title: Comparison of mesenchymal stromal cells derived from osteoarthritis and non-osteoarthritis patients

city: Berlin

first: Julia

last: Sonnleitner

address: Charitéplatz 1

institute: Charité - Universitaetsmedizin Berlin

summary:
Osteoarthritis (OA) is a chronic, multifactorial disease of the joint, which involves synovial inflammation, bone remodeling, and cartilage destruction. It poses a serious burden of global disease, with an incidence rate that has increased by 9.3% between 1990 and 2017. In situ tissue engineering represents a strategy that takes advantage of physiological repair mechanisms and seeks to enhance them. A strong focus has been placed on mesenchymal stromal cells (MSCs) as a source for endogenous regeneration, as they have been shown to contribute to tissue recovery in OA. A potential senescent phenotype of OA MSCs could impose a major limitation on their regenerative potential.
MSCs derived from the bone marrow of osteoarthritis and non-osteoarthritis patients were analyzed upon their expression of senescence markers using an affymetrix microarray to explore their suitability for an in situ tissue engineering approach.

overall_design: 3 biological replicates from OA and non-OA (ND) donors each were analyzed upon expression of selected senescence markers.

first: Tilo

last: Dehne

first: Katja

last: Gulich

first: Axel

last: Pruss

first: Carsten

last: Perka

first: Angelika

last: Gursche

first: Daniel

last: Kendoff

first: Michael

last: Sittinger

first: Shabnam

last: Hemmati-Sadeghi


title: Molecular and phenotypic blueprint of human hematopoiesis links proliferation stress to stem cell aging.

status: Public on Dec 09 2025

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Intestinal adaptations increase basolateral intestinal glucose uptake and glycolysis in a Cystic Fibrosis mouse model

status: Public on Dec 10 2025

city: Cleveland

first: Aura

last: Perez

state: OH

address: 10900 Euclid Avenue

department: Pediatrics

country: USA

institute: CWRU

summary: The intestinal manifestations of Cystic Fibrosis (CF) continue to be a source of morbidity despite major advances in CF therapies over the past several years. CF intestinal disease may include obstruction at birth or throughout the lifespan, dysmotility, constipation, small intestinal bacterial overgrowth, and abdominal pain and discomfort. People with CF also have a five to ten-fold increased risk of developing gastrointestinal cancers earlier in life, the reason for which remains largely unknown. The mechanisms underlying the intestinal manifestations of CF are not fully understood. Impaired chloride and bicarbonate ion transport due to absent or dysfunctional CFTR results in dehydrated, viscous mucus that coats the intestinal lumen and altered pH. These changes are thought to create an environment that hinders digestive enzymatic and immune function to promote dysbiosis, dysmotility, and obstruction. The other major organs of digestion, including the pancreas and hepatobiliary system, are also affected in CF, which can result in a variety of symptoms mainly related to fat malabsorption, in addition to various hepatic and biliary pathologies. Most of what is known about the CF intestines has been garnered from studies on the luminal function pertaining to digestion, absorption, mucus accumulation, and bacterial dysbiosis, but little has been described regarding the serosal side. In the process of evaluating systemic carbohydrate utilization in CF mice, we identified the intestine as a key site of increased glucose uptake from circulation in CF. Consequently, we employed a series of complementary in vivo and ex vivo, transcriptional and functional approaches to characterize intestinal glucose demand and metabolism in a mouse model of CF to gain new insights into mechanisms of intestinal disease.  We show elevated GLUT1 (Slc2a1) expression in both CF intestinal tissue and isolated crypts, suggesting GLUT1 is responsible for the increased intestinal glucose uptake from the circulation in CF mice. We also identified concomitant increases in glycolysis, in addition to evidence of a proliferative adaptive response in the CF intestine. Taken together, these results are indicative of an increased intestinal glucose demand in CF to maintain intestinal homeostasis and offer a novel approach to understanding CF intestinal disease that may result in new markers of disease status and potentially new critical insight into cancer risk in people with CF. Our findings emphasize a continued need to investigate how the interplay of numerous digestive and absorptive defects in CF contribute to disease pathogenesis to develop more effective therapies for the gastrointestinal manifestations of CF.

overall_design: RNA-seq profile of whole tissue duodenum, jejunum, and ileum, and jejunum crypts from WT mice and G542X mice

first: Alexander

middle: F

last: Lesser

first: Chunying

last: Wu

first: Shuyu

last: Hao

first: Bernadette

last: Erokwu

first: Derek

last: Host

first: Anjum

last: Jafri

first: Elisha

last: Barbato

first: Jean

last: Eastman

first: Senthilkumar

last: Sankararaman

first: Chris

middle: A

last: Flask

first: Mitchell

middle: L

last: Drumm


title: scRNA-seq of a knockout village during hPSC-derived islet differentiation

status: Public on Dec 12 2025

city: Washington

first: Bicna

last: Song

state: DC

address: 7144 13th Pl NW

institute: Children's National Hospital

summary: This submission consists of processed single-cell RNA-seq data of knockout village samples, provided as filtered feature–barcode matrices generated using Cell Ranger v7.1.0 with default parameters. We previously deposited the same biological samples and data processed by STAR under GEO accession GSE288587. The corresponding raw FASTQ files are available in ENA under accession ERP168459. The supplementary file (reanalysis_samples.xlsx) provides a reference table linking each sample in this submission to its corresponding GSM in GSE288587, which contains the detailed experimental descriptions of culture information, genotypes, and differentiation stages.

relation:
Reanalysis of: GSM8770302
Reanalysis of: GSM8770313
Reanalysis of: GSM8770303
Reanalysis of: GSM8770314
Reanalysis of: GSM8770304
Reanalysis of: GSM8770315
Reanalysis of: GSM8770305
Reanalysis of: GSM8770316
Reanalysis of: GSM8770306
Reanalysis of: GSM8770317
Reanalysis of: GSM8770307
Reanalysis of: GSM8770318
Reanalysis of: GSM8770308
Reanalysis of: GSM8770319
Reanalysis of: GSM8770309
Reanalysis of: GSM8770320
Reanalysis of: GSM8770310
Reanalysis of: GSM8770321
Reanalysis of: GSM8770311
Reanalysis of: GSM8770322
Reanalysis of: GSM8770312
Reanalysis of: GSM8770323
SubSeries of: GSE315753

overall_design: The knockout village consist of 3 WT and 76 knockout lines targeting 30 pancreas developmental regulators and diabetes genes, including GATA6, PDX1, GATA4, FOXA1, FOXA2, MNX1, NEUROD1, NKX2-2, RFX6, GSC, HHEX, HNF4A, PAX6, PBX1, GLIS3, NEUROG3, ARX, OTUD5, BMPR1A, TLE3, BCOR, QSER1, TET1, TET2, TET3, TADA2B, KDM2B, PROSER1, ONECUT1, and NANOG. Edited lines were generated in two hPSC backgrounds (HUES8 and H1). Individual clonal lines were uniquely barcoded by lentiviral infection with GFP-barcode plasmids from the LARRY library and pooled to form a knockout village for differentiation. Samples were collected at five differentiation stages: day -1 (hPSC, 1 day prior differentiation), day 3 (definitive endoderm, DE), day 7 (posterior foregut, PFG), day 11 (pancreatic progenitor, PP) and day 18 (early SC-islet). In addition, WT cells in H1 and HUES8 backgrounds were differentiated and sequenced in parallel at 17 time points: day -1 (hPSC), 3, 5, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 21, 25, 26, 35.

first: Dingyu

last: Liu

first: Dapeng

last: Yang

first: Renhe

last: Luo

first: Wei

last: Li

first: Danwei

last: Huangfu


title: Single Cell and Spatial Transcriptomics Implicate Vascular Cell Orchestration of Inflammatory Changes After Ultraviolet Light Exposure [Spatial Transcriptomics]

status: Public on Dec 08 2025

city: Seattle

first: Jie

last: An

state: WA

address: 750 Republican Street

institute: University of Washington

summary: To elucidate the complex effects of acute UV radiation (UVR) on the skin, we exposed shaved mouse skin to UVB and performed transcriptomic profiling of the epidermis, deep dermis and adipose tissue. Spatial transcriptomic analysis revealed the most pronounced gene expression changes in the epidermis, peaking at 24 hours post-irradiation. While CD45⁺ immune cells showed differential expression of chemokines, cytokines, and acute-phase proteins, cytokeratin⁺ epidermal cells upregulated genes related to cellular stress and damage (e.g., Usp19, Adam25), as well as structural remodeling and apoptosis (e.g., Krt18, Phlda1). Single-cell RNA sequencing (scRNA-seq) conducted 12 hours after UVR exposure identified 4,849 differentially expressed genes (DEGs), with the epidermis and endothelial cells showing the highest DEG counts. Pathway analysis of upregulated genes in the epidermis revealed enrichment in VEGF, HIPPO, complement, IL-6, and apoptosis signaling pathways. In endothelial cells, UVR induced expression of multiple chemokines and cytokines. Notably, receptor-ligand analysis highlighted endothelial cells as key targets of CXCL chemokines and complement component C3. In fibroblasts, UVR triggered upregulation of inflammatory activation markers (Osmr, Cux1) alongside genes associated with glucose metabolism (Hif1a, Pkm). Cross-species comparison of UVR-responsive DEGs between mice and humans revealed strong concordance, particularly in TGF-β and TNF-associated pathways.

overall_design: Mice used in this study were 12-16 week old C57BL/6 (B6, wild type) females. Mice were anesthetized with isoflurane and a single dose of UVB (500 mJ/cm2) was delivered to the shaved whole back using FS40T12/UVB bulbs (National Biological Corporation) as described previously (Skopelja-Gardner et al., 2021). The narrow band UVB light energy (290-320 nm) at the dorsal surface was measured with Photolight IL1400A radiometer with a SEL240/UVB detector (International Light Technologies). Biopsies were taken at times 0, 6, and 24 hours after UVB exposure (n=3 per group) for spatial transcriptome analysis.

first: Rachael

last: Bogle

first: Rayan

last: Najjar

first: Lam

middle: C

last: Tsoi

first: Michelle

last: Kahlenberg

first: Ksenia

last: Anufrieva

first: Erin

last: Theisen

first: Kevin

last: Wei

first: Johann

middle: E

last: Gudjonsson

first: Keith

last: Elkon


title: Hyperosmotic stress induces a large-scale rewiring of 3D chromatin interactions [mAID2 Hi-C]

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

summary: Cells rapidly adapt to hyperosmotic stress through coordinated molecular responses. To determine how three-dimensional (3D) chromatin structure contributes to this process, we profiled chromatin interactions, architectural protein occupancy, and transcriptional dynamics in human cells exposed to sorbitol-induced hyperosmotic stress. We performed time-resolved Hi-C to measure stress-induced remodeling of chromatin loops and domains, CUT&Tag to quantify CTCF, RAD21, YAP1, and H3K27ac occupancy at loop anchors, and RNA-seq to capture stress-responsive transcriptional programs. These data reveal global loss of pre-existing chromatin contacts and concurrent formation of de novo, transient loops enriched for retained CTCF and cohesin, as well as transcriptional responses that are temporally layered and largely decoupled from loop remodeling. This dataset provides a resource for investigating how nuclear architecture and transcriptional regulation respond to hyperosmotic stress.

