordates except for lamprey larvae, where it serves as forerunner to the adult thyroid. Here, we examine if the acquisition of neural crest in the vertebrate lineage played a role in the elaboration of the endostyle. CM-DiI lineage tracing reveals a neural crest contribution to the endostyle, and CRISPR/Cas9 mutagenesis of key neural crest genes causes endostyle defects including formation of a single rather than bilobed structure. RNA-sequencing reveals gene profiles characteristic of embryonic neural crest cells and Schwann cell precursors in the developing endostyle. Contrasting with the prevailing view that the endostyle is an endoderm-derived organ, we propose that the acquisition of the neural crest played a critical step in promoting thyroid evolution from chordate endostyle.

overall_design: To investigate the expression profiles of the lamprey endostyle, we performed bulk RNA sequencing of several developmental stages of lamprey endostyle.

first: Ayyappa Raja

last: Desingu  Rajan

first: Marianne

last: Bronner


title: Single Cell Multiomics Across Nine Mammals Reveals Cell Type Specific Regulatory Conservation in the Brain [RNA-Seq]

platform_organism:
Felis catus
Equus caballus
Bos taurus
Oryctolagus cuniculus
Rattus norvegicus

overall_design: RNA-seq generated from CRISPRi experiments targeting deeply conserved neuronal cCREs.


title: Adipocyte-specific deletion of gp130 prevents ketogenic AQ1 diet–induced hepatic steatosis

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Metabolic dysfunction-associated fatty liver disease (MASLD), the hepatic manifestation of obesity and type 2 diabetes (T2D), can progress to metabolic dysfunction-associated steatohepatitis (MASH) and fibrosis. MASLD is characterized by elevated hepatic lipid accumulation (steatosis) and insulin resistance. Ketogenic diet (KD), a high-fat, low-carbohydrate diet, induces hepatic insulin resistance and steatosis in animal models through unknown mechanisms. Our studies demonstrate the importance of adipose tissue-liver crosstalk in mediating MASLD progression and identify adipocyte IL-6-gp130 as a potential therapeutic target.

overall_design: Herein, we investigated the mechanisms behind KD-induced MASH and fibrosis at thermoneutrality, identifying upregulated inflammatory and lipogenic pathways, including Il-6, Tnf, Mapk13, Lpl, and Pparg. Given the substantial increase in IL-6 during MASLD progression, we investigated IL-6-gp130 signaling using liver- and adipocyte-specific knockout mice. Liver-specific gp130 deletion failed to prevent KD-induced hepatic steatosis and glucose intolerance. In contrast, adipocyte-specific gp130 deletion significantly reduced KD-induced hepatic steatosis by suppressing lipolysis in white adipose tissue and reducing p-JNK and p-p38 signaling in the liver. In agreement, adipocyte-specific deletion of gp130 protected mice from KD-induced hepatic steatosis in response to recombinant IL-6 treatment.

first: Berkay

last: Senkalfa

first: Tenagne

last: Challa

first: Christian

last: Wolfrum


title: Hypersonic Levitation and Spinning: Paving the Way for Enhanced Single-Cell Analysis via Contactless Tissue Dissociation

city: Tianjin

first: Yang

last: Bai

address: Tianjin

institute: Tianjin University

summary: In the realm of single-cell analysis, effective tissue dissociation is a cornerstone yet often hampered by the drawbacks of traditional methods. Mechanical and enzymatic dissociation methods suffer from long processing times, reduced cell viability, and the loss of rare cell populations. Herein, we introduce a revolutionary tissue dissociation approach, Hypersonic Levitation and Spinning (HLS), which capitalizes on a uniquely designed triple-acoustic resonator probe. This probe enables the target tissue sample to levitate and execute a 'press-and-rotate' operation within a confined flow field, generating microscale 'liquid jets' that exert precise hydrodynamic forces in a non-contact manner. Through this mechanism, the shear forces on the tissue are enhanced, facilitating rapid and efficient dissociation while safeguarding cell integrity. We have further developed an automated tissue dissociation apparatus integrating dissociation, fluid replacement, filtration, and output functions. Our comprehensive experiments, including flow cytometry, primary cell culture, immunofluorescence, and single-cell RNA sequencing, unequivocally demonstrate that the HLS method not only markedly outperforms traditional techniques in tissue utilization and dissociation rate but also excels in maintaining high cell viability and preserving rare cell populations. This non-contact, gentle yet highly efficient dissociation method holds immense promise in diverse fields such as cell biology, single-cell sequencing, and precision medicine, extending new possibilities in tissue dissociation technology and its applications.

