title: Molecular and cellular characterization of planarian stem cell microenvironments

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: A Slide-seqV2 atlas of intact and regenerating tail fragments at 6 hours and 48 hours post amputation (hpa). Intact 8 mm animals were removed from recirculation culture and 1.25 mm biopsy punches were used to amputate tail fragments. Regenerating tail fragments were embedded in OCT around an intact 2-3 mm worm, sectioned, and 2 adjacent sections were processed using the Slide-seqV2 protocol (Stickels et al. Nature Biotechnology 2021). Captured mRNA was sequenced on an Illumina platform. RNA-seq of cells positive and negative for matrix metalloproteinase-1 (mmp-1) mRNA.

overall_design: For each timepoint 8-9 tail fragments were arrayed around a single intact animal in OCT prior to freezing. Tissue sections were slowly removed from the block until reaching the middle of the worm fragments. Two adjacent sections were then cut and laid onto Slide-seqV2 pucks for mRNA capture and library preparation. Each puck resulted in one library, resulting in 4 total libraries that were pooled and sequenced on 2 NextSeq flow cells. Mmp-1 positive cells were identified by performing HCRv3 on fixed cells dissociated from planarians at three timepoints: intact worms, as well as 6 and 48 hours post amputation. Positive cells were sorted by flow cytometry for library construction and sequencing.

first: Blair

middle: W

last: Benham-Pyle

first: Frederick

middle: G

last: Mann Jr.

first: Alejandro

last: Sánchez Alvarado


title: PRDM16 controls smooth muscle cell fate in atherosclerosis: Fixed-cell scRNAseq datasets [scRNA-seq]

status: Public on Aug 28 2025

city: Philadelphia

first: Ryan

middle: Patrick

last: Calhoun

state: PA

address: 3400 Civic Center Boulevard

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: Vascular smooth muscle cells (SMCs) normally exist in a contractile state but can undergo fate switching to produce a variety of cell phenotypes in response to pathologic stimuli. In atherosclerosis, these phenotypically modulated SMCs play a critical role in determining plaque composition and the risk of major adverse cardiovascular events. We found that PRDM16, a transcription factor that has been genetically implicated in cardiovascular disease, is highly expressed in arterial SMCs, and downregulated during SMC fate switching in human and mouse atherosclerosis. Deletion of Prdm16 in SMCs of mice activates the synthetic modulation program in arteries under homeostatic conditions. Upon exposure to atherogenic conditions, these mice form strikingly dense, SMC-rich, fibroproliferative plaques that contain few foam cells. Acute deletion of Prdm16 in SMCs triggers a similar fibrotic response, resulting in the formation of collagen-rich lesions with thick fibrous caps – a hallmark of enhanced lesion stability. Reciprocally, ectopic expression of PRDM16 in cultured cells is sufficient to block SMC synthetic processes, including migration, proliferation, and fibrosis. Mechanistically, PRDM16 binds to chromatin and decreases activating histone marks at synthetic genes. Altogether, our results define PRDM16 as a specific gatekeeper of the synthetic SMC switch and reveal that PRDM16 levels in SMCs predetermine atherogenic lesion composition.

overall_design: All mice for this study were male of the C57BL6/J background. The Prdm16 floxed mouse line was bred with Tagln Cre or Myh11 CreER. Floxed animals without Cre were used as controls. Animals were raised at room temperature on standard chow (LabDiet, 5010) with a 12-h light–dark cycle at room temperature (22 °C) unless specified otherwise. For atherosclerosis experiments, mice were placed at thermoneutrality (30 °C) at weaning (21 days old) and kept at thermoneutrality until the end of the experiment. For iKO studies, tamoxifen (Sigma, T5648; stock 20 mg/mL in corn oil) was injected intraperitoneally at a dose of 100 mg/kg for 4 consecutive days.

first: Josephine

last: Tan

middle: P

first: Patrick

last: Seale


title: PRDM16 controls smooth muscle cell fate in atherosclerosis [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: All mice for this study were male C57BL6/J WT mice obtained from Jackson Laboratory. Animals were raised at room temperature on standard chow (LabDiet, 5010) with a 12-h light–dark cycle at room temperature (22 °C). 12 mice were pooled and divided over the three ChIPs

first: Angela

last: Weller


title: PRDM16 controls smooth muscle cell fate in atherosclerosis [RNA-Seq]


title: Targeting RhoA nuclear mechanoactivity rejuvenates aged hematopoietic stem cells [bulk RNA-seq]

status: Public on Aug 29 2025

city: Hospitalet de Llobregat

first: Maria Carolina

last: Florian

state: Barcelona

address: Gran Via de l’Hospitalet, 199

department: Regenerative Medicine

country: Spain

institute: Bellvitge Biomedical Research Institute (IDIBELL)

summary: Biomechanical alterations contribute to the decreased regenerative capacity of hematopoietic stem cells (HSCs) upon aging. RhoA is a key regulator of mechanosignaling, but its role in mechanotransduction in stem cell aging remains unclear. Here we show that murine HSCs respond to increased nuclear envelope (NE) tension by inducing NE translocation of P-cPLA2, which cell-intrinsically activates RhoA. Aged HSCs experience physiologically higher intrinsic NE tension, but reducing RhoA activity lowers NE tension in aged HSCs. Feature image analysis of HSC nuclei reveals that chromatin remodeling is associated with RhoA inhibition, including restoration of youthful levels of the heterochromatin marker H3K9me2 and a decrease in chromatin accessibility and transcription at retrotransposons. Finally, we demonstrate that RhoA inhibition upregulates Klf4 expression and transcriptional activity, improving aged HSC regenerative capacity and lympho/myeloid skewing in vivo. Together, our data outline an intrinsic RhoA-dependent mechanosignaling axis, which can be pharmacologically targeted to restore aged stem cell function.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data from young, aged and aged treated with RhoA-inhibitor (Ri) LT-HSCs. For each condition, 3 biological replicates were performed. LT-HSCs were sorted from bone marrow cells as Lin- Sca1+ cKit+ CD34- Flt3-.

first: Eva

middle: M

last: Mejía-Ramírez

first: Sara

last: Montserrat-Vazquez

first: Maria

middle: C


title: Spatial Proximity Sequencing Maps Developmental Dynamics in the Germinal Center

city: Chicago

first: Junjie

last: Xia

state: IL

address: 10th floor of KCBD, 900 E. 57th Street

department: Chemistry

institute: University of Chicago

summary: Spatial profiling of proteins and protein interactions with mRNAs is essential for studies understanding cellular signaling. However, technologies capable of integrating these modalities remain limited. Here, we present Spatial Proximity-Sequencing (Sprox-seq), a method that combines proximity ligation assay with spatial transcriptomics to simultaneously profile mRNAs, surface proteins, and their interactions in intact tissues. Applied to human tonsil tissue, Sprox-seq profiled 32 proteins and their   pairwise interactions alongside thousands of mRNAs. We developed a robust computational framework for analyzing protein proximity data, enabling both the statistical identification and interaction strength measurements of protein complexes. Clustering based on protein interaction strength recapitulated RNA-defined tissue architecture. Interaction networks constructed from protein complexes revealed significantly higher interaction complexity in Light zone. Trajectory inference based on protein interaction strength uncovered a maturation path distinct from that inferred by RNA data, and spatially enriched protein complexes were associated with functional gene-expression pathways. Moreover, Sprox-seq also captured cell–cell interactions mediated by protein complex ITGA4–VCAM1 in Light zone. Overall, Sprox-seq provides a spatially resolved, multi-modal view of cell states, offering a powerful tool for studying immune responses, tissue development, and disease progression.

overall_design: The assay was performed on fresh-frozen human tonsil tissue sections, including three biological replicates: two spatially distinct regions from the same donor (samples A1 and B1) and one section from a different donor (sample D1) and analyzed using Spatial Proximity-Sequencing (Sprox-seq) by combing proximity ligation assay with spatial transcriptomics to simultaneously profile mRNAs, surface proteins, and their interactions in intact tissues.

first: Huili

last: Wang

first: Peer Mohamed Suhail Mujibur

last: Rahman

first: Bijentimala

last: Keisham

first: Abinash

last: Padhi

first: Yiyu

last: Deng

first: Luke

last: Vistain

first: Sarh

last: Kim

first: Jose Gabriel Mercado

last: Vasquez

first: Aly

middle: A

last: Khan

first: Marcus

middle: R

last: Clark

first: Savas

last: Tay


title: Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [Foxp3-AID-14D RNA-seq]

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

institute: Princeton

summary: Regulatory T (Treg) cells, characterized by expression of the lineage-defining transcription factor Foxp3, are critical gatekeepers of immune homeostasis. While Foxp3’s essential role in Treg cell development is well established, the precise mechanisms by which Foxp3 governs the Treg-specific transcriptional network remain incompletely understood. Here, we employed a novel chemogenetic model that enables inducible, time-controlled degradation of Foxp3 protein in vivo to dissect its stage-specific functions. We show that Foxp3 is indispensable for the establishment of the Treg transcriptional program and the acquisition of suppressive function during thymic differentiation and in newly generated peripheral Treg cells. In contrast, degradation of Foxp3 in fully differentiated, mature Treg cells resulted in surprisingly minimal transcriptional changes and largely preserved suppressive capacity, affecting only a small subset of genes highly enriched for direct Foxp3 targets. Strikingly, intratumoral Treg cells were uniquely sensitive to Foxp3 loss, leading to impaired suppressive function and enhanced tumor rejection. These findings uncover a differential, context-dependent requirement for Foxp3 across Treg cell ontogeny, highlighting a distinct, largely indirect mechanism by which Foxp3 establishes — and to a more limited extent maintains — Treg identity and function.

overall_design: Here we sought to investigate the role of Foxp3 during Treg cell differentiation, maintenance, and turnover using a novel chemogenetic model, which enabled punctual inducible degradation of Foxp3 protein in vivo.

first: Wei

last: Hu

first: Gabriel

last: Dolsten

first: Giorgi

last: Beroshvili

first: Eric

middle: Y

first: Zhong-Min

first: Aazam

last: Ghelani

first: Lion

middle: F

last: Uhl

first: Regina

middle: B

last: Puerto

first: Xiao

last: Huang

first: Anthony

middle: J

last: Michaels

first: Beatrice

middle: E

last: Hoyos

first: Wenjie

last: Jin

first: Alexander

last: Rudensky


title: Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs [CUT&RUN]

city: Warsaw

first: Monika

last: Dzwigonska

address: 3 Pasteur Street

country: Poland

institute: Nencki Institute of Experimental Biology, PAS

summary: Hypoxia rapidly alters gene expression to allow cellular adaptation to challenging conditions and support tumour growth. Hypoxia also affects the chromatin structure by modifications of histones and DNA methylation. Glioblastoma (GBM) is an aggressive, deadly primary brain tumour for which there is no effective treatment. The tumour microenvironment of GBM is highly heterogeneous, with infiltration of glioma-associated microglia and macrophages (GAMs) and the presence of necrotic, hypoxic regions. The mechanisms through which hypoxia alters the tumour microenvironment and regulates functions of infiltrating immune cells remain poorly understood. Here, we show that hypoxia modulates the expression of myeloid markers in distinct ways: upregulates the monocytic marker Lgals3 expression and downregulates the microglial markers P2ry12 and Tmem119 in microglial and monocytic GAMs in vitro and in vivo, as shown using human and mouse GBM single-cell transcriptomics datasets. The genome-wide hypoxia-dependent transcriptomic changes in microglial cells were determined in microglia-glioma co-cultures. Numerous GAM subtype markers were dysregulated in response to hypoxic stress due to associated changes in chromatin accessibility, as determined using ATACseq. While hypoxia alone drives a decrease of the overall chromatin accessibility at gene promoters, the exposure to glioma cells under hypoxic conditions leads to both increases and decreases of chromatin accessibility at promoter regions in microglial cells. Hypoxia downregulates the chromatin accessibility at the regions enriched in motifs of transcription factors regarded as master regulators of microglial cell identity and function, including SPI1 or IRF8. Moreover, changes in histone acetylation are responsible for Lgals3 upregulation and lipid accumulation in GAMs in hypoxic conditions. Overall, our data highlights the importance of hypoxic stress as a strong intratumoral regulator of myeloid cell functions, which adds complexity to the characterisation of particular GAMs subpopulations.