overall_design: eGFP-YAP HEK293 cells were serum-starved for 1 hour and then exposed to 200 mM sorbitol to induce hyperosmotic stress. Chromatin organization was profiled by in situ Hi-C at eight time points (0 min, 10 min, 30 min, 1 h, 3 h, 6 h, 12 h, and 24 h) to capture the formation, loss, and recovery of chromatin interactions. To assess the generality of chromatin remodeling, additional Hi-C experiments were performed in HEK293 wild-type and HCT116 cells with and without 1 hour of sorbitol treatment. To probe the requirement for architectural proteins, we also performed Hi-C in HCT116 mAID2-CTCF and mAID2-RAD21 degron cell lines treated with 1 μM 5-Ph-IAA to rapidly and reversibly degrade CTCF or RAD21 prior to sorbitol exposure. Transcriptional responses were measured by stranded RNA-seq across a time course (0 h, 1 h, 3 h, 6 h, 9 h, 12 h, and 24 h). To quantify changes in architectural protein occupancy, CUT&Tag for CTCF and RAD21 was performed in untreated and 1-hour sorbitol-treated HEK293 cells.

first: JP

first: Andrea A.

last: Perreault

first: Zack

last: Drum

first: Chenxi

last: Xu

first: Doris

last: Cruz Alonso

first: Gelila

last: Petros

first: Yijia

last: Wu

first: Ivana Y.

last: Quiroga-Barber

first: Isha

last: Sahasrabudhe

first: Justin

last: Demmerle

first: Gang Greg

last: Wang

first: Danfeng

last: Cai

first: Douglas

last: Phanstiel


title: Opposing functions of distinct regulatory T cell subsets in colorectal cancer

status: Public on Dec 15 2025

city: New York

first: Sneha

last: Mitra

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Regulatory T (Treg) cells are considered major contributors to the growth of solid organ tumors, with the notable exception of colorectal cancer (CRC), despite the documented abundance of Treg cells in CRC. Here, we demonstrate that IL-10⁺ and IL-10⁻ Treg cells constitute two distinct subsets with opposing functions: IL-10⁺ Treg cells counteract, while IL-10⁻ Treg cells promote, the growth of genetically engineered CRC tumors. Our findings suggest that the tumor-suppressive function of IL-10⁺ Treg cells is mediated by their suppression of effector CD4⁺ T cell production of IL-17, a cytokine that directly stimulates CRC tumor cell proliferation. Consistently, IL-10⁺ Treg cells were more abundant in both mouse and human CRC tumors than in tumor-adjacent normal colon tissue, whereas IL-10⁻ Treg cells exhibited the opposite distribution. Furthermore, gene expression signatures associated with IL-10⁺ and IL-10⁻ Treg cells correlated with better and worse disease prognoses in human CRC, respectively. This functional dichotomy between Treg subsets provides a rationale for therapeutic strategies aimed at selectively targeting pro-tumoral Treg cells while preserving their anti-tumoral counterparts across various barrier tissue cancers that harbor both subsets.

overall_design: Mouse T cells were sort purified from transcplanted AKP tumor, adjacent cecal tissue, and the draining C1 lymph node two, four, or six week after tumor transplantation.

first: Xiao

last: Huang

first: Dan

last: Feng

first: Emma

middle: S

last: Andretta

first: Nima

middle: B

last: Hooshdaran

first: Aazam

middle: P

last: Ghelani

first: Eric

middle: Y

first: Joe

middle: N

last: Frost

first: Victoria

last: Lawless

first: Aparna

last: Vancheswaran

first: Qingwen

last: Jiang

first: Christina

last: Leslie

first: Alexander

last: Rudensky


title: The DLX2-LAP2α axis licenses ectomesenchymal specification by unlocking chromatin barriers for craniofacial regeneration [CUT&Tag]

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

country: China

institute: Sichuan University

summary: The ectomesenchyme generates much of the craniofacial skeleton, sutures, and diverse connective tissues in the mammalian head, yet its derivation from embryonic stem cells (ESCs) and the underlying molecular drivers remain poorly defined. Here, we identified Dlx2 as a key regulator that efficiently directed murine ESCs towards Msx1+ ectomesenchyme, recapitulating the developmental trajectory. These Msx1+ progenitors expressed classical craniofacial markers and retained robust osteochondral bipotency in vitro and in vivo. Mechanistically, DLX2 utilized a lamina-associated polypeptide 2 (LAP2)-dependent nuclear chaperoning system, engaging LAP2α via a 38-amino-acid homeodomain motif to interact with nucleosomes, thereby opening chromatin and activating a craniofacial ectomesenchymal gene network. Disrupting DLX2-LAP2α interaction or silencing Dlx2 targets largely diminished ectomesenchymal differentiation. Our findings established DLX2 as a pioneer factor in ectomesenchyme specification, offering insights into craniofacial development and stem cell engineering.

overall_design: CUT&Tag profiling was performed for LAP2 and the histone modifications H3K9me3 and H3K27ac in day-2 Dlx2-OE EBs, as well as for DLX2 (FLAG) in day-2 EBs with or without Dox treatment.

first: Ziwei

last: Zhang

first: Zhiheng

last: Xu

first: Hong

last: Hu

first: Yao

first: Youmei

last: Jin

first: Yi

last: Zhong

first: Yunqiu

first: Yike

last: Yin

first: Jing

last: Chen

first: Yufeng

last: Duan

last: Hao


title: Single Cell and Spatial Transcriptomics Implicate Vascular Cell Orchestration of Inflammatory Changes After Ultraviolet Light Exposure [scRNA-seq]

first: Jie

last: An

overall_design: Mice used in this study were 12-16 week old C57BL/6 (B6, wild type) females. Mice were anesthetized with isoflurane and a single dose of UVB (500 mJ/cm2) was delivered to the shaved whole back using FS40T12/UVB bulbs (National Biological Corporation) as described previously (Skopelja-Gardner et al., 2021). The narrow band UVB light energy (290-320 nm) at the dorsal surface was measured with Photolight IL1400A radiometer with a SEL240/UVB detector (International Light Technologies). Biopsies were taken at times 0 and 12 hrs (snRNAseq) or at 0, 6, and 24 hours after UVB exposure (n=3 per group) for spatial transcriptome analysis.

first: Rachael

last: Bogle

first: Rayan

last: Najjar

first: Lam

last: Tsoi

first: Michelle

last: Kahlenberg

first: Ksenia

last: Anufrieva

first: Erin

last: Theisen

first: Kevin

last: Wei

first: Johann

last: Gudjonsson

first: Keith

last: Elkon


title: A role for the cholinergic neuron circadian clock in RNA metabolism and mediating neurodegeneration

city: Chicago

first: Sharon

last: Tam

state: IL

address: 303 E Chicago Ave, Rm 13-270

institute: Northwestern University


title: The DLX2-LAP2α axis licenses ectomesenchymal specification by unlocking chromatin barriers for craniofacial regeneration [scRNA-seq]

first: Zhonghan

last: Li

overall_design: To investigate if Dlx2-induced ectomesenchymal differentiation would follow the known developmental principles, we harvested EBs at day-2, -8, -12, and -16 for single cell sequencing (scRNA-seq)

first: Ziwei

last: Zhang

first: Zhiheng

last: Xu

first: Hong

last: Hu

first: Yao

first: Youmei

last: Jin


title: Uracil-DNA glycosylase deficiency is associated with repressed tumor cell-intrinsic inflammatory signaling and altered sensitivity to exogenous interferons

status: Public on Dec 04 2025

city: Pittsburgh

first: Christopher

middle: J

last: Bakkenist

state: PA

address: 5051 Centre Avenue

department: Radiation oncology

institute: university of pittsburgh

summary: 2’-deoxyuridine (dU) is a common DNA lesion resulting from cytosine deamination and from dUMP incorporation by DNA polymerases, both of which are prevalent in cancer. The primary mechanism that repairs dU lesions in genomic DNA is base excision repair initiated by Uracil-DNA Glycosylase 1 (UNG1). We generated Ung knockout mouse B16 melanoma cells to investigate the consequences of UNG deficiency in a well-characterized, immunoproficient, syngeneic mouse cancer model. We show that UNG-deficient (ΔUNG) B16 tumors have altered growth kinetics in vivo and that their delayed growth is T-cell dependent. Immune profiling revealed reduced CD8+ T cell infiltration but augmented CD4+ Th1 responses in ΔUNG tumors. In vitro, ΔUNG tumor cells exhibit strongly suppressed cell-intrinsic type-I interferon, type-II interferon, and inflammatory signaling gene expression signatures as well as altered cytokine and chemokine secretion. In vivo, ΔUNG tumors exhibit a modified inflammatory cytokine and chemokine milieu. Furthermore, ΔUNG tumor cells have altered sensitivity to exogenous interferons in vitro, with increased sensitivity to IFN-γ but decreased sensitivity to IFN-α/β. Collectively, our data show that tumor cell-specific UNG deficiency results in an altered tumor microenvironment in vivo and provide proof-of-concept data for the use of UNG inhibitors to modulate inflammatory pathways in tumors.

overall_design: B16F10 wildtype (cas9 control) and UNG knockout clones (ΔUNG and ΔUNG_2) cells treated with DMSO or 5uM ATRi (AZD6738) for 48h.  Study was performed using two biological replicate per each condition and each cell line

first: Frank

last: Vendetti

first: Pinakin

last: Pandya

first: Carina

middle: R

last: Sclafani

first: Sudipta

last: Pathak

first: Raquel

last: Buj

first: Reyna

last: Jones

first: Daniel

last: Ivanov

first: Katherine

middle: M

last: Aird

first: Robert

middle: W

last: Sobol


title: Single-nucleus multiomic profiling of mouse substantia nigra across age

status: Public on Dec 03 2025

city: San Diego

first: Kangli

last: Wang

address: 9500 Gilman Drive

institute: University of California San Diego

summary: We used single-nucleus multiomic sequencing (snRNA-seq + snATAC-seq) to analyze the dynamic transcriptional regulation in mouse substantia nigra cell types across aging.

overall_design: Chromium Single-Cell Multiome ATAC + Gene Expression for mouse substantia nigra in four age stages of 2, 6, 12, and 18 months.

first: Allen

first: Bing

last: Ren


title: Expression data from human mesenchymal stromal cells from osteoarthritis donors treated with the chemokine CCL25

first: Julia

last: Sonnleitner

country: Germany

summary:
Osteoarthritis (OA) is a chronic, multifactorial disease of the joint, which involves synovial inflammation, bone remodeling, and cartilage destruction. It poses a serious burden of global disease, with an incidence rate that has increased by 9.3% between 1990 and 2017. In situ tissue engineering represents a strategy that takes advantage of physiological repair mechanisms and seeks to enhance them. A strong focus has been placed on mesenchymal stromal cells (MSCs) as a source for endogenous regeneration, as they have been shown to contribute to tissue recovery in OA and other pathologies like myocardial infarction and injured liver or pancreas tissue. CCL25, also known as TECK, is a chemokine that has been prevsiously shown to recruit MSCs.
We used a microarry analysis to elucidate the broader effect of the chemokine CCL25 on mesenchymal stromal cells derived from patients with osteoarthritis.

overall_design: Mesenchymal stromal cells treated with 1000 nM CCL25 were analyzed in comparison to mesenchymal stromal cells not treated with CCL25. Each group consists of 3 biological replicates.

