title: Enhancer regulation of OSR2 in mandibular incisor agenesis susceptibility [CUT&Tag]

city: Nanjing

first: Liwen

last: Fan

address: Hanzhong Road 140

institute: Nanjing Medical University

summary: Mandibular incisors are the most frequently congenitally absent teeth in Asian populations, affecting mastication, speech, aesthetics, and oral and maxillofacial functions over the long term. However, the genetic etiology of mandibular incisor agenesis (MIA) remains obscure. In this study, we conducted the first genome-wide association study on MIA in a Chinese population and identified an enhancer variant rs71514987 associated with an increased risk of MIA (odds ratio = 2.18, 95% confidence interval = 1.83-2.58, P = 3.62×10-19). Functional characterization indicated that rs71514987 C allele reduced the binding affinity of GATA4 to the OSR2 promoter, leading to increased OSR2 expression via remote regulation. Notably, elevated OSR2 levels promoted cell proliferation but diminished cell differentiation, migration, and apoptosis capabilities in stem cells from human exfoliated eciduous teeth (SHED), as well as abnormal development of pharyngeal teeth in zebrafish models. Mechanistic experiments further revealed that OSR2 bound to the promoter region of CXCR4, promoting its transcription level in the GPCR pathway, thereby influencing odontogenic differentiation during tooth development. Our findings provide novel insights into the molecular etiology of MIA.

overall_design: human exfoliated deciduous teeth (SHED) cells at passage 3 were collected and subjected to CUT&Tag assays using anti-OSR2 antibody (sc-393516X, Santa Cruz). Briefly, cells were incubated with ConA beads, followed by primary antibody, secondary antibody, and pG-Tn5 transposase to tag DNA adjacent to OSR2-bound loci. Tagmentation was performed at 37°C for 1 hour, and the reaction was stopped with EDTA, SDS, and proteinase K. DNA was extracted using phenol-chloroform and ethanol precipitation. A matched IgG control (SHED_IgG) was included as a negative control. Libraries were sequenced on the Illumina NovaSeq 6000 platform (Shanghai Jiayin Biotechnology Ltd). Raw reads were processed with Trimmomatic, and clean reads were aligned to hg19 using BWA-MEM. This experiment aimed to identify genome-wide OSR2 binding sites in SHED cells to understand its transcriptional regulatory mechanisms in mandibular incisor agenesis.

first: Xinyu

last: Zhang

first: Ji

last: Mao

first: Barbara

last: Vona

first: Xinze

last: Xu

first: Mulong

last: Du

first: Lan

last: Ma

first: Yongchu

last: Pan


title: The embryonic origins of site-specific arthritis; Bulk RNA sequencing of CD34+(Pi16+) fibroblasts stimulated with TNF and IL1b.

status: Public on Apr 28 2026

city: Oxford

first: Sarah

last: Davidson

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

type: Expression profiling by high throughput sequencing

summary: The cellular basis for site-specific inflammation remains unclear. In human fingers, proximal interphalangeal (PIP) joints are preferentially affected by inflammatory arthritis, whereas distal interphalangeal (DIP) joints are spared, providing a model to investigate the predilection of inflammation to distinct sites. We combine single-cell RNA sequencing, imaging and X-ray tomography to examine cellular composition, spatial organization and structure of finger joints during foetal development. PIP joints were enriched for Pi16+ fibroblasts, which are located in perivascular regions and at tendon–ligament interfaces. To investigate whether Pi16+ fibroblasts have a specific response to inflammatory cytokines Pi16+ and Pi16- cells were sorted from foetal fingers using the co-expressed marker CD34. Thes cells were cultured in vitro with and without TNF and IL1b and analyzed using bulk RNA sequencing.

overall_design: Embryonic fibroblast populations were isolated from fingers of n=3 donors (16-17pcw) provided by the Joint MRC/Wellcome Trust (grant# MR/X008304/1 and 226202/Z/22/Z) Human Developmental Biology Resource (www.hdbr.org).  Skin was removed, leaving all tendon, ligaments, capsule and synovium intact. DIP and PIP joints were excised, pooled and enzymatically digested for each donor individually. CD45-CD31-PDPN+ fibroblast populations were FACs sorted into Thy1+CD34+ and Thy1+CD34- populations for in vitro culture. For each donor, cells were stimulated +/- TNF and IL1b (in duplicate, total n=6 per condition), for 24h prior to bulk RNA sequencing.

first: Christopher

last: Buckley

first: Mark

last: Coles


title: Transcriptomic comparison of RA vs healthy monocytes undergoing different ex vivo activation conditions

city: Schlieren

first: Bojana

last: Müller-Durovic

state: Zurich

address: Wagistrasse 14

department: Department of Rheumatology

country: Switzerland

institute: University of Zurich

summary: Rheumatoid arthritis (RA) monocytes are primed for inflammatory activation, but their disease-intrinsic molecular features have not been systematically profiled across omics layers. We aimed to define RA-associated alterations in primary human monocytes using an integrated multi-omics approach under controlled differentiation and stimulation conditions. Transcriptomics data showed upregulation of inflammatory and interferon-related programs but downregulation of translation- and mitochondrial matrix-associated gene sets in RA monocytes. Constraint-based metabolic modeling using transcript abundances as proxies for enzyme activities showed widespread downregulation of glycosylation-related metabolic fluxes.

overall_design:
Peripheral blood CD14+ monocytes from RA patients and matched healthy donors were analyzed in the undifferentiated state (M0) or after differentiation into classically activated M(IFNy+LPS) or alternatively activated M(IL-4) macrophages, with or without acute lipopolysaccharide (LPS) stimulation.

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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: Shao Thing

last: Teoh

first: Anastasiya

last: Börsch

last: Müller-Durovic


title: Resilience to Diabetic Retinopathy (RDR) is Associated with a Pre-Retinopathy Transcriptional Program Induced by Diabetes

city: Chicago

first: Andrius

last: Kazlauskas

state: IL

address: 1905 W Taylor St

department: Department of Ophthalmology and Visual Sciences

country: USA

institute: University of Illinois at Chicago

summary: The purpose of this project was to define gene expression changes associated with the acquisition and loss of resilience to diabetic retinopathy (RDR) in individual retinal cell types. Diabetes mellitus (DM) was induced with streptozotocin in male C57Bl6J mice. Single-cell RNA sequencing was performed on retinas from mice that experienced DM for 5 or 15 days, along with retinas from age-matched, non-DM mice. The resulting data sets were analyzed to identify DM-associated differentially expressed genes and pathway enrichments after each duration of DM. We observed that acquisition of RDR, shown to occur after 5 days of DM, was linked to altered expression of genes in a subset of retinal cells, mainly Müller cells. Pathway analysis indicated enhancement of numerous modes of protection, including reinforced neurovascular and structural homeostasis through phagocytosis, integrin signaling, and interferon-mediated defense. After 15 days of DM, when RDR is waning, this pro-protection surge in gene expression subsided. We conclude that a duration of DM that is too short to cause diabetic retinopathy (DR) nonetheless evoked a profound change in the gene expression profile within a subset of retinal cell types.  The nature and timing of this molecular shift indicated that it was not the preamble to DM-related damage that eventually develops. Rather, DM engaged numerous defense programs within Müller cells. These observations provide a molecular foundation for the retina's transient ability to remain healthy in the face of DM.

overall_design: Diabetes was induced in eight-week-old male C57BL/6J mice by five consecutive daily intraperitoneal injections of streptozotocin  prepared in citrate buffer. Age-matched non-diabetic control mice received an equivalent volume of citrate buffer. Retinal tissues were collected at two time points following diabetes induction: 5 days and 15 days. Four experimental groups were analyzed: Control 5D, DM 5D, Control 15D, and DM 15D. For each condition, retinas from three mice were pooled to generate a single-cell suspension (n = 3 pooled per sample). Single-cell RNA sequencing (scRNA-seq) libraries were prepared using the 10× Chromium Single Cell platform (10× Genomics).

first: Janani

last: Rajasekar

first: Maria

last: Paula Zappia

first: Maximilian

middle: A

last: McCann

first: Maxim

middle: V

last: Frolov


title: Disrupted glial-mediated synaptic refinement in Fragile X syndrome

city: New York

first: Lindsey

last: Starr

state: NY

institute: Columbia University

summary: Fragile X syndrome (FXS), the most common inherited cause of intellectual disability and autism, results from the loss of the RNA-binding protein fragile X mental retardation protein (FMRP). FMRP is a translational regulator and is highly expressed in glial cells, where its role in neural circuit development remains poorly defined. Here, it was observed that Fmr1 knockout mice exhibit reduced synapse size and accelerated eye-specific segregation. To examine which cell-types participate in this process, a multi-omic framework was applied to FXS model mice at postnatal day 7, a critical window for synaptic remodeling in the retinogeniculate pathway, an established model system utilized to study synaptic pruning. Single-cell transcriptomics revealed coordinated alterations in microglia, astrocytes, and neurons in genes linked to synaptic pruning. Computational modeling further demonstrated enhanced astrocyte-to-microglia signaling, particularly through Ephrin A (EphA)- and semaphorin-mediated pathways, while lipidomic profiling revealed reductions in EphA-associated lipid species required for lipid raft stability and receptor localization. Consistent with these observations, a glial engulfment assay indicated that FXS microglia and astroglia over-engulf synaptic material in the lateral geniculate nucleus, supporting the transcriptomic profile. Together, these findings identify impaired glial-driven synaptic refinement as an early mechanistic feature of FXS pathogenesis, highlighting the genes involved in this process as potential therapeutic targets during circuit development.

overall_design: This study aimed to characterize transcriptional differences between wild-type (WT) and Fmr1 knockout (KO) mouse brain at single-nucleus resolution.  Single-nucleus RNA sequencing (snRNA-seq) was performed using the inDrops platform on nuclei isolated from mouse brain tissue collected at postnatal day 7. Sixteen libraries were generated, consisting of eight WT and eight KO biological replicates.  Sequencing was performed across four lanes on an Illumina platform, generating paired-end reads. FASTQ files were produced without demultiplexing and therefore contain pooled reads labeled as “Undetermined”. Reads were subsequently assigned to individual libraries based on index sequences specified in a YAML configuration file and processed using the inDrops pipeline.  Gene expression was quantified at the level of individual nuclei, generating gene-by-cell count matrices for each library. These data enable comparative analysis of cell-type-specific transcriptional profiles between WT and Fmr1 KO conditions.

first: Melissa

last: Lee

first: Amy

last: Vo

first: Maia

last: Weisenhaus

first: Lucas

last: Cheadle

first: Archana

last: Yadav

first: Fahad

last: Paryani

first: Michelle

last: Shirasu-Hiza

first: Vilas

last: Menon

first: Carol

last: Mason


title: Type I restriction–modification systems regulate gene expression through DNA topology

city: Leicester

first: Richard

middle: David

last: Haigh

state: Leicestershire

address: Medical Sciences Building, University Road

department: Department of Respiratory Sciences

institute: University of Leicester

summary: RNA-seq analysis of wildtype Escherichia coli MG1655 versus a strain with knockout of the hsdM gene of the Type I restriction enzyme EcoKI

overall_design: Triplicate biological samples of Escherichia coli strain MG1655 and an isogenic hsdM mutant were grown to mid exponetial phase in Luria–Bertani (LB) medium.