overall_design: We performed CUT&RUN assays to profile H3K27ac in BV2 cells cultured under hypoxic conditions, either in monoculture or in co-culture with glioma cells (GL261), and compared them to cells maintained under normoxia.

first: Jakub

last: Mieczkowski

first: Katarzyna

last: Leszczynska


title: Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [transfer organ scRNA-seq]

first: Yuri

overall_design: Transfer: For transfer into Tcrbd KO mice, 4 x 106 cells from the Treg + Tconv pool (1 x 106 ROSA26WT, 1 x 106 ROSA26TIR1(F74G), 2 x 106 Tconv) were injected retro-orbitally in 200 μL of sterile PBS (4 mice total). For continuous endogenous Treg depletion, Foxp3DTRCD45.1 were injected i.p. with 1000 ng of DT in 200 μL sterile PBS on day -1 and day 0 followed by 500 ng on day 3 and day 6. Continuous Foxp3 degradation was maintained by daily 5-ph-IAA injections as described above. On day 7, animals were sacrificed. Cross-tissue organ: Foxp3AID/+ROSA26WT and Foxp3AID/+ROSA26TIR1(F74G) mice were treated with 5-ph-IAA for 7 days (4 per group). For each genotype, cells from individual mice and tissue were stained with a unique hashtag antibody. Tregs from SLOs, lung, liver, and LILP were harvested and digested as described in the Methods.

last: Wang


title: Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs

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

overall_design: Refer to individual Series


title: Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [RNA-seq]

first: Wei


title: Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [scRNA-seq]

first: Gabriel


title: Molecular and developmental deficits in Smith-Magenis syndrome human stem cell-derived cortical neural models

city: Montreal

first: Alain

last: Pacis

state: QC

address: 1010 Sherbrooke #1800

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary: Smith-Magenis syndrome (SMS) is a genomic disorder caused by the deletion of a chromosomal region at 17p11.2. Individuals with SMS are frequently diagnosed with autism and have profound cortical deficits, including reduced cortex volume, mild ventriculomegaly, and epilepsy. Here, we developed human induced pluripotent stem cell (hiPSC)-derived neuronal models to understand how del(17)p11.2 affects cortical development. Hi-C identified local fusion and global reorganization of topological domains, as well as genome-wide miswiring of chromatin 3-dimensional (3D) interactions in SMS hiPSC and 3D cortical organoids. Single-nucleus RNA-seq of SMS cortical organoids identified neuropsychiatric disease-enriched transcriptional signatures and dysregulation of genes involved in catabolic and biosynthetic pathways, cell cycle processes, and neuronal signalling. SMS cortical organoids had reduced growth, enlarged ventricles, and impaired cell cycle progression. In a complementary hiPSC-derived 2D cortical neuronal model, we found SMS cortical neurons had accelerated dendritic growth, followed by neuronal hyperexcitability that was associated with a reduced potassium conductance. Our study demonstrates that del(17)p11.2 disrupts multiple steps of human cortical development, from chromatin wiring, transcriptional regulation, cell cycle progression, and morphological maturation to neurophysiological properties, and hiPSC-derived models recapitulate key neuroanatomical and neurophysiological features of SMS.

overall_design: Nuclei from day-75 cortical organoids (3 control libraries Ctrl 1-3 and 3 SMS libraries SMS 1-3, n=5 organoids per library) were isolated using the Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec), following the manufacturer’s guidelines with gentle MACS Dissociation and C tubes. Nuclei were prepared from samples for snRNA-seq analysis.

first: Yu-Ju

last: Lee

first: Senthilkumar

last: Kailasam

first: Wei-Hsiang


title: Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance [ATAC_bulk_adult]

last: Pritykin

last: Hu

last: Dolsten

first: Giorgi

first: Eric

first: Zhong-Min

first: Aazam

first: Lion


title: Temporal and Context-Dependent Requirements for the Transcription Factor Foxp3 in Regulatory T Cell Development and Maintenance


title: Effects of stress of the endoplasmic reticulum on gene expression in the bovine liver cell model BHF12

status: Public on Aug 27 2025

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

summary: Previous studies have demonstrated that high-yielding dairy cows experience endoplasmic reticulum (ER) stress in the liver during early lactation. To date, most insights into the role of ER stress in metabolism and disease pathophysiology have been derived from rodent and human models. In dairy cattle, however, the specific impact of ER stress on metabolic pathways and its contribution to disease development remain insufficiently characterized. The objective of this study was therefore to investigate the molecular effects of ER stress using a bovine liver cell model (BHF12 cells). ER stress was induced by incubation with Tunicamycin (TM) and Thapsigargin (TG). Molecular responses to ER stress were assessed via whole-genome array analysis and PCR targeting genes involved in selected metabolic pathways. Incubation with both ER stress inducers resulted in a marked upregulation of genes associated with the unfolded protein response within a 4 to 24-hour time frame. Unexpectedly, treatment with TM led to a downregulation of numerous genes involved in lipid biosynthesis, including those related to lipogenesis and cholesterol synthesis. Furthermore, incubation with TM and TG induced upregulation of genes involved in fatty acid oxidation and was accompanied by a reduction in intracellular triglyceride concentrations. Genes associated with inflammatory responses were upregulated by both TM and TG, whereas genes encoding antioxidant enzymes were downregulated. Genes involved in ketogenesis remained unchanged. Overall, several effects of ER stress previously described in rodent models could not be replicated in this bovine liver cell system. Extrapolating these findings to dairy cows suggests that while ER stress may contribute to hepatic inflammation, it is unlikely to play a significant role in the development of hepatic lipidosis or ketosis.

first: Eron

last: Bajrami

first: Gaiping

last: Wen

first: Denise

middle: K

last: Gessner

first: Klaus

last: Eder


title: Discovery and AI-guided mechanistic elucidation of a novel Enterobacteriaceae-specific antibiotic

city: Hamilton

middle: Buquiran

last: Catacutan

state: Ontario

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

institute: McMaster University

summary: Current clinical antibiotics are largely broad-spectrum agents that promote intestinal dysbiosis and colonisation of Enterobacteriaceae, which are often drug-resistant. Indeed, dysbiosis creates an ideal niche for adherent-invasive Escherichia coli (AIEC) in patients with inflammatory bowel disease (IBD). There is an urgent and unmet need for novel narrow-spectrum and microbiome-sparing antibiotics. Here, we screened >10,000 molecules for antibacterial activity against AIEC and discovered enterololin, an antibacterial compound with targeted activity against Enterobacteriaceae species. Molecular substructure- and deep learning-guided mechanism of action investigations revealed that enterololin perturbs lipoprotein trafficking through a mechanism involving the LolCDE complex. Moreover, enterololin can suppress an AIEC infection in mouse models, while largely preserving the overall microbiome composition. This work highlights the utility of deep learning methods for predicting molecular interactions, thereby accelerating mechanism of action elucidation of novel molecules, and identifies a promising Enterobacteriaceae-specific antibacterial candidate for further development to treat challenging infections in IBD patients.

overall_design: RNA-seq profiling of E. coli BW25113 ∆bamB∆tolC (DKO) cells diluted 1:10,000 into 50 ml fresh LB and grown to mid-log (~107 CFU ml-1) at 37°C with shaking at 200 RPM, at which time cultures were supplemented with 5× MIC enterololin or no drug and grown for an additional 2 h or 4 h

first: Vian

last: Tran

first: Autumn

last: Arnold

first: Jeremie

last: Alexander

first: Gabriele

last: Corso

first: Yeganeh

last: Yousefi

first: Megan

last: Tu

first: Stewart

last: McLellan

first: Dominique

last: Tertigas

first: Jakob

last: Magolan

first: Michael

last: Surette

middle: D

last: Brown

first: Brian

last: Coombes

first: Regina

last: Barzilay

first: Jonathan

last: Stokes


title: The astrocytic ensemble is a multiday eligibility trace stabilizing memory

city: Wako

first: Jun

last: Nagai

state: Saitama

address: 2-1 Hirosawa

department: Center for Brain Science

country: Japan

institute: RIKEN

summary: Recalled memories become transiently labile and require stabilization. The mechanism for specifically stabilizing memories of critical experiences essential for survival, which are often emotionally salient and repeated, remains unclear. Here, we identified an astrocytic ensemble that is transcriptionally primed by emotional experience and functionally triggered by repeated experience to stabilize labile memory. Using our novel brain-wide Fos tagging and imaging method, we found that astrocytic Fos ensembles were preferentially recruited in regions with neuronal engrams and were more widespread during fear recall than conditioning. We established the induction mechanism of the astrocytic ensemble, which involves two steps: (i) an initial fear experience inducing day-long, slow astrocytic state changes with noradrenaline (NA) receptor upregulation, and (ii) enhanced NA responses during recall, a repeated experience, enabling astrocytes to integrate coincident signals from local engrams and long-range NA projections, inducing secondary astrocytic state changes, including the upregulation of Fos and the neuromodulatory molecule Igfbp2. Pharmacological and genetic perturbation of the astrocytic ensemble signaling modulate engrams, and memory stability and precision. The astrocytic ensemble therefore is as a multiday trace left in a subset of astrocytes after experience-dependent neural activity, making them eligible to capture future repeated experiences for stabilizing memories.

overall_design: To explore how molecular changes in astrocytes under fear learning and recall may arise, we subjected mice to NoFC, FC, NoFR or FR conditions, freshly dissected the amygdala tissue 90 min after behavioral tests, and then FACS-isolated astrocytes based on astrocyte cell surface antigen-2 (ACSA-2) targeting ATP1B2 (ATPase Na+/K+ transporting subunit b 2), from which we performed single cell RNA sequencing (scRNA-seq) analyses.