first: Tilo

last: Dehne

first: Katja

last: Gulich

first: Axel

last: Pruss

first: Carsten

last: Perka

first: Angelika

last: Gursche

last: Kendoff

first: Michael

last: Sittinger

first: Shabnam

last: Hemmati-Sadeghi


title: Transcriptional profiling of mesothelioma and mesothelial cell lines treated with brefeldin A

status: Public on Dec 07 2025

city: Nagoya

first: Tatsuhiro

last: Sato

state: Aichi

address: 1-1 Kanokoden

department: Division of Cancer Biology

country: Japan

institute: Aichi Cancer Center Research Institute

summary:
This study investigates the transcriptional response of mesothelioma cell lines to low-dose brefeldin A.
Gene expression profiles were compared to untreated controls to identify transcriptional signatures associated with selective cytotoxicity.

overall_design: Gene expression was analyzed in three mesothelioma cell lines (NCI-H2052, Y-MESO-27, NCI-H2452) and mesothelial MeT-5A cell line treated with brefeldin A or vehicle control. Total RNA was extracted after 48 hours of treatment.


title: Loss of FBXO11 establishes a stem cell program in acute myeloid leukemia by dysregulating LONP1 [RNA-seq]

city: Vancouver

first: Aly

last: Karsan

address: 675 West 10th Avenue

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

summary:
Purpose: The goals of this study are to compare the transcriptome profile of human cord blood derived CD34+ cells expressing shRNA targeting FBXO11, LONP1 or non-targeting shRNA, combined with or without over-expression of FLAG-FBXO11 or LONP1 by RNAseq.
Methods: mRNA profiles of CD34+ cord blood cells with combinations of FBXO11 or LONP1 knockdown or over-expression were generated by RNAseq.

overall_design: CD34+ cord blood expressing non-targeting shRNA, shRNA targeting human FBXO11, shRNA targeting human LONP1, empty vector, FLAG-FBXO11, LONP1, or a combination of one of the shRNAs with the over-expression of FLAG-FBXO11 or LONP1.

first: Hayle

last: Kincross


title: The DLX2-LAP2α axis licenses ectomesenchymal specification by unlocking chromatin barriers for craniofacial regeneration [RNA-seq]

first: Zhonghan

last: Li

overall_design: Total RNAs were extracted from mESCs, day-2 Dlx2-OE embryoid bodies (EBs), and day-2 GFP-OE EBs to compare the effects of Dlx2 overexpression on ES cell differentiation toward ectomesenchymal lineages at the early stage (day 2), as well as from day-8  Msx1+ and Msx1-  cells and day-16 Msx1+ and Msx1- cells to evaluate the differences between Msx1 positive and negative populations at two distinct differentiation timepoints (day 8 and day 16).

first: Ziwei

last: Zhang

first: Zhiheng

last: Xu

first: Hong

last: Hu

first: Yao

first: Youmei

last: Jin

first: Yi

last: Zhong

first: Yunqiu

first: Yike

last: Yin

first: Jing

last: Chen

first: Yufeng

last: Duan

last: Hao


title: Transcriptomic analyses of normal human pancreatic acinar cells

city: Gainesville

first: Jason

middle: Orr

last: Brant

state: FL

address: 2197 Mowry Rd

department: Biostatistics

institute: University of Florida

summary: A cohort of 69 normal human pancreatic acinar cell specimens was collected from islet transplantation centers. Total RNA was isolated from uncultured pancreatic acinar cells, and sequencing was performed using Illumina NGS platforms. The resulting transcriptome data for each specimen were analyzed.

overall_design: RNAseq profiling of uncultured normal human pancreatic acinar cells. After adding Matrigel, it was immediately removed from the uncultured Day 0 samples by centrifugation at 4°C before solidification. In contrast, Day 6 samples underwent 6 days of ADM incubation at 37°C before Matrigel removal and subsequent collection.

first: Corey

last: Perkins

first: Jinmai

last: Jiang

middle: O

first: Kalyanee

last: Shirlekar

first: Thomas

last: Schmittgen


title: Investigating and correcting a rare pathogenic mutation in GDF11

status: Public on Dec 02 2025

city: West Hartford

first: Sean

last: Congdon

state: CT

address: 200 Bloomfield Rd

institute: University of Hartford

summary: Single nucleotide variants (SNVs) and small insertions or deletions (indels) underlie most rare monogenic disorders, yet therapeutic strategies to precisely correct these mutations remain limited. Prime Editing enables repair of such pathogenic variants without introducing double-stranded breaks. Here, we applied CRISPR Prime Editing to model and correct a de novo GDF11 nonsense mutation (Tyr336*) identified in a participant from the Undiagnosed Diseases Network (UDN) with growth delay and multisystem abnormalities. Using HEK293T cells, we generated heterozygous GDF11 Tyr336* clones, which exhibited reduced GDF11 protein levels due to post-translational degradation likely mediated by ER- and Golgi-associated quality control pathways.  These cells displayed marked Golgi abnormalities, including an increased number of compact, irregularly shaped Golgi structures, findings consistent with Golgi fragmentation and stress. Transcriptomic profiling of HET cells revealed broad dysregulation of gene networks, including downregulation of metabolic and Golgi-linked biosynthetic genes, and upregulation of cell-adhesion and extracellular matrix genes. These transcriptional shifts paralleled the participant’s developmental, neural, and cardiovascular phenotypes. To correct the mutation, we tested multiple bespoke Prime Editing strategies and identified PE7, in combination with a pegRNA designed by Pridict, as the most effective ribonucleoprotein complex for rescue. Editing efficiency was further enhanced by introducing an additional silent PAM-disrupting mutation, likely preventing both Cas9 re-binding and mismatch repair. Together, these findings support a haploinsufficiency mechanism for the GDF11 Tyr336* allele and establish a generalizable framework for disease modeling and allele-specific correction of pathogenic variants in human cells.

overall_design: This study used CRISPR prime editing in HEK293T cells to generate a heterozygous line carrying the GDF11 Tyr336* allele on two of the three chromosomes, and we compared its transcriptomic profile to that of wild-type HEK293T cells

middle: T

first: John

last: Bennett

first: Rhoddean

last: Opinya

first: Amara

last: Agosto

first: Olivia

last: Dossias

first: Christopher

last: Kokko

first: Aime

last: Levesque

first: Andrew

last: Koob

first: Adam

last: Silver

first: Cindy

last: Thomas-Charles


title: A Stem and Progenitor Cell-Derived Gene Expression Signature is Prognostic for Survival in Myelofibrosis

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

summary: We hypothesized that transcriptomic features among disease-driving hematopoietic stem and progenitor cells (HSPC) could improve the current paradigm for risk stratification in myelofibrosis (MF). Therefore, we performed bulk RNA-seq on blood from 358 MF patients split into training and test cohorts (ClinicalTrials.gov Identifier: NCT02760238). Single-cell (sc) RNA-seq data from Lin-CD34+ MF HSPCs were used to guide the development of a prognostic model trained on the bulk RNA-seq data. A NanoString assay was used to validate our final model in two independent cohorts of MF patients. We identified a 24-gene weighted-sum expression score (termed MPN24) that was prognostic of overall survival (OS). In two independent cohorts of 170 and 99 MF patients, MPN24-High scoring patients had worse 5-year OS compared to MPN24-Low scoring patients (25.5% vs 86.9%, HR = 9.81, P = 4.0e-11 and 23.5% vs 75.9%, HR = 6.40, P = 1.8e-7, respectively). MPN24-High was also associated with clinical, mutation and karyotypic features known to confer adverse risk in MF. The MPN24 score retained independent prognostic significance in multivariable analysis incorporating these covariates as well as existing risk stratification models including DIPSS, DIPSS Plus, MIPSS70, and MIPSS70 Plus v2.0, adding significant prognostic value to these baseline risk stratification models (P = 1.6e-5, 4.0e-6, 1.5e-6, 5.4e-4, respectively). The MPN24 score was particularly useful in improving risk-stratification of DIPSS-Intermediate-1 and Intermediate-2 and MIPSS70 Intermediate and High-risk patients. An HSPC-derived gene expression score is associated with overall survival independent of existing clinical and genomic prognostic variables and improves risk stratification in MF.

overall_design: We profiled the peripheral blood mononuclear cells (PB-MNCs) from 358 myelofibrosis patients (PMc1 cohort) and correlated transcriptomic profiles to overall survival to derive a 24-gene prognostic score (termed, MPN24). We benchmarked the ability of a custom NanoString-based assay to measure the 24-gene score against RNA-seq in 59 PMc1 patient samples. Additionally, we validated MPN24 using the NanoString assay in PB-MNCs from two independent cohorts consisting of 170 (PMc2 cohort) and 99 (MSK cohort) myelofibrosis patients.

first: Jessie

last: Medeiros

first: Andy

middle: G

last: Zeng

first: Michelle

last: Chan-Seng-Yue

first: Hyerin

last: Kim

first: Tristan

last: Woo

first: Suraj

last: Bansal

first: Jessica

last: McLeod

first: Sagar

last: Kothari

first: Andrea

last: Arruda

first: Hubert

last: Tsui

first: Jaime

last: Claudio

first: Dawn

last: Maze

first: Hassan

last: Sibai

first: Mark

middle: D

last: Minden

first: James

last: Kennedy

last: Famulare

first: Raajit

middle: K

last: Rampal

first: Jean

last: Wang

last: Dick

first: Vikas

last: Gupta


title: Multimodal integration of epigenetics, spatial transcriptomics and immune microenvironment in sacral chordoma

status: Public on Dec 01 2025

city: New York City

first: Yee Hoon

last: Foong

address: NYU Grossman School of Medicine

department: Department of Medicine

institute: New York University

type: Methylation profiling by genome tiling array

summary: Multimodal study elucidated the complex epigenetic and immunological landscape in sacral chordomas

overall_design: Bisulfite converted DNAs from 29 sacral chordoma tissues  were analyzed on Illumina EPIC platforms (21 on EPICv1 and 8 on EPICv2)

first: Yee

middle: H

first: George

last: Jour

first: Garima

last: Sinha

first: Jamal

last: Benhamida

first: Nathan

last: Aleynick

first: Yanyun

last: Li

first: Travis

last: Hollmann

first: Mrinal

last: Gounder

first: Rohan

last: Sardana

first: Carla

last: Saoud

first: Max

last: Vaynrub

first: Patrick

last: Boland

first: Rami

last: Vanguri

first: Meera

last: Hameed


title: Stromal Fibroblast Mutant Trp53 Promotes Mammary Tumor Development via Enhanced Secretion of Paracrine Factors

status: Public on Dec 05 2025

city: Houston

first: Bin

last: Liu

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: Mutations in the tumor suppressor gene TP53 have been identified in breast cancer-associated fibroblasts and are associated with poor patient prognosis. However, the functional impact of fibroblastic mutant p53 on breast cancer development remains unclear. To investigate this, we compared female mice harboring HER2-driven mammary tumors with a fibroblast-specific Trp53 mutation (NP) to those with wild-type fibroblastic Trp53 (N). NP mice exhibited significantly shorter median tumor-free survival than N mice. RNA sequencing of NP and N tumors and mammary glands revealed numerous differentially expressed genes (DEGs) between tumors and the corresponding glands in both genotypes. Notably, the NP tumors showed enrichment of several signaling pathways, including PI3K/AKT/mTOR. Additionally, twenty DEGs encoding secreted proteins were identified between NP and N mammary glands. Among these, Saa1 and Saa2 were also upregulated in human breast tumors with mutant TP53 compared to those with wild type TP53. Previous studies have implicated SAA1, SAA2, and THBS4 in promoting tumor progression via the PI3K/AKT pathway. Consistently, supplementing primary HER2 tumor cultures with recombinant SAA1, SAA2, or THBS4 peptides enhanced tumor cell proliferation and migration. Together, these findings uncover a mechanism by which fibroblastic mutant p53 promotes mammary tumorigenesis—through upregulating secretory proteins such as SAA1, SAA2, and THBS4 in the stroma, thereby enhancing PI3K/AKT signaling and tumor progression.

