title: High resolution spatially resolved transcriptomic analysis of mouse pancreatic sections during embryonic development

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

institute: King's College London

summary: The pancreas is an endodermal organ with exocrine and endocrine cell compartments. The embryonic development of the pancreas relies on the the coordinated action of pancreatic progenitors and its surrounding microenvironments. The most abundant cell type of the pancreatic microenviroment are mesenchymal cells. These cells are known to contribute to the pancreas organ growth, morphogenesis and differentiation. In this study, we used hybridization-based in situ sequencing (HybISS) to spatially characterize  pancreatic progenitor populations and microenviroment cell types in the pancreas of the mouse embryos.

overall_design: Pancreatic spatial transcriptomics data were generated by RNA hybridization-based in situ sequencing (HybISS, Cartana part of 10xGenomics)

first: Alejo

last: Torres-Cano

first: Jean-Francois

last: Darrigrand

first: Gabriel

last: Herrera-Oropeza

first: Georgina

last: Goss

first: Anna

last: Salowka

first: Debashish

last: Chitnis

first: Morgane

last: Rouault

first: Alessandra

last: Vigilante


title: mRNA Initiation and Termination are Spatially Coordinated II

status: Public on Oct 09 2025

city: Worcester

first: Athma

last: Pai

state: MA

address: 368 Plantation Street, AS5-2057

department: RNA Therapeutics Institute

country: USA

institute: UMASS Medical School

type: Expression profiling by high throughput sequencing

summary: ABSTRACT: The expression of a precise mRNA transcriptome is crucial for establishing cell identity andfunction, with dozens of alternative isoforms produced for a single gene sequence. The regulationof mRNA isoform usage occurs by the coordination of co-transcriptional mRNA processingmechanisms across a gene. Decisions involved in mRNA initiation and termination underlie thelargest extent of mRNA isoform diversity, but little is known about any relationships betweendecisions at both ends of mRNA molecules. Here, we systematically profile the joint usage ofmRNA transcription start sites (TSSs) and polyadenylation sites (PASs) across tissues andspecies. Using both short and long read RNA-seq data, we observe that mRNAs preferentiallyusing upstream TSSs also tend to use upstream PASs, and congruently, the usage ofdownstream sites is similarly paired. This observation suggests that mRNA 5’ end choice maydirectly influence mRNA 3’ ends. Our results suggest a novel “Positional Initiation-TerminationAxis” (PITA), in which the usage of alternative terminal sites are coupled based on the order inwhich they appear in the genome.To examine the direct influence of promoter (AFE) choice on ALE decisions, we performed a series of CRISPR modulations on HEK293 cells to either activate or repress AFEs and measure the change in ALE usage.

overall_design: K562 cells passage 10-12 were grown in RMPI medium supplemented with  cells were treated with DRB 100uM for 3 hours. During the last 5 minnutes of DRB, 4su was added to a final concentration of 1mM. After PBS wash, cells were resuspended in 4su 1mM for a 10m labeling. Treated cells were transferred to low-bind tubes, spin down 2 minutes at 1000rcf, followed by Trizol/Chloroform extraction. Then, the aqueous phase was cleanup using the zymo-clean up kit. We enriched labeled RNA using MTSEA biotin-XX pulldown, followed by RNAseH-based ribosomal RNA depletion. Then, we did a polyI tailing and direct RNA nanopore library prep. For cDNA libraries, polyI tailing was followed by strand-switching RT and PCR, followed by cdna library prep following manufacture's instructions.

first: Ezequiel

last: Calvo-Roitberg

first: Christine

middle: L

last: Carroll

first: GyeungYun

last: Kim

first: Valeria

last: Sanabria

first: Maritere

last: Uriostegui-Arcos

first: Joseph

last: Paquette

first: Steven

middle: T

last: Mick

first: Sergey

middle: V

last: Venev

first: Job

last: Dekker

first: Ana

last: Fiszbein

middle: A


title: Single-cell RNA-seq analysis of pancreatic progenitor cells and mesenchyme from mouse embryos

first: Francesca

last: Spagnoli

country: United Kingdom

summary: The pancreas is an endodermal organ with exocrine and endocrine cell compartments. The embryonic development of the pancreas relies on the the coordinated action of pancreatic progenitors and its surrounding microenvironments. The most abundant cell type of the pancreatic microenviroment are mesenchymal cells. These cells are known to contribute to the pancreas organ growth, morphogenesis and differentiation. In this study, we used single-cell RNA sequencing to molecularly characterize mesenchymal and pancreatic progenitor populations in the dorsal pancreas of the mouse embryos.

overall_design: Single cells were isolated by FACS from the dorsal pancreatic tissue of Tg(Prox1-EGFP), Tg(Nkx2.5-Cre;mTmG) and Tg(Nkx3.2-Cre;mTmG) transgenic mouse embryos at embryonic day (E) 12.5 and processed for single-cell RNA sequencing using SmartSeq2 method.

first: Alejo

last: Torres-Cano

first: Jean-Francois

last: Darrigrand

first: Gabriel

last: Herrera-Oropeza

first: Francesca M.


title: ERBB2 signaling drives immune cell evasion and resistance against immunotherapy in small cell lung cancer

city: Erlangen

first: Lydia

last: Meder

state: Bavaria

address: Glückstr. 6

department: Experimentelle Medizin 1

country: Germany

summary: Small cell lung cancer (SCLC) represents ~15% of all lung cancers and is characterized by its highly aggressive phenotype and its dismal outcome. Though the addition of immune checkpoint blockade to carboplatin and etoposide treatment has improved outcome in SCLC patients, SCLC cells finally acquire the ability to evade immunosurveillance and resistance against immune check point blockade. To elaborate molecular mechanisms that mediate SCLC immune cell evasion we performed high dimensional profiling of human and murine SCLC specimens. We herein comprehensively analyzed matched human samples of primary and metastatic SCLC and found a loss of MHC-I in SCLC metastases indicating that MHC-I loss mediates SCLC immune cell evasion. Silencing MHC-I in SCLC cells drastically diminished immune cell infiltration and facilitated the formation of metastasis in mice by circumventing immune surveillance. Using mass spectrometry and phospho tyrosine kinase analysis we discovered that ERBB2 signaling suppresses MHC-I expression in SCLC cells and stimulates immune modulating transcripts. Mechanistically, genetic and/or pharmacologic blockade of the ERBB2 signaling axis was sufficient to induce MHC-I expression and to prevent immune evasion in autochthonous murine SCLC in a STING dependent manner. Finally, we demonstrate that ERBB2 signaling axis regulates MHC-I expression on SCLC cells and is critical in maintaining immune evasion in SCLC. Most strikingly, we here uncover synergistic treatment efficacy by combining ERBB2 with anti-PD-1 targeted treatment that elicits profound responses in preclinical SCLC models suggesting this combination for future clinical trials in patients with SCLC.

overall_design: To investigate the role of  ERBB2 in SCLC we created an ERBB2KO cell line and compared it to the wild type regarding antigen presentation pathways.

first: Charlotte

middle: I

last: Orschel

first: Cyrielle

last: Bouchez

first: Rahil

last: Gholamipoorfard

first: Claudia

first: David

last: Stahl

first: Christoph

last: Kreer

first: Mirjam

last: Koker

first: Xinlei

last: Zhao

first: Marieke

last: Nill

first: Leon

last: Ullrich

first: Marie-Lisa

last: Eich

first: Alexandra

last: Florin

first: Holger

last: Grüll

first: Jürgen

last: Wolf

first: Reinhard

last: Büttner

first: Florian

last: Klein

first: Johannes

last: Brägelmann

first: Christian

last: Reinhardt

first: Nima

last: Abedpour

first: Roland


title: Origin of Ewing sarcoma by embryonic reprogramming of neural crest to mesoderm

city: Los Angeles

first: Claire

last: Arata

email: carata@usc.edu, clairearata@gmail.com

state: CA

address: 1425 San Pablo St

department: Stem Cell

institute: University of Southern California

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Ewing sarcoma is a malignant small round blue cell tumor of bones and soft tissues, predominantly affecting children, adolescents and young adults. Ewing sarcoma is caused by chromosomal translocations that generate aberrant chimeric transcription factors, most frequently EWSR1::FLI1. Ewing sarcomas exhibit features of both neural and mesenchymal cells. The cell of origin of Ewing sarcoma and the mechanisms of EWSR1::FLI1-driven cell transformation are the subjects of long-standing debates, largely due to the absence of a representative animal model. By developing a robust Ewing sarcoma model in zebrafish, we provide evidence for a neural crest origin of this cancer. We show that neural crest-derived cells (NCCs) uniquely tolerate expression of the human EWSR1::FLI1 oncofusion protein in vivo and that targeted expression of the oncofusion in NCCs is sufficient to generate Ewing sarcoma tumors. In the trunk, EWSR1::FLI1 reprogrammed NCCs to a mesoderm-like state, including upregulation of the early mesoderm specifier tbxta (Brachyury/T) and mesenchymal genes pdgfra, twist1a, and prrx1a. Mesodermal reprogramming of trunk neural crest was evident by the ability of EWSR1::FLI1-expressing cells to induce ectopic fins throughout the body. Single-nucleus analysis of RNA expression and chromatin accessibility, combined with genome-wide profiling of EWSR1::FLI1 binding, revealed that EWSR1::FLI1 targets single GGAA-containing ETS sites in mesodermal developmental enhancers for neural crest to mesoderm reprogramming during cancer initiation, also binding  to GGAA repeats in established tumors. These findings show that EWSR1::FLI1 hijacks normal ETS-dependent developmental pathways in embryonic NCCs to drive initiation of Ewing sarcoma.

overall_design: Dissected trunks of -28.5Sox10:BFP>dsRed -28.5Sox10:dsRed>eGFP-2A-EF1 zebrafish at 7dpf were dissociated and cells were identified by Fluorescence-activated cell sorting (FACS). Dissected tissue from a wild type fish at 3mpf, a -28.5Sox10:dsRed>eGFP-2A-EF1 trunk tumor at 3mpf, and a EWSFLI mosaic model head tumor at 9mpf  were dissociated and processed with no sorting. All samples were subjected to nuclei isolation and processed for snATACseq and/or snRNAseq with 10x Genomics.

first: Elena

last: Vasileva

middle: E

first: Gage

last: Crump

first: James

last: Amatruda


title: Expression profiling of human foetal and adult aortic valves

city: Marseille

first: Stéphane

last: ZAFFRAN

address: 27 Bd JEan Moulin

country: France

institute: Aix Marseille Université

summary: Bicuspid aortic valve (BAV) is a frequent congenital heart defect with a high heritability. Identification of genes associated with the disease and the molecular mechanisms required genetic studies including genome-wide association studies (GWAS) meta-analysis. To prioritize genes identified through such meta-analysis several additional data are required including transcriptomic of aortic valve at early fetal and adult stages. RNA-sequencing was carried out on human fœtal aortic valves at 9, 13, and 22 post conceptional week (PCW) and adult controls. These data were used to compare gene expression profile of several genes identified in a GWAS meta-analysis. Comparing the expression of these genes in valve RNA-sequencing dataset we identified several genes with higher expression in fœtal tissues suggesting their involvement in aortic valve development. In conclusion, we performed integrative analyses taking advantage of human aortic valve transcriptome data to prioritize candidate causal gene of BAV.

overall_design: To prioritize BAV causal genes, we compared the expression profile of these genes in fœtal and adult stages using RNAseq data performed on fœtal and adult aortic valve tissues.

last: Zaffran

first: Sébastien

last: Theriault

first: Simon

last: Bosdy


first: Lydia

last: Meder

overall_design: We compared vehicle treated to anti-PD-1 and ERBB2 inhibition combination therapy treated mice.

