title: CDK4/6 and SHP2 mediate BRAF/MEK inhibitor resistance in Class 2 and 3 BRAF mutant cancers

city: Montreal

first: April

last: Rose

address: 3755 chem. de la côte ste Catherine

department: Lady Davis Institute

institute: McGill University

summary: Class 2 and 3 non-V600E BRAF mutations are oncogenic drivers in many cancer types.  Currently, there are no established targeted therapies with proven efficacy for cancers with non-V600E BRAF mutations. We developed the investigator-initiated, Phase II BEAVER clinical trial (NCT03839342) to evaluate the efficacy of BRAF and MEK inhibitors in patients with non-V600E BRAF mutations. The best objective response rate was 14% (3/21). By analyzing genomic data from patient tumors, circulating tumor DNA (ctDNA), patient-derived xenograft (PDX) models generated from enrolled patients, and Class 2 & 3 BRAF mutant cell lines, we discovered MAPK-dependent and independent mechanisms of resistance to BRAF/MEK inhibition. These mechanisms included the acquisition of new mutations in NRAS, MAP2K1, RAF1, and RB in ctDNA at the time of disease progression. CDK4/6 and SHP2 were identified as mediators of intrinsic resistance to BRAF/MEK inhibition in Class 2 & 3 BRAF mutant tumors. Therapeutic strategies combining CDK4/6 or SHP2 inhibitors with BRAF/MEK inhibitors were more effective than BRAF/MEK inhibitors alone in these cancers.

overall_design: RNA-seq profiling of PDX tumours at experimental endpoint treated with either Vehicle, Binimetinib+Encorafenib, Palbociclib, TNO155, Binimetinib+Encorafenib+Palbociclib, or Binimetinib+Encorafenib+TNO155. RNA-seq profiling of Non-V600 BRAF mutant cancer cell lines treated with DMSO or Binimetinib+Encorafenib for 24 hours.

first: Jennifer

last: Maxwell

first: Emmanuelle

last: Rousselle

first: Chantel

last: Mukonoweshuro

first: Islam

last: Elkholi

first: Melody

last: Riaud

first: Marco

last: Biondini

first: Erica

last: Cianfarano

first: Isabel

last: Soria-Bretones

first: Chantal

last: Tobin

first: Meghan

last: McGuire

first: Ian

last: King

first: Tong

last: Zhang

first: Trevor

last: Pugh

first: Zaid

middle: S

last: Kamil

first: Marcus

last: Butler

first: Frances

last: Shepherd

first: Natasha

last: Leighl

first: Albiruni

last: Razak

first: Aaron

last: Hansen

first: Sam

last: Saibil

first: Philippe

last: Bedard

first: Peter

last: Siegel

first: Lillian

middle: L

last: Siu

first: David

middle: W

last: Cescon

first: Anna

last: Spreafico


title: Stemness factor Mex3a times translation and protein trafficking to ensure robust differentiation of olfactory sensory neurons [HyperTRIBE]

status: Public on Nov 11 2025

city: New York

first: Rachel

last: Duffié

state: NY

address: Jerome L Greene Sciene Building

department: Biochemistry and Molecular Biophysics

country: USA

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: During the switch from progenitor to terminally differentiated cell, cellular physiology must change to accommodate increased translation and trafficking of membrane-bound proteins. We identify stemness factor Mex3a, expressed in immature olfactory sensory neurons (OSNs), as a key factor in ensuring proper neuronal differentiation by regulating translation and trafficking of cell surface proteins in the context of Unfolded Protein Response (UPR) signaling. Loss of Mex3a in immature OSNs leads to defects in cilia structure, cell surface protein expression, and planar cell polarity in mature OSNs. Proteomics reveal a decrease in proteins related to vesicle organization. We identify putative RNA and ubiquitin targets of Mex3a and provide evidence that Mex3a can confer K27 ubiquitin linkage on targets. Finally, modulating cellular levels of Mex3a changes the recruitment of translational elongation factors to ribosomes with effects on translation. Our data reveal how a stemness factor regulates development post-transcriptionally and post-translationally to ensure robust differentiation.

overall_design: RNA-Seq from FAC sorted cell populations from the Main olfactory epithelium. All mice were transgenic for tetO-HyperTRIBE-mCherry or tetO-Mex3a-HyperTRIBE-mcherry constructs which were either driven by gg8-tTA (Nguyen et al. 2007, PMID: 18045541) or gg8-tTA and OMP-tTA (PMID: 15157418) drivers

first: Marko

last: Jovanovic

first: Stavros

last: Lomvardas

first: Lauren

middle: C

last: Tang

first: Martin

last: Escamilla del Arenal


title: Transcriptomic Regulation Driven by TCF12 Isoform Switching

city: Chicago

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

department: Neurology

institute: Northwestern University Feinberg School of Medicine

summary: TCF12 is a member of the basic helix–loop–helix (bHLH) transcription factor family, which functions through homo- or heterodimerization with other bHLH proteins to regulate gene expression during development. We identified an alternative splicing event at exon 15 (E15) of TCF12 that differs among glioma cell states, with E15 more frequently included in NPC- and OPC-like states, but less included in MES- and AC-like states. To investigate the biological function of this isoform switch, we employed a dCasRx-RBM25/gRNA system to promote E15 inclusion in a patient-derived glioma stem-like cells (GSC1478) and performed RNA-seq to profile transcriptomic changes.

overall_design: RNA-seq profiling of GSC1478 cells treated with dCasRx-RBM25 only, dCasRx-RBM25 with control gRNA, or gRNA-I16 and I19 that induce TCF12 E15 inclusion.

first: Shi-Yuan

last: Cheng


title: A conserved C2H2 zinc finger protein, Rel1, links ribosome biogenesis to sexual development and environmental stress response in a ubiquitous human fungal pathogen

city: Nanchang

first: Fanglin

last: Zheng

state: Jiangxi

address: 1519 Dongyue Avenue, Nanchang County, Jiangxi Province

department: The First Affiliated Hospital of Nanchang University

country: China

institute: Nanchang University

summary: Sexual development is a fundamental process that promotes infection and the emergence of highly virulent and drug-resistant isolates in the human fungal pathogen Cryptococcus neoformans. While the genetic factors involved in sexual life cycle have been extensively investigated in this pathogenic fungus, the critical regulator(s) beyond transcriptional machinery remains poorly understood. Rei1, a conserved C2H2-type zinc finger protein, functions as a 60S ribosome biogenesis factor and plays a crucial role in maintaining cellular growth at low temperature in yeast. In this study, we identified a yeast Rei1-like protein, Rel1, based on its encoding gene that was dynamically up-regulated during unisexual reproduction in C. neoformans. Similar to Rei1’s role in yeast, disruption of REL1 gene results in significant growth retardation under low temperature conditions. Consistent with its upregulation during sexual development, REL1 deletion compromised the entire sexual cycle, including yeast-hyphae morphogenesis, basidial differentiation, meiosis and sporulation. RNA-Seq analysis revealed that Rei1 is required for the transcriptional activation of key sexual reproduction gene sets involved in mating response, morphogenesis and meiosis, suggesting a potential link between ribosome biogenesis and sexual development in C. neoformans. Furthermore, REL1 disruption increased susceptibility to the antifungal drug 5’-flucytosine (5’-FC) but enhanced resistance to fluconazole, indicating its differential role in antifungal drugs resistance mechanisms. Collectively, this study provides critical insights into how C. neoformans utilize a conserved ribosome biogenesis factor to coordinate cold resistance, sexual development, and antifungal susceptibility, highlighting both conserved and divergent functions of this C2H2 zinc-finger protein compared to its ortholog in budding yeast.

overall_design: RNA-seg profiling of wild type Cryptococcus neoformans strain XL280 and its knockout derivative (rel1 mutant) at 24 hours of mating induction on V8 medium.

first: Lili

last: Yan

first: Man

last: Chen


title: Plagl1 and Lrrc58 control mammalian body size by triggering target-directed microRNA degradation of miR-322 and miR-503 [RNA-seq]

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Precise control of microRNA (miRNA) expression is critical for normal development. An important mechanism of miRNA regulation is target-directed microRNA degradation (TDMD), a pathway in which the binding of miRNAs to specialized trigger RNAs induces ubiquitylation and decay of associated Argonaute (AGO) proteins by the ZSWIM8 ubiquitin ligase. ZSWIM8-deficient mice exhibit reduced body size, cardiopulmonary and neurodevelopmental defects, and perinatal lethality. Despite widespread dysregulation of miRNAs in these animals, the vast majority of presumptive trigger RNAs that induce decay of ZSWIM8-regulated miRNAs remain undefined. Here, using AGO crosslinking and sequencing of hybrids (AGO-CLASH), a high-throughput method for identifying miRNA binding sites, we report the identification of Plagl1 as a trigger for TDMD of miR-322-5p, and Lrrc58 and Malat1 as TDMD triggers for miR-503-5p in mouse embryonic fibroblasts (MEFs). In mice, deletion of the miR-322-5p and miR-503-5p trigger sites in the Plagl1 and Lrrc58 3' UTRs, respectively, abrogated TDMD of these miRNAs and resulted in miR-322/503-dependent embryonic growth restriction, recapitulating a key feature of the Zswim8—/— phenotype. Thus, these results demonstrate that the transcripts encoding Plagl1 and Lrrc58 regulate mammalian body size by inducing degradation of miR-322-5p and miR-503-5p and provide a valuable resource for identification of additional TDMD triggers.

overall_design: RNA seq on total RNA from mouse tissues from wildtype and trigger site KO mice at E18.5

first: Collette

middle: A

last: LaVigne

first: Jaeil

last: Han

first: He

last: Zhang

first: Sihoon

last: Cho

first: Minseon

last: Kim

first: Komal

last: Sethia

first: Bret M

last: Evers

first: Asha

last: Acharya

first: Tsung-Cheng

last: Chang

middle: T


title: A human iPSC-based neural spheroid platform for modeling glioblastoma infiltration using high-content imaging

city: London

first: Victoria

last: Tsang

state: Select a State

address: Charterhouse Square Campus

department: Translational Medicine and Therapeutics

country: United Kingdom

institute: Queen Mary University of London

summary: Glioblastoma is the most aggressive adult brain tumor, characterized by resistance to therapy and high recurrence due to diffuse infiltration. To mimic glioblastoma migration, we developed a physiologically relevant co-culture model, combining patient-derived glioblastoma cell lines with cortical-like neural spheroids differentiated from human induced pluripotent stem cells. Using high-content imaging, we demonstrate that GBM1 and GBM20 cell lines migrate directionally along axons toward neural spheroids in live imaging assays and infiltrate spheroids extensively in endpoint assays, unlike non-cancerous neural stem cells. A proof-of-principle drug screen identified PF-573228 (FAK inhibitor) and Motixafortide (CXCR4 inhibitor) as potent suppressors of GBM1 and GBM20 infiltration, respectively. Bulk RNA sequencing revealed gene expression profiles correlating with invasive behavior and drug sensitivity. This platform offers a valuable model for studying glioblastoma infiltration along axons and provides proof-of-principle that migration can serve as a measurable and actionable phenotype to screen therapeutic vulnerabilities in glioblastoma.

