title: Antigen reactivity defines tissue-resident memory and exhausted T cells in tumours

first: Lachlan

last: Dryburgh

state: Victoria

overall_design: scRNAseq of transgenic T cells (either OT-I or gBT-I) isolated from B16-gB, epicutaneous melanoma tumours, and surrounding peritumoural skin. Split across 2 lanes of a 10x genomics, chromium 5' v2 kit. Each T cell type (tissue x transgenic) was hashtagged individually. Naive T cells were uniquely hashtagged and spiked in to allow for normalisation across lanes if required.

first: Laura

last: Mackay

first: Thomas

last: Burn

first: Jan

last: Schroeder

first: Maleika

last: Osman


title: Identification of lncMB3 RNA interactome through lncMB3 Native RNA Pulldown in MYC-amplified D283 Med cells.

status: Public on Oct 02 2025

city: Rome

first: Alessandro

last: Palma

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

type: Expression profiling by high throughput sequencing

summary: Medulloblastoma (MB) stands as the most prevalent malignant pediatric tumor affecting the central nervous system. Categorized into four primary subgroups, each with distinct biological and clinical features, MB presents unique therapeutic implications. Group 3 (G3) and 4 (G4) MBs collectively account for the majority of cases (60%) and exhibit the highest degree of aggressiveness. However, these subgroups remain poorly characterized from a biochemical perspective. Therefore, it is crucial to unveil the fundamental molecular mechanisms underlying G3 e G4 MBs to deepen our overall comprehension of these specific conditions and to pave the way for precision medicine-driven approaches. Compared to normal human cerebella, the MYC-dependent lncRNA MB3 was found to be induced in G3-derived cell lines expressing the proto-oncogene and upregulated in G3-MB primary tumors. Consistently, LncMB3 is downregulated upon MYC inhibition and in vitro studies reveal its potent anti-apoptotic activity. To deepen the study of the LncMB3 molecular mechanism, we employed native RNA Pulldown assays followed by RNA-Sequencing  to identify LncMB3 interactome. Here we provide the data of polyA+ RNA samples derived from two biological replicates of LncMB3 Native RNA Pulldown sample sets (INPUT, EVEN, ODD, LacZ) derived from the MYC-amplified D283 Med cell line that were subjected to RNA-Seq analysis.

overall_design: PolyA+ RNA samples of two biological replicates of lncMB3 Native RNA Pulldown sample sets (INPUT, EVEN, ODD, LacZ) derived from the MYC-amplified D283 Med cell line.

first: Alessia

last: Grandioso

first: Paolo

last: Tollis

first: Monica

last: Ballarino

first: Pietro

last: Laneve


title: Human iPSC-based modeling unveils chromatin remodeling induced by SETBP1 mutation as a potential initiating factor in GATA2 deficiency.

city: Hospitalet de Llobregat

first: Loris

last: Mularoni

state: Barcelona

address: Gran Via de l'Hospitalet, 199

department: P-CMR[C]

country: Spain

institute: IDIBELL

type: Genome binding/occupancy profiling by high throughput sequencing

summary: GATA2 deficient patients are prone to develop myelodysplastic syndrome (MDS) that can evolve to acute myeloid leukemia (AML). The MDS progression is usually associated with the acquisition of cytogenetic and/or additional somatic alterations. Mutations in SETBP1 and ASXL1 genes are frequently observed in pediatric GATA2 patients, although how they contribute to the disease progression remains poorly understood. Here we develop a human induced pluripotent stem cells (hiPSCs)-based model to study the impact of germline  GATA2 mutation along with  selected somatic mutations  on GATA2 deficiency progression. We found that, while germline heterozygous GATA2 mutation alone is insufficient to induce an impairment of myeloid development, SETBP1 and ASXL1 mutations lead to a significant decrease of myeloid differentiation potential with a complete monocytopenia. The prominent loss of myeloid progenitor was associated with a down regulation of myeloid-specific genes and an up-regulation of leukemic stem cell markers. Through epigenomic profiling,  we found that mutation in SETBP1 promotes  chromatin remodeling  in genes involved in myeloid neoplasms that preceded the blockage of myeloid differentiation, a state that persisted after the acquisition  of the ASXL1 mutation. Finally, transcription factors motif analysis revealed an enrichment for MEIS1, PU.1, RUNX1 and HOXA9 motifs in more accessible chromatin regions, suggesting their cooperation in disease progression. Beyond establishing a valuable tool for studying the molecular mechanisms underlying GATA2 deficiency, our findings suggest that mutated  SETBP1 primes the onset of hematopoietic impairment at transcriptomic and epigenomic level in GATA2 deficiency, a process exacerbated by the acquisition of the ASXL1 mutation.

overall_design: On day 15 of hematopoietic differentiation, hiPSC-derived myeloid progenitors (CD34⁺CD43⁺CD33⁺CD45⁺) were sorted, yielding at least 50,000 cells from populations P and G, 28,000 from GS, 25,000 from GA, and 8,000 from GSA.

first: Alessandra

last: Giorgetti


title: Microengineered Patient-derived Endometrium-on-a-Chip for the Evaluation of Endometrial Receptivity and Personalized Translational Medicine

status: Public on Oct 01 2025

city: Seongnam-si

first: Yu-Gyeong

last: Lee

state: Gyeonggi-do

address: 335 Pangyo-ro

department: Life Science

country: South Korea

institute: CHA University

summary: Endometrial receptivity plays a pivotal role in determining the success of embryo implantation and supports early pregnancy development, playing a central role in species propagation. However, current methods for assessing endometrial receptivity lack robust evidence-based validation, and reliable technique for accurately evaluating this process in patients with infertility are lacking. In this study, we introduced a novel patient-derived vascularised endometrium-on-a-chip (EoC) model, comprising three distinct layers, namely the epithelium, stroma, and blood vessels. This EoC was cross-species validated using both mouse and human samples, successfully replicating the dynamic microenvironment and mimicking both temporal and spatial features of the endometrial tissue. Using our EoC, we developed a clinically relevant endometrial receptivity scoring system, ERS², based on the molecular expression profiles of crucial endometrial receptivity markers and the morphological analyses of endometrial angiogenesis. The ERS² enables the personalised analysis of endometrial health and the potential for embryo implantation, addressing the individual variations in endometrial biology that may not be captured by traditional diagnostic methods. By leveraging our EoC, the ERS² replicate the physiological characteristics of the endometrium and provided personalised, patient-specific analyses. While larger-scale validation is required before clinical implementation, this highlights its significant potential for identifying therapeutic candidates tailored to individual patient, advancing the prospects for personalised reproductive care. Furthermore, progressive improvements in the patient’s endometrial microenvironment were observed following platelet-rich-plasma treatments, and the optimal timing for embryo transfer was identified in patients with unexplained repeated implantation failure using the EoC-ERS². This highlights the practical utility of our model not only for assessing individual receptivity but also for evaluating the personalised efficiency of interventions aimed at improving implantation outcomes. This study represents the first use of a microengineered EoC model and its scoring system to assess endometrial receptivity and predict successful pregnancy outcomes, offering new insights into personalised infertility treatments and advancing the potential of targeted therapies in reproductive medicine.

overall_design: This study included endometrial RNA samples derived from two normal women and three women with recurrent implantation failure (RIF). In parallel, patient-derived stromal and epithelial cells were used to construct an EoC model, from which RNA was also extracted. For vascular compartment construction within the chip, human umbilical vein endothelial cells (HUVECs) were incorporated.

first: Gaeun

first: Hwa Seon

last: Koo

first: Sun-Young

last: Hwang

first: Danbi

first: Jungseub

first: Won Jong

last: Yu

first: Yoon Young

last: Kim

first: Seung-Yup

last: Ku

first: Jong-Chan

last: Park

first: Jungho

last: Ahn

first: Youn-Jung

last: Kang


title: Programmable mRNA translation initiation by trans-RNA

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

country: USA

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: The ability to modulate specific gene expression is crucial for interrogating, perturbing, and engineering cellular systems. A wide range of approaches have been developed for gene silencing, but few tools are available to activate individual mRNAs for translation inside cells. 16Guiding ribosomes to specific start codons without altering the original sequence remains a formidable task. Here we design capped trans-RNAs capable of engaging ribosomes to specific initiation sites on individual mRNAs. By positioning the trans-cap near the target start codon, the 19anti-parallel trans-RNA enables the ribosome to select nearby start codons in a simple, specific, robust, and tunable manner. Structural and biochemical data suggest that the capped trans-RNA facilitates ribosome loading and scanning on the target mRNA via a synergistic mechanism. The trans-RNA also acts independently of the original cap, enabling translation of circular RNAs lacking internal ribosome entry sites. We demonstrate that trans-RNAs can be applied in vivo to 24achieve programmable alternative translation of endogenous genes in mouse liver. Finally, we discover the existence of naturally occurring trans-RNAs that differ from antisense RNAs by activating translation of endogenous mRNAs. The discovery and the application of trans-RNAs in programmable mRNA translation holds great potential in advancing fundamental and applied biology.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Ribo-seq of HEK293 cells transfected with trans-RNAs targeting the main ORF of ATF4; Total and capped small RNA-seq of HEK293 cells; RNA-seq of mouse liver


title: Remodeling of T and endothelial cells during total neoadjuvant therapy in rectal cancer

city: Beijing

first: Xinnan

last: Ling

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: BIOPIC

country: China

institute: Peking University

summary: Total neoadjuvant therapy (TNT) is a standard care for locally advanced rectal cancer (LARC), yet the immune remodeling mechanisms underlying its efficacy remain unclear. Using single-cell RNA, T cell receptor, and spatial transcriptome sequencing of matched pre- and post-treatment samples, we depicted tumor microenvironment (TME) dynamics induced by different neoadjuvant therapies. TNT is associated with reduced regulatory T cells and increased IFNG+CD8+ effector memory T cells with high IFNG expression, potentially contributing to improved complete response rates. The abundance of tumor-infiltrating CD8+ T cells is correlated with the enrichment of the ACKR1+ endothelial subset after TNT. We further validated that endothelial cells (ECs), when stimulated by IFNγ, potentially released by CD8+ T cells, acquire an enhanced ability for presenting antigens and activating CD8+ T cells. Together, our study systematically characterizes the TME dynamics and uncovers the unique interaction between activated CD8+ T cells and ECs after TNT.

