title: Lysine Pyruvylation Mediated by HAT1/p300-SIRT3 Couples Glycolytic Flux to Epigenetic Regulation [RNA-seq]

first: xiaohan

last: song

first: Xiaohan

last: Song

first: Panan

last: Peng

first: Haonan

last: Zheng

first: Yanan

first: Qianjing

last: Wang

first: Yu

last: Ge

first: Doudou

last: Tan

first: He

last: Huang


title: Nuclear MBL-1 modulates mitochondrial morphology through carnitine palmitoyltransferase in C. elegans with toxic trinucleotide repeats

status: Public on Jan 08 2026

city: Helsinki

first: Susana

last: Garcia

address: Viikinkaari 5D

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

type: Expression profiling by high throughput sequencing

summary: Expansion of nucleotide repeat sequences is linked to a growing number of neuromuscular degenerative disorders. Metabolic changes, including disruptions in mitochondrial function and dynamics, characterize these disorders and are believed to contribute to organismal toxicity. To investigate how toxic RNA repeats affect mitochondria, we used a Caenorhabditis elegans model that expresses expanded CUG repeat RNAs in muscle cells and recapitulates muscle dysfunction. We found that the RNA-binding protein Muscleblind-like 1 (MBL-1) is essential for normal mitochondrial function and regulates organelle morphology. In animals expressing expanded CUG repeats, where MBL-1 function is impaired, we identified two distinct mechanisms of mitochondrial disruption: altered mitochondrial morphology regulated by MBL-1, and oxidative phosphorylation (OxPhos) dysfunction occurring independently of MBL-1. Our data further show that changes in mitochondrial morphology are specifically linked to nuclear MBL-1 dysfunction, which affects cpt-3 expression, a gene encoding carnitine palmitoyl transferase—an enzyme required for fatty acid transport into mitochondria. This mechanism is conserved, with similar disruptions observed in patients with Myotonic Dystrophy type 1. Importantly, our findings indicate that mitochondrial disruption does not result from increased organelle fragmentation. Instead, OxPhos dysfunction appears to be a primary contributor to cellular toxicity.

overall_design: Comparison of gene expression profiles between wild-type C. elegans (N2) and muscleblind splicing factor mutant mbl-1(tm1563) at different development stages – as L4s and as 2 days old adults. Comparison of gene expression profiles between C. elegans expressing RNAs with 123CUG repeats in the body wall muscle cells, and controls expressing 0CUGs. Two independent strains of each - 123CUG and 0CUG animals – were analyzed. Animals were analyzed at differential developmental stages: as L4s and as 2 days old adults.

first: Joana

last: Teixeira

first: Mikko

middle: J

last: Frilander

first: Ove

last: Eriksson

middle: M


title: Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice [RNAseq]

status: Public on Jan 07 2026

city: Cambridge

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

country: USA

institute: Broad Institute

summary: NMDA (N-methyl-d-aspartate) receptor dysfunction is widely implicated in pathophysiology of autism spectrum disorder (ASD), a neurodevelopmental condition with a strong genetic basis. Here we investigated heterozygous mouse mutants carrying the ASD-linked C456Y mutation of Grin2b, a high-confidence ASD risk gene encoding the GluN2B subunit of the NMDA receptors. Comprehensive transcriptomic analyses across multiple brain regions and postnatal ages revealed large-scale gene expression changes, particularly in pathways related to oxidative phosphorylation and ribosome/translation, suggesting brain-wide alteration of energy metabolism and protein synthesis in Grin2b+/C456Y mice. Starting from transcriptomic evidence, we additionally discovered widespread splicing abnormalities, and impaired hippocampal neurogenesis in Grin2b mutants. Interestingly, the underlying genes and the spatial and temporal patterns of transcriptomic changes in Grin2b+/C456Y mice differed substantially from those observed in mutant mice lacking Grin2a, which encodes the GluN2A subunit of the NMDA receptor but is a schizophrenia risk gene. These findings underscore the distinct role of Grin2b in brain development and function and reveal potential mechanisms by which Grin2b loss of function may lead to neurodevelopmental disorders.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from substantia nigra (SN) at 2, 4, 12 and 20 weeks of age in Grin2a mutant mice.

first: Farsi

last: Zohreh

first: Nicolella

last: Ally


title: Tfam-Mediated Metabolic Perturbation in RORgt+ Lymphocytes Impacts Intestinal Tissue Homeostasis and Promotes GATA3+RORgt+ Innate Lymphoid Cells

city: Gainesville

first: Liang

last: Zhou

address: 1945 SW 16th Ave

institute: University of Florida

summary: Rorc-mediated deletion of Tfam, a mitochondrial transcription factor, causes tuft cell-type 2 immunity-driven small intestine (SI) lengthening in mice. Here, we report an indispensable role for Th2 cells in this process. High-fat diet (HFD) reverts SI lengthening in Tfamf/fRorc-cre mice by suppressing IL-13-producing Th2 cells and IL-17-producing Th2 and ILC2s. HFD reduces conventional GATA3–/loRORgt+ ILC3s, but promotes GATA3+RORgt+ ILCs, especially in Tfamf/fRorc-cre mice. Compared to conventional ILC3s, GATA3+RORgt+ ILCs express type 2 cytokines, increase cell proliferation but decrease cell death with metabolic reprograming. Single-cell transcriptional analyses indicate that GATA3+RORgt+ ILCs represent a distinct population, different from IL-17– natural ILC2s, IL-17+ inflammatory ILC2s, or conventional ILC3s. GATA3+RORgt+ ILCs produce IL-17 but not IL-22, resulting from competition of the aryl hydrocarbon receptor (Ahr) with GATA3 at the Il22 locus. Tfamf/fRorc-cre mice on HFD have worsened DSS-induced colitis. These data highlight the role of ILC metabolism in intestinal tissue remodeling and inflammation.

overall_design: Live Lin–CD90.2+CD45.2+ (Lin: CD3, CD5, CD19, B220, TER119, Ly6G) cells were isolated and purified by FACS sorting from large intestine of 8 mice (Tfamf/f CD, n=2; Tfamf/fRorc-cre CD, n=2; Tfamf/f HFD, n=2; Tfamf/fRorc-cre HFD, n=2).

last: Sun

first: Eric

middle: Y

last: Helm

first: John

middle: W

last: Bostick


title: Epitranscriptomic control of stress adaptations in Escherichia coli

city: Martinsried

first: Kirsten

last: Jung

address: Großhaderner Str. 2-4

country: Germany

institute: LMU

type: Non-coding RNA profiling by high throughput sequencing

summary: Bacterial stress responses have been studied at the phenotypic, transcriptional, and translational levels, demonstrating the presence of an “alarm” phase immediately after stress exposure. However, the contributions of RNA modifications during stress adaptation remain largely unexplored. Here, we map the epitranscriptomic changes of Escherichia coli after exposure to oxidative and acid stress using direct RNA sequencing of mRNA, rRNA, and tRNA, combined with mass spectrometry, deletion mutant phenotyping, and single-nucleotide PCR. We identified widespread, dynamic RNA modifications that include central metabolism transcripts and increased levels of rRNA methylations (m4Cm and m5C) under both stresses, with potential consequences for translation. In uncharged tRNAs, stress-specific modifications via the Mnm and Q pathways accumulated at the wobble position; these modifications proved crucial for survival. Together, these findings reveal a multifaceted layer of post-transcriptional regulation, establishing the first comprehensive view of the bacterial epitranscriptome during the alarm phase of stress adaptation.

