title: A proteomics screen uncovers CTCF as a key G-quadruplex binding protein [CUT&Tag]

first: Vipul

last: Shukla

overall_design: Cut and Tag for CTCF and G-quadruplexes of mESCs treated without auxin (control) or with auxin to promote CTCF deletion (EV+AUX) and cells that had reintroduction of FL CTCF or mutant CTCF (H373R) after auxin treatment

first: Daniela

last: Samaniego-Castruita

first: Isabella

last: Han

first: Roxroy

last: Morgan

first: Samantha

last: Carpenter

first: Bryce

last: Williams

first: Ishwar

last: Radhakrishnan

first: Abhijit

last: Chakraborty

first: Samuel

last: Myers

first: Ferhat

last: Ay

first: Anjana

last: Rao


title: Recurrent oncogenic ZC3H18 mutations stabilize endogenous retroviral RNA [zfmelanoma_ribominus_RNAseq]

status: Public on May 15 2026

city: Boston

first: Tanzina

last: Tanu

state: MA

address: 450 Brookline

department: Medical Oncology

country: USA

institute: DFCI

type: Expression profiling by high throughput sequencing

summary: ZC3H18 (Z18) is a component of multiple nuclear RNA surveillance complexes which detect and degrade aberrant nuclear RNAs. We found recurrent truncating mutations in Z18 (Z18trunc) enriched in many cancer types, and as these truncating forms lack the distal domain required for recruitment of RNA degradation machinery, we predicted that Z18’s target transcripts would be stabilized. Expression of Z18trunc expedited melanoma onset in a zebrafish melanoma model and caused a specific accumulation of endogenous retroviral (ERV) RNA. Z18 mutant human cell lines from the Cancer Cell Line Encyclopedia also had increased ERV expression. In engineered human melanoma cells, Z18trunc caused a more severe accumulation of ERV RNA than loss of one Z18 copy, showing dominant negative activity. Z18trunc was exported to the cytoplasm and failed to recruit RNA degradation machinery, while maintaining binding to two RNA stabilizing proteins. Z18trunc bound ERV RNA via aromatic amino acids in the zinc finger domain but failed to recruit the degradation machinery, so in lieu of destruction, ERV messages were stabilized. We find that Z18 normally specifically identifies ERV messages for destruction, while Z18trunc protects ERV RNA, contributing to oncogenesis. This work demonstrates that mutations in a second nuclear RNA surveillance component are oncogenic, supporting that deficient nuclear RNA surveillance is a broad tumor suppressive mechanism. Our work provides a specific mechanism that results in elevated ERV transcripts in cancer and reveals that nuclear RNA surveillance complexes play a complementary role in suppressing ERV expression.

overall_design: Bulk ribo-minus RNA-sequencing from zebrafish melanomas with melanocyte-specific expression of eGFP or truncated ZC3H18.

first: Anna

middle: M

last: Cox

first: Jennifer

last: Karlow

first: Priyanka

last: Sharma

first: Xueyang

last: He

first: Swathy

last: Babu

first: Jared

last: Brown

first: Kevin

first: Stephen

middle: J

last: Chanock

first: David

last: Liu

first: Tongwu

last: Zhang

first: Kathy

middle: H

last: Burns

first: Paul

middle: L

last: Boutz

first: Megan

last: Insco


title: Role of Nutritional Status on Arsenic Toxicity in Daphnia pulex: A Transcriptomic Perspective on Individual and Interactive Effects

status: Public on Aug 05 2026

city: Keene

last: Roy Chowdhury

state: New Hampshire

address: 229 Main Street

institute: Keene State College

summary: In this study, we investigated the individual and interactive effects of non acutely toxic arsenic exposure, low food quantity, and low dietary phosphorus on genome wide gene expression in the aquatic grazer Daphnia pulex. Our results show that phosphorus limitation was the dominant stressor as a main effect and as a co-stressor. Interaction terms with phosphorus produced exponentially more differentially expressed genes than main effects alone. Our results also indicate that the low phosphorus x arsenic interaction impacts Daphnia pulex gene expression greater than the low food x arsenic interaction. Importantly, all nutrient–arsenic interactions exhibited antagonistic gene expression patterns supporting a growing body evidence that arsenic behaves antagonistically as a co-stressor. This study provides novel mechanistic insight into how phosphorus content, rather than food quantity, modulates arsenic toxicity at the transcriptional level. By using gene expression to assess co-stressor interactions, our approach can help refine predictions of how nutritional status influences organismal responses to environmental contaminants.

overall_design: RNA sequencing of whole animal Daphnia pulex treated with a total of 8 different treatments combining optimal/insufficient concentrations of dietary phosphorus and food quantity in the absence/presence of an environmentally realistic concentration of arsenic (0.132 mg/L). The design: 8 treatments x 3 reps for a total of 24 samples. Control reps = HP_High_NoAr.

first: Anthony

last: Schultz

first: Emily

middle: R

last: DeTemple

first: Craig

middle: E

last: Jackson

first: Thomas

last: Hampton

first: Joseph

last: Shaw


title: A proteomics screen uncovers CTCF as a key G-quadruplex binding protein [RNA-seq]

city: Chicago

first: Vipul

last: Shukla

state: Illinois

address: 303 E. Superior Street

department: Department of Cell and Developmental Biology

institute: Northwestern University

summary: DNA G-quadruplexes (G4s) are non-B form secondary DNA structures that are highly conserved across evolution. G4 structures occupy key regulatory sites in the mammalian genomes and are implicated in several cellular processes. However, the mechanisms by which G4s contribute to distinct facets of genome function are not well understood. Here, we conduct an unbiased proteomics screen with G4s of diverse topologies to uncover novel G4 binding activities in key genomic regulators involved in regulation of nucleosome remodeling, paraspeckle assembly, RNA splicing, transcriptional elongation, and 3D genome organization. Among the most prominent hits, we identify the genomic architectural protein, CTCF as one of the strongest G4 binders. Building on this discovery, we perform extensive biochemical validation of CTCF-G4 interaction and identify CTCF mutants, with pronounced affinity for G4s over its consensus DNA motif. By implementing well-established approaches and newly developed G4 mapping tools, we define a comprehensive catalog of genomic  G4s and study their association with CTCF binding. Furthermore, using genetic reconstitution studies with specific CTCF mutants, we ascribe genomic functions to CTCF-G4 interactions in regulation of CTCF occupancy, chromatin looping and gene expression. Our work establishes the G4 binding activity of CTCF and provides new insights into the functional significance of G4 structures.

overall_design: RNA-seq profile of mESCs treated without auxin (control) or with auxin to promote CTCF deletion (EV+AUX) and cells that had reintroduction of FL CTCF or mutant CTCF (H373R) after auxin treatment

first: Daniela

last: Samaniego-Castruita

first: Isabella

last: Han

first: Roxroy

middle: C

last: Morgan

first: Samantha

last: Carpenter

first: Bryce

last: Williams

first: Ishwar

last: Radhakrishnan

first: Abhijit

last: Chakraborty

first: Samuel

last: Myers

first: Ferhat

last: Ay

first: Anjana

last: Rao


title: Recurrent oncogenic ZC3H18 mutations stabilize endogenous retroviral RNA [zfmelanoma_pAselected_RNAseq]

first: Tanzina

last: Tanu

overall_design: Bulk polyA-selected RNA-sequencing from zebrafish melanomas with melanocyte-specific expression of eGFP or truncated ZC3H18.

first: Anna

last: Cox

first: Jennifer

last: Karlow

first: Priyanka

last: Sharma

first: Xueyang

last: He

first: Swathy

last: Babu

first: Jared

last: Brown

first: Kevin

first: Stephen

last: Chanock

first: David

last: Liu

first: Tongwu

last: Zhang

first: Kathy

last: Burns

first: Paul

last: Boutz

first: Megan

last: Insco


title: Recurrent oncogenic ZC3H18 mutations stabilize endogenous retroviral RNA [hs_pAselected_RNAseq]

overall_design:
A ZC3H18 allelic series was made in A375 human melanoma cells. polyA-selected RNA-sequencing was done.
Transient transfection and antibiotic selection was used to generate ZC3H18 CRISPR KO (n=3) vs. ZC3H18 WT (n=3).
ZC3H18 single cell cloned lines were made by transient transfection, antibiotic selction, and subsequent single cell cloning by limiting dilution. The following lines were generated: ZC3H18 WT (n=2), ZC3H18 trunc/+ (n=3), and ZC3H18 -/+ (n=3).


title: Recurrent oncogenic ZC3H18 mutations stabilize endogenous retroviral RNA [hs_PARCLIP_ribominus_RNAseq]

overall_design: Anti-V5 PAR-CLIP ribo-minus RNA-sequencing from A375 human melanoma cells transicently transfected with V5-tagged ZC3H18, truncated ZC3H18, or truncated aromatic zinc finger mutant ZC3H18 vs. V5-tagged Clover (control).


title: RNA-seq analysis of freshly isolated human cord blood HSCs and MPPs

city: shanghai

first: Yandan

last: Chen

state: shanghai

address: 280, Chong-Qing South Road, West Bldg #2, Shanghai , China

country: China

institute: Shanghai Jiao Tong University School of Medicine

summary: The identification and manipulation of unique genes expressed in human haematopoietic stem cells (HSCs) compared with multipotent progenitors (MPPs) to augment transplantation efficacy remain largely unexplored.To identify genes potentially enriched in human HSCs, we sorted rigorously defined HSCs (CD34+CD38-CD45RA-CD90+)and MPPs (CD34+CD38-CD45RA-CD90-) from freshly isolated human cord blood for transcriptomic analysis.

overall_design: Stringently defined HSCs or MPPs were collected by flow cytometry sorting from fresh isolated human cord blood units to analyzed transcriptomic changes.

first: Bin

last: Guo

first: Xiashiyao

first: Jun

last: Wan


title: ZNF467 nucleoplasmic condensates enhance human haematopoietic stem cell homing

summary: Human hematopoietic stem cells (HSCs) possess a distinct gene expression profile distinguishing them from progenitor cells. Gaining insight into the distinctive features of these signature genes could accelerate the development of effective strategies to enhance the clinical efficacy of HSC transplantation. Research into genes specifically enriched in cord blood (CB) HSCs revealed high expression levels of ZNF467 in both freshly isolated human CB HSCs and ex-vivo cultured CB HSCs. ZNF467, originally identified from a mouse hematogenic endothelial cell line, has been linked to the regulation of adipogenesis and osteogenesis within the mouse bone marrow. However, its biological function in human tissues remains largely elusive. Although neither overexpression nor knockdown of full-length ZNF467 had dramatic effect on ex-vivo expansion of CB HSPCs,nucleoplasmic condensates of truncated ZNF467, resulting from ZNF467 with the amino acids (216-292)deletion,as npZNF467.Overexpression npZNF467 profoundly enhances the long-term reconstituting capacity of human cord blood HSCs.Overexpression of npZNF467 in HSC and progenitor cells induces a unique gene expression profile, notably upregulating genes associated with HSPC migration and adhesion. The npZNF467 condensates significantly amplify the homing efficiency of CB HSPCs, primarily through activating expression of MMP9 and ICAM1.Collectively,the enforced expression of npZNF467 condensate initiates a homing-related gene expression program, fostering both homing and long-term engraftment of human CB HSPCs.

