title: Contribution of cohesins STAG1 and STAG2 to preimplantation development in mice

first: Daniel

last: Gimenez

address: Calle de Melchor Fernández Almagro, 3

institute: CNIO

summary: Cohesin complexes carrying either STAG1 or STAG2 display functional specificities in both cohesion and genome organization. While any variant is sufficient for cell viability, both are essential for embryonic development in mice, and mutations in STAG1 and STAG2 cause human developmental disorders. In the first stages of development, continuous cell divisions are accompanied by de novo establishment of genome architecture and activation of zygotic transcription to replace maternal products. The requirements and regulation of the two cohesin variants at this time remain unknown. Here, we show that Stag1 and Stag2 gene products are stored in oocytes. Maternal STAG1 persists beyond the 2-cell stage while accumulation of STAG2 depends on zygotic transcription. Despite clear differences in STAG1:STAG2 ratio in the two lineages emerging from the first cell-fate transition, both maternal and zygotic STAG1 and STAG2 are dispensable for viability in preimplantation stages if the other variant is present. STAG2 deficiency, however, increases DNA damage and affects transcription. These early-stage alterations may contribute to defects leading to embryo lethality by mid-gestation.

overall_design: RNA-Seq from mouse blastocyscystes microinjected with either buffer or 20µM Antisense Oligonucleotide (ASO). ASOs used were against Hprt, Stag1 or Stag2 .

first: Maria

last: Solé-Ferran

first: María José

last: Andreu

last: Giménez-Llorente

first: Sagrario

last: Ortega

first: Ana

last: Losada


title: Friedreich Ataxia Mice

status: Public on Jul 02 2026

city: Stanford

first: Natalia

last: Gomez-Ospina

address: 265 Campus Drive

country: USA

institute: Stanford

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: TIME-RESOLVED MORPHOLOGICAL AND TRANSCRIPTOMIC CHARACTERIZATION OF EARLY ENTERIC NEURON SUBTYPE EMERGENCE IN CHICK

city: lyon

first: valérie

last: CASTELLANI

address: 8 Avenue Rockefeller

country: France

institute: MeLiS | CNRS UMR 5284 | INSERM U1314

summary: The genetic programs directing nascent enteric nervous circuits and their unique architecture remain poorly characterized. To gain insight, we combined manipulations in the chick embryo model, whole gut 3D imaging, and single-nucleus transcriptomics at very short intervals for time-resolved analyses of neuronal subtype trajectories. In imaging, we found highly dynamic axon network growth, with rapid increase in axon density and spatial orientation diversification. At transcriptomic levels, we correlated these changes to cell-state transitions with specific axon guidance gene sets. Cross-analyses with human and mouse embryo scRNAseq and expression profiles revealed globally conserved enteric lineage trajectories and subtypes specific axon guidance programs in all species. Finally, manipulation of DSCAM and ISLR2 evolutionary conserved networks in chick whole gut cultures altered enteric axon patterns, validating our paradigm and its applicability to advance current knowledge on human enteric circuit wiring.

overall_design: Nuclei were prepared from frozen  pre-umbilic intestine pieces that were micro-dissected from E5, E6 and E7 embryos

first: Maëlys

last: André

first: Guillaume

last: Marcy

first: Julien

last: Falk

first: Valérie

last: Castellani


title: Mapping the Immune Modulation Landscape Induced by Sanguisobae Radix at Single-Cell Resolution

city: Chengdu

first: Yumei

last: Wang

address: 1166 LiuTai

country: China

institute: Chengdu University of TCM

summary: Sanguisorbae radix (SR), a traditional Chinese medicine, is commonly used in China to enhance human immunity. Yet, its effects and underlying mechanisms on various types of immune cells remain to be fully explored. Here, we conduct single-cell transcriptomic analysis across human peripheral blood mononuclear cells (PBMCs) before and after taking SR. Our findings reveal that there were fluctuations in immune cell proportions in the bloodstream, including increased Mega/Platelets, Dendritic cells (DCs), CD8+ T cells, natural killer (NK) cells and Naïve CD4+ T cells, and decreased Mast cells, B cells, and Monocytes after taking SR. Among them, SR increased CD8+ T cells by stimulating the proliferation. Our results suggest that SR enhance viability of these types of immune cells by up-regulating genes related to ribosome protein and mitochondrial energetic metabolism. Notably, SR treatment significantly enhance the activity of Cytotoxic Effector T cells, a subtype of CD8+ T cells, by increasing the cytotoxicity score and the expression of toxic particle-related genes (such as LYZ and GZMK). Furthermore, our findings demonstrate significant inhibition of inflammation-associated genes and pathways by SR across various immune cell subsets, including T cells, Monocytes, and Mega/Platelets. Overall, our study highlights the transcriptional heterogeneity induced by SR treatment and its distinct modulation of various circulating immune cells, providing potential for the development of immunomodulatory therapeutics.

overall_design: There were a total of 8 samples, which came from the peripheral blood mononuclear cells (PBMCs) of 4 normal people before and after administrating SR. To investigate the immune modulation landscape induced by SR, the 8 samples were analyzed using scRNA-seq.

first: Dale

last: Guo

first: Lijun

last: Huang

first: Fang

last: Deng

first: Yan

last: Zhang

first: Yun

first: Dong


title: Role of RXRg in NSC-derived OPCs and their differentiation

city: Illkirch

first: Damien

last: PLASSARD

address: 1 rue Laurent Fries

institute: IGBMC

summary: RXRg is positive regulator of oligodendrocyte progenitor (OPC) differentiation. To address molecular underpinnings of this regulation we performed analyses of the effects of RXRg deletion (RXRgKO) as a function of 24hrs T3 treatment (differentiation inducing factor) in neural stem cells derived OPCs.

overall_design: On the 4th day after seeding OPCs derived from oligospheres (see protol in V.A. Baldassarro Jove 2021) total RNA was prepared from 16 samples of corresponing to WT and RXRgKO OPCs with and without 24hrs T3 treatment (n=4/condition). Approximately 10mln cells were used to prepare each sample. We sequanced and analysed a total of 16 samples correspoding to 4 groups : 1) n=4 WT (RXRg+/+ OPCs non-treated); 2) n=4 RXRgKO (RXRg-/- OPCs non-treated); 3) n=4 WT (RXRg+/+ OPCs T3-treated); 4) n=4 RXRgKO (RXRg-/- OPCs T3-treated).

first: Vito

last: Baldassarro


title: The role of gliovascular crosstalk between vascular pathology and Alzheimer’s disease

city: New York

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

summary: Alzheimer's disease (AD) frequently occurs alongside cerebrovascular pathology (CVP), which together exacerbate cognitive decline and dementia. Gaining insights into the molecular interactions between these conditions is crucial for creating effective treatments that can tackle the complexities of AD. To determine impact of gliovascular interactions on the blood-brain-barrier (BBB) experimentally, we utilized a well-established zebrafish model.We treated double transgenic (Tg(fli1a:eGFP)/Tg(her4.1:dRFP)) zebrafish with vegf receptor inhibitor cocktails to evaluate the BBB integrity. By blocking VEGF signaling we showed that astroglial-endothelial interactions are essential for BBB integrity.

overall_design: 14-month-old double transgenic zebrafish line of both genders were treated with vegfr2 inhibitor cocktails (Semaxanib (SU5416) (10 µM, SelleckChem S2845), Tivozanib (AV- 951) (10 µM; SelleckChem S1207), and ZM 306416 (10 µM; SelleckChem S2845),(TZS))  and cells were dissociated sorted by FACS as described Is et al. 2024 and Cosacak et al. 2019, respectively. The single-cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads aligned to zebrafish genome (GRChZ 11, v 105) were used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.

first: Prabesh

last: Bhattarai

first: Elanur

last: Yilmaz


title: Effects of inflammation on human astroglia in 3D cultures

summary: In this project, we analyzed the effects of inflammatory and anti-inflammatory cytokines on gene expression profiles of primary human astroglia cultured in 3D hydrogels.

overall_design: primary human astroglia cultured in 3D with control medium, TNF-alpha-supplemented medium, and TNF-alpha  + Interleukin-4 supplemented medium are compared for their gene expresison profiles by total RNA isolation and deep sequencing.

first: Mehmet

middle: I

last: Cosacak

first: Hilal

last: Celikkaya


title: Regenerative neurogenesis in adult zebrafish brain after neurodegeneration

summary: Alzheimer's disease (AD) is a debilitating neurodegenerative disease in which accumulation of toxic amyloid-β42 (Aβ42) peptides leads to synaptic degeneration, inflammation, neuronal death, and learning deficits. Zebrafish (Danio rerio) is a regenerative organism, and we can learn the basic molecular programs with which we could design therapeutic approaches to tackle AD. By using our amyloid toxicity model in adult zebrafish brain by injecting synthetic Aβ42, we investigate the neurodegeneration phenotypes reminiscent of human brain pathology (e.g., cell death, microglial activation, synaptic degeneration, and memory deficits) in single cell level.

overall_design: 6-month-old WT zebrafish injected with Amyloid-beta 42 and PBS peptide as descibed (Bhatatrai et al. 2016) and cells were dissociated sorted by FACS as described (Cosacak et al. 2019). The single-cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome (GRChZ 11, v 105) was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.


title: Fibronectin mediates the interaction between vascular pathology and Alzheimer’s disease by inhibiting homeostatic gliovascular crosstalk

summary: Alzheimer's disease (AD) often coexists with cerebrovascular pathology (CVP), contributing to cognitive decline and dementia. Understanding the molecular interplay between these pathologies is vital for developing effective therapies that can address the complexities of AD. The extracellular matrix (ECM) plays a crucial role in maintaining the blood-brain barrier (BBB) and modulating interactions of brain cell types with the vasculature. Elevated levels of a particular ECM component, Fibronectin 1 (FN1) are associated with both AD and vascular dysfunctions. In this study we show the molecular regulation exerted by FN1 to regulate the homeostatic interaction between vasculature and the brain.

overall_design: 16-month-old fn1b-/- knockout zebrafish line injected with Amyloid-beta 42 peptide and PBS as control as descibed (Bhatatrai et al. 2016) and cells were dissociated sorted by FACS as described (Cosacak et al. 2019). The single-cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads aligned to zebrafish genome (GRChZ 11, v 105) were used for gene annotation and assigning reads to genes. Cellranger software version 7.1.0 was used to process the data.


title: Translational and rotational setting of nucleosomes across a human genome

city: Ithaca

first: B. Franklin

last: Pugh

address: 465 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

type: Genome binding/occupancy profiling by high throughput sequencing


title: Genome-wide rotational and translational phasing of nucleosomes with human transcription factors [ChIP-exo]

summary: Eukaryotic DNA is wrapped around a complex of histones, such that one face of the helix is accessible, and the other is buried. Sliding and rotating DNA by 5 bp in either direction reverses this polarity. This has substantial ramifications for regulating transcription factor (TF) binding. Yet, there does not exist a method to measure the rotational setting of DNA on nucleosomes in vivo and on a genomic scale. We developed Benzonase-seq, Benzonase cleaves and marks the accessible rotationally exposed DNA surface, in addition to marking linker regions between nucleosomes. Further, Benzonase robustly maps nucleosomes in CpG-rich mammalian promoters compared, which has been challenging for the commonly used micrococcal nuclease (MNase). When Benzonase cleavages are analyzed in the context of TF binding sites, we determine whether the TF motif has a prefer orientation on the nucleosome surface. When this assay is coupled to chromatin immunoprecipitation (ChIP) of histones, histone variants, and modifications, we find evidence for transcription-linked subnucleosomal structures, some of which may be related to hexasomes and half/split-nucleosomes. Benzonase-seq offers a robust and ultra-high resolution method to map the translational and rotational setting of DNA elements on the nucleosome surface, and provides a means to probe subnucleosomal structures. Benzonase-seq may be useful for probing the pioneering potential of transcription factors.