overall_design: Bulk RNA sequencing of patient-derived glioblastoma cell lines GBM1 and GBM20. Each line was snap-frozen as pellets containing 1 × 10^⁶ cells. Replicates included GBM1A and GBM1B for the GBM1 line, and GBM20A and GBM20B for the GBM20 line.

first: Federica

last: Riccio

first: Hannah

last: Nudds

first: Jason

middle: D

last: Coombes

first: Heiko

last: Wurdak

first: Harry

middle: J

last: Bulstrode

first: Ivo

last: Lieberam

first: Davide

last: Danovi

first: Aimee

last: Wilson


title: PITX2 dosage-dependent pacemaker cell state changes underlie sinus node dysfunction and atrial arrhythmia-susceptibility

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: Reduced spatiotemporal transcription factor levels have been shown to affect traits, organism development and disease predisposition. Here, we investigated the impact of physiologically relevant increases in transcription factor dosage, which has remained largely unexplored. Patients with genomic deletions far upstream of PITX2 present with sinus node dysfunction (SND) and atrial fibrillation. We show that delB mice, which recapitulate the deletion-driven arrhythmia in patients, ectopically express PITX2 in sinus node pacemaker cardiomyocytes (PCs) in a highly heterogeneous pattern from early embryonic development onwards. During development, delB sinus nodes form subdomains of mildly affected PC and strongly affected PCs that have lost their PC identity and switched towards an atrial cardiomyocyte-like state in a PITX2 dosage-dependent manner. Compared to heterozygous delB mice, homozygous delB mice have more PITX2+ PCs that express on average more PITX2, form proportionally larger subdomains of strongly affected PCs and have much more severe SND and atrial arrhythmia susceptibility. Ectopic expression of PITX2 in human induced pluripotent stem cell-derived PCs resulted in PITX2 dosage-dependent transcriptional changes reminiscent of those observed in the sinus node subdomains of delB mice. These results show that genetically driven ectopic expression of PITX2 in PCs causes SND and increased susceptibility for atrial arrhythmias, illustrating how spatiotemporally-defined increases in transcription factor dosage translates into developmental defects and disease predisposition.

overall_design: iPSC-derived cariomyocytes were transduced with AAV6 virus to express PITX2c or mcherry (control). Cells were detached and used for 10X Genomics Chromium Single Cell RNA seq.

first: L

middle: E

last: van der Maarel

first: M

middle: R

last: Mungroo

first: O

last: Mulleners

last: Rivaud

first: F

middle: H

last: Tiel Groenesteege

last: Fokkert

first: C

last: de Gier-de Vries

first: K

last: van Duijvenboden

first: B

last: Jensen

first: H

last: Devalla

first: V

middle: M


title: PITX2 dosage-dependent pacemaker cell state changes underlie sinus node dysfunction and atrial arrhythmia-susceptibility II

overall_design: Wild-type (n=3), delB/+ (n=6), delB/delB (n=3) fetal (E17.5) hearts were analysed using spatial transcriptomics. Regions of interest were segmented based on HCN4 and TNNI3 expression, including the TNNI3+ right atrium (RA), HCN4+ wild-type sinus node, and delB/+ and delB/delB HCN4-high and HCN4-low sinus node.


title: PITX2 dosage-dependent pacemaker cell state changes underlie sinus node dysfunction and atrial arrhythmia-susceptibility I

overall_design: Wild-type (n=3) and delB/delB (n=6) fetal (E17.5) hearts were analysed using spatial transcriptomics. Regions of interest were segmented based on HCN4 and TNNI3 expression, including the TNNI3+ right atrium (RA), HCN4+ wild-type sinus node, and delB/delB HCN4-high and HCN4-low sinus node.


title: CDK4/6 Inhibitor, Palbociclib, overcomes Venetoclax resistance mechanisms and outperforms single agents in Acute Myeloid Leukemia [RNA-Seq]

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

summary: Venetoclax (ven) combined with the hypomethylating agent azacytidine (aza) is a widely used therapy for Acute Myeloid Leukemia (AML), however, most patients develop resistance. Using RNASeq, we identified loss of Ikaros (IKZF1) as a potential resistance mechanism to ven+palbo. Examination of cells with IKZF1-loss revealed upregulation of the receptor, AXL, with concordant AXL inhibitor sensitivity in AML tumors harboring IKZF1 mutations.  This work suggests that the combination of ven+palbo is a potential novel therapy for AML for potential subpopulations that may benefit the most from this treatment, as well as targeting translation as a means to overcome ven resistance.

overall_design: Using RNA-Seq, we compared three OCI-AML2 cell lines with a IKZF1 knock-out to three others with a non-targeting control  to identify differentially expressed genes associated with loss of IKZF1.

first: Melissa

last: Stewart

first: Jessica

last: Gibbs

first: Andy

last: Kaempf

first: Jeffrey

last: Tyner


title: Extracellular BRICK1 drives heart repair after myocardial infarction

city: Hannover

first: Felix

last: Polten

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hanover Medical School

summary: Tissue repair after myocardial infarction entails a vigorous angiogenic response that mitigates scarring and worsening of heart function and may represent a therapeutic target. Angiogenesis in the infarct wound is guided by incompletely defined myeloid cell–endothelial cell interactions. Here we identify the myeloid cell-expressed 75‑amino acid microprotein BRICK1 (short name: BRK1) as an indispensable driver of postinfarction angiogenesis. As a subunit of the intracellular actin-regulatory WAVE complex, BRK1 was not previously known to function outside the cell. We show that BRK1 translocates to the extracellular space after myocardial infarction in mice and humans. We find that BRK1 is not actively secreted but released from dying monocytes and macrophages. Cre-loxP-mediated myeloid cell-selective genetic deletion of Brk1 or antibody neutralization of extracellular BRK1 impaired microvessel formation in the infarct border zone and resulted in severe postinfarction heart failure in mice. Treatment with recombinant BRK1, conversely, preserved heart function after myocardial infarction. Mechanistically, BRK1 induced an angiogenic phenotype in human cardiac endothelial cells by signaling via the small GTPase RAP1 and mitogen-activated protein kinases 1 and 3 to promote retinoblastoma protein hyperphosphorylation and E2F transcription factor activation. BRK1 thus emerges as an angiogenic growth factor linking myeloid cell death to ischemic tissue repair and potentially enabling a protein-based therapy for myocardial infarction.

overall_design: Bulk-RNA sequencing of human coronary artery endothelial cells cultured for 8 hours in the absence (control) or presence of BRK1, VEGFA, PD98059, or PD plus BRK1.

first: Mircea-Andrei

last: Sandu

first: Jan

last: Faix

last: Hegermann

first: Nils

last: Kriedemann

first: Robert

last: Zweigerdt

first: Thomas

last: Thum

first: Johann

last: Bauersachs

first: Hans

last: Niessen

first: Andrew

last: Koenig

first: Kory

last: Lavine

first: Andreas

last: Pich

first: Yong

last: Wang

first: Marc

last: Reboll

first: Mortimer

last: Korf-Klingebiel

first: Kai

last: Wollert


title: CDK4/6 Inhibitor, Palbociclib, overcomes Venetoclax resistance mechanisms and outperforms single agents in Acute Myeloid Leukemia [CRISPR Screen]

first: Daniel

last: Bottomly

summary: Venetoclax (ven) combined with the hypomethylating agent azacytidine (aza) is a widely used therapy for Acute Myeloid Leukemia (AML), however, most patients develop resistance. A genome-wide CRISPR screen showed that loss of genes involved in translation conferred sensitivity to ven but not ven+palbo. Accordingly, we show that increased translation occurs after AML cells are challenged with ven, and ven+palbo blocks this increase. We also found that loss of BAX, which leads to ven resistance, was overcome by combination with CDK4/6 inhibitors. Conversely, loss of RB1, a known mechanism of resistance to CDK4/6 inhibitors, was mitigated by ven+palbo. This work suggests that the combination of ven+palbo is a potential novel therapy for AML for potential subpopulations that may benefit the most from this treatment, as well as targeting translation as a means to overcome ven resistance.

overall_design: Using a genome-wide CRISPR screen on OCI-AML2 cells, we performed comparisons of sgRNA read counts between DMSO and venetoclax, palbociclib as well as their combination at Day 0 and 21.  Genes that were significantly depleted (enriched) relative to DMSO controls were deemed candidates for enhancing drug sensitivity (resistance).

first: Melissa

last: Stewart

first: Jessica

last: Gibbs

first: Shannon

middle: K

last: McWeeney

last: Tyner


title: PITX2 dosage-dependent pacemaker cell state changes underlie sinus node dysfunction and atrial arrhythmia-susceptibility III

first: Vincent

last: Christoffels

overall_design: Wild-type (n=3), delB/+ (n=3) and delB/delB (n=3) adult hearts were analysed using spatial transcriptomics. Regions of interest were segmented based on HCN4 and TNNI3 expression, including the TNNI3+ right atrium (RA), HCN4+ wild-type sinus node, and delB/delB HCN4-high and HCN4-low sinus node.

first: L

last: van der Maarel

first: M

last: Mungroo

first: O

last: Mulleners

last: Rivaud

first: F

last: Tiel Groenesteege

last: Fokkert

first: C

last: de Gier-de Vries

first: K

last: van Duijvenboden

first: B

last: Jensen

first: H

last: Devalla

first: V


title: Silencing of BCL11A by Disrupting Enhancer-Dependent Chromatin Insulation

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Polycomb-dependent breakdown of the intestinal barrier in aging Drosophila

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Aging compromises gut integrity, yet the chromatin changes driving this decline remain unclear. Polycomb mediated repression is essential for developmental silencing, but becomes dysregulated with age. Using single-cell chromatin profiling of the Drosophila intestine, we find that intestinal cell types have distinct repressed landscapes, and that enterocytes — not stem cells — undergo the most significant chromatin shifts in older animals. Aged enterocytes aberrantly repress genes essential for transmembrane transport and chitin metabolism, contributing to gut barrier decline. In contrast, stem cells exhibit increased proliferation, linked to hypertranscription of S-phase histone genes and to activation of JAK-STAT signalling pathways. These findings suggest that aberrant Polycomb repression in old differentiated cells is an example of antagonistic pleiotropy aging animals.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

first: Sarah

last: Leichter

first: Kami

last: Ahmad

first: Steven


title: Gene expression profile at single cell level of Tendon at neonate or adult sample with or without injury

city: 北京市

first: 美莲

last: 蔡

state: 北京市

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

summary: We used single cell RNA sequencing (scRNA-seg) to analyze the  diversity of tendon cells at different ages with or without injury. W

overall_design: We compared the gene expression profiles of cells isolated from control and injury tendon tissues both in neonatal period (postnatal day 3, P3) and adult (6-8 weeks).