overall_design: To investigate the function of ZNF467 in human CD34+ hematopoietic stem and progenitor cells, cord blood derived CD34+ cells were lentivirally infected in duplicates with GFP tagged vector containing either control or overexpression of npZNF467, sorted for GFP at 4 days post infection and collected for RNA sequencing. Differential gene expression analysis was performed on CD34+ cells with npZNF467 overexpression compared to control.


title: Conserved Transcriptional Circuits Regulate Cardiac Fibroblast-Mediated Fibrosis

city: Melbourne

first: Alexander

last: Pinto

state: Victoria

address: 75 commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cardiac fibrosis is a major cause of cardiac dysfunction. Recently, single-cell genomic approaches have revealed in unprecedented resolution the orchestrated cellular responses driving cardiac fibrosis. Yet, the fibrosis-causing phenotypes that emerge in the heart following non-ischemic cardiac stress, and the transcriptional circuits that govern cell identity and drive fibrosis, are not well understood. Applying a paired multiomic approach, we reveal key transcriptional circuits, in mouse and human hearts, which are associated with fibrosis development following non-ischemic cardiac insults, independent of disease model, species or biological sex. Strikingly, we find the key regulatory events driving fibrosis are reversible at the single-cell transcriptional and epigenomic level, further pointing to key factors regulating fibrosis development and resolution. The transcriptional regulators identified in this study represent promising targets to ameliorate the development of fibrosis in the context of chronic stressors such as aging and hypertension.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To determine the core GRNs and corresponding TFs governing non-ischemic cardiac fibrosis, we initially used a hypertension-induced cardiac fibrosis model. To achieve this, we infused both male and female C57BL/6J adult mice (12-14 weeks of age) with AngII (1.4 mg/kg/day) or saline (control) for 14 days. Additionally, we tested the tractability and reversibility of GRN changes elicited by AngII infusion, by analyzing hearts from mice that underwent 14 days of AngII infusion followed by a 14- day recovery period (AngII+Rec), where ectopic AngII infusion was halted.

first: Crisdion

last: Krstevski

first: Gabriella

last: Farrugia

first: Ian

last: Hsu

first: Malathi

middle: S

last: Dona

first: Taylah

last: Gaynor

first: Charles

middle: D

last: Cohen

first: Rebecca

last: Harper

first: Thomas

middle: I

last: Harrison

first: Bethany

last: Claridge

first: Auriane

last: Drack

first: Patrick

last: Lelliott

first: Helen

last: Kiriazis

first: Aascha

first: Julie

last: McMullen

first: Daniel

middle: G

last: Donner

first: Sean

last: Lal

middle: W

last: Greening


title: The C-terminal region of TENT5 Proteins Drives ER-associated mRNA Polyadenylation via FNDC3 interaction [TAIL-Seq]

status: Public on May 14 2026

city: Milano

first: Enrico

last: Milan

state: MI

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

summary: Spatial regulation of mRNA polyadenylation is a key emerging mechanism shaping cellular function. The TENT5/FAM46 family comprises four non-canonical poly(A) polymerases that stabilize transcripts encoding ER-targeted proteins, with mutations linked to diseases of professional secretory cells. Using transcriptomic profiling coupled with systematic mutagenesis, we uncover how paralog-specific evolutionary divergence dictates distinct subcellular localization, interaction, and functional outcomes. TENT5D, the most ER-associated member, triggers widespread proteome remodeling, boosting the concerted expression of ER, ERGIC, Golgi, and lysosomal proteins. In contrast, TENT5B lacks ER targeting and regulates proteins involved in cell division. Mechanistically, a member-specific C-terminal region that binds ER-transmembrane FNDC3 proteins is necessary and sufficient for ER localization. Altogether, our findings reveal a domain-encoded mechanism linking TENT5 localization to transcript selectivity and secretory output. The TENT5–FNDC3 axis thus emerges as a key orchestrator of the cellular translatome and organelle identity.

overall_design: TAIL-seq profiling of LP1 cells expressing TENT5B, TENT5D or control vectors.

first: Lisa

last: Viviani

last: Lacidogna

first: Sara

last: Pennacchio

first: Maria Vittoria

last: Mengozzi

first: Ugo

last: Orfanelli

first: Leone

last: Giordano

first: Tommaso

last: Perini

first: Simone

last: Cenci


title: MicroRNA-124-Targeted Zika Virus-A Dual-Functional Candidate as a Live-Attenuated Vaccine and Oncolytic Agent

city: BeiJing

first: Chao

last: Zhou

address: Dong Da Jie street #20

institute: State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Zika virus (ZIKV) poses a significant dual challenge: its profound neurotropism and neurovirulence are responsible for Congenital Zika Syndrome (CZS) and adult neuropathology, yet this neurotropism offers potential for oncolytic virotherapy against malignant brain tumors like glioma. However, the inherent safety risks of wild-type ZIKV constrain its clinical development as either a vaccine backbone or a therapeutic agent. In this study, we screened a microRNA, miR-124, which is highly enriched in neural cells, but low in glioma cells. Based on this finding, we engineered a recombinant ZIKV by inserting the miR‑124 target sequence (miR‑124T) into the genome, named ZIKV‑miR124T. A highly attenuated neurovirulence phenotype across multiple mouse models, including adult A129, BALB/c neonatal, and pregnant mice was identified for ZIKV-miR124T. Importantly, a single dose of ZIKV-miR124T provided complete protective immunity against lethal challenge for the immunized subject and effectively blocked vertical transmission, conferring protection to the fetus and neonate. Furthermore, in an orthotopic glioma model, ZIKV-miR124T maintained robust oncolytic efficacy while exhibiting a superior safety profile, demonstrated by viral replication being strictly confined to the tumor region and a nearly 1,000-fold reduction in non-tumoral brain viral load compared to a non-specific live-attenuated ZIKV (ZIKV-LAV). Overall, our study provides robust proof-of-concept for a rational, miRNA-targeting approach to develop a next-generation ZIKV candidate with dual potential as a safe live-attenuated vaccine and a precisely restricted oncolytic virus.

overall_design: Total RNA of iPSC-derived neural precursor cells(NPCs), NPCs-derived neuron cells, glioma stem cells(GSCs) and glioma stem cell-derived non-stem cells(NSTC) was extracted and subjected to small RNA sequencing, and micRNA expression differences were analyzed.

first: Lishu

last: Chen

first: Yuyan

last: Li


title: Angiotensin II Type 1 Receptor Blockade Inhibits Gastric Cancer Metastasis Through Tight Junction Restoration

city: Mobile

first: Debanjan

last: Chakroborty

state: Alabama

address: 1660 Spring Hill Ave

department: Pathology

institute: University of South Alabama

summary: Cell-Cell adhesion maintained by tight junctions (TJs) is essential for epithelial integrity; loss of TJs correlates with poor prognosis, metastasis, and adverse clinical outcome in gastric cancer (GC). Restoring TJ integrity is therefore considered a promising therapeutic strategy in GC. The study identifies the stomach renin angiotensin system (stRAS) as a crucial regulator of TJ function in GC. Using integrative analysis of GC patient tissues, human GC cell lines, and orthotopic GC xenografts models, here we show that angiotensin II (ATII), the principal effector peptide of stRAS, drives TJ disassembly through an autocrine loop involving angiotensin receptor type 1 (AT1R) expressed on gastric cancer cells. Both ATII and AT1R are overexpressed in GC, where they suppress the expression of key TJ proteins. By analyzing global RNA-seq data and performing CRISPR/Cas9 gene deletion, chromatin immunoprecipitation, and functional assays, we mechanistically reveal that ATII, which is predominantly produced by cancer cells within the tumor microenvironment (TME), inhibits the expression of krüppel-like factor 4 (KLF4), a transcription factor crucial for the transcription of key TJ genes (CLDN1, 3, 4, and TJP1), leading to reduced synthesis of TJ proteins via AT1R expressed on cancer cells. Notably, the study demonstrates the effectiveness of pharmacological inhibition of AT1R with clinically established AT1R antagonists in preventing GC growth and metastasis by restoring TJ stability in vivo. These findings delineate a previously unrecognized role for ATII in governing TJ disassembly in GC and highlight the ATII/AT1R axis as a promising therapeutic target.

overall_design: RNA-seq profiling of wild type MKN45 and their KLF4 kockout cells (KLF4KO MKN45) and losartan treated (24 hour) cells (MKN45+L).

first: Sooraj

last: Kakkat

first: Prabhat

last: Suman

first: Sandeep

last: Goswami

first: Brusi

last: Kola

first: Kira

middle: A

last: Bruno

first: Wendy

last: Frankel

first: Sujit

last: Basu

first: Elba

last: Turbat-Herrera

first: Veronica

last: Alcantara

first: Martin

last: Heslin

first: Joel

middle: F

last: Andrews

first: Paramahansa

last: Pramanik

first: Chandrani

last: Sarkar


title: The C-terminal region of TENT5 Proteins Drives ER-associated mRNA Polyadenylation via FNDC3 interaction [RNA-seq]

first: Enrico

last: Milan

overall_design: RNA-seq profiling of LP1 cells expressing TENT5B, TENT5D or control vectors.

first: Lisa

last: Viviani

first: Daniel

last: Lacidogna

first: Sara

last: Pennacchio

first: Maria Vittoria

last: Mengozzi

first: Ugo

last: Orfanelli

first: Leone

last: Giordano

first: Tommaso

last: Perini

first: Simone

last: Cenci


title: Intracellular pH dynamics promotes zebrafish larval tail regeneration

city: San Francisco

first: Diane

last: Barber

state: CA

address: 513 Parnassus Ave. HSW618

department: Cell and Tissue Biology

institute: UCSF

summary: Intracellular pH (pHi) dynamics regulates numerous cell behaviors, including migration and proliferation. While these functions are well-established in cell lines, the role of pHi changes in vivo is less well understood. We generated a transgenic zebrafish line expressing a fluorescent ratiometric pHi biosensor and identified functional changes in pHi during zebrafish larval tail regeneration. We found that tail amputation led to a transient decrease in pHi, followed by a prolonged increase in pHi above pre-amputation values. Moreover, we showed that pharmacologically inhibiting Na+/H+ exchanger (NHE) activity or decreasing extracellular pH attenuated the post-amputation increase in pHi, reduced subsequent cell proliferation, and impaired tail regeneration. We further found that inhibiting NHE activity post-amputation led to elevated inflammation, disrupted myeloid cell behavior, decreased reactive oxygen species, and increased glycogen synthase kinase-3 (GSK3) activity. Finally, we showed that the regeneration defects in larvae with disrupted pHi were partially rescued by the GSK3 inhibitor BIO. Our data reveal a previously unrecognized role for pHi dynamics in coordinating tissue behaviors in vivo and enabling zebrafish larval tail regeneration.

overall_design: Bulk RNA-seq of amputated and unamputated zebrafish larval tail tissue treated for 6 or 48 hours with 1% DMSO (vehicle) or 200 uM EIPA.