first: Yasmeen

last: Althari

middle: D

first: Marco

middle: R

last: Oggioni


title: Uncovering ectopic GC-like niches for tumor reactive lymphocyte priming in lung adenocarcinoma using Stereo-XCR-seq

city: Shenzhen

first: Zhong

last: Liu

address: 9 Yunhua Road, Meisha Street, Yantian District

country: China

institute: BGI

summary: This experiment aims to dissect the spatial immune microenvironment of lung cancer by performing Stereo-XCR-seq on fresh-frozen tumor tissues. First, we conduct rigorous sample quality control, perform serial tissue sectioning, use H&E staining for morphological validation, and capture mRNA in situ on Stereo-seq chips. Subsequently, we enrich TCR and BCR transcripts from the constructed Stereo-seq libraries using our in-house developed sscirPCR strategy, via nested PCR-mediated ligating element addition, splint oligo-induced circularization, and two-round specific PCR amplification, enabling the spatial mapping of lymphocyte clonal dynamics within the tumor tissue to uncover immune evasion mechanisms and inform immunotherapeutic strategies.

overall_design:
Spatial transcriptomics profiling of 10 lung adenocarcinoma (LUAD) patient tissues using Stereo-XCR-seq. Stereo-seq was performed to capture in situ mRNA, followed by TCR/BCR enrichment to profile lymphocyte clonal dynamics within the tumor microenvironment.
***The raw sequencing reads are available in the Genome Sequence Archive (GSA, https://ngdc.cncb.ac.cn/gsa-human) under accession number HRA013757.

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Raw files for human/patient samples are being made available in GSA (https://ngdc.cncb.ac.cn/gsa/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Zhan

last: Xiaojuan

first: Huang

last: Mengye

first: Zhang

last: Yang

first: Liu

last: Zhong

last: Chengwu

first: Guo

last: Yanying

last: Yi

first: Zhou

last: Wenwen

first: Yan

last: Yixin

first: Zeng

last: Hui

first: Dong

last: Yingqi

last: Xuan

first: Chen

last: Xiaoyu

first: Yang

last: Haohang

first: Ma

last: Rong

first: Zhu

last: Fan

first: Zheng

last: Xubin

first: Li

last: Xinxing

first: Hou

last: Sen

first: Gao

last: Zhidong

first: Yin

last: Jinwen

first: Chan

last: Francis Ka-ming

first: Wu

last: Qin

first: Deng

last: Senyi

first: Yao

last: Yin

first: Suo

last: Shengbao

last: Chuanyu

last: Longqi

first: Xu

last: Xun

last: Yong

first: Tao

last: Haoran

first: Ai

last: Xinlei

last: Yuliang

last: Tao

first: Sun

last: Hanyong

last: Young

first: Zuo

last: Li

first: Wang

last: Hua

last: Xin

last: Zhifang

last: Jingying

last: Zexian

first: Feng

last: Yu


title: Spinal signatures of entrenched and treated neuropathic pain [Xenium]

city: University of Sydney

first: Lipin

last: Loo

state: New South Wales

address: CHARLES PERKINS CENTRE D-17,

department: Charles Perkins Centre and School of Life & Environmental Sciences

country: Australia

institute: The University of Sydney

summary: Chronic pain arises from an imbalance between excitation and inhibition. For chronic pain caused by peripheral nerve injury, sensory neuron damage leads to changes in spinal pain transduction, where enhanced excitatory and/or loss of inhibitory pathways can drive pain diseases. At the cellular level, the transcriptional changes occurring in entrenched chronic pain are largely unknown. Here we use single nuclei and spatial transcriptomic approaches to investigate the cellular and molecular causes of entrenched and treated neuropathic pain.  Our data show that nerve injury leads to broad upregulation of spinal synaptic and excitatory pathways in dorsal neuronal and glial populations. We confirm these core populations are conserved in the human spinal cord, and show an effective pain therapy acts by dampening these neuropathic transcriptional programs. Overall, our data provides the first high resolution transcriptional analysis of the neuropathic spinal cord, highlighting known and novel pathways that may help us better manage pain diseases.

overall_design: Xenium imaging of Sham, SNI lumbar spinal cord samples. Sections were prepared on imaging slides at 28 days post SNI before imaging on Xenium.

first: Gregory

middle: G

last: Neely


title: Astrocyte-microglia crosstalk via CSF1 and IFNb promotes central nervous system repair

city: Lexington

first: Meifan

last: Chen

state: Kentucky

address: 741 S. Limestone St, BBSRB B457

department: SCoBIRC

institute: University of Kentucky

summary: Despite accumulating evidence of functional interactions between astrocytes and microglia in central nervous system (CNS) injury and disease, mechanisms coordinating their response to CNS insults remain incompletely understood. We report that injury-reactive astrocytes at the lesion border upregulate colony stimulating factor 1 (CSF1) required for microglial proliferation, wound closure, and motor recovery after focal spinal cord injury. Intriguingly, astrocyte-targeted deletion of CSF1 also reduces cell number of border-forming astrocytes, revealing positive feedback regulation between astrocytes and microglia. We further show that microglia produce interferon ? (IFN?), which reciprocally supports astrocyte survival.  Genetic disruption of interferon signaling in astrocytes in turn impairs astrocytic border formation, coordination with microglia in wound healing, and motor recovery. This work uncovers astrocyte-microglia crosstalk via CSF1 and IFN? that synergizes the acute injury response of these cells for neural repair, providing insights into fundamental biology of astrocyte-microglia communication and its therapeutic potential.

overall_design: Controls without injury (n=3), Controls with SCI 7dpi (n=4), Astro-CSF1-KO without injury (n=3), and Astro-CSF1-KO with SCI 7dpi (n=4). Total RNA isolated from spinal cord tissue centered at lesion center or equivalent spinal cord region from naïve control were used for bulk tissue RNAseq.

first: Tuoxin

last: Cao

first: Matin

last: Hemati-Gourabi

first: Yongliang

last: Liu

first: Anna

middle: E

last: Mills

first: Lauren

last: Baur

first: Ellie

middle: P

last: Rice

first: Theo

last: Klippel

first: Yiwen

last: Yan

first: Xiu

last: Xu

first: William

middle: K

last: Fenske

first: Jean

middle: X

last: Jiang


title: Full length transcriptome sequencing of rat  abdominal aorta primary EC

city: Shanghai

first: Tonglin

last: Pan

address: No. 12, Middle Urumqi Road, Jing'an District

institute: Fudan university affiliated Huashan hospital

summary: MicroRNAs are well established as key regulators of cellular function and viability. A growing body of evidence indicates that multiple miRNAs are involved in the formation and rupture of IAs. MicroRNA-337-3p (miR-337-3p), in particular, has been implicated in the pathogenesis of diverse conditions—including tissue injury, osteoarthritis, and malignancies—by modulating cellular proliferation, fundamental biological processes, and oxidative stress-induced inflammatory responses. The abdominal aorta was excised from rats, with tissue segments everted to reveal the endothelium. Cultured endothelial cells (ECs) were transfected with 100 nM hsa-miR-337-3p inhibitor. RNA sequencing was performed to map the genetic differences lining between the WT and miRNA-337-3p-/- EC.

overall_design: RNA sequencing was performed to map the genetic differences lining between the WT and miRNA-337-3p-/- ECs

first: HongFei

last: Zhang

first: TongLin

first: ZongZe

last: Li

first: MingJian


title: Spinal signatures of entrenched and treated neuropathic pain [Visium]

first: Lipin

last: Loo

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Visium Spatial Sequencing of mouse and human lumbar spinal cord tissue. The data is used to locate neurons from identified in snRNAseq, and compare conservation between mouse and human.

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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: Gregory


title: Liver transcriptomic response to partial hepatectomy in intestinal-specific SIRT1 knockout mice

city: Norwich

first: Naiara

last: Beraza

address: Rosalind Franklin Road, Norwich Research Park

institute: Quadram Institute Biosciences

summary: Liver regeneration following partial hepatectomy (PHx) requires coordinated metabolic and inflammatory responses. Here, we investigated the contribution of intestinal SIRT1 to hepatic transcriptional reprogramming during early regeneration. Intestinal-specific SIRT1 knockout mice (SIRTintKO) and wild-type (WT) littermates were subjected to PHx, and liver tissue was collected at 6 h and 24 h post-surgery. Bulk RNA sequencing was performed to characterize genotype- and time-dependent transcriptional changes. This dataset provides insight into gut–liver axis regulation of early regenerative priming and metabolic adaptation.

overall_design: WT and intestinal-specific SIRT1 knockout (SIRTintKO) mice were subjected to partial hepatectomy. Liver samples were collected at two timepoints: 6 hours and 24 hours post-surgery. Bulk RNA sequencing was performed on liver tissue. The study includes two genotypes (WT and SIRTintKO) and two timepoints (6 h and 24 h), with biological replicates for each condition.


title: Osteopontin links acquired resistance to hypoxia-inducing antiangiogenics with refractoriness to anti-PD-L1 agents in breast cancer

city: Madrid

first: Manuel

last: Moradiellos Corpus

address: Calle Melchor Fernández Almagro 3

department: Human Genetics

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: Resistance to antiangiogenics is a major challenge in cancer therapy. These agents can either normalize or exacerbate tumor vascular abnormality and hypoxia. The mechanisms of resistance remain unclear in the latter setting. By integrating data from mouse models and clinical trials, we show that hypoxia-inducing anti-VEGF therapy upregulates programmed cell death ligand 1 (PD-L1), yet fails to sensitize tumors to PD-L1 blockade. Mechanistically, early hypoxic stress triggers epithelial osteopontin (Spp1) production, which recruits monocytes and skews macrophages toward M2 states, suppressing T-cell cytotoxicity. Pharmacologic Spp1 depletion impedes the development of hypoxia, M2 infiltration, restores T-cell activity and enables synergy between antiangiogenics and anti-PD-L1. Genetic dissection – tumor-epithelial Spp1 knockout grafts and bone-marrow chimeras generated by lethal irradiation and reconstitution with Spp1-/- or wild-type hematopoietic donors – show that myeloid Spp1 contributes only marginally compared with epithelial Spp1. These findings identify Spp1 as a central mediator of resistance to hypoxia-inducing antiangiogenics, contribute to a comprehensive model of antiangiogenic resistance, and support Spp1-targeted strategies to personalize immuno/antiangiogenic therapy according to tumor hypoxia.

