title: Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells [RNA-seq]

city: Hongo, Bunkyo-ku

first: Ryuichi

last: Murakami

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

summary: Mechanisms by which diverse transcription factors (TFs), particularly the master regulator Foxp3, shape the heterogeneous transcriptional and epigenetic landscape of regulatory T (Treg) cells remain poorly understood. Here, we discovered that Foxp3 cooperates with BATF to direct cis-regulatory programs and gene expression essential for differentiation of immunosuppressive effector Treg (eTreg) cells. Simultaneous single-cell chromatin accessibility and transcriptome profiling, combined with topic modeling, identified cis-regulatory elements and associated programs jointly regulated by these TFs in eTreg cells. Genome-wide mapping of Treg cell-specific BATF and eTreg cell-specific Foxp3 binding sites revealed their co-binding at some of these cis-elements, synergistically enhancing accessibility and transcription. Furthermore, we provide evidence that Foxp3 interacts with specific TFs to orchestrate diverse cis-regulatory programs among Treg cell differentiation states. Thus, Foxp3 serves as a master, but context-dependent regulator, cooperating with other TFs, including BATF, to shape the heterogeneous cis-regulatory and transcriptional landscape critical for functional Treg cell differentiation.

overall_design: Expression profiling by high throughput sequencing

first: Norihito

last: Hayatsu

first: Zhenan

last: Liu

first: Shohei

last: Hori


title: Relation of small intestine neuroendocrine tumor (SI-NET) properties and epigenetics to normal human enteroendocrine cell differentiation [scATAC-seq]

status: Public on Apr 29 2026

city: Brookline

first: Ramesh

middle: A

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

country: USA

institute: DFCI

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
To investigate the relation of small intestine neuroendocrine tumor (SI-NET) properties and epigenetics to normal human enteroendocrine cell differentiation [scATAC-seq]
We established Neurog3ER inducible cell lines and then performed chromatin analysis at single cell level using data obtained from normal EEC single cell ATAC-seq at various  time points.

first: Pratik

middle: N

last: Singh


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

status: Public on Apr 28 2026

city: Norwich

first: Naiara

last: Beraza

address: Rosalind Franklin Road, Norwich Research Park

country: United Kingdom

institute: Quadram Institute Biosciences

type: Expression profiling by high throughput sequencing

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: 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: 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

first: Wenxue

last: Li

first: Cassandra

middle: S

last: Markham

first: Christian

middle: F

last: Ruiz

first: Stites

middle: C

last: Edward

first: Moitrayee

last: Bhattacharyya

first: Yansheng

middle: D


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

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.

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.

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

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

city: Chicago

first: Seth

middle: David

last: Thompson

state: IL

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

middle: L

last: Rugel

first: Kamil

last: Gebis

first: Richard

last: Lieber

first: Jeffrey

last: Savas

first: Shankar

last: Subramanium

first: Mitra

last: Lavasani


title: Spinal signatures of entrenched and treated neuropathic pain in male mice [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: A progeria syndrome links DNA 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: 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: Macrophage EHD1 promotes inflammation and stabilizes sortilin to accelerate atherosclerosis [scRNA-Seq]

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

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: 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

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

first: Bishuang

last: Cai

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

overall_design: Refer to individual Series


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

country: Spain

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: Divergent cell-type specific hypoxia responses in human stem cell-derived and primary islets

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

summary: The success of stem cell-derived islet (SC-islet) therapy for type 1 diabetes is limited by poor graft survival in the hypoxic post-transplantation microenvironment. While the response of SC-islets to chronic hypoxia has been studied, a direct comparison to primary human islets during the acute hypoxic phase has not been performed. Here, we conduct a comparative single-cell transcriptomic and functional analysis of human SC-islets and primary islets exposed to acute hypoxia (1% O2) over 48 h. Our analysis reveals two divergent response patterns. Primary islets exhibit an energy-conserving response, suppressing β-cell identity genes (PDX1, MAFA) and pro-apoptotic factors like DDIT3, while shifting toward metabolic quiescence. In contrast, the SC-islet response is characterized by lineage instability, a significant metabolic shift toward glycolysis, and the activation of pro-apoptotic pathways. Functionally, these transcriptomic differences result in a loss of glucose-stimulated insulin secretion in both islet types, but through different mechanisms: a suppression of secretion in primary islets versus dysregulated, glucose-unresponsive insulin release in SC-islets. These findings demonstrate that SC-islets are particularly vulnerable under hypoxic stress, exhibiting an unstable, plastic phenotype. This comparative dataset provides a resource for developing source-specific therapeutic interventions to overcome the hypoxic barrier and improve the efficacy of cell replacement therapies.

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: Myc sustains Regional and Sex-biased Organ Zonation in the Drosophila Intestine

status: Public on Apr 30 2026

city: Valencia

first: Santiago

last: Vernia

state: Valencia

address: Calle de Eduardo Primo Yúfera, 3

department: Institute of Biomedicine of Valencia (IBV)

institute: Spanish National Research Council (CSIC)

summary: Organs exhibit distinct transcriptional and metabolic territories; how and why such organ zonation differs between the sexes is unclear. Using adult Drosophila intestines, we combine whole-organ 3D cellular mapping with metabolic profiling to uncover regional differences in enterocyte size and metabolism that vary by sex and genotype. Zonation arises from opposing, region-specific and sex-biased actions of the sex determinant Doublesex (Dsx) and the transcription factor Myc. In enterocytes, male-specific Dsx suppresses Myc, rendering its expression female-biased. Dsx–Myc antagonism enlarges female enterocytes, increasing their ploidy in specific gut regions. It also drives a female-specific lipid profile, marked by sex-biased expression of a cluster of lipases and selective triacylglycerol storage in the anterior midgut. Myc activity in female enterocytes sustains peripheral lipid reserves and fecundity. These findings identify relevant roles for Myc in sex differentiation and the intestine as a key, previously overlooked contributor to sex differences in lipid metabolism.

overall_design: RNA-seq profiling of drosophila melanogaster midgut. 30 midguts were dissected and pooled. Total RNA was extracted from 3-4 independent samples for each sex (virgin males and virgin females) and genotype (Myc RNAi vs. Control)

first: Cristina

last: Galiana

first: Irene

last: Miguel-aliaga


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: Single-phage profiling illuminates viral individuality during cell fate determination

city: Urbana

first: Ido

last: Golding

address: 1110 W Green St.

