title: A Gata4–Loxl2 Axis Controls ECM Remodeling to Enable Scar-Free Spinal-Cord Regeneration in Zebrafish

city: Nashville

first: Valentina

last: Cigliola

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University

summary: Spinal-cord injury in mammals causes permanent loss of sensory and motor function due to scar formation obstructing axon regrowth. In contrast, zebrafish fully regenerate their spinal cord without lasting fibrosis. Here, we identify the transcription factor GATA4 as a key regulator of regeneration. After injury, Gata4 is primarily upregulated in dorsal ependymo-radial glial cells (ERGs). GATA4 preserves glial identity and orchestrates regenerative extracellular matrix (ECM) remodeling. GATA4 loss biases ERGs toward a fibroblast-like state with upregulated Loxl2, a collagen cross-linking enzyme, and can also increase Loxl2 in surrounding non-glial cells. Excess Loxl2 activity promotes pathological crosslinking and formation of a rigid, fibrotic matrix impairing glial and axonal bridging across the lesion, greatly reducing motor recovery. Pharmacological inhibition of Loxl2 in gata4 mutants substantially rescues ECM organization, tissue bridging, and functional recovery. Injury-induced Gata4 activation depends on a short hypoxia-responsive enhancer and is driven, at least in part, by Hif1a signaling. We identify the Gata4–Loxl2 axis as a central regulator of and potential therapeutic target for scar-free spinal-cord repair.

overall_design: Adult zebrafish of two genotypes (gata4wcm6/wcm6 and wild-type fish) were subjected to a spinal cord injury. Complete transection and loss of swimming ability were visually confirmed immediately after surgery and again at 1 day post-injury. At 2wpi, snRNAseq was performed.

first: Nicolas

middle: P

last: Noel

first: Vânia

last: Filipa Lima Fernandes

first: Andrew

last: Kjar

first: Paige

middle: E

last: Pfotenhauer

first: Mawusi

last: Sefogbe

first: Eman

middle: A

last: Akam-Baxter

first: Ethan

last: Lippmann


title: TOR-NOT4 signalling couples translation to co-translational quality control in plants

status: Public on Aug 11 2026

city: Birmimngham

first: Daniel

middle: J.

last: Gibbs

address: School of Biosciences,University of Birmingham

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

type: Expression profiling by high throughput sequencing

summary: Protein homeostasis (proteostasis) is in part maintained by co-translational quality control mechanisms that prevent errors during protein synthesis by targeting aberrant polypeptides for degradation. While such systems are relatively well-characterized in yeast and animals, their identity and regulation in plants remain poorly understood, and broader knowledge of how organisms synchronise protein production with quality control is lacking. In eukaryotes, the Target of Rapamycin (TOR) kinase drives translation, but a direct link to co-translational surveillance has not been established. Here, we identify three NOT4-like E3 ubiquitin ligases (NOT4A-C) as TOR-regulated factors that coordinate co-translational protein quality control to limit proteotoxic stress in Arabidopsis thaliana. Loss of NOT4 function increases TOR activity and global translation rates, and leads to an accumulation of polyubiquitylated proteins, as well as hypersensitivity to proteasome and TOR inhibition and protein misfolding stress. We found that NOT4A co-localizes with TOR in cytoplasmic foci, and not4 mutants phenocopy TOR-inhibited wild-type plants for a subset of transcriptional and growth-related outputs, indicating that NOT4s are downstream of and essential for normal TOR signalling. Furthermore, we found that elevated translation in NOT4-deficient plants provides enhanced resistance to Pseudomonas syringae pv. Tomato, suggesting a functional interplay between translational quality control and defence against pathogens that suppress host translation. Our study uncovers a previously uncharacterised TOR–NOT4 signalling axis that may act to proportionately couple translational throughput with quality control capacity to safeguard the plant proteome under both optimal and challenged conditions. Since TOR and NOT4-like proteins are conserved in plants, animals, and fungi, we suggest this mechanism may operate more broadly across eukaryotic taxa.

overall_design: RNA-seq profiling of Arabidopsis thaliana wild-type (Col-0) and not4abc T-DNA insertion mutants under control conditions and TOR inhibition (1 μM AZD8055)

first: Maximillian

last: Schwarze

first: Rory

last: Osborne

first: Margot

last: Raffeiner

first: Manuel

last: Gonzalez-Fuente

first: Anastasia

last: Kanali

first: Mark

last: Bailey

first: Ross

middle: D

last: Etherington

first: Lina

last: Zhou

first: Suayib

last: Üstün

middle: J


title: Protective efficacy of AAV-expressed bNAbs co-delivered with PD-L1

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

summary: Adeno-associated virus (AAV)-delivered anti-HIV-1 broadly neutralizing antibodies (bNAbs) have demonstrated promise for preventing1-8 and treating HIV-1 infection in preclinical models9,10. However, host immune responses, specifically anti-drug antibodies (ADA), limit sustained bNAb expression11-17. Here, we tested whether PD-L1-mediated immune shielding could improve the consistency of AAV-delivered bNAb expression from muscle tissue in rhesus macaques. We show that AAV9.PD-L1 co-delivery with AAV9.10-1074 or AAV9.3BNC117 reduced the occurrence of ADA responses and improved the durability of bNAb expression for one year post administration. Macaques with sustained serum bNAb concentrations were protected against ten repeated SHIVAD8-EO challenges. In macaques that received AAV9.PD-L1 vectors, we observed reduced inflammation in muscle tissue harvested over one year post-AAV administration. In contrast, in macaques that did not receive AAV9.PD-L1, we detected greater severity of inflammation including the formation of tertiary lymphoid structures (TLSs), which was associated with higher ADA responses and diminished serum bNAb concentrations. Furthermore, spatial transcriptomics confirmed TLS gene signatures, along with muscle fibrosis signatures, when AAV9.PD-L1 was not administered. These findings uncover a role for local immune activation in sustaining ADA and promoting muscle deterioration. Thus, an immune shielding approach could serve as an optimal strategy to prolong transgene expression from muscle-directed AAV-delivered biologics.

overall_design: Two quadriceps muscle biopsies, one from the bNAb only and one from the bNAb plus PD-L1 groups were analyzed using spatial transcriptomics

first: Michael

last: Kuipa

first: Abubakarr

last: Koroma

first: Isai

last: Leguizamo

first: Priya

last: Dhole

first: Yash

last: Barot

first: Michelle

middle: Y

last: Lee

first: Shan

last: Liang

first: Magdalen

last: Chouinard

first: Stephanie

last: Ehnert

first: Stacey

last: Weissman

first: Casey

last: Whitehead

first: Rachelle

middle: L

last: Stammen

first: Jennifer

middle: S

last: Wood

first: Elizabeth

middle: H

last: Curran

first: Deepa

last: Machiah

first: Evan

last: Dessasau

first: Yoshiaki

last: Nishimura

first: Jun

last: Xie

first: Guangping

last: Gao

first: Sumit

last: Verma

first: Deanna

last: Kulpa

first: Ian

middle: N

last: Moore

first: Steven

last: Bosinger

first: Matthew

middle: R

last: Gardner


title: Multidimensional Single-Cell Transcriptomic Profiling of Uterine Leiomyosarcomas Identifies Molecular Subtypes with Distinct Therapeutic Vulnerabilities [Spatial Transcriptomics]

city: Stanford

first: Daniel

last: Delitto

address: 257 Campus Dr

institute: Stanford University

summary: Uterine leiomyosarcoma (ULMS) is an orphan disease that frequently recurs and metastasizes, with patients undergoing multiple lines of chemotherapy due to lack of effective therapeutic targets. To address this gap, we used single-cell RNA sequencing and spatial transcriptomic analysis to comprehensively profile ULMS. We uncovered eight subtypes of tumor cells, including stem cell-like hormone receptor-positive cells, tumor cells with mesenchyme-like features, ischemic tumor cells defined by a MYC program, and inflammatory tumor cells with active interferon signaling. The spatial correlates of these tumor cell subtypes demonstrated unique localization patterns. By correlating these signatures to bulk RNA sequencing data, we demonstrate the scalability of these findings to clinical outcomes. Finally, using the single-cell integration and drug response prediction algorithm, we derive previously undescribed drug predictions targeting specific tumor subtypes that may be more efficacious than existing adjuvant regimens. Our findings highlight new individualized and multifaceted therapeutic avenues to treat ULMS.

overall_design:
Samples were prepared from formalin-fixed, paraffin-embedded (FFPE) patient blocks according to the manufacturer’s protocol. Briefly, FFPE blocks were acquired from the Department of Pathology archive and freshly sectioned at a thickness of 5 µm onto custom gel pads. Regions of Interest (ROIs) were selected based on hematoxylin and eosin (H&E) stains previously performed by the Department of Pathology, with areas of high tumor enrichment annotated by a pathologist. ROIs were manually punched out of the gel pad and transferred onto functionalized glass slides. After deparaffinization, rehydration, and antigen retrieval, hybridization with the Singular G4X breast cancer panel (309 genes) was performed. Ligation of the probes and rolling circle amplification were then performed in situ. The slide was conditioned, framed, and loaded onto the G4X instrument. Fluorescent H&E and spatial sequencing were performed on the G4X instrument.

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

last: Korah

first: James

last: Agolia


title: Multidimensional Single-Cell Transcriptomic Profiling of Uterine Leiomyosarcomas Identifies Molecular Subtypes with Distinct Therapeutic Vulnerabilities [scRNA-seq]

overall_design:
At the time of tumor resection, a sample of the resected tumor was collected. Specimens were transported on ice and immediately dissociated into single-cell suspensions using the standard protocol for the gentleMACS Octo Dissociator. If necessary, red blood cell lysis was performed for 10 minutes at room temperature using RBC lysis buffer. The suspensions were then either cryopreserved in Bambanker freezing media  or carried through to library preparation and sequencing.  All library preparations were performed using 10x Genomics protocols. If cryopreserved, cells were thawed, dead cell removal was performed and cells were counted. Once optimal concentration was achieved, we proceeded with library preparation and sequencing using standard 10x Genomics protocols per chemistry. FASTQ files from all batches were aligned independently using 10x Genomics Cell Ranger v8.0.1 to the reference genome GRCh38-2024-A

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


title: Host Adaptation at the Cost of Biofilm Formation Drives Outbreak Persistence of a Major Human Fungal Pathogen

city: Merced

first: Clarissa

last: Nobile

state: California

address: 5200 N Lake road

department: Molecular and Cell Biology

institute: University of California MERCED

summary: Candida parapsilosis is a major human fungal pathogen, with recent global outbreaks driven by drug-resistant (DR-Cp) isolates that are difficult to eradicate and associated with poor clinical outcomes. However, the microbiological traits underlying the persistence of these outbreak strains remain poorly understood. Here, we show that DR-Cp isolates responsible for prolonged outbreaks across multiple countries exhibit a striking low-biofilm-producing (LBP) phenotype. Unexpectedly, LBP strains (29T and 49B) display enhanced stress tolerance, cell wall masking, and immune evasion, leading to resistance against neutrophil and macrophage killing and increased survival in immune cell-rich organs during systemic infection. Genome-wide transcriptomic profiling revealed extensive metabolic and regulatory rewiring in LBP strains. Together, our findings challenge the prevailing view that robust biofilm formation underlies Candida outbreak persistence and instead reveal that host immune pressure selects for biofilm attenuation as an adaptive strategy promoting long-term persistence. These insights redefine how C. parapsilosis adapts during healthcare-associated outbreaks and inform infection control strategies by shifting attention toward non-environmental reservoirs.