first: Ken

middle: I

last: Dewa

first: Kodai

last: Kaseda

first: Aoi

last: Kuwahara

first: Hideaki

last: Kubotera

first: Ayato

last: Yamasaki

first: Natsumi

last: Awata

first: Atsuko

last: Komori

first: Mika

last: Holtz

first: Atsushi

last: Kasai

first: Henrik

last: Skibbe

first: Norio

last: Takata

first: Tatsushi

last: Yokoyama

first: Makoto

last: Tsuda

first: Genri

last: Numata

first: Shun

last: Nakamura

first: Eiki

last: Takimoto

first: Masayuki

last: Sakamoto

first: Minako

last: Ito

first: Takahiro

last: Masuda


title: Effect of Activated Vitamin D on Acute Kidney Injury in Critically Ill Patients

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

summary: Active vitamin D metabolites, including 25-hydroxyvitamin D (25D) and 1,25-dihydroxyvitamin D (1,25D), have potent immunomodulatory effects and attenuate acute kidney injury (AKI) in animal models. We conducted an NIH-funded, phase 2, randomized, double-blind, multiple-dose, 3-arm clinical trial comparing oral calcifediol (25D), calcitriol (1,25D), and placebo among critically ill adult patients at high-risk of moderate-to-severe AKI. The primary end point was a hierarchical composite of death, kidney replacement therapy, and kidney injury (baseline-adjusted mean change in serum creatinine), each assessed within 7 days following enrollment using a rank-based procedure. We also performed transcriptomic analyses on circulating CD14+ monocytes collected immediately prior to randomization and two days later using RNA sequencing. The global rank score for the primary end point was similar among calcifediol vs. placebo treated patients (P=0.85) and for calcitriol vs. placebo-treated patients (P=0.58). Calcitriol upregulated more individual genes and pathways in circulating monocytes than did calcifediol, including pathways involving interferon (IFN)-alpha, IFN-gamma, oxidative phosphorylation, DNA repair, and heme metabolism. In summary, treatment with calcifediol or calcitriol in critically ill adults did not attenuate AKI, but calcitriol upregulated multiple genes and pathways involving immunomodulation, DNA repair, and heme metabolism.

overall_design: RNAseq on CD14+ monocytes, 2 time points(immediately prior to randomization; two days after treatment initiation), 3-arim design (oral calcifediol, n=51; oral calcitriol, n=50; placebo control, n=49),  randomized, double-blinded,

first: Edy

last: Kim

first: Tomoyoshi

last: Tamura


title: Coxsackievirus B infection invokes unique cell-type-specific responses in primary human pancreatic islets

city: St. Louis

first: Daniel

middle: Andre

last: Veronese-Paniagua

state: Missouri

address: 660 South Euclid Avenue

institute: Washington University in St. Louis

summary: Coxsackievirus B (CVB) infection has long been considered an environmental factor precipitating Type 1 diabetes (T1D), an autoimmune disease marked by loss of insulin-producing b cells within pancreatic islets. Previous studies have shown CVB infection negatively impacts islet function and viability but do not report on how virus infection individually affects the multiple cell types present in human primary islets. Therefore, we hypothesized that the various islet cell populations have unique transcriptional responses to CVB infection. Here, we performed single-cell RNA sequencing on human cadaveric islets treated with either CVB or poly(I:C), a viral mimic, for 24 and 48 hours. Our global analysis reveals CVB differentially induces dynamic transcriptional changes associated with multiple cell processes and functions over time whereas poly(I:C) promotes an immune response that progressively increases with treatment duration. At the single-cell resolution, we find CVB infects all islet cell types at similar rates yet induces unique cell-type specific transcriptional responses with b, a, and ductal cells having the strongest response. Sequencing and functional data suggest that CVB negatively impacts mitochondrial respiration and morphology in distinct ways in b and a cells, while also promoting the generation of reactive oxygen species. We also observe an increase in the expression of the long-noncoding RNA MIR7-3HG in b cells with high viral titers and reveal its knockdown reduces gene expression of viral proteins as well as apoptosis in stem cell-derived islets. Together, these findings demonstrate a cell-specific transcriptional, temporal, and functional response to CVB infection and provide new insights into the relationship between CVB infection and T1D.

overall_design: Cadaveric islets from four donors were treated with either poly(I:C) or GFP-tagged coxsackievirus B3 for 24 hr and 48 hr. Endotoxin-free water served as a negative control. Cells from patients 1-3 were multiplexed for single-cell RNA sequencing. Cells from patient 4 were processed indepedently for single-cell RNA sequencing.

first: Marlie

last: Maestas

first: Diana

last: Hernandez-Rincon

first: Kate

last: Hinshaw

first: Matthew

last: Ishahak

first: Jared

last: Taylor

first: Hubert

last: Tse

first: Jeffrey

last: Millman


first: Senthilkumar

last: Kailasam

state: Quebec

address: 740 Dr. Penfield Avenue, #4200

department: Human Genetics

institute: McGill University

overall_design: The study involved the derivation and maintenance of eight human induced pluripotent stem cell (hiPSC) lines—four from healthy individuals and four from Smith-Magenis syndrome (SMS) patients carrying the del(17)p11.2 deletion. hiPSCs were cultured under feeder-free conditions and validated for pluripotency and genomic integrity. Three-dimensional cortical organoids were generated from each of these lines using the AggreWell system and patterned with STEMdiff media. Organoids were cultured through staged differentiation protocols to promote cortical identity and maintained long-term in maturation media. The experimental design enabled comparative analyses of control and SMS cortical development models.

first: Yu-Ju

last: Lee

first: Ya-Ting

last: Chang

first: Yoobin

last: Cho

first: Adrian

last: Dragoiescu

first: Max

last: Kowalczyk

first: Alain

last: Pacis

first: François

last: Lefebvre

first: Qihuang

last: Zhang

first: Xiaojing

last: Gao

first: Wei-Hsiang

last: Huang


title: Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs [ATAC-seq]

first: Monika

last: Dzwigonska

summary: Hypoxia rapidly alters gene expression to allow cellular adaptation to challenging conditions and support tumour growth. Hypoxia also affects the chromatin structure by modifications of histones and DNA methylation. Glioblastoma (GBM) is an aggressive, deadly primary brain tumour for which there is no effective treatment. The tumour microenvironment of GBM is highly heterogeneous, with infiltration of glioma-associated microglia and macrophages (GAMs) and the presence of necrotic, hypoxic regions. The mechanisms through which hypoxia alters the tumour microenvironment and regulates functions of infiltrating immune cells remain poorly understood. Here, we show that hypoxia modulates the expression of myeloid markers in distinct ways: upregulates the monocytic marker Lgals3 expression and downregulates the microglial markers P2ry12 and Tmem119 in microglial and monocytic GAMs in vitro and in vivo, as shown using human and mouse GBM single-cell transcriptomics datasets. The genome-wide hypoxia-dependent transcriptomic changes in microglial cells were determined in microglia-glioma co-cultures. Numerous GAM subtype markers were dysregulated in response to hypoxic stress due to associated changes in chromatin accessibility, as determined using ATACseq. While hypoxia alone drives a decrease of the overall chromatin accessibility at gene promoters, the exposure to glioma cells under hypoxic conditions leads to both increases and decreases of chromatin accessibility at promoter regions in microglial cells. Hypoxia downregulates the chromatin accessibility at the regions enriched in motifs of transcription factors regarded as master regulators of microglial cell identity and function, including SPI1 or IRF8. Overall, our data highlights the importance of hypoxic stress as a strong intratumoral regulator of myeloid cell functions, which adds complexity to the characterisation of particular GAMs subpopulations.

overall_design: We preformed gene expression profiling with RNAseq in mouse microglia cell line (BV2) or in glioma cell line (GL261) in hypoxic co-culture or in hypoxic monocultures compare to normoxia condition. In addition, for BV2 cells chromatin accessibility with ATACseq was carried out.

first: Jakub

last: Mieczkowski

first: Katarzyna

last: Leszczynska


title: A Role for the Transcriptional Coregulator RIP140 in the Control of Muscle Endurance Fitness [RNASeq_MyogeninCre_flat]

first: Daniel

last: Kelly

address: 3400 Civic Center Blvd

department: Penn Cardiovascular Institute

summary: Poor skeletal muscle fitness contributes to many chronic disease states including obesity, heart failure, primary muscle disorders, and age-related sarcopenia. Receptor Interacting Protein 140 (RIP140) is a striated muscle-enriched nuclear receptor co-regulator. To investigate the role of RIP140 in skeletal muscle, striated muscle-specific RIP140-deficient (strNrip1-/-) mice were generated and characterized. strNrip1-/- mice display a remarkable endurance performance phenotype based on endurance treadmill performance, VO2max testing, and functional assessment of isolated muscle. RNA-sequence analysis of glycolytic fast-twitch muscle from the strNrip1-/- mice identified a broad array of differentially upregulated metabolic and structural muscle genes involved in muscle endurance fitness pathways including mitochondrial biogenesis and respiration, fatty acid oxidation, triglyceride dynamics, muscle fiber type, angiogenesis, and neuromuscular junction (NMJ) remodeling. Assessment of the structural correlates of these processes confirmed the function of RIP140 as placing a “brake” on the transcriptional network controlling these key muscle endurance fitness processes. Integration of the RNA sequence results with CUT&RUN analysis of strNrip1-/- myotubes identified direct RIP140 targets including genes involved in fatty acid metabolism and NMJ biogenesis. We conclude that RIP140 serves as a physiological “rheostat” for a broad network of genes involved in skeletal muscle fitness.

overall_design: RNA-seq profiling of WT control and skmNrip1-/- mouse tibialus anterior (TA) muscle in male mice 8 weeks of age.

first: Elizabeth

last: Pruzinsky

first: Kirill

last: Batmanov

first: Denise

last: Medeiros

first: Tomoya

last: Sakamoto

first: Teresa

last: Leone

first: Tejvir

last: Khurana


title: A Role for the Transcriptional Coregulator RIP140 in the Control of Muscle Endurance Fitness [RNASeq_Training_strKO_flat]

overall_design: RNA-seq profiling of EDL muscle collected from sedentary WT control mice, sedentary strNrip1-/- mice, trained WT control mice, and trained strNrip1-/- mice. Male mice were subjected to sedentary conditions or voluntary wheel training at 8 weeks of age.


title: Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs [RNA-seq]


title: Mosquito salivary sialokinin reduces human primary monocyte activation

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Mosquito saliva contains bioactive factors that enhance viral infection, with sialokinin identified as a key contributor to vascular leakage and viral spread in mice. Understanding effect of sialokinin on human moncoytes, the most important innate cells that responsible for the viral-induced inflammatory, will provide important insight to host-virus-vector interaction in arbovirus infection.

overall_design: Freshly purified human monocytes (1,000,000 cells/well) were incubated with or without sialokinin peptides in complete IMDM supplemented with 10% (vol/vol) HS (Sigma-Aldrich) and 1% (vol/vol) penicillin-streptomycin. Untreated monocytes served as no-treatment controls. Total RNA was isolated from primary human monocytes using a RNeasy Micro Kit (Qiagen), following the manufacturer's instructions.

first: Siew-Wai

last: Fong

first: Jeslin J.L.

last: Tan

first: Vaishnavi

last: Sridhar

first: Siti Naqiah

last: Amrun

first: Vanessa K.X.

last: Neo

first: Nathan

last: Wong

first: Yi-Hao

last: Chan

first: Anthony

last: Torres-Ruesta

first: Liang Hui

last: Loo

first: Anna X.Y.