overall_design: Comparative analysis of enzymatic and acoustic streaming-based dissociation methods for renal carcinoma tissue.


title: The molecular landscape in autosomal dominant polycystic kidney disease is characterized by common alterations in purine metabolism

city: Leuven

first: Jean-Paul

last: Decuypere

address: Herestraat 49

department: Cellular & Molecular Medicine

country: Belgium

institute: KU Leuven

summary: Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease. Cysts develop through dedifferentiation of tubular epithelial cells, but the sequence of molecular events and their relative importance remain unclear. To address this gap in knowledge, 40 cysts from 4 ADPKD kidneys and 4 microcystic tissues were mapped on transcriptomic and histological level. Cyst were heterogenous and we identified 6 cystic subclusters with 2 deviations from the main trajectory, dependent on the rate of interstitial remodeling, inflammation and dedifferentiation. Loss of proximal tubular marker gene expression was more pronounced compared to those of other tubular segments. Altered expression of metabolic pathways was consistent among the cysts, which was further analyzed in human and mouse cell lines. Purine metabolism was similarly altered in all ADPKD cell lines, and its modulation with azathioprine suppressed cyst formation in vitro. In conclusion, by focusing on common altered pathways in cysts and cell models, we have identified purine metabolism as a novel potential target in ADPKD.

overall_design: RNA-Seq profiling of 40 cystic membrane tissues of 4 PKD1 patients, 4 samples of microcystic tissue of 2 PKD1 patients and 4 tissue samples of 4 healthy kidneys.

first: Djalila

last: Mekahli

first: Rudi

last: Vennekens


title: Single Cell Multiomics Across Nine Mammals Reveals Cell Type Specific Regulatory Conservation in the Brain

first: J.

last: Cochran

first: Ashlyn


title: T cell-intrinsic cGAS-CTCF regulation maintains regulatory T cell development and function

first: Hang

last: Yin

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

overall_design: Refer to individual Series


title: Non-enzymatic SETD1A activity drives breast cancer cell proliferation via cyclin K.

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University


title: T cell-intrinsic cGAS-CTCF regulation maintains regulatory T cell development and function [scRNA-Seq]

overall_design: To investigate how cGAS affects the transcription of CD4+CCR7+ thymocytes at single cell level.

first: Hongpeng

last: Li

first: Yuchen

last: Zhang


title: A loss-of-function human ADAR variant activates innate immune response and triggers bowel inflammation

first: pengfei

last: xu

address: Donghu Road 115

institute: Wuhan University

summary: The goals of this study are to compare transcriptomes of mouse Ileal crypts isolated from Adarfl/fl and Adar iΔgut mice at 3 dpi of tamoxifen by RNA-seq.

overall_design: RNA-seq analysis of Ileal crypts were isolated from Adarfl/fl and Adar iΔgut mice at 3 dpi.

first: Yue

last: Xi

first: Pengfei

last: Xu

first: Min

first: Wen

last: Xie


title: Inflammatory Epithelial and Macrophage Pathways Underlie Residual Asthma Exacerbations in Urban Children Treated with Mepolizumab

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: While biologic therapies targeting type 2 (T2) inflammation reduce acute exacerbation rates in children with asthma and T2 inflammation, exacerbations still occur, and the underlying molecular mechanisms are poorly defined. We aimed to identify multiple distinct molecular mechanisms implicated in asthma exacerbations by characterizing respiratory illnesses among urban children with eosinophilic asthma enrolled in a clinical trial comparing treatment with mepolizumab versus placebo

overall_design: The MUPPITS-2 study was a randomized, double-blind, placebo-controlled, parallel- group trial of children with exacerbation-prone asthma in low-income urban centers conducted from Nov 7, 2017 to April 20, 2021, and has been previously described1. MUPPITS-2 stands for “Mechanisms Underlying Asthma Exacerbations Prevented and Persistent with Immune-Based Therapy: a Systems Approach Phase 2” (ClinicalTrials.gov number, NCT03292588). Participants were recruited across urban sites in 9 U.S. cities. An individual was eligible for enrollment if he or she: was 6-17 years of age; was diagnosed with asthma by a clinician greater than 1 year prior to recruitment; had at least 2 asthma exacerbations in the prior year (defined as a requirement for SCS and/or hospitalization); was treated at study entry with at least fluticasone propionate 250 mcg 1 puff twice daily or its equivalent for those aged 6 to 11 years, or with at least fluticasone/salmeterol 250/50 mcg 1 puff twice daily or its equivalent for those aged 12-17 years; had peripheral blood eosinophils ≥ 150 per mm3; and lived in a census tract with a density of ≥1000 families per square mile and at least 10% of families with income below the poverty level.