overall_design: RNA-Seq profiling of Candida parapsilosis isolates 1T and 29T (isolated from Turkey), 35B and 49B (isolated from Brazil), grown under planktonic and biofilm conditions for 90 minutes, 8 hours and 24 hours.

first: Farnaz

last: Daneshnia

first: Deepika

last: Gunasekaran

first: Sean

last: Bergin

first: Lisa

last: Lombardi

first: Austin

middle: M

last: Perry

first: Liuyang

last: Cai

first: Louise

last: Walker

first: Tibor

last: Nemeth

first: Süleyha

last: Hilmioglu-Polat

first: Letal

middle: I

last: Salzberg

first: Arefeh

last: Ebadati

first: Tobias

last: Köhler

first: Gabriel

last: Braune

first: João

last: de Almeida Jr

first: Giuseppina

last: Caggiano

first: Julianne

middle: V

last: Kus

first: Pegah

last: Mosharaf Ghahfarokhy

first: Julieta

last: Munoz

last: Floyd

first: Diego

last: Fuentes-Palacios

first: Samuel

last: Gonçalves

first: Relber

last: Gonçales

first: Mostafa

last: Salehi

first: Jigar

last: Desai

first: Agostinho

last: Carvalho

first: Shenglin

last: Mei

first: Carol

last: Munro

first: Alex

last: Hopke

first: Toni

last: Gabaldón

first: Attila

last: Gacser

first: Oliver

last: Kurzai

first: Geraldine

last: Butler

first: David

last: Perlin

first: Wenjie

last: Fang

first: Michael

last: Mansour

first: Amir

last: Arastehfar


title: Ultrasound-Amplified Exosome Secretion and Antibody-Free SERS Profiling for APOE Genotype-Dependent Signatures

city: Suwon

first: Jong-Chan

last: Park

state: Gyeonggi-do

address: 2066, Seobu-ro

department: Department of Biophysics

country: South Korea

institute: Sungkyunkwan University

summary: Exosomes offer a promising platform for non-invasive diagnosis of neurodegenerative diseases by encapsulating multiple biomarkers and crossing the blood–brain barrier. However, conventional exosome analyses often fail to capture subtle, genotype-specific pathological variations due to limited vesicle yield, low detection sensitivity, and reliance on predefined markers. Here, we present an integrated approach that combines ultrasound-induced exosome amplification with an antibody-free surface-enhanced Raman scattering (SERS) platform to sensitively detect genotype-dependent pathological differences. By applying optimized low-intensity pulsed ultrasound (LIPUS), we achieved up to 100-fold enhancement in exosome secretion via the endosomal sorting complexes required for transport (ESCRT) pathway and monitored the dynamics of this amplification. To improve detection, we developed a gold-coated zinc oxide (ZnO) nanowire-based SERS substrate that amplifies exosomal signal intensity by more than fourfold without requiring antibodies. Using multiplex SERS profiling of intact exosomes combined with principal component analysis (PCA), we successfully distinguished apolipoprotein E (APOE) genotypes, improving the silhouette score from 0.37 to 0.5. Consistently, transcriptome analysis substantiates these findings by showing that LIPUS stimulation increased exosome secretion and upregulated exosome-related genes functionally related to Alzheimer's disease (AD). These findings demonstrate that label-free, intact exosome profiling can reveal genotype-dependent pathological variations, supporting its potential utility in high-sensitivity precision diagnostics for AD.

overall_design: RNA-seq profile of APOE E3E4 iPSC-derived cortical organoids. two groups are divided into Low Intensity Pulsed Ultrasound(LIPUS, test) treated and non-treated(control). human cortical organoids used in the sequencing are matured and prepared at Day 87. LIPUS stimulation was performed at Day 86.

first: Won Jong

last: Yu

first: Jinhee

last: Yoo

first: Youngjun

last: Kim

first: Seongmin

first: Inki

first: Byullee


title: The RNA ac4C Writer NAT10-dependent Post-transcriptional Regulations are Prerequisites for Zygotic Splicing Activation in Mouse [RNA-Seq]

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

country: China

institute: Life Sciences  Institute

summary: Programmed establishment of the zygote epitranscriptome orchestrates epitranscriptome fidelity and developmental potency acquisition during mammalian preimplantation embryogenesis. N4-acetylcytidine (ac4C) is a conserved post-transcriptional RNA modification catalyzed by the only known “writer”, N-acetyltransferase 10 (NAT10), but its landscape and function in early embryos remain further exploration owing to limited materials. In this study, we characterized the ac4C modification reprogramming dynamics throughout preimplantation embryogenesis and identified that Nat10 ablation from primary follicle oocytes leads to female infertility with embryonic arrest at the 2-cell transition. Notably, we found that the maternal protein NAT10 was essential for ac4C deposition on ZGA transcripts and maternal mRNAs, and the loss of Nat10 could also lead to abnormal accumulation of maternal transcripts and major ZGA inactivation. Interestingly, through combinatorial interrogation of RNA-seq and ribo-seq data, we uncovered NAT10 regulates the alternative splicing of transcripts that function during zygotic splicing activation in an ac4C-dependent manner. In summary, our findings demonstrate that the RNA ac4C writer NAT10 is essential for the post-transcriptional regulation of mouse zygotic splicing activation and provide valuable view for further exploration of the epigenetic mechanism during maternal-to-zygotic transition.

overall_design: The oocytes were harvested from mature WT and Zp3-cre Nat10 conditional knockout female mice 32-48h after PMSG and washed by 0.2% containing PBS for 3 times, then 10 oocytes per sample were lysed in lysis buffer (containing 0.2% Triton X-100 and Recombination RNase Inhibitor) and prceeded for cDNA library constribution following the workflow of Smart-seq2. And for each sample, ERCC (1:1000, 0.2μl/sample) were added as spike-in for further calibration.

first: Wenjing

last: Wang

first: Lu

last: Chen

first: Yuke

last: Wu

first: Yunwen

first: Hengyu


title: The RNA ac4C Writer NAT10-dependent Post-transcriptional Regulations are Prerequisites for Zygotic Splicing Activation in Mouse

overall_design: The zygotes were harvested from 6W mature WT and Zp3-cre Nat10 conditional knockout female mice 20h after hCG and lysed in 310 μl ice-cold lysis buffer for 10 min on ice. The lysate was clarified for 10 min at 20,000g at 4 °C, then treated with 1 μl RNase I 100 U ml− and incubated at room temperature for 45 min with gentle mixing. RPFs were extracted from pellet buffer by using 1 ml TRIzol and 200 μl chloroform. The aqueous phase was precipitated by adding 750 μl isopropanol and 20 μg glycogen. the library structuration following the workflow of as described previously. Raw reads were trimmed with cutadapt v1.14with parameters.


title: Clinical, genomic, and spatial transcriptomic features of pancreatic adenosquamous carcinoma

city: Baltimore

first: Luciane

middle: Tsukamoto

last: Kagohara

state: MD

address: 1650 Orleans St - CRB1 Rm 490

department: Oncology

institute: Johns Hopkins University

summary: Pancreatic adenosquamous carcinoma (PASC) is a rare and aggressive disease variant, accounting for 1-4% of all exocrine pancreatic malignancies. Compared to conventional pancreatic ductal adenocarcinoma (PDAC), the clinical and molecular characteristics of PASC remain poorly defined due to its understudied nature. To investigate the spatial biology of PASC, we profiled resected tissue specimens from patients in our institutional cohort using the Visium spatial transcriptomics platform for compartment-specific differential gene expression and pathway enrichment analyses.

overall_design:
Spatial transcriptomics with Visium (10x Genomics) was performed on pancreatic adenosquamous tumors from surgical specimens. Spatial gene expression analyses was performed between the adeno versus the squamous histological compartments.

Please note that each sample is a mix of both adeno and squamous subtype. Each spot of the spatial transcriptomics data has been assigned to one of the histological subtypes or other pancreas cell type if existent, as included in the histological_annotations.csv (in each *processed_data.tar).

**Submitters state that raw data will be shared upon request.

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

last: Haldar

first: Meredith

last: Wetzel

middle: T

first: Nilofer

last: Azad


title: The loss of glucocorticoid receptor accelerates ovarian ageing in zebrafish

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

summary: Ovarian aging and reproductive decline are key indicators of mid-life aging in females, with stress and elevated glucocorticoids (GCs) being significant contributors to the acceleration of this process. GCs act through both the glucocorticoid receptor (GR) and mineralocorticoid receptor (MR). While previous studies have shown that the ubiquitous knockout of GR leads to accelerated ovarian aging in zebrafish, the underlying mechanisms remain poorly understood. This study aimed to investigate the effects of GR loss on reproductive aging by performing RNA-seq to analyze transcriptional changes in the ovaries of adult GR knockout (GRKO) zebrafish. Our findings reveal that GRKO ovaries exhibit a high frequency of typical follicular atresia (TFA), with increased cellular proliferation at 6 months of age. Pathways involved in mitochondrial dysfunction were also upregulated in 6-month-old GRKO ovaries, suggesting that mitochondrial dysfunction and increased reactive oxygen species (ROS) contribute to the accelerated aging observed in GRKO zebrafish. These results indicate that the loss of GR alters key cellular, immune, and metabolic processes, driving accelerated ovarian aging in zebrafish.

overall_design: To examine the role of GR loss in accelerated ovarian aging, we sampled wild-type and ubiquitous GR knockout zebrafish at 3 and 6 months of age. The ovaries were dissected and RNA was extracted from the ovaries using Qiagen RNAeasy kit, following the manufacturer's protocol

first: Vijayan

last: Mathilakath

first: Devan

last: Meera


title: RNA seq of ACKR3 loss in  LUSC  murine cell lines derings from genetically engineereed mouse  models

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: bulk RNA seq of cell lines derived from PL(PTEN; LKB1) and PLA(PTEN:LKB1;ACKR3)LUSC genetically engineereed mouse

overall_design: Bulk RNA seq of LUSC cell line upon ACKR3 loss. The cell lone are derived from the LUSC GEMMs.

first: Angeliki

last: Karatza

first: Kwok-Kin

last: Wong


title: RNA m⁵C–dependent chromatin remodeling enhances radiotherapy response and metastasis control via myeloid reprogramming

city: Chicago

first: Hua

last: Liang

state: IL

department: Department of Radiation and Cellular Oncology

institute: University of Chicago

summary: In this study, we found that Myeloid-specific Tet2 deletion (Tet2 cKO) redirect the trajectory of monocyte differentiation into immunostimulatory antigen presenting myeloid-derived activating cells (MDACs), thereby enhanced control of local tumor and metastasis by ionizing radiation.  Using single-cell RNAseq (sc-RNAseq), we characterized the effects of TET2 on immune cells in the tumor microenvironment of B6 mice.

overall_design: WT/Tet2 cKO mice were inplanted with MC38 tumors, When tumors reached approximately 100 mm³,Mice received either a single 20 Gy dose of tumor-localized radiation or a sham treatment, 3 days after radiation. Sc-RNAseq was performed on the CD45+ cells from tumor tissue.

first: Fei

last: Ji

first: Hua Laura


title: Unique transcriptomic alterations in 5XFAD;PS19 mouse model align with human Alzheimer's disease