first: Jose

middle: L

last: Ruiz-Sepulveda

first: María

middle: J

last: Bueno

first: Silvana

last: Mouron

first: Verónica

last: Jiménez-Renard

last: Muñoz

last: Moradiellos

first: Leonardo

last: Garma

first: Luis

last: García-Jimeno

first: Adam

last: Watson

first: Ghassan

last: Mouneimne

first: Solip

last: Park

first: Rebeca

last: Jimeno

first: Miguel

last: Quintela-Fandino


title: Single-cell transcriptional landscape of muscle-derived stem/progenitor cells reveal hallmarks of aging and rejuvenation

first: Seth

last: Thompson

address: 355 E Erie St

department: Physical Medicine and Rehabilitation

institute: Northwestern University

summary: Muscle-derived stem/progenitor cells (MDSPCs) are an adult stem cell population with demonstrated regenerative and rejuvenative potential distinct from other muscle progenitor cells. However, their molecular identity and developmental status remain poorly defined. Using single-cell transcriptomic and proteomics, we profiled murine MDSPCs comprehensively across age groups. We show that MDSPCs exist along a transcriptional continuum of maturation—ranging from metabolically active, proliferative early-stage cells to late-stage, lineage-committed myogenic populations. While lacking canonical pluripotency markers, early-stage MDSPCs express gene programs associated with embryonic progenitor identity, suggesting a non-canonical, multipotent-like state. These features distinguish them from both satellite cells and committed myoblasts. Aging reshapes this continuum by reducing stemness-associated signatures while enhancing differentiation programs and oxidative stress. The identification of distinct MDSPC states provide critical insights into mechanisms that underly tissue regeneration and aging. These analyses offer a blueprint for development of future regenerative therapies to combat age-related functional decline.

overall_design: Three populations of MDSPCs isolated from young mice and three from old mice were cultured under normal proliferation conditions, then collected from culture flasks and underwent single cell RNA sequencing. Analysis was performed on all cell groups combined, as well as young vs old.

first: Kavitha

last: Mukund

first: Chelsea

last: Rugel

first: Kamil

last: Gebis

first: Richard

last: Lieber

first: Jeffrey

middle: N

last: Savas

first: Shankar

last: Subramanium

first: Mitra

last: Lavasani


title: A high-resolution, sex-stratified atlas of transcriptional and alternative splicing dynamics in the fasting mouse liver.

city: Manchester

first: Jessica

middle: Minnie

last: Treeby

address: Oxford Road

institute: Manchester University

summary: The liver's response to fasting is a fundamental adaptive mechanism, yet its temporal complexity, circadian dimension and sexual dimorphism remain incompletely understood. Here we present a high-resolution transcriptomic atlas of the fasting mouse liver, profiling both male and female C57BL/6 mice every 4 hours across a 36-hour fast initiated at a defined circadian time. Using an integrated framework combining high-resolution time-series analysis with stringent statistical filtering, we identify 2,995 genes organised into eight kinetically distinct clusters that collectively delineate a phased transcriptional transition from acute metabolic remodelling to prolonged nutrient deprivation. Contrary to prior reports, fasting amplifies rather than diminishes circadian transcription, increasing the number of rhythmically expressed genes from 727 to 1,233—indicative of a clock re-gearing rather than clock disruption. Extending our analysis to exon-level quantification reveals that differential exon usage constitutes an independent regulatory layer, targeting processes not captured by transcript abundance alone, including SAM metabolism, ferroptosis and mRNA processing. Circadian rhythmicity in exon usage is demonstrated here for the first time. Sexual dimorphism is pervasive but primarily quantitative, reflecting differences in the magnitude and temporal precision of a conserved programme rather than divergent regulatory logic. This open-access, multi-layered dataset provides a comprehensive resource for the study of nutritional and circadian regulation of liver metabolism.

overall_design: Raw RNA-seq reads from cDNA libraries prepared from liver samples extracted from mice every 4 hours across a 36 hour period. Sampling started at Circadian Time 8 (CT8) and finished at CT44. Mice were fed adlib until CT10. Control mice remained fed ad libitum from CT10 for the duration of the experiment. Fasted mice had food removed at CT10 for the remainder of the experiment.Two male mice and two female mice were used as biological replicates for each treatment group at each time point. Liver from each mouse was dissected for RNAseq analysis.

middle: M

first: Jean-Michel

last: Fustin

first: Benjamin

last: Saer

first: Louise

last: Hunter

first: Shin-Yu

last: Kung


title: Spinal signatures of entrenched and treated neuropathic pain [scRNA-seq]

first: Lipin

last: Loo

overall_design: single nucleus RNAseq of Sham, SNI and SNI+ mouse lumbar spinal cord samples. Nuclei were isolated and sorted via FANS and filtered before running on 10X Genomics Chromium Handler and library preparation for sequencing on Illumina Novaseq 6000

first: Gregory

last: Neely


title: The Gene Regulatory Evolution of the Human Skeleton (human-chimp and human-gorilla hybrid cells)

city: Rehovot

first: Simon

last: Fishilevich

address: 234 Herzl St

country: Israel

institute: Weizmann Institute of Science

summary: This GEO submission accompanies the RNA-seq data of human-chimp and human-gorilla hybrid cells in the study “The Gene Regulatory Evolution of the Human Skeleton”. Changes in gene regulation are key drivers of human evolution. However, which regulatory changes shaped human adaptations, and especially how, remains largely unknown. Skeletal alterations have been particularly central in human evolution, facilitating upright locomotion and large brains, and influencing child- birth and our distinctive faces. Here, we generated human-chimp and human-gorilla hybrid osteochondral progenitor cells to study the cis-regulatory expression changes that distinguish humans from other great apes. We identified 4152 chimpanzee-specific, and 4463 human-specific cis-regulatory expression changes.

sample_organism:
Gorilla gorilla
Pan troglodytes
Homo sapiens

overall_design: RNA sequencing of iPSC-derived limb osteochondral progenitor cells from three replicates of human-chimpanzee hybrids and two replicates of human-gorilla hybrids

first: Yizhi

last: Yan

first: Nadav

last: Mishol

first: Katharina

last: Lange

first: Zicong

last: Zhang

first: Gal

last: Bodek

first: Itamar

last: Nini

first: Noam

last: Priel

first: Omer

last: Ronen

first: Nachshon

last: Egyes

first: Aya

last: Kigel

first: Amit

last: Philosoph

first: Liat

last: Rotenstreich

first: Adi

last: Rozenblatt

first: Lucas

last: Wange

first: Guy

last: Hirsh

first: Sergey

last: Viukov

first: Idan

last: Korenfeld

first: Ariel

last: Afek

first: Yaqub

last: Hanna

first: Assaf

last: Marom

first: Martin

last: Kuhlwilm

first: Tomas

last: Marques-Bonet

first: Fumitaka

last: Inoue

first: David

last: Gokhman


title: Epigenetic and transcriptional alterations in Kmt2c/Kmt2d-deficient gastric cancer [ChIP-Seq]

city: New York City

first: Dan

last: Li

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: KMT2C and KMT2D are two of the most frequently mutated genes in gastric adenocarcinoma, yet their function in cancer initiation remains poorly understood. In this study, we developed mouse models to investigate the molecular mechanism of Kmt2c/d loss in gastric tumorigenesis.

overall_design: Comparision of epigenome and transcriptome in control: TY (Tmprss2CreERT2,loxp-stop-loxp-EYFP), Pten KO: TP (Tmprss2CreERT2,Ptenf/f) and triple KO: TPCD (Tmprss2CreERT2, Ptenf/f, Kmt2cf/f, Kmt2df/f) mouse stomach epithelial cells.

first: Naitao

last: Wang

first: Yu

last: Chen


title: New Insights into Müllerian duct differentiation provided by single cell transcriptomics in the chicken embryo

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

institute: Monash Genomics & Bioinformatics Platform

summary: In vertebrate embryos, Müllerian ducts give rise to the female reproductive tract. Aberrations in duct development cause reproductive disorders, many of which have an unknown etiology. Here, we present a comprehensive analysis of Müllerian duct differentiation using single cell transcriptomics in the chicken embryo, a unique model for duct development. The data reveal greater cellular complexity of Müllerian duct differentiation than previously understood. Duct mesenchyme has two transcriptionally distinct populations, while duct epithelium shows distinct regionalised compartments. Trajectory analysis shows that these populations have different fates. Single cell transcript profiling of the regressing male mesenchyme identifies new genes implicated in duct regression. One of these male-restricted transcripts, DKK4, responds to Anti-Mullerian Hormone induction and can induce duct regression when ectopically expressed in females. Lastly, the right female duct does not regress in the same manner as in males, being transcriptionally distinct. These data provide new insights into Müllerian duct differentiation.

overall_design: Entire Müllerian ducts were dissected, dissociated into single cells, and processed for single-cell RNA sequencing through the 10X Chromium system (10X Genomics). Five samples were processed in triplicate, corresponding to key stages of duct formation and sexual differentiation.

first: Juan Lan

last: Tan

first: Adele

last: Barugahare

first: Andrew Thomas

last: Major

first: Craig Allen

last: Smith


title: PI3K Regulates Wild-type RAS Signaling to Confer Resistance to KRAS Inhibition

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Despite the availability of RAS inhibitors and the dependence of >90% of pancreatic ductal adenocarcinomas (PDAC) on oncogenic KRAS mutations, resistance to KRAS inhibition remains a serious obstacle. We showed here that PI3K plays a major role in this resistance through upstream activation of wild-type RAS signaling – beyond its known KRAS effector function. The combination of proximity labeling, CRISPR screening, live-cell imaging, and functional assays revealed that PI3K orchestrates phosphoinositide-mediated GAB1 recruitment to the plasma membrane, nucleating assembly of RAS signaling complexes that activate MAPK in an EGFR/SHP2/SOS1-dependent manner. Inhibiting PI3K enhanced sensitivity to mutant-specific KRAS inhibitors in PDAC cells, including in cells with clinically identified PIK3CA mutations. These findings refine RAS-PI3K signaling paradigms, reveal that PI3K-driven wild-type RAS activation drives resistance to KRAS inhibition, and illuminate avenues for augmenting KRAS-targeted therapies in PDAC.

overall_design: Genome-wide (Brunello) CRISPR KO screen in 8988T KRAS intact vs. knockout (KO) pooled clones

first: Xiangyu

last: Ge

first: Jaffarguriqbal

last: Singh

first: Wenxue

first: Cassandra

middle: S

last: Markham

first: Christian

middle: F

last: Ruiz

first: Stites

middle: C

last: Edward

first: Moitrayee

last: Bhattacharyya

first: Yansheng

last: Liu


title: The Gene Regulatory Evolution of the Human Skeleton (Massively parallel reporter assay (MPRA))

first: Simon

last: Fishilevich

summary: This GEO submission accompanies the massively parallel reporter assay (MPRA) data in the study “The Gene Regulatory Evolution of the Human Skeleton”. Changes in gene regulation are key drivers of human evolution. However, which regulatory changes shaped human adaptations, and especially how, remains largely unknown. Skeletal alterations have been particularly central in human evolution, facilitating upright locomotion and large brains, and influencing child- birth and our distinctive faces. Here, we employed MPRAs in key skeletal cells - chondrocytes - to uncover the functional role of the 574,290 enhancer and promoter substitutions that distinguish humans from their ape relatives. Using this atlas, we identified 15,077 sequences whose activity has diverged since our split from chimpanzees.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: This submission contains data for 10 MPRA libraries conducted in human fetal chondrocytes. The raw data, and processed oligo-barcode association files are reported for each sub-library. In total, 732,804 sequences (366,402 allelic pairs) were tested. The processed activity data files are combined across all sub-libraries.