first: Charlotte

last: Orschel

first: Cyrielle

last: Bouchez

first: Rahil

last: Gholamipoorfard

first: Claudia

first: David

last: Stahl

first: Christoph

last: Kreer

first: Mirjam

last: Koker

first: Xinlei

last: Zhao

first: Marieke

last: Nill

first: Leon

last: Ullrich

first: Marie-Lisa

last: Eich


city: Guangzhou

first: Kai

last: Yan

state: Guangdong

address: No. 106, Zhongshan 2nd Road, Guangzhou

country: China

institute: Guangdong Provincial People's Hospital

summary: RNA-sequencing (RNA-seq) analysis of liver tissues from WT and AKR1D1KO mice in Hepa1-6-induced HCC model. WT is referred as wild type, KO is referred as Akr1d1-knockout.

overall_design: Liver tissues from WT and AKR1D1KO mice in Hepa1-6-induced HCC model.

first: Haoran

last: Wei


title: Distinct components of nucleoside-modified messenger RNA vaccines cooperate to instruct efficient germinal center responses

first: Roberto

last: Spreafico

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

summary: Nucleoside-modified mRNA vaccines elicit protective antibodies through their ability to promote T follicular helper (Tfh) cells. The lipid nanoparticle (LNP) component of mRNA vaccines possesses inherent adjuvant activity. However, to what extent the nucleoside-modified mRNA can be sensed and contribute to Tfh cell responses remains largely undefined. Herein, we deconvoluted the signals induced by LNP and mRNA that instruct dendritic cells (DCs) to promote Tfh cell differentiation. We demonstrated that the nucleoside-modified mRNA drives the production of type I interferons that act on DCs to induce their maturation and the induction of Th1-biased Tfh responses. Conversely, LNP favors the acquisition of a Tfh cell-inducing program in DCs, a stronger Th2 polarization in Tfh cells, and allows for rapid mRNA translation by DCs within the draining lymph node. Our work unravels distinct adjuvant features of mRNA and LNP necessary for the induction of Tfh cells, with implications for vaccine design.

overall_design: We sought to evaluate the impact of the nucleoside-modified mRNA and LNP vaccine components on the transcriptional program of DCs and utilized the LIPSTIC system to probe this in relation to their antigen-presenting status. We created a construct consisting of the RBD of SARS-CoV-2 spike protein fused via a GS linker to the chicken ovalbumin peptide sequence recognized by OT-II CD4 T cells (RBD-OVA). Mice were immunized with either mRNA-LNP encoding RBD-OVA (mRNA_LNP), recombinant RBD-OVA mixed with empty LNP (protein_LNP), or recombinant RBD-OVA mixed with AddaVax (protein_Addavax) and DCs in the draining lymph nodes were analyzed 24-hours later.

first: Emily

last: Bettini

first: Aleksey

last: Chudnovskiy

first: Giulia

last: Protti

first: Sandra

last: Nakadakari-Higa

first: Simona

last: Ceglia

first: Diana

last: Castaño

first: Joy

last: Chui

first: Hiromi

last: Muramatsu

first: Thandiswa

last: Mdluli

first: Edit

last: Abraham

first: Zoltan

last: Lipinszki

first: Ivan

last: Maillard

first: Ying

middle: K

last: Tam

first: Andrea

last: Reboldi

first: Norbert

last: Pardi

first: Gabriel

middle: D

last: Victora

first: Michela

last: Locci


title: Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq II

city: Houston

first: Tao

middle: P.

last: Wu

state: TX

address: One Baylor Plaza, MS BCM225

department: Molecular and Human Genetics

institute: Baylor College of Medicine

type: Methylation profiling by high throughput sequencing

summary: DNA N6-methyladenine (6mA) is the most widespread type of DNA methylation in prokaryotes. However, the prevalence of 6mA in eukaryotes has recently been challenged due to the limitations of current 6mA detection techniques. Here, we present a chemical-based sequencing method, Nitrite-assisted Amino MEthylation sequencing (NAME-seq), for quantitative, whole-genome mapping of 6mA at single-base resolution. NAME-seq combines nitrite conversion of 6mA to nitrosylated-6mA (6mA-NO) with Klenow Fragment (3'→5' exo-) random priming to induce a 6mA-to-T transversion specifically. We apply NAME-seq to two bacterial species and show that, compared to SMRT-seq, NAME-seq results in a more specific and robust detection of 6mA. NAME-seq can also accurately map 6mA in the C. reinhardtii genome at single-base resolution. Additionally, we show that NAME-seq can be combined with conventional DIP-seq to detect 6mA in the Dam-methylated human genome with high specificity. Therefore, we further perform DIP-NAME-seq to profile 6mA in WT and TASOR KO K562 cell line and revealed that 6mA is enriched at specific motifs (HYYHAG and CACACA) and H3K9me3 regions. In summary, we demonstrate NAME-seq is a specific and sensitive sequencing method for quantitative 6mA mapping at single base resolution across different model organisms.

overall_design: NAME-seq to native genomic DNA with DIP enrichment

first: Xuwen

last: Li

middle: P


title: Dexmedetomidine Inhibits Abnormal Muscle Hypertrophy of Myofascial Trigger Points via TNF-α/ NF-κB Signaling Pathway

city: Jinan

first: Mingjian

last: Liu

address: Wenhua Xi Road 107

institute: Qilu Hospital of Shandong University

summary: Myofascial pain syndrome (MPS) is a chronic pain disorder with inflammation-related primarily characterized by the presence of myofascial trigger points (MTrPs). Myocyte enhancer factor 2C (MEF2C) is involved in the occurrence of a variety of skeletal muscle diseases. However, it is not yet clear if MEF2C is involved in MTrPs. The purpose of this study was to investigate whether MEF2C was involved in the inflammatory pathogenesis of MTrPs. In the present study, we used RNA sequencing (RNA-seq) to compare the differential expression of myocyte enhancer factor 2C (MEF2C) in healthy participants and MTrPs participants. the widely used rat MTrPs model was established to research the upstream and downstream regulatory mechanism of MEF2C and found that MEF2C was significantly increased in patients with MTrPs. Dex was injected intramuscularly in the MTrPs animal to assess its effects on MEF2C. The expression of MEF2C protein and mRNA in skeletal muscle of rats in the MTrPs group were up-regulated. In addition, the expression of TNF-α, p-P65, MLCK, and Myocilin (MyoC) was up-regulated and the mechanical pain threshold was decreased. Peripheral TNF- α injection significantly decreased the mechanical pain threshold and increased the expression of p-P65, MLCK, MEF2C, and MyoC in healthy rats. Maslinic acid increased the mechanical pain threshold and inhibited the expression of p-P65, MLCK, MEF2C, and MyoC. In addition, peripheral injection of dexmedetomidine (DEX) in MTrPs rats also inhibited the expression of TNF- α, p-P65, MLCK, MEF2C, and MyoC. These results suggest that MEF2C is involved in the inflammatory pathogenesis of MTrPs and DEX serves as a potential therapeutic strategy for the treatment of MPS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for healthy and MTrPs participants.

first: Feihong

last: Jin

first: Yu

first: Mei

last: Han

first: Feng

last: Qi


title: An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics

first: Colette

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

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

overall_design: Refer to individual Series


title: Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq I

sample_organism:
Helicobacter pylori
Escherichia coli
Chlamydomonas reinhardtii
Homo sapiens

overall_design: NAME-seq to native genomic DNA without any enrichment


title: Prostaglandin D2 Synthase: A novel Player in the Pathological Signaling Mechanism of the Aldosterone–Mineralocorticoid Receptor Pathway in the Heart

status: Public on Oct 08 2025

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

summary: A deregulated aldosterone (Aldo)–mineralocorticoid receptor (MR) pathway is linked to cardiovascular disease, including hypertension and heart failure. Despite the association of elevated plasma Aldo levels with cardiac stress, inflammation, myocardial fibrosis, and cardiac remodeling, the underlying mechanisms remain elusive. To study the impact of Aldo–MR pathway overactivation on cardiac health, a novel mouse model with AAV9-mediated MR overexpression and Aldo administration via subcutaneous osmotic pumps was generated. Echocardiographic analyses, transcriptome sequencing, and loss-of-function experiments of an identified lead candidate gene were performed. Additionally, cardiac tissue samples from human patients with end-stage heart failure were analyzed in the study. Mice with an overactivated Aldo–MR pathway exhibited increased neutrophil gelatinase-associated lipocalin (NGAL) expression, cardiac dysfunction, hypertrophy, and fibrosis. Transcriptomics identified prostaglandin D2 synthase (Ptgds) as a novel downstream effector of the cardiac Aldo–MR pathway. SiRNA-mediated inhibition of Ptgds in primary cardiomyocytes reduced NGAL levels and the hypertrophic impact of Aldo, suggesting a role in mediating Aldo-induced cardiac pathologies. Elevated expression of PTGDS was observed in hiPSC-CMs treated with the pro-hypertrophic cytokine leukemia inhibitory factor (LIF) and in end-stage heart failure patients, ascertaining its importance in cardiac disease settings. PTGDS is a newly identified mediator of Aldo–MR-induced cardiac remodeling and may represent a potential therapeutic target for CVD.

overall_design: RNA-seq profiling of C57BL/6N mouse heart tissue after AAV9-Empty control treatment, or AAV9-mineralocorticoid receptor (MR) overexpression with aldosterone treatment.

first: Ankita

last: Garg

first: Malte

last: Juchem

first: Sinje

last: Biss

first: Carla

middle: N

last: Borisch

first: Julia

last: Leonardy

first: Christian

last: Baer

first: Shashi

last: Gupta

first: Thomas

last: Thum


title: βIV-spectrin/STAT3 complex regulates the orientation of hypertrophic growth

city: Columbus

last: Hund

state: OH

address: 473 W 12th Ave

institute: Ohio State University

summary: Background: Cardiac hypertrophy, defined as a stress-induced increase in heart mass/size, is a major risk factor for adverse cardiovascular events including heart failure and arrhythmia. Within this general definition, the orientation of cell and organ growth varies considerably depending on stress type and duration with important implications for cardiac function, yet, little is known regarding the mechanisms that regulate hypertrophic orientation. Here, we evaluated the role of the cytoskeletal protein βIV-spectrin and associated pro-hypertrophic signal transducer and activator of transcription (STAT3) to direct the orientation of hypertrophic growth.  Methods: Transgenic mouse models with altered STAT3 signaling through modified interaction with its scaffolding partner βIV-spectrin, or phospho-regulation of STAT3 directly, were evaluated at baseline, and following transaortic constriction (TAC), or aortocaval fistula (ACF). Unbiased screening of gene expression from these structurally divergent states were evaluated for pathways responsible for directing myocyte length/width. These pathways were tested in vitro using primary mouse myocytes and in vivo to tune growth patterns for therapeutic intervention. Results: Loss of βIV-spectrin or direct STAT3 activation promoted a preferential increase in myocyte length over width, resulting in dilation of the left ventricular (LV) chamber (eccentric hypertrophy) and decreased systolic function. Conversely, preservation of βIV-spectrin favored an increase in myocyte width without LV dilation (concentric hypertrophy) and preserved systolic function in response to TAC or ACF. Differential expression of genes associated with microtubules, including the trafficking kinesin motor, KIF20A, were identified in concentric vs. eccentric hypertrophic states. In vitro assays revealed a relationship between βIV-spectrin/STAT3 signaling, KIF20A expression, microtubule density, and spatial distribution of mRNA for the sarcomeric gene actc1. Finally, intervention with pharmacologic STAT3 inhibition following chronic 6-week TAC successfully recovered concentric growth with improved systolic function. Conclusions: These data identify a novel and pivotal role for βIV-spectrin/STAT3 to direct myocyte geometry in response to chronic stress. These studies further illustrate the unique separation of hypertrophic growth and orientation as distinct pathways in cardiac remodeling.