department: Physics

institute: University of Illinois Urbana-Champaign

summary: The choice between cell death (lysis) and viral dormancy (lysogeny) following bacteriophage infection serves as a founding paradigm for the emergence of cellular heterogeneity in a genetically uniform population. The determination of host fate arises through the stochastic transcription from multiple viral genomes present within each cell, but this activity remains hidden from empirical interrogation, which typically stops at the whole-cell level. Here we use parallel sequential fluorescence in situ hybridization (par-seqFISH), followed by spatial clustering of phage-encoded transcripts within each cell, to profile the transcriptional activity of individual phages during synchronized infection of Escherichia coli (E. coli) by bacteriophage lambda. At the whole-cell level, transcription kinetics capture the developmental choice between lysis and lysogeny, and further demonstrate that viral replication is required for the emergence of diverging fate decisions. Zooming in to the single-phage level illuminates an individuality of viral activity during infection. We find that, while cells pursuing lysogeny display consensus activity of all in-habiting phages, lytic cells may contain phages that exhibit lysogenic activity. These findings support an earlier suggestion that consensus among coinfecting phages is required for cell dormancy. More broadly, our results highlight the need to identify how whole-cell behavior emerges from the activity of physically distinct copies of the same genetic circuit.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Total RNA-seq was performed on E. coli MG1655 wild-type cells infected with phage lambda at high or low multiplicity of infection (MOI), or mock-infected with buffer, at multiple time points post-infection. As controls, libraries were similarly generated from uninfected MG1655 host cells and lambda lysogens. Two biological replicates were done for each condition.

first: Tianyou

last: Yao

first: Yuncong

last: Geng

first: Ehsan

last: Homaee


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

country: Switzerland

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

country: China

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: JinAh

last: Lee

first: Minha

first: Meehyun

last: Ko

first: Kannan

last: Vaithegi

first: Ji Hoon

last: Kwon

first: Jung Ho

last: Jeon

first: Dawon

last: Yi

first: Seungtaek

last: Kim

first: Seung Bum

last: Park

first: Peng

last: Zou


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

city: Kingston

first: Amanda

middle: M

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: 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: A single Citrobacter rodentium infection in Pink1 knockout and wild type mice leads to regional blood-brain-barrier perturbation and glial activation without dopamine neuron axon terminal loss

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

institute: McGill University

summary: A growing body of research supports the hypothesis of links between immune system activation and the development of Parkinson’s disease (PD). A recent study revealed that repeated gastrointestinal infection with Citrobacter rodentium can lead to PD-like motor dysfunction in Pink1 knockout (KO) mice and immune cell entry in the brain. In the objective of better understanding the mechanisms leading to immune attack of the  brain in this model, we evaluated here the hypothesis that such mild infections are sufficient to increase blood brain barrier (BBB) permeability and cause brain inflammation. Pink1 wild-type (WT) and KO mice were infected with Citrobacter rodentium and at day 13 and 26 post infection, we conducted gadolinium-enhanced magnetic resonance imaging (MRI) to identify signs of BBB permeability changes. Quantification of MRI results provided evidence of increased blood-brain barrier permeability in both WT and Pink1 KO at 26 days after the infection in the striatum, dentate gyrus, somatosensory cortex, and thalamus. This was not accompanied by any change in global expression of tight-junction proteins or in markers of the integrity of the dopamine (DA) system in the striatum at both time points. However, chronic microglial activation was detected at day 26 post infection, accompanied by an elevation of the inflammatory mediators eotaxin, IFNγ, CXCL9, IL-17 and MIP-2 in the striatum. Neutrophil infiltration in the brains of infected mice was also noted at day 26 post infection, as revealed by immune cell profiling by flow cytometry. Our results support the hypothesis that even after mild gastro-intestinal infection, increased BBB permeability could contribute to perturbations of brain homeostasis including increased microglial activation and the establishment of a chronic state of brain inflammation. Such perturbations could potentially act as a first hit for subsequent induction of PD pathology in the context of genetic vulnerability.

overall_design: RNA-seq profiling of wild type and Pink1 knock-out mice at day 26 of Citrobacter infection.

first: Sriparna

last: Mukherjee

first: Vladimir

last: Grouza

first: Alex

last: Tchung

first: Amandine

last: Even

first: Moein

last: Yaqubi

first: Marius

last: Tuznik

first: Tyler

last: Canon

first: Sherilyn Junelle

last: Recinto

first: Christina

last: Gavino

first: Marie-Josée

last: Bourque

first: Heidi

last: McBride

first: Michel

last: Desjardins

first: Samantha

last: Gruenheid

first: Jo Anne

first: David A.

last: Rudko

first: Louis-Eric

last: Trudeau


title: Dual-targeting pharmacological UFMylation inhibition reprograms tumor and immune microenvironments to achieve long-term glioblastoma regression

city: Haidian

first: Pengcheng

last: Tan

address: 30 Shuangqing Rd

institute: Tsinghua University

summary: UFMylation, a recently identified ubiquitin-like modification, is essential for cellular stress homeostasis, particularly endoplasmic reticulum (ER) stress regulation. However, its biological and therapeutic exploration has been hindered by the absence of potent small-molecule inhibitors. Here, we report the first discovery of two compounds targeting the UFMylation E3 ligase complex core protein DDRGK1: Osimertinib, originally designed as an EGFR T790M selective inhibitor, acting through a previously unrecognized covalent mechanism, and CP-24, a novel non-covalent inhibitor. Both compounds disrupt the DDRGK1-UFL1 interaction, globally suppress UFMylation, inhibit ER-phagy, and induce ER stress. In glioblastoma (GBM), pharmacological UFMylation inhibition markedly reduces tumor cell viability and sensitizes cells to Temozolomide and radiotherapy. Both compounds also exert strong immunomodulatory activity, promoting macrophage polarization toward an anti-tumor M1 state. In vivo, Osimertinib, benefiting from superior pharmacokinetics, significantly suppresses tumor growth in immunodeficient models and achieves tumor-free outcomes in 65% of immunocompetent mice. These tumor-free mice develop durable anti-GBM immune memory, rapidly clearing tumors upon rechallenge, an outcome unattainable by previous GBM treatments. Mechanistically, Osimertinib enhances anti-tumor immunity by promoting macrophage M1 polarization, T cell expansion, and reducing PD-1 protein levels. Collectively, our study introduces Osimertinib and CP-24 as valuable chemical probes for dissecting UFMylation biology and highlights Osimertinib’s potential for off-label use in EGFR-wildtype GBM. More broadly, we establish UFMylation inhibition as a dual-targeting therapeutic strategy that disrupts tumor survival pathways and reprograms the immune microenvironment, offering a promising avenue for durable GBM control.

overall_design: U87 cells were treated with DMSO, 5 μM Osimertinib, or 40 μM CP-24 24 h before RNA extraction. Total RNA of each sample was extracted using Trizol as described previous. The RNA-seq libraries were constructed using the using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® according to manufacturer’s instructions. Sequencing was performed on Illumina Novaseq Xplus-25B platform.

