title: Nociceptor neurons control pollution-mediated neutrophilic asthma; Expression profile of vagal nociceptor neurons in air pollution-exacerbated allergic airway inflammattion

status: Public on Aug 12 2025

city: Kingston

first: Sebastien

last: Talbot

state: ON

address: 18 Stuart st

department: DBMS

country: Canada

institute: Queen's University

summary: Sequencing of TRPV1+ neurons in jugular-nodose complex (JNC) in a mouse model of air pollution-exacerbated allergic inflammation.

overall_design: TRPV1-cre/wt::tdTomato-fl/wt mice were sensitized via intraperitoneal injection with a mix of grade V OVA (200 µg/dose; Sigma-Aldrich A5503) and Imject® Alum (1 mg/dose; ThermoFisher 77161) on days 0 and 7. Subsequently, they underwent intranasal challenges with OVA (50 µg/dose), with or without fine particulate matter (FPM; 20 µg/dose; NIST 2786), from day 14 to 16. Control mice were sensitized but not challenged. The mice were euthanized on day 17, jugular-nodose complex (JNC) were collected, and tdTomato+ cells from naive, OVA-challenged, and OVA-FPM co-exposed mice were sroted by FACS.

first: Theo

last: Crosson

first: Katiane

last: Roversi

first: Jo-Chiao

last: Wang


title: Spatial 3D genome organization controls the activity of bivalent chromatin during human neurogenesis

status: Public on Aug 06 2025

city: San Francisco

first: Mitchel

last: Cole

state: CA

address: 35 Medical Center Way

department: Neurological Surgery

country: USA

institute: UCSF

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Subnuclear compartments including the nuclear lamina and speckles organize the genome in three-dimensional (3D) space and regulate gene expression. By studying the neurogenic cell lineage isolated directly from the human brain, we show that lamina association plays a dominant role in maintaining the lowly expressed, poised state of key developmental genes bivalent for H3K27me3 and H3K4me3. During neurogenesis, large regions of the genome relocate from the lamina to speckles, corresponding to enhanced resolution of bivalent chromatin to monovalent H3K4me3 and a ~7-fold increase in transcription. Using cell culture models of human neurogenesis, we confirm the bivalent state of lamina-associated genes and provide further evidence that lamina association contributes strongly to the low expression of bivalent genes independent of H3K27me3.  These data support a model in which spatial location of genomic regions in relation to subnuclear structures plays a dominant role in regulating the activity of chromatin state and lineage-specific gene expression.

overall_design:
LaminB1 GO-CaRT followed by sequential ChIP (LaminB1 GO-CaRT.ChIP-reChIP) and H3K27me3/H3K4me3 CUT&RUN of iPSC-derived NPCs; LaminB1 CUT&Tag, H3K27me3/H3K4me3 CUT&Tag of iPSC-derived NPCs and iPSC-derived neurons (iN); LaminB1 GO-CaRT and H3K27me3/H3K4me3 CUT&RUN of ESC-derived NPCs treated with DMSO or EZH2 inhibitor, EPZ-6438; H3K27me3 CUT&RUN and LaminB1 GO-CaRT of HEK293T cells with or without Fab blocking

**Raw data for human tissue deposited in dbGAP**

first: Chujing

last: Zhang


title: Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [ChIP-seq]

status: Public on Aug 04 2025

city: Nice

first: Pilar

middle: M

last: Dominguez

state: Provence-Alpes-Côte d'Azur

address: 151 Route de Saint-Antoine

country: France

institute: Centre Méditerranéen de Médecine Moléculaire: C3M

summary: Diffuse large B-cell lymphoma (DLBCL) refers to an aggressive lymphoma that arises from germinal center (GC) B-cells, which differentiate into plasma cells (PC) to produce high affinity antibodies. 40% of DLBCL patients relapse or are refractory to the conventional immunochemotherapy treatment, usually with fatal consequences. DLBCL is characterized by profound alterations in the epigenome, which is correlated with poor survival. The abnormal epigenetic landscape of DLBCL tumors is associated with a blockade in GC exit and differentiation programs, which are regulated by the transcription factor BCL6. This aberrant repression of BCL6-target genes is mediated by 1) increased DNA methylation and 2) loss of acetylation of the lysine 27 of histone 3 (H3K27ac)-through recruitment of histone deacetylase 3 (HDAC3). Thus, we investigated the efficacy against DLBCL of the hypomethylating agent (HMA) 5-Azacitidine (5-Aza) and a specific HDAC3 inhibitor (HDAC3i). We found that treatment with 5-Aza plus HDAC3i had a potent synergistic anti-tumor activity in vitro and in vivo, which was superior to the effect of each single drug or 5-Aza combined with non-specific HDACi and, importantly, was not associated with toxicity in normal cells. We also demonstrated that the combined 5-Aza and HDAC3i treatment induced the epigenetic remodeling of DLBCL cells, which resulted in a more potent re-expression of PC differentiation genes, including XBP1 and ATF4, compared to each drug used as single agents. Our results highlight the importance of specifically targeting multiple layers of the epigenome to maximize the efficacy of epigenetic-based therapies.

overall_design: MD901 lymphoma cells were treated with  5-Azacitidine (or vehicle) daily for 5 days, with a HDAC3 inhibitor (or vehicle) added at day 2 and 4. Cells were analyzed at day 5 (3 replicates per group).

first: Izabela

last: Todorovski

first: Emilio Manuel

last: Serrano-Lopez

first: Matt

middle: R

last: Teater

first: Killian

last: Guiraud

first: Francisco

last: Huertas-Lopez


title: A novel oncolytic neutrophil phenotype is induced by IL-10R inhibition

status: Public on Aug 29 2025

city: New York

first: Yacine

last: Marouf

state: NY

address: 413 E 69th St

department: MCC

institute: Weill Cornell Medecine

summary: While the impact of neutrophils on antitumor T cells has been an active area of study, fewer studies have focused on the potential of neutrophils to directly impact tumor cells. Here we asked whether neutrophils have the capacity to directly kill tumor cells independently of T cells. We find that anti-CD40-based therapy, when combined with interleukin 10 (IL-10) receptor blockade, initiates a Batf3-dependent pathway in which IL-12 and interferon gamma (IFNγ) secretion results in oncolytic neutrophil activity. Using a combination of microscopy, single-cell, and functional assays, we observe that killing of tumor cells by neutrophils is dependent on physical contact and degranulation. This degranulation-mediated killing is associated with an atypical dynamic invasive neutrophil phenotype. In line with our preclinical findings, our phase 1 trial of anti-CD40 shows that circulating IL-12, IFNγ, and IL-10 increase in response to anti-CD40, while our phase 1b/2 PRINCE study shows that lower circulating IL-10 is associated with favorable overall survival specifically among anti-CD40-treated patients. Finally, we find that neutrophil expansion with granulocyte colony stimulating factor (G-CSF) is associated with improved overall survival specifically in patients treated with anti-CD40, suggesting that this pathway may be amenable to therapeutic intervention in patients with advanced cancer.

overall_design: C57BL/6 wild-type mice were intradermally inoculated with B16F10 murine melanoma cells on their flanks, and eight days later, they received Isotype control, anti-IL-10R alone, anti-CD40/Monophosphoryl Lipid A (CM), or a combination of anti-CD40/MPL/anti-IL-10R (CMI). Twelve hours post-treatment, the B16F10 tumors were harvested and processed into single-cell suspensions. Single-cell RNA sequencing (scRNA-Seq) was subsequently performed on these FACS-sorted cell suspensions.

first: Danny Nejad

last: Khalil

first: Ricardo

last: Gomez

first: Amit

last: Regev

first: Fadi

last: Samaan

first: Sadna

last: Budhu

first: Daniel

last: Hirschhorn

first: Isabell

last: Schulze

first: Jessica A.

last: Lavery

first: Nicholas

last: Ceglia

first: Samuel

last: Freeman

first: Vivien I.

last: Maltez

first: Jaynia

last: Garcia

first: Nathan

last: Suek

first: Chien-Huan (Gil)

last: Weng

first: Christopher R.

last: Cabanski

first: Sébastien

last: Monette

first: Yevgeniy

last: Romin

first: Yanyun

last: Li

first: Ronan

last: Chaligne

first: Michael

last: Yellin

first: Tibor

last: Keler

first: Deena M.

last: Maurer

first: Anne-Laure

last: Flamar

first: Lucia

last: Morgado-Palacin

first: Levi

last: Mangarin

first: James

last: Harding

first: Wungki

last: Park

first: Jaclyn P.

last: Lyman

first: Stephen

last: Maddock

first: Mark H.

last: O’Hara

first: Ghassan K.

last: Abou-Alfa

first: Robert H.

last: Vonderheide

first: Eileen M.

last: O’Reilly

first: Ronald N.

last: Germain

first: Jedd D.

last: Wolchok

first: Taha

last: Merghoub


title: Post-transcriptional control of homeostatic B- cell signalling by HuR is required for innate B cell maintenance and function.

status: Public on Aug 28 2025

city: Toulouse

first: Manuel

middle: D

last: Diaz-Munoz

address: CHU Purpan, BP3028

institute: INSERM

summary: Innate B-1 cells constitute a self-maintained layer of defence for early detection of bacteria, clearance of apoptotic cell debris and removal of autoantigens driving autoimmunity. B-1 cells are originated from foetal tissues but, as opposed to B-2 cells, the molecular mechanisms behind their development and homeostatic maintenance remain largely unknown. Here we demonstrate that post-transcriptional regulation by the RNA binding protein HuR is essential for the homeostatic self-replenishment of innate B-1 cells, the expansion of B-1 cell clones targeting self-antigens and the production of natural autoantibodies. HuR KO B-1 cells fail to express the high levels of surface BCR, TACI and BAFFR required for tonic signalling and cell survival. Mechanistically, HuR binds to the 3’UTRs of mRNAs encoding these surface receptors and of pro-survival molecules, like BCL-2 and MCL-1, promoting their translation into protein. In summary, we reveal the need of post-transcriptional regulation in BCR expression, tonic signalling and homeostatic maintenance of functional B-1 cells.

overall_design: Individual cross-linking immunoprecipitation (iCLIP) and sequencing for HuR in B cells isolated from the peritoneal cavity of C57BL/6 mice.