overall_design: RNA-seq profiling of wildtype mice and STAT3 S727A phosphoablated mutant mice from whole heart samples following 4 weeks of transortic constriction to promote hypertrophic growth.

first: Drew

middle: M

last: Nassal

first: Shivangi

last: Mohta

first: Rebecca

last: Shaheen

first: Benjamin

last: Buck

first: Simon

last: Lococo

first: Haiyan

first: Omer

last: Cavus

first: Alexander

middle: J

last: Winkle

first: Jolie

last: Pyles

first: Nicholas

last: Leahy

first: Xianyao

last: Xu


title: The effect of Neurensin-2 overexpression on gene expression in N2a cells

city: Jerusalem

first: Gali

last: Umschweif

address: Ein Karem Campus | Jerusalem

department: pharmacology section. school of pharmacy

country: Israel

institute: The Hebrew University of Jeursalem

summary: Neurensin-2 is a stress-responsive vesicular protein. Nonetheless, the cellular mechanisms by which Neurensin-2 regulates depression and anxiety remain unexplored. To identify the cellular pathways regulated by Neurensin-2, we overexpressed Neurensin-2 in a N2a neuroblastoma cell line, followed by RNA sequencing

overall_design: To investigate the stress-induced gene expression changes, we extract RNA from control and  overexpressed Neurensin-2 in a N2a neuroblastoma cell line .On the RNA, which was extracted from cells , we preformed sequencing, gene expression profiling and pathway analysis.


title: Increased LEF1 protein levels and isoform switching drive cell proliferation in chronic lymphocytic leukemia [CUT&Tag]

city: Barcelona

first: Jose Ignacio

last: Martin-Subero

state: Barcelona

address: c/Rosselló, 149-153

country: Spain

institute: IDIBAPS

summary: The main goal of this study was to assess the role of LEF1 in patient-derived CLL cells.

overall_design: Comprehensive functional analyses to define the role of LEF1 (LEF1 CRISPR in primary CLL cells and LEF1 isoforms overexpression in CLL cell lines).

first: Mateos-Jaimez

last: Judith

first: Charalampopoulou

last: Stella


title: Independent mechanisms of myeloid bias and inflammation driven by UBA1 mutation

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Somatically acquired mutations in the E1 ubiquitin-activating enzyme UBA1 within hematopoietic stem and progenitor cells (HSPCs) were recently identified as the cause of the adult-onset autoinflammatory syndrome VEXAS (vacuoles, E1 enzyme, X linked, autoinflammatory, somatic)1. Most VEXAS-associated mutations occur at Met41 in UBA1 and lead to clonal expansion within the HSPC and myeloid, but not lymphoid, compartments. Despite its severity and prevalence, the mechanisms whereby UBA1 mutations cause multiorgan autoinflammation and hematologic disease are unknown. Here, we employ mRNA-based electroporation of adenine base editing enzymes to mutate endogenous Uba1, generating canonical VEXAS-associated Met41 mutations in murine or human HSPCs and macrophages. Expression of Met41-mutant UBA1 in macrophages aberrantly triggered apoptotic and necroptotic inflammatory cell death programs upon exposure to TNF or LPS, which could be fully reversed by combined deletion of Mlkl or Ripk3 plus Casp8, or partially by genetic or pharmacologic targeting of RIPK1 kinase activity. In mice challenged with TNF or LPS, the UBA1 inhibitor TAK-243 exacerbated inflammation, which was mediated by RIPK1 kinase activity and RIPK3-Caspase-8, respectively. In contrast, Uba1-mutant HSPCs displayed an unfolded protein response signature and spontaneous myeloid skewing that were independent of RIPK3-Caspase-8, thereby propagating an inflammatory cycle driven by their mature myeloid progeny. Mechanistically, we traced the dysregulated cell death response of Uba1-mutant macrophages to a cascading, kinetic defect in Lys63/Met1 (i.e., linear) polyubiquitylation of inflammatory signaling complexes. Collectively, our results link the pathogenesis of VEXAS with that of rarer germline monogenic causes of autoinflammation; highlight specific ubiquitin-associated defects stemming from an apical mutation in the ubiquitylation cascade; and nominate the RIPK1-RIPK3-caspase-8 death axis as a therapeutic target in VEXAS.

overall_design: Mouse HSPCs were electroporated with either the Abe8e-SpRY adenine base editor along with either control sgRNA targeting Rosa26 (Uba1-WT) or an sgRNA designed to introduce the M41T mutation in Uba1 (Uba1M41T/y). Cells were subsequently harvested 5- or 8-days after culture, hashtagged and submitted for single cell RNA-seq.

first: Narendra

last: Varun

first: Lareau

last: Caleb


title: Increased LEF1 protein levels and isoform switching drive cell proliferation in chronic lymphocytic leukemia [RNA-Seq]


title: Targeting p300/CBP abolishes HOXB13 loss-induced lipogenesis and tumor metastasis [RNA-seq]

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: HOXB13 is a prostate-specific homeodomain transcription factor that is mainly known as an androgen receptor (AR) cofactor. Recent studies have revealed AR-independent roles of HOXB13 in recruiting HDAC3 to suppress lipogenic programs in prostate cancer (PCa). As such, HOXB13 down-regulation leads to lipid accumulation and tumor metastasis, the molecular mechanisms of which, however, are incompletely understood. Here, we demonstrate that p300/CBP co-occupies HOXB13/HDAC3-repressed lipogenic enhancers and is required for their activation and target gene expression upon HOXB13 loss. We found that HOXB13 is down-regulated in metastatic hormone-sensitive PCa compared to their matched primary prostate tumors. HOXB13 loss induces matrix metalloproteinases (MMPs), which mediate HOXB13-depleted cell motility. Critically, CCS1477, a pharmacological inhibitor of p300/CBP, abolished HOXB13-loss-induced lipid accumulation, MMP gene expression, cell motility in vitro, and tumor metastasis in vivo. Taken together, our results suggest HOXB13 as a significant metastasis suppressor and identify p300/CBP as critical therapeutic targets in HOXB13-low metastatic PCa.

overall_design: To evaluate whether HOXB13 loss induces lipogenic programs through p300/CBP, we performed RNA-seq in control and HOXB13-KD LNCaP cells with concomitant p300 and/or CBP KD, or treated with DMSO or 250nM CCS1477 for 48 hours

first: Xiaodong

last: Lu

first: Qi

last: Chu

first: Jonathan

middle: C

last: Zhao


title: Targeting p300/CBP abolishes HOXB13 loss-induced lipogenesis and tumor metastasis


title: Increased LEF1 protein levels and isoform switching drive cell proliferation in chronic lymphocytic leukemia [CUT&Run]


title: Oral 4`fluorouridine rescues nonhuman primates from advanced Lassa fever

city: Galveston

first: Jacquelyn

last: Turcinovic

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: There are no approved treatments for Lassa fever (LF) which is estimated to cause 100,000 to 300,000 infections and 5,000 deaths annually in West Africa.  Recently, it was shown that 4`-fluorouridine (4`-FlU; EIDD-2749), an orally available ribonucleoside analog, protected guinea pigs from lethal challenge with the lineage IV prototype Josiah strain of Lassa virus (LASV) when treatment was delayed beyond the onset of clinical signs of disease.  Here, we assessed the therapeutic efficacy of 4`-FlU in a novel African green monkey model of LF using the more contemporary and seemingly more pathogenic lineage VII Togo strain of LASV.  Daily treatment of 4`-FlU beginning 6 days after LASV infection, when animals were viremic and clinically ill, resulted in 100% protection. Our findings support the further development of 4`-FlU as both a postexposure prophylaxis to control outbreaks and a therapeutic to treat symptomatic patients.

overall_design: Time series NanoString data from African green monkeys challenged Lassa virus

first: Robert

middle: W

last: Cross

first: Thomas

last: Geisbert


title: Targeting p300/CBP abolishes HOXB13 loss-induced lipogenesis and tumor metastasis [ChIP-seq]

overall_design: To evaluate whether HOXB13 loss induces lipogenic enhancer activation through p300/CBP, we performed H3K27ac ChIP-seq in control and HOXB13-KD LNCaP cells with concomitant p300 and/or CBP KD, or treated with DMSO or 250nM CCS1477 for 24 hours


title: The paternally derived genome opposes seed dormancy induction by the mother plant in Arabidopsis

city: Norwich

first: Steven

last: Penfield

address: Norwich Research Park, Colney Ln

department: Crop Genetics

institute: John Innes Centre

summary: Seed dormancy in Arabidopsis is known to be mediated by the interaction of maternal and zygotic genomes during seed maturation. While studies have revealed the extensive influence of maternal processes on dormancy and germination, less is known about the influence of the father. Here we exploit differences in ploidy to explore the role of the paternal genome on progeny seed dormancy. We show that paternal genome acts to reduce seed dormancy regardless of maternal genome dose, resulting in lower dormancy in tetraploid Arabidopsis versus genetically identical diploids. We show that this paternal effect requires synthesis of RNA Polymerase IV-dependent RNAs in the male gametophyte which oppose the dormancy- inducing effects of maternal siRNAs on seed coat and endosperm development. We conclude that the paternal genome has evolved to subvert the dormancy-inducing role of the mother plant in progeny seeds.

overall_design: Diploid WT Ler, diploid jas-1 (jas_2n) and triploid jas-1 (jas_3n) seeds were imbibed for 1 hour and endosperm-enriched tissues were then isolated using a glass slide to squeeze the seeds following Iwasaki & Lopez-Molina (2021) for sequencing.

first: Thiago

last: Barros-Galvão

first: Xiaochao

last: Chen


title: DROSHA and DICER RNA products control BMI1-dependent transcriptional repression at DNA damage sites

city: Pavia

first: Sofia

last: Francia

address: Via Abbiategrasso, 207

country: Italy

institute: Istituto di Genetica Molecolare - Consiglio Nazionale delle Ricerche (IGM-CNR)

summary: Genome integrity is safeguarded by the DNA damage response (DDR). Transcriptional modulation of genes around DNA double-strand breaks (DSBs) is important for DNA repair. It has been shown that DSBs repress transcription of DSB-bearing genes in an ATM- and PRC1-dependent manner. However, DSB also induce local de novo transcription of non-coding RNA, which are processed by DROSHA and DICER into small DNA-damage-response RNA (DDRNA). Here we reconcile these apparently contrasting observations by showing that DROSHA and DICER inactivation prevents transcriptional repression of DSB-bearing genes by reducing PRC1 recruitment to DSB and consequent H2A-K119 chromatin ubiquitination. Indeed, DDRNAs generated at DSB associate with the PRC1 component BMI1 and inhibition of DDRNA function with antisense oligonucleotides is sufficient to reduce damage-induce transcriptional silencing in cis genes (DISC). We propose that DROSHA, DICER and DDRNAs control DISC at genomic lesion sites by favoring PRC1-driven chromatin ubiquitination.

