title: The role of Ciliary Muscle Contraction in Myopia Onset

city: Shanghai

first: Peng

last: Zhou

address: 389 Nanjing Xi Rd

institute: Parkway Gleneagles Medical and Surgical Center

summary: To investigate myopia’s pathogenesis involves clinical, animal, and single-cell sequencing studies to reveal underlying mechanisms. We compared cycloplegia (ciliary muscle relaxed) and non-cycloplegia (ciliary muscle contracted) groups to measure axial length in adolescents. Post-mortem mouse eyes underwent single-cell transcriptomic sequencing for cellular analysis.

overall_design: We conducted single-cell RNA sequencing to investigate the cellular and molecular effects of ciliary muscle contraction on the eyes. Our study comprised two experimental groups: the Ciliary Muscle Relaxation Group, treated with tropicamide eye drops administered every 10 minutes for a total of 6 applications, followed by a one-hour waiting period; and the Ciliary Muscle Contraction Group, which received saline drops at the same frequency. Each group included 12 mice, and only the right eyes were analyzed in this study. Due to the small size of mouse eyes and to ensure an adequate number of cells for sequencing, we pooled four eyes to create a single sample. Post-euthanasia, the eyeballs were enucleated. Using scalpels and micro-scissors, we excised the lens, cornea, and iris-ciliary body, preserving only the posterior sclera, choroid, and retina. These residual ocular cup tissues were gently dissociated into single-cell suspensions

first: Zhou

last: Peng

first: Fan

last: Lei


title: GPNMB as a viable CAR Target for MITF pathognomonic fusion-driven cancers: A first-in-person GCAR1 Trial

status: Public on Apr 02 2026

city: Calgary

first: Sorana

last: Morrissy

state: Alberta

address: 3330 Hospital Dr NW

department: Department of Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

summary: CAR T therapy for solid tumours is limited by a lack of safe and uniformly expressed cell-surface targets. We identify the MITF-driven gene GPNMB as being highly, homogeneously and stably expressed from primary and relapsed translocation-positive alveolar soft part sarcoma (ASPS) and renal cell carcinoma (tRCC). We developed a 2nd generation GPNMB-targeting CAR T therapy (GCAR1) that shows activity against cells, organoids and PDX models. First-in-person GCAR1 treatment of a patient with metastatic ASPS was well tolerated and generated stable disease for 6 months, with the majority of non-target lung lesions resolving post-treatment. A diverse population of GCAR1 cells expanded in blood, peaking at 14 days post-treatment. Spatial transcriptomics revealed immunosuppression, including PDL1 expression, in close proximity to T cells infiltrating a treatment-resistant lung lesion, and PDL1 blockade showed synergy with GCAR1 in a PDX model. Our data provide a proof-of-concept for targeting oncogenic translocation-driven genes with CAR T therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A total of four samples were used in this analysis, three of which came from a rapidly progressing stage IV metastatic alveolar soft part sarcoma (ASPS) patient and a single sample from a patient-derived xenograft (PDX) model of ASPS treated with GCAR1. For the prior, the three samples included, one section from the untreated primary thigh tumor and two sections from GCAR1 treatment resistant lung needle biopsies. The PDX model was developed from a separate patient, and the model, but not the patient, was treated with GCAR1. In all cases, GCAR1 treatment was done at a dose of 1e6 GCAR1 CAR T-cells / kg. All of these samples were analyzed using Visium HD spatial transcriptomics.

first: Gill

last: Gurveer

first: Morrissy

last: Sorana


title: CUX1 Manifests Species-Dependent Regulation in Controlling Adipocyte Differentiation [RNA-Seq]

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: Adipocyte differentiation, also known as adipogenesis, is a crucial process for maintaining the adipocyte pool and plays a key role in insulin sensitivity and systemic metabolism. Adipogenesis is governed by master transcription factors, such as C/EBPβ. However, there remains an unmet need to identify novel transcriptional factors within the C/EBPβ regulatory network in the differentiation of primary human adipose-derived precursor cells (hAPCs). Chromatin immunoprecipitation and selective isolation of chromatin-associated proteins (ChIP-SICAP) and CRISPR/cas9 knockout (KO) screening approach was applied in hAPCs. RNA-seq and ChIP-seq were also utilized for pathway and gene enrichment analyses. We also constructed a APCs-specific KO mouse model. Deletion of CUX1 in hAPCs impairs adipogenesis, whereas CUX1 overexpression (OE) increases human adipogenesis. RNA-seq and ChIP-seq analyses reveal that CUX1 promotes the expression of key adipogenic genes, including PPARG, a master regulator of adipocyte fate determination. Interestingly, Cux1 deletion enhances, while CUX1-OE suppresses adipogenesis in mouse APCs (mAPCs). ChIP-seq analysis of CUX1 in mAPCs further supports its contrasting role in mice. Additionally, in vivo tracing of mAPCs shows that Cux1 deletion promotes adipocyte differentiation. Collectively, these findings highlight that CUX1 exerts species-specific regulation of adipogenesis, acting as a differential regulator of fat development in humans and mice.

first: Chen

last: Yang

first: Liu

last: Lin

first: Calhoun

last: Ryan

first: Cheng

last: Lan

first: Steger

last: David

first: Seale

last: Patrick


title: CAR T therapy against the MiTF-driven protein GPNMB

summary: CAR T therapy for solid tumors is limited by a lack of safe and uniformly expressed cell-surface targets. Here, we identify the MiTF-driven protein GPNMB as being highly, homogeneously, and stably expressed from primary and relapsed translocation-positive alveolar soft part sarcoma (ASPS) and renal cell carcinoma. We developed a GPNMB-targeting CAR T therapy called GCAR1 that shows activity against patient-matched cells, organoids and xenograft models. First-in-human treatment of a patient with metastatic ASPS was well tolerated and generated stable disease until 6 months, with many non-target lesions resolving post-treatment. A polyclonal population of GCAR1 cells expanded in blood and were detectable until 6 months. Spatial transcriptomics revealed multiple immunosuppressive niches in proximity to T cells infiltrating a treatment-resistant lesion, and PDL1 blockade showed synergy with GCAR1 in a xenograft model. Our data provide clinical evidence for treating solid tumors with CAR T cells targeting a surface protein driven by an oncogenic gene fusion.

overall_design: Multiome-seq: Single cells were extracted from the single-patient's peripheral blood samples that were collected before and after GCAR1 infusion. Joint scRNA-and-scTCR libraries were preared using the 10x Genomics platform (10x Genomics Chromium Next GEM Single Cell V(D)J + 5′ Gene Expression).


title: Differential IRES-initiated translation during homeostatic stem cell differentiation and stress

city: Boston

first: Lai Ping

last: Wong

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Cell stress commonly induces preferentially reduced m7G-cap-dependent translation initiation while cap-indendepent, IRES-mediated initiation persists. We investigated differential translation initiation in the highly regulated protein production of somatic stem cells by generating a reporter mouse quantifying the ratio of IRES-mediated to cap-dependent translation in vivo. Both hematopoietic and epithelial stem cells exhibited minimal IRES utilization that progressively increased with differentiation. Notably, even within defined differentiation states, lower IRES/Cap was associated with increased clonogenicity regardless of cell cycle and among HSCs, with greater long-term multi-lineage regeneration. The RNA binding protein PTBP1 is a key modulator of IRES utilization during differentiation by CRISPR/Cas9i screening. Even within IRES-low immature stem/progenitor cells, nutrient stress upregulated IRES utilization, pointing to distinct roles of IRES in cell behavior depending on physiologic state.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design:
We sorted SLAM-LKS, GMP, and MEP from the Translator mouse based on IRES-GFP/Cap-RFP using flow cytometry to evaluate how differential translational initiation activity was transcriptomically associated with differentitation status.
Smart-seq IV was performed on 100 Translator SLAM-LKS, GMP and MEP cells gated based on the ratio of IRES/Cap.
Comparative gene expression analysis was performed to evaluate how IRES/Cap associated with gene expression relevant to primative and differentiated cell states.

first: Michael

last: Mazzola

first: Lai

middle: P

first: Ting

last: Zhao

first: Anna

last: Kiem

first: Maris

last: Handley

first: Ruslan

middle: I

last: Sadreyev

first: David

middle: T

last: Scadden


title: MDM2 degradation overcomes feedback regulation of p53 signaling in Merkel cell carcinoma

first: Andrew

last: Cherniack

state: Mass

address: 450 Brookline Ave

department: Molecular Oncology

institute: Dana Farber Cancer Institute

summary: This study explored the efficacy of MDM2 degraders, KTX-049 and KT-253, in treating Merkel cell carcinoma (MCC), an aggressive skin cancer. MCC tumors often exhibit clonal integration of Merkel cell polyomavirus, with virus-positive (MCCP) and virus-negative  (MCCN) tumors showing distinct molecular profiles. MDM2, a target of the ST-MYCL- Tip60 complex in MCCP, inhibits p53-mediated tumor suppression. Our results  demonstrate that KTX-049 is over 100 times more potent than the MDM2 inhibitor DS- 3032 in MCC cell lines with wild-type p53, effectively degrading MDM2 and activating the  p53 response. Mathematical modeling indicates that KTX-049 collapses the p53-MDM2 feedback loop, enhancing its potency. In vivo, KT-253 induced robust and durable p53 pathway activation, producing deep tumor regressions in patient-derived xenograft models. However, the observed resistance was linked to TP53 mutations. These findings highlight the potential of MDM2 degraders as a therapeutic strategy for MCC and other tumor types with wild-type p53 and underscore the need for further investigation of resistance mechanisms and combination therapies.

overall_design: This study includes 1) RNA-seq profiling of Merkel cell carcinoma established cell lines MKL-1 and WaGa treated with DMSO, an MDM2 degrader KTX-049 or an MDM2 inhibitor DS-3032. 2)RNA-seq profiling of Merkel cell carcinoma PDX and CDX derived cell lines treated with DMSO or KTX-049.

first: Varsha

last: Ananthapadmanabhan

first: Simone

last: Bruno

first: Leonard

last: Vonk

first: Yu-Chen

last: Cheng

first: Abeba

last: Teshager

first: Benjamin

middle: K

last: Eschle

first: Charles

middle: L

last: Howarth

first: Joana

middle: S

last: Rodrigues

first: Julia

last: Schnabel

first: Ananya

last: Kodali

first: Prafulla

middle: C

last: Gokhale

first: Rujuta

last: Kshirsagar

first: Susanne

middle: B

last: Breitkopf

first: Kirti

last: Sharma

first: Joao

middle: A

last: Paulio

first: Yvonne

last: Li

middle: D

first: Franziska

last: Michor

first: Yogesh

last: Chutake

first: Joyoti

last: Dey

first: James

last: DeCaprio


title: Mitochondrial L-2-hydroxyglutarate is a physiologic signaling metabolite [PRO-seq]