first: Matt

last: Altman

first: Ryan

last: Murphy

first: Tomasz

last: Janczyk


title: Nuclear Paxillin Modulates Alternative Splicing Programs in Neurons during Sensitive Periods of Brain Development

city: Taipei

first: Pei-Lin

last: Cheng

address: No. 128 Acdemia Rd., Section 2, Nankang

country: Taiwan

institute: Institue of Molecular Biology, Academia Sinica

summary: During sensitive postnatal periods, brain neural circuits undergo significant refinement coincident with widespread neuronal alternative splicing events in which hundreds of genes alter their splice site selection to generate isoforms essential for synaptic plasticity. Here, we reveal that neuronal activity-dependent serine119 phosphorylation of paxillin (p-paxillin S119) acts as a molecular switch in the nucleus to modulate alternative splicing during this period. We report that following NMDA receptor activation, nuclear p-paxillin S119 is recruited to nuclear speckles, where it interacts with U2AFs and splicing factors. Neuronal paxillin expression is required for timely alternative splicing of synaptic factors, including Snap25. Consequently, young mice lacking paxillin S119 phosphorylation exhibit significantly reduced levels of Snap25-5b isoforms, impaired presynaptic function at hippocampal Schaffer collateral-CA1 synapses, and deficits in short-term learning and memory. These findings support the idea that nuclear p-paxillin S119 is a critical mediator of alternative splicing programs in postnatal neurons during a sensitive period essential for neural plasticity.

overall_design:
RNA-seq of mouse primary neuronal cells with/without BDNF treatment and with/without paxillin knockdown by siRNA. Collect cells at DIV(days in vitro) 3, 5, 10.
Nanopore-based RNA-seq of mouse hippocampus tissue from wild type and paxillin KO/paxillin-S119A KI mice. Collect these mice at postnatal day10 (P10), P15 and P21.

first: Chien-Hsin

last: Chu

first: Guan-Zhu

last: Pan

first: Hung-Lun

last: Chiang

first: Chen

last: Chen

first: Ting-Ya

last: Chang

first: Chien-Lin

last: Lin


title: Common and Distinct Circulating MicroRNAs Across Four Neurovascular Disorders

city: Chicago

first: Issam

last: Awad

state: IL

address: 5841 S Maryland Avenue MC 3026, J 341 MC 3026, J 341

department: Neurological Surgery

institute: University of Chicago

summary: Background: Familial cerebral cavernous malformations (FCCM), Sturge-Weber Syndrome (SWS), and hereditary hemorrhagic telangiectasia with brain arteriovenous malformations (HHT) are neurovascular disorders driven by genetic mutations. Cerebral microbleeds (CMBs) are primarily associated with the aging process with less known about genetic drivers. This study hypothesizes that common and distinct circulating microribonucleic acids (miRNAs) reflect shared and different pathobiology and can serve as potential diagnostic and mechanistic biomarkers.  Methods: Common and unique differentially expressed (DE) plasma miRNAs (p<0.05, FDR corrected, absolute fold change [|FC|]>1.5]) were identified between patients with FCCM, SWS, HHT and CMB, compared to age- and sex-propensity-matched healthy subjects. Ingenuity Pathway Analysis as well as transcriptome integration analyses were performed to identify gene targets and their associated pathways. Preselected miRNAs were finally validated using ddPCR.  Results: Eleven DE miRNAs were identified in FCCM, 40 in SWS, 41 in HHT, and 26 in CMB (p<0.05, FDR-corrected, [|FC|]>1.5]). Further analyses showed that 18 DE miRNAs were commonly dysregulated in any two of the studied neurovascular disorders. The PI3K-Akt and ROBO SLIT signaling pathways were identified across all four disorders. The plasma levels of four of the 18 miRNAs were further validated (p<0.05) using ddPCR.  Conclusion: The common dysregulated miRNAs across neurovascular disorders reflect shared pathophysiological pathways, underscoring their potential as biomarkers and therapeutic targets. These findings pave the way for further exploration of these miRNAs, aiming at the clinical application for disease monitoring and therapeutic intervention.