overall_design: RNA-seq profiling of breast tumors and mammary glands with mutant p53 or wild type p53 in fibroblasts from MMTV-Erbb2 mice (The Jax Lab, Strain #:002376), The mammary glands from wild type mice are usd for normal control

first: Yun

last: Zhang


title: Eos maintains Treg homeostasis and plays a critical role in the function of recirculating thymic Tregs

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

summary: Eos, a member of the Ikaros family of transcription factors, is expressed by T regulatory cells (Tregs) and has been postulated to play a role in Treg suppression and maintenance of Treg stability. We demonstrate that expression of Eos was limited to a subpopulation of thymus-derived, activated Tregs and is undetectable in resting or activated T conventional cells (Tconvs). Eos associates with Helios, Foxp3 and Hdac1 and binds directly to the CD25 locus at a site identical to the Foxp3 binding site resulting in enhancement of CD25 expression. Studies in heterozygous female mice demonstrate that Eos is critical for Treg survival and activation. Eos+ Tregs also represent the major population of recirculating thymic Tregs, in which Eos plays a critical role in regulating their migration and suppression of Treg precursors in the thymus by competing for IL-2 and depleting MHC II from thymic dendritic cells (DCs).

overall_design: sc-RNA seq of thymic Tregs

first: Xuan

last: Xie

first: Angela

last: Thornton

first: Shalini

last: Tanwar

first: Patricia

last: Korty

first: Alexandria

middle: C

last: Wells

first: Elisha

last: Segrist

first: Ana

last: Teijeiro

first: Claudia

middle: A

last: Rivera

first: Danping

last: Wei

first: Xi

last: Chen

first: Jinfang

last: Zhu

first: Asya

last: Khleborodova

first: Tovah

middle: E

last: Markowitz

first: Margery

last: Smelkinson

first: Juraj

last: Kubat

first: Tibor

last: Veres

first: Owen

last: Schwartz

first: Francisco

last: Otaizo-Carrasquero

first: Paul

last: Gardina

first: Amirhossein

last: Shamsaddini

first: Craig

last: Martens

first: Kyoungin

last: Cho

first: Cheng-Chao

last: Lin

first: Jaspal

middle: S

last: Khillan

first: Yelena

last: Levin

first: Ying

last: Wu

first: Ethan

last: Shevach


title: A Stem and Progenitor Cell-Derived Gene Expression Signature is Prognostic for Survival in Myelofibrosis [RNA-Seq]

first: Alexander

last: Murison

overall_design:
We profiled the peripheral blood mononuclear cells (PB-MNCs) from 358 myelofibrosis patients (PMc1 cohort) and correlated transcriptomic profiles to overall survival to derive a 24-gene prognostic score (termed, MPN24). We benchmarked the ability of a custom NanoString-based assay to measure the 24-gene score against RNA-seq in 59 PMc1 patient samples. Additionally, we validated MPN24 using the NanoString assay in PB-MNCs from two independent cohorts consisting of 170 (PMc2 cohort) and 99 (MSK cohort) myelofibrosis patients.

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

first: Jessie

last: Medeiros

first: Andy

last: Zeng

first: Michelle

last: Chan-Seng-Yue

first: Hyerin

last: Kim

first: Tristan

last: Woo

first: Suraj

last: Bansal

first: Jessica

middle: L

last: McLeod

first: Sagar

last: Kothari

first: Andrea

last: Arruda

first: Hubert

last: Tsui

first: Jaime

last: Claudio

first: Dawn

last: Maze

first: Hassan

last: Sibai

first: Mark

last: Minden

first: James

last: Kennedy

first: Christopher

last: Famulare

first: Raajit

last: Rampal

first: Jean

last: Wang

first: John

last: Dick

first: Vikas

last: Gupta


title: Dynamics of Tumor Heterogeneity from Primary to Metastatic Dissemination in Prostate Cancer

first: Mathieu

last: Lupien

address: 101 College Street

summary: Identifying drivers of cancer progression to guide treatment selection is hindered by limited abilities to understand tumor heterogeneity’s impact on evolution. Here, we delineated the phenotypic variability across ~300,000 prostate tumor cells collected from multi-loci in primary and matched locoregional metastases. We found inter-patient heterogeneity to be confined to malignant populations. While malignant populations exhibit intra-locus heterogeneity, they maintain inter-loci phenotypic similarity within a patient’s prostate gland. Furthermore, the inter-loci malignant population similarity is paired with a shared clonal architecture. Lastly, we show that malignant populations disseminating to locoregional lymph nodes mirror the clonal architecture and phenotypic heterogeneity observed across primary tumor loci while showcasing cell state transition to inflammatory phenotypes. These findings provide insights into four distinct measures of tumor heterogeneity, revealing diverse evolutionary paths across patients converging to common phenotypic adaptations in early prostate cancer progression.

overall_design:
38 prostate cancer specimens derived from five human patients with ISUP > 3 pathology who underwent radical prostatectomy and pelvic lymph node dissection at surgery as part of the International Cancer Genome Consortium (ICGC) late-onset cohort. Using single-cell multiome (expression and chromatin accessibility from RNA and ATAC, respectively) sequencing assay, we characterized 282,956 nuclei/cells, with a median of 6 primary tumor foci from the prostate gland and 3 locoregional lymph node metastases across all patients.

***************************************************************
These dataset are coming from patients hence we have opted to submit the raw fastq files to EGA.
***************************************************************

first: Kira

last: Furlano

first: Tina

last: Keshavarzian

first: Clarissa

last: Gerhäuser

first: Christoph

last: Plass

first: Thorsten

last: Schlomm


title: The Nuclear Matrix Regulates Gene Induction By Maintaining the Chromatin-Speckle Association and Compartmentalization

city: Daejeon

first: Wonki

last: Cho

address: 291 Daehak-ro Yuseong-gu

country: South Korea

institute: KAIST

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

overall_design: Refer to individual Series


title: Nascent RNA m6A modification are involved in T cell activation gene signature under Hypoxia in CRPC-V16A

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

summary: In this study, we set out to identify m6A modified nascent transcription under Hypoxia in parallel with Normoxia by EU labeling coupled with MeRIP-seq. By comparing Hypoxia and Nomoxia, we identified 5,873 m6A sites specific under Hypoxia.

overall_design: We performed MeRIP-seq in CRPC-V16A cells under Hypoxia and Normoxia conditions.

first: Feifei

last: Zheng

first: Yu-e

last: Guo


title: Therapeutic effects of telomerase-derived peptide GV1001 in experimental autoimmune encephalomyelitis: inhibiting neuroinflammation and promoting remyelination

city: Daegu

first: Jong-Heon

last: Kim

address: 680 Gukchaebosang Street, Jung-gu

department: Brain Science & Engineering Institute

institute: Kyoungpook National University

summary: GV1001, a peptide derived from human telomerase reverse transcriptase, exhibits anti-cancer and anti-inflammatory actions, yet its impact on experimental autoimmune encephalomyelitis (EAE)—an established mouse model of multiple sclerosis—remains unknown. This study assessed the therapeutic potential and mechanism of GV1001 in EAE. Subcutaneous administration of GV1001 reduced clinical scores, inflammatory cytokine transcripts, and spinal cord pathology in EAE mice. Spinal cord RNA-seq showed that GV1001 suppressed immune and neuroinflammatory genes, particularly in microglia. Experiments in cultured mouse and human glia cells identified microglia as the principal cellular target. Mechanistically, GV1001 increased the NF-κB antagonist PRMT1 and boosted microglial insulin-like growth factor-1, promoting oligodendrocyte progenitor cell survival and maturation. Co-culture assays confirmed that GV1001 blunts microglial neurotoxicity and facilitates remyelination during inflammation. Collectively, the data indicate that GV1001 modulates microglial activity to attenuate neuroinflammation and foster spinal cord repair, underscoring its promise as a multitarget therapy for inflammatory demyelinating diseases such as multiple sclerosis.

overall_design: RNA-seq profiling of spinal cords from naïve control, EAE, and EAE treated with GV1001 mice

first: Anup

last: Busal

first: Jiwon

last: Kwon

first: Jun-Yeong

last: Lee

first: Min-Soo

last: Song

first: Won-Ha

first: Long Tai

first: Sangjae

first: Kyoungho

last: Suk


title: Antitumor effect of combining STING agonist (ADU-S100) and Doxorubicin versus Doxorubicin alone or control vehicle in mouse sarcoma cell line (WEHI-164)

status: Public on Nov 28 2025

city: Goyang

first: Wonyoung

last: Choi

state: Gyeonggi

address: 323 Ilsan-ro, Ilsandong-gu

institute: National Cancer Center

summary: Doxorubicin treatment induces the expression of proinflammatory cytokines through the activation of the STING pathway. Our study demonstrates that the combined administration of the STING agonist ADU-S100 significantly enhances the antitumor efficacy of doxorubicin in a syngeneic mouse model of sarcoma using the WEHI-164 cell line.

overall_design: RNA-seq profiling was performed on CD45+ cells magnetically sorted from dissected tumors treated with: 1) ADU-S100 and doxorubicin, 2) doxorubicin alone, and 3) the control.

first: Gi Yeon

first: Sun-Young

last: Kong


title: TREM2 expression level is critical for microglial state, metabolic capacity and efficacy of TREM2 agonism

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Triggering receptor expressed on myeloid cells 2 (TREM2) is a central regulator of microglial activity and sequence variants are major risk factors for late onset Alzheimer’s disease (LOAD). Using a reporter model, we observed a gradual upregulation of TREM2 with increasing plaque proximity. Isolated microglia were sorted based on reporter expression, to determine fluorodeoxyglucose (FDG) uptake and the metabolomic, lipidomic, and transcriptomic signatures. Uptake of FDG correlated with the gradual increase of TREM2 expression.  TREM2 expression improved cellular redox, energetics, and cholesterol homeostasis in the presence or absence of amyloid pathology. Bulk RNA sequencing analysis identified major changes in immunometabolic pathways. Genes associated with oxidative phosphorylation or cholesterol homeostasis were enriched in the TREM2 high expressing clusters. Finally, chronic treatment with a brain penetrant TREM2 agonist identified a window of TREM2 expression where microglia are most accessible for protective responses providing important information for the current efforts to bring TREM2 agonists into the clinic.

overall_design: Inspection of cell type composition, examination of differential expression and assessment of gene co-expression networks in RNA-seq data of healthy and disease mouse microglia with different Trem2 levels.