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

summary: Alzheimer’s disease (AD) is characterized by amyloid-β (Aβ) plaques and tau tangles, yet their combined effects on brain cell types remain poorly understood. To investigate this, we generated a dual-pathology mouse model (5XFAD;PS19) and performed single-nucleus RNA sequencing (snRNA-seq), integrating findings with human AD datasets. We uncovered widespread, synergistic transcriptional disruptions not seen in single-pathology models, including changes in gene co-expression networks and cell type-specific gene expression. Notably, we observed coordinated transcriptomic alterations involving both microglia and oligodendrocytes, particularly in immune-related pathways and suppression of synaptic transmission. The combined model significantly overlapped with human AD transcriptomic profiles at both gene and pathway levels, highlighting its translational relevance. This well-powered, sex-balanced study dissects the synergistic effects of Aβ and tau across multiple brain cell types. Our findings support the importance of modeling combined-pathology to uncover potential pharmacological targets for therapeutic development.

overall_design: Snap-frozen anterior cortex from 2 male and 2 female mice per group was used to generate single-nucleus suspensions for single nucleuse RNA-sequencing (total n=16). The groups included 5XFAD, PS19, 5XFAD;PS19 and wildype littermate controls. All mice were 9 months of age.

first: Jung Hyun

last: Park

first: Byungwook

last: Kim

first: Md Mamun

last: Al-Amin

first: Mason

last: Tate

first: Ahmad

last: Sharify

first: Hande

last: Karahan

first: Hui-Chen

last: Lu

middle: C

first: Jungsu


title: PAX3-SIX2 muscle stem cell heterogeneity drives muscle-specific repair dynamics diversification

city: Creteil

first: Joana

last: Esteves de Lima

address: 8 rue du general sarrail

department: IMRB INSERM U955

country: France

institute: INSERM

summary: The human body contains around 640 distinct muscles, each capable of regeneration following injury through the action of muscle-specific stem cells (MuSCs) that express the transcription factor PAX7. Its paralog, PAX3, a master regulator of embryonic myogenesis, is selectively expressed in a subset of adult quiescent MuSCs. The proportion of PAX3⁺ MuSCs varies across muscles. By combining lineage tracing and skeletal muscle injury, we demonstrate that PAX3 drives MuSC diversity and muscle-specific regeneration rates. PAX3-expressing MuSCs display enhanced proliferation and differentiation capacities, enabling a faster response following injury, whereas loss of PAX3 leads to proliferation arrest and cell death. Single-cell RNA-sequencing analyses revealed the specific expression of Six2 in PAX3+ MuSCs. We show that PAX3 is required for SIX2 expression, and loss of SIX2 in MuSCs reduces proliferation and differentiation rates. Conversely, ectopic Six2 expression promotes a faster response in PAX3- MuSCs. With this work, we establish that PAX3/SIX2 expression correlates with distinct MuSCs behavior, influencing regeneration rates in a muscle-type-dependent context. Our findings highlight a previously unrecognized layer of  regulation in MuSCs behaviour and muscle repair and suggest that PAX3-SIX2 heterogeneity could be leveraged for targeted therapeutic strategies in muscle-wasting diseases.

overall_design: Satellite cells from Pax3GFP/+ 5 days injured muscles were FACS-isolated to separate GFP+ from GFP-. The cells were freshly used to load on the 10x chromium machine.

first: Virginia

last: Zoglio

first: Sarah

last: Chebouti

first: Fayez

last: Issa

first: Benjamin

last: Polin

first: Sylvie

last: Manin

first: Pascal

last: Maire

first: Frédéric

last: Relaix


title: ac4C-RIP-seq in Control, NAT10 KD, NAT10 and Xrp1 KD in Drosophila

city: Shanghai

first: Wang

last: Lin

state: Shanghai

address: 2005 Songhu Road, Yangpu District, Shanghai, China

department: College of Life Science

institute: Fudan University

summary: In our study, we investigated the role of the ac4C RNA modification enzyme NAT10 in Drosophila development. We found that knockdown of NAT10 led to a global reduction of ac4C levels on rRNA and impaired the assembly of the 40S ribosomal subunit and triggered a ribosome biogenesis stress response. This response was associated with increased cell apoptosis, cell competition, and reduced translational efficiency. Through genetic and transcriptomic analyses, we demonstrated that the developmental defects and transcriptional changes observed upon NAT10 knockdown were largely dependent on the upregulation of Xrp1, a key sensor of ribosome assembly stress.  To explore the ac4C epitranscriptomic landscape and its functional implications in mRNA, we performed ac4C-RIP-seq in third instar larvae from three genotypes: Dats-GAL4/+ (control), Dats-GAL4 > UAS-NAT10-RNAi, and Dats-GAL4 > UAS-NAT10-RNAi Xrp1-RNAi. Our results revealed that ac4C modifications were widely distributed across the 5’UTR, CDS, and 3’UTR regions of mRNAs, with relatively higher enrichment in the 3’UTR.Integrated analysis of RNA-seq and ac4C-RIP-seq data revealed that the majority of differentially expressed genes upon NAT10 knockdown were not direct targets of ac4C modification. This indicates that the loss of ac4C on mRNAs has a limited direct impact on the transcriptome. Instead, the observed transcriptional alterations and developmental defects are primarily attributable to ribosome biogenesis stress.

overall_design: ac4C-RIP-seq was from whole third instar larvae from three different genotypes: Dats-GAL4/+ (control), Dats-GAL4 > UAS-NAT10-RNAi, and Dats-GAL4 > UAS-NAT10-RNAi Xrp1-RNAi.  Each genotype included three biological replicates, resulting in a total of nine samples for input and RIP-seq RNA-seq analysis.

first: Yan

last: Dong


title: mRNA-seq in Control, NAT10 KD, NAT10 and Xrp1 KD in Drosophila

summary: Our previous studies demonstrated that knockdown of the ac4C RNA modification enzyme NAT10 significantly activates the ribosomal stress response pathway. To investigate the extent to which NAT10 knockdown-induced transcriptomic changes depend on the activation of this pathway, we performed mRNA-seq on Drosophila wing discs from en-GAL4/+, en-GAL4 > UAS-NAT10-RNAi, and en-GAL4 > UAS-NAT10-RNAi Xrp1-RNAi larvae. Xrp1 is a key transcription factor involved in sensing ribosomal stress. We found that the vast majority of differentially expressed genes caused by NAT10 knockdown were rescued by simultaneous knockdown of Xrp1. This observation is consistent with the developmental phenotypes we observed. These results suggest that the primary function of NAT10 is to regulate ribosome biogenesis.

overall_design: Total RNA was extracted from wing discs of third instar larvae from three different genotypes: en-GAL4/+ (control), en-GAL4 > NAT10-RNAi, and en-GAL4 > NAT10-RNAi Xrp1-RNAi. Each genotype included three biological replicates, resulting in a total of nine samples for mRNA-seq analysis. This experiment was designed to investigate the extent to which transcriptomic changes caused by NAT10 knockdown depend on the activation of the ribosomal stress response pathway mediated by Xrp1.


title: Macrophage-specific targeting of histone demethylases with small-molecule inhibitors suppresses inflammatory responses in vivo [CUT&Run]

city: Pittsburgh

first: Niranjana

last: Natarajan

state: PA

address: 200 Lothrop street, BST1720

institute: university of pittsburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Macrophages are versatile immune cells, with the ability to respond to varied intrinsic and extrinsic cues, and transition between inflammatory and pro-reparative phenotypes. A complex network of epigenetic processes, such as DNA methylation, histone methylation, and acetylation, play key roles in modulating macrophage polarization and inflammatory gene expression. Transcriptional analysis in patients with respiratory failure, long COVID-19, and influenza revealed an augmented expression of chromatin-modifiers including histone demethylases, broadly defined as lysine demethylases (KDMs), in lung macrophages. Therefore, macrophage-specific pharmacological perturbation of these enzymes in vivo holds therapeutic promise in abating inflammation. To investigate the role of KDMs in inflammation, we screened a panel of small-molecule inhibitors of chromatin modifiers for their efficacy in inducing anti-inflammatory macrophage polarization in vitro. We demonstrate that pretreatment with the broad spectrum KDM inhibitor n-octyl-IOX1, KDM5-specific inhibitor PB-IT resulted in a significant decrease of lipopolysaccharide (LPS)-induced expression of the inflammatory genes Il1b, Il6, Tnfa, and iNos in bone marrow-derived macrophages (BMDM). Subsequent RNA sequencing and CUT&RUN analyses revealed that LPS activation led to distinct transcriptomic and epigenomic alterations including expression of master transcription factors (TFs) BLIMP-1 and GFI1 whereas n-octyl-IOX1 and PB-IT treatments rewired these regulatory networks, thereby impeding inflammatory gene expression and response. To further probe the merit of KDM inhibition in perturbing macrophage-mediated inflammation in vivo, we delivered n-octyl-IOX1 selectively to macrophages in mice using a cell-specific, targeted lipidoid nanoparticles. n-octyl-IOX1 loaded nanoparticles significantly diminished LPS-mediated peritoneal macrophage expansion and inflammatory gene expression in this cell population, underscoring the importance of macrophage-specific targeting of KDMs with small-molecule inhibitors in inflammatory disease.

overall_design: Bone marrow cells were isolated from the femurs and tibias of C57BL/6 mice. The cells were cultured in DMEM containing 5.5 mM glucose and supplemented with 20% L929 conditioned medium. The cells were seeded in 12 well plates. After the cells were 80% confluent, the culture was treated with 20mM n-octyl-IOX1 or 20mM PB-IT for 8 hours, followed by 1ng/ml LPS for 24 hours. CUT&RUN was performed according to manufacturer’s suggested protocol (Cell Signaling, #86652). Cells were trypsinized and harvested after treatment, permeabilized, and incubated with H3K4me3 and H3K9me3 antibodies overnight. Next, protein A-MNase was added to the cells after washing and incubated for 1 hour. Then, chromatin digestion was performed followed by release of digested chromatin and purification of digested DNA. Library preparation of CUT&RUN generated fragments was carried out followed by sequencing (~5million reads / sample).

first: Partha

last: Dutta


title: Macrophage-specific targeting of histone demethylases with small-molecule inhibitors suppresses inflammatory responses in vivo [RNA-seq]

overall_design: Bone marrow cells were isolated from the femurs and tibias of C57BL/6 mice. The cells were cultured in DMEM containing 5.5 mM glucose and supplemented with 20% L929 conditioned medium. The cells were seeded in 12 well plates. After the cells were 80% confluent, the culture was treated with 20mM n-octyl-IOX1 or 20mM PB-IT for 8 hours, followed by 1ng/ml LPS for 24 hours prior to RNA extraction, QC and RNA sequencing. untreated cells and LPS treated cells were included as controls.


title: Chimeric Oncoproteins Enhance Native Kinase Activity to Drive Tumorigenesis via Phase-separated Cytoplasmic Condensates

first: Xiaohua

last: Hu

address: 2005 Songhu Rd.