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: L-2-hydroxyglutarate (L-2-HG) is a low-abundance metabolite in mammals, due to the mitochondrial enzyme L-2-HG dehydrogenase (L2HGDH), which oxidizes L-2-HG to 2-oxoglutarate (2-OG) to prevent its accumulation1. In humans lacking L2HGDH activity, L-2-HG builds up, leading to L-2-HG aciduria, a rare childhood neurometabolic disorder2. Thus, L-2-HG is classified as a toxic metabolite2–5. Furthermore, L-2-HG is produced in response to hypoxia, acidic pH, and electron transport chain (ETC) impairment6–10. We investigated the regulation of L-2-HG levels, its impact on gene expression, and whether it has a physiological role in mice. Here, we report that elevated mitochondrial NADH/NAD+ triggers malate dehydrogenase 2 (MDH2) to produce L-2-HG from 2-OG. By contrast, L2HGDH converts L-2-HG to 2-OG in the mitochondrial matrix without requiring a functional ETC. Nascent gene expression analysis in mouse embryonic stem cells (mESCs) demonstrated that the majority of genes were downregulated by elevated L-2-HG levels. To identify proteins involved in L-2-HG-dependent gene regulation, we used proteome integral solubility alteration assays (PISA), which showed that L-2-HG engages the RNA demethylase FTO and H3K9 demethylases KDM4A/B/C in mESC nuclear extracts. The L-2-HG-dependent accumulation of m6A in mRNAs and H3K9me3 at the gene loci negatively correlated with gene expression. Importantly, mitochondrial L2HGDH overexpression during early embryogenesis lowered basal L-2-HG levels and resulted in viable mice at birth but triggered reduced growth, impaired kidney function, and post-natal mortality. Thus, L-2-HG primarily downregulates gene expression and is a signaling metabolite necessary for post-natal mammalian growth and survival. These findings suggest that other previously considered toxic metabolites might also play physiological roles.

overall_design: PRO-seq (Precision Run-On Sequencing) to investigate whether L-2-HG metabolite has a physiological role in mice.

first: Ram

last: Chakrabarty

first: Jonathan

middle: G

last: van Vranken

first: Yuki

last: Aoi

first: Marta

last: Iwanaszko

first: Navdeep

last: Chandel


title: Mitochondrial L-2-hydroxyglutarate is a physiologic signaling metabolite [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of H3K9me3 to investigate whether L-2-HG metabolite has a physiological role in mice.


title: Transcriptom anasys of human induced stem cell-derived endothelial cells and retianl endothelial cells

city: Durham

first: Ying-Yu

last: Lin

address: 534 Research Drive

institute: Duke University

summary: This study conducts a comprehensive transcriptome analysis to compare human induced pluripotent stem cell-derived endothelial cells (iECs) with retinal endothelial cells (iRECs). By examining gene expression profiles, we aims to identify molecular distinctions and similarities between these cell types. With an increasing need to develop tissue-specific endothelial cells for more accurate disease modeling and personalized therapies, this work highlights the unique features of retinal endothelial cells. Understanding these differences is crucial, as retinal endothelial cells play a key role in ocular diseases such as diabetic retinopathy and aged-related macular degeneration. Insights from this study could enhance the development of targeted therapies for retinal vascular disorders.

overall_design: RNA-seq profiling of iECs and matched differentiation of iRECs derived from the same iPSC line (WTC-TJP1) and analyzed at passage1

first: Parker

last: Esswein

first: Sharon

last: Gerecht


title: Distinct cytokines regulate gene expression and anti-tumor activity in regenerated CD8+ T cells derived-from induced pluripotent stem cells.

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Adoptive T cell therapy can induce tumor regression in cancer patients. Tumor-specific CD8+ T cells regenerated from induced pluripotent stem cells (iPSCs), termed regenerated cytotoxic T lymphocytes (CTLs), are promising resources for adoptive T cell therapy. However, it remained unclear what kinds of cytokines enhance the anti-tumor activity of regenerated CTLs. In this study, we examined the effects of exogenous cytokines on the characteristics of regenerated CTLs. We found that IL-15- or IL-21-treatment in vitro enhanced the anti-tumor activity of regenerated CTLs, presumably by different mechanisms. IL-15-treated regenerated CTLs showed early-effector-like characteristics, whereas IL-21-treated regenerated CTLs showed both naïve- and effector-like characteristics. These findings provide useful insights for the clinical application of regenerated CTLs in the future.

overall_design: WT1-specific regenerated CD8+ T cells derived from induced pluripotent stem cells (iPSCs) were stimulated with WT1 peptide-pulsed lymphoblastoid cell line (LCL) in the presence of indicated cytokines for 7 days. RNA of the cytokine-treated cells was extracted and analyzed by RNA-seq.

first: Kenta

last: Kondo

first: Nobuhito

last: Nitta

first: Koji

last: Terada

first: Yusuke

last: Sano

first: Mina

last: Kumode

first: Seiji

last: Nagano

first: Kyoko

last: Masuda

last: Okuzaki

first: Toru

last: Miyake

first: Masaji

last: Tani

first: Hiroshi

last: Kawamoto

first: Yasutoshi

last: Agata


title: Spatial transcriptomic sequencing data of human small cell lung cancer

city: Guangzhou

first: Xiaodong

last: Ma

state: Guangdong

address: No.55, West of ZhongShan Avenue, Tianhe District

country: China

institute: Department of Brain Science and Rehabilitation Medicine

summary: Small cell lung cancer is a lung tumor with extremely poor prognosis, and its tumor heterogeneity and unique microenvironment remain unclear. This study aimed to reveal the early tumorigenesis and microenvironment of small cell lung cancer by performing idle transcriptomic sequencing of patients' small cell lung cancer tissues.

overall_design: In this design, human small cell lung cancer tissue was cryosectioned for spatial transcriptomic sequencing(10X Visium) and downstream bioinformatics analysis.

first: Ming

last: Liu

first: Hua

last: Wu

first: Jun

first: Yang


title: Identification of GLIS2 direct target genes in kidney

city: Research Triangle Park

first: Anton

middle: M

last: Jetten

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

summary: Loss of function of the transcription factor GLIS2 in humans and mice causes nephronophthisis (NPHP). To obtain insights into the role of GLIS2 in the regulation of normal kidney functions and in the development of NPHP, we investigated GLIS2 direct target genes in kidney. Due to a lack of suitable GLIS2 antibody for chromatin immunoprecipitation (ChIP), we  generated Glis2-HA mice in which HA tag was inserted before the TGA stop codon of GLIS2. Thereby, endogenous GLIS2 protein is expressed as a fusion protein with HA tag.  GLIS2 ChIP-Seq was performed using HA antibody with kidneys from Glis2-HA mice. GLIS2 cistrome analysis identified many of genes associated with inflammation, ECM, and cell adhesion as direct targets by GLIS2.

overall_design: ChIP-Seq was performed with kidneys from Glis2-HA mice using anti-HA antibody.

first: Hong Soon

last: Kang

first: Yun-Gil

last: Roh


title: in vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures [day27NMP_scRNAseq]

status: Public on Apr 01 2026

city: Los Angeles

first: Samantha

last: Butler

state: California

address: 610 Charles E Young Drive East

department: Neurobiology

institute: University of California, Los Angleles

summary: Spinal cord injuries (SCI) result in the loss of motor and sensory function. We are working towards restoring sensation by developing directed differentiation protocols to generate dorsal spinal interneurons (dIs; dI1-dI6) from human embryonic stem cells (hESCs). Here, we present an improved method that produces human dIs via a neuromesodermal progenitor state, the physiological intermediate for spinal cord development. We show that retinoic acid (RA), bone morphogenetic protein 4 (BMP4) and growth differentiation factor (GDF) 11 direct dI identity, while GDF11 and extended time in culture promotes posterior spinal identities. Together, these protocols generate the full complement of dorsal subtypes along the entire anterior-posterior axis of the spinal cord. To benchmark in vitro-derived dIs, we constructed a single-cell RNA-Seq atlas of the human embryonic spinal cord and used it to show that hESC-derived dIs closely match their endogenous counterparts. The atlas also reveals that the dI4/dI5 populations dramatically expand in comparison with the other spinal lineages. Moreover, they have mechanosensory circuit signatures linked to autism spectrum disorder, implicating spinal circuits in autistic phenotypes.

overall_design: Single-cell sequencing of embryonic bodies (EBs) generated from H9 hESC-derived NMPs induced for 2, 4, or 10 days that were treated with RA, RA+BMP4, or RA+GDF11 for a total of 14 days.

first: Sandeep

last: Gupta

first: Eric

last: Heinrichs

first: Cristian

last: Rodriguez

first: Emily

last: Friedman

first: Salena

last: Gallardo

first: Talin

last: Dermirjie

first: Teny

last: Panosian

first: Keith

last: Phan

first: Anooshik

last: Tahmasian

first: Yahir

last: Veridin

middle: J


title: in vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures [day43NMP_scRNAseq]

overall_design: Single-cell sequencing of embryonic bodies (EBs) generated from H9 hESC-derived NMPs induced for 2, 4, or 10 days. EBs were treated with RA, RA+BMP4, or RA+GDF11 to induce relevant spinal neuron cell types. At 43 days, a single cell suspension was obtained from the EBs and sent for scRNA-seq.


title: DYRK1B Overexpression Promotes  Senescence-Like Transcriptional and Secretory Programs in A549 Lung Cancer Cells

city: Aachen

first: Walter

last: Becker

address: Pauwelsstr. 30

department: Institute of Pharmacology and Toxicology

country: Germany

institute: RWTH Aachen University

summary: We investigated the transcriptional changes in A549 lung cancer cells to characterize the effects of DYRK1B kinase overexpression on the phenotype of human A549 lung cancer cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from A549 cells with tet-inducible expression of wild type or mutant (Y273F) DYRK1B. Each cell type (WT and Y273F) was treated or untreated with doxycyclin for 7 days.  Data were obtained for three independent cell populations that were cultivated and lysed in parallel.

first: Gerrit

last: Wilms

first: Soraya

last: Sester

first: Aaron

last: Babendreyer

first: Justyna

last: Wozniak

first: Florian

last: Kraft


title: Cellular Crosstalk Drives Hypertrophic Cardiomyopathy in LZTR1 Deficiency

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: LZTR1 deficiency causes Noonan syndrome (NS) and is associated with the manifestation of severe and early-onset hypertrophic cardiomyopathy (HCM). Although paracrine communication is thought to play a critical role in cardiac pathology, little is known about the underlying pathomechanism leading to the development of HCM and cardiac fibrosis in NS. In the present study, we used 2D and 3D iPSC models with LZTR1 deficiency to dissect the impact of non-cardiomyocytes in the development of NS-associated HCM and uncovered a cytokine-mediated intercellular crosstalk, predominantly activated in the disease state, as a major driver of cardiac hypertrophy and cardiac fibrosis.

overall_design: RNA sequecing of LZTR1-KO vs. LZTR1-WT iPSC-derived engineered connective tissues

first: Lukas

last: Cyganek

first: Jakob

last: Fell

first: Mario

last: Pavez-Giani


title: Transduction of Batf family members provide distinct functions to mouse CD8+ T cells.