first: Astrid

last: Feiten

first: Kilian

last: Dahm

first: Kathryn

last: Monroe

first: Christian

last: Haass


title: Metabolic regulation of Th2 cells by L-phenylalanine

status: Public on Nov 27 2025

city: Davos

first: Abhijeet

last: Kulkarni

address: Herman-Burchard-Strasse 9

country: Switzerland

institute: SIAF

summary: RNA-Seq of in vitro differentiated Th2 cells subjected to L-phenylalanine treatment

overall_design: In vitro long differentiated Th2 cells from 5 healthy donors were incubated in RPMI+10%Fetal Calf Serum +100IU recombinant human Interleukin 2 with Vehicle or 1mM additional L-Phenylalanine with or without simultaneous activation with anti-CD2, anti-CD3 and anti-CD28 antibody beads (1:1 beads:cells).

first: Nino

last: Stocker

first: Urszula

last: Radzikowska

first: Ines

last: Jardon Parages

first: Milena

last: Sokolowska


title: CDCA7 facilitates MET1 mediated CG methylation maintenance at pericentromeric and centromeric chromatin [RNA-seq]

city: Los Angeles

first: Shuya

last: Wang

state: California

address: 610 Charles E Young Dr S

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: DNA methylation is a conserved epigenetic modification critical for transposable element (TE) silencing and genome stability. However, how methyltransferases maintain CG methylation within compact heterochromatin remains unclear. In humans, CDCA7 is required for DNA methylation inheritance at juxta-centromeres, and mutations impairing its binding to heterochromatic nucleosomes lead to satellite DNA hypomethylation and ICF syndrome. In Arabidopsis thaliana, we identified two CDCA7 orthologs, CDCA7A and CDCA7B, as key regulators of DNA methylation. Loss of both causes CG hypomethylation specifically at pericentromeric and centromeric regions. Machine learning analysis revealed that nucleosome density, H1 enrichment, the H2A.W variant, and H3K9me2 levels predict methylation loss in cdca7a cdca7b mutants. Notably, H1 depletion restores methylation in these mutants, indicating that CDCA7A and CDCA7B enable MET1 access to H1-containing nucleosomes and are particularly required for methylation maintenance in compact chromatin. Additionally, in h1.1 h1.2 mutants, CG methylation increases modestly at pericentromeric regions but significantly at centromeric sites, revealing an inhibitory role for H1 in centromeric methylation. This hypermethylation is abolished in h1.1 h1.2 cdca7a cdca7b quadruple mutants, demonstrating that CDCA7A and CDCA7B promote MET1 activity at heterochromatic nucleosomes independently of H1. Together, these results establish CDCA7A and CDCA7B as conserved and versatile chromatin remodelers that facilitate MET1 activity within heterochromatin.

overall_design: Employ WGBS and RNA-seq to study the role of CDCA7 in DNA methylation maintenance


title: Single-Cell Integration of Chromatin Accessibility and Transcriptomics Reveals Regulatory Networks in Ovarian Tumor-Infiltrating Adaptive NK Cells

status: Public on Nov 26 2025

city: Huddinge

first: Dhifaf

last: Sarhan

state: Stockholm

address: Alfred Nobels allé 8, floor 8, room 83112

department: Dept. of Laboratory Medicine, Division of Pathology

country: Sweden

institute: Karolinska Institutet

summary: Natural killer (NK) cells are traditionally recognized for their rapid, non-specific responses against virus-infected or malignantly transformed cells, functioning as key effectors of innate immunity. However, a distinct subset known as adaptive NK (aNK) cells has been shown to acquire memory-like properties following viral infections, indicating their capacity for antigen-specific immune recall. Intriguingly, aNK cells have also been identified within the tumor microenvironment, where they can mediate tumor-specific recall responses. Yet, the regulatory mechanisms managing their function in tumor-infiltrating aNK cells remain largely unknown. In this study, we integrated publicly available multiomics datasets from ovarian cancer, including single-cell chromatin accessibility (scATAC-seq) and single-cell RNA sequencing (scRNA-seq), to identify chromatin-accessible regions and construct transcription factors (TF)-gene regulatory networks. To validate and extend these findings, we performed Smart-seq3 on NK cells isolated from ovarian tumors and applied SCENIC analysis to identify TF-driven gene regulation. By integrating results from both analyses, we identified PRDM1 and STAT2 as key TFs, along with their downstream targets CRCP and MTFP1, specifically enriched in tumor-infiltrating aNK cells. The expression levels of CRCP and MTFP1 positively correlated with NK cell infiltration in ovarian cancer tissues, suggesting their potential functions in supporting tumor-specific NK cell memory responses. In addition, external validation using data from the PROMIX clinical trial demonstrated that PRDM1 and STAT2 expression levels are positively associated with both overall survival and aNK cell-associated transcriptional features.

overall_design:
Two high-grade serous ovarian cancer (HGSOC) patient samples were obtained from the IPLA clinical trial and subjected to Smart-seq3 sequencing, combined with ovarian tumor-infiltrated NK cells from 5 patitents from Smart-seq2 sequencing.

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

first: Yizhe

last: Sun

first: Meng

last: Wan

first: Solrun

last: Kolbeinsdottir

first: Kang

first: Shruti

last: Khare

first: Okan

last: Gultekin

first: Sahar

last: Salehi

first: Kaisa

last: Lehti

first: Ramanuj

last: Dasgupta

first: Theodoros

last: Foukakis

first: Martin

last: Enge


title: scMultiome-seq and single-cell spatial HD data for the developing human knee

city: Boston

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Cartilage plays a crucial role in skeletal development and function, and abnormal development contributes to genetic and age-related skeletal disease. Compromises to the integrity of joint-lining articular cartilage in particular lead to debilitating chronic degenerative diseases including osteoarthritis. To better understand how human articular cartilage develops in vivo, we jointly profiled the transcriptome and open chromatin regions in individual nuclei recovered from distal femora at 2 fetal timepoints. We used these multiomic data to predict transcription factor-based regulatory networks that are important for articular chondrocyte differentiation. We developed a human pluripotent stem cell platform for interrogating the function of predicted transcription factors during chondrocyte differentiation and identified new biological roles for CREB5. We expect new regulatory networks we uncovered using multiomic data to be important for promoting cartilage health and treating disease, and our platform to be a useful tool for studying cartilage development in vitro.

overall_design:
Single cell epigenetic and transcriptomic profiling of cells isolated from human fetal femur at E59 and E72
Fresh knee samples were dissected out (along with the soft tissues surrounding them), flash frozen in OCT, and were processed using 10X Genomics visium spatial HD transcriptomics protocol. Each 10X genomics visium run has raw fatq files and input files

first: G

last: Senevirathne

first: Andrew

last: Zhu

first: Divya

last: Venkatasubramanian

first: Terence

last: Capellini


title: T-bet high and low sorted CD4 T cells after acute infection

city: Berlin

first: Max

last: Löhning

address: Chariteplatz 1

institute: DRFZ

summary: The purpose of this study was to understand in detail how T-bet+ CD4 T cells differ depending on their quantitative T-bet levels after acute LCMV infection. For this, the murine T-bet ZsGreen reporter system was used for sorting cells ex vivo without manipulation according to their T-bet brightness into high and low expressors. The bulk RNA Sequencing of these cells showed that T-bet high cells (n=3) have a rather cytotoxic profile, while T-bet low cells (n=3) upregulate multiple Tfh associated markers while still strongly depicting a Th1 phenotype. Overall, only up to 5% of the expressed genes differed between high and low expressors. Furthermore, the bulk ATAC-sequencing also confirmed strong overlap in chromatin accessability of high (n=2) and low (n=2) expressors. Only a couple of the highly differentially expressed genes from the RNA-Seq data also showed differences in chromatin accessability at the TSS. This study provides a further insight into the quantitative differences of T-bet expressing CD4 T cells.

overall_design: Naive Smarta CD4 T cells from T-bet ZsGreen donors (Thy1.1+) were transferred into T-bet ZsGreen recipients (Thy1.2+), which were infected shortly after with LCMV Arm (200pfu). On day 10 p.i. the cells were harvested from the spleen and lymph nodes of the mice. The cells were FACS sorted according to their T-bet ZsGreen brightness into High and Low sorted fractions and bulk RNA- and ATAC-Sequencing was performed. Cells generated in 3 (RNA-seq) or 2 (ATAC-seq) independent experiments were used for the analysis.

first: Valerie

last: Plajer

first: Adrián

last: Madrigal-Avilés

first: Maria

last: Dzamukova

first: Nayar

last: Durán-Hernández

first: Katrin

last: Lehmann

first: Mir-Farzin

last: Mashregi

first: Caroline

last: Peine


title: EBNA1 SUMOylation by PIAS1 Suppresses EBV Lytic Replication and Enhances Episome Maintenance

city: Pittsburgh

first: Febri

last: Sugiokto

state: Pennsylvania

address: 5117 Centre Avenue

institute: University of Pittsburgh

summary: Epstein-Barr virus nuclear antigen 1 (EBNA1) is essential for the replication and stable maintenance of the viral episome in infected cells. Here, we identify the SUMO E3 ligase PIAS1 as a key regulator of EBNA1 through site-specific SUMOylation. Our Chromatin-Immunoprecipitation Sequencing (ChIP-seq) analysis revealed that PIAS1 is enriched at the viral origin of plasmid replication (oriP), where it physically associates with EBNA1 and catalyzes its SUMOylation. Using mutational analysis, we identified three lysine residues on EBNA1 (K17, K75, and K241) as major SUMOylation sites. Disruption of these sites compromises EBNA1’s ability to restrict EBV lytic replication. In addition, both PIAS1 depletion and the disruption of EBNA1 SUMOylation lead to reduced retention of EBNA1-OriP-based EBV mini-replicon, indicating the importance of EBNA1 SUMOylation in viral episome maintenance. Together, these results uncover a conserved post-translational mechanism by which PIAS1-mediated SUMOylation modulates EBNA1 function and EBV episome maintenance and suggests a broader role for SUMOylation in viral latency, lytic replication and persistence.

overall_design: ChIP seq of PIAS1 in Akata (EBV+) Burkitt lymphoma

first: Kun

last: Zhang

first: Yunash

last: Maharjan

first: Renfeng

last: Li


title: Regulation of murine follicle-stimulating hormone β subunit transcription by newly identified enhancers [ChIP-seq; LβT2 cells]

status: Public on Nov 24 2025

first: Michel

last: Zamojski

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: Activin-class ligands of the TGFβ family induce follicle-stimulating hormone (FSH) production by pituitary gonadotrope cells in mice via the actions of the transcription factors SMAD3, SMAD4, and FOXL2, which bind to cis-elements in the FSHβ subunit (Fshb) promoter. An enhancer region for murine Fshb transcription was identified in vitro. The region, however, did not significantly alter basal or activin-stimulated murine Fshb promoter-reporter activity in LβT2 cells. In contrast, three other open chromatin regions enhanced basal and activin A-stimulated Fshb promoter-reporter activity in LβT2 cells, with the two most distal showing the greatest effects. Using ChIP-seq we show that these two regions exhibit enrichment of the enhancer mark H3K27ac, and are bound by SMAD2/3 and FOXL2 in response to activin A in LβT2 cells. These data are part of a SuperSeries that includes ATAC-seq data also showing these regions to be open in response to activin A in LβΤ2 cells, as well as scATAC-seq data of whole mouse pituitaries indicating that there may be as many as four activin-sensitive enhancers upstream of murine Fshb. The data of this series were generated with the help of Next Gen and Bioinformatics Core services at the Salk Institute.