overall_design: RNA-seq,  1 cell line, 6 conditions (siCTL Induced, siCTL Uninduced, siATM Induced,  siATM Uninduced, siDIC-DRO Induced, siDIC-DRO Uninduced), 3 replicates per condition

first: Francesca

last: Esposito

first: Ilaria

last: Capozzo

first: Stefania

last: Modafferi

first: Letizia

last: Manfredi

first: Fabio

last: Iannelli

first: Ubaldo

last: Gioia

first: Alessia

last: di Lillo

first: Sara

last: Tavella

first: Matteo

last: Cabrini

first: Fabrizio

last: d?Adda di Fagagna


title: Emergence of Endothelial Cell Subtypes and Role of Cell Cycle Control in Arterial-Venous Specification During Embryonic Vascular Development [bulk RNA-seq]

city: Charlottesville

first: Jordon

last: Aragon

state: VA

department: Cell Biology

institute: University of Virginia

summary: During embryonic vascular development, endothelial cells that line all blood vessels undergo specification into arterial, capillary, and venous subtypes to form a circulatory network. Regulation of endothelial cell cycle state has been shown to play a critical role in enabling arterial-venous specification and remodeling in a postnatal, blood flow-mediated, and tissue specific manner; however, if a similar cell cycle-mediated mechanism is a common mechanism that regulates embryonic vascular development, even prior to blood flow, is unknown. To investigate this, we first defined the emergence of distinct subtypes by isolating endothelial cells from wild type embryos at embryonic day (E)8.0, prior to blood flow; E8.5, just after flow begins; and E9.5. We performed single cell RNA sequencing and analyses, and found increased specification of arterial, venous and hemogenic subtypes over time, concomitant with decreased primordial and capillary endothelial cells. Gene Ontology analysis revealed that cell cycle control was significantly enriched over time, and we found arterial identity highly correlated with growth arrest. To gain more insight into the potential role of cell cycle control in specification, we isolated similar endothelial cells from Fucci-expressing embryos, sorted them into distinct cell cycle states (early G1, late G1 and S/G2/M), performed bulk RNA sequencing, and bioinformatically correlated endothelial cell cycle states with subtype identities. We found venous endothelial cells are highly enriched in early G1 and arterial endothelial cells highly enriched in late G1, which was corroborated with fluorescent imaging of Fucci embryos. Furthermore, we showed that endothelial cell hyperproliferation, induced by deletion of cell cycle inhibitor Cdkn1b (p27), impaired arterial-venous specification and vascular development. These results support that at the earliest stage of vascular development, endothelial cells in arterial and venous vessels reside in different cell cycle states and endothelial cell cycle control is required for their specification.

overall_design: CD31+ CD45- murine embryonic endothelial cells sorted from Fucci E8.0 (pre-blood flow, E8.5, and E9.5 embyos in early G1, late G1, and S/G2/M.

first: Aragon

last: Jordon

first: Nelson

last: Elizabeth

first: Chavkin

last: Nicholas

first: Jackson

middle: G

last: Madeline

first: Heo

last: Won

first: Cain

middle: R

last: Shelby

first: Markowska

last: Zaneta

first: Bradecamp

last: Grace

first: Genet

last: Gael

first: Cwiek

last: Aleksandra

first: Hirschi

last: Karen


title: Biomimetic Design of Manganese-Doped Carbon Dot Nanozymes with Ultrahigh SOD-Like Activity for ALS Management

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

institute: Chinese Academy of Sciences

summary: Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease without cure. Mitochondrial dysfunction and reactive oxygen species (ROS)-induced oxidative stress are considered critical factors in ALS pathogenesis. Here, we design carbon dot superoxide dismutase (SOD) nanozymes with manganese doping (Mn@CDs) by screening for the optimal active site according to the special structures of natural SODs. Mn interacts with N and O in the CD scaffold, optimizing its structure, enhancing electron transfer and superoxide anion binding, and achieving superhigh specific activity of more than 7×104 U/mg. Theoretical calculations reveal the SOD-like activity of Mn@CDs from both kinetic and thermodynamic perspectives, identifying MnN₂O₂ (with amide-derived N) as the most likely active center. After being applied in ALS therapy, Mn@CDs which target and accumulate in mitochondria, effectively prevent oxidative stress and protect mitochondria from abnormalities in morphology, quantity, and function. Hence, administration of Mn@CDs prolonged survival by 14.5 days, with a 93% increase over the effect of edaravone. These results suggest that Mn@CD hold significant potential as a promising therapeutic candidate for ALS treatment.

overall_design:
In order to investigate the regulation of Mn@CDs in ALS ,  RNA-seq was performed on mouse spinal cord tissues to elucidate the therapeutic mechanism of Mn@CDs in ALS.
We collected four groups of RNA-seq data, abbreviated as H, C, E, and P.  P refers to data obtained from ALS model mice fed with PBS, which can be considered as the negative control group; H represents data from healthy WT mice; C corresponds to data from ALS model mice treated with the material we developed, which can be regarded as the experimental group; and D refers to data from ALS model mice treated with the representative ALS drug Edaravone. Each group of data includes three replicates, with the numbers following the abbreviated letters representing different biological duplication.

first: Yaxin

last: Hou


title: Emergence of Endothelial Cell Subtypes and Role of Cell Cycle Control in Arterial-Venous Specification During Embryonic Vascular Development [scRNA-seq]

overall_design: CD31+ CD45- murine embryonic endothelial cells sorted from C57Bl6J E8.0 (pre-blood flow, E8.5, and E9.5 embyos.

first: Elizabeth

last: Nelson

first: Nicholas

last: Chavkin

first: Madeline

last: Jackson

first: Won

last: Heo

first: Shelby

last: Cain

first: Zaneta

last: Markowska

first: Grace

last: Bradecamp

first: Gael

last: Genet


title: Key Regulatory Elements of the TGFβ-LRRC15 Axis Predict Disease Progression and Immunotherapy Resistance Across Cancer Types

first: Michael

last: Cheng

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: Transforming growth factor-beta (TGFβ) has dual roles in cancer, initially suppressing tumors but later promoting metastasis and immune evasion. Efforts to inhibit TGFβ have been largely unsuccessful due to significant toxicity and indiscriminate immunosuppression. Leucine-rich repeat-containing protein 15 (LRRC15) is a TGFβ-regulated antigen expressed by mesenchymal-derived cancer cells and cancer-associated fibroblasts (CAFs). In preclinical studies, ablation of TGFβ-driven LRRC15+ CAFs increased tumor infiltration of CD8+ T cells. However, the underlying pathobiological mechanisms prompting TGFβ’s upregulation of LRRC15 expression are unclear. Using an integrated approach combining functional compound screening with single-cell RNA sequencing, we reveal key genomic features regulating TGFβ’s ability to increase LRRC15 expression on cancer cells. Construction of gene regulatory networks converged our analyses on four key genes—MMP2, SPARC, TGFβR2, and WNT5B—central to TGFβ-induced LRRC15 pathobiology. Validation of these genes in cell models and their use in predicting immunotherapy responses highlight their potential in refining immunotherapy strategies and personalizing co-treatment options.

overall_design: 3 TGFβ-inducible cell lines (HUO9, RPMI7951, U118) and 3 TGFβ-noninducible cell lines (CALU1, KASUMI2, SAOS2), were FACS sorted for the top 1% of LRRC15+ cells by AlexaFluor647-DUNP19 staining. LRRC15+ and LRRC15- cells for each cell line were sequenced using scRNAseq, totaling to 12 sample.

first: Claire

last: Storey

first: Mohamed

last: Altai

first: Julie

last: Park

last: Tran

first: Smiths

middle: S

last: Lueong

first: Daniel

last: Thorek

first: Liqun

last: Mao

first: Wahed

last: Zedan

first: Constance

last: Yuen

first: Alexander

last: Ridley

first: Marija

last: Trajovic-Arsic

first: Ken

last: Herrmann

first: Sumit

last: Subuhdi

first: Bilal

last: Siddiqui

first: Katharina

last: Lückerath

first: Jens

last: Siveke

first: Robert

last: Damoiseaux

first: Xia

last: Yang

first: David

last: Ulmert


title: Single-cell Multiomics Analysis Reveals CTCF as a Key Regulator of Lung Morphogenesis and Progenitor Maintenance

city: shenzhen

first: Jiang

last: Yamei

address: longfei

institute: The Chinese University of Hong Kong-Shenzhen

summary: Lung development generates a complex tree-like architecture through proximal-distal patterning and branching morphogenesis. However, the gene regulatory programs governing embryonic lung development remain poorly understood. Here, we present a comprehensive single-cell multi-omics atlas of mouse embryonic lungs, integrating gene expression and chromatin accessibility profiles. Through systematic analysis, we identify 13 distinct cell types and map cis-regulatory elements, peak-to-gene linkages, and transcription factors underlying lung development. Leveraging this multi-modal dataset, we uncover lineage-determining transcription factors  driving cell differentiation, including the Activated Protein-1 complex. We further delineate gene regulatory networks involving diverse transcription regulators, including CCCTC-binding factor. Using the Ctcf conditional knockout mouse, coupled with histological and multi-omics analyses, we demonstrate that CCCTC-binding factor  orchestrates lung progenitor maintenance and branching morphogenesis by modulating both gene expression and chromatin accessibility. Thus, our study provides a multi-omics resource and mechanistic insights for transcriptional regulation of lung morphogenesis.

overall_design: To comprehensively study the heterogeneity and regulatory mechanisms of lung morphogenesis, we performed ATAC-seq profiling of nuclei extracted from embryonic day 12.5 (E12.5) lungs.

first: Shenfei

last: Sun

first: Yamei

last: Jiang

first: Fujing

last: Huang

first: Wei

last: Wei

first: Mathias

last: Hochgerner

first: Tianmin

last: Xu

first: Xiaoting

last: Wang

first: Kaijun

last: Lin

first: Xinna

last: Zhang

first: Yanli

first: Hua

last: He

first: Miao

last: Yu

first: Xiaofang

last: Tang

first: Xinhua


overall_design: To comprehensively study the heterogeneity and regulatory mechanisms of lung morphogenesis, we performed RNA-seq profiling of nuclei extracted from embryonic day 12.5 (E12.5) lungs.


title: USP2 is an androgen-repressed survival factor that stabilises oncoproteins to facilitate therapy resistance in prostate cancer

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: In prostate cancer, the development of resistance to androgen receptor (AR)-targeted therapies (ATTs) and chemotherapies is associated with the emergence of new phenotypic states with altered molecular features. Here, we identify ubiquitin-specific peptidase 2 (USP2) as a mediator of this phenomenon. USP2 is induced in response to ATTs and more highly expressed in aggressive, castration-resistant prostate tumours that have lost dependence on AR as an oncogenic driver. Over-expression of USP2 in prostate cancer cells elicited elevated rates of glycolysis, neuroendocrine features and resistance to docetaxel, a taxane chemotherapeutic that is a mainstay treatment for advanced prostate cancer. USP2 stabilises key oncoproteins including Aurora kinase A, cyclin D1 and fatty acid synthase. An unbiased proteomic approach identified potential new USP2 substrates and a USP2-regulated proteome that is associated with metastatic disease. Genetic or pharmacological targeting of USP2 caused cell death in human and mouse models of aggressive prostate cancer, and the USP2 inhibitor ML364 exhibited potent anti-tumour effects against an orthotopic xenograft model of AR-null disease. Collectively, this study identifies USP2 as a key regulator of proteins involved in prostate cancer progression and therapy resistance, positioning it as a viable therapeutic target.

overall_design: RNA-seq profiling of LNCaP cells over-expressing USP2 (LNCaP-USP2) and control (LNCaP-Control) cells


overall_design: To comprehensively study the heterogeneity and regulatory mechanisms of lung morphogenesis, we performed CUTnTag profiling of nuclei extracted from embryonic day 12.5 (E12.5) lungs.