first: Dunja

last: Capitan-Sobrino

first: Mailys

last: Mouysset

first: Orlane

last: Maloudi

first: Yann

last: Aubert

first: Ines

middle: C

last: Osma-Garcia

first: Maia

last: Nestor-Martin

first: Trang-My

last: Nguyen

first: Greta

last: Dunga


title: Disturbed LTB4 metabolism in ILC2 Aggravates Ulcerative Colitis via intercellular ATP accumulation

city: Shan Dong

first: Weijia

last: Li

address: Shandong Province, Jinan City, Lixia District, Shandong University, Baotu Spring Campus

country: China

institute: Shandong University

summary: LTB4 biosynthesis is critically required for cytokine secretion by the group 2 innate lymphoid cell (ILC2), though its underlying regulatory mechanisms remain incompletely characterized. To investigate how LTB4 governs ILC2 functionality, we performed RNA sequencing on sorted murine colonic ILC2s treated with or without SC-57461A—an inhibitor targeting LTA4H, the key enzyme in LTB4 anabolism. This dataset delineates transcriptomic profiles of ILC2 with pharmacologically attenuated versus intact LTB4 synthesis. Here, we identify significant alterations in mitochondria-associated genes (including Fdps, Hmgcs1, and Acat3) upon suppression of LTB4 anabolism in ILC2. These genes encode proteins essential for mitochondrial function and are indispensable for ILC2 energy metabolism. These findings collectively demonstrate that LTB4 synthesis orchestrates mitochondrial functionality in ILC2, thereby modulating their bioenergetic capacity.RNA sequencing was performed for the SC-57461A- or vehicle-treated ILC2 sorted from the large intestine of C57BL/6 mice (n = 4 per group).

overall_design: Sorted large intestinal ILC2s from C57BL/6 mice were cultured in complete IMDM media containing IL-2 (10 ng/mL), IL-7 (10 ng/mL), IL-25 (10 ng/mL), and IL-33 (10 ng/mL) for 5 days, followed by treatment with SC-57461A for 16 hours. The SC-57461A- or vehicle-treated ILC2s were harvested by centrifugation and lysed for RNA extraction.

first: Xiuli

last: Zuo

first: Shiyang

first: Yanqing


title: Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in synovial sarcoma

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [MD901_RNAseq_Day5]

first: Pilar

last: Dominguez

first: Izabela

last: Todorovski

first: Emilio Manuel

last: Serrano-Lopez

first: Matt

last: Teater

first: Killian

last: Guiraud

first: Francisco

last: Huertas-Lopez


title: Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [RRBS]

type: Methylation profiling by high throughput sequencing


title: Response of B cells specific for polyomavirus-derived oncoprotein is predictive of Merkel cell carcinoma tumor control

status: Public on Aug 01 2025

city: Seattle

first: Haroldo

middle: Jose

last: Rodriguez

state: WA

address: 850 Republican St

department: Medicine

institute: University of Washington

summary: Merkel cell carcinomas (MCC) typically arise from clonal integration of the Merkel cell polyomavirus. Immunogenic viral oncoproteins then lead to tumorigenesis. Oncoprotein-specific T cells are essential for anti-MCC immunity, but it is unclear whether B cells promote tumor control. Here, we analyzed the frequency and phenotype of viral oncoprotein–specific and total B cells in blood samples from 47 patients with MCC and tumor samples from another 19 patients with MCC. The phenotype of blood B cells did not correlate with MCC patient outcomes. In contrast, all 11 patients with robust oncoprotein-specific antibody-secreting and/or germinal center B cells in tumors experienced long-term MCC control. In vitro, B cells engineered to be specific for viral oncoproteins increased the sensitivity of oncoprotein-specific CD4+ T cells by over 50-fold. Together, our findings suggest that cancer-specific B cells promote antitumor immunity via increased responses by T cells and that cancer-specific augmentation of B cells could be therapeutically relevant.

overall_design:
Count matrices and B cell receptor sequences from single cell RNA sequencing data are included for immune and tumor cells found in Merkel cell carcinoma patient tumors

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

middle: J

first: Justin

last: Taylor

first: Paul

last: Nghiem


title: miRNA/mRNA analysis of Chlamydial trachomatis-infected endometrial biopsies indicate increased TGF-β pathways drive epithelial-mesenchymal transition and regulatory T cell differentiation

status: Public on Jul 30 2025

city: CHAPEL HILL

first: Xuejun

last: Sun

state: NC

address: Booker Creek Apts, 2525 Booker Creek Rd Apt 15F

institute: University of North Carolina Chapel Hill

type: Non-coding RNA profiling by high throughput sequencing

summary: Chlamydia trachomatis genital tract infection is linked to severe reproductive complications in women, including ectopic pregnancy, infertility, and adverse pregnancy outcomes. Mouse models of infection suggest that chlamydia-induced dysregulation of microRNAs (miRNAs) can drive harmful cytokine responses, pathogenic epithelial-mesenchymal transition (EMT), and fibrosis. To investigate these mechanisms in humans, we profiled miRNA and mRNA expression in endometrial biopsies from women with endometrial infection (Endo+) and compared them to profiles from women with cervix-only infection (Endo-) or no infection. Ingenuity Pathway Analysis (IPA) revealed that Endo+ tissues had upregulated genes associated with innate and adaptive immune response pathways, as well as EMT regulation, while downregulated genes were linked to cell cycle control. An integrative miRNA-mRNA analysis, which combined a review of published miRNA regulation in human infections and immune responses with IPA’s miRNA target filter, identified differentially expressed miRNAs that modulate these pathways in the endometrium of Endo+ women. Functional annotation of these miRNAs showed a predominance of downregulated miRNAs that typically suppress EMT and regulatory T cell (Treg) differentiation, along with miRNAs that usually enhance Th17 responses. Comparisons with previously identified mRNA pathways in blood samples from women with endometrial Chlamydia infection indicated that alterations in TGF-β signaling and EMT were specific to the endometrium. Overall, the miRNA-mRNA interactions inferred from Endo+ tissue suggest increased activity in TGF-β pathways that promote enhanced EMT and Treg differentiation, while reducing Th17 activation. These changes highlight a dual potential for promoting tissue scarring while dampening inflammatory responses that could otherwise limit infection.

overall_design: Endometrial biopsy samples were obtained from cisgender female participants enrolled in two independent cohorts with high exposure to Ct infection. miRNAs were isolated using HTG EdgeSeq reagents and libraries synthesized in the HTSF at the University of North Carolina. Barcodes samples were pooled, and sequencing was performed on an Illumina NextSeq 500 platform (75 cycles, High Output v2 kit). Data were processed into FASTQ files and analyzed using the EdgeSeq parser software (HTG Molecular Diagnostics, Inc.).

first: Toni

last: Darville

first: Yu

last: Zhang

first: Catherine

last: O’Connell

first: Neha

last: Mokashi

first: Weiming

last: Tang

first: Aakash

last: Bhardwaj

first: Bryce

last: Duncan

first: Charles

middle: W

last: Andrews Jr

first: Harold

last: Weisenfeld

first: Xiaojing

last: Zheng


title: Projecting development of TB-IRIS using RNA velocity of whole blood

status: Public on Aug 26 2025

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

summary: TB-associated immune reconstitution inflammatory syndrome (TB-IRIS) is characterised by severe inflammation and immunopathology directed to TB pathogen shortly after commencing antiretroviral therapy (ART) in HIV-TB coinfected patients. This study aims to investigate if RNA Velocity strategy can be used to predict development of TB-IRIS

overall_design: Whole blood was collected from 95 patients with HIV-associated TB at 2 weeks following antiretroviral initiation. Among the 95 patients, 36 developed TB-IRIS by week 2, with another 8 that would eventually develop TB-IRIS. All patients were from the placebo arm of the PredART clinical trial

first: Graeme

last: Meintjes

first: Claire

last: Dunican


title: Bulk RNA-seq of RSC96 Schwann cells after magnetic nanoparticle uptake and magnetic force stimulation

status: Public on Aug 24 2025

city: Jilin

first: wang

last: yang

address: Xin-Min Street NO. 1

institute: Orthopaedic Center, The First Hospital of Jilin University

summary: To explore the effect of magnetic mechanical forces mediated by magnetic nanoparticles on the repair phenotype of Schwann cells in a gradient magnetic field environment, we co-cultured magnetic nanoparticles with RSC96 cells.

overall_design: The magnetic nanoparticles were taken up by the cells, magnetizing the RSC96 cells, and the magnetized cells were exposed to a gradient magnetic field environment and subjected to magnetic force stimulation. Normal cultured control group cells and experimental group cells that received magnetic force stimulation were collected for mRNA transcriptome sequencing to observe the effect of magnetic nanoparticle-mediated magnetic force stimulation on the gene expression profile of Schwann cells.


title: Post-transcriptional control of homeostatic B- cell signalling by HuR is required for innate B cell maintenance and function. [RNA-Seq]

first: Manuel

last: Diaz-Munoz

first: Dunja

last: Capitan-Sobrino

first: Mailys

last: Mouysset

first: Orlane

last: Maloudi

first: Yann

last: Aubert

first: Ines

last: Osma-Garcia

first: Maia

last: Nestor-Martin

first: Trang-My

last: Nguyen

first: Greta

last: Dunga


title: Engineered thoracic spinal cord organoids for transplantation after spinal cord injury

status: Public on Aug 21 2025

city: Shanghai

first: Yanjing

last: Zhu

address: No.727 Zhongshan Road

institute: Tongji University

summary: Human iPSC-derived thoracic spinal cord organoids were transplanted into spinal cord injury mice, and spinal cord tissue was collected after 7 weeks. The transplantation resulted in functional recovery and neural circuit remodeling in the injured mice.

overall_design: Human iPSC-derived thoracic spinal cord organoids (21 days) were transplanted into spinal cord injury mice, and spinal cord tissue for spatial transcriptomics (ST-Seq) was collected after 7 weeks. During the induction of spinal cord organoids from iPSCs, RNA was extracted from 3 or 4 biological replicates at 2 weeks, 3 weeks, and 8 weeks for RNA sequencing. Untreated iPSCs were also collected and subjected to RNA-seq.

first: Ruiqi

last: Huang

first: Liqun

last: Yu

first: Liming

last: Cheng

first: Rongrong


title: Real-time quantitative PCR analysis of extracellular vesicle miRNA from human U2OS cells culture medium [AODRA1]

city: Portland

first: Xiao

last: Shi

state: Oregon

address: 3181 SW Sam Jackson PK Rd

department: dept. of psychiatry

institute: Oregon Health and Science University

summary: Human U2OS cells were stimulated with selective agonist CCPA of adenosine receptor A1(ADORA1) for 24 hours. Extracellular vesicles were isolated from U2OS cell culture media. Total RNAs were purified from extracellular vesicle samples. We used TaqMan Low Density Arrays to quantitate miRNA expression in extracellular vesicles secreted by U2OS cells after GPCR activation.

overall_design: qPCR miRNA expression profiling.  Each GPCR stimulation experiment included its own media control, vehicle control, and treated samples.

first: Aaron

last: Janowsky


title: Real-time quantitative PCR analysis of extracellular vesicle miRNA from human U2OS cells culture medium [ACKR3]

summary: Human U2OS cells were stimulated with selective agonist SDF-1 of atypical chemokine receptor 3 (ACKR3) for 24 hours. Extracellular vesicles were isolated from U2OS cell culture media. Total RNAs were purified from extracellular vesicle samples. We used TaqMan Low Density Arrays to quantitate miRNA expression in extracellular vesicles secreted by U2OS cells after GPCR activation.