overall_design: Chromatin Immunoprecipitation (ChIP-exo) for various histone and histone modification targets in K562 cells.

first: Jordan

middle: E

last: Krebs

first: Haining

last: Chen

first: Olivia

middle: W

last: Lang

first: William

middle: K

last: Lai

first: B

middle: F


title: Genome-wide rotational and translational phasing of nucleosomes with human transcription factors

summary: How transcription factors (TFs) and their binding sites organize and engage nucleosomes at natural genomic locations remains poorly understood. Here we develop Benzonase-seq to measure the rotational phasing of nucleosomes in human cells, and enhance ChIP-exo (v6) to measure rotational phasing on the same DNA molecule bound by a TF. Unbound CTCF sites were found to be rotationally accessible on nucleosomes and this rotational accessibility is encoded by classical dinucleotide periodicities. CTCF binding results in nucleosome displacement to adjacent DNA phasing sequences. Examining 40 TF classes, their unbound sites were phased inward, outward, or lacked phasing. In all examined cases, TF binding (e.g. NFIA and FoxA) results in adjacent rotational and translational phasing, which is not dinucleotide encoded. Benzonase-seq also more robustly maps nucleosome and subnucleosome positions in hard-to-map CpG islands. These findings provide a clearer view of how TFs engage and position nucleosomes to shape the natural chromatin landscape.

overall_design: Benzonaseq-seq nuclease protection assay for chromatin from K562 cell lines and naked DNA

first: Jiayi

last: Hu

first: Devin

middle: C

last: Mellini

first: Judith

last: Hyle

first: Chunliang

last: Li

first: William KM

first: B Franklin


title: Synthetic transcription factor overrides persistent repressive chromatin marks

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital


title: Synthetic transcription factor overrides persistent repressive chromatin marks [ChIP-seq]

summary: The prevailing paradigms of epigenetic control posit that signature patterns of post-translational marks on histones guide specific transcriptional outcomes. Methylation of lysine-9 residue of histone H3 (H3K9me3) is implicated in transcriptional silencing through chromatin condensation by its reader HP-1 proteins. Erosion, erasure and subsequent replacement of H3K9me3 by active acetyl-lysine marks accompanies transcriptional up-regulation. Here, we report that a synthetic transcription elongation factor (SynTEF1), selectively targets the disease-causing GAA repeat expansion in frataxin and stimulates gene expression without erasure of the signature repressive marks or removal of HP1 proteins. Added epigenetic perturbation with a pharmacological agent leads to supra-synergistic frataxin expression that is unexpectedly accompanied by a dramatic rise in H3K9me3 levels. Active placement of the signature repressive mark is readily overridden by SynTEF1, demonstrating the fluidity and context-dependence of these marks in regulating gene expression. While forcing a reconsideration of how signature epigenetic marks are interpreted, our results provide key insights for therapeutic intervention in rationally reconfiguring disease-associated epigenetic states.

overall_design: Examination of specific epigenetic modifications and readers in FRDA in response to SynTEF1

first: Christopher

middle: J

last: Brandon

first: Mangesh

last: Kaulage

first: Sandra

last: Kietlinska

first: Samantha

last: Rider

first: Marcus

last: Valentine

first: Burckhard

last: Hoeckendorf

first: Ashraf

last: Mohammed

first: Wenwei

last: Lin

first: Khaled

last: Khairy

first: Taosheng

first: Beisi

last: Xu

first: Aseem

middle: Z

last: Ansari


title: RNAseq data of mouse B16-F10 melanoma cell lines after siEzh2 knockdown or GSK126 methyl-transferase inhibitor or DZNep treatment

city: Melbourne

first: Pacman

last: Szeto

state: VIC

address: 89 Commercial Road

department: Medicine

country: Australia

institute: Monash University

summary: Enhancer of zeste homolog 2 (EZH2) plays critical roles in the progression of many malignancies including melanoma. The most well-known EZH2 mechanism is regulating gene expression through catalysing tri-methylation of histone H3 at Lys 27 (H3K27me3). However, EZH2 also have methylation-independent activities that limit the therapeutic potential of EZH2 methyl-transferase inhibitors. To investigate the methyl-transferase independent role of EZH2 in melanoma, we performed global gene expression analysis of B16-F10 cells treated with methyl-transferase inhibitor GSK126 or siEzh2 knockdown or the EZH2 degrader DZNep.

overall_design: Gene expression induced by treatment of B16-F10 cells with DMSO (control) or 2 µM GSK126 or 2 µM DZNep was analysed, in parallel with B16-F10 cells treated with scrambled control or siEzh2 knockdown. The RNA sequencing was carried out with 3x replicates for each treatment condition.

first: Gamze

last: Abali

first: Peinan

last: Zhao

first: Nicholas

last: Wong

first: Mark

last: Shackleton


title: Influence of a TLR3 inhibitor on the transcriptome of C. trachomatis infected T24/83 cells

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

summary:
The microarrays show that C. trachomatis induces proinflammtory genes but also different metabolic pathways in the uropithelial T24/83 cell line. A TLR3 inhibitor inhibits some of the proinflammtory genes but also of genes
of metabloic pathways, We used these microarrays to explain the inhibition of the chlamydial inclusion size in T24/83 cells by a TLR3 inhibitor.

overall_design: T24/83 cells were infected with C. trachomatis serovar D for 4 or 24 h in the presence or absence of a TLR3 or TLR4 inhibitor.

first: Simone

last: Albrecht

first: Thomas

last: Miethke

last: De La Torre


title: scATAC seq. on KPC2 PDAC

status: Public on Jul 01 2026

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: Orthotopic KPC2 mice were treated with indicated treatments for 2 weeks and subsequently sac'd to perform sc-ATAC seq. on sorted Live>CD45+ cells

overall_design: Veh, MRTX1133, MRTX1133+anti-CTLA4, MRTX1133+anti-PD1 treatment

first: Krishnan

last: Mahadevan

first: Bingrui

last: Li

first: Raghu

last: Kalluri


title: A transient neurodevelopmental microglial state governs cortical maturation and is disrupted by neonatal inflammation in mouse

city: zhengzhou

first: jinjin

last: zhu

address: Kangfu steet

institute: zhengzhou university

summary: We performed single-cell RNA sequencing of CD45+ brain immune cells isolated from neonatal mouse cortex under control and neonatal inflammation (LPS) conditions at multiple developmental stages. The study aims to characterize developmental microglial states and their disruption by inflammatory insult during early postnatal brain maturation.

overall_design: Single-cell RNA-seq analysis of neonatal mouse brain CD45+ immune cells under control and LPS conditions at P3, P7, and P12.


title: International Phase III Medulloblastoma Trial (SJMB03)

first: Kyle

middle: S

last: Smith

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

summary: Patients 3-21 years old were stratified into average-risk and high-risk treatment groups based on metastatic status and extent of resection. Medulloblastomas were molecularly classified into subgroups (Wingless [WNT], Sonic Hedgehog [SHH], group 3, and group 4) and subtypes based on DNA methylation profiles and overlaid with gene mutations from next-generation sequencing. Coprimary study end points were to assess the relationship between ERBB2 protein expression in tumors and progression-free survival (PFS), and to estimate the frequency of mutations associated with WNT and SHH tumors. Clinical and molecular risk factors were evaluated, and the most robust were used to model new risk-classification categories.

overall_design: SJMB03 was a phase III risk-adapted trial that aimed to determine the frequency and clinical significance of biological variants and genetic alterations in medulloblastoma.

first: Paul

last: Northcott


title: Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response [multiabx]

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St

country: Israel

institute: Bar-Ilan University

summary: Antibiotics are thought to affect host physiology by altering the gut microbiota. But which effects of antibiotics are microbiota-dependent or -independent is not clear. Here, we present a resource encompassing host and microbiota response to antibiotic treatment and computational tools to analyze them. We show how antibiotic administration routes affect host and microbiota responses and how combining antibiotics alters their individual activity. We developed CompoRes, a tool to determine whether perturbation affects the host directly or via the microbiota, and discovered microbiota-independent effects of antibiotic treatment. We found that circadian expression of MHC class II in the colon is functional in germ-free mice and is controlled by feeding via glucose. This expression pattern was lost during vancomycin treatment as the antibiotic altered feeding behaviour in a microbiota-independent manner. Together, our study provides tools for analysis of host response to different microbiota compositions which can also identify microbiota-independent effects of perturbations.

overall_design: Mice were randomly divided into either control or antibiotic treatment groups. Mice were treated twice a day for 3 days, and once more on the 4th day, via either oral gavage, intraperitoneal or intravenous injection. Mice received 2.5mg of either ampicillin, metronidazole, neomycin, vancomycin or a mix of all four antibiotics, in 100µl of PBS. Control mice received 100µl of PBS. Four hours after the last treatment mice were euthanized and tissues extracted.

first: Amir

last: Erez


title: scRNA seq. of PDAC models treated with Kras inhibitors in combination with checkpoint immunotherapy

summary: Multiple KPC models were treated with G12D allele specific inhibitor (MRTX1133) and pan-Ras inhibitor (RMC6236) in combination with anti-CTLA4 and anti-PD1. The mice were sac'd between 10-14 days for single-cell RNA analysis.

overall_design: Veh, Veh/Iso, anti-CTLA4, MRTX1133, MRTX1133+anti-CTLA4, RMC6236, RMC6236+anti-CTLA4, RMC6236+anti-PD1 treatment


title: TOP2A & TOP2B occupancy in MCF7 plus and minus estradiol by ChiP-seq

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

summary: The location of TOP2A and TOP2B was determined in MCF7 cells with and without estradiol treatment.

overall_design: Whole genome TOP2B ChIP-seq was carried out on human MCF7 cells in the presence (30 mins exposure) and absence of the nuclear hormone estradiol. "Input" control samples were also sequenced for background detection and comparison.

first: Caroline

last: Austin


title: RNA sequencing analysis of gene expression in bladder tumor and normal urothelial tissues

city: Chongqing

first: Hongwen

last: Liang

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

summary: RNA sequencing was performed on bladder tumor and normal urothelial tissues to investigate gene expression differences between the two groups. A total of 22 samples (11 tumor and 11 normal samples) were included. Libraries were prepared and sequenced using the Illumina NovaseqTM 6000 platform with paired-end sequencing.

overall_design: Investigation of gene expression differences between bladder tumor and normal urothelial tissue based on RNA sequencing by NGS.