first: Rhonda S.L.

last: Chee

first: Tze-Kwang

last: Chua

first: Angeline

last: Rouers

first: Guillaume

last: Carissimo

first: Fok-Moon

last: Lum

first: Yee-Sin

last: Leo

first: Laurent

last: Renia

first: R. Manjunatha

last: Kini

first: Lisa F.P.

last: Ng


title: Sperm production is comprised in mice exposed to environmentally relevant per- and polyfluoroalkyl substances (PFAS)

status: Public on Aug 31 2025

first: Natalie

middle: Alyce

last: Trigg

state: Pennsylvania

address: 421 Curie Blvd

institute: Children's Hospital of Philadelphia

type: Non-coding RNA profiling by high throughput sequencing

summary: Per- and polyfluoroalkyl substances (PFAS) are a large group of persistent synthetic chemicals that are ubiquitous environmental contaminants. Mounting evidence demonstrates that PFAS can bioaccumulate and induce a suite of adverse health outcomes, including compromise of male reproduction. Despite this knowledge, there remains no clear consensus as to how PFAS elicit these responses. Accordingly, here we aimed to determine how an environmentally relevant cocktail of PFAS impact the fertility of male mice. After twelve weeks of continuous PFAS exposure, blood plasma was isolated for hormone and PFAS profiling and reproductive tissues and spermatozoa were subjected to a comprehensive battery of histological and functional analyses. These analyses revealed that PFAS exposure significantly reduced the rate of daily sperm production linked with reduced levels of circulating testosterone and dihydrotestosterone. Functional profiling of mature spermatozoa from PFAS exposed males failed to identify any overt changes in sperm viability, motility, DNA integrity, or ability to undergo capacitation and support in vitro fertilization and early embryonic development. PFAS exposed spermatozoa did, however, present with pronounced changes in their small non-coding RNA profile and were linked with significant dysregulation of early embryonic gene expression. These observations afford new mechanistic insight into how PFAS exposure impacts male reproductive health.

overall_design: Male mice were exposed to a cocktail of PFAS chemicals for 12 weeks at two different doses (low and high). Following exposure, mice were euthanized and sperm was isolated from the cauda epididymis. Preparations of sperm were either snap frozen for subsequent small RNA-sequenicng or used as donors to fertilize eggs from control females to collect developmentall staged embryos (4-cell stage) for embryo RNA-sequencing.

first: Leah

last: Gillespie

first: Jacinta

middle: H

last: Martin

first: Amanda

middle: L

last: Anderson

first: Ilana

last: Bernstein

first: Simone

last: Stanger

first: John

last: Schjenken

first: Shanu

last: Parameswaran

first: Shannon

last: Smyth

first: Colin

last: Conine

first: Reena

last: Desai

first: David

last: Handelsman

first: Geoffry

middle: N

last: De Iuliis

first: Andrew

last: Eamens

first: Matthew

last: Dun

first: Brett

last: Turner

first: Shaun

last: Roman

first: Mark

last: Green

last: Nixon


title: A Role for the Transcriptional Coregulator RIP140 in the Control of Muscle Endurance Fitness

first: Daniel

last: Kelly


title: Pooled CRISPR screens identifies key regulators of bovine stem cell expansion for cultured meat [RNA-Seq]

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

summary: Cultured meat offers a promising solution to the environmental and ethical challenges of conventional meat production, but faces significant hurdles in scalability and cost-effectiveness. A major bottleneck is the limited proliferation capacity of cell sources such as bovine mesenchymal stem cells (bMSCs). Here, we employ CRISPR knockout screening to identify several key genes and pathways influencing bMSC proliferation. Notably, TP53 and PTEN knockouts emerged as top hits in our pooled CRISPR screen, exhibiting the highest increase in cell abundance over 30 days compared to all other gene knockouts. Subsequent validation using individual knockouts confirmed that both TP53 and PTEN deletion significantly enhanced bMSC proliferation rates relative to non-targeting sgRNA controls. We also identified targets in mitochondrial pyruvate carrier and SMAD signaling pathways that may improve MSC proliferation and differentiation. These findings demonstrate CRISPR technology's potential to enhance stem cell growth for more efficient, cost-effective, and scalable cultured meat production.

overall_design:
To investigate the role of various genes in regulating MSC proliferation  , we established a pooled CRISPR knockout library population targeting 600 genes in adipose-derived bovine MSCs.
We then performed gene expression profiling analysis using data obtained from RNA-seq of three MSCs populations at two time points.
Comparative gene expression profiling analysis of RNA-seq data for CRISPR-Library-KO MSC cells at day 125 compared to early WT at day 25 or late WT at day 125 with three replicated for each.

first: Amit

last: Zirman

first: Mamoun

last: Abed-El Nabi

first: Ella

last: Samuel

first: Zohar

last: Yakhini

first: Leon

last: Anavy

first: Iftach

last: Nachman


title: Pooled CRISPR screens identifies key regulators of bovine stem cell expansion for cultured meat [Short-Term screen]

overall_design:
To investigate genes regulating MSC proliferation, we established a pooled CRISPR knockout library targeting 600 genes in adipose-derived bovine MSCs.
We conducted proliferation screens by expanding the pooled cell population for 30 or 200 days, extracting DNA and PCR-amplifying sgRNA sequences at various time points.
Using MAGeCK, we identified and ranked significantly enriched or depleted sgRNAs over time, inferring which gene knockouts alter proliferation in AD-bMSCs.
We performed Gene Ontology over-representation analysis to identify enriched GO terms associated with increased or decreased proliferation in bMSCs.


title: Pooled CRISPR screens identifies key regulators of bovine stem cell expansion for cultured meat [Long-Term screen]


title: Evaluation of PFHxS, PFOA, PFOS, and PFNA impact on liver metabolism using human liver spheroids

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

state: CA

address: 1450 Biggy Street, NRT 3514

institute: USC

summary: Accumulating evidence suggests that poly- and perfluoroalkyl substances (PFAS), a class of persistent organic pollutants, cause changes in hepatic lipid, amino acid, and glucose metabolism. Our study explores the molecular mechanisms whereby PFHxS, PFOA, PFOS, and PFNA disrupt liver metabolism.

overall_design: 3D InSightTM human liver spheroids (InSphero) composed of hepatocytes (10 donors: 5 males and 5 females), endothelial cells, and macrophages (1 donor). Liver spheroids were maintained in low glucose medium (lean medium) were exposed to 20µM of PFHxS, PFOA, PFOS, or PFNA for 7 days. Control spheroids were cultured in lean medium for the same time. We dissociated spheroids with Trypsin, generating suitable cells for 10x genomics scRNAseq (kit 3’ v3.1).

middle: P

last: Salomon

first: Lucy

last: Golden-Mason


title: Effect of knocking down CERS2 or a double knockdown (KD) CERS5/6 in ventricular cardiomyocytes on gene expression under conditions of hypertrophy induced by phorbol 12-myristate 13-acetate (PMA) or controls.

city: Seattle

first: Melissa

last: Krueger

state: WA

address: 850 Republican St, Box 358052

department: Pulmonary, Critical Care and Sleep Medicine Division

institute: University of Washington

summary: Sphingolipids are an important class of lipids that play imperative structural and functional roles in the body. Ceramides constitute the central essential structural backbone of more complex sphingolipids, thus alterations in the genes that regulate their expression could dysregulate the entire cellular sphingolipid metabolic scheme. The fatty acid acylated to the sphingosine backbones distinguishes ceramide species both structurally and functionally. Higher plasma concentrations of 16:0 ceramide are associated with an increased risk of heart failure, while higher concentrations of 22:0 plus 24:0 ceramide are associated with lower risk. Here, we silenced the ceramide synthase genes (CERS) responsible for the production of long-chain (LC) 16:0 ceramide (CERS5/6) or very long-chain (VLC) 22:0 and 24:0 ceramide (CERS2) in immortalized human ventricular cardiomyocytes and examined how these silenced genes altered the cardiomyocyte’s ability to maintain homeostasis in control conditions and under cardiac hypertrophy in response to PMA treatment. Taken together, our data provides support for the importance of the different ceramide species in maintaining cardiovascular homeostasis and in the development and progression of cardiac hypertrophy.

overall_design:
To investigate the role of LC and VLC ceramides in maintaining cardiomyocyte homeostasis and during the development and progression of cardiac hypertrophy, we silenced CERS2 or CERS5/6 in a human ventricular cardiomyocyte cell line using siRNA.
We then treated the KD or control cells with the hypertrophy inducing compound PMA or controls and analyzed how reductions in the respective ceramide species altered the hypertrophic response.
We performed gene expression analysis using data obtained from RNA-seq of the 8 different treatment groups (n=3).

first: Alexandra

last: Wiley

first: Rheem

last: Totah

first: Sina

last: Gharib


title: A Role for the Transcriptional Coregulator RIP140 in the Control of Muscle Endurance Fitness [CUTnRUN_Ac_flat]

institute: University of Pennsylvania

overall_design: H3K27ac CUT&RUN sequencing of WT control and Nrip1-/- primary skeletal muscle myotubes.

first: Elizabeth

last: Pruzinsky

first: Kirill

last: Batmanov

first: Denise

middle: M

last: Medeiros

first: Tomoya

last: Sakamoto

first: Teresa

last: Leone

first: Tejvir

last: Khurana


title: Oncostatin M induces epigenetic reprogramming in renal cell carcinoma-associated endothelial cells

city: Taichung

first: Hieu-Huy

last: Nguyen-Tran

state: Taichung

address: Xueshi

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

summary: Clear-cell renal cell carcinoma (ccRCC) is the most prevalent and lethal subtype of renal cell carcinoma. Genomic and epigenomic inactivation of the von Hippel-Lindau (VHL) tumor suppressor gene is a crucial early event in ccRCC pathogenesis (~75% of cases). Loss of VHL function leads to dysregulated hypoxia signaling, resulting in an extensive, disorganized, tortuous, and leaky vascular network within ccRCC tissue. It has been shown previously that Oncostatin M (OSM) secreted by the VHL-deficient kidney tubule cells can induce most of these ccRCC-associated vascular phenotypes which in turn promote tumor cell proliferation, immune cell infiltration, and metastasis. The influence of OSM to ECs could induce extensive and long-lasting transcriptomic changes in ECs although these ECs did not harbor any genomic mutations. Further studies indicate that OSM specifically activates endothelial cells (ECs) by inducing acetylation of histone 3 at lysine 14 (H3K14ac). Thus, we performed a variant of chromatin immunoprecipitation analysis, the Cleavage Under Targets and Tagmentation (CUT&TAG) sequencing, on OSM-treated and untreated ECs labeled with anti-H3K14ac antibody to validate the role of H3K14ac in the activation of ECs.

overall_design: 4x104 HMEC-1 cells were seeded in 3.5 cm2 culture dish and grown overnight. The media was replaced with fresh complete media (Control; CT group), 10 ng/mL of rOSM (OSM group). Cells were harvested after 48 hr and performed CUT&TAG sequencing by Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903).

first: Thi-Ngoc

last: Nguyen

first: Tien

last: Hsu


title: Single-cell RNA-seq data of C. elegans early embryos.