title: Single cell RNA sequencing to study the in vivo behaviour of allogeneic HSC-derived MCAR-engineered NKT cells

status: Public on Jul 29 2025

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East

department: Microbiology Immunology & Molecular Genetics

institute: University of California, Los Angeles

summary: Ovarian cancer (OC) poses a significant challenge due to frequent recurrence linked to tumor heterogeneity and an immunosuppressive tumor microenvironment (TME). Here, we generated allogeneic MSLN-targeting CAR (MCAR)-engineered invariant natural killer T (MCAR-NKT) cells, demonstrating high-yield and high-purity production, potent antitumor efficacy, multiple tumor targeting mechanism, and significant in vivo expansion and persistence. Two therapeutic cell products (i.e., CAR-T and CAR-NKT cells) were analyzed at five time points: day 0 (pre-infusion), and days 14, 28, 42, and 56 post-infusion. Day 0 samples were collected prior to cell administration, whereas post-infusion samples were isolated from tumor sites, peripheral blood, spleen, and liver. These findings underscore the feasibility and therapeutic potential of allogeneic MCAR-NKT cell products for OC, laying a foundation for further translation and clinical development.

overall_design: Gene expression profiling of therapeutic cells in an in vivo study using an OVCAR8-FG human OC xenograft NSG mouse model

first: Yan-Ruide

last: Li

first: Zhe

first: Miao

first: Yuning

last: Chen

first: Yichen


title: RNA-seq of retinal microglia and non-microglial retina cells in  WT (Bmal1f/f) and microglial Bmal1-KO (Bmal1-mg/-mg) mice

status: Public on Jul 28 2025

city: Saint Louis

first: Charles

middle: W.

last: Pfeifer

state: Missouri

address: 660 S. Euclid Ave., Campus Box 8096

department: Ophthalmology and Visual Sciences

institute: Washington University School of Medicine in St. Louis

summary: We discovered that Bmal1 knockdown in retinal microglia alters their diurnal clock gene expression, inflammatory gene expression, and morphology. Furthermore, we found that this disruption of diurnal physiology in microglia results in reduced scotopic visual function, retinal neurodegeneration, and abnormal wheel running behavior in mice, suggesting that maintenance of the microglial clock contributes to retinal homeostasis. Subsequently, we investigated transcriptional alterations in retinal microglia and non-microglial cells in the retina to uncover gene expression patterns that may explain these clock-dependent phenotypes and potentially identify homeostatic neuro-glial signaling mechanisms dependent on microglial clock biology.

overall_design: We used tissue dissociation and fluorescent activated cell sorting methods to simulatenously isolate viable microglia (CD11b+, DAPI-) and non-microglia retina (CD11b-, DAPI-) cells from Bmal1f/f and Bmal1-mg/-mg mice and performed RNA-Sequencing on purified mRNA samples (n=4-5/condition).

first: Rajendra

middle: S

last: Apte


title: scRNA-seq Analysis of Dmp1cre-DTAki/wt and wt skin

status: Public on Aug 15 2025

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Utilizing the 10X Genomics Cell Ranger (Pipeline Version 3.1.0) platform, this study investigates the impact of osteocyte ablation on skin aging. Skin and bone share significant structural and molecular homology, including compositional architecture, cellular origins, and signaling pathways. Both tissues exhibit parallel degenerative changes during natural aging and under pathological conditions, characterized by collagen depletion leading to osteoporosis and skin atrophy. Through scRNA-seq analysis of skin following osteocyte knockout, our research provides novel insights into the regulatory role of osteocytes in skin aging.

overall_design: Dorsal skin samples were harvested from 8-week-old wild-type (WT) and osteocyte-ablated mice (Dmp1cre-DTAki/wt), followed by subcutaneous fat removal and single-cell dissociation. Single-cell RNA sequencing (scRNA-seq) was subsequently performed for comprehensive transcriptomic profiling.


title: The ALT-LINC complex mediates cellular responses to matrix mechanics

status: Public on Aug 08 2025

city: St. Louis

first: Helen

last: McNeill

address: 660 S. Euclid Avenue

department: Developmental Biology

summary: Nuclear Envelope Membrane Protein 1 (NEMP1) is crucial for metazoan fertility; loss of Nemp1 causes primordial oocyte death, residing in the mechanically challenging ovarian cortex. Here, we show that softening the ovary rescues oocyte loss and restores fertility in NEMP1 knockout mice. In cell culture, NEMP1 depletion on stiff substrates leads to death, while cells remain viable on soft substrates. We further show that NEMP1 regulates YAP nuclear translocation, essential for mechanotransduction. Mechanistically, Nemp1-depleted cells on stiff substrates or subjected to stretching exhibit reduced nuclear YAP localization, and expressing nuclear YAP5SA restores cell viability. Loss of NEMP1 disrupts actin organization, inhibiting YAP nuclear translocation. Inducing actin polymerization rescues nuclear YAP, indicating an F-actin-dependent mechanism for NEMP1-mediated mechanotransduction. NEMP1 forms a novel complex with NESPRIN2's KASH domain, strengthening the actin cytoskeleton to withstand mechanical forces, independently of SUN proteins. Thus, NEMP1-Nesprin complex, named hereafter ALT-LINC, creates a mechanosensitive pathway parallel to the LINC complex and is crucial for YAP mechanotransduction, enabling cellular response to mechanical stress in vitro and in vivo.

overall_design: RNA-seq profiling of the human epithetial cell line (hTERT RPE-1 - CRL-4000) cultured on soft (10 kPA) and stiff (120 kPA) substrates. This dataset compares control samples and siNemp1-treated samples under both stiffness conditions.

first: Abira

last: Ganguly

first: Nattapon

last: Thanintorn


title: Fat promotes growth and invasion in a 3D microfluidic tumor model of triple-negative breast cancer

status: Public on Jul 22 2025

city: Princeton

first: Celeste

last: Nelson

address: 25 William St

institute: Princeton University

summary: Diet influences the levels of small molecules that circulate in plasma and interstitial fluid, altering the biochemical composition of the tumor microenvironment (TME). These circulating nutrients have been associated with how tumors grow and respond to treatment, but it remains difficult to parse their direct effects on cancer cells. Here, we combine a three-dimensional (3D) microfluidic tumor model with physiologically relevant culture media to investigate how concentrations of circulating nutrients influence tumor growth, cancer cell invasion, and overall tumor metabolism. Human triple-negative breast cancer cells cultured in 2D under media conditions mimicking five different dietary states show no observable differences in proliferation or morphology. Nonetheless, those exposed to high-fat conditions exhibit increased metabolic activity and upregulate genes associated with motility and extracellular matrix remodeling. In the 3D microfluidic model, high-fat conditions accelerate tumor growth and invasion and induce the formation of hollow cavities. Surprisingly, the presence of these cavities does not correlate with an increase in apoptosis or ferroptosis. Instead, RNA-sequencing analysis revealed that high-fat conditions induce the expression of MMP1, consistent with cavitation via cell invasion. Mimicking the flow of circulating nutrients within the TME can thus be used to identify novel connections between metabolic states and tumor phenotype.

overall_design: Bulk RNA-seq of MDA-MB-231 cells cultured in Human plasma-like medium (HPLM) with additives that mimic five different dietary conditions: baseline (A), high-ketone (B), high-insulin (C), high-fat (F) and high-glucose ( G). Additionally, we have also done bulk RNA-seq of MDA-MB-231 cells cultured in DMEM (D).

first: Maryam

last: Kohram

first: Carolina

last: Trenado-Yuste

first: Molly

last: Brennan-Smith

first: Evelyn

last: Navarro Salazar

first: Pengfei

last: Zhang

first: Jasmine

middle: E

last: Hao

first: Xincheng

last: Xu

first: Bharvi

last: Chavre

first: William

last: Oh

first: Sherry

middle: X

first: Susan

last: Leggett

first: Rolf-Peter

last: Ryseck

first: Joshua

last: Rabinowitz


title: Epigenetic de-repression of drivers of neuroendocrine prostate cancer [CUT&Run]

status: Public on Jul 25 2025

city: Boston

first: Varadha Balaji

last: Venkadakrishnan

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

overall_design: CUT&RUN to understand epigenetic de-repression of drivers of neuroendocrine prostate cancer

first: Himisha

last: Beltran


title: The Dream and MEC Complexes reinforce SPR-5; MET-2 maternal reprogramming to maintain the Germline-Soma distinction  [mep-1 RNAseq]

status: Public on Jul 21 2025

city: kennesaw

first: Brandon

middle: Scott

last: Carpenter

state: GA

address: 370 Paulding Avenue, Room 119

department: Molecular and Cellular Biology

institute: Kennesaw State University

summary: Proper regulation of tissue-specific gene expression is essential for cell fate determination and development. In Caenorhabditis elegans, the distinction between germline and somatic cell fates is partially established through maternally inherited histone modifications. During gametogenesis, germline genes acquire transcription-coupled chromatin marks such as histone methylation, which are inherited by the zygote and must be reprogrammed at fertilization to prevent inappropriate germline gene expression in somatic tissues. This maternal reprogramming is mediated by histone-modifying enzymes, including the demethylase SPR-5/LSD1 and the H3K9 methyltransferase MET-2/SETDB1. Together, these enzymes limit DNA accessibility to transcriptional machinery, thereby resetting the chromatin landscape in te newly formed zygote. Failure to reprogram inherited histone methylation, as in spr-5; met-2 mutants, results in the ectopic expression of MES-4-targeted germline genes in somatic tissues, leading to developmental delay and sterility. Here, we investigated whether transcriptional repressor complexes—the DREAM and MEC NuRD complexes—cooperate with SPR-5 and MET-2 to specify germline versus soma. Loss of DREAM or MEC NuRD components alone causes somatic expression of germline genes. Strikingly, combined loss with spr-5; met-2 enhances developmental arrest at the L1 stage and exacerbates germline gene misexpression. By re analyzing previous published ChIP-seq data, we confirmed direct binding of MEP-1 and LIN-35 to these misregulated genes. Our findings demonstrate that maternal reprogramming and conserved chromatin repressor complexes act synergistically to repress germline transcription in somatic tissues, ensuring proper somatic development and preventing soma-to-germline transformation.

overall_design: RNA-seq analysis on spr-5; met-2 L1 progeny from hermaphorites fed either control (L4440) or mep1 RNAi  to determine differentially expressed genes compared to L1 progeny from wild-type ( N2 strain) hermaphrodites fed control RNAi.

first: Sindy

last: Chavez

first: Jazmin

last: Dozier

first: Saahj

last: Gosrani

first: Sandra

last: Nguyen

first: Jovan

last: Brockett

first: Sarah

last: Blancher

first: Sydney

last: Morgan-Benitez

first: Juan

last: Rodriguez

first: Onur

last: Birol

first: Monica

last: Reeves

first: Karen

last: Schmeichel

first: David

last: Katz


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling [ChIPseq]