first: Liujing

last: Chen

first: Meilian

last: Cai

first: Shuai

last: Lin

first: Ruili

last: Yang


title: Single-cell analysis reveals transcriptomic difference between keloid and normal human tissue

city: wuhan

first: jia

last: chen

address: 215 Zhongshan Dadao, Qiaokou District, Wuhan City, Hubei Province

department: Department of Dermatology

institute: Traditional Chinese and Western Medicine Hospital of Wuhan

summary: Keloids are pathological scars characterized by their invasive growth. Currently, keloids remain a therapeutically challenging condition in clinical practice, with high recurrence rates and resistance to treatment, leading to suboptimal therapeutic outcomes. There is a clinical need for new treatment strategies and targets.

overall_design: The aim of this study is to provide evidence at the single-cell level and to explore new approaches for the clinical treatment of keloids.

first: J

first: W

first: Y

last: Wang

first: P

last: Li


title: Developmental convergence and divergence in human stem cell models of autism spectrum disorder

status: Public on Nov 12 2025

city: Santa Monica

first: Lucy

last: Bicks

state: CA

address: 1033 3rd street, apartment 106, apartment 106

institute: UCLA School of Medicine

summary: Two decades of genetic studies in autism spectrum disorder (ASD) have identified over a hundred genes harboring rare risk mutations. Despite this substantial heterogeneity, transcriptomic and epigenetic analyses have identified convergent patterns of dysregulation across ASD post-mortem brain. To identify shared and distinct mechanisms of ASD-linked mutations, we assembled the largest patient hiPS cell cohort to date, consisting of 70 hiPS cell lines after stringent quality control representing 8 ASD-associated mutations, idiopathic ASD, and 20 lines from non-affected controls. We used these hiPS lines to generate human cortical organoids (hCO), profiling by RNAseq at four distinct timepoints up to 100 days after in vitro differentiation. Early timepoints harbored the largest mutation-specific changes, but different mutations converged on shared transcriptional changes as development progressed. We identified a shared RNA and protein interaction network, which was enriched in ASD risk genes and predicted to drive the observed down-stream changes in gene expression. CRISPR-Cas9 screening of these candidate transcriptional regulators in induced human neural progenitors validated their downstream molecular convergent effects. These data illustrate how genetic risk can propagate via transcriptional regulation to impact convergently dysregulated pathways, providing new insight into the convergent impact of ASD genetic risk on human neurodevelopment.

overall_design:
To investigate the effects of ASD-linked mutations on gene expression changes across development in human cortical organoids.

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Submitter states that missing raw data are being made available for controlled access in dbGaP.
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first: Aaron

last: Gordon

first: Se-Jin

last: Yoon

first: Sergiu

middle: P

last: Pasca

first: Daniel

last: Geschwind


title: Oligodendroglial hypothesis of autism: the primary role of master regulator gene Baf155 [RNA-Seq]

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

summary: Autism spectrum disorders (ASD) are polyetiological neurodevelopmental disorders associated with both genetic and non-genetic risk factors with complex and heterogeneous clinical manifestations. A single susceptibility gene usually fails in triggering an intricate array of autistic symptoms, suggesting a primary mechanism may be required to integrate multiple susceptibility genes in casing the disease. Recent evidence highlights the role of myeline disruption in pathogenesis of ASD. However, neither the mechanisms of impaired myelination nor its contribution to ASD symptomatology are fully characterized. We demonstrate the loss of Baf155, a newly recognized autistic susceptibility gene that encodes a core member of the chromatin remodeling complex, affects oligodendroglial differentiation and myelination. BAF155 targets multiple synapse-related genes in oligodendrocyte precursor cells (OPCs), these genes being responsible for regulating the synaptic communication between OPCs and neurons. Heterogeneous target genes affected by BAF155 deficiency in OPCs across various brain regions leads to significant impairments in myelination which may contribute to the diverse manifestations observed ASD patients. Taken together, our findings reveal a primary mechanism that orchestrates multiple ASD susceptibility genes in instigating the disease.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: To investigate whether BAF155 modulates the responses of OPCs to neuronal inputs in distinct brain regions, we assessed the differentially expressed genes in acutely isolated OPCs from mPFC and hippocampus of Baf155 knockout mice and their non-Cre littermates by RNA-seq . In line with that, we analyzed the variability of OPCs from mPFC and hippocampus response to different neurotransmitters(Glutamate/GABA) by RNA-seq.

first: Jianqin

last: Niu

first: Lan

last: Xiao

first: Xiaorui

first: Qi


title: Proximity Labeling reveals role of 14-3-3 protein YWHAB in CDK4/6 inhibitors resistance in breast cancer

city: taipei

first: Jiun-I

last: Lai

state: State...

address: no 155, linong street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming Chiao-Tung University

summary: CDK4/6 inhibitors are currently standard of care for advanced hormone positive (HR+) breast cancer, and CDK6 overexpression induces resistance against CDK4/6 inhibitors. We incidentally discovered that overexpression of a CDK6 D224Y mutant mitigated this resistance. Mechanistic studies revealed that CDK6 overexpression resulted in suppressed apoptosis and increased G1/S progression after treatment with CDK4/6 inhibitors; these features were abolished when CDK6 D224Y was overexpressed. Proximity labeling proteomics revealed CDK6 overexpression, but not CDK6 D224Y overexpression, induced binding of the 14-3-3 protein YWHAB. Co-immunoprecipitation experiments confirmed YWHAB bound overexpressed wild type CDK6 but not CDK6 D224Y, and YWHAB knockdown decreased CDK6 protein expression in a proteosomal dependent manner. Knockdown of YWHAB reversed the resistance conferred by CDK6 amplification. Xenograft studies confirmed that CDK6 D224Y overexpression reversed the resistance conferred by CDK6 overexpression in vivo. In summary, by studying CDK6 D224Y, we uncovered a role for YWHAB that modulates CDK4/6 inhibitor resistance.

overall_design: human breast cancer cell line MCF7 expressing vector, CDK6 overexpression, or CDK6-D224Y overexpression, and sent for RNA-seq

first: Wei-Ting

last: Chung

first: Yi-Ru

last: Tseng

first: Chun-Yu

last: Liu

first: Yi-Fang

last: Tsai

first: Chi-Cheng

last: Huang

first: Ling-Ming

first: Ta-Chung

last: Chao


title: Transcriptional profiling of aged and young mouse hearts [RRBS]

city: Boston

first: Dogacan

last: Yucel

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

type: Methylation profiling by high throughput sequencing

summary: Cardiac aging is a major risk factor for cardiovascular diseases, yet the underlying molecular mechanisms remain poorly understood. Methylation at the CpG islands have been heavily associated with the process of aging. In this study, we performed RRBS sequencing to identify changes in CpG methylation in the aging cardiomyocyte.

overall_design: We isolated cardiomyocyte nuclei using FACS and performed RRBS sequencing. Outputs were analyzed using bismark package.

first: Michael

last: Trembley

first: William

last: Pu


title: Plagl1 and Lrrc58 control mammalian body size by triggering target-directed microRNA degradation of miR-322 and miR-503 [AGO-CLASH]

first: Joshua

last: Mendell

overall_design: AGO CLASH was performed from UV cross-linked mouse brain and lung and sequencing library was prepared for illumina sequencing

first: Collette

last: LaVigne

first: Jaeil

last: Han

first: He

last: Zhang

first: Sihoon

last: Cho

first: Minseon

last: Kim

first: Komal

last: Sethia

first: Bret M

last: Evers

first: Asha

last: Acharya

first: Tsung-Cheng

last: Chang


title: gene expression profiles of Col1α1+Vldlr+ and Col1α1+Vldlr- TSPCs

first: 美莲

last: 蔡

address: 北京市昌平区生命科学园医科路9号院3号楼西门，闹中心二期A2货架

institute: 北京脑科学与类脑研究中心

summary: We here report Reln-VLDLR receptor-ligand interactions are the primary mechanism for communication between lymphatic endothelial cells (LECs) and tendon stem/progenitor cells (TSPCs). The depletion of Vldlr results in impaired tendon regeneration.Specifically, lymphoangiocrine Reelin interacts with Col1α1+Vldlr+TSPCs to activate Notch1-Srebf2 mediated cholesterol metabolism loop, maintaining TSPC stemness and enhancing tendon regeneration.

overall_design: To explore the role of Vldlr+ cells in tendon regeneration, we sorted Col1α1+Vldlr+ and Col1α1+Vldlr- TSPCs by flow cytometry.We then comparare gene expression profiling analysis of RNA-seq data for Vldlr+ and Vldlr- TSPCs.

first: Liujing

last: Chen

first: Meilian

last: Cai

first: Shuai

last: Lin

first: Ruili

last: Yang


title: Gastric Bypass Elicits Persistent Gut Adaptation and Unique Diabetes Remission-Related Metabolic Gene Regulation

first: Margaret

last: Stefater-Richards

summary: Abstract: Objective: We have previously shown that early intestinal adaptation precedes and relates to metabolic improvement in humans after Roux-en-Y gastric bypass surgery (RYGB). We hypothesized that intestinal adaptation would persist at the one-year postoperative timepoint, and that gene expression (GE) signatures would relate to Type 2 diabetes (T2D) remission, providing insight into potential mechanisms for intestinally-mediated metabolic improvement after RYGB. Methods: We determined GE by RNA-seq in jejunum (Roux limb, RL) collected from 28 patients before and 12 months after RYGB. Results: Global GE from paired baseline and 1-year jejunal samples did not separate according to clinical phenotype (T2D remission, sustained weight loss). In general, GE was consistent with persistent RL remodeling, and microvilli were elongated by 39%. Remodeling was not attenuated in patients with lack of diabetes remission or with weight regain. Patients with diabetes remission demonstrated greater jejunal activation of lipogenesis-related pathways driven by RXR, LXR and SREBP. Conclusions: RL adaptation is a key feature of RYGB in all patients, likely reflecting the dramatic alterations to gastrointestinal anatomy, but jejunal lipogenesis appears to be more strongly activated in those patients with diabetes remission. Further study is needed to understand whether these pathways may drive metabolic remission after RYGB.


title: METTL3 dependent m6A RNA methylation is required for self-renewal and cell identity maintenance of human trophoblast stem cells

city: Tianjin

first: Chunxiao

state: Tianjin

address: Xuefu Road

department: College of Life Science

institute: Nankai University

summary: N6-methyladenosine (m6A) is the most prevalent mRNA modification with diverse regulatory functions in mammalian cells. However, its significance in the human trophoblast lineage and human placenta development remains largely unexplored. Here, we found that in human pregnancy, METTL3 and METTL14, the primary enzymes responsible for m6A deposition, specifically mark cytotrophoblast cells in the human placenta. By utilizing a METTL3 inducible knockout (iKO) system, we demonstrated the essential role of METTL3 in generating human trophoblast stem cells (hTSCs) from human expanded potential stem cells (hESPCs). Furthermore, METTL3 is critical for the self-renewal ability and cellular identity in the established hTSCs. Mechanistically, METTL3-dependent m6A modification regulates histone modifiers such as EP300 and EZH2 to maintain the epigenetic homeostasis of hTSCs. The depletion of METTL3 in hTSCs results in epigenetic dysregulation, leading to activation of inflammation and premature senescence, which are associated with the preeclampsia phenotype. Notably, our findings from in vitro model show that inhibiting EP300 could efficiently rescue the preeclampsia signature at the transcriptomic level. These results underscore the critical roles of METTL3-dependent m6A RNA methylation in human placentation and the development of placental diseases.