first: Cambria

last: Chou-Freed

first: Christopher

middle: K

last: Prinz

first: Anush

last: Margaryan

first: Julie

last: Theriot

last: Wagner


title: An orally active dual CBP/p300 degrader targets core dependencies of multiple myeloma [SLAM-seq]

first: Bomin

last: Ku

address: 149 13th street

department: Cancer Center

institute: Massachusetts General Hospital

summary: The enhancer lysine acetyltransferases CBP and p300 are compelling targets for multiple myeloma therapy. Chemical inhibition of these multidomain factors, either through the bromodomain or the catalytic acetyltransferase domain, show promising activity in pre-clinical models of myeloma and other cancers. Some compounds, including the CBP/p300 bromodomain inhibitor inobrodib, have progressed to early-stage clinical trials. Chemical degradation of CBP/p300 is the only modality that can completely disrupt all functional domains of CBP and p300. Our previous attempts to induce CBP/p300 targeted degradation led to dCBP-1, a potent tool compound that induces degradation of both CBP and p300 by hijacking the activity of the E3 ligase CRBN. Here we comprehensively demonstrate across a large panel of cell lines how CBP/p300 degradation compares to inhibition, with pronounced selective antiproliferative activity towards multiple myeloma cells. We use chemical linker optimization strategies to create a compound with better pharmacokinetic properties to enable use in animal models. Through these efforts we define an advanced analog of dCBP-1, dCBP-30, that has improved potency in vitro, along with improved in vivo properties including oral bioavailability. dCBP-30 led to potent and sustained loss of CBP and p300 in myeloma cell lines, potent inhibition of several myeloma-specific dependency programs, and elicits tumor reduction in xenograft models as a single agent and in combination with dexamethasone when delivered orally.

overall_design: Cells were treated with DMSO or dCBP-30 (10 nM) for 2-, 6-. 24-hours in triplicates. Cells were then labelled, lysed, and SLAM-seq procedure was carried out.

last: Ott

first: Ricky

last: Johnstone


title: An orally active dual CBP/p300 degrader targets core dependencies of multiple myeloma [ATAC-seq]

overall_design: 50,000 cells were treated with DMSO or dCBP-30 (10 nM) for 2-, 6-. 24-hours in quadriplicate. Cells were then lysed with appropriate lysis buffers, and ATAC-seq procedure was carried out.


title: Structure and mechanism of inhibition of lysine demethylase 2A (KDM2A) by compound 183c

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

summary: Lysine demethylase 2A (KDM2A) is a key epigenetic regulator and promising target for inhibition since its loss is selectively lethal in cancers reliant on Alternative Lengthening of Telomeres (ALT). Here we investigated the mechanism of compound 183c, a potent KDM2A inhibitor described in the patent literature. Biophysical studies showed that 183c requires the co-factor 2-oxoglutarate (2OG) for binding. A 2.2 Å crystal structure of the KDM2A–183c–2OG ternary complex explained the selectivity of 183c and revealed how 183c occupies the H3K36me2 substrate pocket, with a crucial group mimicking dimethylated lysine 36. In proliferation assays, several ALT-positive cell lines were selectively sensitive to 183c. Comparing ALT-positive SAOS2 and ALT-negative SJSA1 cells, both showed repression of E2F-regulated genes, but only SJSA1 activated EMT, DNA repair, and mTOR pathways, indicating distinct adaptive responses. These structural and cellular insights establish a foundation for designing improved KDM2A inhibitors for ALT-positive cancers.

overall_design: RNAseq of two cell lines (SAOS2 and SJSA) with two different treatments (PR2497 and DMSO) with 3 replicates of each condition.

first: Pavel

last: Mader

first: Linshan

last: Liu

first: Frederic

last: Vallee

first: Francois

last: Denis

first: Victor

last: Pau

last: Mao

first: Lauren

last: Caldwell

first: Kin

last: Chan

first: Igor

last: Kurinov

first: Yael

last: Mamane

first: Paranjay

last: Parikh

first: Zemin

last: Zhang

first: Michel

last: Gallant

first: Mike

last: Tyers

first: W Cameron

last: Black

first: Michael

last: Zinda

last: Durocher

first: Michal

last: Zimmermann

first: Frank

last: Sicheri


title: A recombinant TACI-Fc fusion protein targets IgA plasma cells in a mouse model of systemic lupus erythematosus

city: Charlottesville

first: Loren

last: Erickson

state: Virginia

address: 345 Crispell Drive

department: Department of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

summary: BAFF and APRIL play an important role in driving systemic lupus erythematosus (SLE) immunopathogenesis and kidney damage in lupus nephritis (LN); however, the underlying immune mechanisms contributing to disease pathology and the factors that increase risk of end organ damage are poorly understood. To investigate molecular profiles during the progression of LN, we carried out gene expression analysis on kidneys and spleens from lupus-prone NZM2328 mice treated for four weeks from the time of disease onset. We focused on female mice treated with BAFF and BAFF/APRIL inhibitors alongside cyclophosphamide as a standard therapy to identify mechanisms associated with improved renal outcomes. Inhibition of BAFF alone had a limited impact on gene expression profiles of diseased mice, decreasing myeloid cell and increasing metabolic gene signatures. However, targeting both BAFF and APRIL through competitive inhibition with a TACI-Fc fusion protein significantly altered immune populations in the spleen and depleted IgA plasma cells and also decreased pro-inflammatory immune cells and cytokines in the kidneys of diseased mice. All therapies had a broad impact on kidney pathology through reduction of proteinuria. Targeting both BAFF and APRIL is necessary to reduce autoreactive plasma cell generation and kidney inflammation effectively and especially to decrease IgA secreting plasma cells. The impact of targeting both members of the BAFF family of cytokines in lupus-prone NZM2328 mice provides support for its application in the treatment of human LN.

overall_design: RNA-seq of spleen and kidney tissue from NZM2328 mice treated for 4 weeks with Control-Fc, anti-BAFF monoclonal antibody, TACI-Fc fusion protein, or cyclophosphamide.

first: Claudia

last: Rival

first: Peter

last: Lipsky

first: Andrea

last: Daamen


title: In the Drosophila germline H2Av and Arp6 suppress germline transposons indirectly by driving piRNA pathway expression [RNA-seq]

status: Public on May 18 2026

city: Ithaca

first: Katalin

last: Fejes-Tóth

state: NY

address: Biotechnology Building Room 358, 526 Campus Rd

department: MBG

institute: Cornell University

summary: The spatiotemporal control of transcription and the maintenance of germline genome integrity depend on dynamic chromatin architecture. In Drosophila, the actin-related protein Arp6—a core subunit of the SWR1-like Domino chromatin remodeling complex—mediates the deposition of the histone variant H2Av. Previous studies have established H2Av as a key transcriptional regulator that modulates the +1 nucleosome barrier to promote RNA Polymerase II (Pol II) pause release and productive elongation. Conversely, H2Av is also integral to heterochromatin assembly and gene silencing. Here we demonstrate that Arp6 and H2Av are essential for female fertility and the global repression of transposable elements (TEs) in the Drosophila ovary. Rather than repressing TEs directly, we show that Arp6 and H2Av maintain genomic stability indirectly by driving the transcription of core PIWI-interacting RNA (piRNA) pathway genes. Depletion of either chromatin factor leads to a significant loss of piRNAs and reduced non-canonical transcription of dual-strand piRNA clusters. This defect stems from a failure to express the Rhino-Deadlock-Cutoff (RDC) complex, alongside the downregulation of multiple other piRNA biogenesis factors. Genomic profiling confirms that H2Av acts predominantly as an activating signal at host gene promoters. Upon H2Av or Arp6 depletion, genes that rely on H2Av for their expression exhibit a distinct upstream shift and more precise spatial localization of the Pol II peak at the TSS, indicating an impaired transition from transcription initiation into productive elongation. Together, our findings build upon the known transcriptional activation functions of the Arp6-H2Av axis, revealing that this established chromatin mechanism is critical for licensing piRNA-mediated genome defense and ensuring germline maintenance.

overall_design: Total RNA-seq profiling of Drosophila melanogaster ovaries upon knockdown of H2Av and Arp6.

first: Andrasi

last: Norbert

first: Ryon

last: Hannah

first: Luo

last: Yicheng

first: Fejes-Tóth

last: Katalin


title: Stromal Cell Senescence Augments Hematopoietic Cell Fitness in Clonal Hematopoiesis

city: Munich

first: Anna

last: Navarro Figueredo

state: Bayern

address: Ismaningerstr. 22

department: Hematology/Oncology

country: Germany

institute: Technical University of Munich

summary: Non-cell-autonomous mechanisms impact tumor growth and metastasis, including remodeling of the tissue microenvironment. The extent to which remodeling of the microenvironment promotes pre-malignant clonal fitness remains unknown. Here, using single-cell RNA sequencing of the bone marrow microenvironment in a mouse model of DNMT3A-mutant clonal hematopoiesis, we identify subsets of mesenchymal stromal cells (MSCs) in a molecular state of cellular senescence. Using in vivo and ex vivo approaches, we find MSC senescence is induced by Dnmt3a-mutant hematopoietic cells in a cell contact-independent manner through soluble factors, including the cytokines IL-6 and TNF. Mechanistically, these cytokines activate a STAT3-driven senescence induction pathway selectively in MSCs and not in endothelial cells, underscoring cell context specificity. Depletion of senescent MSCs using genetic or pharmacological methods reduces the fitness of Dnmt3a-mutant hematopoietic stem and progenitor cells, and delays development of myeloproliferation which is a precursor to myeloid malignancy. Together, our work identifies that remodeling of the tissue microenvironment modifies pre-malignant clonal fitness and suggests disruption of the crosstalk between pre-malignant cells and their niche as a cancer prevention strategy.

overall_design: Bulk RNA-seq profiling of sorted healthy human MSC (CD45- CD90+) after 42 hour co-culture with nonCHIP or CHIP HSPC (CD45+ CD34+)

first: Navarro Figueredo

last: Anna

first: Mistry

last: Jayna

first: Trowbridge

last: Jennifer

first: Götze

last: Katharina


title: CD40ag Activated B Cells Elicit Anti-Tumor Immunity [scRNAseq]

status: Public on Aug 13 2026

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: We leveraged mouse models of Triple Negative Breast cancer of varying tumor mutation burdens to elucidate ways that direct activation of B cells can illiciate an anti-tumor effect. These syngenic tranplant models were treated with a combination of CD40 agonist immunotherapy or anti-CD19. Primary tumors of both treated and nontreated conditions were profiled by RNA-SEQ. These tumors that have been profiled describe the impact that B cell acitvation has on CD40 agonist immunotherapy  treatment and tumor progression.

overall_design: Primary tumors were isolated from tumor bearing mice and turned into a single cell suspension using Miltenyi's mice tumor dissociating kit. The resulting single cell suspension was then run through 10x Genomic's single cell protocol to create scRNAseq data sets

first: Kendrick

last: Nguyen

first: Monika

first: Daniel

last: Hollern


title: qMAP decodes RNA fragmentation dynamics

status: Public on May 13 2026

city: Salt Lake City

first: Qi

last: Chen

state: Utah

department: Department of Human Genetics

institute: university of utah

summary: Recent advances in small RNA research reveal that noncanonical small RNAs, such as tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs), are more abundant than well-known microRNAs in various tissue/cell types. Distinct fragmentation of parental RNAs (e.g., tRNA and rRNA) can generate functionally diverse small RNAs. Therefore, we propose a computational tool (qMAP) to identify differential fragmentation of parental RNAs between different biological conditions. Using qMAP, we tested aging-associated differential RNA fragmentation in mouse sperm heads between young and old mice. 28S rRNA was found to exhibit the most significant differential fragmentation. One short rsRNA candidate (17-nt) and one long rsRNA candidate (44-nt) were selected as their involvement of the observed differential fragmentation of 28S rRNA. These two candidate rsRNAs were transfected into mouse embryonic stem cells (mESCs), respectively. mRNA sequencing on these mESCs revealed a distinct transcriptomic response to the 17-nt and 44-nt rsRNAs.

overall_design: V6.5 mESCs were transfected synthetic 28s-rsRNA(17nt length) and 28s-rsRNA(44nt length) seperately by Lipostem reagent.  After 24 hours of transfection, the total RNA were harvested by Trizol reagent for mRNA sequencing.

first: Xudong

last: Zhang

first: Tong

last: Zhou


title: SNP array for Cas9 treated human zygotes

city: North Brunswick Township

first: Jia

last: Xu

state: NJ

address: 675 US Highway One

institute: Genomic Prediction, Inc.