city: San Francisco

first: Binyamin

last: Zuckerman

state: California

institute: UCSF

summary: We performed single-cell transcriptional profiling of Caenorhabditis elegans embryos to benchmark CONCORD, a dimensionality reduction and data integration framework for single-cell analysis. This dataset complements previously published late-stage embryogenesis transcriptomic studies by enriching for early-stage embryos through low-temperature culture conditions, enabling construction of a comprehensive, continuous map of the full embryogenesis process.

overall_design: Wildtype N2 worms were grown on NGM plates and synchronized by bleaching. Eggs hatched on 10-cm plates and grown until L3/L4 stage. Then, plates were transferred to a 12⁰C and incubated for 48 h. Adult worms were lysed by bleaching, and embryos were dissociated into single cells. Cells were loaded onto a Chromium GEM-X chip, libraries were prepared following the 10x Genomics protocol.

first: Qin

last: Zhu

first: Leor

middle: S

last: Weinberger

first: Zev

last: Gartner


title: Functional Genomics and Tumor Microenvironment Analysis Reveal Prognostic Biological Subtypes in Mantle Cell Lymphoma [RNA-seq]

city: Omaha

first: Chengfeng

last: Bi

state: Nebarska

address: 42nd and, Emile St

institute: University of Nebraska Medical Center

summary: Mantle cell lymphoma (MCL) is a genetically and clinically heterogeneous B-cell malignancy. We study two MCL cohorts with differing treatment patterns: one enriched for immunochemotherapy, the other for chemotherapy alone. TP53 alterations are consistently associated with poor prognosis, whereas ATM mutations correlate with improved outcomes following rituximab-based chemotherapy. Based on recurrent genetic events, six clusters are identified and refined into three prognostic groups: high-risk (TP53 mutations and deletions at 17p13.3, 13q14.2, and 19p13.3), intermediate-risk (ATM and epigenetic regulator mutations, or gains at 8q/17q/15q), and low-risk (lacking TP53 alterations, rare ATM mutations without 11q deletions, gains at 3q, deletions at 6q). Transcriptomic analysis reveals enrichment of proliferation, metabolism-promoting gene signatures in high-risk; angiogenesis and NOTCH signaling in intermediate-risk; and proinflammatory-related (i.e., IFNα, TNFα) in low-risk MCLs. Multi-proteomic spatial profiling using imaging mass cytometry (IMC) demonstrates enrichment of CD4⁺ T cells with high expression of exhaustion markers and dominant population of myeloid cells skewed toward an M2-like phenotype. Spatially, TP53-perturbed MCLs are immune infiltrated but exhausted, while ATM-perturbed cases remain immune-cold with dense tumor. Functional analysis shows that p53 represses BCR signaling through PTPN6 activation. Collectively, these findings highlight distinct molecular and immune landscapes and reveal therapeutic vulnerabilities in high-risk TP53-perturbed MCL.

overall_design: 47/51 Human  formalin-fixed paraffin-embedded (FFPE) MCL samples were used for RNA-Seq analysis. The samples were annotated into different genomic clusters and Gene Set Enrichment Analysis (GSEA) was performed to show enrichment in different biological pathways. These samples were also used for Gene Expression Profile (GEP) and copy number alterations (CNAs) analysis.

first: Javeed

last: Iqbal

first: Sunandini

last: Sharma


summary: Clear-cell renal cell carcinoma (ccRCC) is the most prevalent and lethal subtype of renal cell carcinoma. Genomic and epigenomic inactivation of the von Hippel-Lindau (VHL) tumor suppressor gene is a crucial early event in ccRCC pathogenesis (~75% of cases). Loss of VHL function leads to dysregulated hypoxia signaling, resulting in an extensive, disorganized, tortuous, and leaky vascular network within ccRCC tissue. It has been shown previously that Oncostatin M (OSM) secreted by the VHL-deficient kidney tubule cells can induce most of these ccRCC-associated vascular phenotypes which in turn promote tumor cell proliferation, immune cell infiltration, and metastasis. The influence of OSM to ECs could induce extensive and long-lasting transcriptomic changes in ECs although these ECs did not harbor any genomic mutations. The observations suggest a novel interaction mechanism between tumor cells and stromal cells, in which OSM emanating from the tumor cells may induce transcriptomic changes in ECs via epigenetic modification. To further explore the underlying mechanisms, we directly treated HMEC-1, a microvascular endothelial cell, with recombination OSM with or without histone acetylation inhibitors. The total mRNA of these samples was then performed mRNA Sequencing (mRNA-Seq).

overall_design: 4x10^4 HMEC-1 cells were seeded in 3.5 cm2 culture dish and grown overnight. The media was replaced with fresh complete media (Control; CT group), 10 ng/mL of rOSM (OSM group), 30 g/mL PF9363 + 10 ng/mL of rOSM (PF9363 group) or 10 g/mL CBP300 + 10 ng/mL of rOSM (CBP300 group). The total mRNA was harvested after 48 hr for mRNA-Seq.


title: Functional genomics and tumor microenvironment analysis reveal prognostic biological subtypes in Mantle cell lymphoma

overall_design: R273C and R248Q mutations of TP53 were created in TP53-wt MCL cell line Z-138. The isogenic pairs were treated with AMG-232 for 24 hours to activate p53, followed by Cut&Run analysis. Dox-inducible wt-TP53 was introduced into TP53-deficient MCL cell lines Marver-1 and Mino. The isogenic pairs were treated with Dox for 12h, followed by Cut&Run analysis.


overall_design: TP53 KO and R248Q mutation were created in TP53-wt MCL cell line Z-138. The isogenic pairs were treated with AMG-232 for 24 hours to activate p53, followed by RNA-seq. Dox-inducible wt-TP53 was introduced into TP53-deficient MCL cell lines Marver-1 and Mino. The isogenic pairs were treated with Dox for 12h, followed by RNA-seq.


title: Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [ChIP-Seq]

city: San Antonio

first: Hui

last: Yan

state: TX

address: 7703 Floyd Curl Dr.

department: MIMG

institute: UTHSCSA

summary: As “effector” cells, B lymphocytes make antibodies.  They also regulate immune functions through ligand-receptor interactions.  The limited understanding of regulatory roles of B cells prompted us to develop a workflow that profiles B cell ligand and receptor expression, maps in silico interactions involving ligands with high “specificity scores”, validates the function of top ligand-receptor interactions, and unveils transcription regulation of specific ligands.  Using this unbiased approach, here we report the regulatory functions of a new subset of murine B cells that express BATF3 as a hallmark transcription factor.  BATF3+ B cells, as generated upon B cell activation by innate TLR and adaptive CD40 and IL-21 receptor signals, lose their effector cell function (making class-switched antibodies) while expressing new ligands, most notably cytokine IL-27 and chemokine CXCL10.  As elicited by viral infection and immunization, IL-27+CXCL10+ B cells target effector B cells through the IL-27 receptor and, together with IFNg, optimize the antibody response and anti-viral immunity.  Also appearing in tumors and retained there through the autocrine CXCL10-CXCR3 interaction, they enhance B cell expression of immune checkpoint PD-L1 and suppress anti-tumor immunity.  Thus, we have identified new regulatory B cells and provided a paradigmatic framework to investigate immune cell communications.

overall_design: B cells were stimulated with nil,  LPS, or LPS plus CD154 and IL-21 (LC21). Polyclonal rabbit Ab to NF-kB p65 (RELA, Santa Cruz Biotechnology, #sc372) was used to select regions of interest. Input samples were DNA without antibody selection.

first: Zhenming

last: Xu


title: Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [CUT&Tag 1]

overall_design: B cells  were stimulated with LPS or LPS plus anti-CD40 and IL-21 (LA21). Histone H3K27 acetylation or methylation antibody were used to select regions of interest.


title: Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [ATAC-Seq 2]

overall_design: B cells from Batf3 wildtype and knockout mice were stimulated with either LPS or LPS plus anti-CD40 and IL-21 (LA21). Regions of open chromatin was accessed and compared between conditions using ATAC-seq.


title: Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [ATAC-Seq 1]

overall_design: ATAC-seq  samples from 5 different B cell stimulation conditions, namely Nil, LPS, CD154, LPS plus CD154 (LC) and LPS plus CD154 and IL-21 (LC21) were used in this study. Regions of open chromatin was accessed and compared between conditions.


title: Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation [ATAC-Seq]

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

summary: Cohesin- and CTCF-mediated chromatin loops shape enhancer-promoter interactions, but their global impact on gene regulation remains unclear. We show that cohesin and CTCF regulate hundreds of genes in mouse cells, though the magnitude of expression changes is modest. Acute loss of cohesin loops mainly downregulates CBP/p300-dependent enhancer targets, while CTCF depletion can both up- and downregulate putative enhancer targets. Interestingly, beyond regulating enhancer-dependent transcription via loop anchoring, CTCF acts as a transcriptional activator or repressor of sense and antisense transcripts, depending on its binding position and orientation in promoters. Mechanistically, promoter-bound CTCF enhances DNA accessibility and RNA polymerase II recruitment, thereby activating housekeeping genes essential for mammalian cell proliferation. CTCF’s transcriptional activation function—but not its loop-anchoring role—is shared with its vertebrate-specific paralog, CTCFL. These findings resolve cohesin and CTCF’s roles in global gene regulation, offering a unified model that integrates their enhancer-dependent and -independent functions in transcription control.

overall_design: ATAC-seq of mouse ESC, before and after CTCF  depletion using degron system.

first: Takeo

last: Narita

first: Yoshiki

last: Higashijima

first: Chunaram


title: SWI/SNF is a gatekeeper of chromatin access at enhancer networks controlling triple-negative breast cancer progression [RNA-Seq]

city: Odense

first: Simon

middle: Toftholm

last: Jakobsen

state: Syddanmark

address: Campusvej 55

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

summary: Triple-negative breast cancer (TNBC) is a particularly aggressive subtype of breast cancer with high metastatic potential, limited treatment options, and low patient survival rates. By combining proteomics and genomics approaches, we identify an oncogenic transcriptional network in TNBC involving the glucocorticoid receptor (GR), GATA6, the key oncoprotein MYC, and AP-1 transcription factors. Although these transcription factors share cis-regulatory regions, they control largely distinct oncogenic pathways. We demonstrate that SWI/SNF chromatin remodeling complex is a common gatekeeper of chromatin access for these transcription factors, and that inhibition of SWI/SNF-mediated chromatin remodeling decommissions the distinct enhancer repertoires and target gene programs controlled by these transcription factors. Consistently, SWI/SNF inhibition blocks cancer cell proliferation, chemoresistance, and invasion both in vitro and in vivo. Thus, we propose that several key oncogenic pathways in TNBC depend on SWI/SNF-mediated chromatin remodeling, making this disease vulnerable to SWI/SNF inhibitors.