overall_design: 36 microRNA samples from plasma samples from 9 subjects with Familial Cerebral Cavernous Malformation, 10 subjects with Sturge-Weber Syndrome, 8 subjects with Hereditary Hemorrhagic Telangiectasia, and 9 subjects Healthy Young

first: Janne

last: Koskimäki

first: Aditya

last: Jhaveri

first: Abhinav

last: Srinath

first: Akash

last: Bindal

first: Diana

last: Vera Cruz

first: Geetha

middle: P

last: Yeradoddi

first: Rhonda

last: Lightle

first: Justine

last: Lee

first: Agnieszka

last: Stadnik

first: Javed

last: Iqbal

first: Roberto

last: Alcazar-Felix

last: Hage

first: Sharbel

last: Romanos

first: Hanadi

last: Almazroue

first: Robert

last: Shenkar

first: Jeffrey

last: Loeb

first: Marie

middle: F

last: Faughnan

first: Shantel

last: Weinsheimer

first: Helen

last: Kim

first: Romuald

last: Girard


title: Time-course small RNA sequencing across photoperiods in Arabidopsis thaliana

city: New Haven

first: Chun Chung

last: Leung

address: YSB 424, 260 Whitney Avenue

department: MCDB

institute: Yale University

summary: Small RNAs play important roles in photoperiodism, but a comprehensive characterization of miRNAs and the more recently recognized tRFs within this context is lacking. Herein, we characterize the patterns of miRNAs and tRFs in Arabidopsis by performing time-course sRNA-sequencing across three photoperiods. By comparing with our previous mRNA-sequencing time-courses (GSE221846), we identified 14 negatively-correlated miRNA-mRNA pairs between the two co-sequenced datasets that suggest photoperiodic sRNA regulations. Furthermore, we identified 20 patterns of photoperiodic tRFs. These patterns are linked to the tRNA isotypes and positions they derive from, suggesting that tRFs are subjected to photoperiodic regulations.

overall_design: Seeds were sterilized before being sown onto 1/2 Murashige and Skoog medium plates lined with autoclaved filter papers. For germination, seeds were stratified in the dark for 48 hours before being transferred to a growth chamber under a 12L:12D photoperiod . After germination, seedlings were kept in the same condition for 10 days. On day 11, the seedlings were transferred to 16L:8D, 12L:12D, or 8L:16D photoperiod. On day 13, whole seedlings including shoots and roots were harvested and snap-frozen in liquid nitrogen.

first: Daniel A

last: Tarté

first: Joshua M

last: Gendron


title: Adipocyte death drives fat redistribution from adipocytes to hepatocytes in steatotic liver disease via S100A8+ macrophages [RNA-seq]

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

summary: Both adipocytes and hepatocytes have the capacity to store fat, but the factor(s) that determine fat distribution between these cell types remain unknown. In mice fed a high-fat diet, fat initially accumulates predominantly in adipocytes, while hepatic fat accumulation mainly emerges after the onset of epididymal adipocyte death that results in elevated free fatty acids to promote lipid accumulation in hepatocytes. However, it remains unclear whether other signals following adipocyte death are required to direct and/or promote hepatocytes to store fat and subsequently trigger metabolic dysfunction-associated steatotic liver disease (MASLD, formerly known as nonalcoholic fatty liver disease). Using genetically modified mouse models combined with bulk and single-cell RNA sequencing analysis, we demonstrated that adipocyte death induces an accumulation of S100A8+ macrophages in the liver, which is partially induced by fatty acids. Macrophage-specific deletion of the S100a8 gene reduced hepatic fat accumulation and MASLD severity in mice. Mechanistically, S100A8+ macrophages suppress cellular communication network factor (CCN3), a negative regulator of CD36, thereby enhancing CD36 expression in hepatocytes. In conclusion, adipocyte death promotes hepatic infiltration of S100A8+ macrophages, which drive hepatocyte lipid storage and subsequently promote MASLD progression through CD36 upregulation, partially mediated by CCN3 suppression.

overall_design: Male mice aged 8 weeks were placed on an HFD (60% kcal fat, D12492; Research Diets, New Brunswick, NJ) or a chow diet (10% kcal fat) as a control. Total RNA was extracted from whole livers using Trizol (Alkali Scientific, Fort Lauderdale, FL). Liver RNA‐seq was performed.