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

overall_design: Total RNA was extracted from two biological replicates each of wild-type E. coli cultured under standard growth conditions (no stress), medium with HCl added (acid stress), or medium with H2O2 added (oxidative stress) to measure RNA modifications throughout the transcriptome (mRNAe samples). Two replicates of in vitro transcribed RNA were synthesized from no-stress RNA samples as unmodified controls. Putative modifications were detected after samples were processed with direct RNA sequencing via Nanopore. A tRNA-specific preparation and sequencing protocol (Nano-tRNAseq) was also employed for the no-stress, acid-stress, and oxidative-stress samples.

first: Sebastián

last: Riquelme-Barrios

first: Siobhan

middle: A

last: Cusack

first: Luis

last: Rivera-Montero

first: Leonardo

last: Vásquez-Camus

first: Maximilian

last: Berg

first: G

last: Nur Yeşiltaç-Tosun

first: Stefanie

last: Kaiser

first: Pascal

last: Giehr

first: Korinna

last: Burdack

first: Brameyer

last: Sophie


title: Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice [grin2b_bulkRNAseq]

first: Ally

last: Nicolella

overall_design: Comparative gene expression profiling analysis of RNA-seq data from substantia nigra (SN) at 2, 4, 12 and 20 weeks of age in Grin2b mutant mice.

last: Zohreh


title: Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice

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

overall_design: Refer to individual Series


title: Targeting Sufu-mediated Gli transcription alleviates ciliopathic phenotypes [sufu_RNA-seq]

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital

summary: Ciliopathies are incurable, pleiotropic diseases that result from defective cilia. Several ciliopathic phenotypes arise from improper processing and activity of Gli transcription factors yet attempts to rescue these phenotypes by overexpressing activator or repressor Gli isoforms have proven unsuccessful. Gli proteins are regulated by Sufu, and Sufu-Gli complexes accumulate in ciliopathies, fundamentally altering the normal Sufu-Gli interaction dynamics. Herein, we investigated whether targeting Sufu-Gli interactions would provide a therapeutic benefit for ciliopathies. We introduced a single copy of SufuD159R, a point mutation that disrupts Sufu-Gli binding, into a ciliopathic mouse model. This genetic modification restored Gli3 binding to DNA and the subsequent transcription of target genes, and led to a significant rescue of numerous ciliopathic phenotypes. These findings suggest that modulating Sufu-Gli interactions may serve as a promising therapeutic approach for ameliorating ciliopathic pathologies.

overall_design: RNA-seq of E9.5 heads from wild-type control, SufuD159R+/- heterozygous and SufuD159R+/+ homozygous mutant embryos.

first: Ching-Fang

last: Chang


title: Bulk ATAC sequencing in HUVEC after ZBTB16-repression

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ZBTB16 is a transcription factor that is known to induce or repress gene expression. RNA sequencing data from ZBTB16-silenced mice showed that ZBTB16-deletion induces an aged-like phenotype in endothelial cells. In order to understand how ZBTB16 alters gene expression in endothelial cells, ATAC-seq was performed on HUVEC after siTNA-mediated ZBTB16-silencing.

overall_design: HUVEC were transfected with siRNA pools targeting ZBTB16 or with non-targeting siRNAs. Three days after transfection, cells were lysed.

first: Julian

last: Wagner

first: Stefan

last: Günther

first: Elvin

last: Leonard


title: Stc2a inhibits IGF-stimulated somatic growth in favor of organismal survival under hypoxic stress

city: Ann Arbor

first: Hui

last: Xu

state: Michigan

address: 500 S State St

institute: University of Michigan

summary: In response to hypoxia, animals reduce somatic growth to shift energy resources toward the maintenance of vital functions and survival. Although this phenomenon is widespread in the animal kingdom, the factors and mechanisms involved remain poorly understood. Here we report that hypoxia causes major changes in zebrafish transcriptomic landscapes with hormonal activity or hormonal signaling identified as most prominently up-regulated GO term and KEGG pathway. Among the top in this group is Stanniocalcin 2a (Stc2a), a secreted glycoprotein that inhibits insulin-like growth factor (IGF) signaling by binding to pappalysin metalloproteinases and inhibiting their activities. The hypoxic induction of stc2a expression is attenuated in Hif2- deficient fish. Genetic deletion of Stc2a increased the developmental speed and growth rate, resulting in enlarged adult organ and body size. Under hypoxia, stc2a-/- fish grew faster than wild-type fish but showed reduced survival rate. These phenotypes were reversed by inhibiting pappalysin activity or blocking IGF signaling. These findings suggest that Stc2a limits IGF- mediated growth in favor of survival and that the induction of Stc2a is part of a conserved mechanism regulating the trade-off between somatic growth and survival under hypoxic stress.

overall_design: RNA-seq profiling of wild-type zebrafish embryos exposed to normoxia (20.9% O₂) or hypoxia (6% O₂) from 81 to 96 hours post-fertilization (hpf). Each condition included three to four biological replicates, with 30 larvae pooled per replicate.