first: Yizhi

last: Yan

first: Nadav

last: Mishol

first: Katharina

last: Lange

first: Zicong

last: Zhang

first: Gal

last: Bodek

first: Itamar

last: Nini

first: Noam

last: Priel

first: Omer

last: Ronen

first: Nachshon

last: Egyes

first: Aya

last: Kigel

first: Amit

last: Philosoph

first: Liat

last: Rotenstreich

first: Adi

last: Rozenblatt

first: Lucas

last: Wange

first: Guy

last: Hirsh

first: Sergey

last: Viukov

first: Idan

last: Korenfeld

first: Ariel

last: Afek

first: Yaqub

last: Hanna

first: Assaf

last: Marom

first: Martin

last: Kuhlwilm

first: Tomas

last: Marques-Bonet

first: Fumitaka

last: Inoue

first: David

last: Gokhman


title: A distinct CD38+CD45RA+ population of CD4+, CD8+ and double-negative T cells is controlled by FAS [alps]

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: The identification and characterization of rare immune cell populations in humans can be facilitated by their growth advantage in the context of specific genetic diseases. Here, we use autoimmune-lymphoproliferative syndrome to identify a population of FAS-controlled TCRab+ T cells. They include CD4+, CD8+ and double-negative T cells and can be defined by a CD38+CD45RA+T-BET- expression pattern. These unconventional T cells are present in all healthy individuals, generated before birth, enriched in lymphoid tissue and do not expand during acute viral infection. They are characterized by a unique molecular signature that is unambiguously different from other known T-cell differentiation subsets and independent of CD4 or CD8 expression. Functionally, FAS-controlled T cells represent highly proliferative T cells with IL-10 cytokine bias. Moreover, FCT are as highly glycolytic as EBV-induced effector T cells but their metabolic program is uncoupled from T-bet expression and IFNg production. Mechanistically, regulation of this physiologic population is mediated by FAS and CTLA4 signaling and its survival is enhanced by mTOR and STAT3 signals. Genetic alterations in these pathways result in expansion of FAS-controlled T cells, which can cause significant lymphoproliferative disease.

overall_design: FAS-controlled Double Negative T cells (CD3+TCRab+CD4-CD8-CD38+CD45RA+) of three patients with Autoimmune Lymphoproliferative Syndrome-(with pathogenic FAS variants), CD8 T cells (CD3+CD8+CD28+CD57-) of 3 healthy individuals (peripheral blood buffy coats) and CD8 T-cell (CD3+CD8+CD38+) of three healthy individuals with ongoing, serologically confirmed primary acute EBV infection (two peripheral blood samples and one bone marrow blood sample) were sorted.

first: Maria

last: Maccari

first: Anne

last: Rensing-Ehl

first: Melanie

last: Boerries


title: An Epigenetic Progeria Links Hypermethylation to Age-Related Pathology

city: Cambridge

first: Bertie

last: Gottgens

email: bg200@cam.ac.uk, nkw22@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

summary: Declining tissue function and regenerative capacity underlie many chronic diseases.Experimentally establishing the mechanistic basis for such tissue ageing presents substantial challenges, given decades-long timescales and multifactorial origins. Epigenetic alterations have been proposed to have a key aetiological role, but whether they are correlative or causal remains a key unanswered question, as does their contribution to specific age-related pathologies. Here, we establish a novel epigenetically-driven accelerated ageing syndrome. We demonstrate that DNMT3A gain-of-function mutations in Heyn-Sproul-Jackson syndrome recapitulate age-related gains in DNA methylation, cause multilineage stem cell dysfunction, and phenocopy aspects of ageing in humans and mice. We also show that region-specific DNA hypermethylation at lineage-specific genes can explain reduced stem cell output and lineage skewing. Hence, starting from a Mendelian disorder, we causally implicate DNA methylation-mediated stem cell exhaustion in the aetiology of medically important age-related haematological, bone and metabolic pathologies, that might be targetable by future therapies.

overall_design: This study investigated whether gain-of-function mutations in DNMT3A causally drive accelerated ageing phenotypes through altered DNA methylation. Primary samples from individuals with Heyn-Sproul-Jackson syndrome were compared with age-matched healthy controls, alongside a murine knock-in model harboring the equivalent DNMT3A gain-of-function mutation and wild-type littermates. Genome-wide DNA methylation profiling (platform specified in Sample records) was performed on hematopoietic stem and progenitor cells (and/or relevant tissues), with transcriptomic profiling conducted where applicable. Comparisons included mutant versus control methylation landscapes, overlap between mutation-associated and physiological age-associated methylation signatures, lineage-specific DNA hypermethylation at differentiation genes, and cross-species conservation of epigenetic changes. Biological replicates consisted of independent individuals or animals per genotype. The overall objective was to determine whether DNMT3A gain-of-function mutations recapitulate age-related DNA hypermethylation patterns and mechanistically contribute to stem cell dysfunction and lineage skewing.

first: Tomoya

last: Isobe

first: Berthold

first: Andrew P

last: Jackson


title: Arginine deprivation of ASS1-deficient cancers drives mistranslation and neoepitope production

city: Amsterdam

first: Mrittika

last: Adhikary

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Arginine biosynthesis is frequently suppressed in cancer due to loss of ASS1 expression, rendering cancer cells reliant on extracellular arginine. This feature has propelled the development of systemic arginine depletion strategies, which are clinically safe but have limited clinical benefit. Here, we demonstrate that in conditions of arginine scarcity, cancer cells with low ASS1 expression resort to aberrant mRNA translation in the form of ribosomal frameshifts and amino acid misincorporations. While aberrant proteins originated from most arginine codons, the predominant effect was observed at AGA. This codon preference is caused by a selective decrease in tRNAArg(UCU) levels after arginine deprivation, linked to METTL1-mediated tRNA-modification. Using proteomics and immunopeptidomics, we validated that arginine shortage induces aberrant protein production at the endogenous level. We further demonstrate that such inducible neopeptides are immunogenic, laying the foundation for improved cancer therapy combining systemic arginine depletion strategies with T-cell receptor-based targeting of non-classical neoantigens.

overall_design: RNA sequencing to measure mRNA translation

first: Remco

last: Nagel

first: Adva

last: Kochavi

first: Karine Flem

last: Karlsen

first: Yali

last: Gal-On

last: Klaoudatou

first: Julien

last: Champagne

first: Lorenzo

last: Valcanover

first: Heyilimu

last: Palashati

first: Morten

last: Nielsen

first: Xiaodong

last: Feng

first: Pierre-Rene

last: Körner

first: Lisanne

last: Giebel

first: Weiwen

last: Yang

first: Arno

last: Velds

first: Liesbeth

last: Hoekman

first: Onno

middle: B

last: Bleijerveld

first: Olaf

last: van Tellingen

first: Johanna

last: Olweus

first: Reuven

last: Agami


title: Macrophage EHD1 promotes inflammation and stabilizes sortilin to accelerate atherosclerosis

city: Los Angeles

first: Bishuang

last: Cai

state: CA

address: 675 Charles E. Young Dr South, Rm 1220

department: Medicine

institute: University of California, Los Angeles

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

overall_design: Refer to individual Series


title: Inhibition of METTL3 by STC-15 induces RNA misprocessing that results in dsRNA formation and activates innate immunity [RNA-seq]

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

summary: The RNA methyltransferase METTL3 is responsible for the generation of m6A, the most abundant modification mark on mRNA and long non-coding RNA. Accumulating evidence suggests numerous roles of METTL3 in cancer initiation and progression and highlights the potential for targeting this enzyme in oncology. STC-15 is a potent and selective METTL3 inhibitor and the first RNA modifying enzyme inhibitor to enter human clinical development. It is structurally related to the previously published tool inhibitors STM2457 and STM3675. We previously identified the induction of a cancer cell-intrinsic interferon response following pharmacological inhibition of METTL3, leading to activation of T-cell-mediated anti-tumour response. Here, we profiled m6A levels at nucleotide resolution using GLORI and characterised RNA changes following METTL3 inhibition with STC-15 or STM3675. Following loss of m6A, we uncovered aberrant mRNA transcripts arising from intron retention (IR) and transcriptional run-on (RO) events downstream of m6A-enriched exons in human cancer cells and in tumour samples in vivo. We found that these IR and RO events produce double-stranded RNA and are bound by the cytoplasmic dsRNA sensor MDA5.Using preclinical in vitro and in vivo models, we characterised in detail the anti-tumour immune responses induced by STC-15. Our study reveals how METTL3 inhibition leads to dsRNA accumulation, which triggers a type I interferon response and induces anti-tumour immunity. Together, these findings provide a mechanistic rationale for STC-15 as a novel anti-cancer drug both as monotherapy and in combination with anti-PD1 checkpoint inhibitors.

overall_design: rRNA-depleted total RNA-seq on A549, CAOV3, COV644, EFO21, OE21 and SKOV3 treated with DMSO or 1 uM STM3675 for 24h


title: Highly regional generation and heterogenous differentiation of basal cells in mouse trachea

first: Wendong

last: Weng

address: No.320, Yueyang Rd.

institute: Center for Excellence in Molecular Cell Science

summary: The airway epithelium comprises three major cell types: basal cells, secretory cells, and ciliated cells. Among these, basal cells serve as stem cells to generate other cell types. Airway basal cells have been recognized as functionally heterogeneous, with numerous studies with specific cell markers. The regional heterogeneity of basal cells has yet to be fully addressed, despite there being some in vitro evidence. In this study, we utilized a proliferation tracing system to demonstrate regional heterogeneity in the proliferative capacity and differentiation of airway basal cells. We found that dorsal basal cells possess a significantly higher proliferative capacity compared to their ventral counterparts. Further analysis revealed that the proliferating basal cells primarily constitute a subset previously identified as multipotent basal stem cells, which undergo symmetric division to expand the stem cell pool. Furthermore, we identified that the canonical Wnt signaling pathway plays a crucial role in maintaining the proliferation of these multipotent basal cells. These findings may have important implications for understanding airway repair mechanisms in disease and injury.

overall_design: Mice with genotypes P63-CreER; Ki67-lsl-Dre; Rosa26-rsr-GFP; Ctnnb1-fl/+ (control) and P63-CreER; Ki67-lsl-Dre; Rosa26-rsr-GFP; Ctnnb1-fl/fl (Ctnnb1 knockout) were administered tamoxifen to induce genetic labeling of proliferative basal cells and conditional deletion of Ctnnb1 in all basal cells. Tracheae were harvested 10 days after tamoxifen induction, microdissected into dorsal and ventral regions under a stereomicroscope, enzymatically dissociated into single-cell suspensions, and processed for scRNA-seq.