last: GUAN

first: Seonghwan

last: HWANG

first: Dechun

last: FENG

first: Bin

last: GAO


title: Non-enzymatic SETD1A activity drives breast cancer cell proliferation via cyclin K. (ChIP-seq)

first: Masaki

last: Fukuyo

summary: Breast cancer is the most common cancer in women worldwide. SETD1A, a histone H3 lysine-4 methyltransferase, is associated with poor prognosis in breast cancer. While both its enzymatic and non-enzymatic functions have been implicated in cancer progression, the specific role of SETD1A in breast cancer remains unclear. This study aimed to elucidate the molecular mechanisms underlying SETD1A dependency in breast cancer.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for active histone modification H3K4me3 as well as the transcription factor RNAPII and SETD1A in sgRNA-expressing iCas9 KPL-1 cells

first: Kanako

last: Hayashi

first: Takayuki

last: Hoshii

first: Bahityar

last: Rahmutulla

first: Atsushi

last: Kaneda


title: Hippocampus and liver of two starins of inbred rats, F344/N and WNA/NUM exposed to 1-bromopropane vs. fresh filterd air by inhalation

city: Tokyo

first: Yousra

last: reda

state: 千葉県

address: Higashifukai Nagaryama Chiba, Hasumei ikei center E 103

institute: Tokyo University of Science

summary: Transcriptional profiling of hippocampus and liver in F344/N and WNA/NUM rats exposed to 1-bromopropane for 8 hours or 4 weeks

overall_design: filterd air vs. 1-bromopropane exposure for 8 hours or 4 weeks, two inbred rat strains, two organs (hippocampus and liver), Biological replicates: 3 control replicates and 3 exposed repilcates

first: Fen

last: Huang

first: Gaku

last: Ichihara


title: Gene regulatory mechanisms guiding bifurcation of inhibitory and excitatory neuron lineages in the anterior brainstem

city: Helsinki

first: Sami

last: Kilpinen

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

institute: University of Helsinki

summary: Selector transcription factors control choices of alternative cellular fates during development. The ventral rhombomere 1 of the embryonic brainstem produces neuronal precursors that can differentiate into either inhibitory GABAergic or excitatory glutamatergic neurons important for the control of behaviour. Transcription factors (TFs) Tal1, Gata2 and Gata3 are required for adopting the GABAergic neuronal identity and inhibiting the glutamatergic identity. Here, we asked how these selector TFs are activated and how they control the identity of the developing brainstem neurons. We addressed these questions by analysing chromatin accessibility at putative gene regulatory elements active during GABAergic and glutamatergic neuron lineage bifurcation, combined with studies of transcription factor expression and DNA-binding. Our results show that the Tal1, Gata2 and Gata3 genes are activated by highly similar mechanisms, with connections to regional patterning, neurogenic cell cycle exit and general course of neuronal differentiation. After activation, Tal1, Gata2 and Gata3 are linked by auto- and cross-regulation as well as regulatory interactions with transcription factors of the glutamatergic branch. Predicted targets of these selector TFs include genes expressed in GABAergic neurons, glutamatergic neurons, or both. Unlike genes specific to the glutamatergic branch, the genes expressed in GABAergic neurons appear to be under combinatorial control of Tal1, Gata2 and Gata3.

overall_design: CUT&Tag analysis of the DNA interaction of selected transcription factors (Tal1, Gata2, Gata3, Vsx2, Ebf1, Insm1, Tead2) in E12.5 mouse anterior hindbrain (rhombomere 1)

first: Kaia

last: Achim

first: Juha

last: Partanen


title: Spatial Transcriptomic Profiling of the Mouse Adrenal Gland and Adjacent Adipose Tissue

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embryology

country: Poland

institute: Poznan University of Medical Sciences

summary: This study employs spatial transcriptomics to map the molecular landscape of the mouse adrenal gland, focusing on distinct cortical zones (zona glomerulosa, zona fasciculata, X-zone) and the adrenal medulla, as well as adjacent adipose tissue. Using Visium CytAssist technology, we analyzed adrenal sections from male CD-1® IGS mice, identifying seven distinct cell clusters, including brown and white adipose tissues.

overall_design: Four sexually mature male CD-1® IGS mice, 10 weeks old with a body weight of approximately 37 g were used in this study.  Mice were housed in colony cages in a pathogen-free environment with temperature maintained at 21-23°C and relative humidity between 55-60% and under a 12h light/12 h dark cycle. All mice were given standard chow and water ad libitum. The mice were euthanized by decapitation and the harvested adrenals were immediately preserved in 10% buffered formalin for further analysis.

first: Małgorzata

last: Blatkiewicz

first: Szymon

last: Hryhorowicz

first: Marta

last: Szyszka

first: Joanna

last: Suszyńska-Zajczyk

first: Andrzej

last: Pławski

first: Adam

last: Plewiński

first: Andrea

last: Porzionato

first: Ludwik K.