title: Quantitative profiling of DNA 6mA at single-base resolution using NAME-seq

first: Tao

last: Wu

institute: Baylor College of Medicine

platform_organism:
Helicobacter pylori
Escherichia coli
Chlamydomonas reinhardtii
Homo sapiens

overall_design: Refer to individual Series


title: Adenosine to Inosine RNA editing level in ADAR1-deficient or hypoxia-exposed human pulmonary artery endothelial cells

city: Pittsburgh

first: Shu-Ting

last: Cho

state: PA

address: 450 Technology Drive

department: Computational and Systems Biology

institute: University of Pittsburgh

summary: Hypoxia is a PH trigger which significantly downregulates ADAR1 and reduces A-to-(I)G editing in human PAECs. By RNA sequencing of PAECs after ADAR1 knockdown, we have identified the circadian gene Nocturnin (NOCT) as a direct ADAR1 target. NOCT carries two active A-to-I RNA editing sites in the 3’UTR. In addition, hypoxia significantly reduced A-to-G editing in human PAECs

overall_design:
To identify the genes regulated by ADAR1-induced RNA editing, RNA sequencing (RNA-seq) analysis was conducted in PAECs after ADAR1 knockdown.
To investigate the effect of hypoxia on ADAR1-mediated RNA editing in hPAECs, we treated human PAEC with 48 hr hypoxia (1% oxygen) explosure. RNA sequence was perfermed and the overall A-to-I(G) RNA editing level was analyzed.

first: Chen-Shan

last: Woodcock

first: Stephen

last: Chan


title: Adenosine to Inosine RNA editing level in mouse lungs from Adar1 K999N mutants or hypoxia-exposed mice

summary: Hypoxia is a PH trigger which significantly downregulates ADAR1 and reduces A-to-(I)G editing in mouse lungs. Mice have Adar1 misssense mutation K999N were used to determine specific ADAR1-specific RNA editing sites in lungs. We performed RNA sequencing on the lung tissues isolated from mice carrying Adar1 K999N mutations and exposed to 3 week hypoxia.

overall_design: To investigate the effect of hypoxia on ADAR1-mediated RNA editing in mouse lungs, we treated wildtype or Adar1 K999N mice with hypoxia (10% oxygen) exposure for 3 weeks. RNA sequencing was performed and the overall A-to-I(G) RNA editing level was analyzed.


title: G3BP1::CSF1R: a new and actionable gene fusion in acute megakaryoblastic leukemia

city: Hong Kong

first: Margaret

middle: H. L.

last: Ng

address: Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, NT

department: Anatomical and Cellular Pathology

institute: The Chinese University of Hong Kong

summary: Here we report a novel targetable G3BP1::CSF1R fusion in acute megakaryoblastic leukemia. The fusion promotes cytokine-independent growth, leukemic engraftment and megakaryocytic commitment by repressing Kruppel-like factor 1. Disruption of juxta-membrane domain aggravates CSF1R kinase activity and dictates the leukemia phenotype.

overall_design: To explore the mechanisms underlying GC-driven megakaryocytic commitment, RNA-seq was performed in M07E and TF1 cells transduced with EV, GC or GC543 lentivirus for 72 hours, with biological duplicates for each condition.

first: Xi

last: Luo


title: Tel1 is recruited at chromosomal loop/axis contact sites to modulate meiotic DNA double-strand breaks interference

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

institute: CRCM

summary: During meiosis, the programmed formation of DNA double-strand breaks (DSBs) by Spo11, a conserved topoisomerase-like protein, initiates homologous recombination that leads to crossovers between homologous chromosomes, essential for accurate segregation and genome evolution. Because DSBs are a threat to genome integrity, their number, distribution and timing of formation are regulated during the meiotic program. In S. cerevisiae, DSB interference prevents the coincident formation of DSBs in neighboring hotspots through a Tel1/ATM dependent mechanism that remains unexplored. Here, we demonstrate that Tel1 is recruited to meiotic DSB hotspots in response to Spo11-DSB formation. We further show that Tel1 localizes to chromosomal axis sites in a DSB-dependent manner, thus supporting the tethered loop-axis complex (TLAC) model that postulates meiotic DSBs are formed within the chromosome axis environment. Tel1 recruitment to meiotic DSBs, DSB interference and the meiotic DNA damage checkpoint are dependent on both the Tel1-FATC domain and the C-terminal moiety of Xrs2, known to mediate Tel1-Xrs2 interaction in somatic cells. However, in a xrs2-K846/F847 mutant, DSBs interference remains functional despite Tel1 binding to DSB sites being significantly reduced and the Tel1-dependent DNA damage checkpoint abolished. Altogether, this work highlights the complex regulation of Tel1 multiple various functions in meiotic cells, and fine-tuning through interaction with Xrs2.

overall_design: Chromatin immunoprecipitation (ChIP) For each meiotic time point, 2 x 108 cells were fixed in paraformaldehyde (1% final). FLAG-Tel1 cells were fixed for 30min, while FLAG-Spo11 strain were fixed for 15min, quenched by glycine for 5min (125mM final) and washed in TBS 1X two times. Cells were lysed using mechanical lysis (Fastprep, 4 cycles at 6.5M/sec 30sec) together with a Lysis buffer (50mM HEPES-KOH, 140mM NaCl, 1mM EDTA pH8, 1% Triton X100, 0.1% Sodium Deoxycholate) complemented with protease inhibitor cocktail tablet (Roche, Ref 05 892 791 001), PMSF (1mM final), pepstatin (0.1mM final) and leupeptin (1mM final). After cell lysis, chromatin was sheared by sonication into 500 – 1000pb fragment (30sec ON/30sec OFF, 6 cycles, 4°C, Diagenode Bioruptor Pico). 10µl was kept aside as the input, and samples were divided in two halves, for minus and plus antibody treatment. FLAG-Tel1 immunoprecipitation was performed with 2µl of anti-FLAG antibody (M2 monoclonal, Sigma, Ref F1804) and incubation at 4°C for 2 hours. Pan-IgG mouse magnetic beads were incorporated for 2 more hours at 4°C. IP samples were washed by a 500mM NaCl containing lysis buffer and LiCl buffer (10mM Tris-HCl pH8, 0.25LiCl, 1mM EDTA pH8, 0.5% Triton X-100, 0.5% Sodium Deoxycholate). Chromatin was eluted from magnetic beads in elution buffer (TE 1X, 0.5% SDS) at 65°C for 10min. DNA-protein interaction was disrupted by incubation at 65°C overnight for IP and input samples. RNA was digested by RNAse A treatment (20µg total, 15min at 37°C) and proteins by proteinase K treatment (100µg total, 1hour at 42°C). DNA was purified on column (Qiagen DNA purification kit).  ChIP-seq Tel1 and Spo11 ChIP-seq were performed following the ChIP-qPCR protocol with some modifications. For both FLAG-Tel1 and FLAG-Spo11 strain, cells were fixed in paraformaldehyde for 30min. Protein G magnetic beads were washed (0.1M NaHPO4 pH7.5, 0.01%Tween20, pH8.2) and saturated with BSA (0.1M NaP, 0.01% Tween20, 5mg/ml BSA) for 3hours at 4°C. Anti-FLAG antibody (M2 Monoclonal, Sigma) was pre-incubated with saturated-magnetic beads for 4hours at 4°C. Cell lysis was performed as for the ChIP-qPCR protocol. Chromatin shearing was performed in Diagenode tube 15ml with beads (900 – 1000mg) by 7 cycles of sonication (30sec ON/30sec OFF, 4°C). Chromatin was immunoprecipitated with antibody-protein G mix by overnight incubation at 4°C. Samples were washed as for the ChIP-seq protocol, and DNA was eluted with IPure v2 Diagenode kit. DNA quantity was measured by QuBit and fragmentation quality was controlled by Agilent chip (Bio-analyser). DNA was sequenced with a NovaSeq sequencer (Illumina) using a 100nt paired-end protocol (TruSeq) at the Institut Curie sequencing facility (Paris, France).

first: Valérie

last: Garcia

first: Pierre

last: Luciano

first: Marie

last: Dorme

last: Borde

first: Julien

last: Vernerey


title: Effect of Alpelisib treatment and MAEA knockout on gene expression of the EBV+ gastric cancer cell line YCCEL1

city: Boston

first: Yin

last: Wang

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

summary: EBV+ gastric cancer cell line was reported with PI3K pathway activated. Alpelisib is the PIK3CA specific inhibitor. To study the MAEA knockout and alpelisib treatment, RNAseq was conducted to study the gene expression changes in YCCEL1.

overall_design: YCCEL1 cells expressing MAEA or control sgRNAs were treated with 0.5 uM alpelisib or DMSO for 30 hours.

first: Rui

last: Guo

first: Benjamin

last: Gewurz


title: A conserved mechanism of selective mRNA erasure prevents generation antagonism during the sporophyte to gametophyte transition in higher plants Data availability

city: Wuhan

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

summary: The goal of present study is to compare differentially expressed genes between wild type and sgd mutant ovules.

overall_design: About 6000 sgd mutant and wild type ovules at FG1 to FG3 were isolated and collected for RNA sequencing.

first: Xuemei

last: Zhou

first: Bo

last: Wen

first: Meng-xiang

last: Sun


title: Effect of Alpelisib treatment and PIK3CA knockout on gene expression of the EBV+ gastric cancer cell line YCCEL1

summary: EBV+ gastric cancer cell line was reported with PI3K pathway activated. Alpelisib is the PIK3CA specific inhibitor. To compare the drug treatment against the gene knockout, RNAseq was conducted to study the gene expression changes in YCCEL1.

overall_design: Two conditions were included for RNAseq analysis: (1) YCCEL1 treated with 5 uM alpelisib for 6 hours or DMSO, and (2) YCCEL1 cells expressing PIK3CA or control sgRNAs.


title: A Large-Scale Human Toxicogenomics Resource for Drug-Induced Liver Injury Prediction

status: Public on Oct 07 2025

city: Somerville

first: Volker

last: Bergen

address: 101 South St

institute: Cellarity

summary: Drug-Induced Liver Injury (DILI) remains one of the most critical challenges in drug development, causing patient safety concerns, clinical trial failures and drug withdrawals. We introduce ToxPredictor, a toxicogenomics framework combining RNA-seq data from primary human hepatocytes with pharmacokinetic data to predict dose-resolved DILI risks and safety margins. At its core is DILImap, an RNA-seq library tailored for DILI research, comprising 300 compounds at multiple concentrations. ToxPredictor achieves 88% sensitivity at 100% specificity in blind validation, outperforming state-of-the-art methods. It flagged recent phase III clinical failures, including Evobrutinib, TAK-875, and BMS-986142, overlooked by animal studies. Beyond prediction, ToxPredictor provides mechanistic insights into hepatotoxic pathways, enabling early de-risking and actionable safety decisions. Unlike single-endpoint readouts—even from 3D models—transcriptomics offers a multi-dimensional system-level view of hepatocyte responses, capable of detecting diverse DILI mechanisms not captured by conventional assays. Scalable, actionable, and integrated into a broader AI/ML drug discovery platform, this work establishes toxicogenomics as a transformative tool for developing safer therapeutics and addressing one of the most pressing challenges in toxicology.

overall_design:
RNA-seq profiling of 300 DILI positive and negative drug perturbations profiles at multiple concentrations in primary human hepatocytes. The cell metadata (.obs in the h5ad) include all experimental and treatment details.