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Donated 2PN human zygotes were injected with a Cas9 RNP targeting pericentromeric and mid-arm sites on chromosomes 16 and X. The purpose of this experiments was to determine if CRISPR induced genetic changes (e.g. indels or chromosomal changes) differ based on the targeted chromosome and position in the chromosome (pericentromeric vs chromosome mid-arm targets). We found whole and segmental chromosome loss in over one third of chromosomes targeted by CRISPR/Cas9. Chromosome loss was seen after targeting different chromosomes, and different positions in the chromosome. These results highlight additional limitations of CRISPR/Cas9 genome editing, as well as potential mechanisms of origin of aneuploidies in the human embryo.

overall_design: SNP array for Cas9 treated human embryos

first: Dieter

last: Egli

first: Nathan

last: Treff

first: Diego

last: Marin


title: Cartography of emergency myelopoiesis identifies dysregulated metabolism

city: New York

first: James

last: Swann

address: 650 W 168th Street

institute: Columbia University

summary: Hematopoietic stem and progenitor cells (HSPC) respond to infections, inflammation, and regenerative challenges using cellular and molecular mechanisms termed emergency myelopoiesis (EM) pathways. However, it remains unclear whether all parts of the hematopoietic hierarchy are similarly activated by different EM inducers. Here, we generate a generalizable and comprehensive cell annotation method together with a refined quantitative model of hematopoietic differentiation using single cell RNA sequencing (scRNA-seq) of HSPCs, which we apply to a broad range of EM contexts. We uncover multiple strategies to enhance myelopoiesis acting at different levels of the HSPC hierarchy, which are also associated with both unique and shared transcriptional response modules. In particular, we identify a myeloid progenitor-based signature associated with EM pathway engagement across multiple inflammatory challenges, which predicts outcome in both pediatric and adult human acute myeloid leukemia. Collectively, our work illuminates fundamental regulatory mechanisms in hematopoietic regeneration and identifies a common EM signature that informs outcome in disease contexts.

overall_design: Mice were treated with agents to stimuate emergency myelopoiesis (5-fluorouracil, interleukin-1 beta, polyinsolinic:polycytidylic acid) before bone marrow was collected. Hematopoietic stem and progenitor cells from the lineage-/cKit+ (LK) or lineage-/cKit+/Sca-1+ (LSK) fractions were isolated and subjected to single cell RNA sequencing.

first: Oakley

last: Olson

first: Emmanuelle

last: Passegue


title: Analysis of the genomic regions controlled by PPARγ in alveolar macrophages (PPARγ HT-ChIPmentation)

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

country: Spain

institute: CNB-CSIC

summary: The goal of this study was to define the cistrome of PPARγ by HT-ChIPmentation followed by sequencing in alveolar macrophages of wild-type mice, in order to identify genomic regions directly controlled by this transcription factor.

overall_design: Alveolar macrophages (AMs) from wild-type mice were isolated by bronchoalveolar lavage (BAL), stained and FACS-sorted in 200k cell aliquotes. We performed the protocol described in 'Gustafsson et al, 2019' with minor modifications, using the PPARγ antibody (#C15410367, Diagenode)

first: Laura

last: Casablanca

first: Hooman

last: Aghelpasand

first: Pontus

last: Höjer

first: Robert

last: Månsson


title: Codon-dependent regulation of mRNA translation and stability by ZC3H7A and ZC3H7B RNA-binding proteins

city: Belfast

first: Sarah

last: Maguire

address: 97 Lisburn Road

department: PGJCCR

country: United Kingdom

institute: Queen's University Belfast

summary: The reduced translation elongation rate caused by the presence of non-optimal codons can negatively impact mRNA stability through translation-dependent decay. A key aspect of this process is the coupling of sensing the mRNA codon usage with the regulation of translation efficiency and stability. We found that two paralog RNA-binding proteins; ZC3H7A and ZC3H7B; which have only emerged in Chordates, preferentially bind to and reduce the stability and translation of mRNAs enriched in the non-optimal codons with A/U at their wobble sites (A/U3 codons). ZC3H7A/B engage with ribosomes that lack elongation factors and induce mRNA degradation or block translation initiation through their interactions with the CCR4-NOT and the GIGYF2/4EHP translation repressor complex, respectively. Depletion of ZC3H7A and ZC3H7B or 4EHP impairs the repression of non-optimal A/U3-rich mRNAs. This study provides insights into a unique mechanism in higher eukaryotes that couples codon usage with the regulation of translation efficiency and mRNA stability.

overall_design: This dataset is for a catabolic SLAM-seq experiment performed with two cell lines: Flag/HA control and ZC3H7B-OE HEK293 cells, with 4 timepoints each performed in triplicates. The 0 h s4U-labeled RNA timepoint was immediately harvested with the RNeasy Plus Mini kit (Qiagen, Cat. # 74134), with the gDNA column being used to remove contaminating DNA. The RNA samples then underwent alkylation and purification as previously described [Herzog, V.A. et al. (2017) Nature Methods]. Later timepoints were collected every 2 h and were processed in an identical manner. RNA-seq was performed by Genewiz, with poly (A) selection ahead of Illumina NovaSeq X+ paired-end sequencing.

first: Patric

last: Harris Snell

first: Parisa

last: Naeli

first: Aitor

last: Garzia

first: Susanta

last: Chatterjee

first: Joseph

last: Waldron

first: Tom

last: McGirr

first: Reese

last: Ladak

first: Jung-Hyun

last: Choi

first: Sami

last: Leino

first: Jun

last: Luo

first: Naomi

last: Jess

first: S. Ali

last: Shariati

first: Ximena

last: Soto Rodriguez

first: Christos

last: Gkogkas

first: Nahum

last: Sonenberg

first: Thomas

last: Tuschl

first: Seyed Mehdi

last: Jafarnejad


title: A Mitochondria-Driven Quality Control Mechanism for Peroxisomal Membrane Proteins

city: Ramat Gan

first: Tirza

middle: T

last: Doniger

state: Not US or Canada

address: Bar Ilan University

department: The Mina and Everard Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

summary: Peroxisomes are essential organelles involved in lipid and reactive oxygen species metabolism, and their function requires proper targeting of peroxisomal membrane proteins (PMPs). When peroxisome biogenesis fails, as occurs in peroxisome biogenesis disorders, PMP levels decrease markedly, yet the underlying mechanisms remain unclear. Here, using quantitative proteomics and transcriptomics in peroxisome-deficient cells, we observe widespread post-transcriptional downregulation of PMPs driven by increased protein turnover via ubiquitination and proteasomal degradation. An unbiased CRISPR screen uncovers a mitochondrial quality control axis. PMPs that fail to reach their native peroxisomal destination are rerouted to mitochondria, where the mitochondrial outer membrane E3 ligases MUL1 and MARCH5 act redundantly to promote their degradation. Importantly, the transmembrane domain of PMPs is sufficient to drive their mitochondrial turnover. Functionally, simultaneous loss of peroxisomes and mitochondrial E3 ligases severely impairs cell proliferation, underscoring the essential role of this pathway. Together, these findings provide insight into the pathology of organelle dysfunction and reveal an inter-organelle quality control axis in which mitochondria act as a surveillance hub to clear PMPs and maintain cellular proteostasis when peroxisomes are absent.

overall_design: RNAseq experiment comparing the transcriptome of HEK293T WT cells vs. two independent lines of PEX3 KO cells

first: Sarin

last: Segev

first: Itay

last: Koren


title: Establishment and characterization of lymph node fibrosis mouse model via dual TGF-β1 administration routes

city: Beijing

first: niu

last: yaru

address: No. 17, Panjiayuan South Lane, Chaoyang District, Beijing

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: This study establishes two reliable TGF-β1–induced lymph node fibrosis models that recapitulate ECM remodeling and immune suppression, providing a platform to investigate how fibrotic changes disrupt local immune regulation.

overall_design: Mice were subjected to either intra-lymph node or repeated inguinal subcutaneous TGF-β1 injections to induce lymph node fibrosis, followed by tissue and serum collection at defined time points for histological and molecular analyses.


title: Lysosomal dysfunction drives a transcriptional and epigenetic signature found in disease-associated microglia in neurodegenerative diseases [ChIP-seq]

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

summary: Lysosomal dysfunction is causally linked to neurodegeneration in many lysosomal storage disorders and is associated with various age-related neurodegenerative diseases. Here, we investigated the question of underlying mechanisms using a mouse model of mucopolysaccharidosis type IIIA caused by deficiency of the lysosomal hydrolase SGSH. Systematic imaging and transcriptomic and epigenetic studies revealed microglia to be the most profoundly impacted cell type in brains of Sgsh-deficient mice. Further investigation identified dominant and context-dependent roles of members of the MITF/TFE family as major drivers of microglia-specific epigenetic and transcriptional changes resulting from lysosomal stress that are dependent on collaborative interactions with AP-1/ATF, C/EBP, and PU.1/ETS transcription factors. Features of the transcriptomic and epigenetic alterations observed in murine Sgsh deficiency were also observed in microglia derived from mouse models of age-related neurodegeneration and in human Alzheimer's disease patients. These findings reveal common and disease-specific transcriptional mechanisms associated with disease-associated microglia phenotypes.

overall_design: Gene expression analyses across brain cell types by single-nucleus RNA-seq and in sorted microglia by single-cell RNA-seq in WT and SgshKO mice, temporal polyA RNA-seq of sorted ex vivo mouse microglia (WT and SgshKO; 3weeks, 4months, 8 months), polyA RNA-seq of sorted ex vivo mouse microglia following in vivo ASO-mediated knockdowns of Mitf, Tfeb, and Tfe3 (WT) or combination of Mitf+Tfe3 (SgshKO), ATAC-seq and H3K27ac-ChIP-seq of mouse microglia, neurons, and oligodendrocytes (WT and SgshKO) at 4- and 8-months of age, and MITF, TFEB, and TFE3 ChIP-seq from microglia (PU.1+) and oligodendrocyte (OLIG2+) in WT and SgshKO nuclei isolated from mouse forebrains.