overall_design:
26 patients with LARC, treated with three different neoadjuvant therapies including nCT, nRT and nRCT, were enrolled in this study. We employed droplet-based single-cell RNA sequencing (scRNA-seq) and paired T-cell receptor sequencing (scTCR-seq) to profile a set of 92 samples, including 44 blood tissues and 48 tumor tissues. These samples were collected from patients before (pre-treatment, Pre) and after neoadjuvant therapies.
----------------------
Authors state:
The corresponding raw data has been deposited in the Genome Sequence Archive in National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences (GSA-Human: HRA006512) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa-human. When published, raw FASTQ data are publicly available and a data access agreement will be required to evaluate the reasonableness of the data request and to avoid any confidentiality obligations

first: Qianqian

last: Gao

first: Fei

last: Tang

first: Zemin

last: Zhang


title: CDK12 inhibition reveals melanoma dependence on the RUNX1/CBFβ complex for genomic stability

city: Montreal

first: Philippe

last: Roux

state: QC

address: 2950 Polytechnic Rd

country: Canada

institute: Université de Montréal

summary: Cutaneous melanoma is the deadliest form of skin cancer, frequently driven by hyperactivation of the RAS/mitogen-activated protein kinase (MAPK) pathway. Cyclin-dependent kinase 12 (CDK12), a downstream effector of MAPK signaling, has emerged as a therapeutic target due to its essential role in transcriptional regulation and DNA damage repair. To uncover vulnerabilities associated with CDK12 inhibition, we performed a genome-wide CRISPR/Cas9 screen and identified the Runt-related transcription factor RUNX1 and its cofactor CBFβ as synthetic lethal partners of CDK12. RUNX1 inhibition enhanced melanoma sensitivity to CDK12 inhibitors in a p53-independent manner, resulting in DNA damage accumulation and impaired repair capacity. Combined inhibition of CDK12 and RUNX1 suppressed melanoma growth in vivo. These findings uncover RUNX1/CBFβ as a compensatory mechanism in CDK12-inhibited melanoma and establish a novel synthetic lethal interaction with translational potential for combinatorial therapy.

overall_design: RNA-seq profiling of A375 melanoma cells treated with SR-4835 (CDK12 inhibitor, 100 nM), AI-10-49 (RUNX1 inhibitor, 1 µM), or the combination for 48 hours, compared to DMSO-treated controls.

first: Jonathan

last: Boucher

middle: P


title: H4K16ac and RNAPol2 CUT&Tag of Drosophila Melanogaster and Bacillus Grandii

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

summary: This experiment was designed to investigate the epigenetic basis of sex chromosome dosage compensation. Such mechanisms often operate through epigenetic modifications, including histone modifications, which alter chromatin structure and gene expression. In Drosophila melanogaster, dosage compensation is achieved by upregulating the single X chromosome in males through acetylation of histone H4 at lysine 16 (H4K16ac). We therefore used D. melanogaster as a positive control to validate our approach. In contrast, the mechanism of dosage compensation in Bacillus grandii remains unknown. By profiling H4K16ac in this species, we aim to test whether this histone modification may have been convergently recruited to mediate dosage compensation.

sample_organism:
Drosophila melanogaster
Bacillus grandii

overall_design: For D. melanogaster, CUT&Tag targeting H4K16ac was performed using five heads per sample for both males and females. For B. grandii, a single head per individual was used for each sample. In B.grandii, we profiled H4K16ac together with RNA polymerase II. Remark: In absence of an appropriate reference genome of Bacillus grandii we used NCBI genome assembly Brsri_v3 of Bacillus rossius redtenbacheri (GCF_032445375.1) as reference genome instead.

first: Frederic

last: Zimmer

first: Annika

middle: M

last: Fox

first: Qiaowei

last: Pan

first: Peter

last: Andersen

first: Ann-Kathrin

last: Huylmans

first: Tanja

last: Schwander

first: M Felicia

last: Basilicata

first: Claudia

middle: I

last: Keller Valsecchi


title: Tregs stimulate intestinal repair by integrating epithelial IFNy/IL-10 signaling

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

summary: To understand the transcriptional changes on cellular level within the murine intestinal epithelial tissue, we generated small intestinal organoids from wild type mice, co-cultured them with Treg cells +/- rIL10/rIFNg or anti-IFNg/IL10R, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq

overall_design: To understand small intestinal epithelial normal tissue differentiation and growth during the presence of Treg cell and/or IL10/IFNg signaling, small intestinal organoids were generated and co-cultured with indicated wild-type Treg cells +/- anti-IFNg/IL10R or +/- rIFNg/rIL10. Medium was changed after 4 days, stimuli were removed and the organoids were dissagregated, sorted into single cells and profiled by single-cell RNA-seq

first: Sascha

last: Göttert

first: Julius

last: Fischer

first: Paul

last: Heinrich

first: Nicholas

last: Strieder

last: Gebhard

first: Michael

last: Rehli

first: Hendrik

last: Poeck


title: Transciptome profile of liver tissues from CD163KO mice after 8 weeks of Western diet.

city: Odense M

first: Jonas

last: Graversen

address: Campusvej 55

department: Health, IMM

country: Denmark

institute: University of Southern Denmark

summary: Liver macrophages have a high expression of the macrophage-specific scavenger receptor CD163 but during metabolic dysfunction-associated steatohepatitis (MASH) development CD163 undergoes increased shedding and downregulated expression in the liver in humans. Herein, we derived a hepatic-transcriptome based dataset to understand the development of early hepatic steatosis in CD163 knockout mice and their littermate controls.

overall_design: RNA-seq profiling of liver tissue obtained from C57BL/6NTac (CD163tm1(KOMP)Vlcg) mice after 8 weeks of chow (n=4-5 per genotype) or Western diet (n=15 pr. genotype).

first: Maria

last: Skytthe

first: Søren

last: Moestrup


title: ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes

city: San Francisco

first: Vijay

last: Ramani

state: CA

address: 1700 Owen Street

institute: Gladstone Institues

summary: ATP-dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. Here, we investigate effects of two major remodelers, ACF and RSC using chromatin condensates and single-molecule footprinting. We find that both remodelers inhibit the formation of condensed chromatin. However, the remodelers have distinct effects on pre-formed chromatin condensates. ACF spaces nucleosomes without de-condensing the chromatin, explaining how ACF maintains nucleosome organization in transcriptionally repressed genomic regions. In contrast, RSC catalyzes ATP-dependent de-condensation of chromatin.  RSC also drives micron-scale movements of entire chromatin condensates. These additional  activities of RSC may contribute to its central role in transcription. The biological importance of remodelers may thus reflect both their effects on nucleosome mobilization and the corresponding consequences on chromatin dynamics at the mesoscale.

overall_design: Chromatin  was assembled in vitro via salt gradient dialysis. Chromatin arrays were remodeled in vitro with ATP-dependent chromatin remodelers and visualized via microscopy. Chromatin was then profiled with m6A methyltransferase footprinting and SMRT long-read sequencing (SAMOSA-ChAAT). 36 in vitro chromatin samples were analyzed.

first: Camille

last: Moore

first: Emily

last: Wong

first: Upneet

last: Kaur

first: Un Seng

last: Chio

first: Ziling

last: Zhou

first: Megan

last: Ostrowski

first: Ke

last: Wu

first: Iryna

last: Irkliyenko

first: Sean

last: Wang

first: Geeta

last: Narlikar


title: Demyelination-Induced Glutamatergic Imbalance Mediates Hippocampal Hyperexcitability

city: Riverside

first: Seema

last: Tiwari-Woodruff

address: 900 University Avenue

department: Biomedical Sciences

institute: University of California-Riverside School of Medicine

summary: Chronic demyelination is a hallmark of multiple sclerosis (MS) and is associated with increased seizure susceptibility. In this study, we used the cuprizone (CPZ) diet induced demyelination model to investigate the progression of hippocampal demyelination and its impact on seizure activity and neurotransmitter dysregulation. Using EEG recordings, immunohistochemistry, Western blotting, ELISA, Golgi staining, and NanoString transcriptomics, we found progressive hippocampal demyelination accompanied by a striking increase in seizure incidence, from 38% at 6 weeks to 88% by 12 weeks. Structural degeneration of the CA1 pyramidal layer was marked by reduced dendritic arborization and loss of parvalbumin interneurons. Hippocampal glutamate levels increased as early as 3 weeks and remained elevated, with values (~2.2 µM) reaching excitotoxic thresholds, along with astrocyte reactivity (glial fibrillary acidic protein) and downregulation of astrocytic glutamate transporter-1, and glutamate aspartate Transporter-1 and modification of aquaporin-4 in CA1. Stratum pyramidal and stratum radiatum region-specific alterations in glutamate transporters and related enzymes (glutamine synthetase, glutamic acid decarboxylase 67, vesicular glutamate transporter 1), further supported neurotransmitter imbalance. Transcriptomic profiling revealed widespread downregulation of myelin, neuronal, astrocytic, glutamatergic, and GABAergic genes at 6 weeks, with partial recovery by 12 weeks. Together, these findings establish a mechanistic link between chronic hippocampal demyelination, glutamate dysregulation, and epileptogenesis offering potential molecular targets for therapeutic intervention in MS-associated epilepsy.

overall_design: Gene expression profiling analysis of mRNA data from demyelainted C57Bl/6J hippocampus mouse samples. Samples were collected from 6- and 12-week Cuprizone-treated and control mice.

first: Anderson

last: Alyssa

first: Ajayi

last: Moyinoluwa


title: JMJD3 and UTX as Key Targets for Gene-Modified Mesenchymal Stem Cell Therapy in Cartilage Tissue Engineering

city: Caen

first: Catherine

last: Baugé

address: Esplanade de la paix

country: France

institute: Université de Caen Normandie

summary: Histone methylation plays a critical role in cartilage development, making it an appealing target for improving cartilage engineering protocols. In this study, we evaluated the roles of JMJD3 (KDM6B) and UTX (KDM6A), both demethylases of histone H3 at lysine 27 (H3K27), in chondrogenesis and their application in gene-modified mesenchymal stem cell therapy for cartilage tissue engineering. Our findings revealed that JMJD3 is specifically upregulated during chondrogenesis in hBM-MSC, and is crucial for this differentiation process. In contrast, UTX was found to be dispensable for chondrogenesis. Nevertheless, both JMJD3 and UTX share the ability to demethylate similar gene loci, thereby promoting the expression of chondrogenic signature genes, which suggests functional redundancy. Notably, the genes encoding these H3K27me3 demethylases emerge as strong candidates for enhancing gene-modified mesenchymal stem cell therapy for cartilage tissue engineering, as their overexpression during chondrogenesis significantly increased the formation of thicker cartilage discs enriched with type II collagen. These findings emphasize the potential of transient JMJD3 transduction, along with a lesser emphasis on UTX, as effective strategies for improving gene-modified mesenchymal stem cell therapy in cartilage tissue engineering.

overall_design: ChIP-seq of H3K4me3 and H3K27me3 in human bone marrow-derived mesenchymal stem cells. Cells were collected from 2 different patients.