summary: Gene fusions involving receptor tyrosine kinases (RTKs) are potent oncogenic drivers, yet the underlying mechanisms by which these chimeric proteins induce tumorigenesis remain largely elusive. Here we demonstrate that recurrent FGFR3-TACC3 (FT) fusion proteins undergo liquid-liquid phase separation (LLPS) to form cytoplasmic condensates, driving tumorigenesis in lung cancer and glioma. These condensates function as oncogenic signaling hubs, enhancing FGFR3 native kinase activity and promoting hyperactivation of the canonical MAPK/ERK pathway. The coiled-coil domain of TACC3 is essential for condensate formation and the oncogenic potential of FT fusions. CKAP5 and AURKA are recruited to FT phase-separated condensates, thereby amplifying MAPK/ERK signaling and triggering AURKA/MYC oncogenic program. Dual pharmacological inhibition of FGFR3 and AURKA synergistically dissipates LLPS and impedes the growth of FT-driven tumors. Our findings unveil the oncogenic significance of membrane-less protein assembly and highlight the potential of targeting LLPS or its pivotal components as a therapeutic strategy for FT-driven cancers.

overall_design: A549 expressing empty vector, FGFR3, TACC3, FTS,  FTL, or FTLΔCC

first: Xiaoping

last: Wu


title: Multiparity induces persistent myocardial structural, functional and transcriptomic remodelling

city: Melbourne

first: Bing H

last: Wang

state: VIC

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

summary: Pregnancy poses unique hemodynamic and metabolic demands on the heart. We postulated that the repetitive biological and hemodynamic impact of multiple pregnancies could cause persistent myocardial remodelling providing a substrate for subsequent HFpEF. Here we report that C57Bl/6J female mice at 24 months of age with history of multiple pregnancies have a different transcriptomic profile combined with diastolic dysfunction, and persistent remodeling  in the absence of on going stimulus, compared to virgin age matched mice. 128 genes were differentially expressed in the the multiparous mice. The 64 upreguated and 64 downregulated genes were associated organic anion/ion transport and  extra cellular matrix regulation pathway. These genes were also involved in biological processes such as ERBB2-3 signaling and actin polymerisation dependent cell motility, and were associated with 5 cardiac related disease pertubations in the top ten diesease pertubations in GEO UP including dilated cardiomyopathy. Therefore multiparity could provide a potential foundation for heart failure phenotypes including HFpEF later in life.

overall_design:
To investigate the effects of parity per se on cardiac function and transciptomic profile we compared age matched 24 month old C57Bl/6J mice with history of more than 3  pregnancies to virgin C57Bl/6J mice with no experimental interventions.
Comparaitve cardiac gene expression profile was performed on mid sections of n=8 multiparous mice hearts and n=8 virgin mice hearts.

first: Ruth

last: Magaye

first: Bing

first: David

last: Kaye

first: William

middle: W

last: Ho

first: Fumi

last: Takeuchi


title: Single-cell transcriptomic analysis of midbrain organoids of bipolar disorder patients reveals a mechanism of lithium response

city: beijing

first: xinyu

last: She

address: shuangqing road, haidian district

department: school of life sciences

institute: Tsinghua university

summary: Bipolar disorder (BD) is a complex neuropsychiatric disorder involving pathophysiological changes in multiple brain regions, which, however, remain poorly understood.We generated human midbrain organoids (hMOs) to investigate the midbrain pathophysiology of BD.

overall_design: Human midbrain organoids were differentiated from ten iPSC lines,  including four healthy controls (HC), three lithium responders (LR) and three lithium non-responders (NR), and analyzed using scRNA-seq.

first: Xinyu

first: Dan

last: Li

first: Qian

first: Chonglei

last: Fu

first: Bocheng

first: Yanfen

last: Chen

first: Mei

last: Zhao

first: Shuangli

last: Mi

first: Jun

last: Yao


title: Deficiency of m6A RNA methylation promotes ZBP1 mediated cell death

city: Houston

first: Yi-Lan

last: Weng

state: Texas

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: m6A RNA methylation suppresses the immunostimulatory potential of endogenous RNA. Deficiency of m6A provokes inflammatory responses and cell death, but the underlying mechanisms remain elusive. Here we showed that the noncoding RNA 7SK gains the immunostimulatory potential upon m6A depletion and subsequently activates RIG-I/MAVS axis to spark interferon (IFN) signaling cascades. Concomitant excess of IFN and m6A deficiency synergistically facilitate the formation of RNA G-quadruplexes (rG4) to promote ZBP1-mediated necroptotic cell death.

overall_design: RNA sequencing (RNA-seq) was conducted on both wild-type (WT) and METTL3 knockout (KO) HMC3 cell lines, with five replicates each, using the Smart-seq2 protocol.  rRNA-depleted RNA-seq was carried out for both WT and METTL3 KO HMC3 samples, each with three replicates. This process involved rRNA depletion, followed by library construction using the NEBNext Ultra II Directional RNA Library Prep Kit.

first: Li

last: Shuang

first: Weng

last: Yi-Lan


title: The effect of Sphingosine-1-Phosphate Receptor 1 and Complement Component 3 conditional knockouts on primary tumors in MMTV-PyMT mice.

city: Charleston

first: Alhaji

middle: Harune

last: Janneh

state: SC

address: 86 Jonathan Lucas Street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: Sphingolipid metabolism has been shown to regulate intracellular complement activation via sphingosine-1-phosphate receptor 1 (S1PR1) signaling to stimulate NLRP3 inflammasome-induced cancer metastasis. Here, the transcriptomic effects of S1PR1 and complement C3 conditional knockouts on primary tumors in MMTV-PyMT Mice were assessed.

overall_design: Three different strains of mice were generated by breeding MMTV-PyMT mice with MMTV-Cre, MMTV-Cre;S1pr1fl/fl, and MMTV-Cre;C3Tdt strains. These three strains were named: 1) Wild-type= MMTV-Cre; MMTV-PyMT, 2) S1pr1 knockout= MMTV-Cre;S1pr1fl/fl; MMTV-PyMT, and 3) C3 knockout= MMTV-Cre;C3Tdt:MMTV-PyMT. After 4.5 months, the mice were sacrificed, and the primary tumors were collected from all three strains and stored immediately in an RNAlater stabilization solution. The total isolated RNA from these samples was sent to CD Genomics for RNA sequencing.


title: The effect of nitric oxide donor on tumor infiltrated immune cells.

city: Tainan

last: Chung Yen

state: Please Select

address: No.1, University Road, Tainan City 701, Taiwan (R.O.C)

country: Taiwan

institute: NCKU

summary: Low-dose nitric oxide donor, SNAP induced an anti-tumor effect through the immune modulation in tumor microenvironment. We isolated the lived CD45-positive immune cells from LL2 tumor tissue after the day 20 of 0.004 mg/kg SNAP treatment and performed single-cell RNA sequencing via BD Rhapsody Single-Cell analysis system.

overall_design: 2 sample from low-dose SNAP treatment and control group

first: Chung-Yen

first: Ming-Derg

last: Lai


title: Oncogenic KRAS promotes pancreatic ductal adenocarcinoma (PDAC) through post-transcriptionally regulated KRAS-induced granules (KGs)

first: Ronald

middle: J

last: Parchem

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: scRNA-seq analysis of patient-derived organoids treated with JTE-607

status: Public on Aug 10 2026

first: Zhaozhao

address: Songhu Road 2005

institute: FUDAN UNIVERSITY

summary: To evaluate the impact of CPA inhibition on transcriptomic heterogeneity, we treated two lung cancer organoids and one liver cancer organoid with either DMSO or JTE-607, and subsequently pooled them for 3′ tag-based single-cell RNA sequencing using the 10x Genomics Chromium platform. For bioinformatic analysis, profiled cells were first demultiplexed and assigned to their respective organoids of origin based on expression and SNP profiles. We then quantified transcript abundance at polyadenylation site (PAS) resolution to generate a PAS-by-cell count matrix, allowing us to systematically investigate the effects of JTE-607 treatment on PAS usage patterns and cellular states.

overall_design: Two lung cancer organoids and one liver cancer organoid were treated with DMSO or JTE-607. Single-cell RNA-seq (scRNA-seq) libraries were generated using the 10x Genomics Chromium Single Cell 3′ Reagent Kit (v2 chemistry). In addition, standard bulk RNA-seq was performed separately on each of the three organoids to establish baseline expression and SNP profiles.

first: Yue

last: Chu

first: Bing

first: Ting

last: Ni


title: An expanded repertoire of brain microexons is directly impacted by autism-associated genetic variation

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

summary: A major challenge in understanding autism spectrum disorder (ASD) is to establish the underlying convergent genetic and molecular mechanisms. Neuronal microexons represent a highly conserved class of alternative splicing event and are enriched in genes with diverse and critical functions in nervous system biology. Previous studies have provided evidence that microexon splicing is disrupted in the brains of approximately one-third of ASD individuals, in part as a consequence of altered neuronal activity. Moreover, mice with microexon splicing deficiencies display multiple ASD-like phenotypes. However, the full landscape of microexons is not known, and whether these exons are directly impacted human genetic variation has not been previously investigated. Through extensive profiling of brain RNA-Seq data, we have discovered several hundred new neuronal microexons, including many that have highly specific neuronal subtype-specific splicing patterns, and others with the potential to control gene expression by activating nonsense-mediated mRNA decay. By developing a machine learning model that predicts neuronally-spliced microexons from genome sequence, we have defined critical regulatory elements surrounding the expanded repertoire of microexons. Using this model, we identify rare and common variants that are predicted to alter microexon splicing patterns in approximately 30% of ASD-affected individuals, relative to their unaffected siblings, with rare variants having the strongest impact. These variants are mostly detected in idiopathic individuals and converge on a subset of microexons concentrated in synaptic and additional ASD-linked genes, but also in genes not previously linked to autism. Our results collectively define an expanded repertoire of neuronal microexons, delineate their regulatory code, and pinpoint genetic variants that impact their splicing, with implications for the disruption of functions central to neuronal biology and brain disorders.

overall_design: This dataset consists of 10 RNA-seq files associated with the manuscript "An expanded repertoire of brain microexons is directly impacted by autism-linked genetic variation" based on two experiments: 1) siRNA knockdown of the splicing factor Quaking (Qk) in mouse neuroblastoma (N2A) cells followed by RNA-Seq, 2) Treatment of in-vitro differentiated glutamatergic neurons (from mouse embryonic stem cells) with the translation inhibitor cycloheximide (CHX) followed by RNA-Seq. Experiment 1 is controlled by a non-targeting siRNA, while experiment 2 is controlled by the no-drug condition.