first: Zhengyi

last: Wang

first: Jinay

last: Shah

first: Shuang

last: Li

first: Shriya

last: Jaggi

first: Cunming

last: Duan


title: Deciphering functional intra-tumoral heterogeneity in BRAFV600E-driven mouse thyroid cancer reveals EMT trajectory and metabolic remodeling

city: Shanghai

first: Siyi

last: Shen

address: 320 Yueyang Road

country: China

institute: Shanghai Institution of Nutrition and Health, Chinese Academy of Sciences

summary: A better understanding of functional heterogeneity of tumor cells may lead to the improvement of the diagnosis and development of effective therapies for patients with papillary thyroid cancer (PTC). Here, the transcriptional heterogeneity and hierarchical trajectory of malignant thyrocytes were investigated by single-cell RNA sequencing analysis in an adult-onset autochthonous mouse model of PTC driven by a BRAFV600E. Within BRAFV600E thyrocytes, we identified distinct subpopulations exhibiting varying degrees of mesenchymal transformation and stability. Further analysis uncovered an epithelial-mesenchymal transition (EMT) trajectory, where malignant subpopulations progress from an intermediate to a more mesenchymal and malignant state. The EMT-related phenotype of each subpopulation was validated with an organoid culture system. Further analysis demonstrated that major malignant subpopulations maintain distinct EMT states through subpopulation-specific pathway usage, whereas transitioning cells undergo a dynamic shift in molecular strategy by using different pathway combinations or distinct gene sets within the same EMT-related pathways along the EMT trajectory. Moreover, metformin diminished the most malignant subpopulation in the PTC mouse model and inhibited EMT potential in both regular and organoid cultures. Importantly, the functional heterogeneity of tumor cells identified in PTC mouse model have clinical relevance. Furthermore, transcriptome dynamics analysis revealed an EMT trajectory-related gene module with substantial predictive value for human PTCs with BRAFV600E. Lastly, our analysis reveals that p53 deficiency lowers the tumorigenic threshold for BRAFV600E and promotes cell state transition towards a more malignant state, rather than altering cellular heterogeneity or the transition trajectory. Subsequent analysis in vitro demonstrated that p53 loss might confer more malignant potential to BRAFV600E thyrocytes through modulating metabolic plasticity. Collectively, our work not only deciphers the functional intra-tumoral heterogeneity of BRAFV600E-drieven PTC but also thereby provides a theoretical foundation for developing EMT-targeted treatment.

overall_design: To uncover intra-tumoral heterogeneity in PTC mouse models, scRNA-seq was performed on thyroid glands from TB or TBP mice 5-7 months after tamoxifen-induced recombination.

first: Hao

last: Ying

first: Ling

last: Zhang

first: Jing

last: Yu


title: BAP1 deletion in hepatocytes primes an inflammatory transcriptional response

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

summary: BRCA1-associated protein 1 (BAP1) is a deubiquitinase, frequently altered in cancers including hepatocellular carcinoma and cholangiocarcinoma. While Bap1 has been shown to play key roles in metabolism, maintenance of tissue homeostasis, and immune cell development, little is known about its normal functions in the liver in vivo. This study aims to identify Bap1 specific effects on the liver’s immune microenvironment and biological functions. Using AAV8-mediated CRISPR/CAS9 genome editing we generated a mouse hepatocyte-specific model of Bap1 knockout to define the changes that occur in liver biology in an in vivo system and characterize how loss of Bap1 alters the liver’s response to injury. Single-cell resolution spatial transcriptomics were performed in conjunction with immunohistochemistry to analyze cell-type composition and immune cell recruitment changes. Bulk RNA-sequencing was performed for further assessment of the impact of Bap1 loss on transcription. Hepatocyte-specific depletion of Bap1 induced transcriptional changes shared with acute injury. We observed a strong dysregulation of inflammatory pathways associated with BAP1 loss. Moreover, the transcriptional response of Bap1 depletion in hepatocytes to damage was markedly different than in control liver, with Bap1-deleted livers showing a decreased hepatocyte identity based on gene expression. Spatial transcriptomics and quantitative texture analysis of immunohistochemistry revealed an altered immune environment prior to damage and an impaired recruitment of immune cells in Bap1 depleted livers after damage. Using a hepatocyte-specific Bap1 deletion we identified Bap1 as a critical modulator in the liver’s immune cell response. We show that Bap1 loss leads to an inflammatory environment prior to damage and disrupts the recruitment immune cells. Our quantitative spatial analysis highlights the power of such approaches to characterize the spatial distribution of different cell types in a tissue.

overall_design: Bulk RNA-seq profiling of AAV-sgRNA-TBG-Cre mouse livers targeting Bap1 or non-targeting control, subject to either CCl4 or vehicle treatment

first: William

middle: C

last: Nenad

first: Peyton

last: Kuhlers

first: Katherine

last: Hoadley

middle: R


title: Targeted p63 isoform modulation corrects dominant mutations in AEC syndrome without disrupting epidermal homeostasis

city: Napoli

first: Dario

last: Antonini

address: Strada Vicinale Cupa Cintia, 21

country: Italy

institute: University of Naples "Federico II"

summary: The transcription factor p63 is a master regulator of stratified epithelial development. Its disruption leads to severe congenital defects affecting the skin, limbs, and craniofacial structures. Among p63-related disorders, Ankyloblepharon-Ectodermal Defects-Cleft Lip/Palate (AEC) syndrome is caused by dominant mutations predominantly in the SAM/TID domains of the TP63 gene, affecting the p63α isoform. These mutations promote protein aggregation and transcriptional dysregulation, resulting in debilitating skin erosions. To explore a therapeutic strategy based on isoform switching, we developed a conditional mouse model in which exon 13 was deleted, replacing p63α with the shorter p63β isoform, which is expressed in the skin, albeit at lower levels . Despite the essential role of p63α in limb and palate formation, we found that p63β is sufficient to sustain epidermal development, postnatal skin homeostasis, and wound healing. At the molecular level, the switch from p63α to p63β preserved chromatin binding and global transcriptional programs in keratinocytes. We next applied CRISPR/Cas9-mediated exon 13 deletion in human primary keratinocytes. This isoform conversion maintained proliferation and gene expression. Importantly, in AEC patient-derived keratinocytes, p63β expression rescued protein aggregation, restored mechanical integrity, and normalized key epidermal gene expression. Together, these findings demonstrate that p63β can functionally compensate for p63α in the skin and establish isoform switch as a promising therapeutic strategy for AEC syndrome.

overall_design: Skin was harvested from P2 mice, and the epidermis was separated from the dermis by overnight incubation in Dispase solution at 4°C. Single-cell suspensions were then obtained by incubating the tissue in Accutase for 20 minutes at room temperature.

first: Daniela

last: Di Girolamo

first: Gloria

last: Urciuoli

first: Stefano

last: Sol

first: Marco

last: Ferniani

first: Emanuela

last: Marchese

first: Angela

last: De Stefano

first: Marijke

last: Baltissen

first: Marian

last: Ros

first: Jill

last: Dixon

first: Smail

last: Hadj-Rabia

first: Caterina

last: Missero


title: Aberrant mRNA Splicing and Impaired Hippocampal Neurogenesis in Grin2b Mutant Mice [grin2b_snRNAseq]

first: Ally

last: Nicolella

overall_design: snRNA-Seq analysis of hippocampus (HP), striatum (STR), Thalamus (TH) and prefrontal cortex (PFC) at 4 weeks in Grin2b mutant mice.