first: Zhimin

last: Liu

first: Xiaodan

last: Hu

first: Yuxia

last: Zhang

first: Hedi

last: Chen

first: Baoliang

last: Lan

first: Tianhua

last: Ma

first: Sheng

last: Ding


title: Molecular Drivers of Neuroinflammation in Amyotrophic Lateral Sclerosis

city: Chicago

first: David

last: Gate

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


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

middle: S

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: Integrated Phenotypic and Transcriptomic Profiling Positions ONC212 as a Lead Imipridone in Androgen-Independent Prostate Cancer Models

status: Public on Apr 27 2026

city: Beirut

first: AUB

last: Submission

address: Bliss street

country: Lebanon

institute: American University of Beirut

summary: Prostate cancer (PCa) remains lethal at advanced stages, partly due to stem-like subpopulations known as prostate cancer stem cells (PCSCs) that sustain tumor growth and therapeutic resistance. Imipridones are small-molecule anticancer agents, with next-generation derivatives ONC206 and ONC212 designed for enhanced potency and broader activity. This study compared their antitumor efficacy and mechanisms in advanced androgen-independent PCa (AIPC) models, namely DU145 and PC3 cells, using two- and three-dimensional systems encompassing bulk cancer cells and PCSCs. DU145 and PC3 AIPC cells were treated with ONC201 (parent compound), ONC206, or ONC212. Functional assays assessed proliferation, viability, migration, invasion, PCa spheroids formation, cell cycle distribution, and mitochondrial membrane potential and mass, while RNA sequencing defined transcriptional responses. ONC212 was the most potent derivative, inhibiting proliferation and migration and abolishing PCa spheroids at nanomolar doses, whereas ONC201 and ONC206 required higher concentrations. Transcriptomic analyses revealed shared repression of DNA replication and cell-cycle transition programs, with activation of integrated stress and unfolded protein responses (ISR/UPR) and FOXO signaling. ONC206 favored PERK–ATF4-mediated apoptosis with reduced DNA repair, while ONC212 more strongly impacted oxidative phosphorylation-related pathways and mitochondrial RNA processing. Imipridones induced a time-dependent cell-cycle redistribution with increased sub-G1 accumulation and modulated mitochondrial membrane potential and mass in a context-dependent manner. Collectively, these findings position ONC212 as a leading imipridone candidate in AIPC models, combining potent inhibition of tumor and stem-like cell functions with a coherent stress-response signature that supports further translational evaluation.

overall_design: RNA-seq profiling of PC3 and DU145 cell lines after 48 hours treatment with DMSO (Vehicle), ONC206 (0.5 µM), or ONC212 (0.1 µM).

first: Fatima

last: Ghamlouche

first: Amani

last: Yehya

first: Abdallah

last: Kurdi

first: Sana

last: Hachem

first: Varun

middle: V

last: Prabhu

first: Georges

last: Daoud

first: Wassim

last: Abou-Kheir


title: Calling a Truce: Enterococcus faecalis as a mediator between E. coli and C. albicans during polymicrobial CAUTIs

city: South Bend

first: Ellsa

last: Wongso

address: 809 Lindenwood Dr S

institute: University of Notre Dame

summary: Polymicrobial catheter-associated urinary tract infections (CAUTIs) are a severe clinical burden. CAUTIs promotes colonization by different microbes, including E. faecalis, E. coli, and C. albicans. These mixed biofilms can compromise antimicrobial efficacy and promote resistance. Despite their prevalence, the cross-kingdom dynamics driving these infections within the catheterized bladder remain poorly understood. Using established in vitro and in vivo CAUTI models, we elucidate the complex, environment-dependent interactions governing these multispecies biofilms. We demonstrate that E. coli strongly antagonizes C. albicans, by limiting iron uptake, inhibiting filamentation, and inducing cell death. Crucially, we identify E. faecalis as a protective keystone species that mitigates this antagonism. E. faecalis facilitates multispecies coexistence by acting as a spatial bridge on the urothelium, enabling E. coli and C. albicans to co-localize rather than occupy segregated niches. These mechanistic insights into polymicrobial synergy and competition provide a crucial framework for developing targeted therapeutics against recalcitrant CAUTIs.

sample_organism:
Escherichia coli
Enterococcus faecalis
Candida albicans

overall_design: The objective of the RNAseq is to compare transcriptomes of single species biofilm with double species and triple species biofilms. In this project, I used three different species of microorganisms: Enterococcus faecalis, Escherichia coli, and Candida albicans. The cells were grown in urine (in 12 well plates) for 48 hours and treated with TRI-zol. EF stands for E. faecalis single biofilm, EC stands for E. coli single biofilm, CA stands for C. albicans biofilm. EF-EC means it is a combination between E. faecalis and E. coli biofilm (two species), EF-CA is E. faecalis with C. albicans, EC-CA is E. coli and C. albicans, and EF-EC-CA is E. faecalis, E. coli, C. albicans biofilm (triple species biofilm). I want to see how the transcriptomes of each species is different in single biofilm compare to two species and three species biofilm. The numbering is of different replicates.

first: Ana

last: Flores-Mireles


title: U2AF1 mutations rescue deleterious exon skipping induced by KRAS mutations [RNA-Seq]

city: Boston

first: David

last: Walter

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: The mechanisms by which mutations of the splicing factor gene U2AF1 contribute to lung adenocarcinoma pathogenesis are not well understood. Here, we used prime editing to modify the endogenous U2AF1 gene in lung adenocarcinoma cells and assessed the resulting impact on alternative splicing. One specific KRAS mutation, G12S, leads to skipping of KRAS exon 2 and generation of a non-functional KRAS transcript. However, expression of the U2AF1 S34F mutant reverts this exon skipping and restores KRAS function, leading to an enrichment of U2AF1 S34F mutations in KRAS G12S-mutant lung adenocarcinomas. A comprehensive analysis of splicing factor/oncogene mutation co-occurrence in cancer genomes also revealed significant co-enrichment of KRAS Q61R and U2AF1 I24T mutations. Experimentally, KRAS Q61R mutation leads to KRAS exon 3 skipping, which in turn can be rescued by the expression of U2AF1 I24T. Our findings provide evidence that splicing factor mutations can rescue splicing defects caused by oncogenic mutations in a dynamic process of cascading selection.

overall_design: To determine the impact of U2AF1 mutations on splicing of KRAS and other targets, we performed short-read RNA-sequencing of engineered lung adenoarcinoma cell lines with mutations in U2AF1 and KRAS.

first: Katherine

last: Cho

first: Smruthy

last: Sivakumar

first: Daniel

last: Denney

first: Iris

middle: T

last: Lee

first: Anders

last: Dohlman

first: Jakob

last: Heinz

first: Ethan

last: Shurberg

first: Kevin

last: Jiang

first: Akansha

last: Gupta

first: Garrett

last: Frampton

first: Matthew

last: Meyerson


title: RNA-seq analysis of hypothalamus in female mice reveals effects of membrane-initiated estrogen receptor alpha signaling

city: Göteborg

first: Yiwen

address: Vita Stråket 11, Klinfarmlab

country: Sweden

institute: University of Gothenburg

summary: Membrane-initiated estrogen receptor alpha (mERα) signaling plays an important role in bone metabolism, but its contribution in the brain remains unclear. In this study, we performed RNA sequencing of hypothalamic tissue from 16-week-old female mice with selective inactivation of mERα signaling in POMC neurons (POMC-C451Af/f) and wild-type littermate controls. Total RNA was isolated from hypothalamus, and samples were pooled (two animals per sample) resulting in four biological replicates per genotype. Libraries were prepared using poly(A) selection and sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads. Transcript abundance was quantified using Salmon and summarized to gene-level counts. Differential expression analysis was performed using DESeq2. This dataset provides insight into transcriptional changes associated with disrupted mERα signaling in hypothalamic neurons.