overall_design: LβT2 cells stably expressing FLAG-tagged FOXL2 (FLAG-mFoxL2) were generated by lentivirus transduction of a cassette that permits constitutive GFP expression and tetracycline/doxycycline (DOX)-inducible, IRES-mediated tandem expression of a fluorescent reporter.  LβT2-FLAG-mFoxL2 cells were cultured in plates, and DOX-induction was initiated, followed by treatment with either vehicle or activin A.  Cross-linked complexes suitable for ChIP-seq were produced and enriched for SMAD2/3-, FLAG-FOXL2- and H3K27ac-bound complexes, the DNA of which was then isolated and prepared for sequencing.

first: Alissa

last: Blackler

first: Sven

last: Heinz

first: Christopher

last: Benner

first: German

last: Nudelman

first: Hailey

last: Schultz

first: Stuart

last: Sealfon

first: Daniel

last: Bernard

first: Louise

last: Bilezikjian


title: Differentially expressed microRNAs between WT and AtC3H3 OX, and WT and AtC3H26 OX

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

institute: Pusan National University

type: Non-coding RNA profiling by high throughput sequencing

summary: CCCH-type zinc finger (ZF) proteins comprise a diverse family of RNA- and DNA-binding regulators that play crucial roles in plant growth, development, and responses to stress. While tandem CCCH zinc finger (TZF) proteins have been extensively studied, the molecular functions of non-TZF members remain less understood. Here, we characterized Arabidopsis thaliana AtC3H26, a non-TZF CCCH protein and paralog of AtC3H3, and demonstrated its role as a ribonuclease (RNase) in salt stress tolerance and phosphate (Pi) homeostasis. In vitro assays confirmed that AtC3H26 degrades RNA substrates in a dose-dependent manner. mRNA sequencing of OX lines revealed a significant upregulation of phosphate starvation–responsive genes, including SPX1, PS2/PECP2, and SRG3/GDPD1, whereas small RNA sequencing identified the downregulation of miR399 and miR827, which are involved in the Pi starvation response. AtC3H26 OX plants accumulated higher Pi levels than wild type, suggesting that AtC3H26 modulates Pi accumulation. Collectively, these findings establish AtC3H26 as a novel cytoplasmic RNase that coordinates RNA turnover with stress and nutrient signaling in Arabidopsis.

overall_design: Differential gene expression between WT and AtC3H3 OX, as well as between WT and AtC3H26 OX, was examined at 10 days after germination under SD conditions (8-hour-light and 16-hour-dark cycle) on a microRNA level.

first: Hye-Yeon

last: Seok

first: Yunseong

last: Jang

first: Sun-Young

last: Lee

first: Dahyun

last: Kim


title: Reduced TBX5 dosage causes human atrial disease by undermining developmental gene regulation of atrial cardiomyocyte identity [scATAC-seq]

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary: In a TBX5-linked human cellular model of atrial disease, we examined the gene networks controlled by TBX5 during human atrial differentiation using single-cell RNA and ATAC sequencing.

overall_design: Wildtype, TBX5 heterozygous and homozygous mutant iPSCs were differentiated to atrial cardiomyocytes. At day 20 of differentiation, cells were harvested for single-cell ATAC sequencing. Two replicates per genotype per timepoint were harvested. Wildtype iPSCs were also differentiated to ventricular cardiomyocytes and cells were harvested at day 23 for single-cell ATAC sequencing.

first: Kavitha

last: Rao

first: Irfan

last: Kathiriya


title: The Nuclear Matrix Regulates Gene Induction By Maintaining the Chromatin-Speckle Association and Compartmentalization [RNA-Seq]

first: Wonki

last: Cho

summary: Emerging evidence reveals the critical role of the nuclear RNA-protein meshwork complex, termed nuclear matrix, in stabilizing chromatin architecture. While chromatin associates with transcriptional machinery within nuclear bodies to regulate gene expression through hierarchical architecture formation, how the nuclear matrix mediates chromatin-nuclear body associations and their spatial organization remains unclear. Here, we demonstrate that depletion of nuclear matrix factor SAF-A leads to genome-wide chromatin compaction and enhanced chromatin-speckle associations. Using super-resolution imaging and genomic analyses, we show that these chromatin organizational changes alter the inducibility of speckle-associated genes. Mechanistically, we reveal that nuclear matrix exhibits a layered spatial distribution, forming distinct compartments with RNA polymerase II clusters and chromatin in the perispeckle region. Our findings demonstrate that nuclear matrix maintains chromatin architecture and regulates gene expression through spatial coupling with nuclear bodies, providing new insights into the hierarchical organization of nuclear structure-function relationships.

overall_design: RNA-seq profiling of HCT116 osTIR1(F74G) SAF-A-mAID-Halo cells and their acute depletion by 5-Ph-IAA treatment for 3hr and 12hr.


title: Regulation of murine follicle-stimulating hormone β subunit transcription by newly identified enhancers

first: Michel

last: Zamojski

summary: Activin-class ligands of the TGFβ family stimulate follicle-stimulating hormone (FSH) synthesis in pituitary gonadotrope cells through SMAD3/SMAD4 and FOXL2-mediated transcriptional regulation of Fshb. This SuperSeries integrates chromatin accessibility and transcription factor binding datasets to identify activin-sensitive regulatory regions controlling Fshb expression. It includes single-nucleus ATAC-seq of mouse pituitaries, and bulk ATAC-seq and ChIP-seq of gonadotrope-derived LβT2 cells. Together, these datasets indicate that there may be as many as four activin-sensitive enhancers upstream of murine Fshb.

overall_design: Mice were engineered with a previously identified Fshb enhancer knocked out.  Single-nucleus ATAC-seq was performed on whole pituitaries from wild-type, and enhancer knockout mice, as well as from IgG- and Bimagrumab-, an activin type II receptor antagonist, treated mice.  Bulk ATAC-seq and ChIP-seq for SMAD2/3, FLAG-FOXL2 and H3K27ac was performed on vehicle- and activin A-treated LβΤ2 cells.

first: Yangfan

last: Jin

last: Bilezijkian

first: Frederique

last: Ruf-Zamojski


title: Regulation of murine follicle-stimulating hormone β subunit transcription by newly identified enhancers [scATAC-seq; Mouse Pituitaries]

summary: Activin-class ligands of the TGFβ family induce follicle-stimulating hormone (FSH) production by pituitary gonadotrope cells in mice via the actions of the transcription factors SMAD3, SMAD4, and FOXL2, which bind to cis-elements in the FSHβ subunit (Fshb) promoter. An enhancer region for murine Fshb transcription was identified in vitro. However, deletion of the region using CRISPR-Cas9 did not affect FSH synthesis or secretion in mice. Using single-nucleus ATAC-seq of whole pituitaries, we identified three additional chromatin regions upstream of Fshb open exclusively in murine gonadotropes. We found these regions, as well as the Fshb gene, to be fully or partially closed in gonadotropes of FSH-deficient mice with genetically or pharmacologically inactivated activin type II receptors. The data indicate that there may be as many as four activin-sensitive enhancers upstream of murine Fshb. This data is part of a SuperSeries that includes bulk ATAC-seq and ChIP-seq data of gonadotrope-derived LβT2 cells, that substantiate the above conclusions.

overall_design: Two sgRNAs were designed to target a previously identified enhancer region for murine Fshb transcription. Enhancer-knockout mice were generated using CRISPR-Cas9, after electroporation of the two sgRNAs and the Cas9 protein into zygotes. Pituitary glands were dissected from 8- to 10-week-old wild-type and enhancer-knockout mice, and prepared for scATAC-sequencing.  Pituitary glands were similarly collected and processed from wild-type mice treated with either IgG or Bimagrumab, an activin type II receptor antagonist.

first: Luisina

last: Ongaro

first: Shinsuke

last: Onuma

last: Schultz

first: Gauthier

last: Schang


title: Aldosterone-induced myotube to fibroblast signals

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

summary: Here we report the gene expression data following bulk RNA sequencing used to identify the aldosterone-mediated cellular communication from cultured myotubes to fibroblasts isolated from neonatal hind limbs of wild-type (C57) and dystrophic mice (mdx). We found distinct transcriptional changes induced by aldosterone in myotubes, which in turn resulted in distinct transcriptional changes in the CM-treated fibroblasts.

overall_design: Bulk RNA sequencing was performed on vehicle (DMSO, 0.001% v/v) or aldosterone (1 µM)-treated C57 and mdx myotubes following 48 hrs of treatment, and conditioned media (CM)-treated C57 and mdx fibroblasts. CM was collected from myotubes following 15 hrs of incubation with fresh media after 48 hrs of vehicle or aldosterone treatment. Primary myogenic progenitor cells (which were differentiated to myotubes) and fibroblasts were isolated from hindlimbs of neonatal (<5-day-old) C57 and mdx mice.

first: Swathy

last: Krishna

first: Chetan

last: Gomatam

first: Reva

last: Reddy

first: Jeovanna

last: Lowe

first: Christoph

last: Lepper


title: Synergy between regulatory elements can render cohesin dispensable for distal enhancer function

first: Karissa

middle: Lynn

last: Hansen

address: 555 Mission Bay Blvd S, 312

department: CVRI

institute: UCSF

summary: Enhancers are critical genetic elements controlling transcription from promoters, yet how they convey regulatory information across large genomic distances remains unclear. Here, we engineer pluripotent stem cells in which cohesin loop extrusion can be inducibly disrupted without confounding cell cycle defects. Transcriptional dysregulation is cell type-specific, and not all loci with distal enhancers depend equally on cohesin extrusion. Using comparative genome editing, we demonstrate that enhancer-promoter communication over just 20 kilobases can require cohesin. However, promoter-proximal elements can support long-range, cohesin-independent enhancer action – even across strong CTCF insulators. Finally, transcriptional dynamics and the emergence of embryonic cell types remain largely robust despite disrupted extrusion. Beyond establishing novel strategies to study cohesin in enhancer biology, our work provides mechanistic insight into cell type- and genomic context-specificity.

overall_design:
Stranded mRNA-seq and CUT&Tag for H3K27ac and H3K27me3 in mouse ES cells, ES cells exiting pluripotency, neural progenitors, and neural progenitors differentiating into astrocytes in control (DMSO/untreated) and NIPBL-depleted (dTAG-13/IAA) cells.
Bulk ATAC-seq from control (NIPBL) and NIPBL-depleted (dTAG-13) gastruloids. NIPBL depletion was initiated either 48, 72, or 96 hours after aggregation of mouse embryonic stem cells.
ChIP-seq for CTCF in ES cells with a mutation of the CTCF-binding site in the Car2 promoter.
4C-seq in ES cells (WT SRR2 and homozygous SRR2 deletion) from control (DMSO/untreated) and NIPBL- or RAD21-depleted (dTAG or IAA) cells. Viewpoints include the Sox2 promoter, Sox2 SCR, Car2 promoter, Car2 enhancer 1, and Car2 enhancer 2.
Cells harboring an dTAG-inducible (FKBP) or auxin-inducible degron (AID) on endogenous Nipbl or Rad21 alleles and were treated with either DMSO (control) or dTAG-13/IAA (NIPBL or RAD21 depletion). WT parental cells are E14Tg2a (129 X,Y background).