first: Lyess

last: Allas

first: Juliette

last: Aury-Landas

first: Quitterie

last: Rochoux

first: Anais

last: Julien

first: Eva

last: Lhuissier

first: Marion

last: Lenté

first: Sybille

last: Brochard

first: Alexis

last: Veyssiere

first: Karim

last: Boumédiene


title: Eomesodermin+ CD4 T cells are critical for curative immunotherapy outcomes

city: Seattle

first: Scott

middle: N

last: Furlan

state: WA

address: 1100 Fairview Ave N

department: TST

institute: Fred Hutchinson Cancer Research Center

summary: IL-10-producing CD4+ type-1 regulatory T cells (Tr1) promote immune tolerance during chronic infection, autoimmunity, and transplantation. However, specific Eomes-dependent stages of Tr1 differentiation and function remain unclear. Using preclinical models of bone marrow transplantation (BMT) and chimeric antigen receptor (CAR) T cell immunotherapy, we demonstrate a Tr1 differentiation trajectory in vivo from Eomes+IL-10– to Eomes+IL-10+ subsets with the acquisition of cytokine, cytolytic and exhaustion features. The Eomes+CD4+ fraction represents the dominant cytotoxic subset after BMT, mediating graft-versus-leukemia effects while limiting inflammation. In CD19-targeted CAR T cell immunotherapy, Eomes drives the same CD4+ Tr1 phenotype that controls cytolysis, whilst mitigating immune toxicity and promoting persistence. In patients receiving commercial CD19-targeted CAR T cells with long term disease control, Eomes+ Tr1 cells represent a stable population comprising 40-80% of the CD4+ CAR T cell population. Hence, Eomes controls both regulatory and cytotoxic programs in CD4+ T cells, essential for curative immunotherapy outcomes.

overall_design: B6D2F1 recipients were transplanted with TCD BM (5x106) and naive CD4+ T cells (0.5x106) from EomesmCherry/IL-10GFP donors. Spleens (n = 4) were taken on day +14, pooled, enriched to CD4+ T cells with MACS selection and FACS sorted to P1 (Eomes- IL10-), P2 (Eomes+ IL10-) and P3 (Eomes+ IL10+) based on the expression of mCherry and GFP. The sort-purified cells were subsequently processed for single cell RNAseq.

first: Ping

last: Zhang

first: Olivia

middle: G

last: Waltner

first: Shruti

middle: S

last: Bhise

first: Geoffrey

middle: R

last: Hill


title: 3D imaging and single-cells analysis reveal cellular heterogeneity of lymphatic valve endothelial cell types

city: Toulouse

first: Florence

last: Tatin

address: 1 avenue Jean Poulhès

summary: We have used single-cells transcriptomics to analyse the identity of lymphatic endothelial cells in adult dorsal skin. Lymphatic endothelial cells played an important role in skin homeostasis and protection. We showed that lymphatic vasculature has a highly organized architecture dependent to skin microenvironment. Our 3D imaging data associated to single-cells analysis revealed the importance of lymphatic valves in dermal lymphatic vascular network.

overall_design: Lymphatic endothelial cells have been isolated by cell sorting as CD45 negative, CD31 positive and GFP positive from Prox1creERT2; mTmG reporter mouse model and analysed by single-cells

first: F

first: E

last: Marchaud


title: Mapping of Chromatin Architecture and Enhancer-Promoter Interactions in the Cochlea

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

institute: Creighton University

summary: Chromatin interactions, particularly those between promoters and distal enhancers, enable precise gene regulation in specialized tissues, like the cochlea in the inner ear. Disruptions in these long-range interactions between enhancers and gene promoters are linked to hereditary hearing loss. For many genes important to cochlear development and function, the distal regulatory elements that control their expression remain unknown. Identifying these elements and studying their regulatory roles is challenging due to their distance from target genes and the spatial complexity of chromatin architecture. To address this, we employed Micro-C, a high-resolution chromatin conformation capture technique that enables nucleosome-level mapping of chromatin interactions, to construct a cochlea-specific chromatin interaction map. We then integrated epigenomic and transcriptomic data to interpret enhancer-promoter interactions involved in gene regulation.

overall_design: Cochlea organs from P0/1 C57Bl/6 animals were disssected and dissociated for Micro-C, ATACseq, histone or CTCF Cut&Run

first: Tuba

last: Ege

first: Celia

last: Bloom

first: Mi

last: Zhou

first: Huizhan

last: Liu


title: Diagnostic and prognostic biomarkers associated with histotype in advanced epithelial ovarian cancer

city: Göteborg

first: Ella

last: Ittner

address: Medicinaregatan 1F

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

summary: Despite advances in cancer treatments, epithelial ovarian cancer (EOC) remains the leading cause of death among gynecologic cancers. EOC is stratified into five main histopathological subtypes: high-grade serous carcinoma (HGSC), clear cell carcinoma (CCC), mucinous carcinoma (MC), endometrioid carcinoma (EC), and low-grade serous carcinoma (LGSC). However, personalized treatment strategies and reliable biomarkers for all histotypes remain elusive. Building on our previous work with early-stage EOC, we aim to explore diagnostic and prognostic biomarkers in advanced-stage EOC, updated to the latest World Health Organization classification guidelines from 2020, using comprehensive transcriptomic profiling from total RNA sequencing of 146 EOC patients. Differential expression analysis identified top 9 histotype-specific gene panels for HGSC, CCC, MC, and EC, including S100A1 (HGSC), ARID3A (CCC), LGALS4 (MC), and SCUBE2 (EC). We also identified gene candidates associated with overall survival and disease-specific survival, reflecting both favorable (e.g., OTOF, EEF1E1-BLOC1S5, and STAC3) and unfavorable (e.g., SMOC1, GDPGP1, EPRS1) clinical outcome. Additionally, enrichment analysis revealed tumor progression-related pathways unique to each histotype, offering insights into molecular mechanisms underlying disease progression and potential therapeutic targets. These findings provide valuable insights into the molecular landscape of advanced-stage EOC, paving the way for more effective diagnostic and prognostic tools across diverse histotypes.

overall_design: Whole-transcriptome RNA sequencing (RNA-seq) was performed for 146 specimens. Containing benign, borderline and malignant epithelial ovarian tumors (Stage III & IV).

first: Hugo

last: Swenson

first: Lucas

last: Werner

first: Elisabeth

last: Werner Rönnerman

first: Constantina

last: Mateoiu

first: Anikó

last: Kovács

first: Pernilla

last: Dahm-Kähler

first: Ghassan

last: Saed

first: Per

last: Karlsson

first: Toshima

middle: Z

last: Parris

first: Khalil

last: Helou


title: Tandem duplications in UBTF create XPO1-dependent nuclear export signals necessary for leukemic progression [scRNA-seq]

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

summary: UBTF tandem duplications (UBTF-TD) define a high-risk molecular subtype of acute myeloid leukemia (AML) characterized by poor clinical outcomes. While menin inhibitors have shown therapeutic promise, acquired resistance remains a significant challenge. Here, we use proteomic, genomic, and functional analyses to uncover mechanisms underlying UBTF-TD mediated leukemogenesis. We show that TDs create nuclear export signal (NES) motifs, which mediate interactions with Exportin-1 (XPO1) and chromatin-associated partners. These interactions drive aberrant chromatin binding and transcriptional activation of genes commonly dysregulated in UBTF-TD tumors, including the HOXA/HOXB clusters. We demonstrate that these NES motifs are critical for mislocalization of UBTF-TD proteins, cellular transformation, and transcriptional dysregulation. Importantly, we identify the XPO1 inhibitor eltanexor as a potential therapeutic strategy. Eltanexor treatment disrupts UBTF-TD chromatin localization, reduces tumor burden, and promotes differentiation in preclinical models. These findings provide mechanistic insights into UBTF-TD-driven leukemogenesis and highlight XPO1 inhibition as a promising therapy for UBTF-TD AMLs.

overall_design: scRNA-seq data

first: Juan

last: Barajas


title: Oncogenic Kras  cells override homeostatic cell elimination mechanisms in adult pancreas via Wnt signalling and cell dormancy.

city: Cardiff

first: Beatriz

last: Salvador-Barbero

state: Wales

address: Hadyn Ellis Building, Maindy road

department: ECSCRI-BIOSI

country: United Kingdom

institute: Cardiff University

summary: Epithelial tissues use homeostatic defence mechanisms to actively remove aberrant or poorly functioning cells and maintain tissue health. We show that when present in tissues in low numbers, cells expressing KrasG12D or p53R172H  mutations compete with normal cells for survival and are often eliminated. This implies that tumour initiation would require mechanisms whereby mutant cells override tissue homeostasis and remain in a tissue; however, the biology of these initial events is poorly understood. Here, we use an in vivo model of sporadic tumorigenesis in the adult pancreas to show that cell elimination processes are inefficient and a proportion of KrasG12D or p53R172H expressing cells are never eliminated from the epithelium. Using RNA sequencing of non-eliminated mutant populations, we reveal a general activation of the non-canonical  Wnt pathway. We demonstrate that non-eliminated KrasG12D cells express cell dormancy and diapause gene signatures, suggesting non-eliminated KRasG12D cells adopt a dormant cell state in vivo. Using cell competition assays in vitro, we show that active Wnt or cell cycle arrest blocks elimination of RasV12 mutant cells from normal epithelial cell sheets. Importantly, we demonstrate that Wnt signalling is a general mechanism required to promote retention of KrasG12D and p53R172H cells in tissues in vivo . Our results suggest that mutant cells activate Wnt and/or a dormant cell state to avoid homeostatic tissue defence mechanisms and survive in the adult pancreas.

overall_design: To gain an unbiased insight into how non-eliminated mutant cells survive in tissues we performed bulk RNA sequencing. Whole pancreata were harvested from experimental (KC/PC/KPC) and control mice (Control) at 35 days p.i. and digested to cell suspensions. We used anti-leptin antibodies to enrich for acinar/ductal epithelial cells and FACS sorted leptin positive RFP positive cells. We pooled cell suspensions from three mice per genotype to obtain a minimum of 5,000 viable leptin positive RFP positive cells, with n=3 replicates per genotype.

first: Catherine

last: Hogan


title: Tandem duplications in UBTF create XPO1-dependent nuclear export signals necessary for leukemic progression [CUT&Run]

overall_design: CUT&RUN Genomic Occupancy Analysis of UBTF-TD in hematopoeitic cells and actue myeloid leukemia samples


title: Antagonizing Il10 and Il4 signaling via intracerebral decoy receptor expression attenuates Aβ accumulation

city: Atlanta

first: Karen

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

summary: Multiple lines of evidence indicate that immune signaling can impact the pathological progression in Alzheimer’s disease (AD), including amyloid deposition, tau aggregation, synaptic pathology and neurodegenerative trajectory. In earlier studies, we reported that intracerebral expression of the anti-inflammatory cytokines, Interleukin-10 (Il10) and Interleukin-4 (Il4), increased amyloid β (Aβ) burden in TgCRND8 mice, a preclinical model of AD-type amyloidosis. As both Interleukin-10 receptor (IL10R) and Interleukin-4 receptor (IL4R) are upregulated in an age-progressive manner in rodent models of AD and in specific regions of human AD brains, we hypothesized that a decoy receptor strategy specifically targeting Il10 and Il4 signaling could have a disease-modifying effect. We derivatized the ectodomains of mouse Il10R (sIl10R) and mouse Il4R (sIl4R) into corresponding recombinant solubilized receptor forms and delivered these intracranially into neonatal TgCRND8 mice or hippocampally into adult TgCRND8 mice with pre-existing Aβ deposits. AAV-mediated expression of sIl10R and sIl4R robustly attenuated Aβ burden in TgCRND8 mice when expressed neonatally while in the hippocampus injection cohort, AAV-sIl4R, but not sIl10R, reduced Aβ burden. sIl10R and sIl4R had opposing effects on microglial and astrocyte proliferation, with sIl10R generally reducing gliosis. RNAseq analysis showed that sIl10R likely acts as a microglial immune checkpoint inhibitor while both sIl10R and sIl4R expression show unexpected impacts on genes related to circadian rhythm. Notably, neither Il10 nor sIl10R expression altered tau pathology in two tau transgenic models, despite robust expression and impacts on glial proliferation. Together, these data reveal that decoy receptor mediated targeting of physiological Il10 or Il4 signaling can beneficially impact amyloid deposition and thus represent novel immunomodulatory approaches for AD therapy.