overall_design: Hypothalamic RNA was collected from 16-week-old female mice of two genotypes: POMC-C451Af/f (mutant) and wild-type controls. For each genotype, RNA from eight animals was pooled in pairs to generate four biological replicates per group. RNA-seq libraries were prepared using poly(A) enrichment and sequenced on an Illumina NovaSeq 6000 platform (paired-end, 150 bp). Differential gene expression analysis was performed comparing POMC-C451Af/f and wild-type samples.

first: Karin

last: Horkeby

first: Petra

last: Henning

middle: H

last: Nilsson

first: Jianyao

last: Wu

first: Lei

last: Li

first: Sofia

last: Movérare-Skrtic

first: Claes

last: Ohlsson

first: Marie

last: Lagerquist


title: APOE4 Increases Systemic Inflammation and Alters Metabolic and Neuroprotective Pathways following Multiagent Chemotherapy in Older Human APOE Knock-In Mice

city: Washington

first: Christopher

last: Albanese

address: 3800 Reservoir Road NW

institute: Georgetown university

summary: Spatial transcriptomic profiling of APOE4 mice post-chemotherapy compared with APOE3 knock-in mice to assess genotype-specific regional gene expression changes.

overall_design: Mouse brain sections were fixed, sectioned and mounted on positively charged slides with 8μm thickness in the Histology and Tissue Shared Resource

first: Olga

last: Rodriguez

first: Naazneen

last: Khan

first: Adrian

last: Oblak

first: Aisha

last: Naeem

first: Jeff

last: Dage

first: Chris


title: Elongin B orchestrates chromatin and transcriptional programs in H3K27M‑mutant diffuse midline glioma [XIII_ELOBKO_chIP_ELOB_RNAPII]

city: Houston

first: Jamie

middle: N.

last: Anastas

state: TX

address: 1 Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

summary: Recurrent driver mutations in genes encoding histone H3 (H3.3K27M and H3.1K27M) are observed in ~80% of diffuse midline gliomas (DMG), which lead to aberrant gene regulation, yet the specific RNA polymerase 2 (Pol2) regulators inducing aberrant DMG transcription are not fully defined. We identified multiple regulators of Pol2 elongation as DMG genetic dependencies in a chromatin-focused CRISPR screen. Additional studies confirm that knockout (KO) of the Pol2 SIII complex gene Elongin B (ELOB) inhibits DMG cell proliferation in tissue culture and tumor growth in xenograft models. Further genomic analyses reveal that ELOB binding sites are enriched in H3K27M oncohistones and that ELOB knockout alters H3K27me3 and H3K27M incorporation at thousands of genomic regions, suggesting a role for ELOB in maintaining dysfunctional chromatin states in DMG. Correspondingly, ELOB loss disrupts Pol2 transcriptional activity and alters the expression of transcripts involved in metabolism, proliferation, and brain development. These findings suggest that Pol2 elongation factors cooperate with H3K27M oncohistones to maintain the epigenetic and transcriptional landscape driving DMG malignancy.

overall_design: ChIPseq for ELOB or total RNA Polymerase II (RNAPII) was performed on SU-DIPGXIII cells expressing Cas9 and either a cotol or ELOB-targeting sgRNA.

middle: N


title: PDGF signaling regulates the adipocyte-to-fibroblast transition in wound healing

city: Oklahoma City

first: Lorin

middle: E.

last: Olson

state: OK

address: 825 NE 13th St,

department: Cardiovascular Biology

institute: Oklahoma Medical Research Foundation

summary: Adipocytes are a plastic cell type with the ability transition into fibroblast-like cells during tissue repair or physiological remodeling. How such transitions are regulated, and whether they exemplify cell plasticity or merely a transient suppression of adipocyte features, is unclear. Fibroblasts express platelet-derived growth factor receptors (Pdgfra and Pdgfrb) while adipocytes express adiponectin (Adipoq). We developed two-step lineage tracing to label Pdgfra+ and Pdgfrb+ cells originating from Adipoq+ adipocytes. Adipocyte-derived Pdgfr+ cells (ADPCs) are induced adjacent to skin wounds and contribute to the wound fibroblast population. ADPCs lose adipocyte characteristics and acquire fibroblast characteristics including collagen expression, smooth muscle actin expression, and cell proliferation. Active PDGFRalpha signaling in ADPCs increases cell proliferation and improves wound angiogenesis and re-epithelialization, while deletion of Pdgfra has the opposite effect. Wound ADPCs persist as fibroblast-like cells after completion of wound healing, indicating an enduring change rather than a transient downregulation of adipocyte characteristics.

overall_design: Translating RNA profiling by bulk RNA sequencing in NuTRAP mice

first: Sunhye

last: Jeong

first: Hae Ryong

last: Kwon

middle: E


title: Elongin B orchestrates chromatin and transcriptional programs in H3K27M‑mutant diffuse midline glioma [XIII_ELOBKO_RNAseq]

overall_design: Cas9+ BT245 or SU-DIPGXIII cells were transduced with control or ELOB-targeting sgRNAs and selected with 250 ug/mL hygromycin 48 hours later. Equal live cell numbers were collected for RNAseq analysis at day 14 following the start of hygromycin selection and processed for bulk RNAseq of polyA transcripts.

first: Adam

last: Kebede


title: A progeria syndrome links DNA hypermethylation to age-related pathology [human]

city: Edinburgh

first: Dan

last: Sarni

address: Crewe Road

institute: University of Edinburgh

type: Methylation profiling by genome tiling array

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: Bisulphite converted DNA from whole blood samples from 7 HESJAS patients and 9 healthy controls were hybridised to the Illumina Infiniun MethylationEPIC v.1.0 BeadChip following manufacture's protocols. SNPs removed from idat and processed files to anonymise patients and healthy controls.

first: Duncan

last: Sproul

first: Andrew

middle: P

last: Jackson


title: Tumor-intrinsic expression of signal regulatory protein α (SIRPα) contributes to the suppression of anti-tumor immune responses [RNA_CD172KO]

city: NEW YORK

first: LEVI

last: MANGARIN

state: NY

address: 413 E 69TH STREET

department: MEYER CANCER CENTER

institute: WEILL CORNELL MEDICINE

summary: Signal regulatory protein α (SIRPα) is a well-characterized inhibitory receptor expressed on myeloid immune cells. We and others have recently discovered that human and mouse melanoma cells express high levels of SIRPα. However, whether and how melanoma-intrinsic SIRPα contributes to tumor progression and anti-tumor immunity remains underexplored. Here, we identify a novel role of tumor-intrinsic SIRPα in suppressing anti-tumor immune recruitment and activation. Genetic deletion of SIRPα in melanoma cells enhanced tumor control and increased infiltration of immune cells into the tumor. Transcriptomic analysis revealed that loss of melanoma cell-intrinsic SIRPα leads to upregulation of C-X-C motif chemokine 10 (CXCL10) expression in both human and mouse melanoma cells. Notably, knockdown of Cxcl10 in SIRPα-deficient melanoma cells partially rescued tumor growth and reduced CD8+ T cell infiltration, recapitulating the phenotype observed in SIRPα-expressing tumors. These findings indicate that tumor cell-intrinsic SIRPα suppresses anti-tumor immunity by inhibiting Cxcl10 expression, thereby compromising T cell recruitment to the tumor sites. Thus, our work uncovers a previously unrecognized mechanism by which melanoma cell-intrinsic SIRPα suppresses anti-tumor immunity and highlights the therapeutic potential of silencing SIRPα to enhance anti-tumor immune cell infiltration and promote T cell-mediated tumor control. We envision that SIRPα silencing as a therapeutic strategy that could be applied to other cancer types that express SIRPα.