last: Balak

first: Johannes CM

last: Schlachetzki

first: Addison

last: Lana

first: Elizabeth

last: West

first: Christine

last: Hong

first: Jordan

last: DuGal

first: Yi

last: Zhou

first: Benjamin

last: Li

first: Nathanael

last: Spann

first: Payam

last: Saisan

first: Vishal

last: Sarsani

first: Kilian

last: Kleeman

first: Xiaoming

last: Zhang

first: Martina

middle: P

last: Pasillas

first: Sydney

last: O’Brien

first: Juliette

last: Bokor

first: Philip LSM

last: Gordts

first: Oleg

last: Butovsky

first: Beth

last: Stevens

first: Fredrik

last: Kamme


title: Matrix viscoelasticity regulates dendritic cell migration and immune priming [RNA-seq]

city: Boston

first: Wei-Hung

last: Jung

address: 201 Brookline Ave

institute: Wyss Institute

summary: The tumor microenvironment shapes immune surveillance through its mechanical properties, yet the role of matrix viscoelasticity remains unclear. Here, we used a collagen system with tunable viscoelasticity to define how matrix relaxation directs dendritic cell (DC) behavior. Elastic matrices impaired DC migration by limiting actomyosin-driven collagen remodeling, thereby reducing DC-T cell encounters and weakening T cell priming, activation, proliferation, and tumor killing. Blocking DC migration in fast-relaxing gels recapitulated key aspects of the impaired T cell priming seen in elastic matrices. Prolonged confinement in elastic ECM induced a mechanomemory state, locking DCs into reduced motility even after transfer to viscoelastic environments, corresponding to altered chromatin accessibility. Finally, studies with patient-derived glioma samples confirmed these findings, identifying viscoelasticity as a barrier to antitumor immunity with implications for therapeutic intervention.

overall_design: TNF-α–treated primary human monocyte-derived dendritic cells were encapsulated in 2 mg mL⁻¹ type I collagen gels engineered to exhibit either fast or slow stress relaxation for 3 days. After encapsulation, cells were harvested and processed for bulk RNA-seq and ATAC-seq analyses.

first: Joshua

middle: M

last: Price

first: David

last: Mooney


title: Matrix viscoelasticity regulates dendritic cell migration and immune priming [ATAC-seq]

middle: J


title: Codon-dependent regulation of mRNA translation and stability by ZC3H7A and ZC3H7B RNA-binding proteins [ParClip]

first: Sarah

last: Maguire

overall_design: ParClip library preparation and sequencing of Flag and HA tagged ZC3H7A and ZC3H7B HEK293 Cells

first: Patric

last: Harris Snell

first: Parisa

last: Naeli

first: Aitor

last: Garzia

first: Joseph

last: Waldron

first: Susanta

last: Chatterjee

first: Tom

last: McGirr

first: Reese

last: Ladak

first: Jung-Hyun

last: Choi

first: Jun

last: Luo

first: Sami

last: Leino

first: Naomi

last: Jess

first: S. Ali

last: Shariati

first: Ximena

last: Soto Rodriguez

first: Christos

last: Gkogkas

first: Nahum

last: Sonenberg

first: Thomas

last: Tuschl

first: Seyed Mehdi

last: Jafarnejad


title: Codon-dependent regulation of mRNA translation and stability by ZC3H7A and ZC3H7B RNA-binding proteins [RNA-seq]

first: Sarah

last: Maguire

overall_design: RNA-seq profiling of Flag/HA-control, Flag/HA-ZC3H7A, Flag/HA-ZC3H7B, Parental and ZC3H7A/B-Double depletion HEK293 cells

first: Patric

last: Harris Snell


title: UCSF Study 2- Perturb-seq targeting 225 genes expressed during embryoid body formation

status: Public on Aug 12 2026

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

institute: EMBL-EBI

summary: This study phenotypes the knockout of 225 genes by single cell RNAseq during embryoid body formation. Guides targeting 225 genes known to be expressed in the pluripotent state or during embryoid body formation.

overall_design: A dox-inducible CRISPRi-mCherry Kolf2.2J cell line was infected at a low MOI with a BFP and pruro resistance-expressing lentivirus containing a pool of sgRNAs targeting 225 genes. After infection, infected cells were treated with puro, expanded, and exposed to doxycycline. A fraction of the cells were aggregated and converted to EBs using DMEM +20% KSR. On day 8 of EB differentiation, both iPSCs and EBs were isolated and sorted for viability, as well as BFP and mCherry expression and encapsulated using a 10X Chromium X.

first: Aaron

last: Huebner

first: Luke

last: Gilbert

first: Ashir

last: Borah


title: Codon-dependent regulation of mRNA translation and stability by ZC3H7A and ZC3H7B RNA-binding proteins [Ribo-seq]

overall_design: Ribo-seq profiling of Flag/HA-control, Flag/HA-ZC3H7A, Flag/HA-ZC3H7B, Parental and ZC3H7A/B-Double depletion HEK293 cells

first: Parisa

last: Naeli

first: Aitor

last: Garzia

first: Joseph

last: Waldron

first: Susanta

last: Chatterjee

first: Tom

last: McGirr

first: Reese

last: Ladak


title: Analysis of the genomic regions controlled by RXRα in alveolar macrophages (RXR HT-ChIPmentation)

first: Mercedes

last: Ricote

summary: The goal of this study was to define the cistrome of RXR by HT-ChIPmentation followed by sequencing in alveolar macrophages of wild-type and RXRαβ-deficient mice, in order to identify genomic regions directly controlled by these transcription factors. Due to technical antibody limitations, the ChIPmentation was performed using only the antibody against RXRα

overall_design: Alveolar macrophages (AMs) from wild-type and RXRαβ-KO mice were isolated by bronchoalveolar lavage (BAL), stained and FACS-sorted in 200k cell aliquotes. We performed the protocol described in 'Gustafsson et al, 2019' with minor modifications, using the RXRα antibody (#21218-1-AP, ProteinTech)

first: Jesús

last: Porcuna

first: Jorge

last: Mínguez-Martínez


title: Transcriptomic differences in RXRαβ-deficient and WT alveolar macrophages using the CD11c-Cre+ mouse model (RNA-Seq)

summary: The main objective of this study was to compare the transcriptomic profile of alveolar macrophages in mice lacking both RXR subtypes (RXRα and RXRβ), to identify genes that are controlled by these nuclear receptors.

overall_design: WT and RXRαβ-deficient alveolar macrophages were obtained by lung digestion and sorting as individual biological replicates. RNA was extracted using RNeasy Mini Kit (Qiagen) and sequencing was performed on a NextSeq2000 (Illumina).


title: GATA4 loss promotes mutant Kras-driven pancreatic ductal adenocarcinoma in the absence of canonical precursor lesions [ChIP-Seq]

status: Public on May 12 2026

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

summary: GATA6 and GATA4 play key roles in pancreatic development and are essential to maintain the classical transcriptional program in pancreatic ductal adenocarcinoma (PDAC). Using genetic mouse models we show that, in contrast to GATA6, GATA4 is dispensable for the maintenance of acinar homeostasis in the adult pancreas. Deletion of Gata4 in mice expressing mutant Kras in the embryonic pancreas (KG4C) leads to PDAC development in the absence of acinar-to-ductal metaplasia (ADM), pancreatic intraepithelial neoplasias (PanINs), or other canonical precursor lesions present in Gata4-proficient (KC) mice. Similar observations were made when Gata4 was selectively inactivated in adult, Kras-mutant, acinar cells, We identify Pale Acinar Lesions (PALes) as a previously unrecognized pancreatic lesion, distinct from ADM and PanINs, present in KC and KG4C mice but not in control mice. PALes display weak expression of acinar and ductal markers and lack mucins; they have lower proliferation rates than PanINs. RNA-seq and ChIP-seq reveal that GATA4 and GATA6 partially share genomic binding sites and transcriptomic effects, but they exert opposing influences on mutant Kras–induced, hematopoietic cell–dependent, transcriptional inflammatory signatures. Adenoviral-mediated pancreatic expression of IL17 restored the formation of ductal lesions in KG4C mice but failed to rescue PanIN development. Our data suggest that GATA4 functions through the coordinated action of multiple inflammatory factors that are required for ADM/PanIN formation but are dispensable for PDAC development. Collectively, these findings challenge current paradigms of PDAC initiation and progression.

overall_design: To identify genetic programs directly regulated by GATA4, we performed ChIP‑Seq on chromatin from bulk normal pancreas.

first: Francesc

last: Madriles

first: Mónica

last: P. de Andrés

first: Mikhail

last: Chesnokov

first: Francisco X.

last: Real


title: Transcriptionally active genomic regions defined by H3K27ac mark (H3K27ac HT-ChIPmentation)

summary: The goal of this study was to define the acetylation mark H3K27ac profile by HT-ChIPmentation followed by sequencing in alveolar macrophages of wild-type mice, allowing us to identify the transcriptionally-active genomic regions.

overall_design: Alveolar macrophages (AMs) from wild-type mice were isolated by bronchoalveolar lavage (BAL), stained and FACS-sorted in 200k cell aliquots. We performed the protocol described in 'Gustafsson et al, 2019' with minor modifications.

first: Laura

last: Casablanca

first: Hooman

last: Aghelpasand

first: Pontus

last: Höjer

first: Robert

last: Månsson


title: Investigation of sugar transport by Proteus mirabilis during urinary tract infection using a modified Tn-seq approach

status: Public on May 16 2026

city: Ann Arbor

first: Melanie

last: Pearson

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

summary: The experiment was to construct a library of targeted insertion mutants, using the "targetron" method, and compare the fitness of mutants in a murine UTI model by measuring the relative quantity of mutants before and after experimental UTI. Since the targetron disrupts the gene function, enriched mutants after this selection suggests the gene is deleterious for this process and vice versa. Mutations were in genes predicted to enable the bacteria to import sugars. The targetron sequence is provided in a supplementary file.

overall_design: All 47 mutant strains of bacteria were separately cultured and adjusted to the same density. Mutants were then mixed in equal measure in two pools, with 23 mutants in group 1 and 24 in group 2. Thus, the inputs are a mix of mutated P. mirabilis bacteria. Mice (15 per group, numbered 1-15 and 16-30 for groups 1 and 2, respectively) were transurethrally inoculated with the equally mixed pools of 23 or 24 mutants, and after 24 h P. mirabilis was recovered from urine (U), bladder (B), and kidneys (K). Genomic DNA was purified and prepared for Illumina sequencing. The "input spiral" samples in the "Experimental Group" column were cultured on agar before library preparation. This control quantifies differences in bacterial growth in broth (input) vs agar (input spiral).

first: Harry

last: Mobley

first: Shiuhyang

last: Kuo

first: Allyson

last: Shea


title: GATA4 loss promotes mutant Kras-driven pancreatic ductal adenocarcinoma in the absence of canonical precursor lesions [Epithelial RNA-seq]

overall_design: RNA-seq transcriptomic profiling of sorted epithelial cells isolated from pancreas of mice with embryonic mutant Kras-G12Vgeo knockin and Gata4 knockout prior to major histological changes (8-12 weeks old animals, no treatment or intraperitoneal injection of sterile PBS).


title: Comparative transcriptomics of luminescent and low-luminescent states in Photobacterium kishitanii ANT-2200

city: Marseille

first: Capucine

last: Le Cam Ligier

address: 167 Avenue de Luminy

country: France

institute: Aix-Marseille University

summary: RNA-seq was performed to compare gene expression profiles between luminescent and low-luminescent states of Photobacterium kishitanii ANT-2200 across different growth phases. Raw RNA-seq reads were previously deposited in the NCBI Sequence Read Archive under BioProject PRJNA1464527. Processed count matrices are provided in this GEO submission.

overall_design: Single-end RNA-seq analysis of Photobacterium kishitanii ANT-2200 comparing luminescent and low-luminescent states across four growth phases: early growth phase, mid exponential growth phase, late exponential growth phase, and stationary growth phase. The study includes Lum_T1, Lum_T2, Lum_T3, Lum_T4, DimLum_T1, DimLum_T2, DimLum_T3, and DimLum_T4.