first: Daisuke

last: Motooka

summary: BATF family members including BATF, BATF2, and BATF3 has critical roles in various types of immune cells. Several studies have indicated that their functions are redundant as they can compensate for each other’s functions. Here, we show that transduction of Batf family members confers distinct characteristics on CD8+ T cells. Batf- and Batf2-transduced CD8+ T cells exhibited effector and memory-like phenotypes, respectively. Intriguingly, Batf3-transduced CD8+ T cells showed effector- and memory-like phenotypes in response to effector- and memory-associated cytokines, respectively and superior anti-tumor activity in vivo among BATF family members. Our results demonstrated that each BATF family member has distinct functions in CD8+ T cells. These findings help us understand the roles of BATF family members in CD8+ T cells and contribute to the development of optimized adoptive T cell therapies against cancer.

overall_design: Naïve OT-I T cells (CD44low CD62hgih) were isolated from the spleen and stimulated with anti-CD3/28 mAb in the presence of IL-2. On day 1, the activated OT-I T cells were transduced with either an empty or Batf family members-encoding retrovirus. On day 4, the transduced OT-I T cells were cultured in the presence of IL-2 without anti-CD3/28 mAb for 4 days. On day 8, GFP+ OT-I T cells were sorted. RNA of the sorted cells was extracted and analyzed by RNA-sequencing.

first: Kenta

last: Kondo

first: Mina

last: Kumode

first: Koji

last: Terada

first: Yusuke

last: Sano

first: Nobuhito

last: Nitta

last: Okuzaki

first: Kensuke

last: Takada

first: Akira

last: Andoh

first: Makoto

last: Murata

first: Yasutoshi

last: Agata


title: inDropsPilot_29hpf-ef1a-mCherry

city: San Francisco

first: Nicole

last: Aponte Santiago

state: CA

address: 35 Medical Center Way

institute: UCSF

summary: We profiled gene expression during zebrafish development. This inDrops single-cell RNA-seq dataset comprises 12,603 cells collected from 29 hpf Danio rerio embryos. Here, nuclear-tagged mCherry2 is driven by a ~2.2 kb upstream regulatory region of eef1a1l1, enabling ubiquitous nuclear labeling (Tg(eef1a1l1:h2b-mCherry2) /+). Single-cell analysis shows that reporter expression covaries with endogenous eef1a1l1 transcripts, serving as a proxy for eef1a1l1 expression.

overall_design: inDrops scRNA-seq dataset was collected from Tg(eef1a1l1:h2b-mCherry2/+) dissociated zebrafish embryos. Single-cell dissociation was performed on 29 hpf dechorionated embryos (n=57 embryos per sample) and the freshly dissociated samples were encapsulated following the Droplet Genomics protocol.

first: Aponte-Santiago

last: Nicole

first: Wagner

last: Dan


title: Astragaloside IV Modulates Oxidative Stress and Osteoimmune–Wnt Signaling in Ovariectomized Rats: An Integrated Study of RNA Sequencing, Molecular Docking, and Experimental Validation

city: jinzhong

first: xianying

last: yao

address: No. 121, Daxue Street, Yuci District, Jinzhong City, Shanxi Province,

department: The First Clinical College

institute: Shanxi University of Chinese Medicine

summary: Postmenopausal osteoporosis (PMOP) is characterized by high-turnover bone loss and oxidative stress. Astragaloside IV (AS-IV) exhibits antioxidant and immunomodulatory activities, yet its skeletal effects and mechanistic basis in ovariectomized (OVX) models remain incompletely defined.

overall_design: Female Sprague–Dawley rats underwent bilateral ovariectomy. Six weeks after surgery, OVX rats were randomized to model, positive control, or AS-IV treatment (20/40/80 mg/kg, gavage, 8 weeks), with sham-operated controls. Serum bone-turnover markers (CTX-I, OCN, PTH) and oxidative stress markers (SOD, MDA) were measured by ELISA. Femora were assessed by micro-CT (BMD, BV/TV, Tb.N, Tb.Sp) and H&E staining. RNA sequencing was performed followed by GO/KEGG enrichment and WGCNA to identify hub genes, and molecular docking was used to evaluate AS-IV–target interactions. Multiplex immunofluorescence in the femoral trabecular bone quantified Lep, Ptgs2, Gfap, Igfbp2, Wnt1, β-catenin, and NF-κB p65 region (mean fluorescence intensity, normalized to Sham).

first: Xianying

last: Yao


title: mRNA m6A modifications and the RNA-binding protein YTHDF1 affect translational control in both normal and pathological learning

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

summary: Animals learn and adapt to environmental changes. However, neural plasticity can also become maladaptive, leading to neurological and psychiatric disorders. How do we use known molecular mechanisms to harness the power of neural plasticity to prevent and treat diseases? Consolidating learning is known to require new protein synthesis. We found that mRNA m6A modifications and the RNA-binding protein YTHDF1 are required for molecular, cellular, and behavioral adaptations in response to environmental changes. Deletion of Ythdf1 in dopamine D1- or D2 receptor-expressing neurons selectively impaired D1- or D2-dependent learning, respectively, including both adaptive and maladaptive learning. This highlights YTHDF1 as a potential therapeutic target for preventing pathological plasticity. YTHDF1 recognizes m6A modifications on transcripts and regulates their translation. Elevated cAMP triggered increased protein synthesis in control striatal neurons but not in Ythdf1-deficient neurons. Behaviorally, cell-type-specific Ythdf1 deletion resembled learning phenotypes caused by deletion of the m6A methyltransferase gene Mettl14, suggesting YTHDF1 as the main mediator of m6A-dependent regulation in the striatum.

overall_design: Mouse brain tissue was frozen in liquid nitrogen and then thawed in ice-cold RIPA buffer. Tissue was lysed with a douncer and then crosslinked with 245 nm UVC at 45,000 J/m2 total dose. Standard CLIP-seq was performed with monoclonal anti-YTHDF1 antibody (Abcam, ab220162) and RIPA buffer as lysis buffer.

first: Zhuoyue

last: Shi

first: Zhongyu

last: Zou


title: in vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures [day0NMP_bulk RNAseq]

first: Samantha

last: Butler

overall_design: RNA-seq profiling of H9 hESCs induced for 2, 4, or 10 days (in triplicate) with FGF and CHIR, alongside an undifferentiated hESC control.

first: Sandeep

last: Gupta

first: Eric

last: Heinrichs

first: Cristian

last: Rodriguez

first: Emily

last: Friedman

first: Salena

last: Gallardo

first: Talin

last: Dermirjie

first: Teny

last: Panosian

first: Keith

last: Phan

first: Anooshik

last: Tahmasian

first: Yahir

last: Veridin


title: Distinct Dynamics and Composition of Endogenous Neuronal RNA Granules

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

summary: RNA granules are essential regulators of post-transcriptional gene expression, enabling mRNA transport, localization and local translation in neurons. The localized transcriptome is diverse; however, how different mRNAs are organized into granules for efficient localization and translation remains unknown. Here, we combine real time single RNA imaging with protein and RNA proximity labeling to investigate two endogenous neuronal mRNA granule populations, Actb and Arc, in stimulated primary hippocampal neurons. Using orthogonal RNA labeling systems in a dual knock-in mouse model, we show that Actb and Arc mRNAs are packaged into spatially segregated granules with distinct trafficking dynamics, localization kinetics, and responses to synaptic stimulation. While Actb granules displayed rapid and sustained localization, whereas Arc granules showed delayed, transient recruitment, consistent with their respective roles in structural and activity-dependent plasticity. Proximity labeling reveals that these granules are entirely distinct in their RNA signatures, despite sharing core RNA-binding proteins. Using motif analysis, we propose that shared cis-regulatory elements may drive selective co-packaging of mRNAs into unique granules. Together, these findings demonstrate that neuronal mRNAs are differentially sorted into molecularly and functionally distinct granules, providing a framework for understanding how precise spatio-temporal control of mRNA localization and translation is achieved across complex neuronal arbors.

overall_design: Primary hippocampal neurons derived from Actb:24xMBS and Arc:24xPBS transgenic mice were used to characterize the RNA composition of mRNA-containing granules following chemical long-term potentiation (cLTP) stimulation. To identify RNAs in proximity to Actb or Arc transcripts, an APEX2-based RNA proximity biotinylation approach was employed. APEX2 was targeted to specific RNAs via MCP–MBS and PCP–PBS systems, with neurons transduced with lentiviruses expressing MCP-APEX2 or PCP-APEX2 fusion proteins.  Proximity labeling was induced by a 1-minute H₂O₂ treatment at 1 hour post-cLTP stimulation, a time point corresponding to peak cytoplasmic accumulation of Arc mRNA. Following labeling, total RNA was extracted, and biotinylated RNAs were enriched באמצעות streptavidin pulldown and prepared for high-throughput sequencing.  Control conditions included uninfected neurons and scrambled targeting controls (MCP-APEX2 expressed in Arc:24xPBS neurons and PCP-APEX2 expressed in Actb:24xMBS neurons) to account for non-specific labeling.

first: Rogow

last: Jackson

first: Cutler

last: Ronald

first: Das

last: Sulagna


title: in vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures [day0NMP_scRNAseq]

overall_design: Single cell-seq profiling of H9 hESCs induced for 2, 4, or 10 days with FGF and CHIR.


title: Noncanonical PRC1.1 Targets BTG2 to Retain Cyclin Gene Expression and Cell Growth in Neuroblastoma

city: Kita-adachi-gun

first: Shunpei

last: Satoh

state: Saitama

address: Komuro 818, Ina

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: Cancer cells exploit epigenetic modifications and post-transcriptional regulations to form oncogenic gene expression networks. However, how these machineries collaboratively orchestrate malignancy remains elusive. One of aberrant epigenetic pathways in cancer is Polycomb repressive complex 1 (PRC)-mediated H2AK119 monoubiquitination (H2AK119ub1) with subsequent silencing of tumor suppressor genes. Despite previous efforts, the biological and clinical significance of PRC1 remains unclear in neuroblastoma (NB), an aggressive sympathoadrenal solid tumor in children. In this study, we demonstrated that knockdown of RING1A, one of the E3 ubiquitin ligases of PRC1, reduced cell viability and enrichment of H2AK119ub1 in NB cells. Transcriptional profiling revealed RING1A-specific targets, whose lower expression was associated with poor outcomes in NB patients. Among these genes, BTG2, a component of the CCR4-NOT polyA deadenylase complex, harbored a hypomethylated CpG island occupied by H2AK119ub1 and accessory proteins of noncanonical PRC1.1 (ncPRC1.1). Biological experiments uncovered that BTG2 suppressed NB cell growth in vitro and inhibited tumor formation in vivo. Moreover, BTG2 perturbed cell cycle progression and selectively destabilized the mRNAs of the cyclin genes CCNA2, CCNB1, and CCNB2. In NB patient cohorts, lower expression of BTG2 was associated with poor outcomes and inversely correlated with those cyclin gene expression. Collectively, we have uncovered a crosstalk between epigenetic modifications and post-transcriptional regulations, in which ncPRC1.1-mediated silencing of BTG2 retains cyclin gene expression and cell proliferation in NB. This study provides new insights into how epigenetic pathways contribute to NB malignancy.

overall_design: CUT&RUN-sequence of the histone modifications, H2AK119ub1, H3K27me3 and H3K4me3 in NGP cell lines

first: Masayuki

last: Haruta

first: Takehiko

last: Kamijo


title: Downstream genes of HNF4A in H2122 lung adenocarcinoma cells

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary: We performed RNA-seq to determine genes regulated by HNF4A in H2122 lung adenocarcinoma cells.