overall_design: we performed RNA sequencing (RNA-seq) to analyze global gene expression profiles in P0, P2 and P3 hTSCs using two independent cell lines. We performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) to analyze m6A modification profiles in P0 and P2 hTSCs. We performed RNA stability analysis, in which we introduced Actinomycin D to transiently suppress global transcription then performed RNA-seq experiments at different time points to evaluate the transcription dynamics in P0 and P2 hTSCs. we conducted CUT&Tag for H3K27ac, H3K27me3, H3K9me3, H3K4me1 and JUND, as well as ATAC-seq for chromatin accessibility in P0 and P3 hTSCs.

first: Haifeng

last: Fu


title: Knockdown MSLN enhances anti-PD-1 therapy efficacy in high-grade serous ovarian cancer via modulating tumor microenvironment.

city: Shanghai

first: Haiou

last: Liu

address: No.128, Shengyang road, Yangpu distinct, Shanghai, P. R. China.

institute: Fudan University

summary: The role of MSLN in remodulating tumor microenviroment in high-grade serous ovarian cancer and the underlying mechanisms

overall_design: RNA-seq of tumor tissues (shcontrol vs shMsln) - 4 replicates each.

first: Jiaqi

last: Lu

first: Yujing

last: Zhong

first: Yiying

last: Wang

first: Chenyang


title: The effect of an NAT10 inhibitor (remodelin) on inflammation-related genes in the treatment of thalamic hemorrhage based on RNA sequencing data

city: Yangzhou

first: Tianfeng

last: Huang

address: 98 Nantong West Road

institute: Northern Jiangsu People's Hospital

summary: Thalamic hemorrhage is a disease caused by hemorrhage of the thalamic brain parenchyma and is accompanied by an inflammatory response during development. NAT10 has been associated with a wide range of diseases. The aim of this study was to explore the molecular mechanisms associated with the use of the NAT10 inhibitor (Remodelin) for the treatment of thalamic hemorrhage from an inflammatory perspective.

overall_design: First, the total RNA of the sample was isolated and purified by TRIzol (Invitrogen, CA, USA), which was used for quality control by a NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The integrity of the RNA was subsequently detected with a Bioanalyzer 2100 (Agilent, CA, USA) and verified via agarose gel electrophoresis. RNA samples with a concentration >50 ng/μL, a RIN >7.0, an OD260/280>1.8, and >1 μg of total RNA were selected for subsequent experiments. Then, the mRNA captured by oligo(dT) magnetic beads was fragmented at high temperature and reverse transcribed into cDNA. Next, the second strand of cDNA was synthesized by RNase H digestion, and the ends of the double-stranded DNA were aligned to form flat ends. Then, an A base was added at each end of the double-stranded DNA so that it could be ligated to the junction with a T base at the end of the double-stranded DNA. Finally, magnetic beads were used for the selection of fragment sizes and purification so that fragments could be formed into 300 bp±50 bp fragments

first: Yueping

last: Gu

first: Ju

last: Gao

first: Yinggang

last: Xiao


title: An in vivo and in vitro spatiotemporal atlas of human fetal midbrain development

first: George

middle: Thomas

last: Hall

address: Zayed Centre for Research, 20 Guilford Street

department: UCL Great Ormond Street Institute of Child Health

institute: University College London

summary: The dopaminergic system has key roles in human physiology and is implicated in a broad range of neurological and neuropsychiatric conditions that are increasingly investigated using induced pluripotent stem cell-derived midbrain models. To determine the similarity of such models to human systems, we undertook single cell and spatial profiling of first and second trimester fetal midbrain and compared it to in vitro midbrain models. Our initial histological analysis of second trimester fetal midbrain revealed structural complexity already similar to that of adult tissue, although this similarity did not fully extend to transcriptional activity. Moreover, we show that in vitro models recapitulate the transcriptional activity of late first trimester fetal midbrain, while 3D models replicate the spatial organization and cellular microenvironments of first and second trimester fetal midbrain. Understanding the extent of human tissue recapitulation in midbrain laboratory models is essential to justify their use as biological proxies.

overall_design:
For spatial transcriptomics data:
Fetal midbrain samples from four timepoints were profiled with spatial transcriptomics.  Each sample had three biological replicates. Four spatial transcriptomics capture areas (each containing six organoids) were also profiled.
The fetal samples are:
PC_AGE_1_REP_1
PC_AGE_1_REP_2
PC_AGE_1_REP_3
PC_AGE_2_REP_1
PC_AGE_2_REP_2
PC_AGE_2_REP_3
PC_AGE_3_REP_1
PC_AGE_3_REP_2
PC_AGE_3_REP_3
PC_AGE_4_REP_1
PC_AGE_4_REP_2
PC_AGE_4_REP_3
The organoid samples are:
OCT_BLOCK_1
OCT_BLOCK_2
OCT_BLOCK_3
OCT_BLOCK_4
For single-cell transcriptomics data:
In vitro 2D and 3D organoids (both iPSC-derived samples) were profiled throughout neuronal differentiation, along with fetal midbrain from first and second trimester. For 2D models, samples from 2 donors (2 controls) were collected at days 40 and 70 of differentiation. For 3D models, samples from 4 donors (2 controls, 2 patients, one patient-corrected line) were collected at days 40, 70 and 120 of differentiation. Fetal midbrain samples were collected at post-conceptional weeks 10, 12, 16 and 20. To reduce the batch effects between donors, individual donors were pooled at the time of sequencing. The biological samples described below correspond to 10x libraries (samples processes through the same GEM well).
The 2D and 3D models are:
mid_organoids8644112
mid_organoids8644113
mid_organoids8644114
mid_organoids8643920
mid_organoids8643921
mid_organoids8643922
mid_organoids8644016
mid_organoids8644017
mid_organoids8644018
The fetal samples are:
F10121620_A
F10121620_B
F10121620_C
F10121620_D

first: Pau

last: Puigdevall Costa


title: Helicobacter pylori-induced PPFIA4 promotes gastritis and gastric bacterial colonization

city: Chongqing

first: yuan

last: zhuang

address: Gaotanyan Street

institute: Third Military Medical University

summary: Bacterial-modulated gastric epithelial cells (GECs) play key roles in H. pylori-associated pathology. Here we demonstrate both pro-colonization and pro-inflammation roles of GEC-derived PPFIA4, originally expressed in nervous system, in H. pylori infection. PPFIA4 was elevated in gastric mucosa of H. pylori-infected patients and mice. PPFIA4 in GECs was synergistically induced by H. pylori and IL-33 in a cagA-dependent manner. Human gastric PPFIA4 correlated with H. pylori colonization and the severity of gastritis, and H. pylori colonization and inflammation were attenuated in Ppfia4-/- and Ppfia4ΔGEC mice.Overall, we propose a model in which PPFIA4 collectively ensures H. pylori persistence and promotes gastritis.

overall_design: To investigate the function of PPFIA4 in gastric epithelial cells, AGS cells were treated with PPFIA4 sgRNA or non-specific control sgRNA to generate sgPPFIA4-AGS cells and sgNC-AGS cells.

first: Pan

first: Yuan

last: Zhuang


title: Oligodendroglial hypothesis of autism: the primary role of master regulator gene Baf155 [ChIP-Seq]

first: Yixun

last: Su

overall_design: ChIP-seq technology is used to determine BAF155 binding sites in primary oligodendrocyte precursor cell (OPC) culture on day 1 and day 5 during differentiation.

first: Jianqin

last: Niu

first: Lan

first: Xiaorui

first: Qi


title: Multiomics Investigation of the Hypertensive Human Heart

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Biobanked, postmortem human heart tissue presents a unique opportunity to understand the pathogenesis of human cardiovascular disease risk factors through detailed multiomic analyses. We hypothesize that hypertension affects the cardiac transcriptome and cellular subtypes in a site-specific manner. We performed bulk and single-nucleus RNA-seq (snRNA-seq) on spatially distinct ventricular and atrial samples of postmortem hearts from donors with hypertension (n=3) and normotensive referents (n=2), using our rigorous cardiac dissection and preservation protocol. We identified both chamber- and cell-type specific transcriptomic profiles, including altered NAD+/NADH homeostasis and dysregulated metabolic gene expression. We identified a unique proliferative endothelial subtype in cardiac samples from donors with hypertension.  Atrial contractile vascular smooth muscle cells were depleted in tissue from donors with hypertension compared to tissue from normotensive referents. Future studies are needed to understand the contributions of reductive stress and related signaling, and the contributions of unique endothelial and vascular smooth muscle cell states in hypertensive heart disease.

overall_design: Cross-sectional study design consisting of atrial and ventricular cardiac samples collected postmortem from donors with (n = 3) and without (n = 2) systemic hypertension

first: Zachary

last: Milstone

first: Jessica

last: Fetterman

first: Jesse

last: Moreira-Bouchard

first: Deepa

last: Gopal


title: AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis (PRO-Seq)

city: Changsha

first: Bi

last: Shi

address: #2 Lushan South Road

institute: Hunan University

summary: Oncogenic transcription represents a crucial event in MLL rearranged (MLLr) leukemia, yet the precise role of transcription co-activators in MLL-fusion protein-associated transcription and their contribution to leukemogenesis remain incompletely understood. Here, we demonstrate that AKAP95 is notably up-regulated in both MLLr patients and in MLL-AF9-transformed mouse bone marrow. AKAP95 proves essential for initiating mouse MLL-AF9 leukemia, exhibiting widespread DNA binding across the genome, particularly at gene promoters. Interaction with the translocated MLL1 fragment primarily occurs through phase separation mechanisms. AKAP95's RNA-binding properties, coupled with its phase separation behavior, govern its binding to pre-mRNA and concurrent transcriptional regulation. Importantly, we engineered a peptide to disrupt its phase separation, effectively attenuating AKAP95-mediated transcriptional co-activation and inhibiting the growth of MLLr cell lines. These findings illustrate a vivid example of an RNA-binding protein orchestrating transcription and tumorigenesis via phase separation, underscoring the potential for targeting oncogenic condensation mechanisms therapeutically.

overall_design: Overexpression of wild-type AKAP95 and phase separation mutants was performed in HeLa cells to establish the significance of AKAP95's phase separation ability in promoting tumorigenesis. Pro-seq was performed to uncover transcriptional signals in Hela cells.

first: Yongkun

last: Luan

first: Hao

last: Jiang

first: Wei

last: Li


title: AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis (CLIP-Seq)

overall_design: Flag-mEGFP was knocked into the N-terminus of the AKAP95 locus in HeLa cells to tag the endogenous AKAP95. Lentiviruses pLKO.1-shAKAP95, pCDH-CMV-HA-JD-PI95-puro, and pCDH-CMV-HA-H32Q-PI95-puro were packaged in 293T cells with the envelope plasmids psPAX2 and pMD2.G. One million HeLa cells were transduced with 200 μL of concentrated virus by spin infection at 1000 × g for one and a half hours.  Overexpression of wild-type AKAP95 and phase separation mutants was performed in HeLa cells to establish the significance of AKAP95's phase separation ability in promoting tumorigenesis. The binding targets of AKAP95 in pre-mRNA were determined by CLIP-seq.