last: Malendowicz


title: Taurine improves bovine oocytes maturation through recovering mitochondria dysfunction and oxidative stress-induced apoptosis after Microplastics exposure

city: Nanjing

first: Zhaokang

last: Cui

address: No. 50, Zhongling Street,

institute: Jiangsu Academy of Agricultural Sciences

summary: Plastic is widespread in our lives, releasing various Microplastics (MPs) with toxicity. In recent years, the potential threat of MPs on reproductive system arouses public concern. Numerous reports have focused on its damage to spermatogenesis. Nevertheless, the toxicity of MPs on female reproduction is unclear. Here, we explored this question using bovine oocyte. We found that MPs disrupts spindle organization, chromosomes alignment and actin assembly, leading to failed maturation of bovine oocytes. Meanwhile, cortical granule secretion is obstructed, suggesting the failure of cytoplasmic maturation. Therefore, embryonic development is impacted. In transcriptome results, MPs induces the expression change of Mitochondrial-related genes, reflecting the damage of MPs are mediated by mitochondrial functions. MPs indeed causes oxidative stress, DNA damage and apoptosis. Taurine is capable for stabilizing cellular antioxidant level. We surprisingly find that Taurine suppresses mitochondrial dysfunction, reversing the failure of oocyte maturation and embryo development after MPs exposure. Collectively, we reveal the reproduction toxicity of MPs on bovine oocytes, and demonstrates the restorative effect of Taurine against MPs.

overall_design: Transcriptomic analysis of oocytes at M II stage was carried out using a protocol for RNA-Seq. The constructed library was sequenced with Illumina platform.

first: Jianli

last: Zhang

first: Jun

first: Jifeng

last: Zhong

first: Yilong

last: Miao

first: Huili

last: Wang


title: Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq [single_cell]

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Profiling combinations of histone modifications identifies gene regulatory elements in different states and discovers features controlling transcriptional and epigenetic programmes. However, efforts to map chromatin states in defined cell types are hindered by the lack of methods that can profile multiple histone modifications together with transcriptome in individual cells. Here we describe single-cell Multi-Targets and mRNA sequencing (scMTR-seq), which enables simultaneous profiling of six histone modifications and transcriptome in single cells. As a proof of concept, we apply scMTR-seq to uncover the dynamics of chromatin state change during human endoderm differentiation. We also use scMTR-seq to produce lineage-resolved chromatin maps and gene regulatory networks in mouse blastocysts, revealing striking epigenetic asymmetries at gene regulatory regions between the three embryo lineages. We identify the transcription factor Trps1 as a potential repressor in epiblast cells of trophectoderm-associated enhancer networks and their target genes. Together, scMTR-seq enables investigation of combinatorial epigenetic modalities in low-cell number and heterogeneous samples.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We develop scMTR-seq (single cell multi-targets and mRNA sequencing), a multiomics sequencing technology that can simultaneously profile over six histone modifications and transcriptome in the same single cells with high sensitivity, high cell recovery and is highly scalable in terms of starting material requirement.

first: Yang

first: Peter

last: Rugg-Gunn


title: Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq [bulk_RNA]

overall_design: We tested different order of profiling chromatin marks and profiling transcriptome from the same sample.


title: Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq [bulk_DNA]

overall_design: We develop MTR-seq (multi-targets and mRNA sequencing), a multiomics sequencing technology that can simultaneously profile over six histone modifications and transcriptome in the same sample.


title: Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq


title: Effect of deplation of vtRNA1-1 and vtRNA1-2 on gene expression in  Huh7 hepatocellular carcinoma cells

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

institute: University of Bern

summary: Non-coding RNAs (ncRNAs) are pivotal in tumorigenesis and cancer progression, and recent evidence highlights the class of human vault RNAs as important regulators of cellular homeostasis. The human genome encodes four vtRNA paralogs that are differentially expressed in cancer tissues and have thus been implicated in tumor onset and progression. The so far best studied paralog of the vault RNA family, vtRNA1-1, is involved in crucial cellular processes such as resistance to apoptosis, regulation of autophagy, control of lysosomal biogenesis, and drug resistance. In this study, we present a comprehensive characterization of a vtRNA1-2 knockout (KO) hepatocellular carcinoma cell line, marking the first detailed research study on this specific vtRNA paralog. Our findings indicated that the absence of vtRNA1-2 resulted in reduced viability and proliferation of cancer cells, by modulating the MAPK signaling pathway. Significantly, vtRNA1-2 KO cells displayed impaired motility, leading to a marked reduction in the invasiveness of malignant cells. Intriguingly, vtRNA1-2, unlike the vtRNA1-1 paralog, did not affect autophagy or lysosomal activity. Instead, our data demonstrate that vtRNA1-2 is critically involved in angiogenesis, a key process in tumor progression, by reducing vascular endothelial growth factor A secretion and inhibiting tube formation. These insights revealed a distinct role of vtRNA1-2 in tumorigenesis and positioned it as a promising target for the development of novel anti-cancer therapies. Our study advances the understanding of vault RNAs in cancer biology and strongly suggests that each vtRNA paralog possesses a unique role, rather than being mere molecular doppelgangers.