first: Jianli

last: Zuo

first: Yuxi

last: Tan

first: Zhaode

last: Mu

first: Yuhan

last: Dong

first: Yijie

last: Wu

first: Yanzhi

first: Yonghua

last: Yuan

first: Xiaobo

last: Wang

first: Yongjun

last: Dang

first: Lijuan

last: Bai


title: Single-cell variant landscape of the human mitochondrial genome reveals cell type-specific and disease-associated changes

city: Philadelphia

first: Ting

last: Peng

state: PA

address: CTRB 6200

department: Pathology and Laboratory Medicine

institute: Children's hospital of Philadelphia

summary: Mitochondria generate over 90% of the cellular energy and are central to health and disease. Mitochondrial DNA (mtDNA) heteroplasmy represents a significant source of cellular genetic diversity and has been shown to cause impaired mitochondrial function and even mitochondrial diseases. However, mitochondrial genetic heterogeneity across different human cell types at the population level is poorly understood. Here we present scMOCHA, a scalable computational framework that resolves high-confidence, single-cell resolution mtDNA heteroplasmy directly from standard single-cell RNA sequencing (scRNA-seq) data. Applying scMOCHA to all publicly available human peripheral blood mononuclear cells (PBMC) and bone marrow (BM) scRNA-seq datasets comprising 5.5 million cells, we uncover the single-cell landscape of mtDNA single-nucleotide variants (SNVs) and heteroplasmy levels in the human hematopoietic system across ages and cell types, including previously unreported SNVs and recurrent somatic hotspot SNVs in unrelated individuals. PBMCs and BM share many inherited homoplasmic and highly heteroplasmic SNVs but few somatic SNVs. Somatic SNVs are tissue- and cell type-specific and distributed across the mtDNA genome, suggesting that they arise in a largely random fashion. Although mtDNA replication error is the most likely dominant force shaping homoplasmic variants, oxidative stress may drive a significant portion of heteroplasmic and somatic mutations in the mtDNA genome. Importantly, we discover cell type-specific and human disease-associated mtDNA SNVs. By coupling mtDNA genotypes with matched single-cell nuclear transcriptomes and structural modeling, we uncover potential molecular mechanisms of how these disease-associated mtDNA SNVs impact cellular function such as inflammation and contribute to disease. Together, these findings define the single-cell variant landscape of the human mitochondrial genome and reveal previously unrecognized lineage- and disease-associated patterns of mtDNA variation in the human hematopoietic system.

overall_design:
Cell Culture
All cell lines were maintained at 37°C in a humidified incubator with 5% CO2. The human osteosarcoma thymidine kinase-deficient cell line 143B(TK−) (ATCC CRL-8303) and human embryonic kidney HEK293 cells were maintained in Dulbecco’s Modified Eagle Medium GlutaMAX (DMEM; Thermo Fisher Scientific, 10569044) containing high glucose (4.5 g/L) and sodium pyruvate (110 mg/L), supplemented with 1% non-essential amino acids (NEAA) and 10% fetal bovine serum (FBS). The human lung adenocarcinoma cell line A549 and the WAl2A WAL2A lymphoblastoid49 cell line were cultured in RPMI 1640 medium with ATCC modifications (Thermo Fisher Scientific, A1049101), supplemented with 1% NEAA and 10% FBS. Corresponding mitochondrial DNA-depleted (ρ⁰ or Rho0) derivatives were maintained in the same medium supplemented with 50 μg/mL uridine (Sigma-Aldrich, U3750-100G). Adherent cell lines were passaged at 70-95% confluence by washing with PBS (Thermo Fisher Scientific, 14190250) and dissociating with 0.25% trypsin-EDTA (Thermo Fisher Scientific, 25200114). Cells used for comparative experiments were harvested at the same passage number.
Single-cell RNA-seq Library Preparation and Sequencing
For the WT and Rho0 samples, an equal mixture of four cell lines (143B, WAL2A, HEK293, A549) was processed using the Chromium Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Cell barcoding, reverse transcription, cDNA amplification, and 3′ gene expression library preparation were performed according to the manufacturer's protocol. The resulting libraries were sequenced on either a DNBSEQ-T7 or an Illumina NovaSeq 6000 platform.
PacBio Library Preparation and Sequencing
Genomic DNA was extracted from cell pellets and quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q33231). Full-length mitochondrial genomes were amplified by long-range PCR using using PrimeSTAR GXL DNA Premix (Takara, R051B) with custom primers and reaction conditions as previously described50. PCR products were purified with SMRTbell Cleanup Beads (PacBio, 102-158-300), and assessed for fragment size distribution using the Femto Pulse system (Agilent, FP-1002-0275). PacBio libraries were prepared using the SMRTbell Prep Kit 3.0 (PacBio, 102-182-700) according to their standard protocol. Following adapter ligation and nuclease treatment, libraries were size-selected using AMPure PB beads (PacBio, 100-265-900). Libraries were annealed to sequencing primers using the Sequel II Binding Kit 3.2 (PacBio, 102-333-300), bound to Sequel II Polymerase 2.2, loaded onto SMRT Cell 8M (PacBio, 102-281-700), and sequenced on a PacBio Sequel IIe platform using the Sequel II Sequencing Kit 2.0 (PacBio, 102-194-400) with a 30-hour movie collection time.

first: Chunjie

last: Liu

first: Zimu

last: Cen

first: Peiran

last: Lu

first: Prasanth

last: Potluri

first: Po

last: Hu

first: Shiping

last: Zhang

first: Marie

last: Lott

first: Gabrielle

last: Widjaja

first: Douglas

last: Wallace

first: Yi

last: Xing

first: Liming

last: Pei


title: Alpha-melanocyte-stimulating hormone and its impact on myeloid-derived suppressor cells

city: Oldenburg

first: Anna-Galina

last: Arndt

address: Carl-von-Ossietzky-Straße 9-11

department: Department für Humanmedizin

institute: Carl von Ossietzky Universität Oldenburg

summary: Myeloid-derived suppressor cells (MDSCs) are key mediators of tumor-associated immune suppression. Alpha-melanocyte-stimulating hormone (α-MSH) is a neuropeptide with immunomodulatory properties that has been shown to reduce MDSC expansion in a murine carcinogenesis model. However, its molecular effects on human MDSC differentiation remain poorly understood. Here, we investigated the transcriptional effects of α-MSH during GM-CSF and IL-6 induced differentiation of T and B cell depleted, myeloid enriched peripheral blood cells from healthy donors. Whole transcriptome analysis revealed gene expression changes during cytokine induced differentiation and subtle but reproducible transcriptional alterations following α-MSH treatment. Differentially expressed genes were mainly associated with immune regulation, intracellular signaling, cell migration and metabolic processes. These data provide insight into the molecular mechanisms underlying α-MSH-mediated regulation of human MDSC differentiation and serve as a resource for future studies of melanocortin signaling in human myeloid cells.

overall_design: T and B cell depleted, myeloid enriched peripheral blood cells from three independent healthy donors were cultured for 2 days under three experimental conditions: basal medium alone (control), 10 ng/ml GM-CSF and IL-6, and 10 ng/ml GM-CSF and IL-6 supplemented with 1 nM α-MSH (stimulated three times per day). Total RNA was isolated after 2 days of culture and analyzed by whole transcriptome sequencing. Three biological replicates were included per condition.

first: Karin

last: Loser


title: Establishment and characterization of patient-derived in-vitro and in-vivo models of penile squamous cell carcinoma

city: Homburg

first: Johannes

last: Linxweiler

address: Kirrberger Straße 100

institute: Saarland University

summary: Tissue samples from patients with penile squamous cell carcinoma were used to generate primar cell cultures and these cell cultures were injectied under the renal capsule of immunodeficient NSG mice for xenograft development. Four primary cell lines were successfully established (PeCa53, PeCa60, PeCa65, PeCa70). For all four cell lines, the patient tissue sample and primary cell lines were submitted to RNAseq. Stably growing xenografts from PeCa53 and PeCa60 were harvested as well for analysis by RNAseq.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA Seq profiling of patient tumor samples, primary cell lines and primary-cell line-derived renal-subcapsular xenograft tumors

first: Linxweiler

last: Johannes

first: Ayoubian

last: Hiresh

first: Skowron

middle: A

last: Margaretha

first: Mink

last: Jan

first: Stöckle

last: Michael

first: Petzsch

last: Patrick

first: Heckt

last: Jochen

first: Nettersheim

last: Daniel

first: Junker

last: Kerstin


title: Hydrogel delivery of apoptotic neutrophils modulates macrophage angiogenic and inflammatory responses during wound healing

city: Irvine

first: Wendy

last: Liu

email: wendy.liu@uci.edu, enriqud2@uci.edu

state: California

address: 419 S. Circle View Drive

department: Biomedical Engineering

institute: University of California Irvine

summary: Effective wound healing requires coordinated angiogenesis and immune resolution. Biomaterial systems support tissue regeneration but typically lack intrinsic immunomodulatory signals needed to actively direct immune resolution and angiogenesis. In this study, localized delivery of apoptotic neutrophils (AN) encapsulated within Gelatin methacryloyl (GelMA) hydrogels was evaluated for its ability to enhance angiogenic responses and modulate inflammatory activity in vivo. In a murine splinted full-thickness skin wound model, AN-loaded GelMA significantly increased vessel length and CD31⁺ vascular area at 14 days post-wounding, while also enhancing cellular infiltration and hydrogel retention. Single-cell RNA sequencing (scRNA-seq) at day 5 post-wounding revealed that AN incorporation reshapes the early wound landscape, enriching macrophage states associated with tissue remodeling and increasing expression of efferocytosis-associated genes across myeloid populations while reducing inflammatory gene expression and altering chemokine expression. Intercellular communication analysis demonstrateds that AN-loaded GelMA shifts endothelial-myeloid signaling away from pro-inflammatory interactions toward pro-resolving signaling programs and enhances vascular crosstalk. In vitro assays confirmed modulation of macrophage paracrine activity, with reduced pro-inflammatory cytokine production, enhanced anti-inflammatory responses, and differential regulation of angiogenesis-associated gene expression. HUVEC vessel-like tube formation assay demonstrated that conditioned media from both GelMA- and AN-treated macrophages support endothelial network formation in vitro. Together, these findings demonstrate that combining GelMA hydrogel with AN-derived cues establishes a pro-resolving environment that reprograms macrophage states and coordinates vascular remodeling, highlighting a promising immunomodulatory biomaterial strategy for wound healing applications.

overall_design: Single-cell RNA sequencing of cells isolated from 5 mm full-thickness skin excisional wounds 5 days after injury, comparing untreated wounds with wounds treated in situ with gelatin methacryloyl (GelMA) or apoptotic neutrophil-loaded gelatin methacryloyl (AN-loaded GelMA).