***Submitters state that the raw data contain proprietary information and are therefore not publicly available, as agreed with the Nature Communications editor.  Academic researchers may request access for internal, non-commercial use***

***************************************************************
Raw files were not submitted to GEO due to concerns about submitting proprietary information for open access.
***************************************************************

first: Konstantia

last: Kodella

first: Sreenath

last: Srikrishnan

first: Ornella

last: Barrandon

first: Sara

last: Anderson

first: Max

last: Rogers-Grazado

first: Casey

last: Fowler

first: Hirit

last: Beyene

first: Nicole

last: Robichaud

first: Timothy

last: Fulton

first: Nina

last: Lapchyk

first: Mauricio

last: Cortes

first: Nick

last: Plugis

first: Matthew

last: Goddeeris

first: Mahdi

last: Zamanighomi


title: NaBH4-sequencing of LX-2 cells

first: An

last: Zhang

address: Aerodrome Road 13

institute: Huazhong University of Science and Technology

summary: Liver fibrosis is characterized by deposition of excessive extracellular matrix (ECM). The major source of ECM is activated hepatic stellate cells (HSCs).NAT10 is the only known acetyltransferase catalyzing ac4C RNA modification. The purpose of this RedaC:T-seq is to explore the role of NAT10 acting as ac4C acetyltransferase during HSC activation.

overall_design: The changes of ac4C modification in LX-2 cells after TGF-β1 stimulatation were investigated by NaBH4 sequencing.

first: Chunwei

last: Shi


title: Sex Differences in WAT Thermogenesis of NCOA1 Knockout Mice

city: Nice

first: Jean-Francois

last: Louet

address: C3M 151 route Saint Antoine de Ginestière 151 route Saint Antoine de Ginestière

institute: INSERM

summary: To elucidate the sex-specific role of the transcriptional coregulator NCOA1 on thermogenic adipocytes in subcutaneous white adipose tissue (SAT), we performed RNA-seq analysis on  male and female NCOA1 knockout mice after ß3-receptor agonist stimulation(CL316,243)

overall_design: RNA-seq profiling of female and male SAT after administration of CL316,243 (0.5 mg/kg body weight) during seven days

first: Jean-François

first: Mounia

last: Tannour-louet


title: Effect of butyrate stimulation on CD19 CAR-T cells for the treatment of Non-Hodgkin Lymphoma

city: Madrid

first: Roberto

last: Garcia-Vicente

address: Avd Cordoba s/n

department: Translational Hematology

institute: Instituto de Investigacion Hospital 12 de Octubre

summary: Gut microbiota plays a pivotal role in the development and function of the immune system, therefore it has been described as an important factor for the efficacy and safety of immunotherapy, including CAR-T. The mechanisms by which this occurs are not well understood. Short Chain Fatty Acids (SCFAs) are metabolites derived from the microbial fermentation that are involved in the regulation of metabolic, endocrine and immune function. In this study we analyze the transcriptomic changes that SCFA butyrate generates in CAR-T cells.

overall_design: T cells were isolated from peripheral blood of four healthy donors and activated on anti-CD3/28-coated plates. After that, they were transduced with a CD19CAR lentiviral vector and separated into two conditions. One was exposed to SCFA butyrate and the other to the control medium. Comparative gene expression profiling analysis of RNA-seq data for both conditions was performed

first: Andrés

last: Arroyo-Barea

first: Joaquín

last: Martínez-López

first: María

last: Linares


title: Placental transcriptome profiles in late-onset preeclampsia: a cross-sectional observational analysis stratified by fetal sex

first: Claire

middle: Trelford

last: Roberts

state: South Australia

address: HMRB Building, Loading Bay via Sports Road

summary: Background Preeclampsia is a hypertensive disorder of pregnancy with significant maternal and fetal health implications. While the molecular mechanisms underlying early-onset preeclampsia have been studied extensively, less is known about late-onset preeclampsia, particularly with regard to fetal sex-specific effects. Understanding transcriptional changes in the placenta may provide insight into persistent mechanisms or downstream consequences of the disease, thereby contributing to our understanding of its pathophysiology. While the initiating events of late-onset preeclampsia occur earlier in gestation, analysis of term placental tissue can reveal cumulative effects of disease processes and identify biological pathways that remain altered at delivery. Methods We conducted a cross-sectional observational analysis of placental gene expression using RNA sequencing in a subset of 58 term placentas (21 male-bearing and 37 female-bearing pregnancies) drawn from two large prospective birth cohorts. Pregnancies were classified based on clinical diagnosis of late-onset preeclampsia (diagnosed ≥20 weeks’ gestation according to ISSHP criteria) or uncomplicated and assessed for differential gene expression. Cell type proportions were estimated using CIBERSORTx from a placenta-specific reference single-cell dataset. Weighted gene co-expression network analysis identified modules of co-expressed genes associated with late-onset preeclampsia and fetal sex. Results Differential gene expression analysis identified 150 genes with altered expression in male-bearing placentas from pregnancies with late-onset preeclampsia compared to those from uncomplicated pregnancies. No differentially expressed genes were identified in female-bearing placentas. Cell type deconvolution revealed increased abundance of CD14+ monocytes and CD8+ activated T cells (log odds of 1.42 and 1.44 respectively) and reduced fetal GZMK natural killer cells (log odds of 0.60) in male-bearing placentas from affected pregnancies. In female-bearing placentas, late-onset preeclampsia was associated with increased fetal nucleated red blood cells and maternal plasma cells (log odds of 1.33 and 1.40 respectively). Male-specific co-expression analysis identified gene modules enriched for biological processes including RNA processing, immune regulation, and metabolism. Conclusions Placental transcription and cellular responses to late-onset preeclampsia differ by fetal sex. Evidence of altered immune cell composition and gene co-expression in male-bearing placentas suggests a sex-specific vulnerability. These findings highlight the importance of considering fetal sex in molecular investigation and clinical management of preeclampsia.

overall_design: RNA-seq profiling of placental chorionic villous tissue from male- and female-bearing pregnancies complicated by late-onset preeclampsia or uncomplicated outcomes at term.

first: Melanie

last: Smith

first: Seema

last: Plaisier

first: James

last: Breen

first: Konstantinos

last: Bogias

first: Tanja

last: Jankovic-Karasoulos

first: Dylan

last: McCullough

first: Dale

last: McAninch

first: Anya

middle: L

last: Arthurs

first: Melissa

last: Wilson

first: Katherine

last: Pillman

middle: T


title: RNAseq data LUN 156 parental, adagrasib resistant and RMC-4998 resistant LUN156 tumors

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: LUN156 is a patient-derived xenograft (PDX) tumor model derived from 73-year-old male Chinese non-small cell lung cancer (NSCLC) patient with a tumor with a KRASG12C mutation.

overall_design:
PDX model development: To generate an animal tumor model, fresh tumor fragments were obtained from hospitals with informed consents from the patients in accordance with protocols approved by the Hospital Institutional Ethical Committee (IEC). The tumors were cut into 30 to 60 mm3 fragments after arrival at CRO animal facility and serially passaged after implanting subcutaneously into BALB/c nude mice.
Briefly, five to six-weeks-old female Balb/c nude mice were purchased from Vital River Lab Animal Technology Co. Ltd., Beijing, China. Animals were held for a minimum of 7 days for acclimation prior to the beginning of study. Animals were housed in individually ventilated cages (IVC) under specific pathogen free (SPF) conditions with access to standard diet and water ad libitum. During the study period, the animals were monitored daily for any effects of tumor growth and treatments on normal behavior, such as mobility, food, and water consumption. Study-related parameters like body weight and tumor volume (tumor volume = ((width)2 × length)/2, where width and length are measured in mm) were measured twice weekly.
Recovered tumor fragments of about 15-30 mm3 in volume were implanted subcutaneously into right flanks of Balb/c female nude mice and mice were randomized by blocks when average tumor sizes reached ~200 mm3 in volume into three treatment groups with three mice in each group. The animals were administered vehicle for RMC-4998 formulation as a control, RMC-4998 100 mg/kg, and adagrasib 100 mg/kg as a daily treatment through oral gavage for 28 days, and end of study tumor samples were collected. In an independent study, to derive a stable adagrasib or RMC-4998 resistant (adagrasib-R or RMC-4998-R) LUN156 PDX tumor model, animals were treated with 100 mg/kg of each inhibitor for 90 days to determine on-treatment tumor relapse. After treatment period, the mouse showing on-treatment tumor relapse was collected (Passage 0 (P0)). The 30-50 mm3 volume tumor fragments from P0 were further subcutaneously implanted into the right flanks of female Balb/c nude mice and allowed to grow. Once the tumor became palpable (70-100 mm3), respective KRASG12C inhibitor treatments were provided daily and observed for tumor growth until the tumor reached an average of 1,000 mm3 in volume (P1). The animal from each inhibitor resistant cohort showing the least doubling time for a tumor to grow was selected and passaged further to generate P2. The in vivo serial passage procedure with respective KRASG12C inhibitor was repeated until P5 to ensure resistant phenotype in LUN156 tumor model, and samples were frozen for efficacy and single dose pharmacodynamic use. During these passages, snap frozen tumor fragments were collected for resistance mechanism analyses

first: Ida

last: Aronchik

first: Eric

middle: B

last: Haura

first: Ethan

last: Ahler

first: Jiqiang

last: Yao

first: Hitendra

last: Solanki


title: Analysis of transcriptomic alterations in HYDIN2 knockdown as compared to empty vector control in NT2 cells

city: Pune

first: Yash

middle: Lahu

last: Kuber

state: Maharashtra

address: Nccs, inside pune university, ganeshkhind

department: Biotechnology

country: India

institute: National center for cell science

summary: Transcriptomic analysis was performed to identify differentially expressed genes under HYDIN2 knockdown conditions compared to an empty vector control. Pathway enrichment analysis revealed a significant upregulation of neuronal-related pathways and a downregulation of those involved in fundamental cellular processes. Collectively, these findings suggest a potential role for HYDIN2 in modulating neuronal function and cellular dynamics.

overall_design: RNA-seq profiling of HYDIN2 knockdown cells and its empty vector control in NT2 cells.

first: Sharmila

middle: A

last: Bapat

first: Amruta

last: jadhav

first: Sushmita

last: sahoo

first: Khushi

last: tanwar

first: Shubhankar

last: palwankar

first: Avinash

last: mali


title: Leveraging Medulloblastoma Clonal Dynamics to Overcome Treatment Resistance

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

summary: Medulloblastoma (MB) is a common pediatric brain tumor with distinct molecular subgroups, of which, Group 3 MB is associated with increased recurrence, metastatic potential and poor patient outcomes. Small molecule inhibitors targeting BMI1 have been shown to be efficacious against several types of malignant tumors, including pediatric MB. While our previously published in vivo study provides a promising proof-of-concept for the therapeutic targeting of BMI1 in Group 3 MB with small molecule inhibitor, it is not sufficient to eradicate the tumour.

overall_design:
In this study, following preclinical validation of BMI1 inhibitor PTC596, DNA barcoding technology was leveraged to profile in vivo clonal dynamics of Group 3 MB in response to the established chemoradiotherapy regimen alone and in combination with PTC596. Following demonstration of a small number of treatment-refractory clones we sought to identify potential druggable molecular vulnerabilities by utilizing phosphoproteomic profiling and genome-wide CRISPR screening.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: David

last: Bakhshinyan

first: Laura

last: Escudero

first: Kevin

last: Brown

first: Jason

last: Moffat


title: DNA-Diffusion  STARR-Seq Validation

first: Gue-ho

last: Hwang

address: 300 Longwood Ave

institute: Boston Children's hospital

summary: To test how DNA-Diffusion sequences can induce transcription, we select 2150 sequences, including DNA-Diffusion synthetic and natural occurring DHS sites for each cell type (K562, HepG2, and GM12878) and insert them into STARR-Seq plasmids  (N= 6450 sequences). all synthetic and naturally occurring sequences were combined  into a single library, and this same library was experimentally tested using STARR-Seq in different cell lines (K562, HepG2, GM12878).