overall_design: RNA-seq upon GR activation by DEX, siRNA KD of GATA6 , and SWI/SNF ATPase inhibition using BRM014, in BT549 and MDA-MB-231 triple-negative breast cancer cell lines

first: Rikke

middle: A

last: Jensen

first: Mikkel

middle: G

last: Terp

middle: T

first: Tina

last: Ravnsborg

first: Maria

last: Madsen

first: Laurits

last: Sloth

first: Henrik

last: Ditzel

first: Ole

first: Rasmus

last: Siersbæk


title: Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation [ChIP-Seq]

overall_design: EU-seq of mouse ESC, before and after CTCF and/or Rad21 depletion using degron system. EU-seq of CTCF Y226A/F228A mutant mouse ESC before and after CTCF depletion.

first: Elina

last: Maskey

first: Georgios

last: Papas


title: Epigenetic control and inheritance of rDNA arrays [3]

status: Public on Aug 26 2025

city: Kansas City

first: Tamara

last: Potapova

institute: Stowers Institute for Medical Research

type: Methylation profiling by high throughput sequencing

summary: Ribosomal RNA (rRNA) genes exist in multiple copies arranged in tandem arrays known as ribosomal DNA (rDNA). The total number of gene copies is variable, and the mechanisms buffering this copy number variation remain unresolved. We surveyed the number, distribution, and activity of rDNA arrays at the level of individual chromosomes across multiple human and primate genomes. Each individual possessed a unique fingerprint of copy number distribution and activity of rDNA arrays. In some cases, entire rDNA arrays were transcriptionally silent. Silent rDNA arrays showed reduced association with the nucleolus and decreased interchromosomal interactions, indicating that the nucleolar organizer function of rDNA depends on transcriptional activity. Methyl-sequencing of flow-sorted chromosomes, combined with long read sequencing, showed epigenetic modification of rDNA promoter and coding region by DNA methylation. Silent arrays were in a closed chromatin state, as indicated by the accessibility profiles derived from Fiber-seq. Removing DNA methylation restored the transcriptional activity of silent arrays. Array activity status remained stable through the iPS cell re-programming. Family trio analysis demonstrated that the inactive rDNA haplotype can be traced to one of the parental genomes, suggesting that the epigenetic state of rDNA arrays may be heritable. We propose that the dosage of rRNA genes is epigenetically regulated by DNA methylation, and these methylation patterns specify nucleolar organizer function and can propagate transgenerationally.

overall_design: We obtained two iPS cell lines derived from the HG002 B-lymphocytes, designated iPS1 and iPS2, and cultured them in feeder-free conditions. These isogenic cell lines differed in the delivery mode of the reprogramming factors: iPS1 was re-programmed using episomal delivery, and the iPS2 using the Sendai virus. IPS1 and IPS2 were then differentiated into cerebral and intestinal organoids to investigate rDNA activity in tissue.

first: Matthew

last: Borchers

first: Paxton

last: Kostos

first: Sean

last: McKinney

first: Jeff

last: Haug

first: Andrea

last: Guarracino

first: Steven

last: Solar

first: Madelaine

last: Gogol

first: Graciela

last: Monfort Anez

first: Leonardo

last: Gomes de Lima

first: Yan

last: Wang

first: Kate

last: Hall

first: Sophie

last: Hoffman

first: Erik

last: Garrison

first: Adam

last: Phillippy

first: Jennifer

last: Gerton


title: SWI/SNF is a gatekeeper of chromatin access at enhancer networks controlling triple-negative breast cancer progression [ChIP-Seq]

first: Simon

last: Jakobsen

overall_design: ChIP-seq upon GR activation by DEX, siRNA KD of GATA6 , and SWI/SNF ATPase inhibition using BRM014, in BT549 triple-negative breast cancer cell line

first: Rikke

last: Jensen

first: Mikkel

last: Terp

first: Tina

last: Ravnsborg

first: Maria

last: Madsen

first: Laurits

last: Sloth

first: Henrik

middle: J

last: Ditzel

first: Ole

first: Rasmus

last: Siersbæk


title: SWI/SNF is a gatekeeper of chromatin access at enhancer networks controlling triple-negative breats cancer progression [ATAC-seq]

overall_design: ATAC-seq upon GR activation by DEX, siRNA KD of GATA6 , and SWI/SNF ATPase inhibition using BRM014, in BT549 and MDA-MB-231 triple-negative breast cancer cell lines


title: Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation

first: Chunarum

last: Choudhary

overall_design: Refer to individual Series


title: Disentangling the architectural and non-architectural functions of CTCF and cohesin in global gene regulation [EU-Seq]

overall_design: EU-seq of mouse ESC, before and after CTCF and/or Rad21 depletion using degron system. EU-seq of CTCF Y226A/F228A mutant mouse ESC before and after CTCF depletion. EU-seq of mouse NPC, before and after Rad21 depletion using degron system. EU-seq of mouse NPC, before and after A-485 treatment.

first: Takeo

last: Narita

first: Elina

last: Maskey

first: Yoshiki

last: Higashijima

first: Natalie

last: Scherer

first: Georgios

last: Papas

first: Chunaram


title: Clinical testing of transcriptome-wide expression classifiers in high-risk localized and metastatic prostate cancer starting androgen deprivation therapy in the STAMPEDE abiraterone and docetaxel Phase 3 trials

city: San Diego

first: Elai

last: Davicioni

address: 9725 Lusk Blvd

institute: Veracyte, Inc

summary: Gene expression study of the STAMPEDE abiraterone and docetaxel randomized controlled trials

overall_design: Retrospective analysis of 1523 tumor transcriptomes from STAMPEDE abiraterone and docetaxel comparisons

first: M

last: Parry

first: E

last: Grist

first: L

last: Mendes

first: P

last: Dutey-Magni

first: A

last: Sachdeva

first: C

last: Brawley

first: S

last: Lall

first: J

last: Proudfoot

first: Y

last: Liu

first: N

middle: W

last: Clarke

last: James

last: Brown

first: G

last: Attard


title: RNA Sequencing of Mouse Cerebella Expressing the STING-N153S Mutant in Purkinje Cells

city: DALLAS

last: YAN

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: To investigate the transcriptomic changes in mouse cerebella with Purkinje cell–specific expression of the STING-N153S mutant, we performed RNA sequencing (RNA-seq) on cerebellar tissue from N153SLSL/LSLPcp2-cre and N153SLSL/LSL mice.

overall_design: STING-N153S Lox-STOP-Lox (N153SLSL/LSL) mice were crossed with Pcp2-cre mice to  drive Purkinje cell–specific expression of the N153S mutant  (N153SLSL/LSLPcp2-cre). Two-month-old  N153SLSL/LSLPcp2-cre and N153SLSL/LSL mice (3 mice per genotype) were sacrificed and cerebella were collected and snap-frozen in liquid nitrogen. Total RNA was extracted from frozen cerebellar tissue, and mRNA libraries were prepared and sequenced.

last: Yan

first: Kun

last: Yang


title: Synovial MS4A4A correlates with inflammation and counteracts response to corticosteroids in arthritis

city: Rozzano

first: Massimo

last: Locati

state: Milano

address: Via Alessandro Manzoni, 56

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: MS4A4A belongs to the MS4A tetraspan protein superfamily and is selectively expressed by the monocyte-macrophage lineage. In this study, we aimed to evaluate the role of MS4A4A+ macrophages in rheumatoid arthritis (RA) pathogenesis and response to treatment. RNA sequencing and immunohistochemistry of synovial samples from either early treatment-naïve or active chronic RA patients showed that MS4A4A expression positively correlated with synovial inflammation. Synovial macrophages from patients treated with corticosteroids (CS: Dexamethasone) exhibited an enhanced expression of MS4A4A and Fc γ receptor (FcγR) 3. Accordingly, CS enhanced in vitro the expression of MS4A4A and FcγR3 in human and murine macrophages. In an experimental model of arthritis, Ms4a4a deletion had no effect on the diseases course, but was associated with enhanced therapeutic response selectively to CS. These results suggest that macrophage expression of MS4A4A represents a novel biomarker of joint inflammation in RA and that its upregulation in concert with FcgR3 by CS counteracts the therapeutic activity of these drugs. Macrophage MS4A4A may represent a novel biomarker of joint inflammation in RA and a target to amplify the therapeutic activity of corticosteroids.

overall_design: Trascriptional profile of MS4A4A WT and KO Bone Marrow-Derived Macrophages (BMDMs) exposed to Dexamethasone (1 µM Dex) at different time points (0, 2, 8, 24 hours)

first: AR

last: Putignano

last: Troilo

first: EM

last: Borroni

first: D

last: Di Silvestre

last: Lomagno


title: Chromatin accessibility changes in response to TGFB in human pancreatic stellate cells with knockdown of PIN1

city: Portland

first: Ellen

last: Langer

state: OR

address: 2720 SW Moody Ave

department: DOS (Department of Oncological Sciences)

institute: Oregon Health and Science University

summary: Pancreatic stellate cells can be activated to a myofibroblast phenotype in response to TGFB treatment. The goal of this study was to determine how loss of PIN1 affects stellate cell state at baseline and in response to TGFB treatment.

overall_design: Primary human pancreatic stellate cells (PSCs) were cultured in Stellate Cell Media. For knockdown studies, PSCs were infected with a pLKO-shPIN1 lentivirus or an shSCR control lentivirus. Stable pools were generated with puromycin selection. These cells were plated, and then treated for 8 hours with 5 ng/mL TGFB1. Nuclei were isolated and used for single cell combinatorial indexing ATAC-Seq

first: Rosalie

last: Sears

first: Andrew

last: Adey


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

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: Transient Ddx61-enriched condensates refine heart regeneration programs

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

summary: Gene regulatory mechanisms that underlie tissue regeneration have been largely studied at the level of transcription. Here, proximity labeling methods identified enhanced presence of Processing body (P-body) marker, Ddx61, in zebrafish heart muscle cells induced to divide by injury or mitogenic stimulation. We found that Ddx61-containing condensates emerge and develop complex, transient structures in cardiomyocytes during cardiogenic settings in adult zebrafish, developing mice, and human stem cell-derived myocardium. Mutations in zebrafish ddx61 disrupted cardiomyocyte cycling and differentiation after cardiac injury or mitogen presence, and DDX61 knockdown in human cardiomyocytes inhibited similar parameters under maturation conditions in vitro. RNA affinity and proteomic profiling implicated mRNAs preferentially associating with Ddx61 during regeneration, and induced transgenic expression of one of these mRNAs, encoding the BMP signaling inhibitor, Chordin, disrupted indicators of heart regeneration after cardiac injury. Our experiments provide evidence that mRNA sorting by specialized context-dependent condensates can modulate gene expression and impact tissue regenerative capacity.

overall_design: Ddx61/Ddx6 pulldown and isolation of associated mRNAs during heart regeneration in zebrafish. For this 120 hearts were used for one sample. Uninjured and 14 days post injury hearts were used. Dublicate samples for each condition.

first: Mira

last: Pronobis


title: Transcriptional changes in response to TGFB in human pancreatic stellate cells with inhibition of PIN1

state: Oregon

address: 2720 S Moody Ave

department: CEDAR

institute: OHSU

summary: Pancreatic stellate cells can be activated to a myofibroblast phenotype in response to TGFB treatment. The goal of this study was to determine how inhibition of PIN1 affects stellate cell state at baseline and in response to TGFB treatment.