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Transcriptional control in eukaryotes relies on the coordinated action of chromatin-based regulatory mechanisms, including control of nucleosome occupancy and chromatin modifications. We previously identified the ChAHP complex – comprising the chromatin remodeler CHD4, transcription factor ADNP, and HP1 proteins – as a repressor of SINE B2 retrotransposons and site-specific regulator of CTCF engagement with chromatin. However, the molecular basis of these functions remained unresolved. Here, we show that ChAHP-associated CHD4 is essential for SINE B2 repression, while HP1 proteins are dispensable. We further demonstrate that CHD4’s remodeling activity is not required for chromatin binding, but is critical for both retrotransposon silencing and efficient CTCF antagonism. We propose ChAHP is a sequence-specific recruiter of chromatin remodeling activity, facilitating transcriptional control and localized modulation of chromatin architecture.

overall_design: ChIPseq experiments for ADNP, CTCF and Pol III were performed in indepdendent biological duplicates or triplicates in wt and Cas9-engineered mESC.

first: Josip

last: Ahel

first: Michaela

last: Schwaiger

first: Marc

last: Bühler


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling


title: miRNA expression profiling of mouse colon in chronic colitis and colitis-associated cancer models

status: Public on Aug 07 2025

city: Guri

first: Jae Gon

last: Lee

address: 153 Gyeongchun-ro

country: South Korea

institute: Hanyang University Guri Hospital

summary: This study aims to investigate alterations in colonic microRNA expression in mouse models of chronic colitis and colitis-associated colorectal cancer. Using the Affymetrix GeneChip miRNA 4.0 Array, miRNA profiles were analyzed from control mice, DSS-induced colitis mice, and AOM/DSS-induced colorectal tumor mice.

overall_design: A total of 20 mouse colon tissue samples were analyzed, including 6 control samples, 7 DSS-treated samples, and 7 AOM/DSS-treated samples. Total RNA was extracted and hybridized to the GeneChip miRNA 4.0 Array (Affymetrix). CEL and CHP files were generated for each sample and used for downstream analysis.

first: Chang

last: Eun


title: Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis [crispr gRNA knockout screening 3]

city: Philadelphia

first: Joshua

middle: Hunter

last: Rhoades

state: PA

address: 3800 Spruce St

department: Vet School

institute: University of Pennsylvania

summary: Cancer is the second leading cause of death globally, and this is due primarily to metastatic dissemination to distal sites. Metastatic outgrowth requires that cancer cells delaminate from the primary tumor, intravasate, survive in circulation, extravasate, then migrate to and proliferate at a distal site. Recurrent genetic drivers of metastasis have remained elusive, suggesting that, unlike the initial steps of oncogenic transformation and primary tumor development, drivers of metastasis may be variable. Here, we develop a framework for interrogating pathways governing metastasis by applying CRISPR/Cas9-based forward genetic screening in a genetically defined tumor-organoid model of colorectal adenocarcinoma. We conduct in vitro screens for invasion and migration alongside orthotopic, in vivo screens for gain of metastatic potential in a syngeneic mouse model, identifying suppressors of metastasis both unique to the in vivo setting as well as common to both models. Specifically, we identify Ctnna1 and Bcl2l13 as bona fide metastasis suppressors acting through distinct mechanisms, with CTNNA1 loss promoting carcinoma cell invasion and migration through an atypical EMT-like mechanism, and BCL2L13 loss promoting cell survival after extracellular matrix detachment and non-cell-autonomous changes to macrophage polarization. Ultimately, this study provides a proof-of-principle that high-content forward genetic screening can be performed in tumor-organoid models in vivo and identifies novel regulators of colon cancer metastasis.

overall_design:
Engineered colorectal adenocarcinoma organoids were transduced with various sgRNA libraries and implanted into atleast 5 mice and resulting primary and metastatic lesions were harvested after 5-6 weeks. Primary and metastatic lesions were compared to one another and reference organoids collected pre-implantation
Please note that these data (along with GSE263580 and GSE263581) are in accompaniment of the previous single cell dataset GSE237980.

first: Christopher

last: Lengner

first: Zvi

last: Cramer

middle: H


title: Enhanced efficacy of a specific HDAC3 inhibitor in combination with 5-Azacitidine against diffuse large B-cell lymphoma [MAC-seq]

city: Nice

first: Pilar

last: Dominguez

address: 151 Route de Saint-Antoine

institute: Centre Méditerranéen de Médecine Moléculaire: C3M

summary: Diffuse large B-cell lymphoma (DLBCL) refers to an aggressive lymphoma that arises from germinal center (GC) B-cells, which differentiate into plasma cells (PC) to produce high affinity antibodies. 40% of DLBCL patients relapse or are refractory to the conventional immunochemotherapy treatment, usually with fatal consequences. DLBCL is characterized by profound alterations in the epigenome, which is correlated with poor survival. The abnormal epigenetic landscape of DLBCL tumors is associated with a blockade in GC exit and differentiation programs, which are regulated by the transcription factor BCL6. This aberrant repression of BCL6-target genes is mediated by 1) increased DNA methylation and 2) loss of acetylation of the lysine 27 of histone 3 (H3K27ac)-through recruitment of histone deacetylase 3 (HDAC3). Thus, we investigated the efficacy against DLBCL of the hypomethylating agent (HMA) 5-Azacitidine (5-Aza) and a specific HDAC3 inhibitor (HDAC3i). We found that treatment with 5-Aza plus HDAC3i had a potent synergistic anti-tumor activity in vitro and in vivo, which was superior to the effect of each single drug or 5-Aza combined with non-specific HDACi and, importantly, was not associated with toxicity in normal cells. We also demonstrated that the combined 5-Aza and HDAC3i treatment induced the epigenetic remodeling of DLBCL cells, which resulted in a more potent re-expression of PC differentiation genes, including XBP1 and ATF4, compared to each drug used as single agents. Our results highlight the importance of specifically targeting multiple layers of the epigenome to maximize the efficacy of epigenetic-based therapies.

overall_design: MD901 lymphoma cells were treated with  5-Azacitidine (or vehicle) daily for 5 days, with a HDAC3 inhibitor, panobinostat or vorinostat (or vehicle) added at day 2. Cells were analyzed at day 4 (3 replicates per group).

first: Izabela

last: Todorovski


title: Targeting of SUMOylation leads to cBAF complex stabilization and disruption of the SS18::SSX transcriptome in synovial sarcoma [SYATAC_ATAC-seq]

status: Public on Aug 06 2025

city: Richmond

first: Mikhail

last: Dozmorov

address: 830 E Main St

institute: Virginia Commonwealth University

summary: Synovial Sarcoma (SS) is driven by the SS18::SSX translocation event and is often diagnosed in patients under 30. In general, SS is refractory to chemotherapy and other therapeutic approaches. SS18::SSX does not directly bind to DNA. Instead, SS18::SSX alters ATP-dependent chromatin remodeling complex BAF (mammalian SWI/SNF complex) complexes away from a wild-type SS18-containing canonical (cBAF) complex towards a SS18::SSX-containing non-canonical (nc)BAF complex to drive a SS-specific transcription program with subsequent tumor formation. Small molecule targeted therapies are expanding beyond the kinome, providing additional tools to treat cancers that are not yet amenable to targeted therapies. Here, we demonstrate that SS18::SSX activates the SUMOylation program and SS are sensitive to the small molecule SAE1/2 inhibitor, TAK-981 (subasumstat). Mechanistically, we demonstrate TAK-981 de-SUMOylates the cBAF and Polybromo-associated BAF complex (PBAF) complex member, SMARCE1. The result of which is stabilization and restoration of cBAF complexes on chromatin, shifting away from the dominant SS18::SSX-ncBAF-complex driven transcriptome. This phenotypic shift is associated with DNA damage and cell death, resulting in tumor inhibition across both human and mouse SS tumor models. As such, TAK-981 combined with standard-of-care chemotherapy enhances induced synergistic activity through increased DNA damage, leading to tumor regressions. Targeting the SUMOylation pathway in SS restores cBAF complexes and blocks the SS18::SSX-ncBAF transcriptome, identifying a therapeutic vulnerability in SS, and positioning the in-clinic TAK-981 as a novel candidate to treat this refractory cancer.

overall_design: Chromatin Immunoprecipitation DNA sequencing (ChIP seq) for SS18::SSX, SMARCA4, KDM2B and H3K27ac in SYO.1 and SYO.1 synovial sarcoma cell lines

first: Konstantinos

middle: V

last: Floros

first: Carter

middle: K

last: Fairchild Jr

first: Jinxiu

last: Li

first: Kun

last: Zhang

first: Jane

middle: L

last: Roberts

first: Richard

last: Kurupi

first: Bin

last: Hu

first: Vita

last: Kraskauskiene

first: Nayyerehsadat

last: Hosseini

first: Shanwei

last: Shen

first: Melissa

last: Inge

first: Kylie

last: Smith-Fry

first: Li

first: Afroditi

last: Sotiriou

first: Krista

last: Dalton

first: Asha

last: Jose

first: Elsamani

middle: I

last: Abdelfadiel

first: Yanli

last: Xing

first: Ronald

last: Hill

first: Jamie

last: Slaughter

first: Mayuri

last: Shende

first: Madelynk

last: Lorenz

first: Mandy

last: Hinojosa

first: Benjamin

last: Belvin

first: Zhao

last: Lai

first: Sosipatros

middle: A

last: Boikos

first: Angeliki

last: Stamatouli

first: Janina

middle: P

last: Lewis

first: Masoud

last: Manjili

first: Kristoffer

last: Valerie

first: Renfeng

first: Ana

last: Banito

first: Andrew

last: Poklepovic

first: Jennifer

last: Koblinski

first: Trevor

last: Siggers

middle: G

first: Kevin

middle: B


title: Aerobic exercise effects on tumor and skeletal muscle transcriptome in a DMBA-induced carcinogenesis

first: Rafael

last: Correia

address: 2730 S Moody Ave

institute: Oregon Health & Science University

summary: Here we sought to investigate changes caused by aerobic exercise in the skeletal muscle and tumor during the progression of a DMBA-induced carcinogenesis and cachexia. Also, we investigate the cross-talk between the tissues.

overall_design:
We used Sprague-Dawley rats starting at 50 days of age. Cancer was induced using a single dose of DMBA carcinogen (65 mg/kg), and the induction time took 3 months. After induction, we performed aerobic exercise training (treadmill running)  5 times a week for 8 weeks. Tibialis anterior muscle (n=4 per group) and tumor tissue (n=4 per group) were collected.
Snap-frozen tibialis anterior and tumor tissue were homogenized in liquid nitrogen via mortar and pestle. RNA was isolated from ∼50 mg of tissue using the miRNeasy Mini Kit (Qiagen, cat: 217004). The concentration and quality of total RNA samples were assessed using an Agilent 2100 Bioanalyzer, and an RNA Integrity Number (RIN) of 8 or higher was required to pass the quality control.
Library preparation and sequencing was completed at the Massively Parallel Sequencing Shared Resource at Oregon Health and Science University using the Illumina NovoSeq6000. 150ng of total RNA was used for each sample. cDNA library preparation includes mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, and ligation of index adaptors using the KAPA mRNA Hyperprep Kit prep (cat: KK8581). Each resulting indexed library was quantified, and its quality was assessed by NovaSeq 6000. 5μL of 2nM pooled libraries per lane was denatured, neutralized, and applied to the cBot for flow cell deposition and cluster amplification before loading to 100bp paired-end sequencing (Illumina, Inc.). Approximately 30-50 million reads per library were generated.
The processed data were obtained using the software Partek Flow. The quality trimming level (Phred) was 35 (3' end). We aligned the reads to the UCSC Rattus norvegicus (rn7) reference genome using STAR (Spliced Transcripts Alignment to a Reference). To quantify gene expression, we used the annotation model Rn07. The gene counts were filtered using a noise filter reduction filter <=10. The normalization was made using Median ratio (DESeq2) and differential analysis was made using DESeq2.