first: Elphège

middle: P

last: Nora


title: Regulation of murine follicle-stimulating hormone β subunit transcription by newly identified enhancers [ATAC-seq; LβT2 cells]

summary: Activin-class ligands of the TGFβ family induce follicle-stimulating hormone (FSH) production by pituitary gonadotrope cells in mice via the actions of the transcription factors SMAD3, SMAD4, and FOXL2, which bind to cis-elements in the FSHβ subunit (Fshb) promoter. An enhancer region for murine Fshb transcription was identified in vitro. The region, however, did not significantly alter basal or activin-stimulated murine Fshb promoter-reporter activity in LβT2 cells. In contrast, three other open chromatin regions enhanced basal and activin A-stimulated Fshb promoter-reporter activity in LβT2 cells, with the two most distal showing the greatest effects. Using ATAC-seq we show that these two regions were open in response to activin A in LβT2 cells.  This data is part of a SuperSeries that includes ChIP-seq data further showing that these regions exhibited enrichment of the enhancer mark H3K27ac, and were bound by SMAD2/3 and FOXL2 in response to activin A in LβT2 cells. The SuperSeries also includes scATAC-seq data of whole mouse pituitaries indicating that there may be as many as four activin-sensitive enhancers upstream of murine Fshb.

overall_design: LβT2 cells were cultured in 12-well plates, and then treated with either vehicle or activin A, after which cells were collected, trypsinized and prepared for ATAC-sequencing.

first: German

last: Nudelman

first: Hailey

first: Natalia

last: Mendelev

first: Daniel

last: Bernard

first: Stuart

last: Sealfon


title: Evaluation of 5-aminolevulinic acid-mediated radiodynamic therapy after single-dose irradiation in HT-29 xenografted mice

status: Public on Nov 23 2025

city: Kitakyushu

first: Junko

last: Takahashi

state: Fukuoka

address: 2-7 Hibikino, Wakamatsu-ku

department: Graduate School of Information, Production and Systems

institute: Waseda University

summary: We investigated changes in gene expression in HT-29 human colon carcinoma xenografts in nude mice after single-dose X-ray irradiation combined with 5-aminolevulinic acid (ALA)-mediated radiodynamic therapy. Control (non-irradiated, no ALA) and treated tumor samples were analyzed using Aglient Whole Human Genome Microarray 4x44K G4112F.

overall_design: Mice were implanted with HT-29 human colon carcinoma cells and divided into six groups: (1) no treatment (NT); (2) single administration of 5-aminolevulinic acid (5-ALA) without irradiation (ALAT); (3) 12 Gy single-dose X-ray irradiation alone (XT); (4) 100 mg/kg 5-ALA treatment followed by 12 Gy single-dose X-ray irradiation (A100-XT); (5) 200 mg/kg 5-ALA treatment followed by 12 Gy single-dose X-ray irradiation (A200-XT); (6) 10 daily administrations of 100 mg/kg 5-ALA followed by fractionated X-ray irradiation (2 Gy/day, total 20 Gy) (A100-20XT). treatment followed by fractionated irradiation (2Gy/day) (A100-20XT).


title: Harnessing the E3 ligase SPOP for targeted degradation of the NUP98::KDM5A fusion oncoprotein

status: Public on Nov 21 2025

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: NUP98-rearranged (NUP98-r) acute myeloid leukemia (AML) is associated with poor clinical outcomes and represents a major therapeutic challenge due to the lack of strategies for the direct elimination of NUP98-fusion oncoproteins. While targeted degradation of cancer-driving oncoproteins is an attractive strategy, the molecular mechanisms controlling NUP98 fusion oncoprotein stability are not known. Here, we used CRISPR/Cas9 screening to identify the E3 ligase SPOP as a direct regulator of NUP98 oncofusion stability and a novel tumor suppressor in NUP98-r AML. SPOP loss caused a selective increase of NUP98 fusion oncoprotein levels, and promoted leukemia cell proliferation. Leveraging this specificity, we show that induced proximity of SPOP and the NUP98::KDM5A fusion oncoprotein via a bioPROTAC approach induced full clearance of the fusion oncoprotein, and drove terminal differentiation and apoptosis of NUP98-r leukemia cells in vitro and in vivo. Altogether, our study identifies the SPOP E3 ligase as a direct regulator of NUP98 oncofusion stability and presents a blueprint for redirecting the ubiquitin proteasome system to selectively target cancer driving fusion oncoproteins.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
HEK293T cells: NUP98::KDM5A-expressing or wild-type HEK293T cells were subjected to 3' mRNA-sequencing to study effects of the introduction of NUP98::KDM5A.
GFP-NUP98::KDM5A-driven AML cells: Cells were transduced with SPOP-bioPROTAC or empty vector constructs. Doxycycline was added to cells to induce expression of the constructs. On days 3 and 6 post induction, cells were sent for RNA sequencing to assess changes to the transcriptional landscape upon bioPROTAC-mediated NUP98::KDM5A degradation.

first: Ecem

last: Kirkiz

first: Gabriel

last: Kaufmann

first: Simone

last: Bergqvist

first: Pablo

last: Fernandez Pernas

first: Laura

last: Quell

first: Melanie

last: Allram

first: Gabriele

last: Manhart

first: Wencke

last: Walter

first: Torsten

last: Haferlach

first: Florian

last: Grebien


title: Single-cell transciptional profiling of thymic hAPCs in perinatal mice

city: Nashville

first: Bryan

middle: Robert

last: Helm

state: Tennessee

address: 2525 West End Avenue, Suite 1100

department: Center for Quantitative Science

institute: Vanderbilt University Medical Center

summary: This study carried out single-cell transcriptional profiling of FACS purified thymic hematopoietic antigen presenting  cells (hAPCs) to determine changes in cellular composition and gene signatures in neonatal to perinatal (P00, P03, P07, P10, and P14)  mice.

overall_design: CD45+ MHC-II lo to + hematopoietic APCs (HAPCs) were FACS-isolated from C57BL6/J (WT) mice at postnatal ages P00, P03, P07, P10, and P14 mice to identify transcriptional heterogeneity of hAPCs throughout perinatal stages of thymus growth.

first: Lauren

last: Ehrlich

first: Jayashree

last: Srinivasan

first: Aparna

last: Calindi

first: Colin

last: Moore

first: Qi

last: Liu

first: Ken

last: Lau


title: A myeloid trisomy 21-associated gene variant is protective from Alzheimer’s disease

city: Piscataway

first: Ziyuan

last: Ma

state: NJ

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

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

overall_design: Refer to individual Series

first: Mengmeng

last: Jin

first: Peng

last: Jiang


title: Systemic chemotherapy in metastatic TNBC polarizes effector T cell differentiation

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

institute: Incheon National University

summary: In this study, the dynamic changes in the immune landscape in metastatic triple-negative breast cancer (mTNBC) were assessed and compared with healthy donors using single-cell RNA sequencing (scRNA-seq) analysis. This study is the first to provide potential diagnostic and therapeutic targets of East Asian chemotherapy-treated mTNBC with regard to effector T cells.

overall_design: Peripheral blood mononuclear cells (PBMC) of two patients with mTNBC and two healthy donors were obtained from a clinical study. ScRNA-seq libraries were prepared using the Chromium Single Cell 3′ v3.1 platform (10X Genomics) according to the manufacturer’s protocol.

first: Hye-Yeon

last: Ju

first: Hyundong

last: Yoon

first: Seungpil

last: Jung

first: Serk In

last: Park

first: Tae Kon

last: Kim


title: HMGN1 and HMGN2 are recruited to acetylated and histone variant H2A.Z-containing nucleosomes to regulate chromatin state and transcription

city: Chapel Hill

first: Riya

last: Gohil

state: NC

address: 250 Bell Tower Drive, 3314 Genome Sciences Building

institute: University of North Carolina at Chapel Hill

summary: The High Mobility Group Nucleosome-binding (HMGN) proteins are small abundant nuclear proteins that directly bind nucleosomes and constitute a major component of chromatin. HMGN proteins specifically localize to enhancers and actively transcribed genes across the genome, however the roles of HMGN proteins in regulating chromatin structure and transcription remain poorly understood. To investigate the localization and function of HMGN proteins on chromatin, we engineered mouse embryonic stem cells (mESCs) lacking HMGN1 and/or HMGN2 (Hmgn1-/- mESCs, Hmgn2-/- mESCs, and Hmgn1-/-Hmgn2-/- mESCs) and profiled gene expression and localization of architectural proteins. Gene expression was profiled in WT mESCs, Hmgn1-/- mESCs, Hmgn2-/- mESCs, and Hmgn1-/-Hmgn2-/- mESCs via RNA-sequencing.

overall_design: RNA-seq was performed in wildtype mESCs, Hmgn1-/- mESCs, Hmgn2-/- mESCs, and Hmgn1-/-Hmgn2-/- mESCs in triplicate replicates.

first: Jill

middle: M

last: Dowen

first: Zhihan

last: Gao

first: Rebecca

last: Lewis

first: Nathaniel

last: Burkholder

first: Brian

last: Strahl


title: A myeloid trisomy 21-associated gene variant is protective from Alzheimer’s disease (scRNA-Seq)

summary: While challenging, identifying individuals displaying resilience to Alzheimer’s disease (AD) and understanding the underlying mechanism holds great promise for the development of new therapeutic interventions to effectively treat AD. Recent studies indicate that somatic mutations in hematopoietic cells may lead to both the instigation and resilience to neurodegeneration. Down syndrome (DS), or trisomy 21, is the most significant genetic risk factor for AD. Interestingly, some DS individuals show resilience to AD neuropathology and do not exhibit dementia signs. Notably, DS individuals face a heightened risk of myeloid leukemia due to somatic mutations in hematopoietic cells. Microglia dysfunction is a central mechanism in AD etiology. Here we hypothesize that somatic mutations associated with DS myeloid leukemia may impart resilience to microglia against AD. Using CRISPR-Cas9 gene editing, we introduce a DS-linked hotspot CSF2RB A455D mutation into human pluripotent stem cell (hPSC) lines derived from both DS and healthy individuals. Employing hPSC-based in vitro microglia culture and in vivo human microglia chimeric mouse brain models, we show that in response to pathological tau, the CSF2RB A455D mutation suppresses type-1 interferon signaling in both DS and control human microglia, independent of trisomy 21 genetic background. This mutation also reduces neuroinflammation and enhances phagocytic and autophagy functions, ameliorating senescent and dystrophic changes in human microglia. Furthermore, the CSF2RB A455D mutation promotes the development of a microglia subcluster with tissue repair properties. Importantly, human microglia carrying CSF2RB A455D provide protection to neuronal function, such as neurogenesis and synaptic plasticity. When co-transplanted into the same mouse brains, human microglia with CSF2RB A455D mutation phagocytize, outcompete, and gradually replace human microglia carrying the wildtype CSF2RB gene following pathological tau treatment. Our findings suggest the potential use of hPSC-derived CSF2RB A455D microglia to develop effective microglial replacement therapy for AD and other age-related neurodegenerative diseases, even without the need of depleting endogenous senescent microglia prior to cell transplantation.

overall_design: To examine the impact of the CSF2RB A455D mutation on DS microglia, we utilized CRISPR–Cas-9-mediated gene editing to generate DS hiPSC lines carrying the CSF2RB A455D (DS-A455D) mutation. Subsequently, we differentiated DS WT and DS A455D hiPSCs into primitive macrophage progenitor (PMP) cells, denoted as DS-WT and DS-A455D PMP. To investigate potential transcriptomic changes induced by the A455D mutation in DS PMP, we conducted RNA-seq analysis on DS-WT and DS-A455D PMP.