overall_design: We created human HNF4A8 overexpressing H2122 cells in which H2122 cells were infected with lentiviral HNF4A vector. Control lentiviral vector was used as control. RNA was harvested from the cells for RNA-seq. RNA-seq was conducted at CCHMC Genomics Sequencing Facility.

first: Yutaka

last: Maeda


title: Essential lncRNAs in the human transcriptome

city: New York

first: Wen-Wei

last: Liang

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using RNA-targeting CRISPR-Cas13 screens, we probed how loss of ~5,500 lncRNAs impacts cell fitness across five human cell lines and identified 788 lncRNAs with context-specific or broad essentiality. We confirm their essentiality with individual perturbations and find that the majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that loss of essential lncRNAs impair cell cycle progression and drive apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development. Using ~9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13.

overall_design: To identify essential lncRNAs, we engineered five human cell lines, HAP1, HEK293FT, K562, MDA-MB-231 and THP1, to express the nuclear-localized RfxCas13d effector under doxycycline-inducible control. Next, we transduced each cell line with the lentiviral gRNA library at a low multiplicity-of-infection to ensure each cell received only a single perturbation and induced Cas13 expression via doxycycline addition. We harvested genomic DNA from these cells at 0, 7, and 14 days post-Cas13 induction and computed changes in gRNA abundance via amplicon sequencing.


title: Transcriptomic data of 84K poplar were detected at 3, 6, and 9 days under drought conditions.

city: Heilongjiang

first: huijiao

last: li

address: No.26 Hexing Road, Xiangfang District

institute: Northeast Forestry University

summary: This study aimed to elucidate the molecular mechanisms underlying drought stress responses in 84K poplar by analyzing transcriptomic changes at 3, 6, and 9 days of treatment. It sought to identify differentially expressed genes, key biological pathways (including photosynthesis, ROS metabolism, and hormone signaling), and core regulatory networks involved in drought adaptation.

overall_design: The study was conducted under drought conditions. Each treatment group included three biological replicates, and control samples were included in the treatment groups.

first: Huijiao

last: Li

first: Siyue

last: Qi

first: Tongtong

last: Yao


title: Rat somatic genome editing enables ER+ breast cancer modeling

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Genetically engineered mouse models have advanced cancer research but often fail to capture key features of certain human tumors. Rats, with distinct physiology and tumor biology, offer a powerful alternative, yet their use has been constrained by technical barriers to genome editing. Here, we report efficient somatic genome editing in rats, enabling both Indel and substitution mutations. We then apply this approach to model estrogen receptor (ER)-positive breast cancer, which accounts for ~70% of human cases but remains poorly represented in mice. The resulting rat tumors reproduce hallmarks of human ER+ breast cancer, including ductal histology, hormone responsiveness, and immune-microenvironmental features. By contrast, identical genetic alterations in mice failed to yield ER+ tumors, underscoring critical species differences in tumorigenesis. Together, this work establishes a versatile platform for rapid generation of clinically relevant rat tumor models, opening new avenues to dissect tumor biology, therapeutic response, and immune interactions in previously inaccessible cancer subtypes.

overall_design: Multiple group comparison. We compared the transcriptomes of different rat models, involving six genotypes in all.

first: Wen

last: Bu

first: Yi


title: Ethylene glycol poisoning induces nephrolithiasis including complement-fibrinogen-related renal tubular injury in rats

city: Tokyo

first: Toshihiko

last: Aki

address: 1-5-45 Yushima, Bunkyo-ku

institute: Institute of Science Tokyo

summary:
We conducted transcriptome analysis to search clues to find novel mechanisms during ethylene glycol intoxication (8 g/kg body weight, orally, 2 and 5 days) in rat kidney.
Total RNAs from the control and ethylene glycol groups were subjected to DNA microarray analysis.

overall_design: We analyzed kidney from 1 control rat and 2 ethylene glycol-administered ( 8g/kg,  for 2 or 5 days) rtas using the ClariomS platform.

first: Kana

last: Unuma

first: Shintaro

last: Isa

first: Kanako

last: Noritake

first: Atsushi

last: Yamada

first: Akihiro

last: Tojo


title: Combined dopamine receptor inhibition and radiotherapy target mesothelioma-initiating cells and increase survival in a mouse model of mesothelioma

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

summary: Malignant pleural mesothelioma (MPM) is a rare thoracic cancer associated with poor prognosis and low survival rates. In solid cancers, repurposed dopamine receptor antagonists have been shown to have anti-cancer effects. Moreover, in combination with radiotherapy, quetiapine (QTP), a dopamine (D) 2/3 receptor antagonist, has been shown to interfere with self-renewal capacity in glioma-initiating cells and increase survival in mouse models of glioblastoma. In this study we explore combined treatment effects in MPM. Using mesothelioma cell lines, MSTO-211H, H2052, and H2452, and MSTO-211H-derived orthotopic xenograft mouse model of MPM we examined how QTP combined with radiation affects mesothelioma-initiating cells (MICs) in vitro and survival in vivo. Subsequently, bulk and single cell RNA sequencing was used to characterize the transcriptomic landscape of MSTO-211H treated with combined radiation and QTP. We demonstrate that combining QTP with radiation reduces MIC self-renewal capacity and stem cell frequency. In vivo, this combination therapy significantly extends the median survival of mesothelioma-bearing mice. Clonogenic survival assays revealed that QTP does not enhance radiosensitivity in the tested mesothelioma cell lines. Sequencing data revealed, combined treatment upregulated genes involved in cholesterol homeostasis, depleted cancer stem cells, and increased cellular senescence. Taken together, our study highlights the therapeutic potential of radiation with QTP in the treatment of MPM.

overall_design: MSTO-211H mesothelioma-initiating cells were seeded in suspension in a flask. Cells were treated with QTP (10 uM) or vehicle control and irradiated with 4 Gy or sham irradiated the next day. 48 hours after the irradiation, RNA was isolated.

first: Cardenas

last: Anjelica


title: Oxygen-generating microparticles enhance viability and functionality of human pluripotent stem cell-derived cardiomyocytes

first: JIALIANG

last: LIANG

address: 231 Albert Sabin Way

department: Department of Pathology and Laboratory Medicine

institute: University of Cincinnati

summary: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent a promising therapy for myocardial infarction (MI), but their survival is severely limited by the hypoxic infarct environment. The optimal oxygen levels required to maintain the viability and functionality of hiPSC-CMs remain poorly defined. This study aimed to develop a controlled oxygen-delivery system to support engineered heart tissue (EHT) for cardiac regeneration. Oxygen-generating particles (OGPs) were engineered using peroxide (sodium percarbonate) and antioxidant (β-carotene) components encapsulated in PLGA microparticles. The effects of OGPs on hiPSC-CMs were evaluated through oxidative stress assays, cell viability analysis, and contractility measurements. RNA-seq was performed to investigate gene expression changes in hiPSC-CMs in response to OGPs and hypoxic stress. Transcriptomic analysis revealed that genes associated with CM maturation and contractile function were upregulated following OGP pretreatment. RNA-seq further demonstrated activation of oxygen-responsive metabolic pathways that facilitated cellular adaptation to hypoxic stress. OGP-mediated oxygen delivery offers a promising strategy for oxidative preconditioning and significantly improves the regenerative efficacy of hiPSC-CM-based cardiac therapies.

overall_design: Experiment 1: hiPSC-CMs were generated using a Wnt activation/inhibition protocol. Following 10 days of induction, cells were treated with OGPs or vehicle control for 24 hours. Total RNA was then isolated from undifferentiated hiPSCs, vehicle-treated hiPSC-CMs, and OGP-treated hiPSC-CMs for RNA sequencing. Experiment 2: After 10 days of differentiation and subsequent purification, hiPSC-CMs were treated with OGPs or vehicle control and exposed to hypoxic conditions (1% O₂). After 24 hours, total RNA was extracted from both groups for RNA sequencing.

first: Jialiang

first: Xingyu

last: He


title: Distinct signalling centre and progenitor identity dynamics initiate human forebrain patterning

city: London

first: Fursham

last: Hamid

address: 1 Newcomen St

country: United Kingdom

institute: KCL

summary: At which developmental stage does the human brain start to differ from other mammals? We uncover human features of telencephalic patterning as early as the fourth post-conception week, comparing the early mouse and human forebrains using single-cell transcriptomics and 3D spatial multi-transcript imaging. In comparison to mice, the human telencephalon is delayed in ventral SHH signaling, accompanied by a human signature of anterior FGF signaling. These observations correlate with a less-resolved patterning and reduced progenitor diversity along the dorsoventral and anteroposterior axes, as well as a human early neurogenic signature. Our complementary approaches reveal a human divergence in allocation of telencephalic progenitor identities, propelled by temporal and qualitative differences in ventro-anterior signals following neural tube closure in the developing forebrain.

overall_design: Forebrain (telencephalon) was dissected from from fresh human embryo (CS12, CS13, CS15, CS17) and mouse embyro (E9.5, E10.5, E11.5, E12.5) heads and dissociated into single cells suspensions. Single-cell sequencing libraries were prepared using  Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit (v3.1) and sequenced on the HiSeq4000 system (Illumina).

first: Afnan

last: Azizi

first: Dana

last: Fakhreddine

first: Zeno

last: Messi

first: Stephanie

last: Strohbuecker

first: Francois

last: Guillemot

first: Corinne

last: Houart


title: ACSS2 supresses ferroptosis via E2F1-SLC7A11 signaling in breast cancer brain metastasis

city: Philadelphia

first: Mauricio J.

last: Reginato

state: Pennsylvania

address: 245 N. 15th Street.

institute: Drexel University College of Medicine

summary: Brain metastasis in breast cancer patients represents a terminal disease stage, with median survival typically measured in months. Tumors that colonize the brain must adapt to its unique microenvironment, such as high acetate levels. Primary brain tumor cells enhance acetate conversion to acetyl-CoA through phosphorylation of acetyl-CoA synthetase 2 (ACSS2) by cyclin-dependent kinase 5 (CDK5), a process regulated by the nutrient sensor O-GlcNAc transferase (OGT). In this study, we showed that brain-metastatic breast cancer cells exhibited elevated O-GlcNAc, OGT, and phosphorylated ACSS2 (Ser267) compared to their parental counterparts. Both OGT and CDK5 were essential for in vivo tumor growth in the brain, and ACSS2 and a phospho-mimetic S267D mutant drove progression of brain metastatic breast cancer. Mechanistically, ACSS2 supported tumor cell survival by suppressing ferroptosis through E2F1-dependent transcription of the anti-ferroptotic protein SLC7A11. Treatment with brain-penetrant ACSS2 inhibitor AD-5584 induced ferroptosis and significantly suppressed breast cancer brain metastatic growth ex vivo and in vivo. Together, these findings identify ACSS2 as a key metabolic regulator of brain-metastatic breast cancer survival and a promising target for ferroptosis-inducing therapies.

overall_design: To study the contribution of ACSS2 in regulating breast cancer brain metastatic growth, an RNA transcriptional profiles were generated from control shRNA or from shRNA targeting ACSS2 in breast cancer brain tropic MDA-MB-231-BR cells.