first: Farsi

last: Zohreh

first: Nicoellla

last: Ally


title: Epigenetic plasticity is a driver of heritable pollution tolerance in Atlantic killifish [RNA-seq]

city: Saint Paul

first: Caren

last: Weinhouse

state: Minnesota

address: 1988 Fitch Ave

institute: Oregon H

summary: Heritable epigenetic adaptation to environmental stressors is a compelling but highly contested possibility. Previously, we showed evidence of a generationally heritable epigenetic memory at the cytochrome P450 1A (CYP1A) gene in wild Atlantic killifish (Fundulus heteroclitus) with evolved tolerance to PAH. This memory leads to blunted induction of CYP1A by PAH; this blunting that protects against polycyclic aromatic hydrocarbon (PAH)-induced cancer. Here, using Oxford Nanopore long-read sequencing in PAH-tolerant and sensitive wild-type embryos, we show that genome-wide, PAH-tolerant embryos showed reduced plasticity in DNA methylation response to PAH vs. PAH sensitive embryos that was not due to mutational loss of CpG sites. Notably, we observed population differences in gene methylation in pathways linked to the PAH tolerance phenotype, including AHR and voltage-gated potassium channel signaling, as well as developmental processes and energy metabolism. Specifically, we observed PAH-induced loss of CYP1A gene body methylation in PAH-sensitive (86% CpG methylation in control, decreased to 63% in exposed), but not -tolerant (84% control, 86% exposed), embryos. We observed similar patterns at CYP1B, CYP1C, and the aryl hydrocarbon receptor repressor, AHRR, which show similarly blunted expression. This genic methylation loss was correlated with decreased levels of natural anti-sense RNA transcripts in cis (cis-NATs), which may regulate transcription of these genes. Our data support the existence of stable epigenetic responses to chronic environmental stressors in a natural experimental setting, with broad implications for natural or directed adaptation strategies for other populations.

overall_design: Stranded, paired-end RNA sequencing  in four pools of embryos (N=10 embryos/pool): two pools each from PAH-sensitive and PAH-tolerant populations, one control and one challenged with PAH (Elizabeth River sediment extract, ERSE).

first: Mathia

last: Colwell

first: Melissa K.

last: Drown

first: Nicole

last: Flack

first: Carrie

last: Walls

first: Christopher

last: Faulk

first: Samantha

last: Carrothers

first: Emma

last: Weeks


title: Targeting Sufu-mediated Gli transcription alleviates ciliopathic phenotypes [kif3a_CUT&RUN]

last: Brugmann

overall_design: Gli3 CUT&RUN of E11.5 mandibles from wild-type, Kif3a f/f;Gli3 BioFLAG/+;Wnt1Cre knockout mutant and Kif3a f/f;Gli3 BioFLAG/+;Wnt1Cre;SufuD159R+/- embryos.

first: Ching-Fang

last: Chang


title: Identification of a neoplastic Tfh-like cellular subset in a mouse model of angioimmunoblastic T cell lymphoma (AITL)

city: Montreal

first: Saba

last: Mohammaei

address: 110 Pine Ave W

country: Canada

institute: IRCM

summary: Nodal T-follicular helper cell lymphoma, angioimmunoblastic type (nTFHL-AI, or AITL), is an aggressive peripheral T cell lymphoma without effective treatments. It has been shown that genetic and epigenetic changes lead to the expansion of neoplastic CD4+ T cells originating from T follicular helper (Tfh) cells, which subsequently cause B cell expansion and tumor. However, it remains unclear if the Tfh-like cell populations contain a subset that drive tumor progression and, if so, whether such a subset may have druggable targets. Using a mouse model of AITL driven by heterozygous sanroque mutation (Roquinsan/+), we identified a tumor-enriched Tfh cell subset highly expressing CXCR6 and IL-18 receptor, termed “Double-Expressor (DE) Tfh” cells. DE Tfh cells also expressed higher levels of enhancer of zeste homolog 2 (EZH2). In vitro data indicated that IL-18 and EZH2 are required for the proliferation of DE Tfh cells. Furthermore, DE Tfh cells have a potent capacity to expand B cells when adoptively transferred to lymphopenic recipients. On the other hand, depletion of DE Tfh cells via Ezh2 gene deletion, inhibition of EZH2 (using FDA-approved drug, tazemetostat), or anti-CXCR6 mAb led to tumor regression. These findings may be relevant to a subset of AITL cases since we found that ~20-30%  of AITL patient samples have concomittantly elevated expression of CXCR6, IL-18R1, and IFNG. Thus, our study identified a pathogenic Tfh-like subset essential for AITL tumor progression in a mouse model and suggests that identifying and targeting DE Tfh-like subset in AITL patients might be an effective strategy.

overall_design:
Tumor or tumor-free lymph node (control) were isolated from Roquinsan/+ mice and stained to sort live CD4+CXCR5+PD-1+ T follicular helper-like cells (>95% purity), and were analyzed by scRNA-seq.

>>>Submitter states that raw data for this study are no longer available.<<<

first: Antoine

last: Bouchard

first: Woong-Kyung

last: Suh


title: Targeted p63 isoform modulation corrects dominant mutations in AEC syndrome without disrupting epidermal homeostasis [ChIP-seq]

first: Dario

last: Antonini

overall_design: Mouse dorsal skin was harvested P0, and the epidermis was separated from the dermis by overnight incubation in Dispase solution at 4°C and single-cell suspensions were obtained by incubation in Accutase for 20 minutes at RT. Cells were cross-linked in 1% formaldehyde for 10 minutes at 37°C. After quenching with 125mM glycine for 5 minutes at RT, cells were collected by centrifugation and washed twice with ice-cold PBS containing 1mM PMSF and a protease inhibitor cocktail (Roche). Pellets containing 4×10⁶ cells were resuspended in 500µL of SDS lysis buffer (50mM Tris-HCl pH8.1, 1% SDS, 10mM EDTA) supplemented with protease inhibitors, incubated on ice for 10 minutes. Samples were sonicated in 250µL aliquots using a Bioruptor® Plus (Diagenode) at high power (60s ON, 90s OFF) for 45 minutes at 4°C to obtain chromatin fragments of approximately 300bp. Chromatin was diluted in ChIP dilution buffer (16.7mM Tris-HCl at pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS) and incubated overnight at 4°C with p63-specific antibodies (EPR570, Abcam) conjugated with Dynabeads Protein A and G (ThermoFisher Scientific). Immunoprecipitated samples were washed with Low salt buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-Hcl pH 8.1, 150 mM NaCl) High salt buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-Hcl pH 8.1, 500mM NaCl) and LiCl Immune complex wash buffer (10mM Tris-Hcl pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% Na deoxycholate, 1% NP-40) and twice with TE buffer. After immunoprecipitation, DNA was eluted in 1% SDS plus 0.1 M NaHCO3, purified with QiaQuick columns (ThermoFisher Scientific)