overall_design: To investigate the role of vtRNA1-1 and vtRNA1-2 in hepatocellular carcinoma,we sequenced the transcriptome of Huh7 cells in which it was knocked out either the VTRNA1-1 gene or VTRNA1-2 gene via CRISPR/Cas9 editing. RNA was extracted from cells grown to 80% confluency in complete medium

first: Stefano

last: Gallo

first: Deborah

last: Keogh-Stroka

first: Norbert

last: Polacek


title: A Multivariate Cell-Based Liquid Biopsy for Lung Nodule Risk Stratification: Analytical Validation and Early Clinical Evaluation

city: Potomac

first: Jennifer

last: Smith

state: Maryland

address: Windsor View Dr

institute: PreCyte, Inc.

summary: The iCAP is a tool for blood-based diagnostics that addresses the low signal-to-noise ratio of blood biomarkers by using cells as biosensors. The assay exposes patient serum to standardized cells in culture and classifies disease by AI analysis of gene expression readouts from the cells. This method simplifies the complexity of blood into a concise readout in a scalable cell-based assay. We developed the LC-iCAP as a rule-out test for nodule management in CT-based lung cancer screening. The assay achieved an AUC of 0.63 (95% CI 0.50-0.75) in blind temporal validation with retrospective samples. When integrated with CT data after validation, it demonstrated 90% sensitivity, 67% specificity and 95% NPV using an estimated 25% prevalence, significantly outperforming the Mayo Clinic model and potentially reducing unnecessary follow-up procedures. Analytical validation demonstrated LC-iCAP reproducibility, identified unwanted variation from long-term sample storage and indicated enrichment of hypoxia signaling in the differential assay readout.

overall_design: The goal of the experiment was to measure the gene expression response of human indicator cells to serum from  patients with benign or malignant lung nodules and to find a differential pattern between the two conditions that can be used to predict presence of lung cancer in patients from their serum using machine learning tools. SAMPLES are total RNA extracted from cultured human indicator cell that have been exposed to either patient serum or controls.  Control conditions included pooled malignant (pooled serum from multiple patient with malignant lung nodules), pooled benign (pooled serum from multiple patietns with benign lung nodules), DMOG chemical stimulant, or PBS. Global gene expression analysis of the samples was performed by RNAseq.

first: Smith

last: Jennifer

first: Mark

last: D’Ascenzo

first: Jason

last: Berndt

first: Fergal

last: Duffy

first: Leslie

middle: R

last: Miller

first: Sherry

last: Qi

first: G

last: Whitney

first: Sam

last: Danziger

first: Anil

last: Vachani

first: Pierre

last: Massion

first: Rob

last: Lipshutz

first: Stephen

last: Deppen

first: John

last: Aitchison


title: Non-enzymatic SETD1A activity drives breast cancer cell proliferation via cyclin K. (RNA-seq)

first: Masaki

last: Fukuyo

overall_design:
Examination of gene expression in sgRNA-expressing iCas9 KPL-1 cells on day 7 of doxycycline treatment (sgEmpty and sgSETD1A)
Tiling screening for functional domains of SETD1A in iCas9 KPL-1 cells (sgKMT2pool)

first: Kanako

last: Hayashi

first: Takayuki

last: Hoshii

first: Bahityar

last: Rahmutulla

first: Atsushi

last: Kaneda


title: Transcriptomic Landscape of Fibroblasts Under IL-1β Stimulation [ATAC-seq]

city: nanjing

first: xiaoyun

last: chen

state: nanjing

address: nanjing

institute: xiangya

summary: In this study, we investigated the chromatin accessibility changes in human dermal fibroblasts in response to IL-1尾 stimulation, a key pro-inflammatory cytokine. Using ATAC-seq, we compared the open chromatin landscapes between control fibroblasts and those treated with IL-1尾. The data provide insights into the regulatory elements activated during fibroblast differentiation and their potential role in sustaining inflammation within the skin. These findings contribute to our understanding of fibroblast-mediated inflammation in autoimmune diseases like SLE and offer a resource for identifying novel therapeutic targets.