first: Sergei

last: Butenko

first: Daniela

last: Enriquez-Ochoa

first: Li-Mor

last: David

first: Ronald

middle: Q

last: Nguyen

first: Mary

last: Ziegler

first: Eric

last: Pearlman

first: Alan

last: Widgerow

first: Maksim

middle: V

last: Plikus


title: Central amygdala single-nucleus atlas reveals chromatin and gene transcription dynamics in human alcohol use disorder

city: New Haven

first: Matthew

last: Girgenti

state: CT

address: 34 Park St

department: Psychiatry

institute: Yale University

summary: Regulation of gene expression is a highly coordinated process in both the healthy and pathological brain with unique patterns across a multitude of cell types. Here we present a multi-omic single nucleus study of ~175,000 nuclei from 50 donors with alcohol use disorder (AUD) and control donors without AUD, profiling cell type specific gene expression and chromatin accessibility in the human central amygdala. We identify all major CNS cell types and neuronal subtypes and find inhibitory neurons are particularly affected by AUD. We find high numbers of differentially expressed genes (DEGs) including GABRA2, GRM8, and NCAM1 and show significant enrichment for AUD risk genes within these DEGs. We identified 51,431 cell type-specific, disease associated candidate cis-regulatory elements including an interneuron-associated set of chromatin loops at the AUD risk gene CALN1. Transcription factor footprinting identified Kruppel-like factors upstream of AUD GWAS genes and DEGs. Finally, we also perform cell type-specific fine mapping for AUD GWAS to prioritize variants within functional genomic elements.

overall_design: Multiome-seq: human samples of the central amgydala (brain) from control and alcohol use disorder diagnosed according to DSM-V. 8 mouse samples (5 subjected to ethanol vapor) of the brain is also included

first: Che Yu

last: Lee

first: Catharine

last: Duman

first: Rosemarie

last: Terwilliger

first: Genevieve

last: Thibodeau

first: Mario

last: Skarica

first: Jing

last: Zhang

first: Matt


title: Col1a1 Knockdown Suppresses EMT, Migration, and Invasion of Oral Squamous Cell Carcinoma both In Vitro and In Vivo.

city: Hung Hom

first: Xiaofan

last: Xu

address: 11 Yuk Choi Rd

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Oral squamous cell carcinoma (OSCC) is a lethal malignancy characterized by frequent metastasis. Utilizing a 4-NQO-induced murine model and single-cell RNA sequencing, we identified a distinct Collagen Type I Alpha 1 Chain (Col1a1+) epithelial subpopulation that is significantly expanded in OSCC, exhibits the highest epithelial-mesenchymal transition (EMT) signature, and correlates with poor patient survival. Functional studies demonstrated that Col1a1 knockdown in OSCC cell lines (HSC3) attenuated TGF-β-induced EMT, impaired migration and invasion in vitro, and reduced tumor burden in a conditional knockout mouse model. Transcriptomic profiling following Col1a1 silencing revealed the suppression of TGF-β signaling and ECM-receptor interaction pathways. We further identified BMP1 as a key downstream effector, demonstrating a direct physical interaction between COL1A1 and BMP1, and showed that COL1A1 potentiates BMP1's proteolytic activity. Rescue experiments confirmed that BMP1 is essential for COL1A1-driven tumor growth, metastasis, and TGF-β pathway activation in vivo. Furthermore, we uncovered an immunomodulatory role for the COL1A1-BMP1 axis, whereby it promotes M2 macrophage polarization via TGF-β secretion to foster an immunosuppressive tumor microenvironment. This effect was reversible using either BMP1 knockdown or TGF-β neutralization. In conclusion, our study establishes a novel COL1A1-BMP1-TGF-β signaling cascade that drives OSCC progression by autonomously enhancing tumor cell malignancy and non-autonomously reprogramming the immune landscape, nominating this axis as a promising therapeutic target.

overall_design: si-NC(n=4) and si-Col1a1 group (n=4). after knockdown, the total RNA was used for RNA-seq.

first: Xing

first: Yalun

last: Li

first: Lanlan

last: Gao

first: Rihui

last: Lu

first: Yongjin

last: Fang

first: Xiao

last: Yang


title: A thioredoxin-Serinc2-lipid signaling axis modulates mood-related behaviors in mice [ATAC-Seq]

city: Jinan

first: Chong

middle: lei

last: Fu

state: Shandong

address: No. 6699, Qingdao Road

institute: Shandong First Medical University

summary: Bipolar disorder (BD) shows strong heritability and distinct symptomatic subtypes. However, the molecular basis underlying subtype-specific features remains poorly understood. Here, we showed that Serinc2, a BD susceptibility gene encoding a L-serine transporter that regulates membrane lipid synthesis, as a regulator of mood-related behavioral phenotypes. Using patient plasma samples, BD iPSC-derived forebrain organoids, and Serinc2 knockout/overexpression mouse models, we found that Serinc2 expression was increased in bipolar I (BDI) but decreased in bipolar II (BDII); bi-directional manipulation of Serinc2 induced opposite changes in synaptic transmission and depression-related behaviors, accomplied by alterations in PS/SM-dependent redistribution of NMDAR subunits in postsynaptic membranes. Mechanistically, we found that thioredoxin (Txn) bound to the Serinc2 regulatory region and negatively regulate its transcription, and that differential chromatin accessibility of Txn contributed to subtype-associated expression patterns. Together, our results demonstrated a Txn–Serinc2–lipid signaling axis that linked membrane lipid composition to synaptic function and mood-related behaviors, and indicated a potential molecular framework contributing to subtype-specific features of BD.

overall_design: ATAC-seq was performed on human iPSC-derived forebrain organoids from healthy control individuals and patients with bipolar disorder, including bipolar I disorder (BDI) and bipolar II disorder (BDII). The aim was to profile genome-wide chromatin accessibility and identify disease-associated and subtype-specific differentially accessible regions among HC, BDI, and BDII organoids.

first: Chong-Lei


title: Single-nucleus RNA sequencing reveals the pathological process and key transcription factor of sorafenib-induced cardiotoxicity

city: Shenyang

first: Yani

last: Wang

address: General Hospital of Northern Theater Command, Wenhua Road 83

department: State Key Laboratory of Frigid Zone Cardiovascular Diseases, Department of Cardiology and Cardiovascular Research Institute

summary: Background: Sorafenib is a first-line treatment for advanced solid tumors. However, its clinical application is limited by cardiotoxicity. The underlying mechanisms remain unclear. We aimed to identify key mechanisms of sorafenib-induced cardiotoxicity using single-nucleus RNA sequencing (snRNA-seq) and experimental verification. Results: SnRNA-seq demonstrated that cell clustering and component analysis confirmed the reduction in cardiomyocytes (CMs) and endothelial cells (ECs), along with an increase in immune cell populations. DEG enrichment analysis indicated that the upregulated DEGs in CMs, ECs, and fibroblasts (FBs) were consistently enriched in pathways associated with cardiomyopathy, whereas the downregulated DEGs were enriched in myocardial remodeling and repair processes. Gene set scoring revealed activation of fibrosis and inflammation programs in CMs and FBs. Cell communication analysis revealed a widespread disruption of cellular crosstalk in sorafenib-induced cardiotoxicity and identified key ligand-receptor pairs contributing to pro-inflammatory and pro-fibrotic phenotypes. Meanwhile we identified the common transcription factors and main effect genes in the three main effector cells during sorafenib-induced cardiotoxicity. Augur analysis and WGCNA consistently identified CMs as the most significantly affected cell type. Transcriptional regulatory network analysis highlighted melanocyte-inducing transcription factor (MITF) as a core transcription factor involved in sorafenib-induced cardiotoxicity. Functional validation showed that MITF expression was significantly increased in cardiac tissues and CMs after sorafenib treatment and that knockdown of MITF attenuated sorafenib-mediated CM hypertrophy in vitro. Conclusions: By constructing the first snRNA-seq data for sorafenib-induced cardiotoxicity, we identified MITF as a key transcription factor associated with sorafenib-induced cardiotoxicity. Our study provides potential therapeutic targets for mitigating sorafenib-induced cardiotoxicity.

overall_design: SnRNA-seq was performed on cardiac tissue from a mouse model of sorafenib-induced cardiotoxicity. Bioinformatics analyses included weighted gene co-expression network analysis (WGCNA), differentially expressed gene (DEG) analysis, intercellular communication inference, and transcriptional regulatory network analysis. We conducted functional verification both in vivo and in vitro.


title: Genome-wide rotational and translational phasing of nucleosomes with human transcription factors

city: Ithaca

first: B. Franklin

last: Pugh

address: 465 Biotechnology Building

institute: Cornell University

summary: How transcription factors (TFs) and their binding sites organize and engage nucleosomes at natural genomic locations remains poorly understood. Here we develop Benzonase-seq to measure the rotational phasing of nucleosomes in human cells, and enhance ChIP-exo (v6) to measure rotational phasing on the same DNA molecule bound by a TF. Unbound CTCF sites were found to be rotationally accessible on nucleosomes and this rotational accessibility is encoded by classical dinucleotide periodicities. CTCF binding results in nucleosome displacement to adjacent DNA phasing sequences. Examining 40 TF classes, their unbound sites were phased inward, outward, or lacked phasing. In all examined cases, TF binding (e.g. NFIA and FoxA) results in adjacent rotational and translational phasing, which is not dinucleotide encoded. Benzonase-seq also more robustly maps nucleosome and subnucleosome positions in hard-to-map CpG islands. These findings provide a clearer view of how TFs engage and position nucleosomes to shape the natural chromatin landscape.

overall_design: Chromatin Immunoprecipitation (ChIP-exo) with Benzonase for various transcription factor targets in a variety of chromatin preps from K562 and HepG2 cell lines.

first: Haining

last: Chen

first: Jordan

last: Krebs

first: Olivia

last: Lang

first: Jiayi

last: Hu

first: Devin

last: Mellini

first: Judith

last: Hyle

first: Chunliang

first: William KM

last: Lai

first: B Franklin


title: Expression data from arsenite treated wildtype and ATF4-deficient mouse cortical neurons

city: London

first: Sean

middle: Patrick

last: Cregan

state: Ontario

address: 1151 Richmond St N

department: Physiology & Pharmacology

country: Canada

institute: University of Western Ontario

summary:
Microarray data was used to assess ATF4-dependent gene expression and signaling pathways induced by arsenite in mouse cortical neurons.
Pathway enrichment analysis of differentially expressed genes revealed several ATF4-dependent signaling pathways induced by arsenite treatment in mouse neurons.

overall_design:
Cortical neurons derived from wildtype and ATF4-deficient mouse embryos were treated at 7 days in vitro with sodium arsenite (5uM) or vehicle for 12 hours and RNA extracted and hybridized on mouse Affymetrix GeneChips. Probe signals from microarrays were normalized and transformed into log2 transcript expression values in Partek Genomics Suite v6.6 using the Robust Multiarray Average (RMS) algorithm.