first: Riley

last: Young

first: Emily

last: Esquea

first: Lorela

last: Ciraku

first: Jessica

last: Merzy

first: Nusaiba

last: Ahmed

first: Alexandra

last: Talarico

first: Mangalam

last: Karuppiah

first: Wiktoria

last: Gocal

first: Alexej

last: Dick

first: Nicole

last: Simone


title: Deep invaginations of nuclear envelope coordinate spatial organization of chromatin

city: Tampere

first: Elina

last: Mantyla

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University Foundation

summary: Epithelial maturation, increase in cellular packing density and associated suppression of MAPK signaling induces deep invaginations of the nuclear envelope (DINEs). The DINEs are associated with both transcriptionally active and repressed chromatin. Here, ATAC-seq was used to identify global chromatin accessibility in mature epitheliumcontaining DINEs  in comparison a newly (2 h) seeded epithelium detached from mature epithelium (grown for 7 d) and not containing DINEs.

overall_design: ATAC-seq of epithelial Madine Darby canine kidney type II (MDCKII) cells grown for 7 d until full maturity, or from MDCKII cells grown for 7 d until full maturity, detached and reseeded for 2 h.

first: Sanna

last: Korpela

first: Anna

last: Rekonen

first: Sini

last: Hakkola

first: Jenni

last: Karttunen

first: Anni

last: Pörsti

first: Sanni

last: Erämies

first: Fábio Tadeou

last: Arrojo Martins

first: Roselia

last: Davidsson

first: Markus

last: Ojanen

first: Satu

last: Hakanen

first: Peipei

last: Wang

first: Joonas

last: Uusi-Mäkelä

first: Alice

last: Anais Varlet

first: Maija

last: Vihinen-Ranta

first: Daniel

middle: E

last: Conway

first: Keijo

last: Viiri

first: Matti

last: Nykter

first: Jan

last: Lammerding

first: Teemu

last: Ihalainen


title: RNA-seq for intracerebral hemorrhage model in Sprague-Dawley rats

city: Guiyang

first: Ke

last: Zhang

address: No.28, Guiyi Road, Liuguangmen

institute: Gui zhou Medical University

summary: This study aims to explore how inhibition of the Sp1/CTR1 axis affects cuproptosis and axonal repair after intracerebral hemorrhage in rats using RNA-seq

overall_design: Rats were divided into three groups: sham, ICH, and ICH+MA, with 5 rats per group. RNA-seq was performed on brain tissues 72h post-modeling. Differentially expressed genes between sham and model groups were screened, then genes with reversed expression in the inhibitor group were identified. Intersection genes were used for KEGG enrichment, focusing on cuproptosis-related genes


title: Stromal TNF–NFκB signaling impairs acinar differentiation through inflammation-driven epithelial–stromal crosstalk in chimeric salivary gland organoids

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Salivary gland organoids enable long-term epithelial expansion but lack stromal compartments that regulate glandular differentiation in vivo. Here, we developed chimeric salivary gland organoids (cSGOs) by layering embryonic day 13 stromal cells over postnatal day 1 epithelial organoids. cSGOs incorporated fibroblasts, immune cells, endothelial cells, and neuronal populations while preserving acino-ductal architecture. Single-cell RNA sequencing revealed that stromal fibroblasts supply FGF ligands supporting epithelial proliferation, yet acinar differentiation remained stalled. Pseudotime and pathway analyses identified TNF-NFκB signaling from stromal immune cells as selectively enriched in proacinar cells. Dexamethasone suppressed this inflammatory axis, expanded the proacinar population, and restored acinar marker expression. Direct NFκB inhibition with BAY11-7082 phenocopied the glucocorticoid effect, implicating epithelial NFκB as a stromal-derived inflammatory checkpoint limiting acinar maturation. These findings support a mechanistic link between stromal inflammation and impaired acinar differentiation and identify a candidate signaling node for therapeutic intervention.

overall_design: Organoids from four conditions (nSGOs with growth factors, nSGOs without growth factors, cSGOs, and Dexa-treated cSGOs) were used for single-cell RNA sequencing.

first: Yeo-Jun

last: Yun

first: Yongjun

last: Koh

first: Jae-Yol

last: Lim


title: Type-I Interferon drives T-cell responses to amyloid-beta in the central nervous system

city: Heidelberg

first: Julius

last: Michel

address: Im Neueunheimer Feld 280

department: Neuroimmunology and brain tumor immunology

summary: This repository contains raw and processed targeted spatial transcriptomics data generated from cerebral cortex sections of APP23^het transgenic and wild-type mice at 13 and 24 months of age, as well as human Alzheimer’s disease cortical tissue. Spatial profiling was performed using the Molecular Cartography™ platform (Resolve Biosciences), an imaging-based highly multiplexed single-molecule fluorescence in situ hybridization (smFISH) technology.    The dataset includes raw transcript coordinate files, as well as cell segmentation outputs generated by the platform’s segmentation algorithm. Both segmentation-free (transcript-based) and segmentation-based spatial analyses were performed.    These data were used to investigate age-dependent immune cell composition and spatial enrichment of T-cell phenotypes in amyloid plaque-associated regions, as described in the associated manuscript.    Detailed experimental procedures, gene panels, preprocessing steps, normalization, clustering, and spatial analysis methods are provided in the Methods section of the publication.

overall_design: Mouse:Coronal sections of the cerebral cortex of in total eight cryo-preserved APP23-tg and Wt mouse brains (n = 2 per group) were subjected to targeted spatial transcriptomics using the Molecular Cartography™ platform (Resolve Biosciences). For each mouse, a single brain hemisphere was analyzed. Human: Alzheimer’s disease patient tissue from the cerebral cortex of in total 4 patients was used, 1cm3 cryo-conserved tissue cores were sectioned, and two sections per patient were used for spatial transcriptomics using the Molecular Cartography™ platform (Resolve Biosciences).


title: Sensory nerve input is not required for digit tip regeneration

city: Guelph

first: Samantha

last: Payne

state: ON

address: 50 Stone Road East

institute: University of Guelph

summary: Peripheral nerves are a major component of the post-injury microenvironment and are required for successful appendage regeneration in non-mammalians. However, the role of innervation in mouse digit tip regeneration is unclear. We developed a denervation technique that maintains mechanical loading while significantly reducing innervation to the digit. Using this model, we found that denervation does not impair digit tip regeneration. Histological analysis showed the amputation stump proceeds through the expected phases of wound healing, blastema formation, and tissue outgrowth, and that regenerate bone volume is not significantly impaired in denervated digits. Interestingly, despite minimal change in regenerative outcome, bulk RNA sequencing identified significant changes in gene expression over time during regeneration in the absence of innervation. This study is the first to use RNA sequencing to characterize changes in gene expression during digit tip regeneration in the absence of innervation. Overall we show that digit tip regeneration is not dependent on innervation and our results suggest that regeneration may be achieved through activation of redundant signalling pathways.

overall_design: RNA-Seq profiling of SHAM and spared nerve injury (SNI) surgery murine digit tips over 7, 14 and 21 days post amputation.

first: Abby

last: Gloade

first: Ian

last: Tobias

first: Maia

last: Hoover

first: Melissa

last: Hardman


title: Disease-associated microRNA, miR-9-2, is required for the timing of retinal progenitor cell competence and the maintenance of Müller glial identity

city: Seattle

first: Timothy

middle: Joel

last: Cherry

state: WA

department: Pediatrics

institute: University of Washington/Seattle Children's Research Institute

summary: The development of vision is dependent upon precise regulation of cell fate specification. In the mammalian retina, a single pool of multipotent progenitor cells becomes competent to produce the seven major retinal cell classes in distinct but overlapping windows. MicroRNAs (miRNAs) have been implicated in controlling retinal progenitor competence and risk for retinal disease, but it is still unclear which individual miRNAs drive this regulation. Using immunohistochemistry and single-nuclei RNA-sequencing of miR-9-2 enhancer and miR-9-2 knockout mice, we find that specific disruption of miR-9-2, one of three mammalian miR-9 paralogs, delays the emergence of late-born retinal cell classes and leads to misspecification of Müller glial cells to a hybrid neuronal-glial fate. Further, we identify transcription factors and gene regulatory networks directly regulated by miR-9-2 during this process. Thus, this study provides insight into the regulation of the timing of retinal progenitor competence and the risk for retinal disease.

overall_design: Single-nucleus RNA-sequencing profiling of mouse retinas. Mouse retinal development profiled at E16.5, P0, and 3-weeks for litter- and sex-matched pairs of miR-9-2 knockout and wildtype mice. Mature retinas profiled at 5-weeks for litter- and sex-matched pairs of miR-9-2 enhancer knockout and wildtype mice.

first: LuLu

last: Callies

first: Emma

last: Thomas


title: Gene Expression Profiling of T- and NK-cell Lymphoma Cell Cultures

city: Chapel Hill

first: Adam

last: Palmer

address: 116 Manning Drive

department: Pharmacology

institute: University of North Carolina at Chapel Hill

summary: RNA-seq gene expression profiling was performed on 30 established T- and NK-cell lymphoma cell cultures. These data were collected to for the measurement of correlations between gene expression profiling and the sensitivities of T- and NK-cell lymphoma cultures to small molecule therapies used in the treatment of T- and NK- lymphomas.

overall_design: RNA was extracted from 1 M cultured cells, taken after cells had been grown up to a high densitv, >400,000 live cells per mL in RPMI. Total RNA was extracted using Rneasy extraction kit from QIAGEN. Samples were shipped to Novogene corporation where cDNA library perparation and sequencing were performed. NovaSeq 6000 was used (A01426) in one lane of an S4 Flow Cell (ID#H73WJDSX2).

first: Pantazis

last: Jacob

first: Pomeroy

last: Amy

first: Palmer

last: Adam


title: Comparative studies of RNAs in GICs and ISX9-treated GICs

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku

institute: Hokkaido University

summary: To identify genes that increase or decreaes in ISX9-treated GICs, we compare the expression levels of RNAs in ISX9-treated GICs with those in GICs.

overall_design: We cultured GICs with or without ISX9, purified total RNA, and then used them for RNA sequences.


title: Expression profiling of WT mouse liver after saline, TNF, or IL-1 treatment

city: Hiroshima

first: Yoshihiro

last: Tsuchiya

state: Hiroshima

address: 4-13-1 Ushita Higashi Higashi-ku

department: Department of Nutrition and Health Promotion

institute: Hiroshima Jogakuin University

summary:
Microarray analysis of WT mouse liver under saline, TNF, and IL-1 conditions using the Affymetrix Mouse Genome 430 2.0 Array.
This study was designed as an exploratory reference dataset to assess cytokine-associated transcriptional responses in the liver.

overall_design: Total RNA extracted from liver tissues was analyzed on the GeneChip Mouse Genome 430 2.0 Array (Affymetrix). WT mouse liver samples from saline-, TNF-, and IL-1-treated conditions were profiled (n = 1 per condition).