first: Xiuxiu

last: Liu

first: Zhen

last: He

first: Kuo

first: Maoying

last: Han

first: Bin

last: Zhou


title: Macrophage EHD1 promotes inflammation and stabilizes sortilin to accelerate atherosclerosis [scRNA-Seq]

summary: Macrophages are the key players in the pathogenesis of atherosclerosis. Here we explored the role of the endocytic regulator EHD1 in immune responses in macrophages and determined its contribution to atherosclerosis progression. EHD1 expression profile in mouse and human plaques were determined by single cell-RNA sequencing (sc-RNA-seq) and immunofluorescence staining. Bone marrow transplantation (BMT) by transplanting bone marrow cells from Ehd1−/− or littermate wild-type mice to irradiated Ldlr−/− mice was performed to determine the effect of EHD1 deletion on atherosclerosis progression. In vitro mechanistic studies including inflammation signaling and endocytosis assays were performed in bone marrow-derived macrophages. EHD1 expression in macrophages is enhanced as atherosclerosis progresses in both mice and humans. Sc-RNA seq of aortic CD45+ cells demonstrated that EHD1 deletion attenuates pro-inflammatory responses and cell-cell interactions. Mechanistic studies revealed that EHD1 accelerates the endocytic recycling of TNFR2 and activates NF-kB, leading to increased expression of inflammatory cytokines. Moreover, EHD1 interacts with retromer and stabilizes sortilin, a retrograde cargo of retromer and a risk factor for atherosclerosis. Our study reveals novel roles for EHD1-mediated membrane trafficking in macrophage function and paves the way to innovative therapeutic strategies aiming at addressing dysregulated membrane trafficking in atherosclerosis.

overall_design: Single-cell RNA-seq analysis was performed on CD45⁺ aortic cells from irradiated Ldlr⁻/⁻ mice transplanted with either WT or Ehd1⁻/⁻ bone marrow and fed a high-fat diet for 12 weeks.

first: Xin

last: Huang


title: Epigenetic and transcriptional alterations in Kmt2c/Kmt2d-deficient gastric cancer [RNA-seq]

first: Dan

last: Li

first: Naitao

last: Wang

first: Yu

last: Chen


title: Macrophage EHD1 promotes inflammation and stabilizes sortilin to accelerate atherosclerosis [RNA-Seq]

overall_design: Mouse BMDMs treated with siEhd1 and incubated with lipopolysaccharide (LPS)


title: Comparative single-cell transcriptomic analysis of human primary and stem cell-derived islets under acute hypoxia

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

summary: To understand the divergent responses of different islet sources to the hypoxic stress encountered post-transplantation, we performed a direct, comparative single-cell RNA sequencing analysis of human primary islets and stem cell-derived islets (SC-islets, HUES8 line) over an acute time course (0, 6, 24, and 48 hours) of hypoxic exposure (1% O2). Our data reveal that while both islet types activate conserved core stress pathways, they subsequently execute markedly divergent adaptive strategies. Primary β-cells navigate hypoxia through a profound suppression of their mature identity and a shift towards a quiescent, energy-conserving state. In contrast, SC-β cells mount a highly plastic and metabolically dynamic response that is coupled with significant lineage instability and functional dysregulation. These findings highlight fundamental, source-specific differences in hypoxic adaptation, providing a rich resource for developing tailored strategies to improve islet transplantation success.

overall_design: A direct comparison of human primary islets and stem cell-derived islets (SC-islets) under acute hypoxic conditions (1% O2) over a time course of 0, 6, 24, and 48 hours. Islet responses were profiled using single-cell RNA sequencing to identify cell-type-specific transcriptional programs.

first: Kameron

last: Bradley

first: Matthew

last: Ishahak

middle: R

first: Camryn

last: Moore

first: Marlie

last: Maestas

first: Daniel

middle: A

last: Veronese-Paniagua


title: Mitochondrial toxins cause widespread downregulation of pathways in X-linked dystonia-parkinsonism patient-derived neurons

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

institute: University of Lübeck

summary: The genetic mechanism underlying the neurodegenerative movement disorder X-linked dystonia-parkinsonism (XDP) involves a retrotransposon insertion within the TAF1 gene. TAF1 encodes the TATA-box binding protein-associated factor 1, the largest subunit of the basal transcription factor TFIID, which connects transcription activation to the assembly of the RNA polymerase II preinitiation complex at the core promoter of genes. This study investigated how the TAF1 mutation affects the transcriptomes of XDP patient-derived neurons under basal conditions and in response to mitochondrial toxins.

overall_design: RNA sequencing was perfromed from iPSC lines of patients and controls of Filipino origin.

first: Karen

last: Grütz

first: Hauke

last: Busch

first: Christine

last: Klein

first: Philip

last: Seibler


title: Pax6 deficiency results in expansion of dysfunctional limbal epithelial stem cells

city: Chicago

first: Han

last: Peng

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

summary: we took advantage of PAX6 +/- mice and utilized single cell RNA sequencing to characterize the abnormalities in PAX6 +/- mouse corneas at the single cell level.

overall_design: Methods: We conducted scRNA-seq on ocular anterior segmental tissue from 2  wild-type and 2 Pax6 het mice, using a 10X Gemomics pipeline. Cell populations were distinguished by UMAP embedding. Seurat analysis was conducted to compare gene expression profiles between these groups of mice.

first: Nihal

last: Kaplan

first: Parisa

last: Foroozandeh

first: Tsutomu

last: Kume

first: Robert

last: Lavker


title: Tbx16 and mesogenin 1 promote presomitic mesoderm differentiation by repressing the mesodermal progenitor cell state

first: Miriam

last: Genuth

address: 260 Whitney Ave

department: Molecular Cell and Developmental Biology

summary: During zebrafish embryonic body elongation, differentiation of mesodermal progenitors into presomitic mesoderm requires the transcription factors tbx16 and mesogenin 1. Here, we elucidate how these genes promote differentiation. We use temporally controlled tbx16 and mesogenin 1 overexpression and RNAseq to identify immediate downstream changes in gene expression. Using machine learning and game theory, we integrated differentially expressed genes with wild-type scRNAseq data and identified genes downstream of tbx16 and mesogenin 1 during mesoderm differentiation. This data-driven analysis indicates that mesogenin 1 and tbx16 primarily repress expression of genes as mesodermal progenitors differentiate. Strikingly, the genes that are most important for defining transcriptional cell states during mesoderm differentiation are most strongly repressed by tbx16 and mesogenin 1. Moreover, these downstream effectors are enriched for genes with known roles in mesoderm development and body elongation such as Fgf, Wnt and Bmp pathways and the transcription factors tbxta, eve1, hoxd12a, hoxd13b, lef1, cdx4, tbx16l, ved, vent and vox. Gradients of Fgf and Wnt specify the mesodermal progenitor state in the posterior tailbud and activate many of these transcription factors indicating that tbx16 and mesogenin 1 promote mesoderm differentiation by repressing this progenitor state.

overall_design: RNA-seq profiling of pooled zebrafish tailbuds from wildtype embryos and ones overexpressing tbx16 or mesogenin1

first: Guoyu

last: Zhu

first: Yanrong

last: Xiao

first: Abigail

last: Kindberg

first: Kayleigh

last: Hackett

first: Scott

last: Holley


title: Meningioma cell reprogramming and microenvironment interactions underlie brain invasion

city: San Francisco

first: Ayush

last: Aggarwal

address: 1450 3rd St. Helen Diller Family Cancer Research Building

department: Neurosurgery

institute: University of California San Francisco

summary: Meningiomas brain invasion encumbers resection and increases the risk of tumor recurrence, but the molecular mechanisms underlying meningioma brain invasion are poorly understood. To identify molecular and cellular features of brain-invasive meningiomas, we performed spatial transcriptomic of brain-invasive meningiomas. Our results reveal that meningioma brain invasion is defined by molecular remodeling of tumor cells and functional interactions within the tumor microenvironment.

overall_design: Two brain invasive meningioma tumors were analyzed using spatial transcriptomics focusing on regions showing brain invasion

first: Youngblood

last: Mark W

first: Aggarwal

last: Ayush

first: Raleigh

last: David


title: Inhibition of oogenic JNK prevents primary ovarian insufficiency and infertility induced by DNA-damaging anti-cancer agents

city: Pitscataway

first: Shuo

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

summary: Primary ovarian insufficiency (POI) and related infertility, early menopause, and endocrine disorders are major side effects in young female cancer patients undergoing cancer treatment. Current strategies preserving ovarian functions and fertility can be suboptimal due to concerns of feasibility, efficacy, or safety. Herein, we identify c-Jun N-terminal kinase (JNK) as a pivotal factor regulating the DNA damage response (DDR) signaling in oocytes of primordial follicles in response to DNA-damaging chemotherapy. Using pharmacological inhibition of JNK and a mouse model with oocyte-specific deletion of JNK, together with bioinformatic, molecular, and computational approaches, we show that inhibition of oogenic JNK prevents chemotherapy-induced oocyte apoptosis and POI as well as preserve long-term reproductive cycles and fertility. Mechanistically, JNK is activated upon chemotherapy-induced DNA damage in oocytes of primordial follicles, which further activates the transcription factor TAp63α and triggers oocyte apoptosis. we further used a breast cancer mouse model to demonstrate that JNK inhibition preserves the ovarian reserve without interfering with the anti-cancer efficacy of chemotherapy. Together, our research establishes JNK as a crucial determinant of oocyte apoptosis and POI following DNA-damaging cancer therapy, highlighting JNK as a promising target for developing ovarian protectant and preserving the ovarian reserve, fertility, and ovarian endocrine functions in young female cancer patients.

overall_design:
SMART-Seq2 profiling of single oocyte and single granulosa cell from PD5 WT CD-1 mouse ovary at 6 hours post-treatment of solvent (Control) or 10 mg/kb Doxorubicin via i.p..

***************************************************************
GSM9386670: no raw data due to data lost
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first: Wenlong

last: Zhao

first: Jiyang

last: Zhang

first: Yingnan

last: Bo

first: Yingzheng

last: Wang

first: Yunman

last: Song

first: Qiang

first: So-Youn

last: Kim


title: Fucosyltransferase 4-derived Peptide Bioconjugates on Carbon Nanotubes Enhance Antitumor Immunity in an Ovarian Cancer Mouse Model

city: Mexico city

first: José

middle: Jesús

last: Guzmán-Mendoza

address: Av. Instituto Politecnico Nacional 2508,

department: Infectómica y Patogénesis Molecular

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados

summary: This study explored the potential of carbon nanotubes (CNTs) bioconjugated with antigenic epitopes from fucosyltransferase 4 (FUT4) to serve as adjuvants and carriers in ovarian cancer immunotherapy.  We confirmed FUT4 overexpression via flow cytometry and confocal microscopy in an immunocompetent ovarian cancer model in which the ID8-Def29/Vegf-a cell line (ID8DVLuc) was inoculated into C57BL6 mice. Mice were immunized with nonconjugated peptide (PEP37), PEP37 bioconjugated CNTs (f-CNTs), or f-CNTs plus adjuvant, and nonimmunized mice were used as controls. Tumor development, the spleen, and ascitic fluid immune populations, the antibody response, and survival rates were evaluated. The results revealed reduced tumor development and ascitic fluid volume in immunized mice, with the best outcomes in the f-CNT group. Immunized mice presented increased infiltration of leukocytes, M1 macrophages, dendritic cells, T lymphocytes, and CD8+ T cells alongside reduced Tregs. Enhanced IgM, IgG1a, and IgG2a responses were observed in the f-CNT groups. Splenocytes from these groups also showed increased antigen-specific proliferation and enhanced cytotoxicity against ID8DVLuc cells mediated by CD8+ T cells. Survival analysis revealed median survival times of 6, 7.5, 11, and 8.5 weeks for the nonimmunized, PEP37, f-CNT, and f-CNT plus adjuvant groups, respectively. In addition, RNA-seq analysis of f-CNT-immunized mice revealed the overexpression of genes related to antigen processing and presentation, CD8+ T-cell activation, and Th1-type-mediated responses (H2-K1, H2-D1, B2m, Trex1 Cd80, Cd8a, Prf1, IL18r1, Ccr7, Stat4, Tbx21), among others.  These findings suggest that f-CNTs enhance the antitumor immune response mediated by M1 macrophage polarization, enhance antigen processing and presentation to CD8+ T cells, and evoke a robust cytotoxic response against ID8DVLuc cells. These findings suggest the potential of this nanocarrier system in ovarian cancer immunotherapy

overall_design: Total RNA from ascites-derived cells from each immunized mouse was extracted via an RNeasy Mini Kit (Cat. 74104, Qiagen). Following the provider's protocol, the DNA was further cleaned with a DNasa I amplification grade Kit (Cat. 18068015, Invitrogen). The total RNA from each mouse (n=4) in each corresponding group (non-immunized, PEP37, and f-CNT) was pooled for further library construction (TruSeq stranded mRNA) via the NovaSeqX platform and RNA sequencing.