middle: R

first: Teresa

last: Zimmers

first: Giovana

last: Teixeira


title: Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis [crispr gRNA knockout screening 2]

first: Joshua

last: Rhoades

overall_design:
Engineered colorectal adenocarcinoma organoids were transduced with various sgRNA libraries and implanted into atleast 5 mice and resulting primary and metastatic lesions were harvested after 5-6 weeks. Primary and metastatic lesions were compared to one another and reference organoids collected pre-implantation
Please note that These data (along with GSE263580 and GSE263582) are in accompaniment of the previous single cell dataset GSE237980.

first: Christopher

middle: J

last: Lengner

first: Zvi

last: Cramer


title: Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis [crispr gRNA knockout screening 1]

overall_design:
Engineered colorectal adenocarcinoma organoids were transduced with various sgRNA libraries and implanted into atleast 5 mice and resulting primary and metastatic lesions were harvested after 5-6 weeks. Primary and metastatic lesions were compared to one another and reference organoids collected pre-implantation
Please note that these data (along with GSE263581 and GSE263582) are in accompaniment of the previous single cell dataset GSE237980.


title: The Dream and MEC Complexes reinforce SPR-5; MET-2 maternal reprogramming to maintain the Germline-Soma distinction  [lin-35 RNAseq]

status: Public on Jul 19 2025

first: Brandon

last: Carpenter

overall_design: RNA-seq analysis on spr-5; met-2 L1 progeny from hermaphorites fed either control (L4440) or lin-35 RNAi  to determine differentially expressed genes compared to L1 progeny from wild-type ( N2 strain) hermaphrodites fed control RNAi.

first: Sindy

last: Chavez

first: Jazmin

last: Dozier

first: Saahj

last: Gosrani

first: Sandra

last: Nguyen

first: Jovan

last: Brockett

first: Sarah

last: Blancher

first: Sydney

last: Morgan-Benitez

first: Juan

last: Rodriguez

first: Onur

last: Birol

first: Monica

last: Reeves

first: Karen

last: Schmeichel

first: David

last: Katz


title: Gpnmb is required for immune and fibrotic responses during zebrafish heart regeneration

status: Public on Aug 03 2025

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Myocardial infarction occurs when coronary supply of oxygen and nutrients to a part of the heart is interrupted.  In contrast to adult humans, adult zebrafish have a unique ability to regenerate their heart after cardiac injury.  To identify potential regulators of the regenerative response, we performed transcriptomics profiling of regenerating coronary endothelial cells (cECs) at 7 days post cryoinjury, when revascularization is vigorous, and identified gpnmb to be upregulated.  Gpnmb (glycoprotein non-metastatic melanoma protein B) is a transmembrane glycoprotein implicated in inflammation resolution and tissue regeneration.  Expression analyses at earlier time points revealed gpnmb specific expression in infiltrating macrophages post cryoinjury in zebrafish ventricles.  Using newly generated gpnmb mutants, we analyze its role during heart regeneration and find that animals lacking gpnmb exhibit neutrophil retention and decreased macrophage recruitment as well as reduced myofibroblasts numbers.  Moreover, loss of gpnmb impairs coronary endothelial cell regeneration and cardiomyocyte dedifferentiation.  Transcriptomic analyses identified enhanced collagen production and extracellular matrix (ECM) related pathway activated in cryoinjured gpnmb mutant hearts.  Furthermore, gpnmb mutant hearts exhibit larger fibrotic scars revealing defects in cardiac regeneration.  Overall, these data suggest that gpnmb expressing macrophages modulate inflammation and ECM deposition after cardiac cryoinjury and highlight the importance of this subset of immune cells to support a regenerative response.

overall_design: To investigate the role of gpnmb during zebrafish heart regeneration, we generated gpnmb mutants and performed comparative RNAseq analysis on WT and MUT

first: Savita

last: Gupta

first: Didier

last: Stainier


title: microRNA expression profile of human thymus populations corresponding to 8 sequential T-cell developmental stages isolated from 3 independent pediatric thymus samples.

status: Public on Jul 15 2025

city: Madrid

first: María

last: Toribio

state: Madrid

address: Calle Nicolás Cabrera, 1. Campus Cantoblanco

department: Interactions with the environment

country: Spain

institute: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy arising from the neoplastic transformation of immature T cells during their development in the thymus. Deciphering the developmental programs whose dysregulation leads to T-ALL pathogenesis is critical for the development of novel targeted therapies, which remain an urgent unmet need for the treatment of this disease. MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of numerous physiological processes and cancer. However, the specific role of miRNAs in human T-cell development and T-ALL pathogenesis remains largely unexplored. In this study, we comprehensively evaluated miRNA expression profiles across human T-cell development by microarray analysis and identified a dynamic expression pattern of miR-16-2, which is upregulated across early pre-T cell proliferative stages up to the resting state of immature thymocytes immediately preceding TCR expression, and decreased thereafter. We confirmed the coordinated regulation of miR-15b expression, consistent with the reported clustered genomic location of both miRNAs. Notably, functional studies identified the miR-15b/16-2 cluster as a negative regulator of early thymocyte proliferation, and showed that overexpression of miR-15b/16-2 in T-ALL cells impaired leukemic growth in vitro and tumor progression in patient-derived xenotransplantation assays. Mechanistically, miR-15b/16-2 expression represses the genes encoding BCL-2 and CYCLIN D3, leading to T-ALL apoptosis and cell cycle dysregulation, with an accumulation of G0-phase cells and a defective transition to the G2/M phase. Overall, these findings support a novel function for miR-15b/16-2 as tumor suppressors in T-ALL, highlighting their role as promising targets for T-ALL therapy.

overall_design: Thymocyte subpopulations corresponding to sequential T-cell developmental stages were isolated by immunomagnetic sorting from 3 independent pediatric thymus samples (aged 1 month to 4 years). Sortings were performed based on the surface expression markers characteristic of each T-cell developmental stage using Dynabeads (Dynal, Invitrogen) or Microbeads and AutoMACs (Miltenyi Biotec). Individual population purity (>95%) was confirmed by flow cytometry.

first: M

first: S

last: González-García


title: Cell Density Regulates Neural Stem Cells of Cellular Contact and Differentiation in 3D Hydrogel Culture System

city: Changsha

first: Chaoyong

last: He

address: Tianma road

institute: Hunan university

summary: Neural Stem Cells (NSCs) of biological behaviors are frequently regulated by the three-dimensional (3D) niches that they located in. The impact of cell density cue inside niche on cellular outcomes are usually underestimated and understudied. In this study, a facile NSCs of 3D culture system was developed using collagen self-assembled fibril hydrogel. We used RNA sequencing and molecular biology technologies to investigate the NSCs of cell contacts and differentiations in developed 3D hydrogel culture system with low (0.75 million/mL), medium (1.5 million/mL), and high (3 million/mL) cell packing density. Compared with low cell density system, cytoskeletal spreading, gap junction, and tight junction mediated cell contacts were significantly improved in high cell density culture. Moreover, high cell density increased NSCs differentiation into immature (Tuj1) neuron, while there is no discrepancy of NSCs differentiation into astrocytes in different cell densities of 3D culturing system. This study provides new understanding in the regulation of 3D cultured NSCs behaviors through niche of cell density cue.

first: Yuyun

last: Liang

first: Xiaonan

last: Wang

first: Jing

last: Yang

first: Ziyan

last: Chen

first: Hexu

last: Zhang

first: Cheng

last: Zhao

first: Liyang

last: Shi


title: Spatial transcriptional features of MYCN niche in liver tumorigenesis.

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death, often diagnosed at advanced stages and characterized by high recurrence rates. While chronic liver inflammation and metabolic dysfunction are recognized contributors to tumorigenesis, the molecular mechanisms linking early microenvironmental stress to malignant transformation remain poorly understood. MYCN, a proto-oncogenic transcription factor, has emerged as a potential biomarker of cancer stemness, yet its functional role in hepatocarcinogenesis is unclear. Here, we elucidate the oncogenic role of MYCN and its dynamic regulation during metabolic liver tumorigenesis. Transcriptomic profiling revealed that MYCN-driven tumors exhibit features of human HCC subtypes enriched in stress-adaptive transcriptional programs. Time-resolved spatial transcriptomics further uncovered a MYCN-enriched niche characterized by epithelial–mesenchymal transition (EMT) and Wnt/β-catenin signaling, which expanded during tumor progression and was spatially proximate to transformed malignant cells.

overall_design: Spatial transcriptomics using the 10× Genomics Visium platform in a metabolic HCC mouse model STAM (STAM16w, STAM20w), which mimics MASH and type I diabetes, and in a fibrotic HCC mouse model DEN+CCL4 (DEN22w, DEN30w), which mimics DNA damage–driven and fibrosis-promoting tumor evolution.


title: Single-cell transcriptomic and 3D genome atlas of leukemia cells from patients with acute myeloid leukemia (AML)

status: Public on Jul 14 2025

city: Beijing

first: Menghan

last: Liu

address: Yiheyuan Road

institute: Peking University

summary: We applied a single-cell multi-omics assay named “Hi-C and RNA-seq employed simultaneously” (HiRES) to simultaneously profile chromatin structure and transcriptome within the same cell. In our study, this assay was conducted on CD34⁺CD117⁺CD38⁻ hematopoietic stem and progenitor cells (HSPCs) isolated from bone marrow aspirates of acute myeloid leukemia (AML) patients. This dataset represents the first application of single-cell HiRES in primary AML samples, providing paired 3D genome and gene expression information at single-cell resolution.

overall_design:
HiRES：Mononuclear cells were extracted from acute myeloid leukemia patients. Target cells were stained with CD34 and CD117 antibodies and isolated by Fluorescence-activated cell sorting (FACS). Final libraries were prepared strictly follwing HiRES protocol.