title: AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis (ChIP-Seq)

overall_design: Flag-mEGFP was knocked into the N-terminus of the AKAP95 locus in HeLa cells to tag the endogenous AKAP95. Lentiviruses pLKO.1-shAKAP95, pCDH-CMV-HA-JD-PI95-puro, and pCDH-CMV-HA-H32Q-PI95-puro were packaged in 293T cells with the envelope plasmids psPAX2 and pMD2.G. One million HeLa cells were transduced with 200 μL of concentrated virus by spin infection at 1000 × g for one and a half hours.  Overexpression of wild-type AKAP95 and phase separation mutants was performed in HeLa cells to establish the significance of AKAP95's phase separation ability in promoting tumorigenesis. The binding targets of AKAP95 in genomic loci were determined by ChIP-seq.


title: Single cell-RNA datasets from cell lines and dissociated mouse and maize tissues

city: Tainan

first: Po-Min

last: Chiang

state: TAIWAN

address: No. 35, Xiaodong Road,, Rm. 7068

institute: National Cheng Kung University

summary: A generally applicable method to profile RNA from single cells and nulclei with high sensitivity and throughput is desirable.To demonstrate the potential, cells and nuclei from different sources and species were acquired and profiled.

sample_organism:
Zea mays
Homo sapiens
Mus musculus

platform_organism:
Zea mays
Homo sapiens
Mus musculus

overall_design: Human and mouse cell lines were used to benchmark gene detection sensitivity against other platforms or as spike-ins to demonstrate minimal multiplet formation in the same experiments. Tissues from mouse and maize were directly lysed to collect nuclei, demonstrating the method's applicability to complex multicellular structures.

first: Ya-Wen

last: Hsueh


title: Transcriptional profiling of aged and young mouse hearts

first: Dogacan

last: Yucel

summary: We identified Dnmt3a and Esrrg as the putative regulators of CM aging. Here, we overexpressed Esrrg, Dnmt3a and control GFP proteins in adult hearts and performed bulk RNA-seq to discover molecular pathways associated with these proteins.

overall_design: We isolated total RNA from adult ventricles 3-months after AAV injection. Libraries were prepared and sequenced from individual RNA samples.

first: Michael

last: Trembley

first: William

last: Pu


title: Identify the changed genes that are regulated by Ppp2ca [RNA-seq]

first: Haibo

last: Zhou

state: Shanghai

address: Shangdong Middle street

institute: Renji Hospital

summary: Ppp2ca is a subunit of PP2A complex, which plays critical roles in variaty of tumors and autoimmune diseases. Deletion of Ppp2ca in mice led to hematopoietic disorders, showing increased myeloid differentiation and decreased lymphoid differentiation.  Metabolic analysis indicated that Ppp2ca deficiency resulted in aerobic glycolysis in hematopoietic stem cells (HSCs), with elevated levels of lactate. Genetic deletion of LDHA or blocking of  lactate metabolism was found to be able to rescue the phenotypic abnormal caused by Ppp2ca insufficiency. Therefore, this study proposed that LDHA could be served as a novel target for the treatment of Ppp2ca related diseases.

overall_design:
To investigate the genes regulated by Ppp2ca, we isolated hematopoietic stem cells (HSCs) from the bone marrow of wild type Ppp2ca mice or Ppp2ca knockout mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 wild type HSCs and 3 knockout HSCs.
Comparative gene expression profiling anaysis of RNA-seq data for wild type HSCs and knockout HSCs.


title: Tailoring a CRISPR/Cas-based Epigenome Editor for Programmable Chromatin Acylation and Decreased Cytotoxicity [Perturb-seq]

city: Houston

first: Isaac

middle: B

last: Hilton

state: Texas

address: 6500 Main St., BRC Rm 660

institute: Rice University

summary: Precisely engineering histone acylation states can inform mechanistic epigenetics and catalyze new therapeutic epigenome editing opportunities. Here, we developed engineered lysine acyltransferases that enable the deposition of acetylation and longer-chain acylations in a programmable manner using a dead Cas9 (dCas9) fusion protein. We show that targeting an engineered lysine crotonyltransferase, developed by mutagenizing the native human p300 protein, results in relatively weak levels of endogenous enhancer activation yet retains strong potency when targeted to promoters. We further identify a single mutation within the catalytic core of human p300 that preserves enzymatic activity while promoting more target-specific acetylation and substantially reducing downstream transcriptomic perturbations. Further, this novel fusion protein exhibits low cytotoxicity but maintains high levels of H3K27ac deposition, enabling markedly improved lentiviral delivery. We leveraged this enhanced delivery and improved cytotoxicity profile to perform single-cell CRISPR activation screening. Using proteomics and a panel of engineered p300 variants, we also discover acylation-specific interactions and link the cytotoxicity of the wild-type p300 core domain to altered activities among DNA repair machinery components. These new programable epigenome editing tools and insights expand our ability to perform functional genomic screens, multiplexed cell engineering, and, more broadly, understand the mechanistic role of lysine acylation in epigenetic and cellular processes.

overall_design: Perturb-seq of non-coding elements in K562 cells expressing dCas9-p300 variants

first: Jacob

last: Goell


title: Transcriptional profiling of aged and young mouse hearts [scMulti-ome]

summary: Cardiac aging is a major risk factor for cardiovascular diseases, yet the underlying molecular mechanisms remain poorly understood. In this study, we employed a multi-omics approach combining single-nucleus RNA-seq, ATAC-seq, and reduced representation bisulfite sequencing (RRBS) to comprehensively characterize the cellular and molecular landscape of cardiomyocyte (CM) aging in mice.

overall_design: We isolated cardiac cell nuclei and performed concurrent scRNA and scATAC-seq to identify molecular changes between old and young cell types.


title: Cell-cycle-dependent repression of histone gene transcription by histone H4

first: Jorja

last: Henikoff

summary: In all eukaryotes DNA replication is coupled to histone synthesis to coordinate chromatin packaging of the genome. Canonical histone genes coalesce in the nucleus into the Histone Locus Body (HLB), where gene transcription and 3’ mRNA processing occurs. Both histone gene transcription and mRNA stability are reduced when DNA replication is inhibited, implying that the Histone Locus Body senses the rate of DNA synthesis. In Drosophila melanogaster, the S-phase-induced histone genes are repeated in an ~100 copy repeat unit array, whereas in humans, these histone genes are scattered. In both organisms these genes coalesce into Histone Locus Bodies.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: We used a transgenic histone gene reporter and RNAi in Drosophila to identify canonical H4 histone as a unique repressor of histone synthesis during the G2 phase in germline primary spermatocytes.

first: Kami

last: Ahmad

first: Matt

last: Wooten

first: Brittany

middle: N

last: Takushi

first: Velinda

last: Vidaurre

first: Xin

last: Chen

first: Steven


title: Knockdown MSLN enhances anti-PD-1 therapy efficacy in high-grade serous ovarian cancer via modulating tumor microenvironment. [cell line]

first: Haiou

last: Liu

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor tissues ID8-agg celllines with the knockdown of MSLN or not.

first: Jiaqi

last: Lu

first: Yujing

last: Zhong

first: Yiying

last: Wang

first: Chenyang


title: Identify the genomic occupying sites of acetylated H3K27 that are affected by Ppp2ca gene [CUT&RUN]

summary: Ppp2ca is a subunit of PP2A complex, which plays critical roles in a variaty of tumors. Compared with control, ppp2ca deficient hematopoietic stem cells (HSCs) showed increased myeloid differentiation and decreased lymphoid differentiation. We further found that Ppp2ca deficiency led to global increased acetylation of H3K27 in HSCs.  Consistent with these, the acetylation levels of H3K27 in the promoters of myeloid genes were found elevated. Thus, PPP2CA might affect hematopoietic differentiation through epigenetic regulation.

overall_design:
To investigate the genomic sites occupied by acetylated H3K27, we isolated hematopoietic stem cells (HSCs) from the bone marrow of 3 wild type Ppp2ca mice and 3 Ppp2ca deficient mice.
1×10^5 primary cells were prepared by using the Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina (Vazyme, China) according to the protocol.


title: Symptomatic versus asymptomatic host responses to Sclerotinia sclerotiorum

city: chongqing

first: binnian

last: tian

address: tianshenglu

institute: binniantian

summary:
To exploite symptomatic versus asymptomatic host responses to Sclerotinia sclerotiorum to identify  Plasticity of transcription  leading to either an endophytic or a pathogenic lifestyle
We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 different samples after 2 days.

sample_organism:
Brassica napus
Triticum aestivum

platform_organism:
Brassica napus
Triticum aestivum

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 9 samples.

first: Binnian

last: Tian


title: RNA sequencing data of normal glucose tolerant (NGT) and gestational diabetes (GDM) pregnant women

first: Liying

last: Jiang

address: 279 zhouzhugong road

institute: Shanghai University of Medicine and Health Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Total RNA was isolated from lymphocyte. We compared the circRNA, lncRNA and mRNA expression profiles between healthy and GDM women by RNA sequencing, and determined the signaling pathways associated with the changes. Our study offers new insights into circulating biomarkers of GDM and thus provides a valuable resource for future investigations.

overall_design: Sample from 12 pregnant women (6 from normal controls and 6 from GDM patients) were used for RNA sequencing analysis.


title: AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis (RNA-Seq)

first: Bi

last: Shi

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Wild-type and Akap95-/- mouse bone marrow cells were transfected with pMSCV-MLL-AF9-IRES-GFP retrovirus and cultured for multiple passages. Flag-mEGFP was knocked into the N-terminus of the AKAP95 locus in HeLa cells to tag the endogenous AKAP95. Lentiviruses pLKO.1-shAKAP95, pCDH-CMV-HA-JD-PI95-puro, and pCDH-CMV-HA-H32Q-PI95-puro were packaged in 293T cells with the envelope plasmids psPAX2 and pMD2.G. One million HeLa cells were transduced with 200 μL of concentrated virus by spin infection at 1000 × g for one and a half hours. The experiments include RNA-seq data for wild-type and AKAP95-/- bone marrow cells transfected with AKAP95 to demonstrate the importance of AKAP95 in MLL leukemogenesis. Overexpression of wild-type AKAP95 and phase separation mutants was performed in HeLa cells to establish the significance of AKAP95's phase separation ability in promoting tumorigenesis.

first: Yongkun

last: Luan

first: Hao

first: Wei

last: Li


title: Gene expression in lung resident macrophages and recruited macrophages in pulmonary hypertension

first: Shumin

last: Guo

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: We generated a Lineage tracing system to trace the fate of resident macrophages and recruited macrophages using GFP and RFP fluorescence respectively, in a SuHx-induced mouse PH model.          Cx3cr1+GFP+resMФs and RFP+recMФs was achieved through bone marrow transplantation system and flow cytometry sorted.  Gene-expression data was collected via microarray analysis.

overall_design: For lineage tracing of macrophages, we generated fluorescent chimeric mice (RFP→Cx3cr1CreR26iGFP). The mice were divided into normoxia control group and SUHx-induced pulmonary hypertension group. After the induction of pulmonary hypertension, cells were sorted, and RFP-positive macrophages and GFP-positive macrophages were sorted for sequencing, with three independent samples per group


title: AKAP95 condensates regulate transcription and can be targeted in MLL-fusion driven oncogenesis