overall_design: Gene expression profiling of RNA from somatic transgenic mouse brains expressing soluble forms of Il10ra or Il4r or controls (non-injected).

first: Paramita

last: Chakrabarty

first: Todd

middle: E

last: Golde


title: Glial cells missing 1 triggers gliosis and vasculogenesis in the neonatal brain injury

city: Okazaki

first: SHOJI

last: TATSUMOTO

address: Myodaiji

country: Japan

institute: The National Institutes of Natural Sciences NINS

summary: glial cells missing (gcm) in Drosophila plays a crucial role in the fate switch in nervous system and induces glial differentiation. However, function of a mammalian homologue, Gcm1, in the normal neural development and in pathological conditions remains elusive. Here, we report that Gcm1 was upregulated in Nestin+ cells immediately after neonatal brain injury was made, followed by accumulation of GFAP+ and Olig2+ cells in the penumbra region. In addition, Gcm1 strongly induced vasculogenesis in the injury lesion as well as in the developing brain via the action of VEGFA and VEGFC. Lack of Gcm1-mediated vasculogenesis could be one of major causes for dysplasia of placental labyrinths found in Gcm1–/– embryos, which leads to embryonic lethality. Our data suggest that Gcm1 triggers both gliosis and vasculogenesis after brain injury and could be a target for therapeutic intervention.

overall_design: The transcriptome profiles of the GFP-positive tissues from Gcm1 overexpression and control embryonic mouse brains (E16.5) were generated using the Illumina HiSeq platforms. The number of replicates for both Gcm1 overexpression and control samples is five.

first: Yoshitaka

last: Hayashi

first: Seiji

last: Hitoshi

first: Shoji

last: Tatsumoto

first: Yasuhiro

last: Go


title: GnRHR-expressing LAD2 RNA-seq

city: Shiwa-gun

first: Tatsuki

last: Kataoka

state: Iwate

address: 1-1-1, Idaidori, Yahaba-cho

institute: Iwate Medical University

summary: Gonadotrophin releasing hormone (GnRH) from hypothalamus stimulates gonadotrophin secretion from pituitary, followed by the secretion of sex steroid hormones from ovaries. GnRH is also detected in the extra-hypothalamic areas, like trophoblasts at the implantation sites. We have previously studied the association between trophoblasts and mast cells by producing leukemia inhibitory factor (LIF) and matrix metalloprotease (MMP)-9, and here hypothesized another association between the cells via GnRH derived from trophoblasts. We here report the RNA-seq analysis revealed the expressions of LIF, MMP-9, and a NK cell attractor CXCL16 enhanced in a human mast cell line LAD2 with forced-expression of GnRHR (GnRHR-expressing LAD2), when compared to those of control LAD2.

overall_design: Lentivirus was used to force expression of GnRHR or EGFP as a control in LAD2 cells. The GnRH agonist, leuprorelin, or DMSO was added, and cells were cultured for 72 h. Total RNA was then extracted for RNA-seq profiling.

first: Takashi

last: Matsuzaki

first: Hiroaki

last: Hamaguchi

first: Ken

last: Ito

first: Ryota

last: Nakagawa

first: Hiroya

last: Nakamura

first: Chiyuki

last: Ueshima

first: Akihiko

last: Yoshizawa

first: Hironori

last: Haga


title: Integrative Single-Cell RNA-Seq and ATAC-Seq Identifies Transcriptional and Epigenetic Blueprint Guiding Osteoclastogenic Trajectory [scATAC-seq]

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

summary: Osteoclasts (OCs) are multinucleated bone resorbing cells essential for skeletal development and remodeling. In adulthood, OCs originate from the serial fusion of monocytes, yet the transcriptional and epigenetic mechanisms shaping their osteoclastogenic potential at a single cell resolution remain poorly understood. Here, we employed an integrative multi-omics approach, combining single-cell (sc) RNA-seq, scATAC-seq, bulk RNA-seq, and ChIP-seq, to comprehensively define the regulatory landscape of osteoclastogenesis in wild-type (WT) and Irf8 conditional knockout (cKO) mice.

overall_design: 10x Genomics scATAC-seq platform comparing WT and Irf8floxCsf1rCre bone marrow cells (Irf8cKO)

first: Amitabh

last: Das

first: Stefania

last: Dell'Orso

first: Xiaobei

last: Wang

first: Joseph

last: Stains

first: Ryan

last: Riddle

first: Keiko

last: Ozato

first: Hong-Wen

last: Deng

first: Vivek

last: Thumbigere-Math


title: Integrative Single-Cell RNA-Seq and ATAC-Seq Identifies Transcriptional and Epigenetic Blueprint Guiding Osteoclastogenic Trajectory [scRNA-seq]

overall_design: 10x Genomics scRNA-seq platform comparing WT and Irf8floxCsf1rCre bone marrow cells (Irf8cKO)


title: Mislocalisation of MED12L in the nucleolus of female MED12 p.Arg1138Trp patients leads to temporal changes in neural development and dysregulation of the pre-ribosome complex

city: Nedlands

first: Kevin

middle: Guangxing

last: Chen

address: Hospital Avenue

country: Australia

institute: The Kids Research Institute Australia

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

overall_design: Refer to individual Series


title: Mislocalisation of MED12L in the nucleolus of female MED12 p.Arg1138Trp patients leads to temporal changes in neural development and dysregulation of the pre-ribosome complex [Amp-seq]

summary:
Background: A genetic variant MED12 c.3423C>T,p.Arg1138Trp, classified as a variant of uncertain significance, was identified in a female patient with multiple congenital anomalies and developmental delay. MED12, located on the X chromosome, is a subunit of the Mediator complex which is involved in regulation of transcription and RNA polymerase II activity. The functional consequence of these MED12 genetic variants in disease is undetermined, and insight into disease mechanism is required.
Method: We compare disease in seven female MED12 p.Arg1138Trp patients with a disease phenotype including  Blepharophimosis – intellectual disability syndrome, Maat-Kievet-Brunner MKB type, Choleostasis-pigmentary retinopathy-cleft palate syndrome, and non-syndromic MED12-related condition. Inducible pluripotent stem cells were derived from patient PBMCs, followed by neural disease modelling for transcriptomics and functional protein analysis.
Results: The phenotype for female patients with the MED12 c.3423C>T, p.Arg1138Trp genetic variant, indicated overlapping and divergent clinical features. In comparison of MED12 genetic variant neural cells, derived from patient induced pluripotent stem cells (iPSCs), identified altered expression levels for genes that regulate RNA polymerase II activity (ZNF558, ZIM2, ZFP3, TBR1, PEG3, EMX1, DMRTA2), transcription and pre-mRNA processing (ZIM2, and SNRPN) and neural development (BMP3, CNP, EBF2, EMX1, EOMES, LXH5, NHLH1, UNCX). Transcriptomics analysis further revealed a reduction in pathways related to axon development, forebrain differentiation, and cell specification (neural cell specification); and significant upregulation of pathway gene sets related to pre-ribosome complex (nucleolus) in the MED12 genetic variant cells. Comparison of MED12 wild-type and MED12 p.Arg1138Trp neural progenitor cells indicated similar MED12 transcript and protein expression. However, there was a decrease in MED12L expression, at the transcript and protein level, and significantly reduced MED12L localisation to the nucleolus in the MED12 p.Arg1138Trp cells.
Conclusion: Patient iPSC derived stimulated for neural cell differentiation indicate delayed neural development in MED112 p.Arg1138Trp expressing cells providing functional evidence of disease aetiology. Disease mechanism in genetic variant neural cells was linked to decreased localisation of MED12L to the nucleolus and dysregulation of the pre-ribosome complex.

overall_design: To investigate the functional consequences of a variant of unknown significance (VUS), we generated iPSC lines from PBMCs derived from the patient. We then studied two clonal lineages: one of which expressed the MED12 VUS, and one of which expressed the WT MED12 transcript. We compared the transcriptomic profile of both lineages at days 0, 18, and 24.

first: Nicole

middle: C

last: Shaw

first: Saraya

middle: H

last: Harrison

first: Catherine

middle: A

last: Forbes

first: Emma

last: Kuzminski

first: Mitchell

last: Hedges

first: Kathryn

middle: O

last: Farley

first: Michelle

last: Ward

first: Lily

last: Loughman

first: Cathryn

last: Poulton

first: Gareth

last: Baynam

first: Timo

last: Lassmann

first: Vanessa

last: Fear


title: Liver single-nucleus multiome profiling reveals cell-type mechanisms for cardiometabolic traits

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Genome-wide association studies (GWAS) have identified numerous genetic variants associated with cardiometabolic traits, yet their mechanisms in relevant liver cell types remain unclear. Using multiome single-nucleus RNA and ATAC sequencing on liver samples from 39 individuals, we profiled gene expression and chromatin accessibility in 68,398 nuclei across six primary liver cell types. We identified 306,706 accessible chromatin regions, including 70,884 regions undetected in bulk tissue analyses, predominantly representing less abundant cell types. By mapping quantitative trait loci (QTLs), we detected 1,885 chromatin accessibility QTLs (caQTLs) and 67 expression QTLs (eQTLs), highlighting genetic regulation in the different liver cell types. We integrated cell-type QTLs with GWAS signals and revealed cell-types, genes, and chromatin regulatory elements involved in cardiometabolic traits, such as liver enzymes and cholesterol levels. Importantly, non-hepatocyte cell-type QTL analyses elucidated previously obscured mechanisms, such as an eQTL for ADAMTS12 in liver sinusoidal endothelial cells potentially involved in liver fibrosis, demonstrating how single-nucleus approaches capture regulatory events missed in bulk analyses. Furthermore, we annotated bulk liver caQTLs colocalized with GWAS signals to liver cell types, enhancing functional interpretations and predicting cell-type of action for complex trait associations. Our findings provide a comprehensive, high-resolution map of the hepatic regulatory landscape, advancing the understanding of cellular contexts and molecular mechanisms underlying cardiometabolic diseases.

overall_design: 10x Chromium Single Cell Multiome ATAC + Gene Expression performed on frozen liver tissue from 39 human donors

first: Abdalla

last: Alkhawaja

middle: W

last: Currin

first: Hannah

middle: J

last: Perrin

first: Swarooparani

last: Vadlamudi

first: Amy

last: Etheridge

first: Kelsy

last: Broadaway

first: Gabrielle

last: Cannon

first: Carlton

last: Anderson

first: Anne

last: Moxley

first: Erin

last: Schuetz

first: Federico

last: Innocenti

first: Terrence

last: Furey


title: Mislocalisation of MED12L in the nucleolus of female MED12 p.Arg1138Trp patients leads to temporal changes in neural development and dysregulation of the pre-ribosome complex [RNA-seq]

first: Kevin

last: Chen

first: Nicole

last: Shaw

first: Saraya

last: Harrison

first: Catherine

last: Forbes

first: Emma

last: Kuzminski

first: Mitchell

last: Hedges

first: Kathryn

last: Farley

first: Michelle

last: Ward

first: Lily

last: Loughman

last: Poulton


title: Genome-wide maps of deaminated CPDs (dCPDs) in yeast genomic DNA in vitro

city: Pullman

first: John

middle: J.