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

first: Yujing

last: Deng


title: Distinct effects of restricting individual branched-chain amino acids on the development and progression of Alzheimer’s disease in 3xTg mice

status: Public on Jul 30 2025

city: MADISON

first: REJI

last: BABYGIRIJA

state: WI

address: 726 BEAR CLAW WAY, APT 211

institute: UW Madison

summary: Dietary protein is a critical regulator of metabolic health and aging in diverse species, and many of the benefits of low-protein diets are recapitulated by restriction of the three branched-chain amino acids (BCAAs), leucine, isoleucine, and valine. In mouse models of Alzheimer’s disease (AD), dietary supplementation with BCAAs worsens AD neuropathology, while restriction of any of the BCAAs improves cognitive deficits. We recently discovered that each BCAA has distinct metabolic effects, with the restriction of isoleucine alone being sufficient to improve metabolic health and extend lifespan and healthspan in genetically diverse mice. Here, we investigate the effect of restricting each individual BCAA on metabolic health and the development and progression of AD in the 3xTg mouse model. We find that restriction of isoleucine and valine, but not leucine, promotes metabolic health. Restricting any of the three BCAAs improved short-term memory in males, with isoleucine restriction having the strongest effect, while restricting valine has the greatest cognitive benefits in females. Restriction of each BCAA had distinct effects on AD pathology, mTOR signaling, autophagy, and survival. Transcriptomic analysis of the brain revealed both distinct and shared, and highly sex-specific, molecular impacts of restricting each BCAA, and we identify a set of significantly altered pathways strongly associated with reduced AD pathology and improved cognitive performance in males. Our findings suggest that restricting any of the BCAAs, particularly isoleucine or valine, may form the basis of a novel sex-specific approach to prevent or delay the progression of AD.

overall_design: Six month old Male and female 3xTg mice were placed on either of these 4 diets Amino acid defined diet , Isoleucine restricted diet, Leucine restricted diet or Valine restricted diet for 9 months. Brains were colelcted for rna sequencing from all the treatment groups.

first: Reji

last: Babygirija

first: Cara

last: Green

first: Dudley

last: Lamming


title: Gene expression analysis in canine peripheral blood mononuclear cells (PBMCs) from dogs with diffuse large B cell lymphoma (DLBCL)

status: Public on Jul 17 2025

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a veterinary clinical oncology trial in client-owned dogs to determine if immune modulating drugs could be combined in rational approaches to treat spontaneous canine diffuse large B cell lymphoma (DLBCL).

overall_design: Gene expression in peripheral blood mononuclear cells (PBMCs) at Day 0, Day 7, Day 21/28 and relapse from dogs enrolled in three different treatment arms was analyzed using the NanoString canine IO panel Sprint platform.

first: Cheryl

last: London

first: Heather

last: Gardner


title: miRNA/mRNA analysis of Chlamydia trachomatis-infected endometrial biopsies indicate increased TGF-β pathways drive epithelial-mesenchymal transition and regulatory T cell differentiation

city: Chapel Hill

first: xiaojing

last: zheng

address: 111 Mason Farm Road

institute: UNC-CH

summary: Chlamydia trachomatis genital tract infection is linked to severe reproductive complications in women, including ectopic pregnancy, infertility, and adverse pregnancy outcomes. Mouse models of infection suggest that chlamydia-induced dysregulation of microRNAs (miRNAs) can drive harmful cytokine responses, pathogenic epithelial-mesenchymal transition (EMT), and fibrosis. To investigate these mechanisms in humans, we profiled miRNA and mRNA expression in endometrial biopsies from women with endometrial infection (Endo+) and compared them to profiles from women with cervix-only infection (Endo-) or no infection. Ingenuity Pathway Analysis (IPA) revealed that Endo+ tissues had upregulated genes associated with innate and adaptive immune response pathways, as well as EMT regulation, while downregulated genes were linked to cell cycle control. An integrative miRNA-mRNA analysis, which combined a review of published miRNA regulation in human infections and immune responses with IPA’s miRNA target filter, identified differentially expressed miRNAs that modulate these pathways in the endometrium of Endo+ women. Functional annotation of these miRNAs showed a predominance of downregulated miRNAs that typically suppress EMT and regulatory T cell (Treg) differentiation, along with miRNAs that usually enhance Th17 responses. Comparisons with previously identified mRNA pathways in blood samples from women with endometrial Chlamydia infection indicated that alterations in TGF-β signaling and EMT were specific to the endometrium. Overall, the miRNA-mRNA interactions inferred from Endo+ tissue suggest increased activity in TGF-β pathways that promote enhanced EMT and Treg differentiation, while reducing Th17 activation. These changes highlight a dual potential for promoting tissue scarring while dampening inflammatory responses that could otherwise limit infection.

overall_design: Endometrial biopsy samples were obtained from cisgender female participants enrolled in two independent cohorts with high exposure to Ct infection. Total RNA was extracted from endometrial biopsies stored at -80°C in tubes containing RNA/DNA Shield (Zymo Research, Irvine, CA). After thawing, samples were weighed, minced, and processed for simultaneous DNA and RNA extraction using the Quick DNA/RNA™ isolation kit according to the manufacturer's protocol (Zymo) with on column DNase I treatment prior to total RNA elution. Libraries were prepared using the Ovation SoLo RNA-Seq kit (NuGen Technologies) and sequenced on an Illumina HiSeq2500 platform in the High Throughput Sequencing Facility (HTSF) at the University of North Carolina.

first: Toni

last: Darville

first: Xuejun

last: Sun

first: Yu

first: Catherine

last: O’Connell

first: Neha

last: Mokashi

first: Weiming

last: Tang

first: Aakash

last: Bhardwaj

first: Bryce

last: Duncan

first: Harold

last: Weisenfeld

first: Xiaojing

last: Zheng


title: Real-time quantitative PCR analysis of extracellular vesicle miRNA from human U2OS cells culture medium [HRH1]

city: Portland

first: Xiao

last: Shi

address: 3181 SW Sam Jackson PK Rd

institute: Oregon Health and Science University

summary: Human U2OS cells were stimulated with selective agonist PEA of Histamine receptor H1 (HRH1) for 24 hours. Extracellular vesicles were isolated from U2OS cell culture media. Total RNAs were purified from extracellular vesicle samples. We used TaqMan Low Density Arrays to quantitate miRNA expression in extracellular vesicles secreted by U2OS cells after GPCR activation.

overall_design: qPCR miRNA expression profiling.  Each GPCR stimulation experiment included its own media control, vehicle control, and treated samples.

first: Aaron

last: Janowsky


title: Real-time quantitative PCR analysis of extracellular vesicle miRNA from human U2OS cells culture medium [FZD4]

summary: Human U2OS cells were stimulated with selective agonist Wnt3a of Frizzled class receptor 4(FZD4) for 24 hours. Extracellular vesicles were isolated from U2OS cell culture media. Total RNAs were purified from extracellular vesicle samples. We used TaqMan Low Density Arrays to quantitate miRNA expression in extracellular vesicles secreted by U2OS cells after GPCR activation.


title: Single cell RNA-seq analysis of H3.3K4M WT and Hom brain samples (10X Genomics Multiome)

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

summary: Methylation of lysine4 on Histone H3 (H3K4) is require for promoter and enhancer activation at gene loci and presents distinct methylation patterns over developmental gene clusters. Disrupting in the writer, eraser and reader of H3K4 methylation is associated with developmental syndromes. However, less studies focus on the role of H3K4 methylation in development of interneuron and hypothalamus. Here, we explore the role of H3K4 methylation in the medial ganglionic eminence (MGE) derive interneuron and hypothalamus by directly mutating the lysine 4 on H3.3 to the methionine in mice.

overall_design: The Nkx2.1-Cre;H3.3K4M;Sun1-sfGFP mice were generated to harvest all Nkx2.1-lineage GFP+ nuclei via flow cytometry.  Single nuclei from embryonic and adult samples from each genotype were prepared to analyze transcriptome using 10X Genomics Multiome pipeline. Samples: E13.5 MGE and hypothalamus as well as P60 cortex and hypothalamus of H3.3K4M WT and Hom. In addition, one replicate for male and female for each condition.


title: Multimodal antigenic escape to GPRC5D-targeted T-cell engagers in multiple myeloma [scRNA-seq]

status: Public on Jul 05 2025

city: Calgary

first: nizar jacques

last: Bahlis

state: AB

address: 3330 Hospital Dr NW HMRB328

institute: University of Calgary

summary: Tumor intrinsic adaptations with emerging resistant clones following T cell targeted immunotherapies pose a major barrier to durable remissions in multiple myeloma (MM). Through integrated genomic, transcriptomic, and epigenomic interrogation of clonal plasma cells, we observed antigenic drift in 68.4% of relapsed cases following anti-GPRC5D T cell engager (TCE) therapy. These escape events were driven by three distinct mutational mechanisms involving i) focal to large biallelic deletions at the GPRC5D gene locus, ii) monoallelic deletion coupled with GPRC5D single nucleotide variants (SNVs) or insertions/deletions (indels) on the remaining allele, as well as iii) epigenetic GPRC5D promoter/enhancer silencing. Beyond biallelic deletions resulting in complete antigenic loss, we demonstrate that GPRC5D SNVs and indels mutate anti-GPRC5D TCE binding epitopes or more commonly affect G-protein couple receptor family conserved motifs critical for protein membrane trafficking resulting in endoplasmic reticulum (ER) GPRC5D trapping. Multiple subclones bearing distinct genomic alterations at GPRC5D locus co-emerged within individual cases, depicting their convergent evolutionary trajectories. Importantly, anti-GPRC5D TCEs with varying epitope specificity, affinity, and valency differentially targeted mutant subclones, underscoring their non-redundant functional roles in overcoming resistance

overall_design: Experiments were conducted on primary patient bone marrow samples, after informed consent, in accordance with the Declaration of Helsinki and following the approval by the Medical Center Institutional Review Board. Unbiased mRNA profiling were conducted by using scRNA-seq from the GemCode system (10x Genomics) accordingly to the manufacturer’s protocols. Single cell library preparation of CD138+  were carried out on the Chromium platform (10x Genomics) using the Single Cell 3ʹ reagent kits v3 according to the manufacturer’s protocol. Samples were processed with CellRanger suite v7.1.0 against the human reference genome GRCh38 with default parameters

first: Holly

last: Lee

first: Noémie

last: Leblay

first: Sungwoo

last: Ahn

first: Sacha

last: Benaoudia

first: Elham

last: Hasheminasabgorji

first: Mansour

last: Poorebrahim

first: David

last: Jung

first: Paola

last: Neri

first: Nizar


title: Lipid nanoparticles as a tool to dissect dendritic cell maturation pathways

status: Public on Jul 01 2025

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

summary: Dendritic cells (DCs) are short-lived immune cells that continuously roam our body in search for foreign or self-antigens. Upon acquisition of antigen, they mature and start migrating to the lymph node to present the antigen to naïve T cells. Depending on the context wherein the antigen is acquired, DCs will mature in a homeostatic or immunogenic manner. So far, the field is lacking proper tools to distinguish between the two maturation states. Most maturation markers are shared between the two states and therefore inappropriate to use. Still, defining the proper maturation type is crucial as it determines how the DCs will instruct the T cells towards antigen expressing cells. In this study, we used a lipid nanoparticle (LNP)-based approach to steer DC maturation pathways in vivo. CITE-seq analysis allowed us to design a panel of flow cytometry markers that reliably annotates the two DC maturation states, as validated in an infection and in a tumor model. Furthermore, the data corroborated that uptake of empty LNPs in DCs induces their homeostatic maturation, in contrast to uptake of mRNA-LNPs or TLR ligand-adjuvanted LNPs, leading to distinct effector T cell outputs. This reveals that LNPs themselves are not being decoded as “danger” by cDC1s, and that the cargo is essential to provide adjuvants activity, which is highly relevant for targeted design of LNP-based therapies.