first: José Jesús

first: Blanca

last: Sánchez-Ramírez

first: Patricia

last: Talamás-Rohana


title: Unbiased niche labeling maps immune-excluded niche in bone metastasis

city: Houston

first: Xiang

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Microenvironment niches determine cellular fates of metastatic cancer cells. However, robust and unbiased approaches to identify niche components and their molecular profiles are lacking. We established Sortase A-Based Microenvironment Niche Tagging (SAMENT), which selectively labels cells encountered by cancer cells during metastatic colonization. SAMENT was applied to multiple cancer models colonizing the same organ and the same cancer to different organs. Common niche features include macrophage enrichment and T cell depletion. Macrophage niches are phenotypically diverse in different organs. In bone, niche macrophages express estrogen receptor (ER) and exhibit active ER signaling in male and female hosts. Conditional knockout of ER in macrophages significantly retarded bone colonization by allowing T cell infiltration. ER expression was also discovered in human bone metastases of both genders. Collectively, we identified a unique population of ER+ macrophages in metastatic niche and functionally tie ER signaling in macrophages to T cell exclusion during metastatic colonization.

overall_design: For the preparation of mouse tissues from Macrophage-specific Esr1-knockout mice, bone tissues (including bone and tumor) were collected, and live cells were isolated via FACS sorting. The study included both male and female mice, divided into two groups: the control group (LysM-ctrl) and the LysM-cre group (macrophage-specific Esr1 knockout). Each group consisted of three mice, and each mouse had two technical replicates (represented by two barcodes).

first: Xu

last: Zhan

first: Liu

last: Fengshuo

first: Zhang

last: Xiang


title: IL-17A Neutralization Prevents Immune Checkpoint Inhibitor-Associated Myocarditis and Synergistically Enhances Immune Checkpoint Blockade Therapy

first: Yuanyuan

last: Zhu

state: Texas

address: 6565 Fannin St

department: Systems Medicine and Bioengineering

institute: Houston Methodist

summary: Immune checkpoint inhibitor (ICI)-associated myocarditis is a severe and often fatal immune-related adverse event observed in cancer immunotherapy. To investigate its pathogenesis and prevention, we performed spatial transcriptomics on cardiac tissue from mice treated with dual ICIs (anti–PD-1 and anti–CTLA-4) with or without IL-17A neutralizing antibody. Our analysis revealed immune-mediated fibrotic remodeling and distinct spatial immune cell distributions, providing insights into how IL-17A blockade mitigates cardiac toxicity without compromising immune activation.

overall_design: FVB/NJ mice were immunized with MyHCα peptide and treated with either dual ICIs alone or dual ICIs plus IL-17A neutralizing antibody. Heart tissues from both groups were collected and analyzed using 10x Genomics Visium Spatial Transcriptomics. Two samples per group were used to assess spatial immune infiltration, fibrosis, and transcriptional responses.

first: Stephen T. C.

last: Wong

first: Kun

last: Han

first: Yin

last: Zheng

first: Lin


title: Gene expression analysis in hepatocytes in response to hepatocyte-specific Succinate Receptor 1 (SUCNR1) deletion

city: Barcelona

first: Anna

last: Díez-Villanueva

state: Catalonia

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB

summary: The liver plays a crucial role in metabolic adaptations in response to nutrients, a function that is critically dependent on its zonated structure. Succinate, a key intermediate of the tricarboxylic acid cycle, has emerged as a postprandial signaling metabolite that regulates metabolic adaptations to food intake in adipose tissue and pancreatic beta cells through its receptor SUCNR1. Considering that SUCNR1 is also expressed in hepatocytes, we hypothesized a role for the succinate-SUCNR1 axis in liver metabolic homeostasis. To better understand the role of Sucnr1in hepatocytes, we generated a mouse model specifically lacking Sucnr1 in hepatocytes (Hep-Sucnr1 KO mice) and performed an RNA-seq of isolated hepatocytes from controls (Sucnr1 fl/fl mice) and Hep-Sucnr1 KO mice.

overall_design: Comparative gene expression analysis of RNA-seq data for murine primary hepatocytes from Hep-Sucnr1 KO mice (n=3) and Sucnr1 fl/fl mice (n=3).

first: Sonia

last: Fernández-Veledo


title: Folic acid drives metabolic reprogramming to alleviate Toxoplasma gondii antigen-induced vascular injury

city: Nanjing

last: LAB

address: Longmian Street num101

institute: nanjingmedicaluniversity

summary: Infection with parasites is usually accompanied by vascular problems. To investigate the detrimental effects of parasites on blood vessels. We used Toxoplasma gondii (T. gondii), a prevalent intracellular parasite with the potential to induce vascular damage, as an example. In addition to a murine model, a novel human pluripotent stem cell-derived blood vessel organoid (VO) model was emoployed to examined the effect of T. gondii antigens on vessels. We found that T. gondii antigen-induced vascular injury is correlated with inflammation, cellular apoptosis, degradation of extracellular matrix, and disruption of cellular tight junctions. T. gondii antigens also promotes the phenotypic transition of smooth muscle cells (SMCs) from contraction phenotype to secretion phenotype. Interestingly, we found that prophylactic addition of folic acid (FA) appears to counteract all such effects, partially restoring vascular homeostasis. Previous studies on the protective effects of FA on blood vessels remains in its infancy. To reveal the mechanism of FA-mediated vasoprotective effects, we performed transcriptomic and metabolomic analyses. The results show that T. gondii antigen disrupts several vital metabolic pathways crucial for vessel function. Significantly, FA alleviates these metabolic disorders. The protective effect of FA is associated with vascular metabolic reprogramming. This study not only elucidates the mechanisms underlying T. gondii antigen-induced vascular injury, but also reveals a metabolic regulatory role of FA in vascular repair, which has potential value in clinical applications. Additionally, VOs derived from human stem cells are amenable systems for modelling and identifying the regulators and drugs of vascular injury.

overall_design: To investigate the detrimental effects of T. gondii on blood vessels, we employed human pluripotent stem cells to develop self-organizing human VOs.To evaluate the effects of STAg on VOs, we treated VOs with STAg for 96 h (day 11−15).Since 100 nM FA has been shown to restore cell viability of HUVEC , we treated VOs with the same dosage of FA until the end of exposure (from day 10 to day 15). Then STAg was added from day 11 to day 15.

first: Jingfan

last: Qiu

first: Yingyi

last: Quan

first: Jiang

last: Jiang

last: Gao

first: Jing

last: Guo

first: Wei

last: Shi

first: Linfeng

first: Chenlu

last: Shao

first: Yang

last: Yang


title: Autoimmune antibody-induced neuronal hyperactivity triggers pathological Tau in IgLON5 disease

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Anti-IgLON5 disease is an autoimmunity/neurodegeneration overlap disorder in which autoantibodies (AABs) against the neuronal cell surface protein IgLON5 lead to profound brain dysfunction. Brains of patients show Tau pathology, neuroinflammation, and neurodegeneration in multiple brain regions. Through administering patient-derived α-IgLON5 AABs to mice and cultured neurons, we here deciphered the cellular mechanisms of Tau pathology and neurodegeneration in α-IgLON5 disease, highlighting a central role of neuronal activity modulation in the disease pathology. Pathogenic human α-IgLON5 AABs induced acute neuronal hyperactivity, which triggered Tau changes typically found early in Tau-related neurodegenerative diseases like Alzheimer’s disease (AD). α-IgLON5 AAB-induced Tau phosphorylation and somatodendritic resorting selectively occurred in key hippocampal connections, involving dentate gyrus granule cells, mossy fiber projections and commissural fiber tracts. These changes were accompanied by a Tau-specific neuroinflammatory response, involving the complement pathway, microglial MHC class II proteins, T cell receptors, and deregulation of synaptic activity and cell-cell interactions. These findings provide new insights into the origin of autoimmune-triggered α-IgLON5 disease pathology and highlight that, similar to recent reports in AD patients, neuronal hyperactivity may be a disease-overarching driver of Tau pathology.

overall_design: Eight weeks-old male C57Bl/6J wild-type mice were randomized for the different treatment groups by an independent investigator. α-IgLON5 AABs and non-reactive human monoclonal IgG (mCtrl),  and PBS as controls - were delivered continuously into the right lateral ventricle over the course of 14 days, with a flow rate of 0.25 μl/h. Antibody cerebroventricular infusion was performed unilaterally using osmotic pumps (model 1002, Alzet, Cupertino, CA), which were loaded 24 h prior to surgical implantation. For pump implantation, mice were placed in a stereotaxic frame and a cannula was inserted into the right ventricle (Coordinates: 0.2 mm posterior and ± 1.00 mm lateral from bregma, depth 2.2 mm). For RNA analysis, brain tissues were promptly dissected on ice, flash-frozen by placing on dry ice, and stored at -80°C until further use.

first: Bilge

last: Askin

first: Pia

last: Grundschoettel

first: Thomas

last: Ulas

first: Susanne

last: Wegmann


title: Genetic Deletion of the Inflammatory Bowel Disease -Associated Risk Gene Rgs14 Aggravates Experimental Colitis

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: Regulators of G protein signaling (RGS) deactivate G protein-coupled receptors (GPCRs), one of the most prominent receptor families with diverse functions. Of the twenty RGS, Rgs14 single-nucleotide polymorphism is associated with inflammatory bowel disease. This manuscript describes a novel conditional mouse line that allows deletion of Rgs14 in defined cell lines. We show that deletion of Rgs14 in macrophages affects macrophage function and aggravates colitis severity. This novel conditional mouse model will help to investigate further the function of Rgs14 for inflammatory bowel disease and possibly other conditions, such as metabolism, neuroscience, and aging

overall_design: CCR2 and/or CD64 positive lamina propria cells from four tamoxifen-treated Rgs14f/fCx3cr1+ mice and four tamoxifen-treated Rgs14wt littermate mice were sorted out, then those cells were sent to be prepared for library preparation.