last: Wyrick

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: Here, we describe a genome-wide map of uracil lesions arising form deaminated UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast (Saccharomyces cerevisiae) genomic DNA that were UV-irradiated and deaminated as naked DNA in vitro. Deaminated CPDs (dCPDs) were mapped at single nucleotide resolution across the yeast genome using the new dCPD-seq method. We used these data to analyze CPD deamination in different trinucleotide sequence contexts.

overall_design: We used the new dCPD-seq method to map cytosine-containing UV-induced cyclobutane pyrimidine dimers (CPDs) that had undergone deamination to uracil. Deaminated CPDs were mapped at single nucleotide resolution across the yeast genome in UV-irradiated yeast genomic DNA that was deaminated for 0, 6, 24, or 48 hours (hr) in solution in vitro.

first: Marian

middle: F

last: Laughery


title: Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling [CUT&Tag]

city: Philadelphia

first: Emily

last: Feierman

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: A cell’s ability to respond and adapt to environmental stimuli relies in part on transcriptional programs controlled by histone proteins. Histones affect transcription through numerous mechanisms including through replacement with variant forms that carry out specific functions. We recently identified the first widely expressed H2B histone variant, H2BE and found that it promotes transcription and is critical for neuronal function and long-term memory. However, how H2BE is regulated by extracellular stimuli and whether it controls activity-dependent transcription and cellular plasticity remain unknown. We used CUT&Tag and RNA-sequencing of primary neurons, single-nucleus sequencing of cortical tissue, and multielectrode array recordings to interrogate the expression of H2BE in response to stimuli and the role of H2BE in activity-dependent gene expression and plasticity. We find that unlike Further, we show that neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity in neurons after long-term stimulation. In summary, these data demonstrate that H2BE expression is inversely correlated to activity and necessary for long-term activity-dependent responses, revealing the first instance of a histone variant involved in the homeostatic plasticity response in neurons.

overall_design: WT primary cortical neurons were isolated from E16.5 mice and cultured for 12 days . Neurons were treated with BDNF 24h prior to collection for RNA-sequencing (n=3 biological replicates per genotype/condition, 2 technical replicates per WT control sample).


title: Novel molecular signatures of peripheral Regulatory T Cells in Kidney Disease associated with Type 1 Diabetes

city: Campbelltown

first: Mugdha

middle: V.

last: Joglekar

state: NSW

address: Cnr Goldsmith and David Pilgrim Ave

department: School of Medicine

institute: Western Sydney University

summary: Diabetic kidney disease (DKD) is a common complication of type 1 diabetes (T1D). T1D and some kidney disorders are often associated with abnormalities in regulatory T cells (Tregs). However, it is unknown if Treg subsets, and their molecular architecture are altered during the onset and progression of DKD in T1D. We addressed this critical knowledge gap by characterising changes in Tregs isolated from 31 participants (10 control, 13 with T1D, and 8 T1D with albuminuria) using flow cytometry, RNA-sequencing, and microRNA profiling. We identified that the effector and central memory Tregs were significantly different between groups. Similarly, multiple gene transcripts were also significantly different between groups that also overlapped with other publicly available datasets. Machine-learning based data analyses discovered a set of important microRNAs associated with clinical eGFR values. Importantly, our analyses identified two differentially expressed Treg ligand genes (LRRC4B, TGM2), which interacted with the receptors on kidney cells (PTPRD/F/S, ADGRG1) in silico, providing potential mechanistic insights into the role of Tregs in DKD progression. Together, our work supports the yet unappreciated role of Tregs in DKD and opens new research avenues to further consolidate their causal relationship.

overall_design: RNA-seq data on Treg cells samples from donors which do not have diabetes, have Type 1 Diabetes (T1D) without albuminuria, or have T1D with albuminuria.

first: Amita

last: Bansal

first: Soon Wei

last: Wong

first: Wilson KM

first: Giles

last: Best

first: Steven

last: James

first: Sarah

last: Glastras

first: Alexia

last: Pena

first: Cheng Xue

last: Qin

first: Sih Min

last: Tan

first: Devy

last: Deliyanti

first: Darling M

last: Rojas-Canales

first: Mugdha V

first: Elif I

last: Ekinci


title: Tandem duplications in UBTF create XPO1-dependent nuclear export signals necessary for leukemic progression [RNA-seq]

first: Jeffery

last: Klco

overall_design: RNA-seq in cbCD34+ cells expressing FKBP12-F36V-UBTF-TD54 via lentiviral tansduction. Data was collected in triplicates (n=3)/Condition. The three conditions include DMSO (control), Eltanexor treated (25nM), and dTAG-13 (1uM) treated for 24 hours.

middle: M

first: Juan

last: Barajas


title: HMGA2 overexpression drives a leiomyoma-like phenotype by modulating the epigenomic environment in primary myometrial cells [ChIP-Seq]

city: Chicago

first: Debabrata

last: Chakravarti

state: IL

address: 303 E Superior St.

department: Obstetrics and Gynecology

institute: Northwestern University

summary: With the utilization of advanced tools for genome-wide studies, the role of the epigenome in regulating gene expression is becoming more evident in both normal tissue development and disease states. Uterine fibroids, also known as leiomyomas, are a major reproductive disease that manifests as benign tumors and altered extracellular matrix composition leading to severe pathological symptoms. Several genomic alterations have been associated with leiomyoma. HMGA2 overexpression has been noted in approximately 10% of all patients with leiomyoma. HMGA2 is a chromatin-targeted protein and is therefore an important contributor to altered transcriptomic outcomes. However, due to a lack of specific antibodies against HMGA2 and appropriate in vitro cellular models, there is a lack in understanding of HMGA2 interaction with and regulation of chromatin in the context of leiomyoma. To address this gap, we engineered primary myometrial cells that express V5-tagged HMGA2 at levels comparable to those observed in leiomyoma. We observed transcriptomic and H3K27 acetylation changes that appeared to drive a leiomyoma-like phenotype in the engineered HMGA2v5 cells. HMGA2 was found to be diffusedly bound to chromatin, with most of the binding occurring at promoter- distal regions. Moreover, altered chromatin accessibility was observed in HMGA2v5 cells, with enrichment of AP-1 family transcription factor binding motifs at various sites. Thus, our study suggests that overexpression of HMGA2 modulates the genomic architecture of myometrial cells to cause leiomyoma-like gene expression and epigenomic changes.

overall_design: Primary myometrial cells were obtained from three patients and treated with empty or V5-tagged HMGA2 vector using lentiviral transduction. ChIP-sequencing was performed for histone modification -H3K27ac and V5-tagged HMGA2 using antibody against V5 epitope.

first: Priyanka

last: Saini

first: Austin

middle: G

last: Holmes

first: Jian-Jun

last: Wei

first: James

middle: B

last: Parker


title: Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling.

first: Emily

last: Feierman


title: HMGA2 overexpression drives a leiomyoma-like phenotype by modulating the epigenomic environment in primary myometrial cells [ATAC-seq]

overall_design: Primary myometrial cells were obtained from three patients and treated with empty or V5-tagged HMGA2 vector using lentiviral transduction. ATAC libraries were generated from these samples and used for next generation sequencing.


title: PHF6 regulates stress susceptibility in the pituitary intermediate lobe [CUT&Tag]

city: Shanghai

first: Bing

last: Liu

address: No. 280, South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: We revealed that stress triggers PHF6 to bind to the promoters of various stress-regulated genes in IL-melanotrophic cells and regulate their expression levels.

overall_design: CUT&Tag assays were conducted using a PHF6 antibody on enriched pituitary tissue obtained within 3 hours (8 AM - 11 AM) from 100 control and 100 RS-treated wild-type mice (6-7 weeks old), followed by high-throughput sequencing.

first: Jingjie

last: Wang

first: Xiaohua

last: Wu

first: Linhua

last: Gan

first: Jingjing

last: Sun

first: Guangzhong

first: Qian

last: Li

first: Ju

last: Huang


title: Modelling co-development between the somites and neural tube in human trunk-like structures

city: London

first: Naomi

last: Moris

address: 1 Midland Way

institute: Francis Crick Institute

summary: Human stem cell-based embryo-like models have opened new avenues of research into the principles of embryonic development using experimentally amenable in vitro systems. One of the benefits of embryo-like models over organoids is their multilineage differentiation, which allows the co-development of different populations and interaction between tissues. Here, we develop a method of generating somite- and neural tube-containing models, called human Trunk-like Structures (hTLS). These hTLS contain SOX2+ TBXT+ neuromesodermal progenitors, presomitic mesoderm, and somitic epithelial tissues, alongside a neural tube structure. As well as the expression of Wnt/FGF ligands posteriorly and Retinoic Acid (RA) pathway components anteriorly, we observe oscillatory HES7 expression, and show that increasing exposure to a Sonic Hedgehog signalling agonist (SAG) increasingly ventralises tissue identity. Additionally, we show that RA and noncanonical Wnt interactions likely occur between the somites and neural tube. In particular, we observe medially-localised ALDH1A2 expression in the somites - at the interface with the neural tube – which we validated in mouse embryos, whereas in somite-only structures, ALDH1A2 is anteroposteriorly polarised. This suggests that interactions between the neural tube and the somites might be responsible for mediolateral somitic organisation, both in vitro and in vivo, and highlights the value of embryo models to reveal insights into mammalian tissue co-development.

overall_design: Human trunk-like structures were sampled at 3 timepoints (72, 96, 120h), dissociated to single cells, and sequenced using the 10x transcriptomic platform.


title: Distinct Autoreactive CD19– Plasma Cell Subsets Accumulate in Lupus

city: Berlin

first: Andreia

middle: C.

last: Lino

address: Charitéplatz 1

institute: Charité – Universitätsmedizin Berlin

summary: Plasma cells (PCs) play a pathogenic role in autoimmune diseases by secreting autoantibodies and inflammatory cytokines. While PC elimination therapies exist, they risk depleting protective long-lived plasma cells. Using single cell RNA sequencing, including B cell receptor repertoire analysis, and genetic models, we identified disease- and organ-specific PC subsets in systemic lupus erythematosus (SLE) mice. We uncovered a substantial expansion of autoreactive CD19– PCs, particularly switched CXCR3+ and phosphatidylcholine-specific B-1-derived subsets, which exhibit unique gene expression profiles in SLE. Notably, our findings suggest that CD19– PCs originate from CD19+ PCs in a unidirectional manner, complicating the effectiveness of CD19-targeted therapies in advanced disease stages. This study highlights the crucial role of timing in anti-CD19 therapy and the necessity to broaden therapeutic targets beyond CD19+ PCs. The emergence of CD19– subpopulations underscore the need for novel therapeutic strategies that target these elusive PCs, offering new avenues for intervention in SLE treatment.