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The raw data (.CEL files) are not available due to file loss.
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middle: P

first: Matthew

middle: D

last: Demmings


title: Stem cell factor 248 shapes ILC2 transcriptional programs and promotes mucosal inflammation in allergic asthma

city: Ann Arbor

first: Ramon

last: Ocadiz Ruiz

state: Michigan

address: 109 Zina Pitcher, BSRB

institute: University of Michigan

summary: Stem cell factor (SCF), also known as Kit ligand, is a pleiotropic cytokine that Q5 signals through the c-Kit receptor to regulate cellular development, survival, and proliferation. Although SCF is classically recognized for its essential role in hematopoiesis and mast cell biology, c-Kit is also expressed by innate lymphoid cell progenitors (ILCp) and subsets of mature innate lymphoid cells (ILCs), suggesting broader immunoregulatory functions. Group 2 innate lymphoid cells (ILC2s) are critical mediators of type 2 airway inflammation and serve as an important source of type 2 cytokines during allergic responses. We previously demonstrated increased expression of the pro-inflammatory SCF248 isoform in the lungs of mice with chronic allergic inflammation, while elevated soluble SCF levels have also been reported in patients with asthma. In the present study, we further observed that SCF248 is upregulated in the bone marrow during allergic inflammation, suggesting that SCF248 may contribute to both local and systemic regulation of allergic immune responses. To define the role of SCF/c-Kit signaling in ILC2 biology, we first performed transcriptional profiling of SCF-deficient ILC2s, which revealed reduced expression of genes associated with cytokine signaling, activation, and effector function, including  Il4, Stat5b, and PI3K-AKT pathway components, consistent with impaired inflammatory responsiveness. Mechanistically, pro-inflammatory and type 2 cytokines induced SCF248 expression in mesenchymal cells in vitro. To define its functional impact, ILC progenitors were cultured on OP9-DL1 stromal cells with upregulated SCF248 expression, which increased expression of ILC2-associated markers and the maturation program, supporting a role for SCF248 in enhancing ILC2 maturation and activation. In vivo validation using tamoxifen-inducible whole-body SCF-deficient mice (SCFfl/fl; UBC-CreERT2) in an Alternaria alternata model of allergic airway inflammation demonstrated that SCF deficiency reduced SCF248 expression, attenuated type 2 cytokine production, diminished lung inflammation, and decreased circulating and pulmonary ILC2 populations. Similarly, SCF248 blockade reduced allergic inflammation and altered bone marrow ILC compartments. Together, these findings identify SCF248 as a regulator of ILC2 maturation and activation, amplifying mucosal type 2 inflammation during allergic airway disease.

overall_design: Bone marrow from allergic and control Kitlfl/fl-UBC-cre-ERT mice was collected. We combined bone marrow samples from 3 mice per groupand sequenced them to assess sample heterogeneity.

first: Nobuhiro

last: Asai

first: Grace K

last: Lombardo

first: Yao

last: Gu

first: Andrew J

last: Rasky

first: Dana S

last: Garcia

first: Angela J

last: Montoya

first: Sarita

last: Montaño

first: Kazuma

last: Yagi

first: Wendy

last: Fonseca


title: Compartmentalisation of m6A (N6-methyladenosine) methylated RNA in somatic or axonal subcellular locations is dependent on Nerve Growth Factor (NGF) state in sympathetic neurons [Axon-meRIP-seq]

first: Braulio

last: Martinez De La Cruz

address: Gower Street

department: LMCB

institute: UCL

summary: Sympathetic neurons were culture in compartmentalised chambers in medium with NGF (control condition). Cells were then subjected to NGF starvation for 18 hours followed by 1 hour of restimulation. RNA was collected from either cell bodies (CB) or axons (Ax) from these neurons for meRIP-seq. Here, we find a strong compartmentalisation effect, in which RNA is hypermethylated in axons in both control and restimulated conditions. We also find that a select few RNA species are hypermethylated in restimulated axons compared to control axons, suggesting a fast time-dependent function for m6A marks in these RNAs.

overall_design: meRIP-seq of Control NGF or Restimulated RNA collected from cell bodies or axons. Each condition has 4 biological repeats. Each sample has a corresponding input sample for normalisation. Reads are paired-end (Labelled R1 or R2).

first: Simon

last: Galkin

first: Shiqi

last: Wang

first: Yuxuan

last: Jing

first: Subramanian

last: Raju Nurani

first: Pierre-Luc

last: Germaine

first: Gerhard

last: Schratt

first: Antonella

last: Riccio


title: Compartmentalisation of m6A (N6-methyladenosine) methylated RNA in somatic or axonal subcellular locations is dependent on Nerve Growth Factor (NGF) state in sympathetic neurons [Axon-TRAP-seq]

summary: Sympathetic neurons were culture in compartmentalised chambers in medium with NGF (control condition). Cells were then subjected to NGF starvation for 18 hours followed by 1 hour of restimulation. Following a TRAP protocol, translating RNA was collected from either cell bodies (CB) or axons (Ax) from these neurons for RNA sequencing. Here, we find a strong compartmentalisation effect. We also find that only a few RNA are translated in restimulated distal axons within 1 hour compared with control condition axons.

overall_design: Axon-TRAP-seq of Control NGF or Restimulated RNA collected from cell bodies or axons. Each condition has 4 biological repeats. Each sample has a corresponding input sample for normalisation. Reads are paired-end (Labelled R1 or R2).


title: Comparative RNA-seq analysis of PM2.5-induced transcriptional responses in wildtype mouse mammary epithelial cells

city: Linz

first: Tamara

last: Lang

address: Krankenhausstraße 5

department: Pathophysiology

country: Austria

institute: Johannes Kepler Universität

summary: Fine particulate matter (PM2.5) is an environmental pollutant associated with adverse health effects, including increased cancer risk. To investigate early transcriptional responses to PM2.5 exposure in non-malignant epithelial cells, we performed bulk RNA sequencing of wildtype mouse mammary epithelial EpH4 cells cultured under two-dimensional (2D) conditions. Cells were either left untreated or exposed to PM2.5. This dataset captures genome-wide gene expression changes induced by PM2.5 in wildtype epithelial cells and provides insight into stress response and pathophysiological pathways activated upon particulate matter exposure.

overall_design: Bulk RNA sequencing was performed on wildtype EpH4 mouse mammary epithelial cells cultured in 2D. Cells were divided into two experimental groups: untreated controls and PM2.5-treated samples, each in duplicates. Total RNA was isolated and subjected to RNA-seq to assess global transcriptional changes induced by PM2.5 exposure.

first: Wechselberger

last: Christian

first: David

last: Demmel

first: Johannes

last: Pröll


title: Human tubuloids from cryopreserved adult tissue: building a biobank for 3D modeling and precision medicine

city: Zaragoza

first: Maria del Mar

last: Encabo Berzosa

address: San Juan Bosco

country: Spain

institute: IACS

summary: Tubuloids offer a powerful tool for advancing renal research and improving patient care. To facilitate this, we have established a robust biobank of 40 adult human kidney organoids derived from fresh or frozen biopsies. These organoids exhibit diverse morphologies, distal and proximal tubules, closely resembling their tissue of origin. We have extensively characterized these organoids using a combination of techniques, including histological staining, immunofluorescence, gene expression analysis (qPCR and RNA-seq), and genetic profiling (STRs). This comprehensive characterization ensures the quality and reliability of the organoids for downstream applications.  Molecular analysis revealed the expression of genes characteristic of various kidney cell types.  Furthermore, we have successfully cultured these organoids within microfluidic chips, demonstrating their compatibility with advanced culture systems. This platform of well-characterized, living human kidney organoids from fresh and frozen tissues provides a valuable resource for a wide range of biomedical research, including drug screening, disease modeling, and personalized medicine.

overall_design: RNA-seq profiling of kidney patient-derived organoids cultured for one week across passages 1–5, compared with their corresponding original tissues

first: Cindy

last: Giraldo

first: Alodia

last: Lacueva-Aparicio

first: Rebeca

last: Sanz-Pampona

first: Ester

last: Raigón-Gómez

first: Laura

last: Martínez-Gimeno

first: María Pilar

last: Torcal

first: Ignacio

last: Giménez

last: Ochoa

first: Celia

last: del Agua

first: Paula

last: Bermúdez-Javierre

first: Izaskun

last: Arenaz

first: Irene

last: Mora

first: Purificación

last: Catalina-Carmona

first: José Antonio

last: Carrillo

first: Carlos Hugo

last: Mora Cevallos

first: Jorge

last: Subirá

first: Delia

last: Recalde-Frisón

first: Teodora

last: Ranđelović

first: Mª del Mar

last: Encabo-Berzosa


title: DNMT3B plays antagonistic roles with SMARCB1 and is a targetable vulnerability in rhabdoid tumors [RNA-seq]

city: Paris

first: Franck

last: Bourdeaut

address: 26 rue d'ulm

institute: Institut Curie

summary: Purpose: Rhabdoid tumors (RTs) are highly aggressive pediatric cancers driven by the biallelic inactivation of the SMARCB1 tumor suppressor gene, the sole recurrent genetic alteration. SMARCB1 encodes a core subunit of the SWI/SNF chromatin remodeling complex; its loss disrupts epigenetic gene regulation, supporting the classification of RTs as prototypical epigenetically driven cancers and highlighting the therapeutic potential of targeting epigenetic modifiers. Notably, previous studies have reported the overexpression of DNMT3A and DNMT3B, enzymes responsible for de novo DNA methylation, in RTs. Experimental Design: Using patient samples, cell lines, and an ex vivo brain organoid system, combined with immunohistochemistry and bioinformatics, we investigated the role of DNMT3 enzymes in RT progression. Results: In a composite tumor case, SMARCB1-deficient and -proficient regions displayed distinct methylation profiles. SMARCB1 loss correlated with increased DNA methylation and DNMT3A/B overexpression. To assess their respective roles in RTs, we used CRISPR-Cas9 to knock out DNMT3A/B in a SMARCB1-inducible RT cell line. DNMT3B loss impaired viability more strongly than DNMT3A. DNMT3B knock-out and SMARCB1 re-expression regulated overlapping gene programs related to development and cell adhesion at methylation and transcriptional levels. We next demonstrated that the cytotoxicity of the DNMT inhibitor decitabine, which impairs RT cell growth in human iPS-derived cerebral organoids, is primarily mediated by DNMT3B. Conclusions: These results show that DNMT3B plays a key role in the cascade of epigenetic effects following SMARCB1 loss and is pivotal in the RT sensitivity to decitabine; our study therefore supports the development of DNMT3B-specific inhibitors for RT.

overall_design: RNA-seq profiling of I2A rhabdoid tumor cells under basal condition (day 0), SMARCB1-reexpressing derivatives (days 7 and 14), DNMT3A- and DNMT3B-knock-out derivatives, and cells treated for 21 days with decitabine (DAC) or DMSO as a control. RNA-seq profiling of G401-i rhabdoid tumor cells under basal condition (day 0) and their SMARCB1-reexpressing derivatives (days 7 and 10). RNA-seq profiling of 64 ATRT patient samples, 23 extra-cranial rhabdoid tumors (ECRT) and 1 meningioangiomatosis (MAM).