first: Daniela

last: Di Girolamo

first: Gloria

last: Urciuoli

first: Stefano

last: Sol

first: Marco

last: Ferniani

first: Emanuela

last: Marchese

first: Angela

last: De Stefano

first: Marijke

last: Baltissen

first: Marian

last: Ros

first: Jill

last: Dixon

first: Smail

last: Hadj-Rabia

last: Missero


title: snATAC Sequencing of the aging mouse heart to study chromatin remodeling on single cell level

first: Yousef

last: Alayoubi

institute: Max-Planck-Institute for Heart and Lung Research

summary: To study chromatin remodelig of the aging mouse heart, hearts from young and gaed mice were taken and nuclei were isolated via FACS. SnATAC Seq was performed using the 10X Genomics kit. Michail Yekelchyk (AG Braun) analysed the data)

overall_design: n=2 young (3 months) versus n=2 aged (22 months) mice (C57Bl\6J) were used for this experiment. Mice were sacrificed with cerval dislocation under isofluran. Hearts were taken and flushed with PBS. Nuclei of each heart were isolated via FACS and the 10X Genomics ATAC kit was used.

first: Michail

last: Yekelchyk

first: Julian

last: Wagner

first: Kathrin

last: Stilz


title: ExExE interactions in the transcriptomic response of E. coli exposed to a combination of antibiotic, temperature and salinity stresses

city: Girona

first: Marie

last: Rescan

address: c/ Emili Grahit,101 (edifici H2O- ICRA)

department: Water Quality

country: Spain

institute: ICRA

summary: Beyond individual effects, environmental variables can interact non-additively, thereby reducing our ability to predict demographic responses under multiple simultaneous stressors. The role of gene expression-level interactions remains poorly understood, with most studies limiting their analyses to stressors in isolation, neglecting potential interactions. What is the distribution of interaction between stressors at the gene expression level? do these interactions generally amplify or buffer the individual effects of stressors? Can additional stressors restore expression levels affected by one single stress? Can interactions emerge de novo in genes that are not responsive to individual stressors? And do higher-order interactions also occur at the transcriptomic level? We addressed these questions in the context of a major environmental issue: antibiotic pollution. Third-order interactions have been reported among azithromycin (AZI), temperature, and salinity, and altered by up to 100-fold the antibiotic concentration required to halve bacterial growth rate or yield. We show that most interaction emerge de novo or are antagonistic, pushing expression  back to its baseline level. A metabolic switch between carbon and nitrogen and an enhanced general stress response can explain the interactions observed at the fitness level.

overall_design: Transcriptoimic analysis (mRNA) of 24 isogenic populations of Esherichia coli K12 MG1665  grown in BHI broth from an initial density around 10^8 and exposed to all combination of two concentrations of atythromycin (0 vs. 1 µg/mL), two temperature (30 and 25 °C) and two salinities (0.085 and 0.585 M), for 6 hours.

first: Marc

last: Dachs Rojo

first: Carles

last: Borrego


title: Effect of Moderate-Intensity Treadmill Exercise on Bone Quality in Adult Rats and the Underlying Mechanisms

city: beijing

first: Chenchen

last: Li

address: 37 Xueyuan Road

institute: beihang university

summary: While exercise is widely recognized to enhance bone mass, the underlying molecular and cellular mechanisms remain incompletely elucidated. The present study was designed to investigate the effect of moderate-intensity exercise on skeletal quality, morphological characteristics, and metabolic homeostasis in adult Sprague-Dawley (SD) rats. Herein, we aim to investigate the expression profile of mRNAs in rats with exercise and identify promising targets for osteoporosis diagnosis and treatment. RNA sequence were performed in the bones from 3 exercised rats and 3 healthy controls.

overall_design: RNA sequence were performed in the bones from 3 exercised rats and 3 healthy controls. Significantly differentially expressed mRNAs were selectively verified in 6 exercised rats and 6 healthy controls by real-time PCR.

first: Xitong

first: Peipei

last: Shi

first: He

last: Gong


title: AML PATIENTS WITH WILDTYPE TP53 AND DEFECTIVE TP53-MEDIATED APOPTOSIS HAVE A DISMAL SURVIVAL

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

summary: The survival of 10% of patients with acute myelogenous leukemia (AML) carrying mutations in TP53 is dismal. Here, we estimated the fraction of AML patients with impaired TP53-mediated apoptosis despite TP53 WT status and their survival. We report the results of a detailed characterization of responses to treatment with the MDM2 inhibitor MI219, a p53 protein stabilizer, ex vivo in AML blasts from 165 patients. In total 33% of AML were resistant to MDM2 inhibitor induced apoptosis, of which 15% carried TP53 mutation and 18% were TP53 WT.  We conducted array-based expression profiling of ten resistant and ten sensitive AML cases all with WT TP53, respectively, at baseline and after 2h and 6h of MDM2 inhibitor treatment. While sensitive cases showed the induction of classical TP53 responses genes, this was largely absent in resistant cases. The sensitive and resistant AML samples at baseline furthermore differed in the expression of inflammation-related and mitochondrial genes. Clinically, the survival of TP53 mutated AML or AML with defective MDM2 inhibitor induced TP53-mediated apoptosis despite WT TP53 in this cohort was 0% and 11%, respectively. In summary, we show prevalent multi-causal defects in TP53-mediated apoptosis in AML resulting in extremely poor patient survival.

overall_design: we obtained IC50 values to MDM2 inhibitor treatment in purified AML cell samples.  We selected 10 samples each that were sensitive or resistant and conducted array based expression analysis at baseline (0h), 2h and 6h.