first: Guillermo

middle: E

last: Parada

first: Hannes

last: Bretschneider

first: Jack

middle: D

first: Brett

last: Trost

first: Worrawat

last: Engchuan

first: Mehdi

last: Zarrei

first: Manuel

last: Irimia

first: Martin

last: Hemberg

first: Michael

last: Wainberg

first: Stephen

last: Scherer

first: Quaid

last: Morris

first: Benjamin

last: Blencowe


title: Skeletal muscle reprogramming of metabolic, ribosomal and developmental pathways contributes to Roux-en-Y gastric bypass-induced adaptation in women

city: Ottawa

first: Mary-Ellen

last: Harper

state: ON

address: 451 Smyth Rd

institute: University of Ottawa

type: Methylation profiling by genome tiling array


title: The Maternal-to-Zygotic Transition Is a Critical Window for PFOA-Induced Disruption of Developmental Programming

city: Durham

first: Zainab

last: Afzal

state: NC

address: 700 George Street, BBRI/Kumar Lab

institute: North Carolina Central University

summary: Early embryogenesis is governed by precisely timed gene regulatory programs that coordinate cell fate specification, tissue patterning, and morphogenesis. The maternal-to-zygotic transition (MZT) represents a pivotal developmental milestone during which regulatory control shifts from maternally deposited transcripts to activation of the zygotic genome. Disruption of this transition has the potential to alter developmental trajectories with lasting consequences. Per- and polyfluoroalkyl substances (PFAS), environmentally persistent contaminants, have been linked to developmental abnormalities, yet their impact on core embryonic gene regulatory networks especially with exposure during MZT is not well understood. Using zebrafish (Danio rerio), a tractable vertebrate model and New Approach Methodology (NAM), we investigated how PFAS exposure during the MZT alters early developmental programming. Embryos were exposed starting at different times before and within the MZT time window and collected at 24 hours post-fertilization (hpf) for transcriptomic analysis. Targeted qRT-PCR revealed dysregulation of genes controlling transcriptional activation, lineage specification, proliferation, and differentiation. Whole-transcriptome RNA sequencing (RNA-seq) further identified widespread perturbations in gene networks governing transcriptional regulation, cell signaling, and embryonic morphogenesis. Temporal analysis revealed that exposure beginning at 3.5 hpf, followed by 8 hpf, corresponding to early zygotic genome activation and near completion of zygotic activation, respectively, resulted in the greatest differential gene expression changes at 24 hpf. Consistent with these early gene regulatory perturbations, larvae exposed starting at 8 hpf also exhibited altered behavior at 5 days post-fertilization. Together, these findings demonstrate that PFAS exposure during MZT disrupts the establishment of embryonic gene regulatory networks, linking environmental toxicant exposure to altered developmental patterning and organismal outcomes. This work underscores the vulnerability of early developmental transitions to environmental perturbation and positions MZT as a critical window of susceptibility during development.

overall_design: Wild-type zebrafish embryos were assigned to untreated control or 700 ng/L PFOA exposure groups. PFOA exposure was initiated at different developmental timepoints, the 1-cell, 3.5 hpf, 5 hpf, or 8 hpf developmental stage. Four independent biological replicates (spawning events) were analyzed per condition. All embryos were collected at 24 hpf for total RNA extraction and bulk paired-end RNA sequencing.

first: Vandana

last: Veershetty

first: Evan

last: Pittman

first: Charles

last: Hatcher

first: Deepak

last: Kumar


title: Transcriptomic profiling (RNA-seq) of the mid-region heart tissue from wild-type (WT) and TET2KO mice following 28 days of Angiotensin II treatment.

city: London

first: Hashum

last: Sum

address: 125 Coldharbour Lane

institute: King's College London

summary: Chronic Angiotensin II (Ang II) infusion is a known inducer of cardiac remodeling, hypertrophy, and fibrosis, processes that are intricately linked to endothelial dysfunction. To determine how endothelial-specific deletion of TET2 affects the cardiac microenvironment under stress, we performed total RNA sequencing (RNA-seq) on the mid-ventricular region of the heart harvested from wild-type (WT) and endothelial-specific TET2 knockout (TET2KO) mice after 28 days of Ang II infusion. This dataset captures the global transcriptomic landscape of the heart, facilitating the identification of gene expression shifts, extracellular matrix remodeling, and hypertrophic markers associated with endothelial TET2 deficiency.

overall_design: Mid-ventricular heart tissue samples were harvested from adult wild-type (WT) and endothelial-specific TET2 knockout (TET2KO) mice (n=3 biological replicates per group) following a 28-day continuous infusion of Angiotensin II (1.0 mg/kg/day). Total RNA was extracted from all samples, followed by poly(A)-selected mRNA library preparation and paired-end sequencing on the Illumina NovaSeq 6000 platform. The dataset captures transcriptomic alterations in the heart tissue, reflecting secondary remodeling and fibrotic responses driven by endothelial TET2 deficiency in the context of hypertensive stress.

first: Alison

last: Brewer


title: Transcriptomic profiling (RNA-seq) of lung endothelial cells from wild-type (WT) and TET2KO mice following 28 days of Angiotensin II treatment.

summary: Chronic hypertension and Angiotensin II infusion induce systemic vascular and endothelial dysfunction. To investigate cell-autonomous transcriptional changes resulting from endothelial-specific TET2 deficiency in the pulmonary microenvironment, we performed total RNA sequencing on lung endothelial cells isolated from wild-type (WT) and endothelial-specific TET2 knockout (TET2KO) mice after 28 days of Angiotensin II treatment.

overall_design: Lung endothelial cells were isolated from wild-type (WT) and endothelial-specific TET2 knockout (TET2KO) mice following 28 days of chronic Angiotensin II (Ang II) infusion. Total RNA was extracted, followed by poly(A)-selected mRNA library preparation and paired-end sequencing (2x150 bp) on the Illumina NovaSeq platform. Reads were mapped to the Mus musculus GRCm38 reference genome using STAR.


title: EZH2 inhibitor GSK126 promotes human iPSC hematopoietic differentiation

city: Bethesda

first: Jianyi

last: Ding

address: 9000 Rockville Pike

department: CMTB

institute: NHLBI, NIH

summary: The de novo generation of human hematopoietic stem cells (HSCs) from induced pluripotent stem cells (iPSCs) represents a promising avenue for the cellular therapy of blood disorders. However, existing protocols often result in the production of immature progenitors with limited multilineage engraftment capacity in vivo. This limitation is believed to be due to an epigenetic barrier, particularly involving the Polycomb Repressor Complex 2 (PRC2), which mediates transcriptional repression during hematopoietic development through H3K27me3 methylation. In this study, we explored the suppression of EZH2, a key component of PRC2, using the small molecule inhibitor GSK126 at various stages of iPSC differentiation. Our findings revealed that EZH2 inhibition leads to an increase in phenotypic HSCs and enhances long-term colony-forming unit (CFU) colony formation. Single-cell RNA sequencing further demonstrated that GSK126 promotes iPSC hematopoietic differentiation. These results highlight the potential of EZH2 inhibition to overcome epigenetic barriers and enhance iPSC-derived hematopoietic differentiation, paving the way for advancements in regenerative medicine and transplantation therapies.

overall_design: EZH2 inhibitor or DMSO were used for iPSC HSC differentiation at day 3-day12, and after 12 days of iPSC HSC differentiation, CD43CD45+CD34+ cells were sorted and used for scRNA seq.

first: Andre

last: Larochelle


title: Suppressing phosphatidylserine externalization overcomes cancer immune evasion and enhances immunotherapy

city: Boston

first: Teng

last: Teng

state: MA

address: 201 Brookline Ave Suite 901

institute: Tango Therapeutics

summary: Immune checkpoint blockade (ICB) has transformed cancer therapy, yet many tumors remain refractory to treatment due to diverse immune evasion mechanisms. To uncover novel drivers of ICB resistance, we performed an in vivo CRISPR-Cas9 screen in mice with increasing levels of immune pressure. This screen identified phosphatidylserine (PS) externalization as a potent mediator of immune escape. Tumors with elevated surface PS exposure prevented reinvigoration of CD8+ T cells upon PD-1 blockade, which was associated with increased recruitment of immunosuppressive myeloid cells. Targeting of PS Synthase 1 (PTDSS1) or either of the scramblases, XKR8 or ANO6, sensitized tumors to ICB in vivo. These findings demonstrate that elevated PS exposure constitutes a mechanism of resistance to ICB, and that targeting regulators of PS externalization represents a promising strategy to enhance the efficacy of immunotherapy in refractory tumors.

overall_design: For in vitro CRISPR screen, HCT116 (RRID:CVCL_0291) and SiHa (RRID:CVCL_0032) cells with stable Cas9 expression were infected with lentivirus encoding sgRNA against TMEM30A and selected by hygromycin. Cells were then infected with a genome-wide CRISPR KO library and sorted for Annexin V-high and Annexin V-low  populations to represent PS high and PS low population. For in vivo CRISPR screening, we constructed an immune evasion context discovery library consisting of 20 essential genes as controls for KO efficiency, 18 IO control genes, and 471 tumor suppressor genes and genes associated with immune evasion. MC38 cells were first infected with lentivirus encoding enCas12a and a blasticidin resistance gene (BSD) flanked by LoxP sites. Stable cells were then infected with a CRISPR KO library encoding a puromycin resistance gene and RFP flanked by Lox2272 sites and two gRNA sequences outside the floxed region. Cells were then infected with an insertion-deficient lentivirus encoding Cre recombinase and EGFP (IDV-Cre) and cultured for an additional two weeks before injected subcutaneously into the right flank of C57BL/6 (RRID:MGI:2159769) (n = 50) or BALB/c-nude (RRID:IMSR_RJ:BALB-C-NUDE) BALB/c-nude (n = 15) mice (1.0 x 106 cells per mouse). A sub-population of cells was also maintained in culture for collecting gDNA on the day of inoculation and on the day tumors were harvested. C57BL/6 (RRID:MGI:2159769) C57BL/6 mice were randomized for anti-PD-1 (n = 30) or IgG2a (n = 20) treatment when mean tumor volume reached 50 mm3, as described above. Tumors were harvested when mean tumor volume for a single group reached 1,000 mm3 for gDNA isolation and subsequent analysis by next-generation sequencing (NGS).

first: Johann

last: Bergholz

first: Grace

last: Trombley

first: Gwendolyn

last: Cusing

first: Zhaoqi

last: Li

first: Margaret

last: Torrence

first: Geneva

last: Sganga

first: Jennifer

last: Casey

first: Shangtao

last: Liu

first: Ashley

last: Choi

first: Samuel

last: Meier

first: Tenzing

last: Khendu

first: Yi

last: Yu

first: Binzhang

last: Shen

first: Hannah

last: Stowe

first: Salam

last: Shaaban

first: Jannik

last: Andersen

first: Serge

last: Gueroussov


title: Acetate, a short-chain fatty acid, inhibits Coxiella burnetii replication via direct bacteriostatic effect and through vacuolar modulation and host cell perturbations.

city: Glendale

first: Dhritiman

last: Samanta

state: Arizona

institute: Midwestern University

summary: Coxiella burnetii, the etiologic agent of Q fever, is an obligate intracellular pathogen that replicates within a specialized acidic compartment termed the Coxiella-containing vacuole (CCV). Current treatment options for chronic Q fever require prolonged antibiotic therapy and are limited by toxicity and reduced efficacy within the acidic intracellular niche. Short-chain fatty acids (SCFAs) are host- and microbiota-derived metabolites with documented immunomodulatory and antimicrobial properties; however, their effects on C. burnetii remain unknown. We investigated whether acetate, the most abundant SCFA in the human body, influences C. burnetii growth and CCV biology. C. burnetii axenic and intracellular growth was measured by colony-forming unit (CFU) assay. Acetate MIC and MBC were determined using standard broth microdilution coupled with CFU assays. Confocal microscopy followed by quantitative measurements was used to determine the CCV expansion and CCV luminal pH. Uninfected and C. burnetii-infected HeLa cells were processed and sent for RNA-seq to Plasmidsaurus®. Acetate significantly inhibited C. burnetii replication in axenic ACCM-2 medium, completely preventing bacterial growth at concentrations of 20 - 80 mM. Broth microdilution assays identified a minimum inhibitory concentration (MIC) of 1.25 mM and a minimum bactericidal concentration (MBC) of 5 mM, demonstrating marked bacterial sensitivity to acetate. In infected HeLa cells, 24 h acetate treatment reduced intracellular bacterial burden by approximately 50% and markedly impaired CCV expansion, decreasing vacuolar size by 61–67% relative to control cells. Further, acetate elevated CCV luminal pH from approximately 5.2 to 5.5–5.7, indicating reduced vacuolar acidity, a condition known to be unfavorable for C. burnetii replication. Transcriptomic analysis revealed extensive host-cell reprogramming following acetate treatment, characterized by altered expression of genes involved in lipid metabolism, membrane trafficking, stress responses, apoptosis, complement activation, and inflammatory signaling pathways. Acetate restricts C. burnetii through multiple mechanisms, including direct antibacterial activity, disruption of CCV maturation and acidification, and broad modulation of host-cell transcriptional programs. These findings identify acetate as a previously unrecognized inhibitor of C. burnetii and highlight metabolic perturbation of the intracellular niche as a potential vulnerability of this pathogen. More broadly, our results demonstrate that host-derived metabolites can profoundly influence obligate intracellular bacterial survival and pathogenesis.