overall_design: Human dermal fibroblasts were cultured and treated with IL-1B (10 ng/mL) for 24 hours to mimic the inflammatory conditions. Control fibroblasts were cultured under identical conditions but without IL-1B stimulation. ATAC-seq was performed to map genome-wide chromatin accessibility in both control and IL-1B-treated fibroblasts. The experimental design allows for the identification of differentially accessible regions in the genome, which may reveal key regulatory elements involved in fibroblast activation and their interaction with immune cells. Data were generated in biological triplicates for each condition to ensure robustness and reproducibility.

first: Ming

last: Zhao

first: Xiaoyun

last: Chen

first: Yueqi

last: Qiu


title: CXCR4 Antagonist-Loaded Nanoparticles Reprogram the Tumor Microenvironment and Enhance Immunotherapy in Hepatocellular Carcinoma

city: Hsinchu City

first: ShengLiang

last: Cheng

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

department: Institute of Biomedical Engineering

institute: National Tsing Hua University

summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer death, with limited treatment options for advanced stages. Although PD-1 inhibitors like nivolumab and pembrolizumab are approved for advanced HCC, their effectiveness is often hampered by the immunosuppressive tumor microenvironment, driven by hypoxia-driven CXCL12/CXCR4 axis activation. Herein, we develop 807-NP, a lipid-coated tannic acid nanoparticle to encapsulate and deliver BPRCX807, a potent antagonist of CXCR4, into HCC tumors. 807-NP enhances pharmacokinetics and improves tumor availability of BPRCX807 without systemic toxicity. Our findings show that 807-NP blocks the CXCR4/CXCL12 pathway, inhibiting Akt and mTOR activation in HCC cells and M2 macrophages, promoting their repolarization to an anti-tumor M1 phenotype. In orthotopic murine HCC models, systemic administration of 807-NP significantly remodels the immunosuppressive tumor microenvironment by reprogramming tumor associated macrophages (TAMs) towards an immunostimulatory phenotype and promoting cytotoxic T cell infiltration into tumor. This suppresses primary tumor growth and metastasis while enhancing the efficacy of cancer immunotherapies, including PD-1 blockades and whole cancer cell vaccines, by facilitating T cell activation. Our work demonstrates the potential of nanotechnology-enabled delivery of CXCR4 antagonists to improve cancer immunotherapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine HCC tumors with or without treatment of nanoparticle loaded with CXCR4 inhibitor BPRCX807.

first: Yunching

first: Kak-Shan

last: Shia

first: Yu-Ting

last: Yen


title: A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [TAF_15_KO_splicing ]

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Department of Biochemistry and Biophysics

institute: UCSF

summary: RNA-binding proteins (RBPs) are multifunctional regulators of gene expression with complex and context-dependent mechanisms of action, yet the regulatory grammar that underlies RBP-mediated functions remains underexplored. Here, we performed a multi-omic data integration to systematically decipher the context-specific functions of RBPs. First, we report a compendium of in vivo proximity-dependent biotinylation (BioID) datasets of 50 human RBPs, which we used to generate a large-scale map of RBP protein neighborhoods. In parallel, we took advantage of CRISPR-interference with single-cell RNA-seq read-out (Perturb-seq) to capture rich transcriptomic phenotypes downstream of each RBP knockdown. By combining these physical and functional interaction readouts, along with the ENCODE transcriptome-wide atlas of RBP binding sites from eCLIP assays, we generated an integrated map of functional RBP interactions. This map not only captures well-studied post-transcriptional processes, but also reveals numerous previously unknown RBP-mediated regulatory functions. For a number of these cases, we have validated their predicted context-specific RBP functions using biochemical and genetic approaches. By deciphering these complex modes of functional interactions between RBPs, we have taken the first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar.

overall_design: We obtained transcriptome-wide gene expression measurements for 68 RBPs (representing a variety of regulatory processes) knockdowns using single-cell RNA sequencing and used the resulting high-dimensional data to systematically delineate genetic interactions between RBPs.  Perturb-seq experiment was performed as previously described (Datlinger et al. 2017).

first: Matvei

last: Khoroshkin

first: Andrey

last: Buyan

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middle: V

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