overall_design: We performed bulk RNA-seq analysis using in vitro cultured B16-F10 melanoma cells that were either Sirpa-wild type (WT) or Sirpa-knockout (KO) to assess steady state gene express patterns among Sirpa-WT and KO murine B16 melanoma tumor cell lines. We also performed scRNA-seq analysis of live-sorted CD45+ cells from tumor-draining lymph nodes and tumors from wild-type C57BL6/j mice that were implanted with Sirpa-WT or Sirpa-KO B16 tumors. The experimental design of these in vivo experiments was to understand the impact of tumor-intrinsic Sirpa expression on immune modulation.

first: Chien-Huan

last: Weng

first: Levi

last: Mangarin


first: David

last: Gate

overall_design: 18 sections of cervical spinal cords from 9 controls, 4 sporadic cases and 5 C9orf72 cases.

first: Zhang

last: Ziyang

first: Gate

last: David


title: Progeria syndrome links DNA hypermethylation to age-related pathology

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

overall_design: Refer to individual Series


title: Thrombospondin-1:CD47 signaling contributes to the development of T cell exhaustion in cancer [scRNA_CD172KO]

summary: T cell exhaustion, a hyporesponsive state of antigen-specific CD8+ T cells exhibiting elevated expression of multiple inhibitory surface receptors, is a major obstacle for the treatment of cancer. Current immune checkpoint blockade (ICB) therapies aimed at reinvigorating exhausted CD8+ T cells have demonstrated clinical effectiveness. However, not all cancer patients achieve long-term disease control due, at least in part, to the refractory nature of terminally exhausted CD8+ T cells to be functionally reinvigorated. Besides persistent antigen stimulation, the environmental sources and mechanisms that lead to CD8+ T cell exhaustion in cancer remain to be thoroughly characterized. Here, we show that the expression of CD47 [a.k.a. integrin-associated protein (IAP) and ‘‘don’t eat me’’ signal is upregulated in tumour-associated, exhausted CD8+ T cell compartments in both human and murine tumours. Our findings reveal a novel role of the extracellular matrix protein thrombospondin-1 (TSP-1) and CD47 in promoting T cell exhaustion. Engagement of TSP-1 with CD47 drives the upregulation of TOX and inhibitory immune checkpoint molecules and compromises the effector function of CD8+ T cells during tumour progression. Mechanistically, the interaction of TSP-1 with CD47 on CD+ T cells activates the calcineurin-NFAT signaling, thereby promoting TOX expression and the T cell exhaustion program in cancer.

overall_design: For the analysis of scRNA-seq of tumor-associated T cells of interests, we performed adoptive transfer of naïve-sorted CD8+ T cells from Pmel-1 CD47+/+ and Pmel-1 CD47+/- mice and combined them in 50% to 50% for adoptive transfer into B16 melanoma implanted mice. After 14 days of transfer, tumors from each mouse were dissected to get all the tumor-associated T cells for sorting. We then sorted live, CD8+ T cells that were transferred to perform scRNA-seq analysis separately.


title: Negative control of Candida albicans biofilm formation by combined action of white-opaque regulator Wor2 and biofilm regulator Bcr1

city: Athens

first: Katharina

last: Goerlich

state: GA

address: 120E Green St

department: Microbiology

institute: University of Georgia

summary: Biofilm formation is vital for survival and pathogenicity of the fungus Candida albicans.  Expression of biofilm-promoting genes is coordinated by a transcription factor network that governs the yeast-filament transition and other processes.  A second cell type transition, the white-opaque transition, that is coordinated by its own transcription factor network.  Initial studies suggested that the two transcriptional networks have a mutually exclusive relationship, driven in part by reciprocal repression of biofilm regulator Efg1 and white/opaque regulator Wor1.  However, recent studies have shown that biofilm regulators and white/opaque regulators can promote one another’s function in many situations.  Here we test the function of white/opaque regulator Wor2 in biofilm formation.  We find that Wor2 has a functional relationship with biofilm regulator Bcr1.  We characterized the phenotype of bcr1Δ/Δ wor2Δ/Δ mutants in five strain backgrounds, and conducted RNA-sequencing (RNA-seq) analysis in the SC5314 reference strain background.  The combined Bcr1-Wor2 impact is unexpected: although Bcr1 is known as a positive regulator of biofilm formation and biofilm-related genes, the bcr1Δ/Δ wor2Δ/Δ mutants have increased biofilm or filamentation capacity, depending on the strain, and increased expression of biofilm-related genes.  Those properties suggest that Wor2 and Bcr1 function together as negative regulators of biofilm formation.  Our findings argue that Bcr1 can act as both a positive and negative regulator of downstream effector genes in the biofilm network and establish a new connection between the biofilm and white-opaque regulatory networks.

overall_design: RNA-seq profiling of WT (SC5314 A22) C. albicans cells and their mutant derivatives (wor2△/△, bcr1△/△, and wor2△/△bcr1△/△). Cells were grown for 4h at 37C in YPD.

first: Aaron

last: Mitchell


title: Rpd3L regulates Transcription-Replication Conflict via H3K4 Methylation-Dependent and Independent Chromatin Mechanisms

city: Yilan City

first: Shin Yen

last: Chong

state: Yilan County

address: No.1, Shennong Rd.,

department: Department of Food Science

country: Taiwan

institute: National Ilan University

summary: Faithful genome duplication requires coordination between transcription and replication. Disruption of this coordination causes transcription-replication conflicts (TRCs), leading to replication stress and genome instability. How chromatin regulators modulate these processes remains unclear. Here, we show that the Rpd3L histone deacetylase complex dynamically modulates chromatin state to control replication fork progression and buffer TRCs in Saccharomyces cerevisiae. Rpd3L is targeted through both histone H3 lysine 4 methylation-dependent recruitment and methylation-independent mechanisms engaged under replication stress. Loss of H3K4 methylation or Rpd3L function promotes histone acetylation, accelerates fork progression through transcribed regions, and increases transcription-associated genome instability. Balanced acetylation at multiple histone lysines is required to stabilize replication forks under stress. While histone deacetylase complexes have been implicated in repairing damaged forks, our findings reveal that Rpd3L acts preemptively to modulate chromatin state and replication dynamics during TRCs, defining a chromatin-based mechanism that safeguards genome stability.