first: Jan

last: Niess

first: Mao

last: Chen

first: Florian

last: Geier


title: Host-Directed Antiviral Activity of SB2960 Through Selective Induction and Remodeling of Stress Granules

city: Beijing

first: Songrui

last: Zhao

address: 292 Chengfu Road, Haidian District

institute: Peking University

summary: The increasing prevalence of emerging infectious diseases highlights the urgent need for broad-spectrum antiviral therapeutics. Here, we report the discovery of SB2960, a small molecule that promotes stress granule (SG) formation and exhibits potent antiviral activity across diverse viral species. Here, we applied genetically-encoded photosentisizer miniSOG induced RNA labeling technique CAP-seq to profile RNA components in SG induced by poly(I:C) and drug SB2960 to investigate how SB2960 modulates the RNAs composition of SGs.

overall_design: RNA-seq profiling of SG induced by poly(I:C) and SB2960 drug

first: Wan Gi

last: Byun

first: Sumin

last: Son

first: Meehyun

last: Ko

first: JinAh

last: Lee

first: Ju Hee

last: Kim

first: Kannan

last: Vaithegi

first: Jung Ho

first: Dawon

last: Yi

first: Peng

last: Zou

first: Seungtaek

first: Seung Bum

last: Park


title: Dynamic Reprogramming of Stromal Pdgfra-expressing cells during WNT-Mediated Transformation of the Intestinal Epithelium [Figure 3]

city: Piscataway

first: Michael

last: Verzi

address: 145 Bevier Road,

department: Department of Genetics

summary: Stromal fibroblasts of the mesenchyme regulate critical signaling gradients along the crypt-villus axis1 and provide a niche that supports intestinal stem cells in the intestine. Here we report that Pdgfra-expressing fibroblasts secrete ligands that promote a fetal-like state in the intestinal mucosa during early WNT-mediated tumorigenesis. Using a mouse model of WNT-driven oncogenesis and single-cell RNA sequencing (RNA-seq) of mesenchyme cell populations, we revealed a dynamic reprogramming of Pdgfra+ fibroblasts that facilitates WNT-mediated tissue transformation. Functional assays of potential mediators of cell-to-cell communication between these fibroblasts and the oncogenic epithelium revealed that TGFB signaling is notably induced in Pdgfra+ fibroblasts in the presence of oncogenic epithelium, and TGFB was essential to sustain fetal-like growth of organoids ex vivo. Genetic reduction of Cdx2 in the β-catenin mutant epithelium elevated the fetal-like transcriptome and accelerated WNT-dependent onset of oncogenic transformation of the tissue in vivo. These results demonstrate that Pdgfra+ fibroblasts are activated during WNT-driven oncogenesis to promote a fetal-like state in the epithelium that precedes and facilitates formation of tumors.

overall_design: Duodenum-derived enteroids, control or β-cateninGOF, were co-cultured with 50,000 Pdgfra-lo cells and plated in 20ul Matrigel droplets in culture medium lacking EGF, R-SPONDIN1 and NOGGIN. Culture media was replaced every day for optimal growth conditions.   Pdgfra-lo controls were seeded in Matrigel without organoids. After 7 days of coculture, enteroids and Pdgfra-lo cells were physically and enzymatically separated from Matrigel using Recovery Cell Solution (Corning 354253). Then, Matrigel-free enteroid and Pdgfra-lo cells were dissociated into single cells by incubating with TrypLE (Gibco 12604013) at 37°C. Cells were then washed twice with 1% BSA/PBS and filtered with a 40-μm cell strainer. For cell sorting, cells were incubated in 1% BSA/PBS with 200 U/ml of DNase I. GFP+ cells were sorted with Beckman Coulter Astrios EQ High Speed Cell Sorter according to the described culture conditions. Dead cells were eliminated using 0.5 μg/ml DAPI. Kaluza analysis 2.1.3 software was used for FACS data analysis. For treatments, co-cultures were treated daily with SB525334 (Selleckchem Catalog No. S1476) dissolved in DMSO at a final concentration of 10 µM.

first: Oscar

last: Pellon-Cardenas

first: Prateeksha

last: Rout

first: S

last: Hassan

first: E

last: Fokas

first: Ping

last: He

first: I

last: Patel

first: J

first: O

last: Plotsker

first: A

last: Wu

first: R

last: Kumar

first: M

last: Akther

first: Alexandra

last: Logerfo

first: DE

last: Wagner

first: D

last: Boffelli

first: KD

last: Walton

last: Manieri

first: Kevin

last: Tong

first: Jason

last: Spence

first: NJ

last: Bessman

first: RA

last: Shivdasani

middle: P


title: Dynamic Reprogramming of Stromal Pdgfra-expressing cells during WNT-Mediated Transformation of the Intestinal Epithelium [Figure 2]

first: Michael

last: Verzi

overall_design: To appreciate changes in non-epithelial cells in response to oncogenic activation of the WNT pathway in the epithelium, we conducted scRNA-seq during a very early time course of oncogenic transformation. β-cateninGOF; Villin-CreERT2 mice were used to model β-catenin hyperactivation and led to tissue transformation and exacerbated cell proliferation within 5 days. Tissues were collected from control and tamoxifen-treated mice at different times post-tamoxifen treatment, smooth muscle and epithelial cells were removed, and the remaining stromal cells were dissociated into single cells for scRNA-seq

first: Oscar

last: Pellon-Cardenas

first: Prateeksha

last: Rout

first: S

last: Hassan


title: Nociceptor clock genes control excitability and pain perception in a sex and time-dependent manner

city: Kingston

first: Amanda

last: Zacharias

state: Ontario

address: 99 University Avenue

country: Canada

institute: Queen's University

summary: Nociception is critical for pain perception and survival and begins with the activation of nociceptors, specialized sensory neurons located in the dorsal root ganglia (DRGs). Both sex and circadian rhythms, governed by clock genes, seem to play a significant role in modulating pain perception. However, the potential interaction between circadian rhythms and sex differences in nociception at the peripheral level has been largely overlooked. Here, we first report that DRGs from mice express clock genes in a time- and sex-dependent manner. Using whole-cell recordings in whole-mounted DRGs and optogenetic stimulation of Nav1.8-expressing neurons, we demonstrate that male nociceptors exhibit reduced excitability during the night, while female nociceptor excitability remains stable across time points. Disruption of the core clock gene Bmal1 in Nav1.8-expressing neurons not only diminished nociceptor activity but also abolished the nighttime reduction in heat sensitivity, highlighting a pivotal role for the molecular clock in regulating nociception. Transcriptomic analyses, voltage-clamp recordings, and pharmacological experiments identified the voltage-gated chloride channel ClC-2, controlled by Bmal1, as a key mediator for the observed fluctuations in male nociceptor excitability. This work opens new avenues for chronobiology-inspired strategies in pain management tailored to sex-specific mechanisms.

overall_design: RNA-seq profiling of DRG tissues (L1 - L6) from male C57BL/6J mice. Tissues were collected at zeitgeber time (ZT) 2, 8, 14, and 20.

first: Courtney

last: Bannerman

first: Qingling

last: Duan

first: Nader

last: Ghasemlou


title: Progressive cell fate specification in morphallactic regeneration [scRNA-seq]

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute

summary: Through regeneration variable species replace lost parts of their body. This is achieved either by growth of new structures at the amputation side (epimorphosis), as is the case of axolotl limb regeneration, or through remodeling of the remaining tissue (morphallaxis), as happens in Hydra. Whereas work on epimorphic regeneration support a gradual proximal to distal establishment of cell identities, morphallactic regeneration is believed to rely on initial establishment of boundary conditions that organize the adjustment of the pattern. Performing single cell RNA sequencing during regeneration in Hydra, we revealed the sequence of cells’ transdifferentiation into the missing identities. We provide evidence that morphallaxis proceeds with progressive specification of cell fates, unifying its mechanism with the one found for epimorphosis.

overall_design: To study the molecular processes underpinning Hydra  regeneration we bisected Hydra vulgaris animals and collected samples at different time points after bisection (0, 3, 6, 12, 24, 48, 72 and 96 hours). For each time point, we processed the oral and aboral halves separately. These halves correspond to the regions that will regenerate a new foot or a new head structure, respectively. Using scRNA-seq, we monitored the dynamics of axial identity emergence over time for both regeneration types.

first: Clara

last: Nuninger

first: Sebastien

last: Smallwood

first: Jacqueline

last: Ferralli

first: Charisios

last: Tsiairis


title: Spatial transcriptomic analysis of developing hearts at embryonic and neonatal stages

city: Pittsburgh

first: guang

last: li

state: PA

address: 530 45th St. 8116 Rangos Research Center

institute: university of pittsburgh

summary: Cd1 wildetype mice, Wt1-CreER;Rosa-mTmG mice, and Wt1-CreER;Rosa-DTA mice derived hearts were isolated and directly embeded. The hearts were then sectioned for spatial transcriptomic analysis.

overall_design: Visium from 10X genomics and Slide-seq from Curio-bio were used to profile the genome-wide genes expression of heart sections.

first: Junqi

last: Hu

first: Haoting

last: He

first: Guang

last: Li


title: Arginine deprivation of ASS1-deficient cancers drives mistranslation and neoepitope production [Ribo-Seq]

city: Amsterdam

first: Mrittika

last: Adhikary

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

summary: Arginine biosynthesis is frequently suppressed in cancer due to loss of ASS1 expression, rendering cancer cells reliant on extracellular arginine. This feature has propelled the development of systemic arginine depletion strategies, which are clinically safe but have limited clinical benefit. Here, we demonstrate that in conditions of arginine scarcity, cancer cells with low ASS1 expression resort to aberrant mRNA translation in the form of ribosomal frameshifts and amino acid misincorporations. While aberrant proteins originated from most arginine codons, the predominant effect was observed at AGA. This codon preference is caused by a selective decrease in tRNAArg(UCU) levels after arginine deprivation, linked to METTL1-mediated tRNA-modification. Using proteomics and immunopeptidomics, we validated that arginine shortage induces aberrant protein production at the endogenous level. We further demonstrate that such inducible neopeptides are immunogenic, laying the foundation for improved cancer therapy combining systemic arginine depletion strategies with T-cell receptor-based targeting of non-classical neoantigens.

overall_design: Ribosome profiling to measure mRNA levels and mRNA translation

first: Remco

last: Nagel

first: Adva

last: Kochavi

first: Karine Flem

last: Karlsen

first: Yali

last: Gal-On

first: Maria

last: Klaoudatou

first: Julien

last: Champagne

first: Lorenzo

last: Valcanover

first: Heyilimu

last: Palashati

first: Morten

last: Nielsen

first: Xiaodong

last: Feng

first: Pierre-Rene

last: Körner

first: Lisanne

last: Giebel

first: Weiwen

last: Yang

first: Arno

last: Velds

first: Liesbeth

last: Hoekman

first: Onno

last: Bleijerveld

first: Olaf

last: van Tellingen

first: Johanna

last: Olweus

first: Reuven

last: Agami


title: Resolving human α versus β cell fate allocation for the generation of stem cell-derived islets