overall_design: Primary human pancreatic stellate cells (PSCs) were cultured in Stellate Cell Media. For inhibitor studies, cells were pre-treated for 48 hours with 10 uM all trans retinoic acid (ATRA), 10 uM KPT-6566 (KPT), or DMSO as a control. Media was then changed to replenish this treatment as well as to treat with and without 5 ng/mL TGFB1. Cells were collected 24 hours later, RNA isolated and used for RNA sequencing.


title: Epigenetic control and inheritance of rDNA arrays [1]

status: Public on Aug 25 2025

first: Tamara

last: Potapova

overall_design: Chm13 cells were cultured in the presence of DNMT1 inhibitor GSK-3484862 to induce genome-wide demethylation of 5-methylcytosine. Analysis of rDNA and the whole genome was performed to confirm reduced methylation. The transcriptional activity of the rDNA was assayed with immuno-FISH for UBF.

first: Matthew

last: Borchers

first: Paxton

last: Kostos

first: Sean

last: McKinney

first: Jeff

last: Haug

first: Andrea

last: Guarracino

first: Steven

last: Solar

first: Madelaine

last: Gogol

first: Graciela

last: Monfort Anez

first: Leonardo

last: Gomes de Lima

first: Yan

last: Wang

first: Kate

last: Hall

first: Sophie

last: Hoffman

first: Erik

last: Garrison

first: Adam

last: Phillippy

first: Jennifer

last: Gerton


title: Transcriptional changes in response to TGFB in human pancreatic stellate cells with knockdown of PIN1

first: Ellen

last: Langer

overall_design: Primary human pancreatic stellate cells (PSCs) were cultured in Stellate Cell Media. For knockdown studies, PSCs were infected with a pLKO-shPIN1 lentivirus or an shSCR control lentivirus. Stable pools were generated with puromycin selection. These cells were plated, and then treated for 24 hours with 5 ng/mL TGFB1. Cells were collected, RNA isolated and used for RNA sequencing.

first: Rosalie

last: Sears


title: Selective targeting of HIV infected clones by cognate peptide stimulation and antiproliferative drugs

city: Baltimore

first: Isha

last: Gurumurthy

state: MD

address: 1650 Orleans Street, CRB1, 4M

department: Oncology

institute: Johns Hopkins University

summary: Clonal expansion of HIV infected CD4+ T cells is a barrier to HIV eradication. We previously described a marked reduction in the frequency of the most clonally expanded infected CD4+ T cells in an individual with elite control (ES24) after initiating chemoradiation for metastatic lung cancer with a regimen that included paclitaxel and carboplatin. We tested the hypothesis that this phenomenon was due to a higher susceptibility to the chemotherapeutic drugs of CD4+ T cell clones that were sustained by active proliferation. We studied a CD4+ T cell clone with replication-competent provirus integrated into the ZNF721/ABCA11P genes, termed ZNF721i. We stimulated the clone with its cognate peptide and then exposed the cells to paclitaxel and/or carboplatin or the antiproliferative drug, mycophenolate mofetil. While treatment of cells with the cognate peptide alone led to a marked expansion of the ZNF721i clone, treatment with the cognate peptide followed by culture with either paclitaxel or mycophenolate mofetil abrogated this process. The drugs did not affect the proliferation of other CD4+ T cell clones that were not specific for the cognate peptide. This strategy of antigen-specific stimulation followed by treatment with an antiproliferative agent may lead to the selective elimination of clonally expanded HIV-infected cells.

overall_design:
PBMCs were cultured with peptides 42 and 61 for 20 hours and then washed and cultured as described above. On day 4, paclitaxel (58nM) was added and on day 7, CD4 isolation was performed on these samples and on freshly obtained PBMCs. An annexin V column was used to remove dead cells. ES24_1 corresponds to cells non stimulated (DMSO) and treated with DMSO on day 4.  ES24_2 corresponds to cells non stimulated (DMSO) and treated with paclitaxel on day 4.  ES24_3 corresponds to cells stimulated with gag peptides and treated with paclitaxel on day 4. ES24_4 corresponds to cells stimulated with gag peptides and treated with DMSO on day 4. ES24_5 corresponds to CD4s freshly isolated from uncultured PBMCs.

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

first: Joel

last: Blankson

first: Francesco

middle: R

last: Simonetti

first: Kellie

last: Smith


title: Induction of regulatory functions in BATF3+ B cells through ligand-receptor interactions [CUT&Tag 2]

first: Hui

last: Yan

overall_design: Wildtype B cells were stimulated with LPS, anti-CD40 plus IL-27 (A21), or LPS plus anti-CD40 and IL-21 (LA21). Batf3 knockout (KO) B cells  were stimulated with LPS plus anti-CD40 and IL-21 (LA21). BATF3 ployclonal antibody were used to select regions of interest.

first: Zhenming

last: Xu


title: Gene expression of wild-type C57BL/6 mouse nasal turbinates infected with C2-202 human metapneumovirus (HMPV)

city: Pittsburgh

first: John

last: Williams

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh School of Medicine

summary: Human metapneumovirus (HMPV) is a primary causative agent of acute upper respiratory tract infections. We used single cell RNA-sequencing (scRNA-seq) to assess nasal immune profiles in a mouse model of HMPV infection.

overall_design: Mice were either infected with C2-202 HMPV (5E5 total PFU) or mock-infected with cell lysate (resuspended in PBS to total 100-uL volume and delivered intratracheally). Cells were collected from nasal turbinates of mice euthanized day 1 post-infection, processed to single cell suspensions, and analyzed using scRNA-seq.

first: Jorna

last: Sojati

middle: V


title: Transplanted human striatal progenitors exhibit functional integration and modulate host circuitry in a Huntington’s disease animal model

city: Milan

first: Elena

last: Cattaneo

address: Via Celoria, 26

department: Bioscience

institute: University of Milan

summary: Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion in the HTT gene, leading to progressive loss of striatal neurons and motor-cognitive decline. While current gene-targeting approaches aiming at reducing somatic instability show promise – especially in case of early treatment – they cannot restore the already compromised neuronal circuitry at advanced disease stages. Thus, cell replacement therapy offers a regenerative strategy to rebuild damaged striatal circuits. Here, we report that human striatal progenitors (hSPs) derived from embryonic stem cells via a morphogen-guided protocol survive long-term when transplanted into a rodent model of HD and recapitulate key aspects of ventral telencephalic development. By employing single-nucleus RNAseq (snRNAseq) of the grafted cells, we resolved their transcriptional profile with unprecedented resolution, identifying transcriptional signals of D1- and D2-type medium spiny neurons, MGE- and CGE-derived interneurons, and regionally specified astrocytes. Moreover, we demonstrate that grafted cells undergo further maturation 6 months post-transplantation (MPT), acquiring the expected regionally defined transcriptional identity. Immunohistochemistry confirmed stable graft composition over time and supported a neurogenic-to-gliogenic switch post-transplantation. A plethora of techniques exploiting virus-based tracing and electrophysiology assays demonstrated anatomical and functional integration of the grafts. Notably, chemogenetic modulation of graft activity regulated striatal-dependent behaviors, further supporting effective graft integration into host basal ganglia circuits. Altogether, these results provide preclinical evidence that hSP-grafts can reconstruct striatal circuits and modulate functionally relevant behaviors. The ability to generate a scalable, molecularly defined progenitor population capable of in vivo functional integration supports the potential of hSPs for clinical application in HD and related basal ganglia disorders.

overall_design: RNA-seq profiling of brain grafted cells at 6 months post transplantation and in-vitro cells at Day15 and Day35 of hESC differentiated into MSN enriched culture.

first: Linda

last: Scaramuzza

first: Marta

last: Ribodino

first: Christian

last: Cassarino

last: Morrocchi

first: Gabriela

middle: B

last: Gomez-Gonzalez

first: Roberta

last: Parolisi

first: Edoardo

last: Sozzi

first: Giacomo

last: Turrini

first: Valentina

last: Cerrato

first: Paola

last: Conforti

first: Eriola

last: Hoxha

first: Riccardo

last: Tognato

first: Greta

last: Galeotti

first: Chiara

last: Cordiglieri

first: Maria

last: Crosti

first: Stefano

last: Zucca

first: Martina

last: Lorenzati

first: Serena

last: Bovetti

first: Paolo

last: Spaiardi

first: Claudio

last: de'Sperati

first: Gerardo

last: Biella

last: Ottoboni

first: Malin

last: Parmar

first: Simone

last: Maestri

first: Dario

last: Besusso

first: Annalisa

last: Buffo


title: PB2 and NP of North American H5N1 virus Drive Immune Cell Replication and Systemic infections

city: Daejeon

first: Woohyun

last: Kwon

address: expo-ro

country: South Korea

institute: Institute for Basic Science

summary: The 2022 North American outbreak of 2.3.4.4b H5N1 avian influenza virus revealed significant mammalian adaptation and pathogenicity, yet mechanisms remain unclear. To address this knowledge gap, we investigated the North American H5N1 strain (GA/W22-145E/22), which demonstrated unique immune cell-mediated systemic dissemination, neuroinvasion, and 100% mortality in ferrets, unlike the non-lethal Eurasian strain (KR/W811/21). Genomic and reverse genetics studies identified PB2478I and NP450N mutations as key determinants of enhanced polymerase activity, immune cell tropism, and pathogenicity. Mutant GA/W22-145E/22 virus carrying PB2478V/NP450S showed complete survival without systemic dissemination. Furthermore, GA/W22-145E/22 demonstrated robust replication in human PBMCs and bovine mammary gland organoids, raising concerns about zoonotic spillover. These findings underscore PB2478I and NP450N as pivotal markers of pathogenicity, emphasizing the urgent need for enhanced surveillance and targeted interventions

overall_design: Single cell RNA seq profiling of North American H5N1 strain (GA/W22-145E/22) and Eurasian strain (KR/W811/21) infected to brain (0,3,5dpi), cervical lymph node(0,3,5dpi), peripheral and mesenteric lymph node (4dpi), lung (3dpi,5dpi). Moreover, North American H5N1 strain PB2-478I and/or NP-450N mutation virus infected to cervical lymph node (4,6dpi).

first: Young-Il

last: Kim

first: Seung-Gyu

last: Jang

first: Dongbin

last: Park

first: Se-Mi

first: Young Ki

last: Choi


title: Decoding cellular stress states for toxicology using single-cell transcriptomics [scRNA-Seq]

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

summary: Single-cell transcriptomics (SCTr) offers a powerful platform for decoding the complexities of cellular stress responses to chemical exposures, capturing rare and transient subpopulations that can be obscured in bulk measurements. This study employs SCTr to profile the responses of HepaRG liver cells to various stress-inducing chemicals, providing detailed insights into adaptive stress response pathways (SRPs), encompassing the response to unfolded proteins, oxidative stress, heat shock, and DNA damage. By leveraging SCTr, we identify distinct cellular subpopulations and elucidate their transcriptomic profiles, linking specific gene expression patterns to biological mechanisms underlying stress responses. Our findings demonstrate the utility of SCTr in discerning the dose-dependent effects of chemicals at a granular level, highlighted by key differences between pseudo-bulk and single-cell analysis. Chemicals such as troglitazone, brefeldin A, rotenone, and tunicamycin induced unique transcriptional signatures associated with specific stress response pathways. Single-cell connectivity mapping with signatures of SRPs and cell fates, including autophagy and apoptosis, revealed clusters of cells with adaptive and potentially adverse phenotypes. These SCTr data have implications for identifying toxicological and disease mechanisms involving adaptive stress pathways. The data can also provide unique insights into toxicological processes by beginning to resolve adaptive chemical exposures, where cells recover, from those that are adverse from which cells do not recover, offering potentially new approaches for chemical safety assessments.