first: Céline

last: Chauvin

first: Ryszard

last: Wimmer

first: Ludovica

last: Brunetti

first: Joanna

last: Cyrta

first: Ana

last: Boranijasevic

first: Mamy

last: Andrianteranagna

first: Julien

last: Masliah-Planchon

first: Kévin

last: Beccaria

first: Sandrina

last: Turczynski

first: Grégory

last: Thomson

first: Maëva

last: Veyssière

first: Rachida

last: Bouarich-Bourimi

first: Zhi-Yan

last: Han

first: Owen

last: Hoare

first: Aurore

last: Coulomb

first: Mylène

last: Bohec

first: Sylvain

last: Baulande

first: Gaëlle

last: Pierron

first: Olivier

last: Delattre

first: Arnault

last: Tauziède-Espariat

first: Nicolas

last: Servant

first: Alexandre

last: Baffet


title: Comprehensive single cell RNA profiling of the spleen in murine myelofibrosis identifies targetable immune-stromal interactions

city: Aachen

first: Mohamed

last: Saad

address: Pauwelsstraße 30

department: Institut für Zell- und Tumorbiologie

institute: Uniklinik RWTH Aachen

summary: Splenomegaly is a defining feature of myelofibrosis, yet the contribution of splenic mesenchymal stroma to disease progression remains unclear. We perferomed spatial transcriptomics of murine spleens to map extramedullary hematopoiesis niches. Activated red pulp reticular cells localize near hematopoietic stem and progenitor cells, and early disease shows marginal zone disruption with lymphoid depletion preceding stromal remodeling. Trajectory analyses reveal a shift of reticular cells from hematopoiesis-supportive to inflammatory and pro-fibrotic states driven by macrophage- and megakaryocyte-derived signals that activate complement and induce TNFα, TGF-β, extracellular matrix, and Thbs1 programs. Stromal deletion or pharmacological inhibition of complement component C3 suppresses these pathways, restores splenic architecture, and reduces splenomegaly and bone marrow fibrosis. These findings identify complement-dependent stromal reprogramming as a mechanism governing hematopoietic niches and a targetable axis in myelofibrosis.

overall_design: scRNA-seq Transcriptomics profiling of murine spleens from 3 conditions; WT, ThPO and  MPLW515L

first: Bérénice

last: Dugué

first: Pia

last: Wanner

first: Mayra

last: Ruiz Tejada Segura

first: Lucas

last: Greven

first: Katrin

last: Gotz

first: Carmen

last: Schalla

first: Stijn

last: Fuchs

first: Gerjanne

last: Vroeg in de wei

first: Hélène

last: Gleitz

first: Anna Katharina

last: Galyga

first: Jessica

last: Ellen Pritchard

first: Tobias

last: Schlangen

first: Niklas

last: Lutterbach

first: Salim

last: Atakhanov

first: Lina

last: Schmidt

first: Marie

last: Parrens

first: Armelle

last: Peyrat

first: Damien

last: Luque Paz

first: Marie-Christine

last: Copin

last: Guy

first: Victor-Emmanuel

last: Brett

last: Mansier

first: Susanne

last: Schmitz

first: Paul

last: Wanek

first: Bella

last: Banjanin

first: Stephani

first: Martina

last: Crysandt

first: Marian

last: Clahsen-van Groningen

first: Konnie

last: Hebeda

first: Sascha

last: Dietrich

first: Harald

last: Voehringer

first: Matthias

last: Meyer-Bender

first: Kristin

last: Séré

first: Chloé

last: James

first: Adam

last: Benabid

first: Ivan

last: Costa

first: Charles

last: Dussiau

first: Rebekka

last: Schneider


title: Synthetic transcription factor overrides persistent repressive chromatin marks [RNA-seq]

city: Memphis

first: Wojciech

last: Rosikiewicz

address: 262 Danny Thomas Place

institute: St. Jude Childrens Research Hospital

summary: The prevailing paradigms of epigenetic control posit that signature patterns of post-translational marks on histones guide specific transcriptional outcomes. Methylation of lysine-9 residue of histone H3 (H3K9me3) is implicated in transcriptional silencing through chromatin condensation by its reader HP-1 proteins. Erosion, erasure and subsequent replacement of H3K9me3 by active acetyl-lysine marks accompanies transcriptional up-regulation. Here, we report that a synthetic transcription elongation factor (SynTEF1), selectively targets the disease-causing GAA repeat expansion in frataxin and stimulates gene expression without erasure of the signature repressive marks or removal of HP1 proteins. Added epigenetic perturbation with a pharmacological agent leads to supra-synergistic frataxin expression that is unexpectedly accompanied by a dramatic rise in H3K9me3 levels. Active placement of the signature repressive mark is readily overridden by SynTEF1, demonstrating the fluidity and context-dependence of these marks in regulating gene expression. While forcing a reconsideration of how signature epigenetic marks are interpreted, our results provide key insights for therapeutic intervention in rationally reconfiguring disease-associated epigenetic states.

overall_design: Examination of the relationship between SynTEF1 and RGFP109

first: Christopher

last: Brandon

first: Sandra

last: Kietlinska

first: Samantha

last: Rider

first: Marcus

last: Valentine

first: Burckhard

last: Hoeckendorf

first: Ashraf

last: Mohammed

first: Wenwei

last: Lin

first: Khaled

last: Khairy

first: Taosheng

last: Chen

first: Beisi

last: Xu

first: Aseem

last: Ansari


title: A thioredoxin-Serinc2-lipid signaling axis modulates mood-related behaviors in mice

first: Chong

last: Fu

overall_design: Human iPSC-derived forebrain organoids were generated from healthy control individuals and patients with bipolar disorder, including bipolar I disorder (BDI) and bipolar II disorder (BDII). RNA sequencing was performed to characterize transcriptomic differences among HC, BDI, and BDII organoids and to identify disease-associated and subtype-specific differentially expressed genes. Pairwise comparisons were conducted between BD and HC groups and between BDI and BDII groups, followed by functional enrichment analysis of differentially expressed genes.

first: Chong-Lei


title: Effect of curing the phi027 prophage for gene expresson in Clostridioides difficile clinical isolate 500/12

city: Gdansk

first: Adam

last: Iwanicki

address: Debinki 1

department: Department of Medical Biotechnlogy

country: Poland

institute: Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk

summary: Clostridioides difficile is a clinically important nosocomial pathogen whose virulence is primarily associated with toxin production and can be influenced by prophage carriage. In this study, we investigated the molecular basis of phi027-dependent phenotypic differences previously observed between the clinical RT176 strain 500/12 and its prophage-free derivative CKH08. Comparative transcriptomic analysis revealed that loss of phi027 was associated with reduced expression of the sinR/R' operon, downregulation of multiple flagellar biosynthesis genes.

overall_design: RNA profiling of C. diffcile clinical isolate 500/12 lysogenic with phi027 bacteriophage and its prophage-free derivative strain CKH08 at late logarithmic growth phase in BHI medium.

first: Michał

last: Obuchowski

first: Krzysztof

last: Hinc


title: Gene expression of activated CD8+ Tc1 and Tc2 cells

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

country: Sweden

institute: KI

summary: RNA sequencing identified distinct transcriptional programs associated with Tc2 cell metabolism, including enhanced lipid metabolism and monoamine oxidase A (MAOA)-mediated serotonin catabolism. These data provide a resource for investigating the molecular regulation of human Tc2 cells and their role in type 2 immune responses and allergic disease. Due to restrictions in participant consent and the approved EU ethical approval (Swedish Ethical Review Authority), raw sequencing data (FASTQ files) cannot be deposited in a public repository.

overall_design:
Bulk RNA sequencing was performed to compare transcriptional profiles of in vitro differentiated human CD8+ type 1 cytotoxic T cells (Tc1) and CD8+ type 2 cytotoxic T cells (Tc2). Memory T cells were isolated from peripheral blood of healthy donors and cultured for 7 days under lineage-polarizing conditions to generate Tc1 and Tc2 populations. Following culture, cells were lysed and processed using the Takara SMART-seq v4 Ultra Low Input RNA Kit. Libraries were prepared using the Illumina Nextera DNA Library Preparation Kit and sequenced on Illumina NextSeq 500 and NextSeq 2000 platforms. The study was designed to identify differentially expressed genes and pathways associated with Tc2 cell identity, metabolic regulation, lipid metabolism, and serotonin metabolism compared with Tc1 cells.

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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: Christopher Andrew

first: Sabrina

last: de Souza Ferreira


title: Comparative toxicogenomic profiling of human epithelial cell lines exposed to hazardous chemicals

city: Busan

first: BuHyun

last: Youn

address: Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Biological Sciences

country: South Korea

institute: Pusan National University

summary: Human exposure to chemically diverse hazardous substances has increased the need for human-relevant models for toxicity assessment. In this study, we performed bulk RNA sequencing of four human epithelial cell lines representing major exposure-relevant tissues: HIEC-6 intestinal epithelial cells, HL7702 hepatic epithelial cells, BEAS-2B bronchial epithelial cells, and HaCaT keratinocytes. Cells were exposed to nine hazardous chemicals, including DBP, DINCH, BPA, BPS, PFOA, PFTeDA, DEHP, NiCl2, and AlCl3, at cell line-specific IC01 concentrations, with vehicle controls included for each cell line. Biological triplicates were generated for all conditions, resulting in 120 samples. Comparative transcriptomic analysis was used to evaluate shared and cell line-dependent responses to hazardous chemical exposure. The dataset provides a toxicogenomic resource for investigating chemical-induced molecular perturbations across human epithelial models.

overall_design: This study includes bulk RNA-seq samples from four human epithelial cell lines representing major exposure-relevant tissues: HIEC-6 intestinal epithelial cells, HL7702 hepatic epithelial cells, BEAS-2B bronchial epithelial cells, and HaCaT keratinocytes. Each cell line was exposed to nine hazardous chemicals, including DBP, DINCH, BPA, BPS, PFOA, PFTeDA, DEHP, NiCl2, and AlCl3, at cell line-specific IC01 concentrations. Vehicle control samples were included for each cell line. All conditions were prepared as biological triplicates, resulting in 120 samples in total.

first: Junhyeong

last: Park

first: Soomin

last: Yum

first: Byeongsoo

last: Kim

first: Wooseok

last: Kang

first: Changjong

last: Moon

first: Hyewon

last: Jang


title: LEF1 and niche determinants define T cell stemness across chronic diseases

city: New York

first: Andrea

last: Schietinger

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: CUT&RUN analysis CD8 T cells

overall_design: Naïve TCR-P14 CD8 T cells were isolated and sorted from spleens and subjected to CUT&RUN

first: Svetlana

last: Miakicheva

first: Katrina

middle: M

last: Hawley

first: Simon

last: Grassmann

first: Paul

last: Zumbo

first: Doron

last: Betel


title: LEF1 and niche determinants define T cell stemness across chronic diseases [scMultiome]

summary: Paired scRNA and scATAC sequencing of IGRP-specific from non-obese diabetic mice pancreatic lymph nodes and of GP-33 specific CD8 T cells from LCMV clone 13 infected non-obese diabetic mice spleens.

overall_design: For multiomic analysis of IGRP-specific CD8+ T cells, pancreatic lymph nodes (pLN) were harvested from euglycemic NOD mice (13–20 weeks old) and IGRP-specific (live, CD8+, Kd/NRP-V7 tetramer+ ) T cells were sorted and frozen in BamBanker freezing medium, and stored in  −80°C until further processing. IGRP-specific cells were pooled from over n=150 mice.  For multiomic analysis of exhausted GP33-specific T cells, NOD mice (8 weeks old) were infected with LCMV-cl13 and spleens were harvested 21 days post-infection; CD8+ T cells were pre-enriched using the EasySep negative selection kit (STEMCELL Technologies) prior tto sorting on GP33-specific (live, CD8+, GP-33 tetramer+) T cells.

first: Ronan

last: Chaligne


title: Age-related changes in the phenotype and function of mouse skin macrophages