overall_design: BM (healthy/sick: each n= 6), spleen (healthy/sick: each n= 6) and kidney (sick: n= 13)  of SLE123 mice were collected and pooled. PCs from those tissues were enriched using anti-CD138 magnetic beads followed by cell sorting. Mice without proteinuria (9-12 weeks) were included as healthy control compared to mice with proteinuria (>24 weeks). Sequencing was performed using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit v1.1 (single index) and Illumina NextSeq2000.

first: Van

middle: D

last: Dang

first: Franziska

last: Szelinski

first: Marta

last: Ferreira-Gomes

first: Gabriela

last: Guerra

first: Pawel

last: Durek

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi


title: HMGA2 overexpression drives a leiomyoma-like phenotype by modulating the epigenomic environment in primary myometrial cells [RNA-Seq]

first: Debabrata

last: Chakravarti

summary: High-mobility group AT-hook 2 is a non-histone chromatin binding nuclear protein that belongs to the high-mobility group A family, which are known as "architectural transcription factors". Overexpression of HMGA2, resulting primarily due to chromosomal rearrangements of 12q15 loci, is considered a driver event in approximately 10% of uterine leiomyoma cases. To better understand how HMGA2 overexpression contributes to the formation of uterine leiomyoma, we generated primary myometrial cells engineered to overexpress HMGA2 (n=3) and determined the effect of HMGA2-overexpression on genome-wide mRNA levels, H3K27ac deposition, and chromatin accessibility.

overall_design: Primary myometrial cells were obtained from three patients and treated with empty or V5-tagged HMGA2 vector using lentiviral transduction. RNA was harvested from these cells and used for next generation sequencing.

first: Priyanka

last: Saini

first: Austin

last: Holmes

first: Jian-Jun

last: Wei

first: J

last: Parker


title: WWOX promotes osteosarcoma development via upregulation of Myc

city: Jerusalem

first: Rami

last: Aqeilan

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem


title: PHF6 regulates stress susceptibility in the pituitary intermediate lobe [RNA-seq]

first: Bing

last: Liu

overall_design: We performed SMART-RNA sequencing on pituitary intermediate lobe tissues meticulously dissected and captured by laser-capture microdissection (LCM) from both Phf6cKO and control mice under control and RS-stress conditions

first: Jingjie

last: Wang

first: Xiaohua

last: Wu

first: Linhua

last: Gan

first: Jingjing

last: Sun

first: Guangzhong

first: Qian

last: Li


title: Genome-wide maps of deaminated CPDs (dCPDs) in yeast cells

first: John

last: Wyrick

summary: Here, we describe a genome-wide map of uracil lesions arising form deaminated UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast (Saccharomyces cerevisiae). Deaminated CPDs (dCPDs) were mapped at single nucleotide resolution across the yeast genome using the new dCPD-seq method in repair-deficient (rad14∆), G2/M-arrested (cdc13-1) yeast cells immediately after UV irradiation (0 hour) and following 6 hour (6hr), 24hr or 48hr of deamination in arrested, repair-deficient yeast cells. We used these data to analyze CPD deamination in different trinucleotide sequence contexts, yeast genes, transcription factor binding sites, and nucleosomes.

overall_design: We used the new dCPD-seq method to map cytosine-containing UV-induced cyclobutane pyrimidine dimers (CPDs) that had undergone deamination to uracil. Deaminated CPDs were mapped at single nucleotide resolution across the yeast genome, both immediately after UV-irradiation of yeast cells (0 hour) and following 6 hour (6hr), 24hr or 48hr of deamination in arrested, repair-deficient yeast cells. We also mapped deamination in unirradiated cells (No UV) as a control.

first: Marian

last: Laughery


title: WWOX promotes osteosarcoma development via upregulation of Myc [ChIP-Seq]

summary: Osteosarcoma (OS) is an aggressive bone tumor that primarily affects children and adolescents. This malignant tumor is highly aggressive, associated with poor clinical outcomes, and metastasizes mainly to the lungs. Due to its rarity and biological heterogeneity, limited studies of its molecular basis exist, thus hindering the development of effective therapies. WW domain-containing oxidoreductase (WWOX) spans one of the most active and common fragile sites that is frequently altered in human OS. The combined deletion of Wwox and Trp53 using Osterix1-Cre transgenic mice has been shown to accelerate OS development. In this study, we generated a traceable OS mouse model, SKO-Trp53 or DKO-Wwox/Trp53, expressing a tdTomato reporter. By tracking tomato expression at different time points, we detected the early presence of tdTomato-positive cells in the bone marrow (BM) mesenchymal stem cells (MSCs) of non-OS bearing mice, young BM (yBM). We found that DKO yBM cells, but not SKO yBM cells, exhibited tumorigenic traits both in vitro and in vivo. Molecular and cellular characterization of these DKO yBM cells revealed their resemblance to OS tumor cells. Interestingly, one of the observed significant transcriptomic changes in DKO yBM was the upregulation of Myc and its target genes, as compared to SKO yBM cells. Intriguingly, Myc-chromatin immunoprecipitation sequencing (ChIP-Seq) revealed increased enrichment on Myc targets, which were upregulated in DKO yBM cells. Restoration of WWOX in DKO-yBM cells reduced Myc protein levels. As a prototype target, we demonstrated upregulation of MCM7, a known Myc target, in DKO yBM relative to SKO yBM.  Inhibition of MCM7 expression using Simvastatin resulted in reduced proliferation and tumor cell growth of DKO yBM cells. Our findings revealed BM-MSCs as a platform to study OS and Myc and its targets as WWOX effectors and early molecular events during osteosarcomagenesis.

overall_design: ChIP-Seq c-Myc DKO WWOX and p53 deletion

first: Rania

last: Akkawi

first: Osama

last: Hidmi

first: Ameen

last: Haj Yehia

first: Judith

last: Diment

first: Yotam

last: Drier

middle: I

first: Gary

last: S Stein


title: Gene expression data from DLPFC of schizophrenia patients

city: Barcelona

first: Sergi

last: Mas

state: BARCELONA

address: Casanova 143, Unidad Farmacologia, Facultad de Medicina, Barcelona

department: Pharmacology Unit

institute: University of Barcelona

summary: We analyzed gene co-expression modules (clusters of genes with highly correlated expression) in the dorsolateral prefrontal cortex (DLPFC) of postmortem brains from patients with schizophrenia and healthy controls. We aimed to identify the co-expressed modules that reflect the genetic differences between clozapine-treated and non-clozapine-treated patients with schizophrenia as a proxy of TRS.


title: Hippocampus RNA-sequencing of aging rats with cognitive decline

city: Beijing

first: Shi

last: Cuige

address: 12 Dahuisi road

institute: National Research Institute for Family Planning

summary: Aging is an inevitable process for everyone. Aging is mostly characterized by decline of cognitive function. Themechanisms are still not clear. Hippocampus has been shown to participate in cognition process,the basic mechanism of which are involved in molecularalterations in genes expression. Objective of the present research was to find the transcriptomic changes influenced by aging in hippocampus using RNA-sequencing. The 22-monthrats with cognition decline were used as a model system to analyze the changes in transcriptional networks. There were121 differentially expressed genes identified in the hippocampus of aged rats, including 54 genes upregulated and67 genes downregulated. After GO analysis,differentially expressed genes were found to be enriched inprotein hetorotrimerization, positive regulation of kinase activity, multivesicular body,mitochondrial membrane, oxygen binding and protease binding. KEGG analysesshowed thatDEGs were mainly observed at biochemical signaling pathways, containing Neuroactive ligand-receptor interaction (likeAplnr,Htr2a,Nmur2,Rxfp3), Apelin signaling pathway(likeAplnr,Cdh1,Serpine1),Serotonergic synapse（like Htr2a,Tph2）,Tryptophan metabolism（Tph2）,and so on. These DEGsin the hippocampusmay be involved in the formation of learning and memory. At last, quantitative reverse transcription-polymerase chain reaction was applied to verify the RNAsequencing data.Altogether, the above analysis help to identify specific genes in the aging hippocampus, which might be used as potential molecular targets for the prevention and treatment of aging-related cognition disorders.

overall_design: Male,adult (4 months; n = 10) and aged (22 months; n =10) Sprague Dawley rats were used.Cognitive function in both rat groups were evaluated by Morris water maze. After the MWM test, three male rats from each group were randomly selected and the ventral hippocampus was harvested and processed for transcriptome sequencing.

first: Li

last: Hou

first: Cuige

last: Shi


title: ZNF180 modulates tumor intrinsic immunotherapy resistance in melanoma through driving plasticity [ATAC-seq]

status: Public on Sep 30 2025

city: New York

first: Won-Min

last: Song

state: NY

address: 1399 Park Avenue

department: Genetics and Genomic Sciences

institute: Icahn school of medicine at Mount Sinai

summary: Through analyzing publicly available single-cell and bulk sequencing data from ICI-treated cohorts, ZNF180-regulome was predictive of ICI responses in independent bulk sequencing cohorts, and ZNF180+ tumors persisted after the therapy with immune-suppressive features such as MHC-I loss and CD155 expressions, the primary ligand to TIGIT inhibitory receptor. To investigate regulatory roles of ZNF180 to confer these immune suppressive phenotypes, we performed ZNF180 knock-down in melanoma cells in vitro with different genetic backgrounds, namely A375 (BRAF-mutant) and SKMEL147 (NRAS-mutant) cells, and performed RNA- and ATAC-sequencing. The integrative analysis revealed ZNF180 silencing promoted tumor immunogenicity through gain of accessibility on MHC-I/-II coding genes, CD155 down-regulation to avoid TIGIT/CD155 checkpoint signaling, and suppressed AP-1 transcription factor activities as the drivers of melanoma reprogramming towards MITFlowAXLhigh de-differentiated cells. Further, ZNF180 silencing increased CD4 helper T-cell infiltrations in tumors and regressed the tumors in vivo. Collectively, these results indicate ZNF180 is a tumor intrinsic regulator of melanoma plasticity to drive de-differentiated phenotypes with immune-suppressive features including loss of immunogenicity, T-cell inhibitory signals through TIGIT/CD155 checkpoint and exclusion of CD4 helper T-cells. As ZNF180-regulome manifests in non-metastatic melanoma in contrast to the current focus of standard-of-care ICI on the metastatic disease, these results establish ZNF180-regulome as a biomarker and novel therapeutic avenue for early stage melanoma to intervene ICI resistance.

overall_design: ZNF180 knock-down by shRNAs (shZ1, shZ3) was performed on A375 and SKMEL147 cells with two biological replicates per shRNA. The ATAC-seq was performed on the ZNF180 KD cells and the respective non-transfected controls.