overall_design: A STARR-Seq plasmid library containing 6,000 enhancer candidates was synthesized and constructed following methods described previously (Neumayr et al., Gordon et al.). Each candidate was uniquely barcoded with five random nucleotides during synthesis, PCR amplified using specific primers (forward: TAGAGCATGCACCGG, reverse: TCGACGAATTCGGCC), and cloned into the STARR-Seq plasmid vector (hSTARR-seq_ORI, Addgene #99296) via NEBuilder HiFi assembly. Recombinant plasmids were electroporated into NEB® 10-beta electrocompetent E. coli and amplified plasmid libraries were purified using PureLink HiPure plasmid midiprep kits. Library complexity was assessed by sequencing PCR-amplified inserts prepared with NEBNext Ultra II DNA kits. Subsequently, plasmids of sufficient complexity were electroporated into three cell lines (K562, HepG2, GM12878), and post-transfection RNA and DNA were isolated after 6 hours. Following DNase treatment and reverse transcription of isolated RNA, both RNA-derived cDNA and genomic DNA underwent targeted amplification with specific primer pairs and were sequenced using Illumina-compatible NEBNext library preparations. Counts of enhancer sequences were quantified using Kallisto, aligning reads to a constructed index with k-mer size 23, filtering for the presence of specific homology arms. The final enhancer activity (mRNA/DNA ratio) was computed with the R "mpra" package (version 1.14.0), employing voom normalization and limma analysis to generate log2 fold changes (log2FC) and associated error ranges across all cell line replicates, considering only sequences with non-zero DNA counts.

first: Lithin

middle: K

last: Louis

first: DaSilva

last: Ferreira

first: Senan

last: Simon

first: Hwang

last: Gue-Ho

first: Emily

last: Wong

first: Pinello

last: Luca


title: Tumor-Initiating Stem Cells Fine-tune the Cell States of Neutrophils to Drive Cancer Relapse from Immunotherapy [SCC bulk RNA-Seq]

city: Chicago

first: weijie

last: guo

state: IL

address: 929 East 57th Street, GCIS W423N

institute: university of Chicago

summary: The highly heterogeneous and plastic nature of tumor-associated neutrophils (TANs) has been recognized, but how different cell states of TANs emerge, evolve, distribute, and impact cancer immunotherapy efficacy remains elusive. Using single-cell RNA sequencing, spatial transcriptomic analysis, and genetic manipulations, we show that, while anti-PDL1/CD40 agonist immunotherapy can reprogram TANs to gain strong anti-tumor activities in squamous cell carcinomas (SCCs), a subset of neutrophils residing at the tumor-stroma interface can preserve their immune-suppressive state. Importantly, we identified a group of Sox2Hi tumor-initiating stem cells (tSCs) at the tumor-stroma interface that can activate Fatty Acid Desaturase 1 (Fads1) and produce arachidonic acid (AA) to induce autocrine prostaglandin E2 signaling which can disrupt the interferon responses in neutrophils. Thus, through this interaction, tSCs fine-tunes the cell states of neutrophils, shapes neutrophil heterogeneity, and sculpts a protective micro-niche to drive cancer relapse following immunotherapy.

overall_design: To investigate the mechanisms by which tSCs modulate neutrophils, we isolated Itga6hi CD80+ tumor stem-like cells and Itga6low CD80⁻ differentiated cancer cells from DMBA/TPA-induced skin squamous cell carcinoma (SCC), and performed bulk RNA sequencing on these populations.

first: Weijie

last: Guo

first: Yuxuan

last: Miao


title: Overexpression of Meis factors in late-stage retinal progenitors yields complex effects on temporal patterning and neurogenesis.

city: Baltimore

first: Patrick

last: Leavey

state: Maryland

address: 733 N Broadway, 332

department: Neuroscience

institute: Johns Hopkins School of Medicine

summary: The vertebrate retina serves as a model for studying neurogenesis and cell fate specification, with retinal progenitor cells following a tightly regulated temporal sequence to generate distinct cell types. Meis1 and Meis2 are transcription factors implicated in early retinal development, but their role in late-stage RPCs remains poorly understood. Here, we investigate whether Meis1 and Meis2 overexpression in postnatal mouse RPCs can alter temporal identity and induce early-born cell types. Using electroporation and single-cell RNA sequencing, we find that while these factors modestly upregulate early-stage gene regulatory network components, they do not repress late-stage transcription factors or induce early-born retinal cells. Meis1 overexpression reduces proliferation and inhibits neurogenesis, whereas Meis2 overexpression  accelerates neurogenic progression without altering fate commitment. Our findings suggest that overexpression of Meis1 and Meis2 modulate largely non-overlapping aspects of temporal identity and neurogenic competence but are insufficient to fully reprogram late-stage progenitors. These results have implications for regenerative strategies aimed at reprogramming retinal cells for therapeutic purposes.

overall_design: Wildtype CD1 murine retinal explants were treated with a pCAGIG- empty control, a pCAGIG-NR2F1, a pCAGIG-NR2F2, or a 50:50 combination of pCAGIG-NR2F1 and pCAGIG-NR2F2 for 2 or 5 days prior to collection and library generation. Retinal explants were lysed into a single cell suspension, GFP+ cells were isolated and run on the 10x Genomics Chromium Single Cell System platform using the Single Cell 3’Reagents Kit v3.1. Libraries were sequenced on Illumina NovaSeq 6000 and processed through the Cell Ranger pipeline using a modified MM10 reference genome with an added loci for GFP transcripts.

first: Clayton

middle: P

last: Santiago

first: Nicole

last: Pannullo

first: Lizhi

last: Jiang

first: Seth

last: Blackshaw


title: Comparison of the ApoE allelic variants in the formation of intracerebral and vascular Aβ deposits.

city: Atlanta

first: Karen

middle: N

last: McFarland

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

summary: Using different experimental models, we investigated how APOE isoforms impact Alzheimer-type amyloidosis and associated neuropathological features.

overall_design: Bigenic knock-in lines of mice were generated by breeding SAA-APP mice (RRID:IMSR_JAX:034711) to APOEtr mice generating a model of Abeta with the murine Apoe gene or homozygous for human APOE2, APOE3 or APOE4 alleles. RNA was extracted from the forebrains of mApoe, APOE2, APOE3 and APOE4 mice. RNA profiling was done using the NanoString nCounter Mouse Neuropathology panel.

first: McFarland

last: Karen N

first: Chakrabarty

last: Paramita

first: Quan

last: Vo


title: Fibroblast STAT3 activation drives organ-specific premetastatic niche formation

city: Ann Arbor

last: Lasse-Opsahl

state: Michigan

address: 1500 E Medical Center Dr Rm 6110

department: Cancer Biology

institute: University of Michigan

summary: Pancreatic cancer is associated with a high rate of metastasis and poor prognosis. The formation of a premetastatic niche (PMN) facilitates cancer cell spread and contributes to cancer mortality. Using murine pancreatic cancer models based on expression of oncogenic KRAS in the pancreas epithelium, we discovered that remodeling of the lung microenvironment occurred in mice bearing pancreatic precursor lesions prior to cancer formation. This early lesion premetastatic niche (EL-PMN) resembled the PMN in cancer-bearing mice, and both feature characteristics of overt metastasis, such as transcriptional reprogramming, activation of fibroblast STAT3 signaling, and infiltration of immunosuppressive ARG1+ macrophages. Both pancreatic cancer patients and mouse models demonstrated elevated serum IL6. Inactivating oncogenic KRAS reduced serum IL6 and reverted fibroblast STAT3 phosphorylation in mouse lungs; loss of lung fibroblast STAT3 phosphorylation was similarly observed when mice were treated with the pan-RAS inhibitor RMC7977. While ARG1+ macrophage infiltration was dispensable for fibroblast STAT3 activation, IL6 blockade inhibited lung fibroblast STAT3 activation. Functionally, fibroblast STAT3 activation was necessary for lung metastasis establishment and growth. Interestingly, activation of STAT3 in the PMN was present in the lungs but not in the liver, where fibroblast reprogramming occurred only in overt metastasis, pointing to organ-specific PMN formation. In human metastasis samples, phosphorylated STAT3 in fibroblasts was similarly more abundant in the lungs than liver. Together, these data point to organ-specific mechanisms driving formation of the PMN and indicate that reprogramming of the microenvironment prior to metastasis might support early dissemination of pancreatic cancer.

overall_design: We harvest the right lung and pancreas from iKRAS mice on doxycycline for 16 weeks at which point they have precursor lesions in the pancreas, but no tumor. We also harvested the right lung and bone marrow from iKRAS;p53 mice on doxycycline for 20 weeks a which point all mice had primary pancreatic cancer. Mice were split into groups based on the prescence or absence of lung metastases. Additionally, we harvested the right lung from KC or KPC mice with pancreatic tumors. All samples were taken for single cell RNA sequencing - Samples were run using 50-cycle paired-end reads on the Illumina NovaSeq 6000 to a depth of 100,000 reads with an intital expected cell count of 10,000 cells per sample.

last: Lasse Opsahl

first: Marina

last: Pasca di Magliano


title: Procollagen C-propeptide Processing Impacts Bone Matrix

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Classical Osteogenesis imperfecta (OI), characterized by short stature, fragile bones and low bone mass, is predominantly caused by genetic defects in the structure or synthesis of type I collagen.   Unexpectedly, there is a rare high bone mass form of OI (HBM OI) with extremely high bone mineralization by quantitative backscattered electron imaging (qBEI) and a moderately severe skeletal phenotype. HBM OI is caused by dominant missense mutations at residues comprising the type I procollagen C-propeptide cleavage site, preventing processing of the C-propeptide.  To elucidate the role of C-propeptide processing in bone mineralization and development, we generated heterozygous HBM OI mice, with substitutions in the Col1a1 C-propeptide cleavage site.  Femoral extracts from HBM OI mice contain increased monomeric proα1(I) C-propeptide and pC-collagen, resulting in a “barbed-wire” appearance to bone collagen fibrils.  The decrease in type I procollagen cleavage has a profound impact on bone, leading to diminished bone strength and integrity despite normal collagen helical primary sequence. HBM OI femora have thin cortices with decreased BV/TV leading to decreased stiffness, yield and fracture load, which does not improve with age. Their femora are also extremely brittle, with increased mineral content and HP crosslinks.  Similar to the high to normal DXA bone density of HBM OI patients, µCT bone density is normal in femora.  However, murine HBM OI cortical bone is hypermineralized in excess of other OI mouse models, with thinner, more disorganized mineral particles.  Increased expression of ossification genes is detected in both murine and human HBM OI osteoblasts, with enhanced mineral deposition in culture.  There is decreased expression of genes involved with extracellular matrix organization, correlating with changes in actin and vinculin staining when osteoblasts are grown on mutant matrix. Murine HBM OI bone mineralization is increased throughout life and increases with age, raising concerns for long-term management of HBM OI patients.

overall_design: Bulk RNA-seq on cultured osteoblasts from WT and high bone mass (HBM) mice over multiple time points.