first: Gwénola

last: Simon

first: Charlotte

last: Berthelier

first: Corinne

last: Valette

first: Elisa

last: Lefeuvre

first: Marc

last: Gare

first: Casalot

last: Laurie


title: Signal-responsive transcription factors cooperate to establish alveolar macrophage identity

first: Mercedes

last: Ricote

summary:
This study includes RNA-Seq, ATAC-Seq, and HT-ChIP-mentation-Seq assay data performed on alveolar macrophages from wild-type and RXRαβ-deficient mice. Through this multifaceted analysis, we aimed to elucidate the transcriptional and epigenetic landscape orchestrated by RXRs in alveolar macrophages.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Long-term maintenance of H3K27me3 in postmitotic neurons is dispensable for gene expression regulation [ATAC-seq]

city: Tallinn

first: Kärt

last: Mätlik

address: Akadeemia 15

country: Estonia

institute: Tallinn University of Technology

summary: Neuronal maturation is associated with extensive changes in gene expression and 3D chromatin architecture. However, the molecular mechanisms that control the epigenetic landscape in terminally differentiated neurons are poorly understood. Here, we show that maturing neurons undergo a striking increase in the levels of the repressive histone modification H3K27me3 broadly across the genome. Using mice with a conditional deletion in the catalytic domain of EZH1, the primary H3K27 methyltransferase in postmitotic neurons, we show that H3K27me3 maintenance depends on EZH1. Strikingly, an almost complete loss of H3K27me3 in postmitotic neurons induces minimal changes in gene expression and chromatin accessibility at 7 months of age. The amino acid composition of EZH1 suggests reduced sensitivity to H3K36 methylation, resulting in distinct activities of EZH1 and EZH2 in different chromatin contexts. Together, our results show that a postmitotic switch from EZH2 to EZH1 establishes novel chromatin domains in neurons with a minimal role in transcriptional maintenance.

overall_design: Chromatin accessibility analysis from proliferating cerebellar granule cell progenitors (GCPs) at P5-P7, mature granule cells at P21, and granule cells from wild-type and Ezh1 cKO x Neurod1-Cre at 7 months of age.

first: Mary

last: Hatten

first: Matthew

last: Paul

first: Thomas

last: Carroll


title: Long-term maintenance of H3K27me3 in postmitotic neurons is dispensable for gene expression regulation [ChIP-Seq]

overall_design:
ChIPseq of the histone modifications H3K36me2, H3K36me3, H3K9me3, and H3K27ac from  P7 mouse cerebellar granule cell progenitors and P21 mature cerebellar granule cells. Scaled ChIPseq tracks of the histone modification H3K27me3 from GSE223487.

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The table below lists GEO accessions reused/reanalyzed for this study.
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title: Long-term maintenance of H3K27me3 in postmitotic neurons is dispensable for gene expression regulation [bisulfite-Seq]

type: Methylation profiling by high throughput sequencing

overall_design: Cerebellar granule cell progenitors isolated from P7 mouse brain, migrating granule cells isolated from P12 mouse brain, and mature cerebellar granule cells isolated from P21 mouse brain were subjected to bisulfite sequencing (BSseq) and oxidative bisulfite sequencing (oxBSseq).


title: Long-term maintenance of H3K27me3 in postmitotic neurons is dispensable for gene expression regulation [snRNA-Seq]

overall_design: Nuclei from cerebral cortices of 7-month-old Ezh1wt/wt;Neurod1-Cre and Ezh1cKO/cKO;Neurod1-Cre mice were isolated and used for single-nucleus RNA sequencing.


title: Asialogycoprotein receptor subunit ASGR1a deficiency leads to cholesterol malabsorption in zebrafish on a high-cholesterol diet

city: Baltimore

first: Steve

last: Farber

state: MD

address: 3520 San Martin Dr

department: JHU Biology

institute: Farber Lab

summary: One of the major pathways to clear glycoproteins from circulation is via the liver-specific asialoglycoprotein receptor (ASGPR). Recently, loss of asialoglycoprotein receptor 1 (ASGR1), the major subunit of ASGPR in humans, was found to correlate with lower levels of plasma apolipoprotein B-containing lipoproteins (B-lps) and a profound reduction in cardiovascular disease risk. However, the cell and molecular biology underlying this effect was unclear. Given that rodents carry their cholesterol largely in HDL, we selected the zebrafish model to better understand the mechanism(s) of action of ASGR1. We first characterized all possible zebrafish ASGR1 orthologs to identify zebrafish ASGR1 (asgr1a) from a collection of lectin-binding proteins. We then generated two independent mutations in asgr1a using CRISPR/Cas9. Neither mutation altered larval, juvenile, or adult B-lp numbers or sizes. However, when challenged with a Western diet, asgr1a mutant zebrafish exhibited less hepatic steatosis and lower hepatic triglyceride levels compared to control animals. Asgr1a mutant animals also exhibited increased levels of fecal cholesterol, which we found was due to malabsorption after a meal and upregulation of liver proteins known to be involved in B-lp metabolism (e.g. MTP, APOA4). These data are consistent with the atheroprotective role of ASGR1 and reveal a previously unappreciated role for ASGR1 in modulating whole animal cholesterol flux.

overall_design: RNA-seq profiling of zebrafish adult liver tissues comparing wild-type (nluc) to two different ASGR mutants (c830 and c865). Animals were roughly 1-year old and had been fed a western diet for 6 days beforehand. Mutants were combined in the analysis because they showed the same phenotype in other lipodomic assays

first: Joshua

last: Derrick

first: Tabea

middle: O

last: Moll

first: Darby

last: Sweeney

first: Jeffery

last: Shin

first: Monika

last: Svelca

first: Giuseppe

last: Danilo Norata

first: Steven


title: A High Dimensionality Approach Reveals Immunopathogenic Responses Driving Severe Pediatric Acute Respiratory Distress Syndrome

city: Singapore

first: Pavanish

last: Kumar

state: Not Applicable

address: 20 collage road, The Academia, Discovery Tower, Level-8 Translation Immunology Institute (TII)

country: Singapore

institute: Translational Immunology Institute (TII), SingHealth-DukeNUS

summary: Mechanisms underlying paediatric acute respiratory distress syndrome (PARDS) remain poorly understood, limiting advances in diagnosis and treatment. To address this gap, we adopted a high-dimensional multi-omics approach to better understand immune dysregulation in PARDS, aiming to identify distinct pathogenic pathways. We show that severe PARDS is marked by interferon-driven immune dysregulation, with pulmonary T cells and myeloid cells exhibiting strong interferon responses and suppressed IL-1 pathways, resulting in impaired immune cell function and reduced IL-1α/β levels.

overall_design:
CD45+ live cells were FACS sorted targeting 16,000 live CD45+ cells at a final single cell suspension of 1000cell/uL which was then loaded on the 10X Genomics chip for each sample (PARDS n=10, controls n=4). Single cells were subsequently encapsulated into droplets via a gel bead in the emulsion (GEMs) method using the 10X Chromium controller. For gene expression the Chromium Single Cell 3ʹ Gene Expression protocol (V3 Chemistry, 10X Genomics) was used. Downstream library construction was done using 10X 3ʹ Gene Expression Library Construction kit and barcoded with i7 Illumina adapter indexes. Pooled libraries were then sequenced on the Illumina HiSeq 4000 platform using paired-end 151bp reads to achieve 50,000 reads per cell for gene expression.

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

first: Judith Ju Ming

last: Wong

first: Sharifah Nur

last: Hazirah


title: Mapping the sequence logic of DNA repair enzyme binding reveals mechanistic principles and evolutionary links [WT UDG]

city: Rehovot

first: Noga

last: Levy

address: 234 Herzl St.

institute: Weizmann Institute of Science

summary: In the study, we developed a high-throughput DNA microarray-based strategy (BER-Map) to comprehensively map how DNA repair enzymes recognize damaged bases across diverse sequence contexts.

overall_design: This library was designed to assess the influence of extended sequence context on UDG binding, examining flanking effects up to five nucleotides from the lesion site. The library consists of oligonucleotides with variable 5-mer flanking sequences in the format 5′-XNNNNN-3′, where N represents all possible nucleotides (A, C, G, T) and X denotes a fixed uracil-containing lesion (U:A pair). All other positions for each DNA oligo in the library are held constant. The lesion position is invariant, and all possible combinations of the defined flanking sequence space are represented. Control probes lacking the lesion are included in the raw dataset. Each probe is represented by 9–10 technical replicates.

first: Ariel

last: Afek


title: Mapping the sequence logic of DNA repair enzyme binding reveals mechanistic principles and evolutionary links [WT TDG binding + ARP]

sample_organism:
Homo sapiens
synthetic construct

overall_design: This library was designed to assess the influence of sequence context on TDG damage binding and product formation (as measured by ARP reagent). The library consists of oligonucleotides with variable flanking sequences in the asymmetric format 5-NNXNNNN-3, where N represents all possible nucleotides (A, C, G, T) and X denotes a fixed T:G mismatch damage. All other positions for each DNA oligo in the library are held constant. The lesion position is invariant, and all possible combinations of the defined flanking sequence space are represented. Control probes lacking the lesion are included in the raw dataset. Each probe is represented by 9-10 technical replicates.


title: Mapping the sequence logic of DNA repair enzyme binding reveals mechanistic principles and evolutionary links [WT TDG]

overall_design: This library was designed to assess the influence of sequence context on TDG damage binding. The library consists of oligonucleotides with variable flanking sequences in the format 5′-NNNXNNNN-3′, where N represents all possible nucleotides (A, C, G, T) and X denotes a fixed T:G mismatch damage. All other positions for each DNA oligo in the library are held constant. The lesion position is invariant, and all possible combinations of the defined flanking sequence space are represented. Control probes lacking the lesion are included in the raw dataset. Each probe is represented by 9–10 technical replicates.


title: Mapping the sequence logic of DNA repair enzyme binding reveals mechanistic principles and evolutionary links [2′-fluoroarabino analogue of deoxyuridine]

overall_design: This library was designed to assess the influence of extended sequence context on UDG and TDG binding to 2′-fluoroarabino analogue of deoxyuridine (UF). The library consists of oligonucleotides with variable flanking sequences in the format 5′-NNXNNN-3′, where N represents all possible nucleotides (A, C, G, T) and X denotes a fixed UF lesion (UF:G pair). All other positions for each DNA oligo in the library are held constant. The lesion position is invariant, and all possible combinations of the defined flanking sequence space are represented. Control probes lacking the lesion are included in the raw dataset. Each probe is represented by 7–10 technical replicates.


title: Mapping the sequence logic of DNA repair enzyme binding reveals mechanistic principles and evolutionary links [WT MBD4]

overall_design: This library was designed to assess the influence of sequence context on MBD4 damage binding and product formation (as measured by ARP reagent). The library consists of oligonucleotides with variable flanking sequences in the format 5-NNNXNNNN-3, where N represents all possible nucleotides (A, C, G, T) and X denotes a fixed T:G mismatch damage. All other positions for each DNA oligo in the library are held constant. The lesion position is invariant, and all possible combinations of the defined flanking sequence space are represented. Control probes lacking the lesion are included in the raw dataset. Each probe is represented by 9-10 technical replicates.