first: Praveen

last: Agrawal

first: Sree

middle: K

last: Kondapuram

first: Xianxiao

last: Zhou


title: Targeting AEBP1 to mitigate pro-tumor activity of cancer-associated fibroblasts and increase therapeutic efficacy to anti-PD-1 [scRNA-Seq]

city: South San Francisco

first: Heyuan

last: Li

state: California

address: 213 E Grand Ave

institute: Merck Research Laboratories

summary: Cancer-associated fibroblasts (CAFs) are one of the components in tumor microenvironment (TME) that can facilitate tumor progression, invasion, and metastasis directly through tumor-CAF interactions, or indirectly by crosstalking with tumor infiltrating immune cells and inducing immunosuppressive TME. Indeed, high stromal signature has been associated with reduced therapeutic efficacy and resistance to Immune Checkpoint Blockade. AEBP1 is highly expressed in myofibroblast cells whose expression is further upregulated in activated fibroblasts and the extracellular matrix (ECM)-producing CAFs. AEBP1 has two alternatively spliced isoforms that the extracellular isoform binds to collagen and promotes collagen remodeling, and the intracellular isoform modulates transcription and signaling. We observed expression of both isoforms of AEBP1 in primary human CAFs.  Our data showed that combined knock out (KO) of both isoforms of AEBP1 by gene editing technology decreased CAF proliferation, collagen gel contractility and CAF-mediated tumor cell proliferation in vitro. Pan AEBP1 KO mouse fibroblasts also showed reduced activity in vitro and in vivo in the co-implantation mouse model.  We found that knocking out both isoforms of AEBP1 downregulated the collagen biosynthesis and ECM organization related pathways in both mouse fibroblasts and primary human CAFs through RNA sequencing studies. In addition, loss of AEBP1 in fibroblasts impacted tumor cell phenotypes resulting in significant decrease of tumor cells with,with epithelial-mesenchymal transition signature in the co-implantation mouse model. Furthermore, AEBP1 KO in CAFs enhanced the anti-PD-1 induced effector T cell activity and the anti-PD-1 efficacy in this co-implantation model. Altogether, our results demonstrate that AEBP1 is important in regulating CAF function in the TME.  Inhibiting AEBP1, therefore, may be a novel strategy in targeting CAF tumor-supporting activity and overcoming cancer resistance to anti-PD-1 immunotherapy.

overall_design: Single-cell RNAseq of MC38-NIH3T3 co-injected tumors 13 days after implatation. MC38 tumor cells were co-injected with wild-type or Aebp1 KO NIH3T3 cells. Whole tumor and CD45 depleted tumors are sequenced in parallel.

first: Suchitra

last: Natarajan

first: Khoa

last: Nguyen

first: Elysia

last: Saputra

first: Cindy

first: Gukhan

last: Kim

first: Yu

last: Liu

first: Hong

last: Sun

first: Ramli

last: Muhammad

first: Ling

first: William

last: Monis

first: Wendy

last: Blumenschein

first: Dewan

last: Hossain

first: Aleksandra

last: Olow

first: Xin

last: Yu


title: ZC3H13 Loss Drives Cancer Metastatic Progression by Disrupting m6A RNA Methylation

city: Salamanca

first: Sandra

last: Blanco

address: Campus Universitario

institute: CSIC

summary: Aggressive metastatic cancer remains a major clinical challenge due to the unclear underlying mechanisms and the limited treatment options available. N6-methyladenosine (m6A) is a reversible modification of RNA that is frequently altered in cancer, and inhibitors targeting regulators of this process have been shown to block tumorigenesis. A better understanding of the role of m6A modifications in driving metastatic properties could help reveal potential strategies to prevent and treat metastasis. In this study, we discovered loss of the m6A writer complex component ZC3H13 as a key regulator of metastatic progression. Co-loss of ZC3H13 together with RB1 and BRCA2 occurred in patients with metastatic prostate cancer. Functional in vitro and in vivo assays demonstrated that ZC3H13 loss changes m6A writer complex activity and target specificity, leading to decreased m6A methylation and increased stability of transcripts that promote migration and invasion. Treatment with FDA-approved m6A demethylase inhibitors effectively reduced the metastatic capabilities of ZC3H13-deficient cells. Together, these findings provide insights into how the m6A writer complex selectively methylates mRNAs, highlight the pathological consequences of altered writer complex composition in cancer, and reveal therapeutic avenues for patients with metastatic cancer.

overall_design: RNA-seq and m6A MeRIP-seq profiling of wt BPH1 cells and ZC3H13 overexpressing cells (dCas and OEsg1) and control and ZC3H13 KO cells (EmpVec and ZC3KO) cells.

first: Óscar

last: Monteagudo-García

first: Paz

last: Nombela

first: Ángel C

last: Román


title: Interferon Mediated Bronchial Epithelium Cellular Senescence in Chronic Obstructive Pulmonary Disease

city: Belfast

first: Clifford

last: Taggart

state: Northern Ireland

address: 97 Lisburn Rd

department: Wellcome-Wolfson Institute for Experimental Medicine

institute: Queen's University Belfast

summary: Cellular senescence has been implicated in chronic obstructive pulmonary disease (COPD) pathogenesis.  We used single cell RNA sequencing (scRNA-seq) to analyze gene expressions in bronchial epthelium, finding increased expression of cellular senescence signature in COPD samples.

overall_design: Bronchial epithelial cells from COPD and healthy controls were cultured in an air-liquid interface (ALI) model, at 28 days ALI culture, cells were trypsinized and anylized using scRNA-Seq.

last: Guo-Parke

first: Oisín

last: Cappa

first: Dermot

last: Linden

first: Jeremy

last: Domis

first: Lee

last: Borthwick

first: Andrew

last: Fisher

first: Sinéad

last: Weldon

first: David

last: Simpson

middle: C

first: Joseph

last: Kidney


title: Granulosa cell-secreted KITL is involved in maintaining zinc homeostasis in the oocytes of neonatal mouse ovaries

city: Guangzhou

first: Yan

last: Du

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: South China University of Technology

summary: Proto-oncogenic receptor tyrosine kinase (KIT) ligand (KITL) secreted by granulosa cells and its receptor KIT on oocytes are crucial for primordial follicle formation and activation, and follicular development. In the present study, ZnSO4 decreased the number of primordial and growing follicles in cultured neonatal mouse ovaries when KITL-KIT signaling was inhibited by ISCK03. ZnSO4 also significantly increased the mRNA and protein levels of Zrt/Irt-like protein 6 (ZIP6, a zinc importer) and zinc levels in the oocytes of cultured neonatal mouse ovaries in the presence of ISCK03, suggesting that the increase of ZIP6 levels results in zinc overload in the oocytes of cultured neonatal mouse ovaries. Further experiments indicated that zinc overload resulted in oocyte apoptosis in cultured neonatal mouse ovaries via oxidative stress-driven dual mechanisms: irreversible DNA damage in the nucleus and autophagic flux blockade in the cytoplasm of oocytes. Moreover, intraperitoneal injection of ZnSO4 and ISCK03 significantly increased ZIP6 expression, DNA damage, autophagic flux blockade, and apoptosis of oocytes in neonatal mice. Taken together, these findings indicate that granulosa cell-secreted KITL is involved in maintaining zinc homeostasis in the oocytes of neonatal mouse ovaries. This study not only reveals a novel function of granulosa cells in supporting oocyte homeostasis, but also provides a theoretical basis for identifying individuals susceptible to zinc dyshomeostasis caused by the impaired KITL-KIT signaling.

overall_design: Effects of ZnSO4 and ISCK03 treatment on ovarian oocytes in neonatal mice


title: Bi-allelic loss-of-function variants in CLCN2 cause retinal degeneration via impairing phagocytosis in patient retinal pigment epithelium

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: CLCN2 encodes a two-pore homodimeric chloride channel protein (CLC-2) widely expressed in human tissues. Previous studies reminded the retinopathy in several individuals carrying the loss-of-function variants in CLCN2, but the genotype-phenotype relationship and the underlying mechanisms remain unknown. In this study, we followed up a patient carrying the homozygous c.2257C>T (p.R753X) nonsense mutation in CLCN2 for more than 6 years, and comprehensively characterized the ocular features by multimodality imaging and functional examinations. The patient presented severe bilateral retinal degeneration with the loss of photoreceptor and retinal pigment epithelium (RPE). Moreover, the pathogenicity of this mutation was explored using an overexpression system and the patient specific induced pluripotent stem cells (iPSCs) derived RPE cells and retinal organoids (ROs). The mutant CLC-2 maintained the correct subcellular localization but displayed lower channel function than wild-type CLC-2 in HEK293T cells. Especially, the mutation also caused dysfunction of both ClC-2 chloride channel and outer segment phagocytosis in patient iPSC derived RPE cells, which were verified by RNA-seq analysis. And these impairments were rescued by repairing the CLCN2 mutation with CRISPR-Cas9 editing. However, this variant did not cause evident changes of photoreceptors in patient ROs, where RPE cells were not opposite to them as in vivo, implying the dysfunctional RPE is the primary cause of the disease. Collectively, we firstly defined the ocular features mediated by bi-allelic CLCN2 variants in detail and illustrated the pathogenetic mechanisms. Our findings will facilitate the diagnosis, treatment and prevention of CLCN2 related retinal degeneration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC-RPE cells derived from control individual and the LKPAT patient hiPSCs. HiPSC-RPE cells were collected at day 28. Total RNA from three independent biological replicates of hiPSC-RPE cells were extracted using Trizol reagent kit (T9424, Sigma). Illumina TruSeq RNA Sample Prep Kit (FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina Casava2.19 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2.Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et. al.

first: Ping

last: Xu

first: Zhuolin

last: Chen

first: Jianchi

last: Ma

first: Yongli

last: Shan

first: Yuan

last: Wang

first: Bingbing

last: Xie

first: Dandan

last: Zheng

first: Fuying

last: Guo

first: Xiaojing

last: Song

first: Guanjie

last: Gao

first: Ke

last: Ye

first: Yizhi

last: Liu

first: Guangjin

last: Pan

first: Bin

last: Jiang

first: Fuhua

last: Peng


title: Targeting STING–induced immune evasion with nanoparticulate binary pharmacology improves tumor control in mice

city: Hangzhou

first: Fanchao

last: Meng

address: 79 Qingchun Road

department: NHC Key Laboratory of Combined Multi-Organ Transplantation

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

summary: Harnessing the stimulator of interferon genes (STING) signaling pathway to trigger innate immune responses has shown remarkable promise in cancer immunotherapy; however, overwhelming resistance to intratumoral STING monotherapy has been witnessed in clinical trials, and the underlying mechanisms remain to be fully explored. Herein, we show that pharmacological STING activation following the intratumoral injection of a non-nucleotide STING agonist (i.e., MSA-2) results in apoptosis of the cytolytic T cells, interferon-mediated overexpression of indoleamine 2,3-dioxygenase 1 (IDO1), and evasion from immune surveillance. We leverage a noncovalent chemical strategy for developing immunomodulatory binary nanoparticles (iBINP) that include both the STING agonist and an IDO1 inhibitor for treating immune-evasive tumors. This iBINP platform developed by dual prodrug engineering and subsequent nanoparticle assembly enables tumor-restricted STING activation and IDO1 inhibition, achieving immune activation while mitigating immune tolerance. A systemic treatment of preclinical models of colorectal cancer with iBINP resulted in robust antitumor immune responses, reduced infiltration of regulatory T cells, and enhanced activity of CD8+ T cells. Importantly, this platform exhibits great therapeutic efficacy by overcoming STING–induced immune evasion and controlling the progression of multiple tumor models. This study unveils the mechanisms by which STING monotherapy induces immunosuppression in the tumor microenvironment and provides a combinatorial strategy for advancing cancer immunotherapies.