first: Sami

middle: N

last: Malek


title: Ecdysone-mediated intestinal growth contributes to microbiota-driven developmental plasticity under malnutrition

city: Lyon

first: Longwei

last: Bai

address: 32-34 Avenue Tony Garnier

country: France

institute: ENS Lyon

summary: Organ and systemic growth must remain coordinated during development, even under nutritional stress. In Drosophila larvae, the intestinal microbiota contributes to this coordination by promoting growth and maturation under chronic undernutrition. Using gnotobiotic models, we show that association with Lactiplantibacillus plantarum (Lp) selectively enhances midgut growth relatively to other organs, providing an adaptive mechanism that buffers the impact of dietary restriction. Transcriptomic profiling of larval midguts revealed a strong Ecdysone signaling signature upon Lp association. Functional analyses showed that local conversion of Ecdysone to its active form, 20-hydroxyecdysone, by the cytochrome P450 enzyme Shade, together with enterocyte Ecd receptor activity, is required for Lp-dependent intestinal and systemic growth. Pharmacological activation of Ecd signaling partially mimicked the bacterial effect, confirming its sufficiency to drive adaptive midgut expansion. Our results uncover an unexpected role of intestinal Ecd signaling in microbiota-driven developmental plasticity, revealing how commensal bacteria modulate local steroid signaling to fine-tune organismal growth and maturation.

overall_design: To uncover transcriptional programs underlying microbiota-dependent intestinal growth, we performed RNA sequencing on midguts dissected from size-matched GF and Lp-associated larvae at early and late third-instar (L3) stages

first: Stéphanie

last: Bellemin

first: Elodie

last: Guillemot

first: Maura

last: Strigini

first: Benjamin

last: Gillet

first: Cathy

middle: I

last: Ramos

first: François

last: Leulier


title: Ablation of VEGFA following a lumbar intervertebral disc injury attenuates intradiscal neurovascular features and prevents chronic low back pain symptoms

city: St. Louis

first: Simon

last: Tang

state: MO

address: 425 S. Euclid Ave, Campus Box 8233, Tang Lab, Washington University School of Medicine

department: Orthopaedic Surgery

institute: Washington University in St. Louis

summary: There are currently no therapies for the staggering disability and public health costs of chronic low back pain (LBP). Innervation of the degenerating intervertebral disc (IVD) is suspected to cause discogenic LBP, but the mechanisms that orchestrate the IVD’s neo-innervation and subsequent symptoms of LBP remain unknown. We hypothesize that Vascular Growth Endothelial Factor-A (VEGFA) critically mediates the neurite invasion in the IVD and contributes to prolonged LBP.  Initiating IVD degeneration through a mechanical injury, we evaluated the progression of neurovascular features into the IVD, as well as resultant LBP symptoms and locomotive performance at acute (3-weeks) and prolonged (12-weeks) time points following IVD injury. To determine the role of VEGFA, we used a mouse model with ubiquitous inducible recombination of the floxed VEGFA allele (UBC-CreERT2; VEGFAfl/fl).  The ablation of VEGFA attenuated the neurite and vessel infiltration into the degenerating IVD, and the VEGFA-null animals exhibited alleviated mechanical allodynia and improved locomotive performance. To determine the effects of IVD-derived VEGFA on endothelial cells and neurons, we cultured HMEC-1 endothelial cells and SH-SY5Y neurons using conditioned media from VEGFA-silenced (siRNA) human primary IVD cells stimulated by IL1b.  The endothelial cells and neurons exposed to the secretome of the VEGFA-silenced IVD cells exhibited reduced growth, suggesting that the inhibition of IVD-derived VEGFA may be sufficient to attenuate intradiscal neurovascular features. Together, we show that VEGFA orchestrates the growth of intradiscal vessels and neurites that cause low back pain and impaired function, and the inhibition of VEGFA can prevent prolonged low back pain.

overall_design: Human intervertebral disc (IVD) cells were isolated from the IVD tissue of eight patients removed during elective discectomy surgeries. IVD cells were plated and 1 ng/mL of IL-1β was added to the stimulate the cells for 24 hours. IL-1β was removed and cells were then transfected with Control, Scrambled siRNA (Scram) or VEGF siRNA (Vegfa)for 24 hours. Next, the IL-1β stimulated and siRNA transfected IVD cells were co-cultured with either SH-SY5Y neuronal cells (Nerves) for 48 hours or HMEC-1 endothelial cells (Endo) for 24 hours. The co-cultured nerve and endothelial csells were submitted for RNA sequencing.

first: Ryan

middle: S

last: Potter

first: Remy

middle: E

last: Walk

first: Hong

last: Moon

first: Addison

middle: L

last: Liefer

first: Sade

last: Clayton

first: Liufang

last: Jing

first: Lori

last: Setton

first: Munish

last: Gupta


title: Targeted p63 isoform modulation corrects dominant mutations in AEC syndrome without disrupting epidermal homeostasis [RNA-seq Mouse]

first: Dario

last: Antonini

overall_design: Mouse dorsal skin was harvested from embryos at E18.5, and the epidermis was separated from the dermis by overnight incubation in Dispase solution at 4°C and single-cell suspensions were obtained by incubation in Accutase for 20 minutes at RT. RNA was isolated using Direct-Zol micro prep kit (Zymo Research, R2061)

first: Daniela

last: Di Girolamo

first: Gloria

last: Urciuoli

first: Stefano

last: Sol

first: Marco

last: Ferniani

first: Emanuela

last: Marchese

first: Angela

last: De Stefano

first: Marijke

last: Baltissen

first: Marian

last: Ros

first: Jill

last: Dixon

first: Smail

last: Hadj-Rabia

first: Caterina

last: Missero


title: Targeted p63 isoform modulation corrects dominant mutations in AEC syndrome without disrupting epidermal homeostasis [human RNA-seq]

overall_design: NHEK and mutant (I537T) human keratinocytes (HK) were nucleofected with Cas9 with or without sgRNA1 and sgRNA2 for the generation of p63alpha KO. After 72 hours from nucleofection, RNA was isolated using Direct-Zol micro prep kit (Zymo Research, R2061)


title: Aged bone marrow myeloid and mesenchymal cells develop unique senescence phenotypes

city: Rochester

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Cellular senescence was originally characterized in mesenchymal cells and subsequently this concept was extended to immune cells. However, the extent to which immune cells differ from mesenchymal cells in their senescence phenotype, or “senotype”, is unclear. Here, we evaluated the senotypes of bone marrow/bone immune versus mesenchymal cells. Among immune cells, myeloid cells exhibited the highest expression of p16. However, targeted clearance of p16+ myeloid cells using LysM-Cre x p16-LOX-ATTAC mice only had minor effects on age-related bone loss in male mice, with no effects in females. After clearance, p16+ myeloid cells were only transiently reduced, unlike when targeting p16+ mesenchymal cells. In the same bones, aged myeloid cells demonstrated lower expression of senescence markers than mesenchymal cells and, when induced in culture, the senescence phenotype of myeloid cells differed substantially from that of mesenchymal cells. Our findings indicate that aged bone marrow myeloid cells do not achieve the fully developed senescent phenotype originally described in mesenchymal cells, justifying further characterization of senotypes of immune cells across tissues.