title: Mapping the sequence logic of DNA repair enzyme binding reveals mechanistic principles and evolutionary links [WT_UDG]

overall_design: This library was designed to assess the influence of sequence context on UDG damage binding and product formation (as measured by ARP reagent). The library consists of oligonucleotides with variable flanking sequences in the format 5-NNXNNN-3, where N represents all possible nucleotides (A, C, G, T) and X denotes a fixed uracil damage (U:G pair). All other positions for each DNA oligo in the library are held constant. The lesion position is invariant, and all possible combinations of the defined flanking sequence space are represented. Control probes lacking the lesion are included in the raw dataset. Each probe is represented by 7-10 technical replicates.


title: Cardiomyocyte-specific lamin A re-expression via AAV-Lmna/DJ8 ameliorates cardiac dysfunction in Lmna⁻/⁻ mice

city: Tokyo

first: Takahiro

last: Jimba

state: Bunkyo

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

summary: Mutations in LMNA, which encodes the nuclear envelope protein lamin A/C, cause laminopathies that frequently present as dilated cardiomyopathy (DCM). We investigated whether re-expression of lamin A in cardiomyocytes can rescue the severe phenotype of Lmna⁻/⁻ mice. An adeno-associated virus vector expressing wild-type Lmna (AAV-Lmna/DJ8) was administered intrathoracically to neonatal mice. Three weeks after injection, treated Lmna⁻/⁻ mice exhibited robust cardiac Lmna mRNA induction and nuclear localization of lamin A protein, reflecting efficient cardiotropic gene delivery. Compared with PBS treatment, AAV-Lmna/DJ8 treatment promoted body weight maintenance, improved left ventricular systolic function, and significantly prolonged survival in Lmna⁻/⁻ mice. To explore the underlying mechanisms, we performed single-nucleus RNA sequencing of cardiomyocytes from wild-type mice, PBS-treated Lmna⁻/⁻ mice, and AAV-Lmna/DJ8–treated Lmna⁻/⁻ mice. AAV-mediated lamin A re-expression shifted the cardiomyocyte transcriptome toward the wild-type profile, and restored oxidative phosphorylation–related gene programs, which were diminished in untreated Lmna⁻/⁻ mice. These findings demonstrate that targeted re-expression of Lmna ameliorates cardiac dysfunction in Lmna⁻/⁻ mice and highlight the therapeutic potential of LMNA gene replacement for laminopathy-associated cardiomyopathy.

overall_design: Study design: Left ventricule tissue of heart was snap frozen, and nuclei extraction was performed using a Singulator Nuclei Isolation System. WT-ctrl, Lmna-KO, and Lmna-KO+AAV-Lmna/DJ8 mice were analysed (n=2/group). Raw and processed data are provided.

first: Miho

last: Izawa

first: Kenji

last: Onoue

first: Shungo

last: Hikoso


title: Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling [scRNA-seq]

city: Detroit

first: Benjamin

middle: L

last: Kidder

address: 4100 John R St

department: Oncology

institute: Wayne State University

summary: Mouse embryonic stem cells (ESCs) occasionally transit into a rare two-cell-like (2C) state characterized by transient activation of endogenous retroviruses such as MERVL and expression of 2C-specific genes including the Zscan4 cluster. These 2C-like cells (2CLCs) resemble early blastomeres and display expanded developmental potential, but their unstable and sporadic nature has hindered mechanistic studies. Here, we demonstrate the transiently stable maintenance of MERVL-positive ESCs that exhibit persistent MERVL expression and activation of 2C-associated genes. Live-cell imaging revealed uniform and sustained MERVL activity in these MERVL-positive ESCs, contrasting with the heterogeneous and transient expression observed in conventional ESCs. Transcriptome profiling demonstrated robust induction of 2C-specific regulatory networks, and embryoid body differentiation combined with machine learning uncovered increased lineage variability and altered developmental trajectories. Single-cell RNA sequencing revealed clear separation of control ESCs from MERVL-positive populations and redistribution across distinct transcriptional states, with Red and Mosaic lines showing graded shifts within a shared transcriptional manifold. Epigenomic profiling further revealed distinct chromatin states, specialized super-enhancer landscapes, and active enhancer marking at MERVL loci. Together, these findings demonstrate that stable maintenance of MERVL-positive ESCs is achievable in vitro, providing a powerful model to dissect ERV-driven transcriptional regulation, epigenomic remodeling, and 2C-like transcriptional and epigenetic programs.

overall_design:
FLEX-Seq scRNA-Seq of ESC samples:
ZHBTc4_noDox_ESC_rep1
ZHBTc4_noDox_ESC_rep2
1_19_red_ZHBTc4_2c_HisD_ESC_rep1
1_19_red_ZHBTc4_2c_HisD_ESC_rep2
2_1_mosaic_ZHBTc4_2c_HisD_ESC_rep1
2_1_mosaic_ZHBTc4_2c_HisD_ESC_rep2


title: 5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [CUT&Run]

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

summary: MYCN-amplification is a strong predictor of poor prognosis in neuroblastoma, an embryonal malignancy that accounts for 15% of pediatric cancer deaths. Here, we found that MYCN-amplified neuroblastoma tumors have increased 5-hydroxymethylcytosine (5-hmC) deposition on Polycomb Repressive Complex 2 (PRC2) target genes. 5-hmC and H3K27me3, a catalytic product of PRC2, directly co-localize at the nucleosomal level in MYCN-amplified neuroblastoma. Genes with co-localization of 5-hmC/H3K27me3 are involved in development related pathways and are transcriptionally repressed in MYCN-amplified neuroblastoma. Chemical and genetic inhibition of 5-hmC deposition results in a loss of H3K27me3 deposition on protein-coding genes. Furthermore, 5-hmC deposition predisposes H3K27me3 marked genes to transcriptional activation upon PRC2 inhibition with tazemetostat. Low expression of genes marked by 5-hmC/H3K27me3 is associated with poor clinical outcome. Our results suggest that 5-hmC/H3K27me3 co-operate to repress mediators of development highlighting a novel link between DNA modifications and chromatin modifications with potential therapeutic implications in MYCN-amplified neuroblastoma.

overall_design: CUT&RUN, nano-HMC-seal, and RNA-Seq performed under various conditions in neuroblastoma cell lines

first: Mohansrinivas

last: Chennakesavalu

first: Gabriel L.

last: Lopez

first: Varsha

last: Gupta

first: Kelley

last: Moore

first: Yuxing

last: Xue

first: Josie

last: Majowka

first: Sahil

last: Veeravalli

first: Ryan

last: Borchert

first: Monica

last: Pomaville

first: Alexandre

last: Chlenski

first: Chuan

last: He

first: Andrea

last: Piunti

first: Mark A.


title: Isolation, Validation, and Long-Term Culture of Mouse Ear Fibroblasts

city: Madison

first: Laura

middle: J.

last: Knoll

state: WI

address: 1550 Linden Dr.

department: Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

summary: Primary fibroblasts are essential cell culture models for studying cellular homeostasis, disease mechanisms, and host-pathogen interactions. Primary cells offer physiological relevance that immortalized cell lines cannot recapitulate. However, existing protocols for isolating and culturing primary fibroblasts lack standardization for long-term applications. Contamination by alternate cell types, variable media formulations, and poorly monitored passage numbers remain critical challenges for reproducibility. Here, we present a streamlined, cost-optimized protocol for isolating and culturing mouse ear fibroblasts (MEarFs) suitable for extended passages. We demonstrate that enriched media (Advanced DMEM F/12 + 15%FBS) consistently promoted adipocyte-like cell contamination in long-term MEarF cultures. In contrast, minimal media (DMEM + 10% FBS) proved sufficient for both isolation and long-term culture, maintaining fibroblast identity through at least 13 passages. Cells displayed characteristic fibroblast morphology, expressed the mesenchymal marker vimentin, and maintained fibroblast-associated transcripts with minimal epithelial and adipocyte marker expression throughout culture. Bulk RNA sequencing revealed 17% of mapped genes exhibited differential abundance between passage 3 and passage 9, with enrichment in functional categories related to cell cycle regulation and paracrine signaling. This protocol provides an accessible primary fibroblast cell culture model with broad research applications emphasizing reproducibility and resource- conscious practices.

overall_design: Bulk RNA-seq of mouse ear tissue from wildtype C57BL/6 mice after 3 passages and 9 passages in tissue culture.

first: Katie

last: Barnes

first: Nicole

last: Davis

first: Billy

last: Erazo

last: Cataldo

first: Emmaly

middle: H

last: Bertges


title: Regulation of endothelial cell chromatin availability and transcription factor activity in arterial-venous specification - Murine Fucci Retinal EC ATACseq

city: Charlottesville

first: Nicholas

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

summary: Arterial-venous specification of endothelial cells during vascular development requires coordination between intracellular signaling, cell cycle state, and transcription factor activity. However, the intrinsic regulatory mechanisms that govern these processes are poorly understood. To investigate this, we assessed endothelial chromatin accessibility during vascular development. Murine postnatal day (P)6 and P15 retinal endothelial cells were analyzed by single cell Assay for Transposase Accessible Chromatin (ATAC) sequencing, revealing heterogeneous accessibility of chromatin across an arterial-venous continuum. Enhancer regulatory network analysis predicted transcription factors with high activity, including Sox17. Transcription factors with differential arterial-venous activity showed dual activator and repressor functions, with many regulated by cell cycle-dependent chromatin accessibility. We validated SOX17 function in human endothelial cells, identifying that SOX17 inhibits proliferation and promotes arterial gene expression. Our findings suggest that dual roles of key endothelial transcription factors are regulated by chromatin accessibility in a cell cycle- and subtype-specific manner to control arterial-venous specification.

overall_design: Mice at age P6 were euthanized according to approved protocols, and retinal tissue was immediately harvested from isolated eyes by microdissection removal of cornea, adventitial, and vitreous body tissue. Retinal tissue was then enzymatically digested in a digestion solution containing 1.0 mg/mL Collagenase Type II and 10% FBS in DMEM for 20 min at 37°C. Digested cells were washed and resuspended in staining buffer containing 10% FBS, 20 mM HEPES, and 1.0 mg/mL D-Glucose in HBSS with fluorescently-conjugated anti-CD31 and anti-CD45 antibodies. Immuno-stained cells were washed, resuspended in FACS buffer containing 1% FBS in PBS, stained with Propidium Iodide (PI), and sorted by FACS using a FACSMelody sorter (BD Biosciences) to isolate the PI-CD31+CD45- population as endothelial cells. Endothelial cells were sorted to isolate 3 samples of early G1 (blank fluorescence) cells and 4 samples of late G1 (red fluorescence) cells, then nuclei were isolated as described for single cell ATAC sequencing preparation. Isolated nuclei were incubated in Transposition Mix containing 25 µL TD Buffer, 2.5 µL TDE1 enzyme, 0.5% Digitonin, and 22.5 µL H2O (items from Nextera XT DNA Library Preparation Kit) at 37°C for 30 min. DNA was purified using a MinElute PCR Purification Kit. Tagmented DNA samples were PCR amplified with unique barcoded primers for demultiplexing after sequencing. PCR products were purified using MinElute PCR Purification Kit and cleaned with AMPure Beads. Samples were submitted to Novogene for next-generation sequencing. Sequencing reads were sorted and filtered for size, including trimming by trimmomatic for ATAC chromatin signal, alignment to mm10 reference genome by STAR, and sorting by bedtools.