overall_design: RNA-seq profile of HeLa cells, uninfected or infected with WT Coxiella burnetii Nine Mile phase 2 strain, and treated with either PBS or 50 mM sodium acetate.

first: Yazen

last: Germukly

first: Brooke

last: Hall

first: Alexandria

last: Quinonez Sandelin


title: Longitudinal single-cell and spatial transcriptomics reveals intratumor heterogeneity, therapeutic response, and comparative value of canine marginal zone lymphoma [spatial data]

city: Minneapolis

first: Grace

last: Walker

state: Minnesota

address: 425 East River Parkway

department: Masonic Cancer Center

institute: University of Minnesota

summary: Diffuse B-cell lymphomas are the most prevalent canine hematologic malignancies, and their clinical presentation resembles that of human B-cell non-Hodgkin lymphomas (NHLs). However, a lack of a clear subtyping framework perpetuates imprecise treatment approaches that fail to address mechanisms of therapy resistance. Here, we employed deep phenotyping via serial sampling and longitudinal transcriptomics to evaluate intratumoral composition and therapy response in a 6-year-old neutered male goldendoodle with stage 5A marginal zone lymphoma (MZL). Following sequential treatment consisting of a single IV dose of oncolytic vesicular stomatitis virotherapy (VSV) and standard CHOP chemotherapy 30 days later, we performed scRNAseq on seven serial lymph node biopsies and spatial sequencing on a resection taken 10 days post-VSV treatment. B cells (>90%) comprised three transcriptionally distinct and temporally stable subpopulations, with specific copy number profiles and robust spatial organization despite disrupted lymph node architecture. Analysis across subpopulations revealed downregulation of the quiescence program including KLF2, suggesting similarity to KLF2-deficient human MZL. While VSV successfully reached target B cells, downstream transcriptional responses were predominantly localized to the T-cell compartment. T cells (≤6%) showed increased proliferation and upregulation of cytotoxicity markers post-VSV administration, enriching for leukocyte-mediated cytotoxicity pathways consistent with an anti-viral immune response. Ultimately, these results provide an in vivo proof-of-concept for the treatment paradigm in canine lymphoma, while emphasizing the need for improved subtyping frameworks and multidimensional treatment strategies targeting intratumoral heterogeneity.

overall_design: On day-10 post VSV administration, a 1cm2 section of malignant lymph node was resected and flash-frozen for spatial transcriptomics sequencing.

first: Marissa

last: Macchietto

first: Kelly

last: Reid

first: Lauren

last: Burt

first: Amber

last: Winter

first: Sara

last: Pracht

first: Michelle

last: Buettner

first: Velia

last: Penza

first: Caitlin

last: Yung

first: Rose

last: Dicovitsky

first: Alana

last: Kuzmik

first: Daniel

middle: A

last: Vallera

first: Kim

last: Demos-Davies

first: Davis

last: Seelig

first: Antonella

last: Borgatti

first: Mike

last: Henson

last: Feiock

first: Jaime

middle: F

last: Modiano

first: Shruthi

last: Naik

first: Aaron

middle: L

last: Sarver

first: Amy

last: Treeful


title: Sunitinib Induces Macrophage Dysfunction and Impaired Tissue Regeneration Through Suppression of PPARγ

first: zhouchen

last: zhang

address: Zhongguancun South Avenue No. 22

institute: Peking University School and Hospital of Stomatology

summary: Sunitinib, a widely used multi-target tyrosine kinase inhibitor, has side effects that Q6 may impact tissue repair and regeneration, potentially contributing to the onset of medication-related osteonecrosis of the jaw. Macrophages play a central role in tissue homeostasis and regeneration, and their dysfunction may be a key factor. In this study, using a zebrafish model, we found that sunitinib treatment impaired macrophage migration and tissue regeneration. Transcriptomic analysis further revealed that sunitinib significantly suppressed the PPARg signaling pathway, reparative gene program and mitochondrial metabolism, confirmed by immunofluorescene staining, RT-qPCR and seahorse mitochondrial stress assays. Treatment with rosiglitazone (PPARg agonist) effectively rescued the regeneration defects induced by sunitinib, an effect that was abolished upon macrophage depletion. Rosiglitazone also recovered the oxidative phosphoryla_x0002_tion in macrophages. Collectively, our results demonstrate that sunitinib impairs tissue regeneration by suppressing PPARg signaling and oxidative phosphorylation in macrophages, and that targeting the PPARg pathway represents a promising therapeutic strategy to reverse sunitinib-associated deficits in tissue repair.

overall_design: In this study, a zebrafish tail fin injury regeneration model was used to investigate the effects of sunitinib on macrophage function and tissue regeneration. Transcriptomic analysis, immunofluorescence staining, RT-qPCR, and Seahorse mitochondrial stress assays were performed to elucidate the underlying mechanisms.

first: Zhouchen

last: Zhang

first: Qiao

last: Qiao

first: Jiannan

last: Li

first: Qingxiang

first: Yuanning

last: Yang

first: Ying

last: Zhou

first: Hongyuan

last: Huang


title: RNA seq of Tunicamycin treated liver with or without CHOP

city: IOWA CITY

first: Thomas

last: rutkowski

state: Iowa

address: 51 newton Rd

department: Anatomy and Cell Biology

institute: uiowa

summary: AAV-Tbg-Flpo was injected to Chop FluL/FluL animals to restore CHOP expression in the liver a week prior to experiment. On the day of experiment, mice (2 males and 2 females in each group) were I.P. injected with tunicamycin to induce ER stress. 8 hrs post injection, mice were sacrificed and RNA seq from the liver was performed. AAV-Tbg-EGP was used as virus control.

overall_design: Chop FLuL/FLuL mice(2 males and 2 females each group) were I.P. injected with either AAV-Tbg-EGFP or AAV-Tbg-Flpo at least a week before experiment. On the day of experiment,  mice were I.P. injected with tunicamycin (TM) at 1 mg/kg.bw. Mice were sacked 8 hrs post tunicamycin injection. GFP control = 368 (M), 369 (M), 392 (F), 393 (F); GFP TM = 434 (M), 370 (M), 394 (F), 435 (F); FLpo control = 436 (M), 395 (M), 441 (F), 439 (F); FLPo TM = 438 (M), 437 (M), 442 (F), 440 (F);

first: Kaihua

last: Liu

first: Chaoxian

last: Zhao


title: Jellyfish-Derived Peptide Hydrolysate Alleviates Diet-Induced Obesity in Mice and Improves Aging-Related Healthspan in Caenorhabditis elegans

first: Zhou

last: Peng

address: 720 Xianxia Rd.

institute: Shanghai tongren hospital

summary: To Investiage th cooperative gene expression of peptide treated or untreated Caenorhabditis elegans

overall_design: Comparative gene expression frofiling analysis of RNA-seq data for Caenorhabditis elegans with or without Jellyfish treatment

first: Xiaoyu

last: Wang


title: CHOP CHIP-seq on WT mouse liver post TM treatment

summary: ChIP-seq on pooled livers from three tunicamycin-challenged wild-type animals.

overall_design: ChIP-seq was performed by Zymo Research using pooled samples from 3 mice treated with 1 mg/kg b.w. TM for 8h. IP was with CHOP antibody B-3 (sc7351, Santa Cruz), previously validated for specificity (Chikka et al. 2013), and validated prior to ChIP-seq against control Ig (12-371, Millipore Sigma) for the known CHOP-binding region in the Gadd34 promoter (Marciniak et al. 2004). Approximately 100-250 μg of chromatin was used. ChIP-seq libraries were prepared using a proprietary library preparation protocol from Zymo Research. ChIP-Seq libraries were diluted to 2 nM before being multiplexed and run on the Next-Gen Sequencing platform –HiSeq using single-end reads. For sequencing data analysis, FastQC was applied to conduct quality control for ChIP-seq data. Reads were aligned to the mouse reference genome mm10 by Bowtie with at most 2 mismatches. Reads that appeared more than twice at the same position on the same strand were discarded to remove PCR duplication. After filtering bam files by Samtools v1.9 and Sambamba v0.7.1, we used MACS2 v2.1.2 to call peaks with default parameters. The R package ChIPseeker was applied to annotate peaks. ChIP-seq motif analysis was performed with HOMER, searching against IMAGE known motifs. Pathway analysis for RNA-seq and ChIP-seq was performed using DAVID (Dennis et al. 2003), and enriched transcription factor binding sites were analyzed using ChEA3 (Keenan et al. 2019) and the ReMap database.

last: Rutkowski


title: Transcriptomic analysis of perfluorobutane Sulfonic Acid (PFBS) in two human placental models

city: San Diego

first: Elana

last: Elkin

state: CA

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

summary: Perfluorobutane sulfonic acid (PFBS) is a short-chain replacement per- and polyfluoroalkyl substance (PFAS) increasingly detected in drinking water and human serum. Prenatal PFBS exposure has been epidemiologically associated with hypertensive disorders of pregnancy, including preeclampsia, and increased offspring adiposity; however, the toxicological mechanisms underlying these associations and the effects of PFBS on human placental tissue remain poorly characterized. With a transplacental transfer efficiency of approximately 97%, PFBS undergoes near-complete transfer to the fetal compartment, underscoring the placenta as a critical target for PFBS toxicity. This study investigated the transcriptional and functional effects of PFBS in human trophoblast cells and term placental villous explants, stratified by fetal sex, to characterize mechanisms of PFBS bioactivity relevant to placental function. Term chorionic villous explants (obtained from with informed consent from elective non-laboring c-sections) from male and female placentas were exposed to 5 or 20 µM PFBS and analyzed by RNA-seq with sex-stratified differential gene expression and gene set enrichment analysis (GSEA) using the MSigDB Hallmark gene set collection.

overall_design: Term placental villous explants were obtained from seven placentas (four male and three female fetuses) and cultured for 24 h in the presence of 5 µM or 20 µM perfluorobutane sulfonate (PFBS) or vehicle control. Differential gene expression analyses were performed by comparing treated and control samples, with analyses stratified by fetal sex. In parallel, HTR-8/SVneo trophoblast cells were exposed to 5 µM PFBS for 24 h, and differential gene expression was assessed relative to untreated controls.

first: Maggie

middle: G

last: Drelichman


title: RNAseq analysis of H69 cholangiocyte cell line stimulated with imidazole propionate

city: Oslo

first: Peder

middle: Rustøen

last: Braadland

address: Sognsvannsveien 20

country: Norway

institute: Oslo University Hospital

summary: Primary sclerosing cholangitis (PSC) is a chronic inflammatory disease of the bile ducts associated with inflammatory bowel disease and an altered gut microbiota. Here we studied the transcriptomic impact of the gut microbial metabolite imidazole propionate and its precursor urocanate on a human cholangiocyte cell line.