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

overall_design: Refer to individual Series


title: Multiscale profiling of tyrosine kinase inhibitor cardiotoxicity reveals mechanosensitive ion channel PIEZO1 as cardioprotective [snMultiome]

status: Public on Nov 10 2025

city: Palo Alto

first: Yu

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: Tyrosine kinase inhibitors (TKIs) have improved cancer outcomes but are limited by cardiovascular toxicity, most notably hypertension and heart failure. The underlying mechanisms remain poorly understood, hindering the development of protective strategies. Here, we investigated the role of endothelial mechanotransduction in mediating vascular and cardiac injury caused by the VEGFR-targeting TKI sunitinib. Using patient-specific induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) and a mouse model of TKI-induced hypertension, we identified downregulation of PIEZO1, a mechanically activated ion channel, as a central driver of endothelial dysfunction. Restoring PIEZO1 expression, either pharmacologically with Yoda1, a selective agonist, or through inducible overexpression in iPSC-ECs, reversed sunitinib-induced endothelial dysfunction and mitigated its hypertensive effects, providing both mechanistic and genetic validation of PIEZO1’s protective role against vascular toxicity. In mice, Yoda1 co-treatment prevented the long-term cardiac dysfunction observed following sunitinib exposure, and normalized elevations in circulating cardiac stress biomarkers. Single-nuclei multiomic profiling of mouse hearts revealed that sunitinib exposure activated chromatin remodeling and fibrogenic programs, which were reversed with PIEZO1 activation. Human engineered cardiac organoids further demonstrated that sunitinib impaired cardiomyocyte function only in the presence of endothelial cells, confirming a role for disrupted endothelial-cardiomyocyte crosstalk in TKI cardiotoxicity. Together, these findings identify endothelial PIEZO1 as a critical mediator of TKI-induced hypertension and cardiac dysfunction and highlight PIEZO1 activation as a potential therapeutic strategy for protecting cardiovascular health during cancer therapy.

overall_design: snMultiome of heart tissues collected from mice treated with vehicle, sunitinib, and sunitinib + Yoda1

first: Nazish

last: Sayed


title: Identify the Ppp2ca binding sites in the genome [CUT&TAG]

first: Haibo

last: Zhou

summary: Ppp2ca is a subunit of PP2A complex. In addition to functioning through its phosphatase activity, PPP2CA has been demonstrated to form a complex with the INTEGRATOR in the promoter of genes and regulate downstream gene expression at the transcriptional level.  We found that Ppp2ca deficiency resulted in a global increased transcripiton of genes, with most significantly changed genes enriched in metabolic pathways.

overall_design:
To investigate the genomic sites occupied by PPP2CA, we isolated hematopoietic stem cells (HSCs) from the bone marrow of wild type Ppp2ca mice.
1×10^5 primary cells were prepared by using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, China) according to the protocol.


title: Multiscale profiling of tyrosine kinase inhibitor cardiotoxicity reveals mechanosensitive ion channel PIEZO1 as cardioprotective

overall_design: scRNA-seq of vacular tissues collected from mice treated with vehicle, sunitinib, and sunitinib + Yoda1


title: Reconstructing Epigenomic Dynamics through a Single-Cell Multi-Epigenome Data Integration Framework

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

summary: Transcriptional regulation arises from the dynamic and combinatorial actions of multiple regulatory factors on genomic DNA. Although many epigenomic regulators have been identified, the precise order in which these factors accumulate at individual gene loci to activate transcription remains unclear. Here we show a single-cell data integration framework that infers the binding order of multiple chromatin factors at single-cell resolution. Central to this framework is sci-mtChIL-seq, a scalable single-cell method that simultaneously profiles genome-wide binding of RNA polymerase II (RNAPII) and diverse epigenomic regulators. By defining transcriptional states through RNAPII occupancy and integrating multiple sci-mtChIL-seq datasets, we systematically link the combinatorial patterns of transcription factor binding, histone modifications and chromatin remodeling. This framework reveals the temporal coordination among chromatin factors during transcriptional activation, providing a powerful approach to uncover context-dependent epigenomic dynamics and the principles of gene regulation in complex cellular systems.

overall_design: Sci-mtChIL-seq for H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3, H3K36me3, H3.1/3.2, and RNA PolII in SP2 cells and sci-mtChIL-seq for RNA PolII-H3K4me3, RNA PolII-H3K27me3 and RNA PolII-MyoD in embryo and for RNA PolII-H3K4me3, RNA PolII-H3K27me3, RNA PolII-MyoD, RNA PolII-H3K27ac, RNA PolII-Brg1 and RNA PolII-Myog in  NIH3T3 cells.

first: Takeru

last: Fujii

first: Akihito

last: Harada


title: Polyamine-dependent metabolic shielding regulates alternative splicing

city: Derio

first: Arkaitz

last: Carracedo

address: Bizkaia Science and Technology Park, building 801A

country: Spain

institute: CIC bioGUNE

summary: Metabolites are central to cellular homeostasis. Whereas much emphasis has been placed on their relevance to meet energetic and biosynthetic demands, metabolic intermediates also function as signaling molecules. Here we show that polyamines, small polycations critical to cellular homeostasis1-3, regulate the process of alternative pre-mRNA splicing. We find that the inhibition of polyamine synthesis increases the phosphorylation of spliceosomal proteins, concomitant with a remarkable perturbation of alternative splicing in cells and tissues. Mechanistically, molecular modeling combined with biochemical assays revealed that polyamines bind to acidic phosphorylatable motifs in splicing factors of the U2 snRNP SF3 subcomplex, thus preventing the action of kinases. The molecular process through which polyamines regulate protein phosphorylation is a phenomenon that we define as “metabolic shielding”.

overall_design:
Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in DU145 cells.
Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing upon the absence or presence of U2 snRNP SF3A3 subcomplex member.
Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in the skeletal muscle of wild-type mice.
Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in HeLa cells.
Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in mouse embryonic stem cells under the effect of SAM486A and DFMO
Deep-coverage RNA-seq analysis to test the effect of polyamine biosynthesis inhibition on splicing in mouse embryonic stem cells under the effect of SAM486A, DFMO and BENSpm

first: Amaia

last: Zabala-Letona

first: Mikel

last: Pujana-Vaquerizo

first: Belen

last: Martinez-Laosa

first: Maria

last: Ponce-Rodriguez

first: Saioa

last: Garcia-Longarte

first: Isabel

last: Mendizabal

first: Ana

last: Gimeno

first: Malgorzata

last: Rogalska

first: Joycelyn

last: Tan

first: Diana

last: Cabrera

first: Sebastiaan

last: van Liempd

first: Pilar

last: Ximenez-Embun

first: Sergio

last: Espinosa

first: Maider

last: Fagoaga-Eugui

first: Francesca

last: Peccati

first: Ianire

last: Astobiza

last: Arana-Castañares

first: Sarah

last: Cherkaoui

last: Sendino

first: Inés

last: Martín-Barros

last: Ercilla

first: Laura

last: Bozal

first: Onintza

last: Carlevaris

last: Arruabarrena-Aristorena

first: Encarnación

last: Pérez-Andrés

first: Telmo

last: Santamaría-Zamorano

first: Juan

last: Ferrer-Bonsoms

first: Fernando

last: Carazo

first: Maciej

last: Cieśla

first: Cesar

last: Lobato

first: Joan

last: Seoane

first: Natalia

last: Martín-Martín

first: Rosa

last: Barrio

first: James

last: Sutherland

last: Aransay

first: Juan Manuel

last: Falcón-Pérez

first: Barbara

last: Martínez-Pastor

first: Angel

last: Rubio

first: Francisco

last: Blanco

first: Michael

last: Hogarty

first: Raphael

last: Morscher

first: Edurne

last: Berra

first: Remigiusz


title: The origin of hepatocellular carcinoma is regulated by metabolic zonation [Xenium]

city: Dallas

first: Hao

last: Zhu

address: 5323 Harry Hines Blvd

institute: UTSW

summary: The origin of cancer is poorly understood because premalignant cells are rarely followed in their native environments. While the spatial compartmentalization of metabolic functions is critical for proper liver function, it is unknown if cancers arise from some zones but not others, and if there are metabolic determinants of cancer risk. Zone-specific, mosaic introduction of Ctnnb1 and Arid2 mutations, commonly co-mutated genes in hepatocellular carcinoma (HCC), showed that position and metabolic context determine clone fates. Ctnnb1/Arid2-driven cancers were much more likely to arise in zone 3. The zone 3 genes Gstm2 and Gstm3 were required for efficient HCC initiation, in part through inhibition of ferroptosis. In the liver, the zonal determinants of HCC development can reveal metabolic vulnerabilities of cancer.

overall_design: Genetic mouse models with zone-specific CreER were given tamoxifen at P28 to induce zone-specific tumor drivers and livers were collected one month later. One mouse each from our zone 1 and zone 3 tumor models were collected and compared to a wild type mouse of the same age.

first: Jason

last: Guo

first: Boyuan

last: Li


title: The origin of hepatocellular carcinoma is regulated by metabolic zonation [Single Nuclear Genotyping]

type: Genome variation profiling by high throughput sequencing

overall_design: Genetic mouse models with zone-specific CreER were given tamoxifen at P28 to induce zone-specific tumor drivers and euthanized at 5 months post-tamoxifen prior to tumor formation

first: Benjamin

last: Kroger


title: The impact of small molecule L-2-hydroxyglutarate on mRNA m6A in renal cancer

city: Birmingham

first: Sunil

last: Sudarshan

state: AL

address: FOT 1120 -  510 20th Street South

institute: University of Alabama at Birmingham

summary: To investigate L-2HG's impact on RNA methylation (m6A), we performed a comparitive analysis of m6A IP profiles in high L-2HG RCC cells  compared with low L-2HG Cells.

overall_design: RCC cells with high basal L-2HG were stably transduced with control vector (CV) or L2HGDH cDNA.  RNA was then extracted from high L-2HG cells (CV) and low L-2HG Cells (L2HGDH).  m6A methylated RNA was then immunprecipiated followed by RNAseq (MeRIP).


title: The origin of hepatocellular carcinoma is regulated by metabolic zonation


title: The effect of HSD17B1 inactivating mutation in adult mouse ovary gene expression

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

summary: We compared the mRNA expression in ovaries of female mice with an inactivating Ser143Ala mutation of HSD17B1 (HSD17B1-KI) and wild-type (WT) littermates. We aimed to identify the possible differences in gene expression patterns due to the disruption of estrogen biosynthesis caused by the lack of HSD17B1 activity.

overall_design: Ovaries were collected from 6-month-old HSD17B1-KI and WT females during the estrus phase of the estrous cycle.