first: Yusuke

last: Sotomaru


title: Secreted Protein Combination GAPDH/S100A8/S100A9 from Human Expanded Potential Stem Cells Counteracts Mesenchymal Stem Cell Senescence

city: Guangzhou

first: Guang

last: Shi

address: 135 Xingang Xi Road, Haizhu District

department: School of Life Sciences

institute: Sun Yat-sen University

summary: Human mesenchymal stem cells (hMSCs) remain the most clinically advanced adult stem cell source; however, their therapeutic potential is limited by rapid replicative senescence during ex vivo expansion. Replicative senescence in hMSCs is characterized by cell cycle arrest, acquisition of senescence-associated β-galactosidase (SA-β-Gal) activity, and secretion of the senescence-associated secretory phenotype (SASP) factors. We investigated whether conditioned medium derived from human extended pluripotent stem cells (hEPSCs), which possess both embryonic and extra-embryonic developmental potential beyond that of conventional hESCs, could attenuate replicative senescence in hMSCs. Using sequential ultrafiltration (10 kDa and 3 kDa) followed by LC-MS/MS, we identified several proteins from hEPSC-conditioned medium. We then tested the combination of S100A9/GAPDH/S100A8 proteins for their effects on doxorubicin-induced and replicative senescence.hEPSC-conditioned medium markedly attenuated replicative senescence in hMSCs. Notably, the combination of S100A9/GAPDH/S100A8 proteins not only mitigated doxorubicin-induced senescence but also counteracted replicative senescence, as evidenced by a significant reduction in SA-β-Gal-positive cells and downregulated mRNA expression of senescence-associated genes, including p16, p21, and the SASP factor IL-6. Furthermore, EdU incorporation assays revealed significantly enhanced proliferative capacity following treatment. Collectively, our findings establish a defined protein combination (S100A9/GAPDH/S100A8) that counteracts both replicative and stress-induced senescence, offering a novel, cell-free strategy to enhance the clinical utility of hMSCs.

overall_design: RNAseq profiling of wildtype hMSCs, EGFP-treated hMSCs and S100A9/GAPDH/S100A8-treated hMSCs at day 20.


title: Glypican-1 upregulation elicited in response to a cell-impermeable kinase inhibitor and its overexpression enhance HIV infection

city: Bronx

first: Ronald

last: Cutler

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Studies of herpes simplex virus (HSV) entry uncovered a previously unappreciated “outside-in” signaling pathway whereby activation of the calcium (Ca2+) responsive enzyme phospholipid scramblase 1 (PLSCR1), which is known to trigger the bidirectional movement of phosphatidylserines (PS) between the inner and outer leaflet of the plasma membrane, also induces the movement and subsequent extracellular activation of intracellular proteins, including Akt. We hypothesized that HIV-1, which has been shown to elicit PS externalization by the scramblase TMEM16F, may trigger a similar “outside-in” signaling cascade involving exofacial kinase activity to promote its entry into CD4+ T cells. To study this process, we utilized a cell impermeable broadly active kinase inhibitor based on staurosporine, CIMSS, which blocks HSV-induced exofacial Akt phosphorylation and HSV infection. Using multiple cell types including TZM-bl, Jurkat T cells, and human peripheral blood mononuclear cells (PBMCs), we show that inhibition of exofacial kinase activity via CIMSS promotes HIV-1 infection in a post-entry manner that is not linked to its utilization of TMEM16F. To identify potential targets of CIMSS, we performed bulk RNA-sequencing and whole cell proteomics and found that CIMSS treatment of cells robustly upregulates the cell-surface proteoglycan glypican-1 (GPC1). GPC1 overexpression and knockdown reveal that the presence and absence of GPC1 independently of CIMSS treatment significantly impacts HIV-1 infection. Further, we identify that the influence of GPC1 on HIV-1 infection is in part mediated by TGF-b signaling. Collectively, these findings implicate exofacial kinase activity in restricting HIV-1 infection and identify GPC1 as a novel modulator of HIV-1 infection.

overall_design: RNA-Seq profiling of Jurkat-CCR5 cells and the effect of alkyl-CIMSS in the context of HIV-1BaL infection.

first: Vinzant

last: Kelsey

first: Cutler

last: Ronald

first: Herold

last: Betsy


title: DNA methylation shapes transcription factor binding beyond canonical CpG contexts - array 6

city: rehovot

first: irina

last: miodownik

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

summary: Here, we systematically profile the methylation sensitivity of 18 human TFs spanning 11 structural families using chemically synthesized DNA libraries containing position-specific 5-methylcytosines (5mC) in CpG, non-CpG, and hemi-methylated contexts, measured via high-throughput protein-binding microarrays. Our results reveal extensive TF  sensitivity to methylation state, position, and strand orientation—including strong binding of several TFs to non-CpG and hemi-methylated sites. The presence of 5mC can dramatically alter TF-DNA interactions: transforming low-affinity sites into high-affinity ones by enabling new contacts, or silencing otherwise favorable motifs through steric hindrance. Genomic analyses further show that the methylation-sensitive sequences identified in vitro are represented within enhancers and regulatory elements, exhibiting distinct methylation patterns across cell types. Together, our findings uncover a previously hidden layer of methylation-dependent TF-DNA recognition, broadening the understanding of epigenetics in transcriptional regulation.

overall_design: Each sequence includes a 8-12 bp region containing a known TF binding site from previously published literature. For each binding site, we generated a comprehensive set of variants by introducing all possible single-base mutations at each position, including 5mC:G base pairs on both strands. To explore CpG methylation effects, every pair of adjacent bases was systematically altered to create unmethylated, hemi-methylated, or fully methylated CpG dinucleotides. For binding sites containing multiple CpG dinucleotides, all combinations of methylation states (methylated and unmethylated cytosines) at those positions were incorporated. Finally, many control sequences were added (e.g.: randomized sequences, sequences with 5mC outside of the binding site).

first: Irina

last: Miodownik

first: Ruben

last: Solozabal

first: Michael

last: O'Hagan

first: Shira

last: Albeck

first: Yoav

last: Peleg

first: Martin

last: Takac

first: Ariel

last: Afek


title: Regulation of Cyclic Lipopeptide Orfamide A Biosynthesis in Pseudomonas protegens by the Gac-Rsm-LuxR Cascade

city: Suzhou

first: Chenjie

last: Yu

state: Jiangsu

address: Xiyuan road 279

institute: Suzhou Polytechnic Institute of Agriculture

summary: Orfamide A, a lipopeptide produced by Pseudomonas protegens Pf-5, is a key determinant of its biocontrol properties. In this study, we investigated the regulatory interactions among the GacS/A two-component system, small RNAs (sRNAs), repressor proteins, and two LuxR-type transcription factors in orfamide A biosynthesis. We found that GacS/A indirectly regulates orfamide A production by enhancing transcription of three sRNAs (RsmX, RsmY and RsmZ). RsmY and RsmZ synergistically relieve repression by RsmA and RsmE, while RsmX plays a lesser role, likely counteracting only one repressor. LuxR-type transcription factors LuxR1 and LuxR2, which positively regulate orfamide A synthesis, are directly repressed by RsmA and RsmE via binding to their 5′ untranslated regions, linking them to the Gac-Rsm signaling cascade. We further demonstrate that LuxR2 activates luxR1 expression, which in turn facilitates orfamide A production by binding to the promoter of the orfamide A biosynthetic gene cluster. Importantly, we show that this entire regulatory cascade operates in the rhizosphere and directly influences biocontrol efficacy. These findings provide a comprehensive understanding of the Gac-Rsm-LuxR pathway in orfamide A biosynthesis and offer valuable insights for the development of biocontrol agents based on Pseudomonas strains.

overall_design: RNA-seq profiling of wild-type Pf-5 and  ΔgacA mutant at 12 h of culture time.


title: DNA methylation shapes transcription factor binding beyond canonical CpG contexts - array 5


title: DNA methylation shapes transcription factor binding beyond canonical CpG contexts - array 2


title: Exploratory microarray analysis of liver tissues from four mouse genotypes with spontaneous hepatitis-associated transcriptional alterations

summary:
Gene-expression profiling was performed to explore genotype-associated transcriptional alterations in the setting of spontaneous hepatitis. Total RNA extracted from liver tissues of four mouse genotypes (IKKβF/F, IKKβΔhep, Tg, and Tg-IKKβΔhep) was analyzed using the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
This dataset was generated as an exploratory reference microarray dataset and was used to identify candidate transcriptional changes for subsequent validation by independent RT-qPCR analyses.

overall_design: Total RNA isolated from liver tissues of one representative 6-week-old male mouse from each of four genotypes (IKKβF/F, IKKβΔhep, Tg, and Tg-IKKβΔhep) was analyzed using the Affymetrix GeneChip Mouse Genome 430 2.0 Array. The experiment was designed as an exploratory reference dataset (n = 1 per genotype) to identify genotype-associated transcriptional alterations in the context of spontaneous hepatitis.

first: Akinori

last: Kanai


title: DNA methylation shapes transcription factor binding beyond canonical CpG contexts - array 1


title: Sex difference in miRNA expressions of lungs post bleomycin-induced acute lung injury

city: Omaha

first: Hanjun

last: Wang

state: Nebraska

address: 984455 University of Nebraska Medical Center 985850 University of Nebraska Medic