summary: The High Mobility Group Nucleosome-binding (HMGN) proteins are small abundant nuclear proteins that directly bind nucleosomes and constitute a major component of chromatin. HMGN proteins specifically localize to enhancers and actively transcribed genes across the genome, however the roles of HMGN proteins in regulating chromatin structure and transcription remain poorly understood. To investigate the localization and function of HMGN proteins on chromatin, we engineered mouse embryonic stem cells (mESCs) lacking HMGN1 and/or HMGN2 (Hmgn1-/- mESCs, Hmgn2-/- mESCs, and Hmgn1-/-Hmgn2-/- mESCs) and profiled gene expression and localization of architectural proteins. ChIP-sequencing was performed for the RAD21 subunit of cohesin and CTCF to assess the functional implications of loss of HMGN1 and HMGN2 on cohesin and CTCF localization.

overall_design: ChIP-seq was performed in wildtype mESCs (as a control) and Hmgn1-/-Hmgn2-/- mESCs in duplicate for RAD21 and CTCF.


title: CDCA7 facilitates MET1 mediated CG methylation maintenance at pericentromeric and centromeric chromatin [BiSulfite-seq]

first: Shuya

last: Wang

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a conserved epigenetic modification critical for transposable element (TE) silencing and genome stability. However, how methyltransferases maintain CG methylation within compact heterochromatin remains unclear. In humans, CDCA7 is required for DNA methylation inheritance at juxta-centromeres, and mutations impairing its binding to heterochromatic nucleosomes lead to satellite DNA hypomethylation and ICF syndrome. In Arabidopsis thaliana, we identified two CDCA7 orthologs, CDCA7A and CDCA7B, as key regulators of DNA methylation. Loss of both causes CG hypomethylation specifically at pericentromeric and centromeric regions. Machine learning analysis revealed that nucleosome density, H1 enrichment, the H2A.W variant, and H3K9me2 levels predict methylation loss in cdca7a cdca7b mutants. Notably, H1 depletion restores methylation in these mutants, indicating that CDCA7A and CDCA7B enable MET1 access to H1-containing nucleosomes and are particularly required for methylation maintenance in compact chromatin. Additionally, in h1.1 h1.2 mutants, CG methylation increases modestly at pericentromeric regions but significantly at centromeric sites, revealing an inhibitory role for H1 in centromeric methylation. This hypermethylation is abolished in h1.1 h1.2 cdca7a cdca7b quadruple mutants, demonstrating that CDCA7A and CDCA7B promote MET1 activity at heterochromatic nucleosomes independently of H1. Together, these results establish CDCA7A and CDCA7B as conserved and versatile chromatin remodelers that facilitate MET1 activity within heterochromatin.

overall_design: Employ WGBS and RNA-seq to study the role of CDCA7 in DNA methylation maintenance


title: A myeloid trisomy 21-associated gene variant is protective from Alzheimer’s disease (bulk RNA-Seq)


title: Metabolic Adaptations Rewire CD4 T Cells in a Subset-Specific Manner in Human Critical Illness with and without Sepsis

first: Matthew

middle: Tyler

last: Stier

state: TN

address: 1161 21st Avenue South

department: Internal Medicine

summary: Bioenergetic dysfunction is an archetypal finding in critical illness, particularly among patients with severe sepsis. A central feature of sepsis is the shift towards pathologic immunosuppression, especially among CD4 T cells, predisposing to secondary infections and ineffectual organ recovery. However, it remains unknown whether metabolic abnormalities contribute to CD4 T cell dysregulation in critically ill sepsis patients. We collected PBMC from medical and surgical ICU patients at Vanderbilt University Medical Center or community-matched healthy controls. We performed single cell RNA-sequencing with 10x Genomics droplet-based technology on a subset of 9 healthy controls, 19 ICU patients without sepsis, and 19 ICU patients with sepsis to generate a 644,147 cell map of critical illness.

overall_design:
Peripheral blood mononuclear cells (PBMCs) were collected from critically ill patients in the medical and surgical intensive care units (ICUs) at Vanderbilt University Medical Center 48-72 hours after admission to the ICU. This includes crtiically ill patients with sepsis (CI-Sep) and non-septic critically ill patients (CI-NS). Non-acutely ill healthy control participants (NHC) were recruited from the community including bedside surrogates of enrolled ICU patients. Cryothawed PBMC were analyzed by scRNA-seq.

***************************************************************
Raw files for human/patient samples are available in dbGaP (accessions phs004377.v1.p1 and phs004258.v1.p1) for controlled access to the personally identifiable sequence data. All subjects with age >89 have been assigned an age of 90 consistent with current HHS policy regarding de-identification of protected health information.
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first: Paul

last: Lindau

first: Jeffrey

last: Rathmell


title: A myeloid trisomy 21-associated gene variant is protective from Alzheimer’s disease [WGS]

first: Ziyuan

last: Ma

overall_design: To accurately assign cell identities in the CAGG-WT and Cont-A455D microglia co-transplanted scRNA-seq samples, we conducted whole genome sequencing (WGS) on their respective pluripotent stem cell lines. Single nucleotide polymorphisms (SNPs) were identified from the aligned WGS data and used to assign identities to individual cells.

first: Jin

last: Mengmeng

first: Ma

last: Ziyuan

first: Jiang

last: Peng


title: Dual promoter–enhancer activities reflect a unified regulatory logic

status: Public on Nov 20 2025

city: Ithaca

first: Haiyuan

last: Yu

state: New York

address: 237 Tower Road

department: Department of Computational Biology, Weill Institute for Cell and Molecular Biology

institute: Cornell University

summary: Accumulating evidence indicates that both putative promoters and enhancers can exert dual promoter and enhancer functions. However, how these activities are related within individual elements and what determines this dual functionality remain poorly understood. We developed a massively parallel dual reporter assay that enables simultaneous assessment of the intrinsic promoter and enhancer potential exerted by the same sequence. Parallel quantification for thousands of elements reveals that canonical human promoters and enhancers can act as both promoters and enhancers under the same contexts, and that promoter activity may be necessary but not sufficient for enhancer function. Perturbations to element transcription factor binding motifs lead to disruptions in both activities, implicating a shared syntax for the two regulatory functions. Combinations of elements with different minimal promoters reveal reciprocal activity modulation, which, together with a strong correlation between promoter and enhancer functions, imply a bidirectional feedback loop to sustain environments of high transcriptional activity. Finally, we validate this reciprocity and correlation in situ using CRISPR activation at the human β-globin locus. Our approach reveals that the functional convergence between promoters and enhancers arises from a shared regulatory logic and sequence syntax, advancing a unified model for regulatory element biology.

overall_design: Quantitative Unifying Assay for Simultaneously Active Regulatory Regions by sequencing (QUASARR-seq), a massively parallel dual-reporter assay that simultaneously measures the intrinsic promoter and enhancer activities exerted by the same DNA sequence.

first: Mauricio

middle: I

last: Paramo

first: John

last: Lis


title: Chimeric brain models to study human glial-neuronal and macroglial-microglial interactions [Bulk RNA-seq]

summary: Human-mouse chimeric brain models, generated by transplanting human induced pluripotent stem cell (hiPSC)-derived neural cells, are valuable for studying the development and function of human neural cells in vivo. Understanding glial-glial and glial-neuronal interactions is essential for unraveling the complexities of brain function and developing treatments for neurological disorders. To explore these interactions between human neural cells in vivo, we co-engrafted hiPSC-derived neural progenitor cells together with primitive macrophage progenitors into the neonatal mouse brain. This approach creates human-mouse chimeric brains containing human microglia, macroglia (astroglia and oligodendroglia), and neurons. Using super-resolution imaging and 3D reconstruction techniques, we examine the dynamics between human neurons and glia, and observe human microglia pruning synapses of human neurons, and often engulfing neurons themselves, as well as the interactions between human oligodendrocytes and neurons. Single-cell RNA sequencing analysis of the chimeric brain uncovers a close recapitulation of the human glial progenitor cell population, along with a dynamic stage in astroglial development that mirrors the processes found in the human brain. Furthermore, cell-cell communication analysis highlights significant neuronal-glial and macroglial-microglial interactions, especially the interaction between adhesion molecules neurexins and neuroligins.  This innovative co-transplantation model opens up new avenues for exploring the complex pathophysiological mechanisms underlying human neurological diseases. It holds particular promise for studying disorders where glial-neuronal interactions and non-cell-autonomous effects play crucial roles.

overall_design: Cultured primitive neural progenitor cells (pNPCs) were used for bulk RNA-sequencing experiments.

first: Mengmeng

last: Jin

first: Haiwei

last: Zhang

first: Peng

last: Jiang


title: CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire

city: East Lansing

first: Yu

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

summary: Dynamic genome folding is important for V(D)J recombination at the immunoglobulin kappa (Igk) locus, which recombines Jk and Vk gene segments across a 3.2 Mb region in both deletional and inversional orientations. Chromatin loop extrusion and diffusion are considered two key mechanisms underlying Igk folding, but how they coordinate remains unclear. Here we show that CTCF is a key regulator coupling loop extrusion and diffusion during Igk V-J rearrangement, promoting recombination in both orientations across long genomic distances. Mechanistically, the CTCF N-terminus promotes long-range loop extrusion that facilitates distal Vk usage by stabilizing cohesin against WAPL release, and also forms loop barriers enabling chromatin diffusion for inversional Vk joining. In CTCF N-terminal-deficient B cells, defects in inversional Vk joining are not restored by WAPL depletion but are instead largely rescued by a dCas9-blockade targeted to the Vk-Jk intergenic region, mimicking the CTCF barrier. Our findings thus highlight how CTCF coordinates distinct genome-folding mechanisms through its dual roles in cohesin stabilization and extrusion barrier formation to ensure the generation of a diverse Igk repertoire.

overall_design: We performed PRO-Seq in WT and CTCF N-terminal mutant v-Abl transformed pro-B cells to study the molecular basis of CTCF's role in Igk recombination


title: Chimeric brain models to study human glial-neuronal and macroglial-microglial interactions [scRNA-seq]

overall_design: Two hMAN (human microglia-astrocyte-neuron co-transplanted) Rag2−/− IL2rγ−/− hCSF1KI chimeric mice were anesthetized and perfused with cold 1x Dulbecco's Phosphate-Buffered Saline (DPBS). Brains were then dissected and dissociated using the Adult Brain Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s instructions. Human cells were isolated using the Mouse Cell Depletion Kit (Miltenyi Biotec), following the manufacturer’s protocols. The isolated cell suspension from the two mice were subsequently loaded into the Chromium Controller respectively for single-cell RNA sequencing (scRNA-seq) library preparation, utilizing the Chromium Next GEM Single Cell 3’ Kit v3.1 and Dual Index Kit TT Set A, in accordance with the manufacturer’s guidelines. Quality control of the scRNA-seq libraries was performed using an Agilent 2100 Bioanalyzer, and the libraries were sequenced on a NovaSeq 6000 system using S4 flow cells.


title: CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire [ChIP-Seq]

overall_design: We performed CTCF and SMC3 ChIP-Seq in WT and CTCF N-terminal mutant v-Abl transformed pro-B cells to study the molecular basis of CTCF's role in Igk recombination


title: CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire [3C-HTGTS]

overall_design: We performed 3C-HTGTS in v-Abl transformed pro-B cells and the various mutant derivatives to study the molecular basis of CTCF's role in Igk recombination