overall_design: ChIP H3K9/14, K18Ac and Pho23-Myc in indicated strains under HU induced replication stress

first: Ya-Ling

last: Chen

first: Yueh-Tzu

last: Hsu

first: Chia-Ling

first: Tsai-Ming

last: Lu

first: Yi-Chen

last: Lo

first: Cheng-Fu

last: Kao


title: Age- and Tissue-dependent Diversity of Human Plasmacytoid Dendritic Cells Uncovers a Cycling Subset Dominant in Early Life and Cancer

city: Saint Louis

first: Shitong

last: Wu

address: 660 S Euclid Avenue

institute: Washington University in St. Louis

summary: Plasmacytoid dendritic cells (pDCs) are innate sentinels that produce type I interferons (IFN-I) during infection. Here, we asked how developmental stage and tissue context shape human pDC transcriptional states. Single-cell RNA sequencing of pDCs from blood, thymus, lymph nodes, and tonsils across fetal, infant, and pediatric stages revealed tissue-enriched programs, including IFN-I-imprinted pDCs in the thymus, NFκB-imprinted pDCs in tonsils, and resting pDCs in blood and lymph nodes. Across tissues, we identified a pDC subset characterized by prostaglandin D2 production and dopamine responsiveness, indicating a potential neuromodulatory axis. Cycling pDCs were abundant in fetal and infant lymphoid tissues and declined with age, while remaining enriched in bone marrow (BM) throughout life. Blastic pDC neoplasm associated with enrichment of cycling, mutation-bearing pDCs in the BM, suggesting that this niche serves as a reservoir for malignant pDCs. Thus, early in life, various lymphoid tissues can generate pDCs. This tissue-specific hematopoiesis may result in distinct cellular and functional outputs.

overall_design: Dendritic cells were isolated from the skin, skin-draining lymph nodes (sLN), mesenteric lymph nodes (mLN), spleen, thymus, and lung of three C57BL/6 mice. Tissues were processed into single-cell suspensions and enriched for CD11c⁺ cells. cDC1 (CD19⁻ CD3⁻ Bst2⁻ SiglecH⁻ CD11c⁺ MHC-II⁺ XCR1⁺ CD11b⁻), cDC2 (CD19⁻ CD3⁻ Bst2⁻ SiglecH⁻ CD11c⁺ MHC-II⁺ XCR1⁻ CD11b⁺), and pDC (CD19⁻ CD3⁻ Bst2⁺ SiglecH⁺) subsets were sort-purified from all tissues except the skin (pDCs were not sorted from skin due to their absence at steady state). Prior to sorting, each tissue suspension was labeled with a unique TotalSeq-A Hashtag antibody (HTO). For Sample 1, mouse 1 was labeled with HTO-1 (Skin), HTO-4 (sLN), and HTO-7 (mLN); mouse 2 with HTO-2 (Skin), HTO-5 (sLN), and HTO-8 (mLN); and mouse 3 with HTO-3 (Skin), HTO-6 (sLN), and HTO-9 (mLN). For Sample 2, the same mouse-specific HTO assignments were used, such that spleen samples were labeled with HTO-1, HTO-2, and HTO-3, thymus with HTO-4, HTO-8, and HTO-9, and lung with HTO-5, HTO-6, and HTO-7 across the three mice. Following sort-purification, cells from each tissue were pooled per sample and resuspended in PBS containing 0.04% BSA at approximately 1,000 cells/μL, and subsequently loaded into a 10x Genomics Chromium Single Cell Controller at the McDonnell Genome Institute (Washington University in St. Louis).  Single-cell libraries were prepared using the Chromium Next GEM Single Cell 3′ Kit v3.1, Chromium Next GEM Chip G Single Cell Kit, and Dual Index Kit TT Set A. Approximately 20,000–23,000 cells were partitioned into Gel Bead-in-Emulsions (GEMs), enabling barcoded cDNA synthesis with unique molecular identifiers (UMIs), followed by cDNA amplification (11 cycles) and size-selection using SPRIselect beads. Gene expression (GEX) and Hashtag-oligo (HTO) libraries were generated according to the manufacturer’s protocol (10x Genomics Single Cell 3′ Reagent Kits v3.1, Dual Index). Libraries were quantified using the KAPA Library Quantification Kit (Roche). Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell using a 28×10×10×150 read configuration. Target sequencing depth was ~50,000 reads per cell for GEX libraries and ~5,000 reads per cell for HTO libraries.

first: Alina

last: Ulezko Antonova

first: Patrick

last: Rodrigues

first: Marina

last: Cella

first: Marco

last: Colonna


title: Pioneer-factor activity requires stable chromatin occupancy mediated by both sequence-specific binding and disordered protein domains [ChIP-seq]

city: Madison

first: Melissa

last: Harrison

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

summary: Pioneer transcription factors overcome the restrictive barrier imposed by chromatin to drive cell-fate specification, yet how their domains collectively support this activity remains unclear. Here, we use the deeply conserved pioneer factor Grainy head to define the protein-intrinsic features that govern pioneering activity. By integrating biochemistry, genomics and quantitative live-cell imaging, we determined that both the conserved DNA-binding domain and the extended, intrinsically disordered N-terminus are required for the stable chromatin occupancy that supports access to closed chromatin and the induction of chromatin accessibility. The disordered N-terminus supports pioneer activity through interactions that do not rely on strict amino acid sequence but instead overall composition. While our results show that pioneering activity depends on the combinatorial contributions of structured and disordered domains, mitotic retention depends solely on sequence-specific DNA binding. These results support stable chromatin occupancy mediated by multiple protein domains as necessary for pioneering function and that this is separable from the mechanisms required for mitotic retention.

overall_design: This data set contains ChIP-seq samples from S2 cells. Stable cell lines containing transgenes under a copper inducible promoter were induced with CuSO4. ChIP-seq was done using antibodies that recognize Grh and HA. Stable cell lines contained various Grh transgenes including wt Grh, HA-Grh, HA-GRHL2, HA-GRHL2.Grh, HA-Grh.GRHL2, Grh_Scrambled, Grh_ScrambledwSD, GrhC800AK807A, or GrhR806A.

first: Meghan

last: Freund

first: Javier

last: deHaro-Arbona

first: Sarah

last: Baloul

first: Ali

last: Torhorst

first: Charalambos

last: Roussos

first: Abby

middle: J

last: Ruffridge

first: Andrew

middle: Q

last: Rashoff

first: Ryen

last: Hazzard

first: Peter

middle: W

last: Lewis


title: Pioneer-factor activity requires stable chromatin occupancy mediated by both sequence-specific binding and disordered protein domains [ATAC-seq]

overall_design: This data set contains ATAC-seq samples from S2 cells. Stable cell lines containing transgenes under a copper inducible promoter were induced with CuSO4. Uniduced cells were harvested as a control. Stable cell lines contained various Grh transgenes including wt Grh, HA-Grh, HA-GRHL2, HA-GRHL2.Grh, HA-Grh.GRHL2, Grh_Scrambled, Grh_ScrambledwSD, GrhC800AK807A, or GrhR806A.