overall_design: The purpose of this particular bulk RNAseq study is to compare the transcriptomes of AP20187 (AP) versus Vehicle in the spleen, flushed diaphysis, inguinal fat and quadricepts of male, 24 month old p16-LOX-ATTAC mice crossed with the LysM-Cre mosue driver.

first: Madison

last: Doolittle

first: Mitchell

last: Froemming

first: David

middle: G

last: Monroe

first: Sundeep

last: Khosla


title: An in vitro methodology demonstrates the five steps of trained immunity in mice: implications on biomarker discovery, adaptive immune responses, mouse strains, sample cryopreservation and genetic ablation [RNA-Seq]

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

summary: Trained immunity is defined by increased inflammatory cytokine production by macrophages that are sequentially activated by two stimuli, separated by a resting period. The models used to study trained immunity should reflect the definition of this process, which includes five different steps. Here, we developed an in vitro methodology to study trained immunity using murine bone marrow-derived macrophages (BMDM), following sequential stimulation with β-glucan and lipopolysaccharide (LPS). Kinetic analysis of cytokine production demonstrated, for the first time, that trained BMDM secrete high levels of tumor necrosis factor (TNF) and interleukin 6 (IL6) following stimulation with β-glucan (stimulus 1), compared to unstimulated BMDM (step 1). After a resting period, trained BMDM do not secrete significant levels of these cytokines (step 2), but rapidly produce enhanced levels of TNF and IL6 after secondary stimulation with LPS (stimulus 2), compared to BMDM stimulated with either β-glucan (step 3) or LPS (step 4) alone. In addition, the sum of cytokine levels produced by both BMDM stimulated with either β-glucan (stimulus 1) or LPS (stimulus 2) individually, was significantly lower than the cytokine levels produced by trained BMDM stimulated with both β-glucan and LPS (stimulus 1+2) (step 5). Our findings also demonstrate that trained BMDM produce higher levels of serum amyloid A3 (SAA3) protein due to metabolic and epigenetic reprogramming. Functionally, trained BMDM upregulate the expression of stimulatory molecules such as MHC-II, CD80, CD86, OX40L and PDL1; downregulate the inhibitory molecules ICOSL and CD206; and induce CD4+ and CD8+ T cell proliferation in vitro through a cell contact-dependent mechanism. Our results also revealed strain-specific differences in the training response among mice, the negative impact of cell cryopreservation on trained immunity, and the potential use of genetically modified mice in elucidating mechanistic pathways through which different training stimuli may induce long-lived memory macrophages. These results also highlight the applicability of mouse in vitro methods as an additional tool to study trained immunity, as the use of inbred mice reduce the genetic variability present in humans and minimize variables that affect trained immunity such as infections, vaccinations and lifestyle-related stimuli. The standardization of trained immunity protocols using murine BMDM will facilitate the development of therapeutic strategies that target the innate immune memory response for the treatment of multiple immune-based diseases.

overall_design: In vitro trained immunity models in murine bone marrow-derived macrophages using sequential β-glucan and LPS stimulation, comparing naive, activated, and trained BMDMs for transcriptomic and epigenetic analyses.

first: Maria

last: Gonzalez-Perez

first: Jana

last: Baranda

first: Leticia

last: Perez-Rodriguez

first: Patricia

last: Conde

first: Carlos

last: de la Calle-Fabregat

first: Marcos

last: Berges Buxeda

first: Alexander

last: Dimitrov

first: Javier

last: Arranz

first: Sergio

last: Rius-Rocabert

first: Alessia

last: Zotta

first: Ana

last: Dopazo

first: Nikita

last: Poddar

first: Xuedi

last: Wang

first: Estanislao

last: Nistal-Villán

first: Raphaël

last: Duivenvoorden

first: Joren

last: Madsen

last: Williams

first: Dan

last: Hasson

first: Daniel

last: Ojalvo-Lozano

first: Florent

last: Ginhoux

first: Luke A.J.

last: O'Neill

first: Jordi

last: Ochando


title: Incomplete developmental silencing of cancer-testis antigen BORIS in humanized mouse model promotes cancer susceptibility

city: Bethesda

first: Emma

last: Price

state: MD

address: 9000 Rockville Pike, Bld 29B

department: LIG

institute: NIAID/NIH

summary: Cancer-testis antigens are genes normally restricted to the germline but aberrantly activated in many cancers, where their role in tumorigenesis remains unclear. BORIS (CTCFL), a testis-specific paralog of the chromatin organizer CTCF, is one such antigen that shows limited conservation between humans and mice, complicating in vivo functional studies. Here, we generated humanized mice in which both alleles of the endogenous Boris locus are replaced with the full-length human BORIS gene, including its highly diverged cis-regulatory elements. These fully humanized mice maintain normal fertility, indicating accurate germline expression and preserved BORIS function despite evolutionary divergence. However, unlike the strictly testis-specific expression of mouse Boris, human BORIS escapes complete somatic silencing, producing mosaic expression in a minority of mouse somatic cells. This ectopic expression is associated with reduced survival, increased tumor incidence and a shift of tumor spectrum toward aggressive lymphomas. Transcriptomic and chromatin profiling revealed that ectopic human BORIS reactivates testes-specific genes in the soma, including regulators of meiosis and DNA repair, through direct chromatin binding. This transcriptional reprogramming was consistent across tissues and clonal cell lines, revealing a dominant tissue-independent gene activation program. These findings demonstrate that when human BORIS escapes epigenetic silencing in somatic cells, it connects aberrant germline gene activation with increased cancer susceptibility in vivo.

overall_design: To assess the impact of humanizing the BORIS/CTCFL locus in mice, ChIP-seq was performed to profile binding of humanized BORIS/CTCFL and endogenous mouse CTCF in male germline and somatic tissues from mice. Additional ChIP-seq and RNA-seq experiments were conducted in mouse embryonic fibroblasts (MEFs). RNA-seq was used to evaluate downstream effects on gene expression associated with BORIS/CTCFL humanization.