first: Arttu

last: Junnila

first: Nataliia

last: Petruk

first: Hanna

last: Heikelä

first: Guillermo

last: Martinez-Nieto


title: Optineurin Shapes Basal and LPS-Induced Transcriptomes in BV2 Microglia

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

summary: The OPTN gene is linked to neurodegenerative diseases like amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which are characterized by chronic microglial activation. Optineurin regulates inflammatory signaling, autophagy, and trafficking, but its role in microglia is not well understood. We used bulk RNA sequencing to profile CRISPR-Cas9-mediated optineurin knockout (KO) and wild-type (WT) BV2 microglia under basal conditions and upon LPS stimulation. At baseline, optineurin KO altered approximately 7% of the transcriptome, with a notable downregulation of type I interferon and antiviral pathways. LPS stimulation in wild-type cells triggered a broad transcriptional shift (~35% of genes). This LPS-induced response was blunted in optineurin-deficient microglia, with ~16% of genes changed relative to the KO baseline. Furthermore, LPS-treated optineurin KO microglia notably diverged from LPS-treated wild-type cells, with ~26% differentially expressed genes. Our findings establish optineurin as a key regulator of the microglial transcriptome. Its loss weakens basal interferon-mediated immune surveillance and decouples the canonical inflammatory response from cell cycle arrest upon activation.

overall_design: Bulk RNA sequencing was performed on four conditions: untreated wild-type (CTRL), optineurin knockout (KO), LPS-treated wild-type (LPS), and LPS-treated optineurin knockout (KO_LPS) BV2 cells. Triplicate samples were used for each condition.

first: Sara

last: Cappelli

first: Josip

last: Peradinoviƒá

first: Alessandra

last: Longo

first: Nikolina

last: Mohoviƒá

first: Purba

last: Mandal

first: Cristiana

last: Stuani

first: Jason R.

last: Cannon

first: Priyanka

last: Baloni

first: Benedetta

last: Leoni

first: Gordana

last: Apic

first: Robert R.

last: Russell

first: Emanuele

last: Buratti

first: Ivana

last: Munitic


title: Differential activity of transcription factors and neuronal effectors during the development of pikeperch brain

city: České Budějovice

first: Radka

last: Symonova

address: Branisovska 1645/31a

department: Department of Applied Informatics

country: Czech Republic

institute: Faculty of Science, University of South Bohemia

summary: Juvenile pikeperch (Sander lucioperca) undergo several ontogenetic shifts whose timing determines the survival of their first winter. The shift from a planktivorous phenotype to a more active predatory (piscivorous) behavior is accompanied by moving from pelagic to demersal habitat with much more stimuli and hence by potential brain functional reorganizations. During two consecutive years, we collected planktivores and piscivores, with different body sizes between the years recording distinct stages relative to the shift and analyzed their whole-brain transcriptomes framed by detailed ecological knowledge. The differential gene transcription analysis identified a distinct non-overlapping group of transcription factors (TFs) significantly upregulated in each phenotype: TFs upregulated in planktivores correspond to initial establishment of brain regions and overall architecture; TFs upregulated in piscivores correspond to the refinement of neuronal populations and the formation of specific neuronal circuits. The planktivorous phenotype independently of body size was characterized by interconnected activity of two TFs, fosab and junba. Gene set enrichment revealed extracellular matrix and collagen-related Gene Ontology terms in piscivores from both years. A highly increased activity of solute carrier (Slc) transporters was identified in the smaller-bodied piscivorous phenotype (20 members of 12 Slc families). The overall count of Slc genes transcribed in pikeperch brain was 334, which is higher than known for humans (287). The neurotranscriptomics results reflected differences in body size and matched with ecological data and survival rates. The multidimensional brain regulome indicated that the intra-phenotypic body size difference can translate into the specific gene activity of the brain in juvenile pikeperch. The period of transition to piscivory appears to be an important ontogenetic step accompanied by increased specific transcription activity.

overall_design: RNA-seq profiling of juveinle pikeperch brains of planktivorous (N) and piscivorous (L/C) phenotypes during 2 consequtive seasons 2022-2023


title: H3K9 Trimethylation Dictates Neuronal Ferroptosis through repressing Tfr1

city: Beijing

first: Liye

last: Hu

address: #10 YouAnMenWai XiTouTiao, Fengtai District

institute: Capital medical university

summary: Chromatin immunoprecipitation sequencing (ChIP-seq) for histone modifications H3K9me3 in N2A cells.

overall_design: Cultured N2A cells treated with hemin or DMSO. Data of experiments were presented in triplicate. The chromatin DNA was immunoprecipitated with anti-H3K9me3 or IgG from N2A cells followed with purification.

first: Ting

last: Lan

first: Qian

last: Li

first: Chenguang

last: Zhang


title: Transcriptomic profile of embryoid bodies under hypoxia at single cell level

city: Madrid

first: Yosra

last: Berrouayel

address: Arturo Duperier, 4

institute: Universidad Autónoma de Madrid

summary: Despite their limitations, embryoid bodies can mimic early embryonic development stages. Our previous results showed that hypoxia induces angiogenesis in this model, increasing the number of endothelial cells. This observation is concomitant with a reduction of the percentage of endothelial cells in S-phase. Our hypothesis is that the increase in the number of endothelial cells is due to a higher rate of differentiation of progenitor cells.

overall_design: Embryoid bodies were generated from murine stem cells and differentiated at two distinct time points: 1) 8 days either in complete normoxia or with a final 16-hour pulse of hypoxia, and 2) 10 days either in complete normoxia or with a hypoxic exposure during the last 48 hours.

first: Luis

last: del Peso Ovalle

first: Benilde

last: Jiménez Cuenca

first: Bárbara

last: Acosta Iborra

first: Laura

last: Puente Santamaría

last: Berrouayel Dahour


title: Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell [RNA004]

city: singapore

first: YUE

last: WAN

address: 1, #20-10 Fusionopolis Way, Connexis, North Tower, 138632

country: Singapore

institute: Genome Institute of Singapore,A*STAR

summary: RNA structure-based gene regulation remains under-explored in eukaryotes. While RNA can form different conformations in solution, the extent to which it folds into structure ensembles and how the different conformations regulate gene expression still needs to be fully understood. We coupled the SHAPE compound NAI-N3 with direct RNA sequencing to identify structure modifications along a single RNA molecule (sm-PORE-cupine). Using a combination of base mapping and direct signal alignment, we boosted the percentage of mappable RNA molecules from direct RNA sequencing. Using Bernoulli Mixture Model (BMM) clustering, we show that we can separate RNA structure ensembles from ligand-bound and unbound riboswitches accurately, identify isoform-specific structure ensembles along the SARS-CoV-2 genome, and determine RNA structure ensembles in the transcriptome of a eukaryote, C. albicans, at yeast (30°C) and hyphae (37°C) states. We observed that RNAs are more structurally homogenous at 37°C compared to 30°C, are more variable in vivo than in vitro, and show higher homogeneity in 3’UTRs than in the coding region. We also identified structure ensembles that are associated with changes in translation efficiency and decay in C. albicans at 30°C and 37°C and validated translational changes using reporter assays. Our work shows that single-molecule RNA structure probing using direct RNA sequencing can be applied to diverse transcriptomes to study the complexity and function of RNA structures.

overall_design: We first treated the IVT RNA and C. albicans cell using structure probing compounds to label the RNA structures, and then sequencing the labeled RNAs using Nanopore direct RNA-seq, the RNA structure signals were then analysized by sm-PORE-cupine approach. (see methods for more details)

first: Jiaxu

last: Wang

first: Han

last: Jian

first: Wenting

last: Tan

first: Anthony

last: Cheng

first: Jong Ghut Ashley

last: Aw

first: Yue

first: Guisheng

last: Zeng

first: Niranjan

last: Nagarajan

last: Wan


title: Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell [nanopore_DRS]

sample_organism:
Candida albicans
synthetic construct

platform_organism:
Candida albicans
synthetic construct


title: Age-dependent immune responses and resident cell dynamics in young mice following pneumonia [RNA-Seq]

city: Philadelphia

first: Sylvia

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

summary: A developmental murine model of pneumonia was used to investigate how lower respiratory tract E. coli infections differentially affects lung immune responses and cell behavior in young mice (neonates; PND5 and juveniles; PND12). Acutely, juveniles recover more quickly than neonates, but alveolar simplification occurred in both groups 6-8 weeks post-infection. Single-cell RNA sequencing revealed transient inflammatory responses in neutrophils, macrophages, and fibroblasts at 48 h post infection in both age groups with a partial return to baseline by 96h. The highly proliferative neonatal alveolar type 2 (AT2) cells showed a modest decrease at 48h post infection, whereas the quiescent juvenile AT2 cells exhibited a proliferative response only post-infection. Neonatal PDGFRα+ fibroblasts had higher expression of inflammatory genes post infection than juveniles and in vitro stimulation of PDGFRα+ fibroblasts with LPS-exposed primary macrophages alone, induced expression of the inflammatory marker SAA3. We conclude that early-life pneumonia alters lung homeostasis in an age-differential manner, potentially affecting lung structure and function in adulthood.

overall_design: Sorted AT2 cells or fibroblasts from the lungs of mice infected with E. coli or PBS (controls) at the neonatal (PND5) or juvenile (PND12) time-points were collected for bulk RNA-seq.

first: Benjamin

last: Singer

first: Sharon

last: McGrath-Morrow


title: Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell

overall_design: C. albicans were treated with Thiolutin to stop transcription, and the RNA were then collected for a seria time points, and we then do the RNA seq for each time points to determin the RNA half-life.


title: Selecting specific bio-markers and researching mechanisms of immune regulation from inhalation injury (ILI) and traumatic lung injury (TLI) based on single cell RNA sequencing technology

city: ShangHai

first: Chenru

last: Wei

address: NO.168,Changhai Road,Yangpu District ,Shanghai,China

institute: the first  Affiliated Hospital of Naval Medical University

summary: To profile the circulating immunological traits of patients with traumatic lung injury (TLI) and inhalation injury (ILI),providing a new direction for the depth research of the pathogenesis, and providing new immune-related targets for diagnosis of the severity of lung injury and treatment, we performed scRNA-seq of neutrophil and PBMCs from fresh circulating blood from 3 patients with TLI and 3 patients with ILI at longitudinal timepoints,as well as peripheral blood from 3 health controls(HCs).We conclude that at different stages of the course of TLI or ILI, there are differences in the proportion of immune cell subsets. PMN function is disordered in the acute stage and the progressive stage, and immature neutrophil subsets of different degrees appear which indicates acute myeloid cells are generated. At the same time, the interactions among the subpopulations of myeloid cells are significantly enhanced during the acute phase, which synergistically promote the development of TLI or ILI.

overall_design: We performed single-cell transcriptomic sequencing (BD Rhapsody) on neutrophil and PBMCs extracted from the fresh circulating blood from 3 patients with TLI and 3 patients with ILI at longitudinal timepoints,as well as peripheral blood from 3 health controls(HCs). Three time points are chosen by clinical conditions of patients with TLI or ILI: day 1 post hospital admission, day 3 post hospital and the day before discharged which matched to acute stage, progressive stage and convalescence.