title: Chromosomal instability drives ECM remodelling and drug vulnerabilities in the first Afro-Caribbean breast cancer cell lines

city: Kingston

first: Simone

last: Badal

address: Mona, Kingston 7

department: Department of Basic Medical Sciences

country: Jamaica

institute: University of the West Indies

summary: Women of African ancestry develop more aggressive breast cancer (BCa) with poorer survival outcomes, yet only 8% of available cell lines represent this population, impeding targeted treatment development. Here, we aimed to establish and characterize new cell lines from an Afro-Caribbean patient to better understand population-specific BCa biology. We developed three lines (ACRJ-BC24 parent, α, and β) from a patient with 100% African ancestry. Karyotype analysis revealed progressive chromosomal instability, with the β-clone showing X-11 translocations correlating with higher Ki-67 expression and enhanced tumorigenic capacity. Immunohistochemistry and immunoblotting demonstrated their transition from hormone-positive to triple-negative phenotypes. Transcriptional profiling identified significant enrichment in extracellular matrix organization pathways mechanistically linked to chromosomal instability, explaining their distinct drug responses. The β-clone's enhanced sensitivity to PARP inhibitors correlates with its chromosomal abnormalities, while the parent line's sensitivity to gemcitabine possibly relates to ECM-mediated nucleoside transporter regulation. These lines provide valuable tools for studying BCa disparities.

overall_design: RNA-seq profiling of breast cancer cell lines from a Jamaican population. This included the original samples and two clones (alpha and beta)

first: Camille

last: Ragin

first: Albert

last: Doughan

first: Shannique

last: Clarke

first: Isabella

last: Allen

first: Jovanka

first: Sophia

last: George


title: RNA-seq of SW620 colorectal cancer cells: control (sh-control) versus ANO1 (TMEM16A) knockdown (sh-ANO1)

city: Changchun

first: Sui

last: Yujie

address: 265 Ziqiang Street

institute: The Second Hospital of Jilin University

summary:
The calcium-activated chloride channel ANO1 (TMEM16A) is overexpressed in colorectal cancer (CRC) and associated with poor prognosis, but its role in regulating metastatic plasticity is not fully understood. To elucidate the transcriptomic networks governed by ANO1, we performed RNA sequencing on SW620 CRC cells stably expressing sh-control or sh-ANO1. Total RNA was extracted using Trizol reagent. Sequencing libraries were constructed with the NEBNext® Ultra RNA Library Prep Kit for Illumina® and sequenced on an Illumina Novaseq platform, generating 125-150 bp paired-end reads. Bioinformatics analysis included read alignment with HISAT2 (v2.0.5) and differential expression analysis using DESeq2 (v1.20.0) with a threshold of |log2(Fold Change)| ≥ 1 and adjusted p-value < 0.05. Functional enrichment analysis for Gene Ontology (GO) and KEGG pathways was performed with clusterProfiler (v3.8.1). Gene Set Enrichment Analysis (GSEA) was conducted using gene sets from MSigDB.
Transcriptomic profiling identified 1,894 differentially expressed genes (DEGs) upon ANO1 knockdown, with 1,523 downregulated and 371 upregulated. Downregulated genes included key EMT and signaling components (e.g., PIK3C2A, PIK3CA, KRAS, ZEB1). GO analysis revealed enrichment in processes related to genomic integrity and cell division. KEGG pathway analysis highlighted significant enrichment in “Homologous recombination” and “Platinum drug resistance”. A trend-level downregulation was observed for the “mTOR signaling pathway”. This dataset illustrates that ANO1 knockdown drives broad changes in a pro-metastatic transcriptome network and implicates mTOR signaling as a potential downstream mechanism, providing a resource for understanding how ANO1 promotes CRC progression.

overall_design: RNA-seq profiling of SW620 cells stably transfected with sh-control and their knockdown derivatives (sh-ANO1)

first: Fei

last: Wu

first: Kun

last: Zhang

first: Zhenwu

last: Du

first: Xin

last: Li

first: Longfei

last: Yang

first: Linxian

last: Zhao

first: Bo

last: Cheng

first: Lili

last: Nie

first: Qiwei

first: Yujie

last: Sui


title: Elimination of myotonia improves myopathy in a muscleblind knockout model of myotonic dystrophy: Deep RNAseq of quadriceps muscle to assess myotonia dependent changes in transcript expression and splicing.

city: Rochester

first: John

middle: D

last: Lueck

address: 601 Elmwood Ave

department: Pharmacology and Physiology

institute: University of Rochester

summary: A cardinal sign of myotonic dystrophy type 1 (DM1) is myotonia, slow muscle relaxation after voluntary contraction. Myotonia results from mis-regulated splicing of chloride channel 1 (ClC-1), leading to loss of channel function and runs of involuntary action potentials in muscle fibers. Heralding the onset of weakness, myotonia is often the first symptom of DM1, and thus this raises the possibility that muscle hyperexcitability promotes the subsequent development of myopathy. We used genome editing to test this possibility by deleting the alternatively spliced and frameshift inducing ClC-1 exon 7a (E7a) in the Mbnl1 knockout model of DM1. Although several ClC-1 exons exhibit mis-regulated splicing in DM1, deletion of this single cryptic exon was sufficient to restore ClC-1 function and eliminate myotonia systemically and permanently. Through direct comparison of quadriceps muscle from myotonic (Mbnl1 knockout) and non-myotonic (Mbnl1 knockout; Clcn1 delta E7a) DM1 model mice, we were able to observe significant changes in transcript expression and splicing regulated by muscle hyperexcibility.

overall_design: Total RNA was isolated from quadriceps muscle from 4-6 month-old WT, Clcn1 delta E7a, Mbnl1 knockout, and Mbnl1 knockout; Clcn1 delta E7a mice with 4 biological replicates per group. This allowed for assessment of transcript expression and splicing changes between myotonic Mbnl1 KO and non-myotonic Mbnl1 KO; Clcn1 delta E7a with WT and Clcn1 delta E7a controls.

first: Matthew

last: Sipple

first: Vanessa

last: Todorow

first: Peter

last: Meinke

first: Charles

last: Thornton


title: Post-Hoc Trial and Preclinical Data Identify IL1RAP as a Tumor Microenvironment Vulnerability to Improve Chemoimmunotherapy Sensitivity in Pancreatic Cancer