overall_design: RNAseq of wild-type H69 cells treated with either imidazole propionate, urocanate or vehicle for four hours.

first: Antonio

last: Molinaro

first: Peder Rustøen

first: Guido

last: Carpino

first: Alba

last: Carreras Palou

first: Marios

last: Nikolaidis

first: Petra

last: Hanzely

first: Katharina R

last: Beck

first: Ahmad H

last: Ali

first: Lars

last: Bossen

first: Anna

last: Frank

first: Annika

last: Lundqvist

first: Brian D

last: Juran

first: Diletta

last: Overi

first: Lei

last: Geng

first: Enya

last: Amundsen-Isaksen

first: Henrik Mikael

last: Reims

first: Ida

last: Björk

first: Krzysztof

last: Grzyb

first: Andreas

last: Abildgaard

first: Trine

last: Folseraas

first: Martin

last: Cornillet

first: Hólmfríður

last: Helgadóttir

first: Bryan M

last: McCauley

first: Laura

last: Cristoferi

first: Marco

last: Carbone

first: Vincenzo

last: Cardinale

first: Marte L

last: Høivik

first: Lise Katrine

last: Engesæter

first: Sara

middle: K

last: Tjønnfjord

first: Adrian

last: McCann

first: Per M

last: Ueland

first: Mette

last: Vesterhus

first: Tom H

last: Karlsen

first: Henning

last: Grønbæk

first: Eugenio

last: Gaudio

first: Konstantinos

middle: N

last: Lazaridis

last: Bergquist

first: Espen

last: Melum

first: Fredrik

last: Bäckhed

first: Johannes

last: Hov Roksund


title: TH-positive pulmonary nerve fiber-epithelial interaction promotes adipose thermogenesis in male mice [Lung_RNA-seq]

city: Shanghai

first: Junkun

last: Jiang

address: 500 Zhennan Road, Putuo District

institute: Tongji University

summary: Cold exposure activates sympathetic neurons in adipose tissue to maintain thermal homeostasis. However, whether sympathetic activation in non-adipose tissues contributes to cross-organ regulation of adipose thermogenesis remains unclear. Here, we demonstrate the activation of TH-positive pulmonary nerve fibers (TPNFs) by cold exposure, which further promotes adipose thermogenesis. Specifically, cold exposure activates TPNFs that innervate bronchial Club cells in the lung and leads to a reduction in Secretoglobin family 3A member 1 (SCGB3A1) expression via Adrenergic Receptor β2 (ADRB2). SCGB3A1, a Club cell-specific secretory factor, binds the choline transporter SLC44A2 on adipocytes to restrict choline uptake and impair thermogenic activation. Meanwhile, TPNFs activation induces NGF secretion from Club cells, which in turn strengthens TPNFs innervation of Club cells in a feedforward loop. Importantly, the stimulation of this mechanism via tracheal infusion of the ADRB2 agonist norepinephrine (NE) enhances thermogenesis in mice.

overall_design: Transcriptomic profiling of mouse lung tissues under cold exposure. Lung samples were collected from mice exposed to cold (4 °C, 6 h) or room temperature control conditions. Three biological replicates were analyzed for each group.

first: Bing

last: Luan


title: Neuronal Nrf/SKN-1B controls a sexually dimorphic neuroendocrine pathway for C. elegans exploratory behaviour

city: Canterbury

first: Jennifer

middle: M. A.

last: Tullet

state: Kent

address: Giles Lane

department: School of Natural Science

institute: University of Kent

summary: The SKN-1/Nrf transcription factor family is integral to metabolic homeostasis. There are three SKN-1 isoforms in Caenorhabditis elegans, each with different functions. One of these, SKN-1B, is expressed specifically in neurons and controls hermaphrodite behaviour in response to food. In a laboratory environment C. elegans hermaphrodites must allocate energy efficiently between exploratory food-seeking behaviour, reproduction, and survival, whereas males have to balance both food-seeking with mate-seeking exploratory behaviours. Here, we evaluate the role of SKN-1B in male behaviour and show that SKN-1B acts in a sexually dimorphic manner to control exploratory behaviour, mitochondrial morphology, and mitochondrial function. Moreover, we show that SKN-1B is expressed in a sexually dimorphic pattern, and that SKN-1B influences gene expression on a much broader scale in males compared to hermaphrodites. This analysis identified a neuronal signalling pathway, specifically in males between SKN-1B, the TGF-β ligand DAF-7 and the chemosensory regulator ODR-10, and that this pathway contributes to increased exploratory behaviour in skn-1b mutant males. Taken together our findings identify SKN-1B as a sex-specific neuronal switch to control food searching and mating behaviours. Sexual dimorphism is essential for optimizing survival and reproductive success and our findings establish SKN-1B as a regulator of sex-specific behavioural and metabolic traits. This work provides new insights into neuronal regulation of metabolism and behaviour, with implications for sex-specific physiological adaptations in other species.

overall_design: RNA-Seq profiling of male and hermaphrodite wild-type and skn-1b mutant animals at day 1 of adulthood (24h post-L4).

first: Noviann

last: Mclean

first: Minaxi

last: Gami

first: Nathan

last: Dennis

first: Yasir

last: Malik

first: Justin

last: De Araujo

first: James

last: Evans

first: Lydia

last: Bennett

first: Marina

last: Ezcurra


title: Giant viruses encode vitamin K–based redox modules for lipid modification

city: Bloomington

first: Cristina

last: Landeta

state: Indiana

address: 1001 E 3rd St

department: Biology

institute: Indiana University

summary: Viruses with large DNA genomes often carry auxiliary metabolic genes that reprogram host physiology, yet their contributions to host redox and membrane homeostasis remain poorly understood. Here we report the discovery and functional reconstitution of viral homologs of vitamin K epoxide reductase (VKOR) encoded by giant viruses. Using phylogenetic and genomic context analysis, we find that viral VKOR genes are frequently located adjacent to -carboxylase-like epoxidase and fatty acid desaturase domains, consistent with a putative modular redox pathway for membrane lipid modification. To investigate their function, we expressed viral VKORs in an Escherichia coli strain lacking disulfide bond–forming enzymes and examined both their membrane topology and activity. Remarkably, a minimal set of residue substitutions enabled proper membrane insertion and restored bacterial motility, demonstrating that viral VKORs are catalytically competent electron shuttles. Structural modeling supports their integration into the endoplasmic reticulum–like environment in the host. Finally, we show that VKORs and gamma-carboxylase-like epoxidase-desaturases from Fadolivirus and Yasminevirus giant viruses are expressed during infection of Vermamoeba vermiformis, where they may couple vitamin K epoxidation to desaturation-driven lipid remodeling. These findings expand the known functional repertoire of giant viruses and uncover a previously unrecognized viral strategy for manipulating host redox metabolism and membrane composition.

sample_organism:
Vermamoeba vermiformis
synthetic construct

overall_design: To investigate the role of VKOR, VKE and VKED during infection, we performed transcriptomic and proteomic analyses of V. vermiformis strain CDC19 infected with Fadolivirus algeromassiliense FV1/VV64 or Yasminevirus saudimassiliense A1/GU-2018. Poly-adenylated RNA was analyzed by RNA-Seq across an infection time course (at 0.5, 2, 4, 6, 8 10, 12 and 16 h post-infection) using a mock-infected culture as negative control.

first: Julien

last: Andreani

first: Philippe

last: Colson

first: Bernard

last: La Scola


title: Bulk RNA sequencing of STK11-deficient and parental Lacun3 murine lung adenocarcinoma cells

city: Pamplona

first: Ruben

last: Pio

state: Navarra

address: Cima Building

department: Cancer Division

country: Spain

institute: Cima Universidad de Navarra

summary: STK11 mutations are associated with primary resistance to immune checkpoint inhibitors in lung adenocarcinoma, but the tumor cell-intrinsic mechanisms underlying this phenotype remain incompletely understood. To investigate transcriptional changes induced by STK11 loss independently of the tumor microenvironment, bulk RNA sequencing was performed on parental Lacun3 murine lung adenocarcinoma cells and CRISPR-generated Stk11-deficient Lacun3 cells cultured in vitro. Differential gene expression analysis identified increased expression of several mediators associated with complement activation and neutrophil extracellular trap (NET) formation, supporting a tumor cell-intrinsic transcriptional program that promotes a pro-NETotic tumor microenvironment.

overall_design: Bulk RNA sequencing was performed on parental Lacun3 murine lung adenocarcinoma cells and Stk11-knockout Lacun3 cells cultured under identical in vitro conditions. Four independent biological replicates were analyzed for each genotype. The study was designed to identify tumor cell-intrinsic transcriptional changes associated with STK11 loss while excluding the influence of the tumor microenvironment.

first: Daniel

last: Ajona


title: IL-1β+ Macrophages Promote CD Intestinal Mucosal Barrier Injury by Inducing Ferroptosis in Intestinal Epithelial Cells

city: Changsha

first: Qi

last: Sun

state: Hunan

address: 139 Renmin Middle Road

department: Department of Geriatric Surgery

institute: The Second Xiangya Hospital, Central South University

summary: This RNA-seq dataset was generated to investigate transcriptomic changes in human intestinal epithelial cells co-cultured with IL-1β-low or IL-1β-high THP-1-derived macrophages. FHC and NCM460 cells were co-cultured with IL-1β⁻ Mac or IL-1β⁺ Mac, followed by RNA sequencing to identify gene expression changes associated with epithelial injury, oxidative stress, lipid peroxidation, and ferroptosis-related pathways.

overall_design: FHC and NCM460 human colonic epithelial cells were co-cultured with IL-1β-low or IL-1β-high THP-1-derived macrophages. For each epithelial cell line and treatment condition, three independent parallel samples were prepared and subjected to RNA sequencing.

first: Lianwen

last: Yuan


title: GDF15 Suppresses Liver Inflammation Independently of Weight Loss through Neuroendocrine Glucocorticoid Signaling

city: Hamilton

first: Dongdong

last: Wang

address: 1200 Main Street West

department: Department of Medicine

institute: McMaster University

summary: Growth differentiation factor 15 (GDF15) is strongly associated with metabolic dysfunction-associated steatohepatitis (MASH), yet whether it promotes or protects against liver injury remains unclear. Using thermoneutral mouse models that closely resemble human MASH, genetic deletion of GDF15 or its receptor GFRAL selectively worsened hepatic inflammation and fibrosis without altering steatosis or insulin resistance. Conversely, recombinant GDF15 reduced liver inflammation and fibrosis more effectively than matched caloric restriction despite identical reductions in food intake, body weight, and steatosis, demonstrating weight loss-independent hepatoprotection. These effects required GFRAL but were independent of β-adrenergic signaling. Instead, GDF15 activated the hypothalamic-pituitary-adrenal (HPA) axis, increasing circulating corticosterone and hepatic glucocorticoid receptor signaling. Spatial transcriptomics and RNA sequencing demonstrated that GDF15 remodeled the hepatic immune-fibrotic niche by suppressing inflammatory macrophages, plasma B cells, and activated stellate cells while promoting pro-resolving immune programs. Together, these findings identify a GDF15-GFRAL-HPA axis that restrains liver inflammation independently of weight loss.