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München German Research Center for Environmental Health

summary: Stem cell-derived glucagon-(α) and insulin-producing (β) cells allow to engineer in vitro biomimetics of islet of Langerhans, the micro-organ controlling glycemia; however, a knowledge gap in the mechanism by which human stem cell-derived α and β cells are specified persists. Mouse studies postulated that Aristaless Related homeobox (Arx) and Paired box 4 (Pax4) transcription factors cross-inhibit each other in endocrine progenitors to promote α/β fate allocation, respectively. To test this model in human, we combined lineage labeling with single-cell multiomic analysis in our newly generated ARXCFP/CFP; PAX4mCherry/mCherry knock-in induced pluripotent stem cell reporter line. Lineage tracing, proteomic and gene regulatory network analysis and potency assays revealed a human specific regulation of α/β cell fate allocation. Pharmacological perturbations previously proposed to trigger α-to-β transdifferentiation or identified by our gene regulatory network led to enhanced endocrine induction and directed α/β cell fate. Studying mechanisms of endocrinogenesis and fate segregation enables to engineer islets in vitro, and has broader implications for cell-replacement therapy, disease modelling and drug screening.

overall_design: ARXnCFP/nCFP; PAX4mCherry/mCherry transgenic double-reporter hiPSCs were differentiated into pancreatic endocrine cells and live PAX4-mCherry+, ARX-CFP+/PAX4-mCherry+, and ARX-CFP+ cells were sorted by FACS and analyzed by paired scRNA-seq and scATAC-seq. Transgenic double-reporter hiPSCs were also treated with artemether during stages 4 and 5 of differentiation and live cells were sorted by FACS and analyzed by paired scRNA-seq and scATAC-seq.

first: Melis

last: Akgün Canan

first: Corinna

last: Cozzitorto

first: Michael

last: Sterr

first: Lama

last: Saber

first: Eunike

last: Setyono

first: Alessandro

last: Dema

first: Kei

last: Kozawa

first: Xianming

last: Wang

first: Juliane

last: Merl-Pham

first: Tobias

last: Greisle

first: Ingo

last: Burtscher


title: Progressive cell fate specification in morphallactic regeneration [RNA-seq]

first: Panagiotis

last: Papasaikas

overall_design: To investigate whether tissue differentiation initiates in the regenerative extremities, we bisected Hydras and collected samples from the oral end of regenerating Hydras at one-hour intervals over a 48-hour period, with two replicates per time point, and RNA-sequenced them. We then monitored the dynamic gene expression profile of the regeneration front.

first: Clara

last: Nuninger

first: Sebastien

last: Smallwood

first: Jacqueline

last: Ferralli

first: Charisios

last: Tsiairis


title: Piezo1 mediates the growth of myoblasts in a microgravity environment

city: Wuhan

first: Xiaojian

last: Cao

state: Hubei

address: No.1095 Jiefang Avenue

department: Department of Rehabilination Medicne

institute: Tongji Hospital

summary: Skeleton muscle atrophy during prolonged spaceflight poses a significant health challenge for manned space missions, with its underlying molecular mechanisms remaining incompletely understood, particularly regarding how microgravity affects skeletal muscle through mechanotransduction pathways. This study investigates the pivotal role of mechanosensitive Piezo1 channels in myoblast regeneration. Utilizing a two-dimensional clinostat to simulate microgravity and integrating multi-dimensional approaches including 3D genomics and cellular dynamics analysis, we systematically revealed that microgravity promotes C2C12 myoblast proliferation via Piezo1 activation while inducing 3D chromatin structural remodeling. This work pioneers in elucidating a novel mechanism where aberrant mechanotransduction leads to chromatin conformation dysregulation and subsequent skeleton muscle atrophy, providing theoretical foundations and innovative directions for developing mechanobiology-based countermeasures.

overall_design: RNA-seq profiling of C2C12 myoblats in normal gravity and simulated gravity condition at day3

first: Yizhou

last: Liu

first: Danxia

last: Huang

first: Hongmei

last: Luo

first: Hong

last: Chen


title: Impact of Histone Hypercetylation on genome organization

city: PHILADELPHIA

first: Yu

middle: Sunny

address: 333 Cottman Ave, P3165

department: Cancer Epigenetics Institute

institute: Fox Chase Cancer Center

summary: We systematically examined the impact of HDAC inhibitor on genome organization by Hi-C and ChIP-seq

overall_design: Hi-C and ChIP-seq analysis on HAP1 and derived HAP1 cells and nuclei after TSA treatment for 3hour. Hi-C analysis of HCT-116 RAD21 degron cells, with and without degrading RAD21 (1uM 5'-Ph-IAA, 3 hours) in the presence of DMSO or TSA treatments for 3hours.


title: Dynamic Reprogramming of Stromal Pdgfra-expressing cells during WNT-Mediated Transformation of the Intestinal Epithelium [Figure 5]

first: Michael

last: Verzi

overall_design: To test for the effects of TGFB activity in stroma fibroblasts,  cultures of primary Pdgfra-lo-H2B-GFP cells was treated with exogenous TGFβ-1 . In parallel, Tgfbr2KO cells were used to measure any non-canonical TGFB1-induced activities.

first: Oscar

last: Pellon-Cardenas

first: Prateeksha

last: Rout

first: S

last: Hassan

first: E

last: Fokas

first: Ping

last: He

first: I

last: Patel

first: J

first: O

last: Plotsker

first: A

last: Wu

first: R

last: Kumar

first: M

last: Akther

first: Alexandra

last: Logerfo

first: DE

last: Wagner

first: D

last: Boffelli

first: KD

last: Walton

last: Manieri

first: Kevin

last: Tong

first: Jason

last: Spence

first: NJ

last: Bessman

first: RA

last: Shivdasani


title: Dynamic Reprogramming of Stromal Pdgfra-expressing cells during WNT-Mediated Transformation of the Intestinal Epithelium [D8]

first: Michael

last: Verzi

overall_design: RNA-seq analysis of primary crypt epithelium shows activation of regenerative and fetal-like gene signatures in control vs β-cateninGOF/+ crypt cells at day 8-10 post-induction of a single mutant β-catenin allele

first: Oscar

last: Pellon-Cardenas

first: Prateeksha

last: Rout

first: S

last: Hassan


title: Changes in Muscularis Macrophage Populations in Diabetes

city: Rochester

first: Yuanhang

last: Liu

state: MN

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Macrophages in the muscle layers of the stomach (Muscularis Macrophages - MMs) play a crucial role in regulating gastric motility and immune homeostasis by interacting with cells in their shared environment and play a central role in development of diabetic gastroparesis, a diabetic complication. The lack of knowledge of the subtypes of murine MMs that reside in the stomach limits a comprehensive understanding of their function and their involvement in disease development.

overall_design: In this study, we used single-cell sequencing analysis of CD45+ immune cells and combined it with previously available data to assess the composition and plausible origin of gastric MMs in healthy and diabetic mice.

first: Cipriani

last: Gianluca

first: Ji

last: Sihan

first: Liu

last: Yuanhang

first: Farrugia

last: Gianrico

first: D'Ambrosio

last: Mario


title: Dynamic Reprogramming of Stromal Pdgfra-expressing cells during WNT-Mediated Transformation of the Intestinal Epithelium

institute: Rutgers University

overall_design: RNA-seq analysis of primary crypt epithelium shows activation of regenerative and fetal-like gene signatures in control vs β-cateninGOF/+ crypt cells at day 4 post-induction of a single mutant β-catenin allele

first: E

last: Fokas

first: Ping

last: He

first: I

last: Patel

first: J

first: O

last: Plotsker

first: A

last: Wu

first: R

last: Kumar

first: M

last: Akther

first: Alexandra

last: Logerfo

first: DE

last: Wagner

last: Boffelli


title: Identification of a novel interleukin-9 receptor complex in non-hematopoietic cells

city: Indianapolis

first: Cheuk Lam

last: Cheung

state: Indiana

address: 635 North Barnhill Drive

institute: Indiana University School of Medicine

summary: Beyond cell-cell contact, communication at a distance requires the secretion of cytokines that bind to specific receptors on responsive cells. Interleukin (IL)-9 is a cytokine with pleiotropic effects not only on immune cells that contribute to the progression of tumor and autoimmunity, but also on structural cells including airway and intestinal epithelial cells involved in the development of inflammatory and allergic diseases. Typically, IL-9 receptor (IL-9R) functions as a complex of two subunits – the α-chain (IL-9Rα) and a common γ (γc) chain, that is shared with other cytokine receptors. Although structural cells express IL-9Rα, they lack expression of the γc chain. Thus, it is still unclear how IL-9 transmits a signal through a single IL-9Rα chain in non-hematopoietic cells. This study aimed to explore the possibility that like the type II IL-4Rα, the IL-9Rα chain can pair with the IL-13Rα1 chain, forming a type II IL-9R and can mediate IL-9 responses in epithelial cells. We demonstrated that the IL-9Rα /IL-13Rα1 complex was detected in situ in mouse tracheal epithelial cells and human small airway epithelial cells (SAEC) using proximity ligation assay. STAT3 was activated after exposure to IL-9 in vitro in SAEC when co-cultured with neutralizing antibody targeting γc chain but STAT3 activity returned to its basal level in the presence of anti-IL-13Rα1 antibody, providing further evidence of a type II IL-9R on epithelial cells. Strikingly, asthma-associated genes are upregulated in SAEC upon IL-9 stimulation in RNA-seq analysis. Collectively, our results identify a putative receptor complex - a type II IL-9R composed of IL-9Rα and IL-13Rα1, providing a mechanism for responses of structural cells to IL-9 and a potential role in asthma.

overall_design: human small airway epithelial cells (hSAEC) were stimulated with 40ng/ml recombinant IL-9 for 6 hours vs no treatment control

first: Cherry CL

first: Mark H

last: Kaplan


title: Molecular Drivers of Neuroinflammation in Amyotrophic Lateral Sclerosis

city: Chicago

first: David

last: Gate

state: IL

address: 745 N Fairbanks Ct

department: Neurology

institute: Northwestern University

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder marked by progressive motor neuron (MN) degeneration in the brain and spinal cord. Although neuroinflammation is increasingly recognized as a hallmark of ALS, the precise molecular programs linking immune responses to MN pathology remain poorly defined. Using an integrated approach that combines single-cell and bulk RNA sequencing with spatial proteogenomics, we characterized both shared and distinct immune dynamics in peripheral blood and spinal cord tissues from sporadic ALS patients and patients carrying C9orf72 repeat expansions. Our analysis revealed broad immune remodeling in C9orf72-ALS, ALS subtype-specific and progression-associated differences in monocyte activation, and antigen-experienced CD8 effector memory T cells with clonal features consistent with antigen-driven responses. Spatial mapping revealed complement activation and lipid-programmed myeloid states converging at sites of MN loss and TDP-43 pathology. Together, these findings connect peripheral and central immune alterations to ALS heterogeneity and highlight stratified immunomodulation as a potential therapeutic strategy.

overall_design: 18 Human Control PBMC Samples, 9 ALS fast PBMC samples, 9 ALS slow PBMC samples, and 4 PBMC samples from ALS patients with C9orf72 repeat expansion