city: Miami

first: Jashodeep

last: Datta

state: FL

address: 1425 NW 10th Ave

department: Surgery

institute: University of Miami Miller School of Medicine

summary: INTRODUCTION: Pancreatic ductal adenocarcinoma (PDAC) remains highly resistant to chemotherapy and immunotherapy due to a tumor microenvironment (TME) dominated by myeloid-stromal immunosuppressive circuitries and T-cell dysfunction. Key mediators of this chemoimmunoresistance are interleukin-1 (IL-1) family cytokines (IL-1α/β, IL-33, IL-36), which converge on IL-1 receptor accessory protein (IL1RAP) signaling to reinforce a tolerogenic, pro-inflammatory TME. We hypothesized that IL1RAP-expressing myeloid-stromal compartments sustain a therapeutic barrier in PDAC, and that disrupting this via pharmacologic IL1RAP inhibition could reprogram the TME to enhance chemoimmunotherapy efficacy. METHODS: Chemoresistance in PDAC samples from Human Tumor Atlas Network (HTAN) was stratified by cell-type IL1RAP expression. Clinical outcomes in patients treated with anti-IL1RAP Ab nadunolimab (Nadu)+gemcitabine+nab-paclitaxel (GnP) in Phase II CANFOUR trial (NCT03267316) were stratified by immune and stromal IL1RAP expression; paired PDAC biopsies pre-/post-treatment were analyzed by mIF. Preclinical studies were conducted in the IL1RAPhi stromatogenic Ptf1aCre/+;LSL-KrasG12D;Tgfbr2fl/fl (PKT) murine model. Nadu surrogate Ab-treated tumors were analyzed by scRNAseq, flow cytometry, and histology. Combination Nadu, GnP, and anti-PD1 therapy was tested in survival \ studies. RESULTS: In HTAN dataset, IL1RAP expression was elevated across multiple TME compartments—myeloid, cancer-associated fibroblast (CAF), and tumor cells; notably, IL1RAP was selectively enriched in chemotherapy-resistant (vs sensitive) samples, predominantly in myeloid and CAF/stromal transcriptomes. Stratification of evaluable specimens from CANFOUR trial revealed correlation between high stromal/CAF (p=0.0058) and myeloid (p=0.014) IL1RAP expression and prolonged duration of response to Nadu+GnP. In PKT mice, Nadu treatment reduced tumor volume (p=0.019) and stromal fibrosis. Flow cytometry showed reduced trafficking/persistence (p=0.0077) and increased T-cell abundance (p=0.0033), which were corroborated by mIF in paired human PDAC biopsies pre/post Nadu treatment, showing diminished CD11b+CD14+/CD15+ myeloid infiltration and expansion of GzmB+Ki67+CD8+ T-cells. scRNAseq in PKT tumors revealed reprogramming in myeloid (↑antigen presentation and Type IIFN response; ↓IL-1/TNF signaling) and T-cell (↑activation/memory, TCR engagement, IL-2 signatures; ↓regulatory/exhausted states) subsets. Phenotypic skewing toward memory progenitor-exhausted CD8+ subsets (Ly108+CD69+/-) supported enhanced immune responsiveness. Triple therapy with Nadu, GnP, and anti-PD-1 significantly prolonged survival versus controls (p<0.001). CONCLUSIONS: IL1RAP-expressing myeloid-stromal networks may represent a distinct therapeutic barrier in PDAC, which can be disrupted pharmacologically to invigorate immunotherapy-permissive CD8+ T-cell subsets and improve chemoimmunotherapy sensitivity. These findings support an upcoming neoadjuvant trial combining nadunolimab with chemoimmunotherapy in patients with operable PDAC.

overall_design: RNA-seq of Ptf1aCre/+;LSL-KrasG12D;Tgfbr2fl/fl (PKT) murine tumors treated with mNadunolimab (Cantargia AB; anti-mouse surrogate of human IgG1 IL1RAP inhibitor; 10 mg/kg7) or isotype control, twice on the first day of treatment (at 4-4.5 weeks of age), followed by 3x weekly dosing for two weeks, after which mice were sacrificed and tumors were processed for scRNA-seq.

first: Erin

last: Dickey

first: Harper

last: Marsh

first: Camilla

last: Rydberg Millrud

first: Haleh

last: Amirian

first: Karthik

last: Rajkumar

first: Manan

last: Patel

first: Andrew

last: Adams

first: Nipun

middle: B

last: Merchant

first: Anna

last: Bianchi

last: Hosein

first: David

last: Lidberg


title: Deciphering the Single-Cell Molecular Landscape of Ampullary Cancer: A Rare Gastrointestinal malignancy

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

country: France

institute: CRCT

summary: Ampullary carcinoma (AC) is a rare epithelial cancer, representing around 0.2% of all gastrointestinal malignancies worldwide, with an estimated incidence of 0.73 per 100,000 people. The rarity of AC, combined with the intricate anatomy of its site of origin, often complicates histopathological diagnosis. Recent advances in molecular research, however, have begun to illuminate its underlying biological complexity. In this study, we present the first comprehensive single-cell transcriptomic atlas of AC, encompassing both malignant epithelial populations and the tumor immune microenvironment (TIME). We identified upregulation of oncogenic drivers previously linked to AC, along with an AC-specific transcriptional program featuring potential biomarkers for minimally invasive diagnostics. Furthermore, we characterized an immunosuppressive TIME, enriched in anti-inflammatory-like TAMs and T cell subsets with limited antitumor activity. Collectively, these findings provide a foundational resource for the identification and validation of candidate biomarkers for early detection and targeted therapies in AC.

overall_design: Fresh samples of ampullary carcinama from three patients, and two fresh samples of ampulla of vater from healthy donors were used to perform a 10X genomics single cell RNA-Sequencing 3' assay.

last: Cerapio Arroyo

first: Karina

last: Cancino Maldonado

first: Stéphane

last: Bertani


title: Clusterin marks maladaptive regenerative responses throughout the kidney following ischemia reperfusion.

city: Montreal

first: Alex

last: Gregorieff

institute: Research Institute of the McGill University Health Centre (RI-MUHC)

summary: The proliferative capacity of the kidney declines after birth due to loss of its reserves of nephrogenic progenitors. Nevertheless, kidney tubules maintain a limited capacity to regenerate following various insults, through transient de-differentiation of the tubular epithelium into a progenitor phenotype. Recent studies describing the transcriptional changes underlying this process have primarily focused on proximal tubules with few studies examining the regenerative potential of other renal segments. To address this knowledge gap, we employed single cell RNA sequencing (scRNAseq) and lineage tracing experiments to dissect the transcriptional changes in cells expressing the secreted factor Clusterin (Clu), a known biomarker and potential regulator of acute kidney injury (AKI) in mice and humans. Our data indicates that de novo induction of Clu mRNA serves initially as a robust marker of injured distal tubules and collecting duct cells following ischemia reperfusion injury (IRI). Fate mapping revealed that while Clu+ nephron progenitors were multipotent, Clu+ collecting duct cells in the adult initially activated a transient proliferative program but ultimately persisted in a de-differentiated state or were lost. By scRNAseq, we also identified delayed and maladaptive responses in injured proximal tubules and the loop of Henle that are marked by Clu. Furthermore, we uncovered a “mixed lineage” gene signature comprised partly of podocyte and glomerular parietal epithelial cell identity markers that is activated in converging epithelial, mesenchymal and macrophages within the medulla. Together these data indicate that Clu marks maladaptive responses in the kidney and highlights the medulla as a particularly vulnerable site to the fibro-inflammatory cascade triggered by ischemic injury.

overall_design: BAC-CluGFP mice subjected to 35 min IRI treatment. Kidneys were harvested at days 2, 7, or 30. GFP+ cells isolated by FACS for RNA-seq.

first: Agnieszka

last: Masztalerz

first: Loïck

last: Joumier

first: Sunny

last: Zhen

first: Tomoko

last: Takano

first: Serge

last: Lemay

first: Mohan

last: Malleshaiah