first: Zong

last: Shen

first: Guosheng

last: Wu

first: Tao

last: Tang

first: Wenjia

last: Hou

first: Banghui

last: Zhu

first: Yu

last: Sun


title: Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment

city: New York

first: Nicholas

last: Tolman

state: NY

department: Ophthalmology

institute: Columbia University

summary: Since the trabecular meshwork (TM) is central to intraocular pressure (IOP) regulation and glaucoma, a deeper understanding of its genomic landscape is needed. We present a multimodal, single-cell resolution analysis of mouse limbal cells (includes TM). In total, we sequenced 9,394 wild-type TM cell transcriptomes. We discovered three TM cell subtypes with characteristic signature genes validated by immunofluorescence on tissue sections and whole-mounts. The subtypes are robust, being detected in datasets for two diverse mouse strains and in independent data from two institutions. Results show compartmentalized enrichment of critical pathways in specific TM cell subtypes. Distinctive signatures include increased expression of genes responsible for 1) extracellular matrix structure and metabolism (TM1 subtype), 2) secreted ligand signaling to support Schlemm’s canal cells (TM2), and 3) contractile and mitochondrial/metabolic activity (TM3). ATAC-sequencing data identified active transcription factors in TM cells, including LMX1B. Mutations in LMX1B cause high IOP and glaucoma. LMX1B is emerging as a key transcription factor for normal mitochondrial function and its expression is much higher in TM3 cells than other limbal cells. To understand the role of LMX1B in TM function and glaucoma, we single-cell sequenced limbal cells from Lmx1bV265D/+ mutant mice (2,491 TM cells). In V265D/+ mice, TM3 cells were uniquely affected by pronounced mitochondrial pathway changes. Mitochondria in TM cells of V265D/+ mice are swollen with a reduced cristae area, further supporting a role for mitochondrial dysfunction in the initiation of IOP elevation in these mice. Importantly, treatment with vitamin B3 (nicotinamide), to enhance mitochondrial function and metabolic resilience, significantly protected Lmx1b mutant mice from IOP elevation.

overall_design: All sequencing data were obtained from mouse ocular limbal strips, a portion of the anterior eye. Briefly, the posterior eye was removed by cutting between the limbus and sclera, followed by removal of the lens. A small circular incision was then made in the anterior cornea to excise the central one-third of the corneal area. Only limbal tissues were collected. In total, six samples were generated: five by single-cell RNA sequencing (scRNA-seq) and one by single-nucleus RNA and ATAC sequencing (multiome). Three samples were from 2-month-old C57BL/6J mice and sequenced at Columbia University (two scRNA-seq and one multiome). One sample was from 3-month-old C57BL/6J mice and sequenced at Duke University. Two samples were from 2-month-old C57BL/6J mice carrying the Lmx1b^V265D mutation and sequenced at Columbia University. Each sample consisted of limbal strips pooled from eight eyes for a single sequencing run. Columbia samples included both sexes, whereas the Duke sample consisted only of male mice.

first: Revathi

last: Balasubramanian

first: Taibo

last: Li

first: Guorong


title: Inhibition of the SETD8 H4K20-mono-methyltransferase Limits the Global Accessibility of the Infecting Herpes Simplex Virus Genome [ATAC-seq]

city: Bethesda

first: Jesse

last: Arbuckle

state: MD

address: 33 North Dr, Bldg 33, Rm 3W10A

department: Laboratory of Viral Diseases

institute: National Institutes of Health, NIAID

summary: Epigenetic modulation of herpes simplex virus (HSV) immediate early (IE) genes is a critical regulatory parameter governing lytic infection, latency, and viral reactivation. Multiple factors, including epigenetic complexes associated with the cellular transcriptional coactivator HCF-1, modulate the state of HSV-1 chromatin. As an approach to identify novel epigenetic factors that regulate the initial stage of HSV-1 infection, an epigenetic chemical probe library was screened for their impact on viral IE gene expression. This screen identified several epigenetic inhibitors that modulated IE expression. Notably, UNC0379, an inhibitor of the histone H4K20 mono-methyltransferase SETD8, potently repressed HSV-1 infection in vitro and in vivo. Furthermore, SETD8 inhibition suppressed HSV-1 reactivation in a mouse ganglia explant model. Importantly, these results correlated with enhanced heterochromatin suppression and decreased accessibility of HSV-1 chromatin. Reduced IE transcription was concomitant with disruption in recruitment of HCF-1 and RNA polymerase II (RNAPII). These results are consistent with the established roles of SETD8 in promoting chromatin accessibility through H4K20me1 deposition and regulating transcriptional elongation, suggesting that SETD8 may facilitate multiple steps in regulation of HSV-1 IE gene expression.

overall_design: ATAC-seq of HFF cells treated with UNC0379 or vehicle and infected with HSV-1. Samples are in triplicate.

first: Tovah

last: Markowitz

first: Thomas

last: Kristie


first: YUE

last: WAN

overall_design: We first treated the IVT RNA using structure probing compounds to label the RNA structures, and then sequencing the labeled RNAs. (see methods for more details)

first: Jiaxu

last: Wang

first: Han

last: Jian

first: Wenting

last: Tan

first: Guisheng

last: Zeng

first: Anthony

last: Cheng

first: Jong Ghut Ashley

last: Aw

first: Yue

first: Niranjan

last: Nagarajan

last: Wan


title: cFLIP suppresses Caspase-1- and MLKL-independent perinatal lethality driven by autoprocessing impaired caspase-8 D387A

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

summary: Death ligands, including FAS ligand (FASL) and tumor necrosis factor (TNF), trigger apoptosis by promoting caspase-8 dimerization and activation. Impaired FAS signaling causes unconventional lymphocytes to accumulate, resulting in lymphadenopathy. Although autoprocessing of caspase-8 is considered important for apoptosis, autoprocessing-deficient Casp8 D387A/D387A mice do not develop lymphadenopathy. We show that this is because heterodimers of caspase-8 D387A and cFLIP, besides suppressing MLKL-driven necroptosis, can also induce apoptosis. Interestingly, caspase-8 D387A elicited MLKL- and caspase-1-independent intestinal atrophy and perinatal lethality in mice lacking cFLIP. Caspase-8 D387A interacted with FADD and RIPK1 in the intestine, where there was aberrant cleavage of N4BP1 and caspase-3, plus enhanced NF-κB signaling. Eliminating FADD, the adaptor protein that promotes caspase-8 oligomerization, prevented this perinatal lethality. Collectively, our results suggest that cFLIP forms heterodimers with caspase-8 D387A to promote apoptosis in some contexts, while limiting the activity of caspase-8 D387A homodimers in others.

overall_design: Mlkl KO with Casp8 KI and Casp1 KOs in different tissues and cell lines

first: R

first: N

last: Rohatgi


title: Filovirus Infection Disrupts Epithelial Barrier Function and Ion Transport in Human iPSC-Derived Gut Organoids

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: Gastrointestinal (GI) dysfunction, characterized by severe diarrhea and dehydration, is a central contributor to morbidity and mortality in filovirus disease in patients, yet the role of the epithelium in this clinical outcome remains poorly defined. Here, we employ induced pluripotent stem cell (iPSC)-derived human intestinal (HIOs) and colonic organoids (HCOs) to model Ebola virus (EBOV) and Marburg virus (MARV) infection. These organoids are permissive to filovirus infection and support viral replication. Bulk RNA sequencing revealed distinct intestinal and colonic epithelial responses, including apical and junctional disruption and a delayed virus-specific induction of interferon-stimulated genes. Moreover, infection impaired adenylate cyclase signaling and CFTR-mediated ion transport, providing mechanistic insight into virus- induced secretory diarrhea. This platform recapitulates key features of human GI pathology in filoviral disease and serves as a powerful system to dissect host-pathogen interactions and identify therapeutic targets.

overall_design: To assess the effects of filovirus infection on the human gastrointestinal tract, we exposed induced pluripotent stem cell (iPSC)-derived human colonic organoids (HCOs) to Ebola virus (EBOV) and Marburg (MARV) virus. Bulk RNA sequencing (bulk RNA-seq) was performed on proximal HIOs (n = 3), distal HIOs (n = 3), and mock-infected controls (n = 3) at 1 and 3 days post-infection to identify transcriptomic changes. These findings were further supported by immunohistochemistry and immunofluorescence assays to validate viral infection.

first: Elizabeth Yvonne

last: Flores

first: Aditya

last: Mithal


title: Inhibition of the SETD8 H4K20-mono-methyltransferase Limits the Global Accessibility of the Infecting Herpes Simplex Virus Genome [ChIP-seq]

first: Jesse

last: Arbuckle

overall_design: ChIP-seq of HFF cells treated with UNC0379 or vehicle and infected with HSV-1. IP was done with anti-RNAPII-NTD. Samples are in duplicate.

first: Tovah


overall_design: To assess the effects of filovirus infection on the human gastrointestinal tract, we exposed induced pluripotent stem cell (iPSC)-derived human intestinal organoids (HIOs) and colonic organoids (HCOs) to Ebola virus (EBOV) and Marburg (MARV) virus. Bulk RNA sequencing (bulk RNA-seq) was performed on proximal HIOs (n = 3), distal HIOs (n = 3), and mock-infected controls (n = 3) at 3 days post-infection to identify transcriptomic changes. These findings were further supported by immunohistochemistry and immunofluorescence assays to validate viral infection.


title: The origin of hepatocellular carcinoma is regulated by metabolic zonation [RNA-seq]

first: Hao

last: Zhu

state: TX

overall_design: Genetic mouse models with zone-specific CreER were given tamoxifen at P28 to induce zone-specific tumor drivers and followed for 6-12 months post-tamoxifen for tumor formation. WT C57/BL6 mice used for controls were treated with AAV-Cre and were maintained on normal chow diet for up to 12 months.

first: Jason

last: Guo

first: Yunguan

first: Yi

last: Han

first: Tao


title: FSP1 and histone deacetylases suppress cancer persister cell ferroptosis

city: La Jolla

first: August

last: Williams

address: 9500 Gilman Dr.

department: Dermatology

institute: UC San Diego

summary: Cancer persister cells which survive oncogene targeted therapies are sensitized to ferroptosis but mechanistic understanding of this vulnerability remains limited. Here, we found that while levels of iron, glutathione and various ferroptosis suppressing enzymes vary among persister cell types, ferroptosis suppressor protein 1 (FSP1) is downregulated in multiple persister cell types and persister cells which survive glutathione peroxidase 4 (GPX4) inhibition rely upon residual FSP1 to survive. Furthermore, persister cells which survive GPX4 inhibition downregulate oxidative phosphorylation, a key source of mitochondrial reactive oxygen species which are required for persister cell ferroptosis. We also found that persister cell treatment with histone deacetylase inhibitors induce reactive oxygen species and sensitize multiple persister cell types to GPX4 inhibition. Together, these findings reveal that FSP1 and histone deacetylases suppress persister cell ferroptosis.

overall_design: Single cell RNA sequencing of PC9 cells with 10X Genomics. PC9 lung cancer cells were untreated (parental) or treated with 100 nM erlotinib for 10 days to derive persister cells. Additionally, parental and persister cells were both separately treated with 1 µM GPX4 inhibitor, RSL3, for 24 hours; or with 7.5 nM HDAC inhibitor, panobinostat, for 48 hours.

middle: F

first: Matthew

last: Hangauer