overall_design: We profiled reference perturbagens known to induce stress responses, including the unfolded protein response (UPR), oxidative stress response (OSR), heat-shock response (HSR), response to hypoxia (HPX), and DNA damage response (DDR), in the differentiated HepaRG human liver cell model at three different concentrations. HepaRG cells were dissociated and fixed for single-cell transcriptomic (SCTr) assessments. Here, cells were profiled with the Parse Biosciences Single Cell Whole Transcriptome Kit v1.3.1.

first: Brian N.

first: Imran

last: Shah

first: Dennis J.

last: Eastburn


title: RNA-seq of kidney transcriptome following UUO injury

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: The role of endothelial dysfunction in tubulointerstitial fibrosis associated with chronic kidney disease (CKD) is not well understood. In this study, we demonstrate that the activation of the endothelial tyrosine kinase TIE2 alleviates renal pathology in experimental CKD in mice. TIE2 activation was achieved using a human angiopoietin-2 (ANGPT2)-binding and TIE2-activating antibody (ABTAA), or through adult-induced endothelial-specific knockout of the vascular endothelial protein tyrosine phosphatase gene (Veptp). Both methods significantly protected CKD mice from endothelial dysfunction, peritubular capillary loss, tubular epithelial injury, and tubulointerstitial fibrosis. Conversely, silencing TIE2 through adult-induced endothelial-specific knockout of the Tie2 gene exacerbated CKD pathology. Additionally, we found that endothelial dysfunction promotes renal fibrosis not through endothelial-to-mesenchymal transition as previously expected, but by inducing the expression of pro-fibrotic PDGFB in tubular epithelial cells, a process that is inhibited by TIE2 activation. Our findings suggest that TIE2 activation via ABTAA warrants investigation in human CKD, where there is a significant unmet medical need.

overall_design: Bulk RNA-seq of whole kidneys was used to investigate transcriptional changes in IgG, ABTAA, VeptpWT, VeptpKO, PdgfbWT and PdgfbKO mice 3 days post-UUO compared to CL (contralateral control kindey)

first: Marie

last: Jeansson


title: SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [ChIP-seq 2]

city: Yokohama

first: Shinsuke

last: Ito

state: Kanagawa

address: 1-7-22 Suehirocho

department: IMS

institute: RIKEN

summary: Polycomb group (PcG) proteins are evolutionarily conserved repressors of developmental genes. Paradoxically, the same PcG proteins also play roles in gene activation via mechanisms that are not yet fully understood. Here, we found that S-phase kinase-associated protein 1A (SKP1A), an essential factor of SCF (SKP1A/CULLIN1/F-box) ubiquitin ligases and a subunit of the PCGF1 (Polycomb group RING finger protein 1) component of Polycomb repressive complex 1 (PCGF1-PRC1), mediates the link between PcG-dependent gene regulation and ubiquitin-dependent proteasomal degradation. By using differentiating mouse embryonic stem cells, we found that SKP1A removes EED, a core component of Polycomb repressive complex 2 (PRC2) that is bound to PcG target gene promoters, via proteasomal degradation, and it thereby sensitises these genes for subsequent activation. Furthermore, we show that SKP1A removes EED from the Meis2 promoter in the midbrain of developing mouse embryos, leading to Meis2 gene expression. In summary, we reveal here a previously unknown role of SKP1A in activating PcG-target genes via the proteasomal degradation of PRC2. This implies that SKP1A-containing PCGF1-PRC1 may confer reversibility on PcG-mediated gene silencing for robust spatiotemporal regulation of target genes.

overall_design: ChIP-seq analysis to investigate the localization PcG factors, ubiqutin pathway, abd histone modifications using SKP1a WT, SKP1a KO, and EED KO of embryonic stem cell or embryoid body.

first: Takashi

last: Kondo

first: Takaho

last: Endo

first: Junichiro

last: Takano

first: Haruhiko

last: Koseki


title: Interplay between Genetic Variation and Nutrition Challenge Controls Hepatic Diurnal Rhythms [ATAC-seq]

city: Houston

first: Dongyin

last: Guan

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

summary: Variation in diurnal rhythms contributes to the risk of multiple diseases, yet the genomic and epigenomic basis remains largely unknown. Here, we show that SNPs in enhancer and promoter regions genome-wide contribute to variations in human diurnal rhythms. Differential rhythmic gene expression and physiological responses to diet-induced obesity in mice with different genetic backgrounds are linked to time-dependent enhancer-promoter interactions (EPI) regulated by cis-regulatory SNPs and transcription factors (TFs) like ESRRγ. Hepatocyte-specific Esrrγ knockout alters rhythmic processes in liver, including triglyceride synthesis and lipid droplet formation, across mouse strains. Moreover, motifs of ESRRγ and other lipid metabolism-related TFs are enriched in individual-specific EPIs harboring SNPs to control rhythmic genes in patients with MAFLD. SNPs located in these sites are correlated with hepatic metabolic traits. Thus, SNPs and TFs interdependently form the genomic and epigenomic basis for diurnal rhythm variation, contributing to disease risk.

overall_design: ATAC-sequencing in livers from high-fat diet fed mice with C57BL/6J and 129S1/SvImJ genetic background.

first: Dishu

last: Zhou

first: Ying

last: Chen

first: Panpan

last: Liu

first: Donyin


title: SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [4C-seq]

overall_design: ChIP-seq analysis to investigate the localization of EED using EED WT and KO of embryonic stem cell or embryoid body.


title: Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models

city: Bei Jing

first: Jie

last: Zhao

address: Shuangqing Street

department: Department of Basic Medical Sciences

country: China

institute: Tsinghua University

summary: Macrophage-mediated phagocytosis plays a pivotal role in eradicating cancer cells and modulating anti-tumor immunity. Yet, the mechanisms through which cancer cells evade phagocytosis remain elusive. We employed a genome-wide CRISPR screen in murine pancreatic cancer cells co-cultured with macrophages and discovered that disabling the tumor-intrinsic pyrimidine synthesis pathway (specifically Cad, Dhodh, and Umps) leads to enhanced phagocytosis by macrophages. Mechanistically, macrophages suppress the UMP salvage pathway in tumor cells, increasing their dependence on de novo UMP synthesis. This suppression resulted in tumor cells with impaired de novo pyrimidine synthesis becoming more susceptible to apoptosis in the presence of macrophages, thereby enhancing macrophage-mediated elimination, both in vitro and in mouse models. Mechanistically, we show that pro-inflammatory cytokines released by macrophages, including TNFα and IL-1, are essential for upregulating Upp1 and decrease UMP pool in tumor cells. Thus, our findings uncover how tumor pyrimidine metabolism pathway shape their sensitivity to macrophage-mediated elimination.

overall_design: To investigate how macrophage and TNFa affect the pyrimidine salvage synthesis pathway in tumor cells, we established Panc02-Cad knockout cell lines using CRISPR/Cas9. Then performed gene-expressing profiling analysis using data obtained from RNA-seq of four experimental groups: cad ko control group, cad ko co-culture group, control group, and TNFa treatment group.

first: Deng

last: Pan

first: Lijian

last: Wu


title: Cwh8 Moonlights as a Farnesyl Pyrophosphate Phosphatase and is Essential for Farnesol Biosynthesis in Candida albicans

city: Hanover

first: Daniel

middle: John

last: Gutzmann

state: NH

address: Vail Building 208, Geisel School of Medicine at Dartmouth

department: Microbiology and Immunology

institute: Dartmouth College

summary: In the opportunistic pathogen Candida albicans, hyphal growth and virulence factor expression are regulated by environmental and chemical cues. Farnesol is a secreted autoregulatory molecule that represses filamentation. It is derived from farnesyl pyrophosphate (FPP), an ergosterol biosynthesis pathway intermediate. Although Dpp1, Dpp2, and Dpp3 were proposed to synthesize farnesol, a mutant lacking all three had only a modest reduction in farnesol. To identify other farnesol biosynthesis genes, we employed transcription factor mutants that underproduced or overproduced farnesol in a screen and analyzed their transcriptomes. CWH8 was the only transcript correlated with farnesol production. Cwh8 is a lipid phosphatase known to recycle dolichyl pyrophosphate during glycosylation of cell wall proteins. The cwh8ΔΔ mutant had a >99% reduction in farnesol compared to the parent strain and was hyperfilamentous in embedded conditions. It had ~900-fold lower levels of farnesyl phosphate, the product of FPP dephosphorylation, suggesting Cwh8 acts directly on FPP. Complementation of the C. albicans cwh8ΔΔ mutant with CWH8 from C. albicans restored cell wall integrity and farnesol production. However, complementation with CWH8 from Clavispora lusitaniae, a species lacking farnesol signaling, restored cell wall integrity but failed to rescue farnesol production. This indicates that while Cwh8’s role in maintaining cell wall integrity is conserved, differences in substrate specificity or interactions with species-specific cofactors underlie its involvement in farnesol biosynthesis in C. albicans. Finally, fluconazole was fungicidal for cwh8ΔΔ rather than fungistatic. These studies demonstrate how an extracellular signaling system can arise and be co-opted to promote fungal fitness in complex environments.

overall_design: To identify genes involved in the synthesis of farnesol we performed an RNA-seq experiment on two farnesol underproducing transcription factor deletion mutants, msn4 and cas5 that were identified from previous work by our group (Gutzmann et al. 2023 G3). We additionally performed two additional RNA seq experiments, one comparing MAY1375 and cwh8∆∆ cells, and another comparing MAY1375, pTDH3-CWH8 cells, and MAY1375 + 50µM FOH treated cells.

first: Cory

last: Boone

first: Brigid

last: Toomey

first: Shyanne

last: Urbin

first: Wayne

last: Riekhof

first: Kenneth

last: Nickerson

first: Audrey

last: Atkin

first: Deborah

last: Hogan


title: Intracellular Salmonella gene expression profile at onset (0h), early (4h), middle (8h), and late (12h) stage of bone marrow-derived macrophage infection

city: Hamilton

first: Marie-Ange

last: Massicotte

state: ON

address: MDCL 2108, 1200 Main St W, McMaster University

department: Biochemistry

institute: McMaster University

summary: We used next generation sequencing to sequence the transcriptome of Salmonella and identify the genes that are differentially regulated throughout the infection of primary macrophages.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Wild-type Salmonella was enriched from infected bone marrow-derived macrophages (C57BL/6J) and RNA was extrated from intracellular Salmonella at 0, 4, 8, and 12 hour post-infection. Transcriptome were sequenced using the Illumina NextSeq 2000 instrument and the processed data was used for differential gene expression analysis to identify the gene that are differentially regulated throught the infection.

first: Aline

last: Fiebig

first: Andrei

last: Bogza

first: Brian

middle: K

last: Coombes