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

institute: Medical University Vienna

summary: Skin ageing is accompanied by chronic low-grade inflammation (“inflammaging”) and progressive remodelling of the dermal extracellular matrix, yet the cellular changes that initiate these processes early in life remain poorly defined. Here we used single-cell RNA sequencing (scRNA-seq) of dorsal skin from young (8-week), middle-aged (26-week) and aged (52-week) male C57BL/6 mice to map age-related shifts in cellular composition, with a focus on macrophages. Whereas the relative proportions of most cell types remained largely stable, the macrophage compartment expanded markedly in the oldest skin. Sub-clustering resolved four macrophage populations, three of which expanded or emerged with age. The Mac4 population, marked by S100a8 and S100a9 and a Cd14-high monocyte-derived signature, was detected only in aged skin and was confirmed in situ by F4/80, S100a8 and S100a9 co-staining. Cell–cell communication analysis predicted increased macrophage-to-fibroblast signalling in aged skin, including the pro-fibrotic mediators Thbs1 and Spp1, accompanied by up-regulation of collagen and fibrosis-associated genes in a subset of fibroblasts (FB3/FB4). Notably, collagen transcripts increased while COL5A3 protein decreased and dermal collagen architecture appeared disorganised by second-harmonic-generation imaging, pointing to post-transcriptional control of matrix remodelling. Ex vivo treatment of aged skin with the secretome of γ-irradiated peripheral blood mononuclear cells (PBMC-sec) reduced the macrophage expansion towards a more youthful composition and down-regulated fibrosis-associated fibroblast genes. Together, these findings identify the early emergence of monocyte-derived, pro-inflammatory and potentially pro-fibrotic macrophage subsets as a feature of mouse skin ageing and suggest that PBMC-sec can partially counteract these changes.

overall_design: The dorsal skin of 8 week, 26 week and 52 week old  C57BL/6 mice was sequenced with 3 animals pooled per condition. Whole skin was dissociated and isolated cells were analysed using scRNA seq. In addition, dorsal mouse skin of the same age was treated with PBMCsec ex-vivo and underwent a simmilar pooling and processing.

first: Melanie

last: Salek

first: Katharina

last: Klaas

first: Attila

last: Sachslehner

first: Daniel

last: Bormann

first: Bahar

last: Golabi

first: Sophie

last: Röder

first: Hendrik

last: Ankersmit

first: Michael

last: Mildner


title: mTORC2-HIF-1β signaling creates a targetable sphingolipid vulnerability in lung cancer [RNA-Seq]

city: Liège

first: Morgane

last: Paque

address: Quartier Hôpital, avenue de l'Hôpital 1

department: University of Liège

country: Belgium

institute: GIGA Institute

summary: Despite extensive genetic heterogeneity, lung tumors frequently converge on shared signaling dependencies that remain therapeutically underexploited. Here, we identify mTORC2 signaling as a convergent dependency across genetically distinct lung cancer subtypes and demonstrate that RICTOR-dependent mTORC2 activity promotes tumor progression through HIF-1β-dependent sphingolipid reprogramming. Elevated mTORC2 signaling in lung adenocarcinoma was associated with poor overall survival, metastatic dissemination and metabolic rewiring. Using complementary genetically engineered mouse models of Rictor deletion or overexpression in Kras-driven lung tumors, we show that mTORC2 activity is dispensable for normal lung homeostasis but required for tumor progression and metabolic adaptation in vivo. Mechanistically, mTORC2 stabilized HIF-1β by preventing its ubiquitin-independent proteasomal degradation through a non-canonical PKCα-CK2 signaling axis, independently of AKT. Integrated multi-omics analyses revealed that mTORC2-HIF-1β signaling drives extensive sphingolipid remodeling through the regulation of key metabolic enzymes, including SPHK1 and SPTLC2. Accordingly, pharmacological inhibition of sphingolipid metabolism markedly impaired the growth of mTORC2-driven lung tumors in vivo. Together, our findings uncover a previously unrecognized mTORC2-HIF-1β-sphingolipid signaling axis that creates targetable metabolic vulnerabilities in lung cancer.

overall_design: RNAseq of RNA on A549 lung cancer cell line: wild type and over-expressing HIF-1β.

first: Pierre

last: Close

first: Arnaud

last: Blomme


title: mTORC2-HIF-1β signaling creates a targetable sphingolipid vulnerability in lung cancer [Polysome-seq]

overall_design: Polysome profiling experiment in control and RICTOR-depleted (siRICTOR) A549 and H460 lung cancer cell lines. Total and polysomal fractions were sequenced.


title: SIRT7 acts as a core regulator in resveratrol-mediated gene transcription to alleviate diabetic cardiomyopathy.

city: Changchun

first: Naixin

last: Chen

address: No. 126, Xiantai Street

institute: China-Japan Union Hospital of Jilin University

summary: Diabetic cardiomyopathy (DCM), a severe diabetic complication manifesting as myocardial hypertrophy, oxidative stress, cardiomyocyte apoptosis and extracellular matrix (ECM) remodeling, lacks effective therapeutic interventions. Resveratrol (Res) confers cardioprotection, and SIRT7 participates in high-glucose (HG)-elicited myocardial damage. This study aimed to clarify whether Res-activated SIRT7 modulates transcriptional profiles to counteract HG-induced DCM lesions. HG-challenged cardiomyocytes and diabetic mouse models were established; a SIRT7 inhibitor was administered to verify the underlying mechanism. Transcriptome sequencing was conducted to identify pivotal functional genes, followed by GO and KEGG enrichment analyses. Immunofluorescence, western blot and multiple histopathological staining assays were adopted to assess oxidative stress, apoptosis, myocardial hypertrophy and cardiac fibrosis. HG exposure boosted reactive oxygen species (ROS) production, facilitated cardiomyocyte apoptosis, increased hypertrophy-related protein levels, and dysregulated genes linked to inflammation and ECM remodeling. Res treatment upregulated SIRT7, rescued all HG-triggered pathological phenotypes, and modulated PI3K-Akt, NF-κB and Hippo signaling cascades. Notably, pharmacological suppression of SIRT7 completely abrogated Res-elicited cardioprotection. Res ameliorates HG-induced DCM through SIRT7-dependent transcriptional reprogramming, which offers promising molecular targets for DCM treatment.

overall_design: Normal glucose, High glucose, High glucose treated with resveratrol, High glucose treated with resveratrol and SIRT7 inhibitor

first: Feng

last: Qian


title: Inotodiol prevents age-related muscle wasting by restoring mitochondrial function through liver X receptor beta signaling

city: Suwon

first: Ju-Hyeon

last: Bae

state: Gyeonggi-do

address: Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 2066

department: school of medicine

institute: Sungkyunkwan University

summary: Sarcopenia is characterized by a progressive decline in muscle mass and strength, and represents a major contributor to increased mortality in elderly population. Mitochondrial dysfunction, leading to impaired energy metabolism and elevated oxidative stress, is a key driver of muscle wasting and associated metabolic disorders. Thus, mitochondria targeting is promising strategy for combating sarcopenia. In this study, we investigated the therapeutic potential of a phytosterol inotodiol (Ino) in mitigating age-related muscle wasting and metabolic dysfunction. Ino treatment significantly improved muscle mass and function in aged mice and also prevented dexamethasone-induced muscle atrophy. Mechanistically, Ino enhanced mitochondrial function and restored muscle metabolism, as evidenced by increased mitochondrial content, elevated oxidative capacity, reduced lipid accumulation, and decreased oxidative stress. These effects are mediated by activation of the LXRβ/SIRT3/PGC-1α signaling axis, a central regulator of mitochondrial function. Collectively, our findings identify Ino as a promising therapeutic candidate that mimics key benefits of exercise.

overall_design: Bulk RNA sequencing was performed on gastrocnemius (GAS) muscle total RNA isolated from vehicle (Veh)- and inotodiol (Ino)-treated aged male mice (20 months old, n = 3 per group) to identify transcriptional changes induced by treatment.

first: Yideul

last: Jeong

first: Gyu-Un

first: Jong-Sun

last: Kang


title: Transcriptome Analysis Identifies Proteostasis and Cell Survival Pathway Disruption in Peripartum Cardiomyopathy, Leading to Heart Failure

city: Torrance

first: Michelle

middle: L

last: Matter

state: CA

address: 1124 West Carson Street

department: Genomics

institute: The lundquist Institute

summary: Peripartum cardiomyopathy (PPCM) is a pregnancy-associated form of systolic heart failure that develops when hemodynamic, metabolic, and hormonal stress of late gestation exceeds maternal cardiac adaptive capacity. While vascular, inflammatory, and genetic contributions have been implicated in PPCM, the integrated molecular programs connecting pregnancy-related stress to cardiomyocyte failure remain poorly defined. To elucidate these mechanisms, we performed a transcriptome-wide RNA seq of left ventricles from females with PPCM and non-failing female normal donor controls. Differential expression analysis identified 2891 genes with altered expressions (1491 upregulated, 1400 downregulated; fold change ≥ 2, FDR < 0.05). Ingenuity pathway analysis (IPA) revealed the activation of protein ubiquitination pathways, EIF2 signaling, mitochondrial dysfunction, and apoptosis pathways. Upstream regulator analysis indicated the suppression of mitochondrial protease CLPP (Z = −4.075) and activation of COPS5 (Z = +5.982) and TEAD1 (Z = +5.00), delineating dual regulatory modules of disease remodeling. Integrated network analysis demonstrated a loss of protein quality control and survival signaling with the activation of stress response and translational repression programs. This signifies a collapse of proteostasis and maladaptive adaptation. Collectively, these data define PPCM as a disorder of failed proteostasis and impaired translational homeostasis. Our analysis provides a systems-level framework connecting PPCM to ventricular dysfunction with potential therapeutic targets in mitochondria, protein quality-control, integrated stress–response, and COP9 signaling pathways.

overall_design:
RNA-seq of LV tissue from donor and PPCM patients. The hypothesis tested in the present study was that pregnancy induced stress alters gene expression that may lead to maternal heart failure. Results identify up-and down-regulated genes that are altered in PPCM/DCM.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Pooja

last: Choubey

first: Vanessa

last: Montoya-Uribe


title: Macrophage-Induced Senescent Cancer-Associated Fibroblasts Promote SASP-Mediated Chemoresistance in Colorectal Cancer

city: Zhengzhou

first: Yukang

state: Henan

address: No. 1 Jianshe East Road, Erqi District

department: Department of Interventional Radiology

institute: The First Affiliated Hospital of Zhengzhou University

summary: Cancer-associated fibroblasts (CAFs) play a crucial role in the tumor microenvironment (TME) by influencing tumor progression and therapy resistance. Accumulating evidence suggests that CAFs undergo senescence, which can impact their effects on the TME. In this study, we integrated single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and multiple preclinical models to explore the mechanisms underlying CAF senescence and its impact on chemotherapy resistance in colorectal cancer (CRC). First, we developed a machine learning-based prediction model, the Cellular Senescence Prediction Model (CSPM), to accurately identify senescent CAFs based on single-cell RNA sequencing data. We used publicly available CRC single-cell cohorts and in-house CRC single-cell data to demonstrate the reliability of the model. By combining in silico analysis and preclinical models, we demonstrated that senescent CAFs induced by IL1B-IL1R1 signaling mediated by macrophages secrete components of the Senescence-Associated Secretory Phenotype (SASP) that impair chemotherapy responsiveness in CRC, suggesting that stromal senescence could be a therapeutic target.