overall_design: We performed CITE-seq to compare cDC1 maturation across various conditions within the spleen. Combining the measurement of the transcriptome and the surface epitopes of cDC1s facilitated a detailed analysis of the various stages cDC1s go through during this maturation process.

first: Sofie

last: Rennen

first: Victor

last: Bosteels

first: Clint

last: De Nolf

first: Karo

last: Van Lil

first: Sandra

last: Maréchal

first: Jessica

last: Vetters

first: Evelien

last: Van De Velde

first: Farzaneh

last: Fayazpour

first: Ria

last: Roelandt

first: Niels

last: Van Damme

first: Kevin

last: Verstaen

first: Rein

last: Verbeke

first: Sabrina

last: Marion

first: Bruno

last: De Geest

first: Ine

last: Lentacker


title: Effects of the FOXF1 on herpes simplex virus 1 and host chromatin accessibility in Neuro-2a cells

status: Public on Jun 30 2025

city: Hangzhou

first: Xiang

last: Yuhang

address: Yuhang Tang street

summary: This is a part of the study that shows that a host gene,FOXF1, promote herpes simplex virus 1 (HSV-1) genome accessibility. These ATAC analyses viral and host genome accessibility in Neuro-2a cells. Neuro-2a cells were transfected with pFOXF1 and pcDNA plasmids for 42 hours then infected with herpes simple virus1 for 3 hours.

overall_design: P represents cell samples transfected with pcDNA plasmid as control group. F represents cell samples transfected with pFOXF1 plasmid as the experimental group.Comparison of cells overexpressing FOXF1 with control cells. Infect the cells for viral and host genome accessibility identification

first: Dongli

last: Pan

first: Yuhang

last: Xiang


title: Genome-Wide Silencer Screening Reveals Key Silencer Modulating Reprogramming Efficiency in Mouse Induced Pluripotent Stem Cells

city: shenzhen

first: Guoli

last: Li

address: penfei street

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

summary: The majority of the mouse genome is composed of non-coding regions, which harbor numerous regulatory sequences essential for gene regulation. While extensive research has focused on enhancers that activate gene expression, the role of silencers that repress gene expression remains less explored. In this study, we conducted the first genome-wide identification of silencers in the mouse cell genome. In mouse embryonic fibroblasts (MEFs) and mouse embryonic stem cells (mESCs), we identified 89,596 and 115,165 silencers, respectively. These silencers are ubiquitously distributed across the genome and are predominantly associated with low-expression genes. Additionally, We have identified that these silencers predominantly exhibit cell-specific presence and exert their function through binding with repressive transcription factors (TFs). Furthermore, these silencers are notably enriched with the histone modification H3K9me3. In terms of biological effects, we identified a silencer within an intron of the pluripotency gene NANOG. Knockout of this silencer in (MEFs) resulted in a twofold increase in the induction efficiency of induced pluripotent stem cells (iPSCs). Collectively, our work provides the first comprehensive silencer landscape in the mouse genome and provides strong evidence for the role of silencers in the induction of iPSCs.

overall_design: We identified genome-wide silencers in mouse cell lines MEFs and mESCs using Ss-STARR-seq. We then performed a joint analysis of these silencers with other multi-omics data to elucidate the fundamental characteristics of mouse silencers. Finally, we investigated the biological effects of these silencers by conducting CRISPR knockout experiments. Genome assembly mm10.


title: Tuft cells in the gut limit cognitive disorders by regulating gut homeostasis

city: Nanjing

first: LU

last: CHEN

address: Longmian Road 101

institute: Nanjing Medical University

summary: Cognitive deficits, such as Alzheimer's disease (AD), encompass not only abnormalities in the brain but also dysfunctions in the gut. However, the characterization and influence of colonic epithelial cells during AD development have remained elusive. In this study, we identified a reduced abundance of tuft cells and dysfunction of CD4+ T cell response in the colon of AD model mice (APP/PS1-21), which may result from the specific inhibition of tuft cell differentiation by Aβ. The cognitive function was found to be further impaired when tuft cells were deficient in APP/PS1-21 mice. Remarkably, activation of tuft cells using succinic acid—a specific promoter—restored cognitive function and gut homeostasis in AD mice. In addition, tuft cell deficiency in normal mice (10-month-old) is sufficient to induce gut leakage, immune imbalance, and subsequent cognitive dysfunction. Thus, tuft cell is necessary for gut homeostasis during cognitive disorders.

overall_design: We performed single-cell RNA sequencing analysis on the colonic epithelium of wild type (WT) and transgenic Alzheimer's disease (AD) model (APP/PS1-21) mice. We generated tuft cell-deficient AD mice and stimulated tuft cells using succinic acid to assess the impact on behavioral performance and CD4+ T cell responses in the colon. We utilized colonic organoids to directly evaluate the effect of β-amyloid (Aβ) on tuft cell differentiation. Furthermore, we compared behavioral performance and CD4+ T-cell responses between different ages of tuft cell-absent mice and age-matched wild-type littermates.

first: Lu

last: Chen

first: Yuxuan

last: Yang

first: Cailong

first: Yong

last: Zhang

first: Xiangyu

first: Xinmei

first: Lin

first: Zhipeng

last: Xu

first: Wenqing

first: Zhi-Yuan

first: Minjun

last: Ji


title: Plasticity of regulatory grammar in human promoters uncovered by MPRA-trained deep learning

city: Amsterdam

first: Noud

last: Klaassen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Insitute

summary: One of the major challenges in genomics is to build computational models that accurately predict genome-wide gene expression from the sequences of regulatory elements. Promoters play a key role in gene regulation, yet their regulatory logic remains incompletely understood. Here, we present PARM, a cell-type specific deep learning model trained on specially designed massively parallel reporter assays that query human promoter sequences. PARM is computationally light-weight and reliably predicts autonomous promoter activity across the genome from DNA sequence alone, in multiple cell types. PARM can also design purely synthetic strong promoters. We leveraged PARM to systematically identify binding sites of transcription factors (TFs) binding sites that are likely to contribute to the activity of each natural human promoter, and to detect the rewiring of these regulatory interactions upon various stimuli to the cells. We also uncovered and experimentally confirmed striking positional preferences of TFs that differ between activating and repressive regulatory functions, as well as a complex grammar of motif-motif interactions. Our approach provides a foundation towards a deeper understanding of the dynamic regulation of human promoters by TFs

overall_design: Various cell lines were transfected with various different massively parrallel reporter assay (MPRA) libraries. Data contain raw read counts as well as normalized data.


title: Epigenetic de-repression of drivers of neuroendocrine prostate cancer [RNA-seq]

city: Boston

first: Varadha Balaji

last: Venkadakrishnan

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

overall_design: RNA-Seq to understand epigenetic de-repression of drivers of neuroendocrine prostate cancer

first: Himisha

last: Beltran


title: The role of adaptor protein PINCH mediated signaling pathway in morphogenesis of vasculature

city: Shanghai

first: Chunxiao

last: Wang

address: Siping road

institute: Tongji university

summary: In order to investigate the underlying molecular mechanisms of the integrin-PINCH signaling pathways in angiogenesis, arterial samples from E14.5 mice were obtained for RNA extraction and RNA-seq sequencing. RNA-seq analysis showed that the enriched regulated genes were associated with various biological processes, including the ERK1/2 cascade, collagen biosynthetic process, and multiple cell behaviors , cell adhesion, migration, extracellular matrix remodeling, muscle contraction, etc. The results suggest that the PINCHs play an essential role in angiogenesis by modulating gene expression and signaling pathways as well as regulating cell behaviors of vascular wall, and deletion of PINCHs lead to altered biological processes, influencing the development and functionality of blood vessels, which are associated with cell adhesion, proliferation, apoptosis, and migration.

overall_design: In order to investigate the functional roles of PINCHs in the development of vascular medial layer cells and angiogenesis, we used vascular medial layer cell specific mouse model (Pdgfrb Cre/+; PINCH1f/+; PINCH2-/- mice and PINCH1f/f; PINCH2-/-, dmut).  Then we performed RNA-seq analysis of the aortic smooth muscle tissue at E14.5/18.5 and comparative gene expression profiling analysis of RNA-seq data for control and PINCH-null (mut) mice.

first: Xingqun

last: Liang

first: Yunfu

last: Sun

first: Zeyue

last: Zhu

first: Yao

last: Jin

first: Qicheng

last: Zou


title: The role of adaptor protein PINCH mediated signaling pathway in morphogenesis of vasculature [CUT&Tag]

summary: To uncover direct targets of PINCH that could account for its role in vasculature, we performed cut tag analysis on wild type aortic smooth muscle using PINCH1 antibody at E18.5. Our analyses uncovered 50789 significant binding peaks for PINCH, mainly located at intergenic or intronic regions.

overall_design: CUT&Tag analyses were performed using the aortic smooth muscle tissue of ctrl mice at E18.5. Tissue samples were dissected under fluorescence microscope.


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling [gNOMEseq]

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: Transcriptional control in eukaryotes relies on the coordinated action of chromatin-based regulatory mechanisms, including control of nucleosome occupancy and chromatin modifications. We previously identified the ChAHP complex – comprising the chromatin remodeler CHD4, transcription factor ADNP, and HP1 proteins – as a repressor of SINE B2 retrotransposons and site-specific regulator of CTCF engagement with chromatin. However, the molecular basis of these functions remained unresolved. Here, we show that ChAHP-associated CHD4 is essential for SINE B2 repression, while HP1 proteins are dispensable. We further demonstrate that CHD4’s remodeling activity is not required for chromatin binding, but is critical for both retrotransposon silencing and efficient CTCF antagonism. We propose ChAHP is a sequence-specific recruiter of chromatin remodeling activity, facilitating transcriptional control and localized modulation of chromatin architecture.

overall_design: gNOMeseq experiments for ADNP PxVxL and N-terminal mutants were performed independent duplicates in mESC.

first: Josip

last: Ahel

first: Michaela

last: Schwaiger

first: Marc

last: Bühler


title: RNA-seq of equine alveolar macrophages and blood monocyte-derived macrophages exposed to an inflammatory stimulus

city: Guelph

first: Heng

last: Kang

state: Ontario

address: 50 Stone Rd E

department: Pathobiology

institute: University of Guelph

summary:
The obejective was to investigate how equine alveolar macrophages (AMs) and monocyte-derived macrophages (MDMs) response to a stimuli which contained fungal spores, lipopolysaccharide, and silica microsphere (FLS), and whether different responses existed between AMs and MDMs.
RNA-seq was used to profile gene expression of AMs and MDMs from six clinically healthy horses were incubated with and without FLS for six hours.