first: Chavkin

last: Nicholas

first: Hirschi

last: Karen


title: Regulation of endothelial cell chromatin availability and transcription factor activity in arterial-venous specification - HUVEC FUCCI SOX17 CUT&RUN

overall_design: HUVEC-FUCCI were generated by lentiviral infection of the FastFUCCI plasmid (pBOB-EF1-FastFUCCI-Puro was a gift from Kevin Brindle & Duncan Jodrell (Addgene plasmid # 86849 ; http://n2t.net/addgene:86849 ; RRID:Addgene_86849)). HUVEC-FUCCI were cultured in EGM-2 media on 10 cm tissue culture plates pre-coated with 0.1% Gelatin. CUT&RUN for library preparation of SOX17-bound chromatin was performed on HUVEC-FUCCI that were sorted by FACS into early G1 or late G1 using the CUT&RUN Assay Kit with anti-SOX17 antibody. Prepped libraries were submitted to Novogene for library pooling and next-generation sequencing. Computational analysis of sequencing output as performed using the standard nf-core pipeline for CUT&RUN, including trimming by Trimgalore, aligning to the hg19 reference genome by STAR, filtering by Samtools, sorting and clipping by bedtools.


title: Cancer stem cells are hyper-responsive sensors of tumor microenvironment in orchestrating metastasis dynamics

city: Bethesda

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary: Cancer stem cells (CSCs) are key drivers of metastasis and therapy resistance but have been challenging to visualize and study in situ. Using a fluorescent CSC reporter, we observed very different population  dynamics for CSCs and nonCSCs during metastatic lung colonization in breast cancer models. CSC  expansive self-renewal drives early lesion formation before switching to a maintenance mode of balanced self-renewal and differentiation, whereupon nonCSC proliferation takes over as the main  driver of metastatic expansion. Mechanistic analyses showed that CSCs are hyper-responsive to  microenvironmental cues such as cell crowding and nutrient availability, suggesting a novel role for CSCs  as sensors and early responders to fluctuating local conditions in the tumor. Most inputs converge on YAP/TAZ/TEAD, with heightened CSC sensitivity and response supported by elevated receptor  expression and increased chromatin accessibility around enhancers with TEAD binding sites. Targeting inputs to the YAP/TAZ/TEAD node reversed chemotherapy-induced enrichment of CSCs in lung metastases.

overall_design: Two independent preparations of MDAMB231-LM2 cancer stem cells (CSCs) and non-cancer stem cells (nonCSCs) were generated by FACS sorting MDAMB231-LM2 cells transduced with the SORE6>dsmCherry cancer stem cell reporter.  After recovery in culture overnight,cells were harvested for processing with the Active Motif ATAC-seq Kit according to the manufacturer’s instruction.

first: Binwu

last: Tang

first: Hualong

last: Yan

first: Jing

last: Huang

first: Maxwell

last: Lee

first: Lalage

last: Wakefield


title: Regulation of endothelial cell chromatin availability and transcription factor activity in arterial-venous specification - HUVEC FUCCI RNAseq

overall_design: RNA isolation and purification for library preparation was performed on HUVEC-FUCCI that were sorted by FACS into early G1 or late G1 using the RNeasy Mini Kit. Purified RNA was submitted to Novogene for sequencing. Raw sequencing output was aligned to the hg19 reference genome by STAR.


title: Quantitative profiling of RNA modifications enriched in non-membrane bound cellular structures using APEX-RNA-MS

city: Princeton

first: Ralph

middle: E

last: Kleiner

address: 359 Frick Chemistry Lab

department: Chemistry

institute: Princeton University

summary: The dynamic behavior of RNA underlies fundamental biological processes. RNA function is controlled by post-transcriptional modifications that are spatiotemporally regulated, but characterizing the distribution of modified RNA transcripts with subcellular resolution is a major challenge. Here we present APEX-RNA-MS, which combines APEX2 proximity labeling with LC-MS quantification of modified ribonucleotides. We use APEX-RNA-MS to characterize RNA modifications proximal to RNA-binding proteins enriched in non-membrane bound cellular structures. We measure changes in protein-proximal RNA modification levels upon induction of DNA damage foci and stress granules, consistent with previous studies using antibody-based imaging and biochemical fractionation. Further, we show that tRNA-specific modifications are proximal to G3BP1 and use RNA sequencing and RNA FISH to demonstrate the accumulation of multiple tRNAs in stress granules. Taken together, our work provides a general approach for characterizing the subcellular distribution of RNA modifications and reveals new insights into the composition and function of cellular condensates.

overall_design: tRNA sequencing of bulk RNA from untreated and NaAsO2-treated HeLa cells; tRNA sequencing of enriched tRNA using G3BP1-APEX proximity labeling

first: Kyung

last: Seo

first: Dhruv

middle: Y

last: Dhingani


title: Analysis of the genomic regions controlled by RBPJ in alveolar macrophages (RBPJ HT-ChIPmentation)

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

institute: CNB-CSIC

summary: The goal of this study was to define the cistrome of RBPJ by HT-ChIPmentation followed by sequencing in alveolar macrophages of wild-type mice, in order to identify genomic regions directly controlled by this transcription factor.

overall_design: Alveolar macrophages (AMs) from wild-type mice were isolated by bronchoalveolar lavage (BAL), stained and FACS-sorted in 200k cell aliquotes. We performed the protocol described in 'Gustafsson et al, 2019' with minor modifications, using the RBPJ antibody (#25949, Abcam)

first: Laura

last: Casablanca

first: Hooman

last: Aghelpasand

first: Pontus

last: Höjer

first: Robert

last: Månsson


title: Feeder-free generation of functional dendritic cells from human pluripotent stem cells

first: Wei-Hung

last: Jung

state: MA

address: 201 Brookline Ave

institute: Wyss Institute

summary: The scarcity of primary conventional dendritic cells (cDCs) and the limited effectiveness of monocyte-derived dendritic cells (moDCs) have long hindered progress in human dendritic cell research and immunotherapy. We developed a feeder-free differentiation platform that generates CD1c⁺CD141⁺ hPSC-cDCs phenotypically aligned with CD141⁺ tissue-resident cDC2 subsets found in human tissues. We further optimized the differentiation process using a Design-of-Experiments framework to refine cytokine and serum conditions, enhancing differentiation efficiency while reducing cytokine demand. These hPSC-cDCs exhibit efficient antigen uptake, defined cytokine responses, and robust priming of antigen-specific CD8⁺ T cell proliferation and effector differentiation, outperforming moDCs in direct comparison. Together, this work establishes a robust, and generalizable platform for mechanistic studies and translational development of dendritic cell-based vaccines and standardized ex vivo T cell expansion.

overall_design: FACS-sorted hPSC-cDCs derived from three lines (H1, iPS-11, and PGP-1), as well as H1-derived cells differentiated under DoE-optimized conditions, were subjected to bulk RNA-seq along with primary cDC1 and cDC2 isolated from PBMCs of three donors.

first: Joshua

last: Price

first: David

last: Mooney


title: Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling

first: Benjamin

last: Kidder

state: MI

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

overall_design: Refer to individual Series


overall_design: RNA-Seq of embryoid bodies (EBs). The 2C::tdTomato reporter plasmid (Addgene #40281) was modified to include the HisD cassette from pENTR-R2L3-cGR-ID plasmid (Addgene #139541). ZBHTc4 ES cells were transfected with this modified plasmid and stably selected. 1-5 red and 1-19 red are 2C::tdTomato reporter positive. ZHBTc4 ESCs were differenitated following culture in the absence of dox and LIF.


overall_design: ChIP-Seq of ESCs. The 2C::tdTomato reporter plasmid (Addgene #40281) was modified to include the HisD cassette from pENTR-R2L3-cGR-ID plasmid (Addgene #139541). ZBHTc4 ES cells were transfected with this modified plasmid and stably selected. 1-5 red, 1-19 red, 2-10 red, 2-1 mosaic, 3-1 mosaic, and 3-2 mosaic are 2C::tdTomato reporter positive. ZHBTc4 ESCs were cultured in the presence or absence of dox.


title: 5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma [5-hmC]

first: Mark

last: Applebaum

summary: Purpose: Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high- risk neuroblastoma.  Methods: 5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunopre- cipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models.  Results: In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found in- creased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma.  Conclusion: Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma.

overall_design: hmC-seal derived 5-hydroxymethylcytosine profiles of 8 neuroblastoma cell lines grown under normoxic and hypoxic conditions.

first: Mohansrinivas

last: Chennakesavalu

first: Kelley

last: Moore

first: Gepoliano

last: Chaves

first: Sahil

last: Veeravalli

first: Rachel

last: TerHaar

first: Tong

last: Wu

first: Ruitu

last: Lyu

first: Alexandre

last: Chlenski

first: Chuan

last: He

first: Andrea

last: Piunti


title: PM20D1-derived treatment induces microglia association with amyloid plaques and improves Alzheimer’s disease pathologies

city: Alicante

first: Jose Vicente

last: Sanchez Mut

state: Alicante

address: C/Santiago Ramón y Cajal, s/n

institute: CSIC

summary: There is increasing evidence of microglia participation in Alzheimer's disease (AD), which incentives their modulation to intercept the disease. Here, we describe a new mechanism by which the recently AD-associated Peptidase M20 Domain Containing 1 (PM20D1) instructs microglia to tackle AD. We show that the PM20D1-derived N-oleoyl-Leucine (OLE) improves AD pathologies in two animal models of AD. OLE induces microglia association with amyloid beta (Aβ) plaques, reduce their size, number and toxicity, and leads to enhanced neuroprotection and cognition. Furthermore, OLE also increases Aβ chemotaxis and clearance in microglia cultures and enhances cell viability in neurons subjected to AD-related stressors. Finally, we also find evidence for a PM20D1- and OLE-mediated microglia association with amyloid plaques and neuroprotection in human AD brains. In sum, our results provide further insight into the protective role of PM20D1 in AD and support the use of OLE as a microglia-modifying treatment for AD.

overall_design: C18:1-Leu (25 mg/kg/day) and/or vehicle (DMSO) in alkaline drinking water was administered from 15 to 18 months of age in Male APP/PS1 mice. Entorhinal cortex samples from five mice were pooled and analyzed by snRNA-seq (10X Genomics)

first: Victoria

last: Pozzi-Ruiz

first: Aida

last: Giner de Gracia

first: Liliane

last: Glauser

first: Mario

last: Romani

first: Fatima

last: Gunter-Rahman

first: Alejandro

last: González-Ramón

first: Mahmood

last: Haj-Yahya

first: Rajasekhar

last: Kolla

first: Allison M

last: Burns

first: Hilal A

last: Lashuel

first: Johan

last: Auwerx

first: Johannes

middle: V

last: Gräff

first: Jose V

last: Sanchez-Mut


title: Analysis of the genomic regions controlled by SMAD4 in alveolar macrophages (SMAD4 HT-ChIPmentation)

first: Mercedes

last: Ricote

summary: The goal of this study was to define the cistrome of SMAD4 by HT-ChIPmentation followed by sequencing in alveolar macrophages of wild-type mice, in order to identify genomic regions directly controlled by this transcription factor.

overall_design: Alveolar macrophages (AMs) from wild-type mice were isolated by bronchoalveolar lavage (BAL), stained and FACS-sorted in 200k cell aliquotes. We performed the protocol described in 'Gustafsson et al, 2019' with minor modifications, using a combination of SMAD4 antibodies (#38454 and #46535, ProteinTech)

first: Jesús

last: Porcuna

first: Jorge

last: Mínguez-Martínez