overall_design: Spatial transcriptomics


overall_design: We then performed gene expression profiling analysis using data obtained from liver tissue of mice treated with vehicle, GDF15, or were pair-fed the same weight of food matched to GDF15 treatment group.


title: Whole transcriptome  analysis of salivary glands from the salivary glands of NIH COVID-19 autopsies

first: Blake

middle: M

last: Warner

state: MD

address: 10 Center Drive, Room 1A01

institute: NIDCR

summary: Salivary glands are recognised targets of SARS-CoV-2 infection, with viral RNA and protein detected in both major and minor glandular tissue; however, the transcriptional response of salivary gland epithelium and stroma to infection remains poorly characterised. Here, we present a bulk RNA sequencing dataset from major (parotid, submandibular) and minor salivary gland samples obtained at autopsy from individuals with confirmed COVID-19 and controls. Transcriptomic profiling reveals dysregulated innate immune signalling, interferon response pathways, or glandular epithelial stress responses in COVID-19 compared to control tissue, with differences observed between both major and minor gland compartments; gland-specific features were identified. These data provide a tissue-level transcriptional resource for investigating salivary gland pathology in acute COVID-19 and its potential contribution to oral manifestations of infection and post-acute sequelae.  Manuscripts to site: Huang N, Pérez P,...Warner BM, Byrd KM. SARS-CoV-2 infection of the oral cavity and saliva. Nat Med. 2021 May;27(5):892-903. doi: 10.1038/s41591-021-01296-8. Epub 2021 Mar 25. PMID: 33767405; PMCID: PMC8240394; Stein SR, ...et al., ...Hewitt SM, Kleiner DE, Chertow DS. SARS-CoV-2 infection and persistence in the human body and brain at autopsy. Nature. 2022 Dec;612(7941):758-763. doi: 10.1038/s41586-022-05542-y. Epub 2022 Dec 14. PMID: 36517603; PMCID: PMC9749650.

overall_design: Case/control. Matching on gland type only

last: Martin

last: Chertow

first: Stephen

last: Hewitt

first: David

last: Kleiner

first: Billel

last: Gasmi


title: Systematic Benchmarking of Ambient RNA decontamination Tools to Advance Precision in Single-Cell transcriptomic analysis

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

summary: Ambient RNA contamination in single-cell RNA sequencing introduces exogenous transcripts from lysed cells, distorting cell-type annotation and biological interpretation. We performed a systematic benchmark of 7 decontamination tools using datasets with well-defined ground truth. Our evaluation across accuracy, robustness, and subtype sensitivity reveals complementary strengths: CellBender and scCDC excel in contamination estimation accuracy, SoupX is the most robust and sensitive for rare subtypes. For overall decontamination efficacy, scAR best balanced robustness and accuracy at the cell-type level. Our study offers a practical guideline for context-dependent tool selection and highlights key directions for future algorithmic development.

overall_design: Lung and kidney tissues were profiled using 10x Genomics single-cell multiome assays.

first: Jing

last: Tan


title: Nuclear GDOWN1 functions as a robust tumor suppressor by triggering premature termination and nuclear export of Pol II CTD phosphatases to facilitate RB activation (TT-seq)

city: Lanzhou

first: Wenyuan

last: Zhu

state: Gansu

address: South Tianshui Road

institute: Lanzhou University

summary: Dysregulated transcription and aberrant cell cycle progression represent core cancer hallmarks, yet not many transcriptional regulators are known to simultaneously govern both pathways as potent tumor suppressors. GDOWN1 is a Pol II-interacting factor mainly sequestered in the cytoplasm in somatic cells, and its nuclear biological functions remain largely undefined. We previously generated a nuclear-localized GDOWN1 mutant (nGDOWN1(10M)) that strongly represses transcription and cell proliferation. Here, we systematically dissect the underlying molecular mechanisms and validate its broad-spectrum anticancer potential. Combining genetic manipulation, multi-omics profiling and multiple functional assays, we demonstrate that nGDOWN1(10M) disturbs Pol II CTD phosphorylation homeostasis and triggers promoter-proximal premature termination, causing global repression of nascent transcription. Terminated Pol II complexes undergo cytoplasmic translocation alongside associated the CTD phosphatases PP2A and PP1, leading to massive cytoplasmic accumulation of these phosphatases. Concurrently, TP53 and CDKN1A are targeted by nGDOWN1(10M) and transcriptionally upregulated. The above dual regulatory circuit synergistically activates RB family tumor suppressors: p53-p21 signaling inhibits cyclin-dependent kinases, while cytoplasmic PP2A/PP1 enhance cellular phosphatase activity to dephosphorylate and stabilize RB and p130. Activated RB and p130 form functional RB and DREAM complexes and inhibit the transcription of their target genes to induce robust cell cycle arrest. Notably, nGDOWN1(10M) exerts profound antiproliferative effects across cancer cell lines, mouse xenograft models and patient-derived tumor organoids, independent of p53 status. Collectively, this work uncovers a novel interconnected regulatory cascade triggered by nuclear translocation of GDOWN1: it remodels Pol II phosphorylation landscape and induces global transcriptional repression, which further drives cytoplasmic kinase-phosphatase coordination to activate master cell cycle suppressors and ultimately arrest cell cycle progression. Our results illuminate a coordinated molecular circuit governing two central cancer hallmarks and establish nuclear GDOWN1 as a promising therapeutic candidate for both p53-proficient and -deficient malignancies.

overall_design: TT-seq of untreated and doxycycline-induced nGDOWN1 inducible HeLa cells (1 day after induction)

first: Zhanwu

first: Jinjing

last: Hu

first: Yonghong

last: Li

first: Bo

last: Cheng


title: Nuclear GDOWN1 functions as a robust tumor suppressor by triggering premature termination and nuclear export of Pol II CTD phosphatases to facilitate RB activation

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

overall_design: Refer to individual Series


title: Nuclear GDOWN1 functions as a robust tumor suppressor by triggering premature termination and nuclear export of Pol II CTD phosphatases to facilitate RB activation (ChIP-seq)

overall_design: ChIP-seq of Pol II-NTD, pSer2, pSer5 and Flag tagged nGDOWN1 in untreated and doxycycline-induced nGDOWN1 inducible HeLa cells (1 day and 4 days after induction)


title: Nuclear GDOWN1 functions as a robust tumor suppressor by triggering premature termination and nuclear export of Pol II CTD phosphatases to facilitate RB activation (CUT&Tag)

overall_design: CUT&Tag of Flag tagged nGDOWN1 in doxycycline-induced nGDOWN1 inducible HeLa cells.(1 day after induction)


title: A comparative brain cell atlas of Astyanax mexicanus

city: Columbia

first: Wesley

last: Warren

state: MO

address: 1201 Rollins St.

department: Bond Life Sciences Center

institute: University of Missouri

summary: Adaptation of organisms to extreme environments, such as caves, requires dramatic phenotypic changes. Studying these changes can elucidate mechanisms underlying phenotypic differences in the context of both evolution and human disease. The Mexican tetra, Astyanax mexicanus, is a useful model of extreme adaptation over a short evolutionary time scale. This fish species includes surface- and cave-dwelling ecotypes, with cavefish displaying many adaptations to subterranean life, including behavioral changes such as sleep loss, increased appetite, and reduced aggression. Unraveling the mechanisms underlying these changes has been challenging, presumably because they are complex traits that required coordinated changes across multiple cell types to evolve. Here, we present a spatially integrated comparative cell atlas of whole adult brains of surface and cavefish. After establishing the molecular signatures of 35 cell types, we show that cave colonization drove canalized regulatory changes to gene expression that persist in the laboratory environment. Cavefish brains show shifts in cell type composition compared to their surface counterparts, as well as complex regulatory changes to pathways governing hypoxia response and circadian rhythm. Microglia in the cavefish brain underwent extensive transcriptional remodelling, including changes in senescence and AMPK pathways. Further, cell-cell communication analysis identified a cave-enriched ligand-receptor communication pattern centered on signals sent from glial cells to diverse populations of neurons. This atlas highlights discoveries on how brains adapt to new environments and provides a resource for future studies of brain evolution in A. mexicanus, an emerging model for translational research into neurodegenerative disease in humans.

overall_design: We sequenced single nuclei and spatial data from whole brains of A. mexicanus

first: Edward

middle: S

last: Ricemeyer

first: Kathryn

last: Gallman

first: X

last: Maggs

first: Yulia

last: Nussbaum

first: Rachel

last: Carroll

first: Robert

last: Peuss

first: Nicolas

last: Rohner

first: Alex

last: Keene


title: Nuclear GDOWN1 functions as a robust tumor suppressor by triggering premature termination and nuclear export of Pol II CTD phosphatases to facilitate RB activation (RNA-seq)

overall_design: RNA-seq of untreated and doxycycline-induced nGDOWN1 inducible HeLa cells (1 day and 4 days after induction).


title: E2F3a transcription factor mediates behavioral, cellular, and DNA-protein regulation of cocaine reward in the nucleus accumbens

city: New York

first: Molly

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Drug addiction is characterized by orchestrated transcriptional changes in brain reward regions, including the nucleus accumbens (NAc). The transcription factor E2F3a has emerged as a novel regulator of cocaine’s rewarding effects, yet its sex- and cell-specific mechanisms, as well as its genome-wide targets, remain undetermined. Here, we investigated the motivational and reinforcing roles of E2F3a in cocaine reward using conditioned place preference (CPP) and self-administration, combined with behavioral economics and viral-mediated gene manipulation. Selective overexpression of E2F3a in D1-type medium spiny neurons (MSNs), but not D2-MSNs, increased cocaine CPP in both male and female mice, whereas knockdown produced the opposite effects. Genome-wide mapping revealed increased E2F3a binding to DNA at genes associated with cocaine exposure. Together, these results establish E2F3a as a central substrate of cocaine reward via the recruitment of D1-MSNs and proven molecular drivers

overall_design: Female and male mice were injected (i.p.) with saline or cocaine (20 mg/kg) for 7 consecutive days in their home-cages before brain tissue collection. Bilateral punches of the NAc were used for nuclei collection and subsequent CutAndRun sequencing, with E2F3a antibody and IgG antibody.

first: Freddyson

last: Martinez-Rivera

first: Yun Young

last: Yim

first: Leanne

last: Holt

first: Arthur

last: Godino

first: Angelica

last: Minier-Toribio

first: Solange

last: Tofani

last: Torres-Berrio

first: Rita

last: Futamura

first: Caleb

last: Browne

first: Tamara

last: Markovic

first: Peter

last: Hamilton

first: Rachael

last: Neve

first: Li

last: Shen

first: Eric

last: Nestler


title: E11.5 Branchial Arches RNA-seq and CUT&RUN

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania


title: E11.5 Branchial Arches CUT&RUN from control neural crest

summary: GLP and G9a repress alternative fate pathways in the neural crest. Analyses of H3K9me2 and H3K27ac profiles from 3 lineage traced control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre)  E11.5 embryos.

overall_design: Branchial arches from 3 control (Ehmt1+/+, Ehmt2+/+, Rosa26 TdTomato/+, Wnt1-cre) E11.5 mice were used with Cut&Run for H3K9me2, H3K27ac, and IgG.

first: Diana

middle: B

last: Fulmer

first: Cheryl

last: Smith

first: Rajan

last: Jain

first: Jonathan

last: Epstein