overall_design: Single-cell RNA sequencing profiles of primary colon adenocarcinoma tissues from 12 patients

first: Zaoqu

last: Liu


title: Individual Host Variation in Single-cell Responses to Enteroaggregative Escherichia coli Infection Modeled with Human Colon Organoids

city: Houston

first: Tajhal

last: Patel

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We performed single cell RNA sequencing of human colon organoids (HCOs) derived from three healthy adult donors with and without EAEC 042 infection.

overall_design: Day 4 differentiated HCO monolayers were either mock-infected with media only or infected with EAEC 042(serotype O44:H18) at MOI=10 for 90 minutes. Single cell gene expression libraries were generated using the Chrominum Single Cell 3' v3.1 kit and sequenced through the Illumina platform.

first: Anthony

middle: W

last: Maresso

first: Cristian

last: Coarfa

first: Ling

last: Qiu


title: Class II trehalose phosphate synthase genes regulate spikelet fertility in rice

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

institute: Rothamsted Research

summary: The trehalose 6-phosphate (T6P) pathway is a sugar signalling regulatory system in plants that integrates sucrose supply with metabolism, growth and development. The pathway consists of multigene families of trehalose phosphate synthases (TPSs) and trehalose phosphate phosphatases (TPPs). TPSs consist of class I and II enzymes. Class I enzymes are catalytically active but the function of class II TPSs has been enigmatic as they do not possess catalytic activity. To decipher physiological function of class II TPSs in cereals, we target a clade of three TPSs - OsTPS2, OsTPS3 and OsTPS6 in rice - with closest similarity to Arabidopsis TPS7. Gene editing with CRISPR-cas9 of OsTPS2, OsTPS3 and OsTPS6 together resulted in delayed flowering and poor grain set. Investigation of pollen showed abnormal structure, poor adherence to stigmas and reduced starch accumulation. RNAseq analysis of panicles at pre-anthesis developmental stages showed large effects on genes involved in flowering time, pollen viability and reproductive development. The study provides first direct functional information acquired through gene editing of class II TPSs in cereals.

overall_design: Transcriptonal changes were compared between two genotypes: wild type (Wt; Oryza sativa indica cv. IR64) against triple gene edited plants of tps2, tps3 and tps6 genes in the same genetic background (Mt). Young panicle tissues were collected in successive developmental differentiation stages corresponding to: Stage 5 (pollen mother cell formation), Stage 6 (pollen mother cell meiosis), Stage 7 (pollen content filling), and Stage 8 (pollen maturation). After harvesting, the samples were flash-frozen in liquid nitrogen and total RNA was extracted through the TRIzol method for 3 independent biological replicates for each genotype from each developmental stage. Following RNA integrity analysis and quantitation (Bioanalyser; Agilent, USA), 24 cDNA libraries were generated and sequenced on Illumina NovaSeq sequencing platform generating 13-20 million 150 bp paired end reads per sample. The trimmed paired-end reads were mapped to the rice reference genome (Oryza sativa IR64) using the STAR aligner. Gene or transcript abundance was quantified using HTseq count with the High Confidence Oryza sativa IR64 annotation. The raw mapped reads were counted and converted to TPM's (transcripts per million). The raw data (.fastq) and TPM values for all expressed genes are included in this submission.

first: Matthew

last: Paul

first: Swati

last: Puranik


title: Sex-specific disruption of VTA transcriptome at acute vs. extended morphine abstinence timepoints

city: Philadelphia

first: Dana

last: Zeid

address: 1701 North 13th St

institute: Temple University

summary: Incubation of craving is a phenomenon characterized by the progressive augmentation of drug craving over a period of extended abstinence. Gene expression analyses can be leveraged to define transcriptomic changes associated with neural adaptions occurring during abstinence, informing understanding of mechanisms underlying craving and relapse. Previously, we identified differential disruptions to the nucleus accumbens transcriptome between acute and extended morphine abstinence timepoints in a rat model. Here, we expand this work to further test effects of morphine abstinence on gene expression in the ventral tegmental area (VTA), in both females and males. We additionally compare small RNA expression from plasma exosomes collected from a separate cohort of heroin-exposed males at the same acute and extended abstinence timepoints. Alterations to the VTA transcriptome diverged significantly between abstinence timepoints and sexes; specifically, VTA gene expression was altered at the acute abstinence timepoint in both sexes, but at the extended abstinence timepoint only in females, contrasting our previous findings in NAc. In heroin-abstinent males, exosomal small RNA was also altered exclusively during acute abstinence. This research expands understanding of VTA-specific regulation of abstinence and craving, in addition to identifying candidate systemic biomarkers for opioid exposure.

overall_design: RNA-sequencing was performed using RNA extracted from ventral tegmental area (brain tissue). Samples were collected from three experimental groups: 1) Saline controls = collected 1 day post completion of saline intravenous self-administration; 2) Day 1 MOR ABS = collected at the 24 hour (Day 1) morphine abstinence timepoint; 3) Day 30 MOR ABS = collected at the 30 day morphine abstinence timepoint. Samples from males and females were included (see "title" or "Sex" for sex, in Sample record "Characteristics" field). RNA expression was compared between sexes and morphine abstinence timepoints.

first: Joanna

last: Perez

first: Hannah

last: Mayberry

first: Mathieu

middle: E

last: Wimmer


title: Oxygen-dependent transcriptional landscape of equine skeletal muscle derived cells.

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

institute: University of Agriculture in Krakow

summary: Growing interest in equine regenerative biology and oxygen-dependent muscle physiology has highlighted the need for reliable in vitro models that accurately reflect the behaviour of equine skeletal muscle cells. In this study, we established an equine skeletal muscle cell line derived from post-mortem tissue. We confirmed its myogenic identity using qPCR analysis of key myogenic regulators, including MYOD1, MYF5, MYOG, and PAX7. This cell system was then used to characterise transcriptional responses to differential oxygen conditions via whole-transcriptome profiling using next-generation sequencing (NGS). By exposing cultures to normoxia and controlled hypoxia (1% and 3% O₂) for defined time periods, we aimed to investigate how oxygen availability shapes the transcriptional landscape of equine skeletal muscle cells and to provide a robust platform for future studies on muscle adaptation, metabolism, and environmental stress responses.

overall_design: Equine skeletal muscle cells were isolated from post-mortem tissue obtained from a 10-month-old preterm foal. Muscle tissue was collected aseptically from the gluteus medius region, transported to the laboratory at 4 °C, and processed within 4 hours. After removal of connective tissue and fat, samples were minced, enzymatically digested with 0.1% pronase, and mechanically dissociated. The resulting cell suspension was filtered, centrifuged, and pre-plated to reduce fibroblast contamination. Myoblast-enriched cultures were maintained in DMEM GlutaMax supplemented with FBS, horse serum, and antibiotics, with subsequent passages performed once appropriate confluence was reached. For the oxygen-dependent experimental setup, approximately 2 × 10⁵ cells were seeded in gelatin-coated flasks and allowed to equilibrate overnight under standard conditions (37 °C, 5% CO₂, atmospheric O₂). The following day, cultures were assigned to normoxic or hypoxic environments. Hypoxic conditions (1% or 3% O₂) were achieved using a HypoxyLab workstation with precise oxygen control, while normoxic cultures remained in standard incubators (~21% O₂). Cells were exposed to differential oxygen tensions for either 48 or 72 hours. Experimental groups included prolonged normoxia (21% O₂, 72 h), moderate hypoxia (3% O₂, 72 h), severe hypoxia (1% O₂, 72 h), shorter severe hypoxia (1% O₂, 48 h), and shorter normoxia (21% O₂, 48 h). At the end of each exposure period, cells were harvested for downstream molecular analyses.

first: Monika

last: Stefaniuk-Szmukier

first: Katarzyna

last: Ropka-Molik

first: Anna

last: Steg

first: Magdalena

last: Profaska


title: MYCN drives pediatric glioma transformation from neural progenitors and creates distinct therapeutic vulnerabilities

last: Mack

state: Tennessee

institute: St. Jude Children’s Research Hospital

summary: MYCN functions as a developmental oncogene, but its role in pediatric high-grade gliomas (pHGGs) remains unclear. In co-operation with Trp53 and Pten loss, MYCN initiates tumorigenesis and establishes an origin for MYCN-driven pHGGs. This transformation creates a vulnerability to PI3K and mTOR inhibition. However, prolonged treatment drives adaptive resistance through MYCN protein rebound, mediated by the attenuation of IGFBP5 and the induction of insulin-like growth factor 2. Although insulin pathway feedback has been implicated in resistance to PI3K targeted therapies, MYCN emerges as the central node of this adaptive program. Resistance can be overcame by sustained MYCN suppression using PI3K and mTOR inhibitors, combined with insulin-like growth factor 1 receptor and insulin receptor inhibitors or dietary intervention. A degradation-resistant MYCN isoform abolishes this response, establishing MYCN as both an initiating oncogene and a resistance driver and revealing a mechanistically defined therapeutic vulnerability.

overall_design: MYCN and H3K27ac ChIPseq in P53/PTEN KD cells and MYCN+ P53/PTEN KD cells

first: Srinidhi

last: Varadharajan


title: Plasma small RNA sequencing during obesity-induced leptin resistance in sheep

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA sequencing of plasma samples collected from Polish Longwool ewes during high-fat diet-induced obesity and leptin resistance. Six ovariectomized ewes received a high-fat diet (OBESE group) and six received a standard diet (CTRL group). Plasma samples were collected at three timepoints: week 7 (T1), week 10 (T2) and week 14 (T3) of the dietary intervention. Libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN) and sequenced on the AVITI platform (Element Biosciences) using 1x76 single-end reads. This study was supported by the National Science Center, Poland (Grant no. UMO-2023/51/B/NZ9/00651).

overall_design: miRNA-seq profiling of plasma from 6 CTRL and 6 OBESE Polish Longwool ewes at three timepoints (T1: week 7, T2: week 10, T3: week 14) of high-fat diet-induced obesity protocol

first: Ewa

last: Oclon

last: Szmatola

first: Dorota

last: Zieba


title: Methylobacterium nodulans ORS 2060 gene expression comparison of phosphate-limited methanol growth with lanthanum chloride or oxide.

city: Berkeley

first: Nathan

last: Good

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: UC-Berkeley

summary: The physiological impact of lanthanum solubility on Methylobacterium nodulans ORS 2060 was assessed using RNA-seq transcriptomics. Differential gene expression analysis was applied to samples of M. nodulans ORS2060 grown in phosphate-limited minimal media with methanol where lanthanum was added in the highly soluble chloride or poorly soluble oxide form.

overall_design: RNA-seq transcriptomics comparison of Methylobacterium nodulans ORS 2060 grown in phosphate-limited methanol minimal media with lanthanum chloride or oxide.

first: Trinity

middle: K

last: Reimer

first: Cecilia

last: Martinez-Gomez