department: Anesthesiology

institute: University of Nebraska Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed miRNA sequencing to comprehensively and unbiasedly examine the post-transcriptional landscape of lung tissue in female and male rats following bleomycin acute lung injury (ALI). Male animals displayed the greatest miRNA perturbation following lung injury with 112 miRNAs differentially expressed (75 upregulated, 37 downregulated). Female animals demonstrated markedly fewer differentially expressed miRNAs, with 66 total miRNAs (45 upregulated, 21 downregulated). Direct comparison between female and male animals’ post-injury revealed 54 differentially expressed miRNAs (8 upregulated, 46 downregulated). Baseline comparison between female and male miRNA profiles turned up 23 miRNAs (6 upregulated, 17 downregulated). Among the sex-biased miRNAs, miR-490-5p showed significant downregulation in females versus males following bleomycin-induced lung injury (log2FC = -2.40). This was particularly intriguing as miR-490-5p is predicted to target Bmpr2 (TargetScan score = 88), a critical component for vascular endothelial integrity and the BMP/TGF- signaling pathway. Correlation analysis of Bmpr2 expression and miR-490-5p expression revealed a negative correlation with females having a lower expression of miR-490-5p and a higher expression of Bmpr2 compared to males. Protein validation of BMPR2 revealed a baseline trend towards females having higher BMPR2 levels compared to males (p = 0.09), with females having significantly higher BMPR2 induction following lung injury compared to males (p = 0.009) . rno-miR-672-3p emerged as a noteworthy differentially expressed miRNA, a sex-specific regulator with opposing expression patterns between sexes. In males, miR-672-3p was significantly downregulated following bleomycin injury (log2FC = -2.46, p = 0.0003), while females showed no significant change (log2FC = 0.375, p = 0.202). Direct comparison revealed that miR-672-3p was significantly higher in bleomycin-treated females compared to bleomycin-treated males (log2FC = 2.21, p = 0.006). qPCR validation revealed a more nuanced pattern than the sequencing data suggested. Both sexes showed suppression of miR-672-3p expression following ALI compared to their respective sham controls. Male animals demonstrated the most dramatic reduction (p < 0.0001), with approximately 95% suppression relative to sham. Females also showed downregulation (approximately a 50% reduction, p = 0.0516), although the magnitude was substantially less pronounced. The direct comparison between injured males and females showed a trend toward significance (p = 0.0801), indicating high retention of miR-672-3p expression in injured females compared to males. Target prediction identified 242 potential miR-672-3p targets among male bleomycin versus sham and female versus male bleomycin DEGs, including high-confidence targeting of inflammatory mediators: Cxcr3, Cxcl11, C3ar1, Cd80, Cd4, and Serpina3a, all of which were upregulated in males in the parallel RNA-seq performed. The biological coherence of these targets, which encompass chemokine signaling, complement activation, and acute-phase responses, suggests a functional significance. To examine whether predicted miR-672-3p targets showed expression patterns consistent with mRNA expression, we analyzed correlations between miR-672-3p and target gene expression. In males, comparing injury to baseline, miR-672-3p showed negative correlations with inflammatory mediators including Cxcl11 (r = -0.88, p = 0.0008), Cxcr3 (r = -0.84, p =0.0022), Cd80 (r = -0.83, p = 0.0029), Cd4 (r = -0.78, p = 0.0083), Serpina3a (r = -0.73, p = 0.017), and C3ar1 (r = -0.77, p = 0.0086) (Figure 6D). These inverse relationships were also observed in the sex comparison with similar correlation strengths: C3ar1 (r = -0.81, p = 0.0045), Serpina3a (r = -0.80, p = 0.0054), Cd80 (r = -0.78, p = 0.0085), Cxcl11 (r = -0.78, p = 0.0148), Cxcr3 (r = -0.65, p = 0.042), and Cd4 (r = -0.77, p = 0.0089). A more granular analysis of top differentially expressed miRNAs uncovered multiple miRNAs that were upregulated in both bleomycin-treated females and males relative to their respective sham, notably miR-511-3p_R+1, though with males having higher miR-511-3p_R+1 expression relative to females following bleomycin-induced lung injury (Figure 5B. Figure S5A-D). Another miRNA mirroring a similar pattern of upregulation in both sexes post-ALI, but higher in males than females was miR-212-3p (Figure 5B). Together, these support the previous evidence of a more perturbed miRNA response in males than females.  This coordinated dysregulation suggests that multiple miRNA networks beyond miR-672-3p alone contribute to sex-specific-post-transcriptional programs.

overall_design: Sham and ALI with male and female rats


title: Systemic Consequences of Chronic Ethanol Intake: From Microbiome Shifts to Metabolic Impairment

city: Columbus

last: Tranter

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

summary: Chronic ethanol (EtOH) consumption is a major contributor to multi-organ dysfunction, yet its systemic effects remain incompletely understood. To address this, we utilized a physiologically relevant long-term mouse model, administering 20% EtOH in drinking water for 60 weeks, to investigate the integrated consequences of chronic exposure. EtOH-consuming mice (0.4-0.5 mL/day) exhibited >30% reductions in both chow and fluid intake, resulting in a 12% decrease in total caloric intake compared to controls (P<0.001). Body mass remained similar until week 52, after which EtOH-treated mice had lower body mass due to reductions in both lean and fat mass (P≤0.004). Functional assessments revealed impaired treadmill endurance (-17%) and grip strength (-11%) (P≤0.037), while motor coordination remained unaffected (P=0.203). Chronic EtOH exposure significantly altered gut microbiota composition, reducing Lactobacillus and enriching Faecalibaculum, Clostridium, and Bifidobacterium at the genus level. These changes were accompanied by marked depletion of short-chain fatty acids (P≤0.05). Indirect markers of gut permeability (serum LPS & zonulin) and liver injury (serum ALT & AST, hepatic amyloid content) were elevated, alongside increased total cholesterol and >62% upregulation of hepatic TNFα, IL-6 & serum amyloid A (P≤0.046). EtOH also induced dyslipidemia and glucose intolerance (P≤0.041), although transcriptomic changes in white adipose tissue were minimal despite elevated free fatty acids. In conclusion, chronic EtOH consumption disrupts energy balance, compromises gut barrier integrity, and impairs hepatic metabolism, collectively driving systemic and metabolic dysfunction. These findings underscore the gut-liver axis as a key mediator of EtOH-induced pathology and highlight the gut microbiome as a promising therapeutic target.

overall_design: RNA-seq profiling of subcutaneous white adipose tissue from female C57BL/6 mice following 60 weeks of 20% EtOH in drinking water (n=6), and fresh drinking water controls (n=6)

first: Cory

middle: W

last: Baumann


title: Sex difference in mRNA expressions of lungs post bleomycin-induced acute lung injury

summary: We performed mRNA sequencing to comprehensively and unbiasedly examine the transcriptional landscape of lung tissue in female and male rats following bleomycin acute lung injury (ALI). Comparative analysis of bleomycin-induced ALI transcriptional responses demonstrated marked sex differences in both magnitude and directionality. Males exhibited significantly greater transcriptional perturbation with 2,393 differentially expressed genes (DEGs) (1,602 upregulated, 791 downregulated) versus 1,533 DEGs in females (1,129 upregulated, 404 downregulated) (|log2FC| ≥ 1, FDR < 0.05). Direct comparison of bleomycin-treated animals identified 826 DEGs (307 female-enriched, 519 male-enriched). Baseline sex differences were minimal, with only 262 DEGs between sham-treated animals (51 female-enriched, 211 male-enriched), indicating that observed transcriptional divergence primarily reflects sex-specific injury responses rather than constitutive sexual dimorphism.  Gene Ontology (GO) analysis of these 826 DEGs began to define this polarity. The biological processes with the most divergent expression patterns included proteolysis (GO:0006508) and immune response (GO:0006955). Cellular components included both membrane and extracellular space (GO:0016020, GO:0005615), and molecular functions included protein binding (GO:0005515). KEGG pathway analysis further highlighted the contrast. Direct comparison between females and males revealed divergent pathways, including: cytokine-cytokine receptor interaction (ko04060), complement and coagulation cascades (ko04610), and ECM-receptor interaction (ko04512). A more granular analysis of the DEGs comprising these divergent functional categories and pathways identified male lungs selectively upregulating chemokines (Cxcl10, Cxcl11, Ccl17), complement/coagulation factors, (F7, Plg, C1qa), and components of the acute-phase protease inhibitor system (Timp1, Serpina3a, Tmprss9), whereas females induced BMP signaling genes (Bmpr2, Smad9, Bmp6) and an integrin scaffolding proteins (Itga1/2/9/11, Itgb3, Flrt3) . Notable findings from within-sex analyses showed females with enriched GO and KEGG themes related to extracellular matrix organization and cell-cycle progression, while males were more focused on immune pathways, specifically cytokine induction and viral response modules. A complete list of all DEGs across comparisons is provided in the supplementary materials.


title: EGF-induced EMT in MDA-MB-468 breast cancer cell line

city: Trondheim

first: Ellen Marie

middle: Botne

last: Quinsgaard

address: Erling Skjalgsons gate 1

country: Norway

institute: Norwegian University of Science and Technology

summary: The Epithelial-Mesenchymal Transition (EMT) is an early  metastatic process found to promote disease progression and poor prognosis in cancer. Here, EMT was induced in the breast cancer cell line MDA-MB-468 using epidermal growth factor (EGF). Gene expression data was used to determine effects on metabolic pathways, as well as to assess the degree of EMT induction.

overall_design: MDA-MB468 cells were seeded, serum-starved and treated with 50ng/mL Epidermal Growth Factor (EGF) for 0h, 12h, 24h, 48h and 72h respectively before lysis and RNA-extraction.


title: RAS pathway activation drives clonal selection and monocytic differentiation in FLT3 and BCL2 inhibitor resistance

city: San Francisco

first: Catherine

last: Smith

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

summary: Despite efficacy of FLT3 and BCL2 inhibition in acute myeloid leukemia (AML), relapse limits survival.  Mutation status and AML monocytic differentiation are implicated in resistance. On-treatment tumor evolution may select for genetically distinct clones or shifts in differentiation not resolvable by bulk sequencing.  We performed multiomic single cell (SC) DNA/protein and RNA/protein profiling of patients treated on a clinical trial of the BCL2 inhibitor venetoclax and the FLT3 inhibitor gilteritinib (Ven/Git) to characterize immunophenotypic, transcriptional, and genetic clonal evolution on therapy. We found that while Ven/Gilt effectively eliminated FLT3 mutant clones, it selected for RAS mutations, RAS pathway activation and RAS-associated monocytic differentiation. In an in vitro model of monocytic differentiation associated with heightened RAS pathway activation, we demonstrated that MEK inhibition re-sensitized to Ven/Gilt.  These data indicate RAS signaling is central to FLT3 and BCL2 inhibitor resistance, is tightly coupled to monocytic differentiation and can be overcome by RAS pathway inhibition.

overall_design:
Fro DAB-seq, briefly, cryopreserved cells were thawed and normalized to 10,000 cells/μL in 180 μL PBS (Corning). Samples with more than one million viable cells recovered were additionally incubated with Human TruStain FcX (Biolegend) and salmon sperm DNA (Invitrogen) for 15 minutes at 4C. A pool of 9 oligo-conjugated antibodies (CD3, CD4, CD11b, CD13, CD19, CD33, CD34, CD117, CD45) (Table S3) was added, and cells were incubated for an additional 30 minutes. In addition, individual samples were also incubated with unique hashtags (BioLegend) to provide sample-level identifiers, and groups of 3 individual patients were pooled together in multiplexed runs. Next, samples were resuspended in cell buffer (MissionBio), diluted to 4-7e6 cells/mL, and loaded onto a microfluidics cartridge, where individual cells were encapsulated, lysed, and barcoded using the Tapestri instrument. DNA from barcoded cells was amplified via PCR using a custom targeted panel that included 288 amplicons across 66 genes associated with acute leukemia generally and known clinical mutations in these samples specifically (Table S2). DNA PCR products were isolated, purified with AmpureXP beads (Beckman Coulter), used as a PCR template for library generation, and then repurified with AmpureXP beads. Protein PCR products (when applicable) were isolated from the supernatant from AmpureXP bead purification via incubation with a 5’ Biotin Oligo (ITD). Protein PCR products were then purified using Streptavidin C1 beads (Thermo Fisher Scientific), used as a PCR template for library generation, and then repurified using AmpureXP beads. Both DNA and protein libraries were quantified and assessed for quality via a Qubit fluorometer (Life Technologies) and Bioanalyzer (Agilent Technologies) prior to pooling for sequencing on an Illumina Novaseq.
For CITEseq, Cryopreserved bone marrow or peripheral blood mononuclear cells from 4 patients across 8 samples were thawed. For each specimen 1-2 million cells were blocked with Human TruStain FcX (BioLegend) and stained with a panel of TotalSeq-C antibodies from the Human Universal Cocktail (1 μg/each, BioLegend) in Cell Buffer (BioLegend) for 20 minutes at 4C. After staining, cells were washed in Staining Buffer, resuspended at 1,000 cells/μL, and immediately processed with the 10x Genomics controller and the Single Cell 5’ reagent kit with feature barcoding technology for cell-surface proteins. 5’ gene expression and feature barcoding libraries were constructed using a 10x Genomics library preparation kit. Library quality was assessed using Agilent High Sensitivity DNA kit and Bioanalyzer 2100, and libraries were quantified using dsDNA High-Sensitivity (HS) assay kit (Invitrogen) on Qubit fluorometer before being sequenced on an Illumina Novaseq. Targeted read depth for gene expression libraries was 100,000 reads/cell and for cell-surface libraries was 40,000 reads/cell.