first: Aileen

middle: M

last: Barnes

first: Joan

last: Marini


title: Loss of NF2 drives malignant transformation of human pancreatic acinar cells and enhances cell fitness under nutrient deprivation and therapeutical stress [single_cell_RNAseq]

city: San Antonio

first: Pei

last: Wang

address: 7703 Floyd Curl Dr

institute: UT Health San Antonio

summary: Pancreatic ductal adenocarcinoma (PDAC) occurs as a complex, multifaceted event driven by the interplay of tumor permissive genetic mutations, nature of cellular origin and microenvironmental stress. In this study, we present a novel model to screen previously underappreciated tumor suppressor genes in human pancreatic acinar-derived PDAC and probe their implications under nutrient deprived environmental context. Primary human pancreatic acinar 3D organoids were engineered to harbor triple PDAC driver mutations—KRAS G12V, TP53 inactivation, and CDKN2A deletion (designated as KPT organoids). Using a pooled CRISPR knockout library targeting 199 potential tumor suppressors curated from recurrent mutations in clinical PDAC samples, we performed in vivo and in vitro screening with KPT cells and revealed significant enrichment of a list of candidate tumor suppressors, with NF2 emerging as the top target. Functional validation confirmed that loss of NF2 promotes the transition of PDAC from a non-invasive to an invasive state, potentially through extracellular matrix (ECM) modulation. Additionally, we found that the fibroblast heterogeneity in these organoids-derived tumors correlates with the cancer progression, suggesting the important roles of cancer-stroma communications in tumor evolution. Strikingly, NF2 inactivation was found to enhance PDAC cell fitness under nutrient starvation, a condition reflective of the harsh tumor microenvironment. This adaptation not only reinforces the oncogenic state but also confers therapeutical resistance. These findings establish NF2 as a critical tumor suppressor in PDAC and uncover its role in mediating nutrient adaptation and drug resistance. Importantly, this study provides new insights into drug resistance mechanisms and potential therapeutic targets in PDAC.

overall_design: In order to investigate the gene expression changes induced by NF2 knockout, single cell RNA seq was performed using wild type, KPT and KPTN organoid samples, as well as KPT-derived and KPTN-derived xenograft tumor samples.

first: Yi

last: Xu

first: Michael

last: Nipper

first: Angel

last: Dominguez

first: Chenhui

last: He

first: Francis

last: Sharkey

first: Sajid

last: Khan

first: Daohong

last: Zhou

first: Lei

last: Zheng

first: Yu

last: Luan

first: Jun

last: Liu


title: Loss of NF2 drives malignant transformation of human pancreatic acinar cells and enhances cell fitness under nutrient deprivation and therapeutical stress [bulk_RNAseq]

overall_design: In order to investigate the gene expression changes induced by NF2 knockout, bulk RNA seq was performed using 6 independent KPT organoid samples, 6  KPTN organoid samples, 3  KPT-derived xenograft tumor samples and 3  KPTN-derived xenograft tumor samples,


title: A Dock8-dependent mechanosensitive central actin pool maintains T cell shape and protects the nucleus during migration

city: Montreal

first: Judith

last: Mandl

state: QC

address: 3649 Promenade Sir William Osler

institute: McGill University

summary: Immune cells navigate through complex tissue architectures by extensive cellular deformation, low adhesion, and high cell velocities. Loss-of-function mutations in dedicator of cytokinesis 8 (Dock8) are associated with immunodeficiency as immune cells becoming entangled during migration through dense environments, but their migration on two-dimensional surfaces remains entirely intact. Here, we investigated the specific cytoskeletal defect of Dock8-deficient activated T cells and describe a central pool of F-actin in wild-type murine and human T cells that is absent in Dock8 knockout T cells. The appearance of the central actin pool is mechanoresponsive and emerges only when cells are very confined. We identified mammalian sterile 20-like (Mst1) as a necessary component in this mechanosensitive pathway in addition to Dock8, allowing for cell shape integrity and survival during migration through complex environments. Our work shows that loss of the central actin pool results in greater nuclear deformation, accrual of DNA damage, and premature cell senescence.

overall_design: CD8+ T cells were isolated from WT or Dock8 KO mice (n=3 per group), activated and expanded in vitro for 3 days, and then cultured in media or in bovine collagen gels (2 mg/mL) for an additionnal 24h. Finally, the cells were recovered from the gels and RNA was extracted for bulk RNA sequencing.

first: Jérémy

last: Postat

first: Connie

last: Shen


title: Chromatine structure in Female and Male mice subcutaneous WAT depot

first: Jean-Francois

last: Louet

summary: To determine  chromatine structure differences in Female and Male mice subcutaneous WAT depot, we performed ATAC-seq experiment.

overall_design: ATAC-seq in Female and Male mice subcutaneous WAT depot

first: Jean-François

first: Mounia

last: Tannour-louet


title: WEE1 inhibitors trigger GCN2-mediated activation of the integrated stress response.

city: Toronto

first: Daniel

last: Durocher

address: 600 University

institute: Lunenfeld Tanenbaum Research Institute

summary: The WEE1 kinase negatively regulates CDK1/2 to control DNA replication and mitotic entry. Genetic factors that determine sensitivity to WEE1 inhibition (WEE1i) are largely unknown. A genome-wide insertional mutagenesis screen revealed that mutation of the alternative translation initiation factor EIF2A sensitized to WEE1i. Mechanistically, WEE1i triggers a translational shut-down, which is lethal in combination with the reduced translation of EIF2AKO cells. A genome-wide CRISPR-Cas9 screen revealed that inactivation of integrated stress response (ISR) kinases GCN1/2 rescued WEE1i-mediated cytotoxicity. Accordingly, WEE1i induced GCN2 activation, ATF4 upregulation, and altered ribosome dynamics. Accordingly, loss of the collided ribosome sensor ZNF598 increased sensitivity to WEE1i. Notably, the ISR was not required for WEE1i to induce DNA damage, premature mitotic entry nor sensitization to DNA-damaging chemotherapeutics. Conversely, ISR activation was independent of CDK1/2 activation. WEE1i-mediated ISR activation was independent of WEE1 presence, pointing at off-target effects, which are shared by multiple chemically distinct WEE1 inhibitors. This response was also observed in peripheral blood monocytic cells. Importantly, WEE1 inhibition at doses that do not induce ISR activation still synergized with PKMYT1 inhibition. Taken together, WEE1i triggers cytotoxic ISR activation and translational shutdown, which can be prevented by low-dose treatments, while retaining the cell cycle checkpoint-perturbing effects.

overall_design: mRNA-seq  was performed on RPE1 TP53.KO PAC.KO cells after 48 h of treatment with DMSO or 250nM AZD1775 for differential expression analysis.

first: Timothy

middle: F

last: Ng


title: The role of DPF2 in mouse radiation-induced intestinal injury by ATAC-seq

city: Suzhou

first: Mintao

last: Ji

address: Renai road

institute: Soochow University

summary: We have employed ATAC-seq to study the role of DPF2 in intestinal immune cells. The intestinal immune cells have been increasingly recognized for their roles in regulating intestinal inflammation. This study represents the SWI/SNF chromatin-remodeling subunit DPF2 mediates the inflammatory network in intestine.

overall_design: The immune cells of intestines from WT and Dpf2 KO mice were isolated by FACS and analyzed using ATAC-seq.

last: Chang


title: The role of DPF2 in mouse radiation-induced intestinal injury by spatial transcriptome

summary: We have employed spatial transcriptomes to study the role of DPF2 in macrophages of Radiation-induced intestinal injury (RIII). The intestinal macrophage has been increasingly recognized for their roles in regulating intestinal inflammation. This study represents the SWI/SNF chromatin-remodeling subunit DPF2 mediates the inflammatory network in intestinal injury and provides new insights in RIII.

overall_design: Following 10 Gy X-ray irradiation, the intestines of WT and Dpf2 KO mice were analyzed using spatial transcriptome.


title: Brain immune responses to systemic inflammation in postnatal mice

city: Mitaka

first: Atsuyoshi

last: Shimada

state: Tokyo

address: 5-4-1 Shimorenjaku

department: Health Sciences

country: Japan

institute: Kyorin University

summary: In newborn mouse, systemic bacterial infection damages the brain even in the absence of direct bacterial invasion.  However, the early immune reactions by intracranial tissues remain an enigma.  We injected lipopolysaccharide (LPS) intraperitoneally into 7-day-old mice to induce systemic inflammation.  Brains were removed and dissociated 24 h after LPS injection, and CD11b(+) cells were isolated using the magnetic-activated cell sorting.  Total RNA samples were extracted from the brain CD11b(+) cells and were analyzed with Gene Expression Microarray.  The results indicated that the transcript expressions of the following nine genes were strikingly increased: Saa3, Saa1, Saa2, Cxcl13, Ccl5, Irg1, Cxcl9, Lcn2, and Slfn4.  In situ hybridization indicated that Saa 3, 2, and 1, Cxcl13, Irg1, and Ccl5 were expressed by macrophages in the meningeal and perivascular space and choroid plexus, whereas Cxcl9 and Lcn2 were expressed by arachnoid, pial, and perivascular fibroblasts.  In conclusion, immune reactions of the brain to systemic inflammation were initiated by leptomeningeal and choroid plexus macrophages and leptomeningeal and perivascular fibroblasts in postnatal mice.

overall_design: We prepared 8 tubes (4 tubes for saline-injected mice and 4 for LPS-treated). Two brains from two mice that were treated with the same way were dissociated in a single tube. CD11b(+) cells were isolated using the magnetic-activated cell sorting. Total RNA samples were extrtacted from the CD11b(+) cells. Four RNA samples prepared from the LPS-treated mice were compared with for samples from the saline-injected mice.


title: HIF-2-dependent Regulation of PTHrP and Paraneoplastic Hypercalcemia in Aggressive Clear Cell Renal Cell Carcinoma [ATAC-seq]

city: Dallas

first: Bingqing

last: Xie

state: Texas

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

summary: Hypercalcemia (HC) in renal cell carcinoma (RCC) patients is associated with reduced survival. HC often involves PTHrP. PTHrP is induced by hypoxia, but whether HIF-2 plays a role in HC is unknown. Here we show that HC is reproduced by transplanting patient tumors (tumorgrafts, TG) in mice resulting in functional deterioration, weight loss, calcium deposition and organ damage. Treatment with PT2399, a specific HIF-2 inhibitor, rapidly normalized calcium levels, downregulated PTHrP and reduced HIF-2 binding to the PTHLH promoter. Interestingly, while the PTHLH locus was generally more accessible in TG(HC), PT2399 did not grossly affect chromatin accessibility, which was consistent with genome-wide studies where promoter accessibility was only reduced in a minority of PT2399-downregulated genes. As in TGs, paraneoplastic HC in humans was associated with clear cell histology and sarcomatoid/rhabdoid differentiation. Interestingly, HC (and PTHrP) was swiftly corrected by the related PT2977/belzutifan drug in a prospective patient with sarcomatoid ccRCC. Our data supports the evaluation of HIF-2 antagonists for ccRCC patients with humoral hypercalcemia of malignancy, which may serve as a predictive biomarker of response (along with PTHrP reduction).

overall_design: ATAC-seq performed on RCC PDX lines and one HCC PDX line without treatment, vehicle treated, and PT2399 treated. The normocalcemic PDX lines are XP1487, XP374, XP1657d, XP1676, XP296, XP490, XP143 and hypercalecmic ones are XP1631, XP771b, XP1139, XP165, XP289, XP1059, XP899, HCC4068, XP1087, XP1152, XP945.

first: Arijit

last: Mal

first: Charlotte

last: Small

first: Alana

last: Christie

first: Vanina

last: Tcheuyap

first: Brooklyn

last: Jackson

first: James

last: Brugarolas


title: HIF-2-dependent Regulation of PTHrP and Paraneoplastic Hypercalcemia in Aggressive Clear Cell Renal Cell Carcinoma [RNA-seq]

overall_design: RNAseq profile of hypercalcemic ccRCC PDXs (XP771b, XP945, XP1169d, XP1139, XP899, XP1087, XP1152, XP1059 and XP1631) and normocalcemic ccRCC PDX (XP374, XP1487) on vehicle and PT2399 treatment. Additionally, matched RNAseq profile of PDX lines without treatment for which ATAC seq have been performed. The additional normocalcemic PDX lines are XP143, XP165d7, XP1676 and hypercalecmic ones are XP1139, XP945, XP165, XP289.