overall_design: Differential gene expression analysis between control and FLS-exposed AMs, and MDMs, respectively. In additon, a comparison between AMs and MDMs in their gene expression change affected by FLS.

first: Gary

last: Lee

first: Dorothee

last: Bienzle

first: Jutta

last: Hammermueller

first: Luis

last: Castro

first: Brandon

last: Lillie

first: Janet

last: Beeler-Marfisi


title: Forward genetic screening in engineered colorectal cancer organoids identifies novel regulators of metastasis

city: Philadelphia

first: Joshua

last: Rhoades

address: 3800 Spruce St

institute: University of Pennsylvania

summary: Cancer is the second leading cause of death globally, and this is due primarily to metastatic dissemination to distal sites. Metastatic outgrowth requires that cancer cells delaminate from the primary tumor, intravasate, survive in circulation, extravasate, then migrate to and proliferate at a distal site. Recurrent genetic drivers of metastasis have remained elusive, suggesting that, unlike the initial steps of oncogenic transformation and primary tumor development, drivers of metastasis may be variable. Here, we develop a framework for interrogating pathways governing metastasis by applying CRISPR/Cas9-based forward genetic screening in a genetically defined tumor-organoid model of colorectal adenocarcinoma. We conduct in vitro screens for invasion and migration alongside orthotopic, in vivo screens for gain of metastatic potential in a syngeneic mouse model, identifying suppressors of metastasis both unique to the in vivo setting as well as common to both models. Specifically, we identify Ctnna1 and Bcl2l13 as bona fide metastasis suppressors acting through distinct mechanisms, with CTNNA1 loss promoting carcinoma cell invasion and migration through an atypical EMT-like mechanism, and BCL2L13 loss promoting cell survival after extracellular matrix detachment and non-cell-autonomous changes to macrophage polarization. Ultimately, this study provides a proof-of-principle that high-content forward genetic screening can be performed in tumor-organoid models in vivo and identifies novel regulators of colon cancer metastasis.

overall_design: Engineered colorectal adenocarcinoma organoids expressing a control or Bcl2l13-targeted sgRNA were implanted into the ceca syngeneic mice. 2 replicate primary tumors from both genotypes were isolated and subjected to scRNA-seq. 2 liver metatases were isolated from sgBcl2l13-implanted mice. Control sgRNA cells were used as reference

first: Christopher

last: Lengner

first: Zvi

last: Cramer


title: ChAHP Displaces Transcriptional Regulators Through Active Chromatin Remodeling [RNAseq]

overall_design: RNA-seq and TT-seq experiments for ADNP PXVxL and N-terminal mutants and for CHD4-ADNP wt and mutant fusions were performed independent triplicates in wt and Cas9-engineered mESC.


title: Identification of RNAs regulated by ZMAT3 and p53

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Identify the transcriptome regulated by p53 and ZMAT3 in HCT116 colorectal cancer cell line. The hypothsis of this study is that ZMAT3 regulates the expression of a subset of RNAs that are also regulated by p53 to mediate its biological functions.

overall_design: To identify the RNAs regulated by p53, mRNA-seq was performed from total RNA isolated from HCT116 cells transfected with a control (CTRL) siRNA or p53 siRNAs (SMART pool of 4 siRNAs) in biological duplicates for 72 hours. To identify the RNAs regulated by ZMAT3, mRNA-seq was performed from total RNA isolated from a ZMAT3-wild type clone and a ZMAT3 knockout clone in biological triplicates.

first: Ashish

last: Lal

first: Xinyu

last: Wen


title: Polycomb repression works without Siesta [TRIP]

city: Umeå

first: Anastasiya

last: Yushkova

address: Försörjningsvägen 2A, Byggnad 6L, NUS

department: Molecular biology

country: Sweden

institute: Umeå University

summary: Polycomb group proteins are essential for epigenetic repression of developmental genes. They act as multi-subunit complexes whose biochemical functions are yet to be fully characterised. One of the complexes, canonical Polycomb Repressive Complex 1 (PRC1), acts as an E3 ligase, depositing a single ubiquitin molecule on histone H2A. It can also bind to histone H3 tri-methylated at lysine 27 (H3K27me3), which is critical to propagate the repressed state of regulated genes epigenetically. The RING1 subunit of PRC1, responsible for the ubiquitin ligase activity, forms other complexes. These complexes can ubiquitylate H2A but cannot bind H3K27me3. It was proposed that H2A ubiquitylation is an essential part of the repressive mechanism and that variant RING1 complexes evolved from ancestral canonical PRC1 to diversify the Polycomb system and enable the evolution of vertebrate-specific traits. However, systematic tracing of genes encoding subunits of distinct variant RING1 complexes argues that these complexes appeared early in animal evolution and likely had functions unrelated to epigenetic repression. To address this problem, we leveraged the power of Drosophila genetics to discover that canonical PRC1 and variant RING1 complexes monoubiquitylate H2A across distinct genomic regions. We found that the sole Drosophila PCGF protein specific for variant RING1 complexes, which we named Siesta, is not required for epigenetic repression of homeotic genes, but controls larval locomotion independently of H2A ubiquitylation. Exploiting the division of labour between PRC1 and Siesta-RING1 complexes, we employed thousands of reporters integrated in parallel to conclude that H2A ubiquitylation has no major repressive effect on transcription. We propose that variant RING1 complexes are not part of the Polycomb regulatory system and that the current PRC1 nomenclature needs revision.

overall_design: TRIP experiments in cultured Drosophila cells. Two experiments started from independently grown cell cultures were performed for each genetic background and condition.

first: Tatyana

last: Kahn

first: Andres

last: Garrido

first: Maria

last: Kim

first: Alexander

last: Glotov

first: Sweda

last: Sreekumar

first: Jan

last: Larsson

first: Yuri

last: Schwartz


title: Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos [scRNA-seq]

status: Public on Jun 25 2025

city: New York

first: Yinwen

last: Liang

email: liangy@mskcc.org, liangyinwen@gmail.com

state: New York

address: 1275 york avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Although specific transcription factors (TFs) are known to regulate cell fate decisions, the degree to which they can stimulate formation of specific cell organelles is less clear. We used a multiomics comparison of the transcriptomes of ciliated and unciliated embryonic cells to identify TFs up-regulated in ciliated cells. We also used conditional genetics in mouse embryos and stem cells and found that the TFs SP5 and SP8 regulate cilia formation and gene expression. In embryos lacking Sp5 and Sp8, primary and motile cilia were shorter than normal and reduced in number across cell types, contributing to situs inversus and hydrocephalus. Moreover, expression of SP8 was sufficient to induce primary cilia in unciliated cells. This work will facilitate the study of cilia assembly using stem cell models and promote further understanding of human ciliopathies.

overall_design: To investigate transcriptome differences of Sp8 GOF and control yolk sac tissue, we performed scRNA-seq analysis of yolk sac tissue of E8.5 mouse embryos.2 yolk sac tissues pooled for each library, 2 replicates per genotype. For each libarry, 2 embryos at E8.5 stages were dissected out and dissassoicated into single cells, sorted for lvie cell and loaed for single cell sequencing.

first: Alexandra L

last: Joyner


title: Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos [ChIP-seq]

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4me3 and FLAG in Sp8 overexpression (iSp8-3xFLAG) EpiSC cells.

first: Richard

last: Koche

first: Alexandra


title: Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos

overall_design: To investigate transcriptome differences of ciliated cell types versus unciliated visceral endoderm lineage cell types in yolk sac tissue, we performed scRNA-seq analysis of yolk sac tissue of E8.75 mouse embryos.3 yolk sac tissues from 3 embryos at E8.75 stages were dissected out and dissassoicated into single cells, multiplexed and pooled for single cell sequencing.


title: Single cell 10X Genomics Multiome Analysis of H3.3K4M Mutant Brain Samples

first: Timothy

last: Petros

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

overall_design: Refer to individual Series


title: Polycomb repression works without Siesta [ChIP]

overall_design: ChIP-seq experiments in cultured Drosophila cells. Two experiments started from independently grown cell cultures were performed for each genetic background and antibody.


title: Elementary 3D organization of active and silenced E. coli genome (RedC)

status: Public on Jun 24 2025

first: Ilya

last: Shamovsky

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery.

overall_design: Using the Micro-C technique, we generated contact maps of the E. coli genome at a resolution up to 10 bp. We analyzed wild-type E. coli cells, cells subjected to heat shock, cells treated with different antibiotics and drugs (rifampicin, bleomycin, novobiocin, ciprofloxacin, netropsin), as well as different knockout strains (deltaHNS, deltaStpA, deltaHNSdeltaStpA, deltaFis, deltaMukBEF). We performed gene expression profiling analysis using data obtained from Red-C and RNA-seq. We also performed Hi-C analysis of wild-type E.coli cells.

first: Alexey

last: Gavrilov


title: Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos [ATAC-seq]

overall_design: Examination of chromatin accessibility profile in Yolk sac mesoderm, Yolk sac viseral endoderm and Gut viseral endoderm cells obtained from fluorescence-activated cell sorting of E8.75 (12 somite) Afp-GFP/+ embryos.


title: A PLURIPOTENT STEM CELL PLATFORM FOR IN VITRO SYSTEMS GENETICS STUDIES OF MOUSE DEVELOPMENT [ATAC-seq]

status: Public on Jun 21 2025

summary: The directed differentiation of pluripotent stem cells (PSCs) from panels of genetically diverse individuals is emerging as a powerful experimental system for characterizing the impact of natural genetic variation on developing cell types and tissues. Here, we establish new PSC lines and experimental approaches for modeling embryonic development in a genetically diverse, outbred mouse stock (Diversity Outbred mice). We show that a range of inbred and outbred PSC lines can be stably maintained in the primed pluripotent state (epiblast stem cells) and establish the contribution of genetic variation to phenotypic differences in gene regulation and directed differentiation. Using pooled in vitro fertilization, we generate and characterize a genetic reference panel of Diversity Outbred PSCs (n = 250). Finally, we demonstrate the feasibility of pooled culture of genetically diverse PSCs as “cell villages”, which can facilitate the differentiation of large numbers for forward genetic screens. These data can complement and inform similar efforts within the stem cell biology and human genetics communities to model the impact of natural genetic variation on phenotypic variation and disease-risk.

overall_design: We converted embryonic stem cells (ESCs) from the 7 of the 8 Diversity Outbred founder strains (129S1/SvImJ, C57BL/6J, NOD/ShiLtJ, NZO/HiLtJ, CAST/EiJ, PWK/PhJ, WSB/EiJ) to epiblast stem cells (EpiSCs) and collected them for ATAC-sequencing at low passage.  We then performed directed differentiation to definitive endoderm (DE) from these cells.  Following 40 hours of differentiation, cells were collected and sorted using magnetic activated cell sorting (MACS) to perform ATAC-sequencing on the CXCR4-positive population.

first: Rachel

last: Glenn

first: Thomas

last: Vierbuchen

first: Ragavi

last: Vijayakumar