first: Vanessa

last: Kennedy

first: Cheryl

last: Peretz

first: Anushka

last: Walia

first: Brenda

last: Chyla

first: Yan

last: Sun

first: Jason

last: Hill

first: Elaine

last: Tran

first: Andrew

last: Koh

first: Timothy

last: Ferng

first: Samantha

last: Pintar

first: Matthew

last: Jones

first: Bogdan

last: Popescu

first: Farid

last: Chehab

first: Natalia

last: Murad

first: Ritu

last: Roy

first: Adam

last: Olshen

first: Christine

last: Berryhill

first: Christopher

last: Davis

first: Steven

middle: P

last: Angus

first: Jose

last: Rivera

first: Alicia

last: Meshulam

first: Elliot

last: Stieglitz

first: Sunil

last: Joshi

first: Elie

last: Traer

first: Monique

last: Dail

first: Habib

last: Hamidi

first: Jessica

last: Altman

first: Naval

last: Daver

first: Mark

last: Levis

first: James

last: McCloskey

first: Alexander

last: Perl


title: Pharmacologic HIF-2α inhibition preserves T cell transcriptome in clear cell renal cell carcinoma

city: New Haven

first: Katrine

last: Madsen

state: CT

address: 300 George St.

department: CMCO

institute: Yale School of Medicine

summary: Belzutifan is a selective HIF-2α inhibitor currently in clinical trials for clear cell renal cell carcinoma (ccRCC). As belzutifan is being evaluated in combination with immune checkpoint inhibitors, we investigated whether pharmacologic HIF-2α inhibition affects T cell transcriptional programs. Primary human pan T cells isolated from blood from healthy donors and ccRCC patients and tumor-infiltrating T cells were isolated from ccRCC patients. These cells were treated with belzutifan (2 μM, 5 days) vs. control DMSO under hypoxic conditions. RNA sequencing revealed that belzutifan treatment preserved T cell transcriptional programs, supporting the rationale for combining belzutifan with immunotherapy in ccRCC.

overall_design: Primary human pan T cells were isolated by negative selection from PBMCs obtained from healthy donors, or from ccRCC tumor specimens as tumor-infiltrating lymphocytes (TILs). T cells were activated with anti-CD3/CD28 Dynabeads and cultured under hypoxic conditions (1% O₂). Cells were treated with belzutifan (2 μM) or DMSO vehicle control for five days. Total RNA was extracted using the RNeasy Mini Kit (Qiagen). DNase treatment and poly(A)-selected library preparation were performed by the Yale Center for Genome Analysis using the Illumina TruSeq Stranded mRNA Library Preparation Kit. Samples were sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads (~25 million reads per sample).

middle: N


title: ChIP-seq of RNA polymerase II and HNF4alpha in mouse liver after cytokine stimulation (WT vs TG)

first: Yoshihiro

last: Tsuchiya

summary: ChIP-seq was performed on liver samples from 6-week-old male mice (WT and TG) following a single intravenous injection of mouse TNFalpha (BioLegend, 7.5 ug/kg) or vehicle. Livers were collected 4 h post-injection. ChIP was carried out using anti-RNA polymerase II (Active Motif) or anti-HNF4alpha (Abcam) with matched input controls. Single-end reads were sequenced on an Illumina HiSeq 2000 platform, aligned to the mouse reference genome (mm10) using Bowtie, and peaks were called using MACS2 (v2.0.10.20120913) with matched input controls.

overall_design: Factors: genotype (WT vs TG), treatment (vehicle vs TNFalpha), and ChIP target (RNA polymerase II vs HNF4alpha). Matched input controls were provided for WT, WT+TNFalpha, and TG conditions.


title: Single intranasal dose of L-MYC–immortalized human neural stem cells enhances neuroprotection and tissue repair after controlled cortical impact in male rats

city: Duarte

first: Margarita

last: Gutova

address: 1500 E Duarte Rd

department: Stem Cell and Regenerative Medicine

institute: City of Hope

summary: Traumatic brain injury (TBI) initiates cellular and molecular cascades that impair neurogenesis and promote chronic neuroinflammation, ultimately contributing to cognitive and functional decline. We previously demonstrated that L-myc–expressing human neural stem (LMNSC01) cells migrate to sites of injury and modulate biomarkers associated with neuroprotection and repair after repeated intranasal (IN) administration. Here, we tested whether a single bulk IN dose of LMNSC01 is sufficient to induce neuroprotective changes in gene and protein expression following injury. Immunocompetent male rats underwent controlled cortical impact (CCI) or sham surgery, followed by a single bulk IN dose of LMNSC01 or vehicle on postoperative day 7. Transcriptomic profiling of brain tissue from injured and LMNSC01-treated rats revealed upregulation of immune modulation and tissue repair genes (Il22ra1, Il1rn, Gfi1, Ddx60) and downregulation of genes involved in microglial activation and cytokine signaling (Xcr1, Ccl21a, Ccl9) compared to controls. Proteomic analysis confirmed reduced levels of inflammatory cytokines and endothelial activation markers (ICAM-1, PDGF-AA, TCK-1). Multiplex immunohistochemistry showed LMNSC01-mediated changes in microglial activation, macrophage infiltration, and vascular remodeling. These findings highlight the potential of single IN LMNSC01 dose to reprogram neuroinflammatory and tissue remodeling networks and offer a clinically translatable strategy to improve long-term outcomes after TBI.

overall_design: Male rat brain tissue was dissected and mRNA was isolated from snap frozen tissues according to a diagram in figure 1 and half was used for NanoString genomics analysis and half for protein ELISA assays. mRNA expression in the ipsilateral and contralateral hemispheres of LMNSC01 and VEH-treated TBI brains was analyzed using the NanoString nCounter platform by digitally detecting and counting mRNA expression in a single reaction without amplification. Each assay included six positive and eight negative RNA assay controls, plus ten mRNA housekeeping controls. RNA was hybridized with the Codeset from the gene panel at 65°C for 16 h. The post-hybridization probe-target mixture was quantified using the nCounter Digital Analyzer, and all data analyses were performed with ROSALIND (Version 3.39.28.7; https://rosalind.bio/). All raw data were first normalized with internal positive and negative controls to eliminate variability unrelated to the samples, then normalized to the selected housekeeping genes using Geometric Means methods. Statistically significant (p<0.05) and < 1.5 fold up- or down- regulated genes were analyzed and clustered as described below. Further downstream pathway and network analysis were performed by using Qiagen IPA software.

first: Brecken

last: Enright

first: Jeffrey

last: Cheng

first: Yate-Ching

last: Yuan

first: Vikram

last: Adhikarla

first: Isabella

last: Vasquez

first: Corina

last: Bondi

first: Russell

last: Rockne

first: Anthony

last: Kline


title: DNA methylation shapes transcription factor binding beyond canonical CpG contexts - array 4

first: irina

last: miodownik

first: Irina

last: Miodownik

first: Ruben

last: Solozabal

first: Michael

last: O'Hagan

first: Shira

last: Albeck

first: Yoav

last: Peleg

first: Martin

last: Takac

first: Ariel

last: Afek


title: Epigenetic reprogramming drives cellular and phenotypic plasticity in liposarcoma

city: Houston

first: Zhao

last: Zheng

address: 1901 East Rd

department: Genomic Medicine

institute: md anderson cancer center

summary: Single-cell multiomic profiling were performed to characterize the cellular and regulatory heterogeneity of liposarcoma (LPS), including well-differentiated liposarcoma (WDLPS) and de-differentiated liposarcoma (DDLPS), which exhibit markedly different clinical behaviors. Integrated scRNA and scATAC were used to resolve tumor cell states, gene regulatory programs, and tumor microenvironment composition across LPS subtypes. The results reveal distinct differentiation landscapes, with DDLPS enriched for progenitor-like mesenchymal cells, sclerotic WDLPS displaying broader lineage plasticity, and adipocytic WDLPS dominated by terminally differentiated adipocytes. Analysis of the tumor microenvironment further demonstrates differences in immune composition, with DDLPS enriched for immunosuppressive macrophages. Sclerotic WDLPS exhibits intermediate cellular and molecular features between the two subtypes. Together, these datasets provide a comprehensive resource describing the transcriptional, epigenomic, and microenvironmental diversity of liposarcoma.

overall_design: Tumor samples from well-differentiated and de-differentiated liposarcoma were dissociated into single cells and profiled using droplet-based single-cell multiomic sequencing to jointly measure gene expression and chromatin accessibility. Libraries were sequenced on an Illumina platform and processed using standard pipelines for alignment, barcode demultiplexing, and quality control. Spatial profiling was performed on matched tissue sections when available. Integrated single-cell RNA and chromatin accessibility analyses were used to identify tumor cell states, regulatory programs, and immune microenvironmental features across liposarcoma subtypes.

first: Denu

last: Ryan

first: Zheng

last: Zhao


title: DNA methylation shapes transcription factor binding beyond canonical CpG contexts - array 3


title: HIF-1α and HIF-2α regulate overlapping and distinct transcriptional programs in primary human T cells [RNA-Seq]

first: Katrine

last: Madsen

summary: Hypoxia-inducible factor 2α (HIF-2α) is a central oncogenic driver in clear cell renal cell carcinoma (ccRCC). Here, we investigated the cell-intrinsic effects of HIF-2α perturbation in primary human T cells. CRISPR/Cas9-mediated deletion of HIF-2α downregulated transcriptional programs associated with T cell effector function.

overall_design: Primary human pan T cells were isolated by negative selection from peripheral blood mononuclear cells (PBMCs) obtained from healthy donors. T cells were activated with anti-CD3/CD28 Dynabeads and cultured under hypoxic conditions (1% O₂) to stabilize hypoxia-inducible factors prior to genetic perturbation.  CRISPR/Cas9-mediated knockout of HIF1A or EPAS1 (HIF-2α) was performed using ribonucleoprotein (RNP) electroporation. Briefly, synthetic crRNAs targeting HIF1A or EPAS1 were annealed to tracrRNA and complexed with recombinant Cas9 protein to generate RNP complexes. Activated T cells (48 hours post-stimulation) were electroporated using the Lonza 4D-Nucleofector system (program EO-115) and recovered in CTS OpTmizer medium supplemented with IL-2. Knockout efficiency was validated by RT-qPCR five days post-electroporation.  Following recovery, edited T cells were maintained under hypoxic conditions (1% O₂) for a total of five days post-electroporation. Non-targeting CRISPR controls served as wild-type comparators. Independent biological replicates represent T cells derived from distinct donors.  Total RNA was extracted using the RNeasy Mini Kit (Qiagen) with on-column DNase I treatment. Poly(A)-selected libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit and sequenced at the Yale Center for Genome Analysis on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads (~25 million reads per sample).