overall_design: Mice bearing  MC38 tumors received intratumoral injections of vehicle (Saline containing 10%DMSO) or MSA-2 every three days. After a total of three doses, tumors were collected, minced and dissociated (n = 3 mice or samples were pooled to control for biological variability).

first: Hangxiang


title: Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling [single-nucleus Drop-seq]

first: Emily

last: Feierman

summary: A cell’s ability to respond and adapt to environmental stimuli relies in part on transcriptional programs controlled by histone proteins. Histones affect transcription through numerous mechanisms including through replacement with variant forms that carry out specific functions. We recently identified the first widely expressed H2B histone variant, H2BE and found that it promotes transcription and is critical for neuronal function and long-term memory. However, how H2BE is regulated by extracellular stimuli and whether it controls activity-dependent transcription and cellular plasticity remain unknown. We used CUT&Tag and RNA-sequencing of primary neurons, single-nucleus sequencing of cortical tissue, and multielectrode array recordings to interrogate the expression of H2BE in response to stimuli and the role of H2BE in activity-dependent gene expression and plasticity. We find that unlike Further, we show that neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity in neurons after long-term stimulation. In summary, these data demonstrate that H2BE expression is inversely correlated to activity and necessary for long-term activity-dependent responses, revealing the first instance of a histone variant involved in the homeostatic plasticity response in neurons.

overall_design: Seizures were induced in 2-4 month old WT and H2BE-KO mice by intraperitoneal injection of pentylenetetrazol (PTZ). Nuclei were isolated from cortical tissue by sucrose gradient and ultracentrifugation. Nuclei capture and library preparation was performed using single-nucleus Drop-seq (n=2-3 biological replicates per genotype/condition).


title: Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling [RNA-seq]

overall_design: WT and H2BE-KO primary cortical neurons were isolated from E16.5 mice and cultured for 12 days . Neurons were treated with BDNF for 30min and 24h prior to collection for RNA-sequencing (n=4 biological replicates per genotype/condition).


title: ZNF180 modulates tumor intrinsic immunotherapy resistance in melanoma through driving plasticity [RNA-Seq]

first: Won-Min

overall_design: ZNF180 knock-down by shRNAs (shZ1, shZ3) was performed on A375 and SKMEL147 cells with two biological replicates per shRNA. The transcriptomes of the ZNF180 KD cells were compared to the respective non-transfected controls.

first: Praveen

last: Agrawal

first: Sree

last: Kondapuram

first: Xianxiao

last: Zhou


title: WWOX promotes osteosarcoma development via upregulation of Myc [RNA-Seq]

first: Rami

last: Aqeilan

overall_design: collect yBM from non tumor bearing mice at different time points in addition to the collection of BMT and tumors at the time of tumor detection to validate the genetic makeup in all these gropups compared to the control BM cells (Cre negative mice)

first: Rania

last: Akkawi

first: Osama

last: Hidmi

first: Ameen

last: Haj Yehia

first: Judith

last: Diment

first: Yotam

last: Drier

first: Gary

last: S Stein


title: Transcriptomic analysis of Hela Ezrin Ko cells

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary: Ezrin (EZR), a cell membrane to cytoskeleton linker protein,  plays key roles in maintaining cellular homeostasis. Its deregulation at various levels strongly correlates with cancer progression, metastasis and higher patient mortality.  However, the precise mechanistic basis for its role remains unknown. Recently, we demonstrated that Ezrin participates in EGFR/AKT signaling pathways. Importantly, transitions between active (phosphorylated open) and inactive (dephosphorylated closed) forms of Ezrin is crucial for its function in cancer. Gene expression analysis suggested dysregulation of genes that are functionally linked to cell energetic metabolism with potential implications for cell proliferation, survival and apoptosis. Total RNA was extracted from n=4 for each experimantal group: Transcriptomic analysis was performed on HeLa WT and HeLa Ezrin KO cells.

first: Ivan

last: Conte

first: Giuliana

last: Giamundo


title: CRISPRi Screening of Enhancers in Human Primary Astrocytes Identifies Regulatory Circuitry Disrupted in Alzheimer’s Disease [NanoString]

city: Kensington

first: Irina

last: Voineagu

address: High St

department: Biotechnology and Biomolecular Sciences

institute: The University of New South Wales

summary: We used CROP-seq to perform a high-throughput, parallel screen of 979 candidate enhancer perturbations in normal human astrocytes (NHAs), a primary cell-line. We identified the target gene(s) for 145 of these candidates, which were enriched for transcription with eRNA, transcription factor footprinting, and superenhancer annotation. Most regulatory interactions were <50kb, targeting the nearest gene in ~50% of cases, but were not typically captured by eQTL or in silico predictions. These data elucidate the regulatory network of an understudied-but-crucial brain cell-type.

overall_design: To validate results from our CRISPRi scRNA-seq screen, we selected 19 enhancers linked to 14 genes to validate in singleton experiments. The top performing sgRNA for each enhancer was cloned in CROP-seq-opti-GFP and transduced into NHA cells that stably express dCas9-KRAB at an MOI of 1. We also generated 4 pooled lines, where sgRNA for 2-3 enhancers linked to the same gene were transduced into the NHA-dCas9-KRAB cells at an MOI of 1 for each sgRNA. After 4 days, cells were selected with 3 µg/mL of puromycin and 10 µg/mL blasticidine S hydrochloride, and RNA was extracted after 7 days. Gene expression was then measured using a Nanostring nCounter Elements TagSets.

first: Nicole

last: Green

first: Gavin

last: Sutton

first: Hannah

last: Danon


title: A comprehensive tRNA pseudouridine map dependent on   human stand-alone pseudouridine synthases

city: Oxford

first: Linzhen

last: Kong

address: University of Oxford Old Road Campus Research Building

department: Nuffield Department of Medicine

institute: Ludwig Institute for Cancer Research

summary: Pseudouridine (Ψ) is one of the most abundant RNA modifications in human cells, which is introduced post-transcriptionally by pseudouridine synthases (PUS). Despite its prevalence, the biological functions of Ψ remain poorly understood, largely due to the limited knowledge linking specific PUS enzymes to their targets. To address this gap, we systematically knocked out or knocked down 9 stand-alone PUS in HCT116 cells and mapped their Ψ profiles using 2-bromoacrylamide-assisted cyclization sequencing (BACS). Through this approach, we uncovered previously unknown targets of several PUS enzymes, including RPUSD1, RPUSD2, PUS3, PUSL1, and PUS7L. Additionally, we revealed that TRUB1 and PUS10 function redundantly to catalyze the highly conserved Ψ55 modification in cytosolic tRNAs. Intriguingly, we found that RPUSD3 and TRUB2 do not exhibit noticeable enzymatic activities in human cells. By integrating these findings with earlier results for TRUB1, PUS7, and PUS1, we constructed a comprehensive map of stand-alone PUS-dependent Ψ modifications across human tRNAs. Using this map, we further demonstrated that different PUS enzymes introduce Ψ modifications at distinct stages of pre-tRNA processing.

overall_design: Pseudouridine detection using BACS in HCT116/HeLa WT cells, TRUB2 KD, PUSL1 KO, RPUSD1 KO,RPUSD2 KO,RPUSD3 KO,RPUSD4 KD, PUS10 KO,PUS3 KO and PUS7L KO cells. Two monoclones for each KO were selected for BACS.

first: Haiqi

last: Xu

first: Mengjie

last: Li

first: Giuseppina

last: Pisignano

first: Jingfei

last: Cheng

first: Feng

last: Feng

first: Parinaz

last: Mehdipour

first: Chun-Xiao

last: Song


title: Pharmacologic inhibition of PCBP2 biomolecular condensates relieves Alzheimer’s disease

city: Chongqing

first: Lu

last: Wang

address: 1 Youyi Road, Yuzhong District

institute: the First Affiliated Hospital of Chongqing Medical University

summary: Biomolecular condensates are involved in a variety of neurodegenerations. These condensates are formed through phase separation mechanism. However, how they may be functional in the pathophysiology of Alzheimer’s disease (AD) remains poorly understood. Here, we report that in the brain of AD patients and animal models, an elevation of poly(C)-binding protein 2 (PCBP2) correlates with biomolecular condensation that involves phase separation. These condensates sequester large numbers of mitochondrial and mRNA-binding proteins, leading to the outside impairment of mitochondrial morphology and function, and BACE1 mRNA decay relative to amyloid deposition. We then identify a small molecule CN-0928 that inhibits the condensates by reducing PCBP2 protein level and mitigates AD pathology and cognitive decline, in which CN-0928 binding to a target protein integrator complex subunit 1 (INTS1) allows to regulate PCBP2 expression. Our findings place PCBP2 condensates as a key player that cooperates the seemingly disparate but important pathways, and show pharmacological modulation of PCBP2 as an effective approach for treating AD.

overall_design: SH-SY5Y cells were transfected with NC (Ctrl) or siPCBP2. After 48 hours, cells were harvested for transcriptome sequencing.

first: Guo-Jun

last: Chen


title: Mouse Spinal Cord Transcriptome Data

city: Stockholm

first: Keying

last: Zhu

state: -- select state --

address: L8:04, Center for Molecular Medicine, Karolinska University Hospital

institute: Karolinska Institutet

summary: To compare the transcriptomic profile of mouse spinal cord homegenates from different conditions using the NanoString nCounter Mouse Glial Profiling Panel with additional customized probes.

overall_design: In this study, we extracted mRNA from mouse spinal cord homogenates from the following groups: wild-type 1-year-old female (WT-OF), wild-type 1-year-old male (WT-OM), wild-type 2–3-month-old female (WT-YF), wild-type 2–3-month-old male (WT-YM), 1-year-old female 10 days post-microglial Tgfbr2 deletion (KO-OF-D10), 1-year-old female 20 days post-microglial Tgfbr2 deletion (KO-OF-D20), 1-year-old female 30 days post-microglial Tgfbr2 deletion (KO-OF-D30), 1-year-old male 30 days post-microglial Tgfbr2 deletion (KO-OM-D30), 2–3-month-old female 30 days post-microglial Tgfbr2 deletion (KO-YF-D30), and 2–3-month-old male 30 days post-microglial Tgfbr2 deletion (KO-YM-D30). The samples were hybridized to the nCounter Mouse Glial Profiling Panel CodeSet (XT-CSO-M-GLIAL-12, NanoString). This CodeSet includes 757 probes for genes of interest, 13 probes for internal reference genes, and 10 additional customized probes for Smad4, Smad7, Nrros, Tgfbr2, Tgfbr3, Smurf1, Tgfb2, Cxcr4, Adgre4, and Clec4b1. A total of 3–5 mice were included for each group.

first: Robert

last: Harris

first: Harald

last: Lund