first: Victor

last: Lobanenkov


title: Sleep restores glia-mediated engulfment in aged flies

city: College Station

first: Alex

last: Keene

state: Texas

address: 3258 TAMU Department of Biology Butler Hall 203A

department: Biology

institute: Texas A&M University

summary: Neuronal injury due to trauma or neurodegeneration is a common feature of aging. The clearance of damaged neurons by glia is thought to be critical for maintenance of proper brain function. Sleep loss has been shown to inhibit the motility and function of glia that clear damaged axons while enhancement of sleep promotes clearance of damaged axons. Despite the potential role of glia in maintenance of brain function and protection against neurodegenerative disease, surprisingly little is known about how sleep loss impacts glial function in aged animals. Axotomy of the Drosophila antennae triggers Wallerian degeneration, where specialized olfactory ensheathing glia engulf damaged neurites. This glial response provides a robust model system to investigate the molecular basis for glial engulfment and neuron-glia communication. Glial engulfment is impaired in aged and sleep-deprived animals, raising the possibility that age-related sleep loss underlies deficits in glial function. To define the relationship between sleep- and age-dependent reductions in glial function, we restored sleep to aged animals and examined the effects on glial clearance of damaged axons. Both pharmacological and genetic induction of sleep restores clearance of damaged neurons in aged flies. Further analysis revealed that sleep restored post-injury induction of the engulfment protein Draper to aged flies, fortifying the notion that loss of sleep contributes to reduced glial-mediated debris clearance in aged animals. To identify age-related changes in the transcriptional response to neuronal injury, we used single-nucleus RNA-seq of the central brains from axotomized young and old flies. We identified broad transcriptional changes within the ensheathing glia of young flies, and the loss of transcriptional induction of autophagy-associated genes. We also identify age-dependent loss of transcriptional induction of 18 transcripts encoding for small and large ribosomal protein subunits following injury in old flies, suggesting dysregulation of ribosomal biogenesis contributes to loss of glial function. Together, these findings demonstrate a functional link between sleep loss, aging and Wallerian degeneration.

overall_design: To identify age-dependent changes in ensheathing glia we performed single-nucleus RNA-sequencing (snRNA-seq) on the central brains of both young (5 day) and old (40 day) flies under intact and axotomized conditions.

first: Jiwei

last: Zhang

first: Elizabeth B.

last: Brown

first: Evan

last: Lloyd

first: Isabella

last: Farhy-Tselnicker

first: Akhila

last: Rajan

first: Alex C.


title: Orai1 in pancreatic ductal cells mediates pancreas-intestinal crosstalk in experimental acute pancreatitis via the secretion of antimicrobial peptide REG3B in pancreatic juice

city: Beijing

first: Xiaoyu

last: Guo

state: Beijing

address: Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.

institute: Peking Union Medical College Hospital

summary: Pancreatic ductal epithelial cells (PDECs) play a crucial role in the development of acute pancreatitis (AP). We and others have previously shown that Orai1 inhibitor confers protection against AP severity. In this study, we aim to investigate the effect and the underlying mechanisms of Orai1 in PDECs on experimental AP and its-associated intestinal damage. We found that Orai1 deletion in PDECs markedly mitigated the prolonged elevation of calcium and preserved the decreased mitochondrial membrane potential due to sodium taurocholate (NaT) or palmitoleic acid (POA) exposure. PDECs-specific Orai1 deletion notably lessened pancreatitis severity and restored the impaired pancreatic juice secretion during AP. Increased expression of tight junction proteins and decreased intestinal permeability and inflammation were observed in duodenal and colonic tissue of PDECs-specific Orai1 knockout mice. Furthermore, the deletion of Orai1 protected against pancreatitis-associated dysbiosis in the duodenum, but not in the colon. Mechanically, this protective effect was partially attributed to the enhanced secretion of REG3B in pancreatic juice during AP. Finally, intraperitoneal administration of REG3B partially alleviated AP severity and pancreatitis-associated intestinal injury and inflammation. Collectively, these findings suggest that Orai1 inhibitor may serve as potential therapeutic strategy for the management of AP and associated intestinal injury.

overall_design: we performed gene expression profiling analysis using data obtained from RNAseq of isolated pancreatic ductal epithelial cells during alcoholic pancreatitis.

first: Li

last: Wen


title: Expression data from mice megakaryocyte proginters and platelets

city: Montpellier

first: Said

last: Assou

state: Languedoc-Roussillon

address: 80 av Augustin fliche, IRMB

institute: IRMB, Hôpital Saint Eloi

summary:
Despite lacking a nucleus, platelets harbor a reservoir of megakaryocyte-derived RNAs and possess the necessary machinery for mRNA translation. Interestingly, the platelet transcriptome has been extensively analyzed in both health and cancer, leading to the identification of cancer-specific molecular signatures. The concept of "tumor-educated platelets" (TEPs) raises the question of whether RNA changes in platelets originate from their progenitor cells, megakaryocytes. Comparative analysis of platelet and megakaryocyte microarray data revealed that RNA alterations occur in both cell types.
In the current study, we emphasize how CTC-derived EVs influence megakaryocytes, leading to alterations in platelet function, contributing to cancer-associated coagulation, and potentially driving cancer progression.

overall_design: Platelets and megakaryocytes from each mouse group were pooled for RNA isolation, and RNA quality was assessed using an Agilent BioAnalyzer 2100. Biotinylated cDNA was prepared from 3 ng of total RNA, fragmented, and hybridized onto a Clariom D Mouse microarray. The arrays were washed, stained, and scanned, and data were analyzed using Affymetrix software, with normalization performed via the MAS5.0 algorithm. Differentially expressed transcripts were identified using a Wilcoxon test and a false discovery rate (FDR) threshold of <5% with a fold change ≥1.5. Gene annotation, pathway enrichment, and Gene Ontology (GO) analysis were conducted using tools like DAVID and TAC, while volcano plots and bar graphs were created to visualize significant findings, highlighting key pathways and genes associated with each condition.

first: Zahra

last: Eslami-S

first: Catherine

last: Alix-Panabières


title: The Loss of Glycoprotein Nonmetastatic Melanoma Protein B (GPNMB) Worsens Endothelial Cell Permeability, Metabolism, and Survival During Infectious Challenge

city: Nashville

first: Ryan

last: Stark

state: Tennessee

address: 2200 Children's Way, 5121 Doctors' Office Tower

institute: Vanderbilt University Medical Center

summary: During severe systemic infections, also known as sepsis, excessive cytokines and reactive oxygen species lead to endothelial dysfunction. Glycoprotein nonmetastatic melanoma protein B (GPNMB) has been implicated in regulating cellular functions, particularly within the vasculature during inflammation, but its effect on infection-mediated endothelial injury remains unclear. Data obtained from the Gene Expression Omnibus (GEO) show that GPNMB expression is systemically reduced following an infectious challenge. Therefore, to investigate the role of GPNMB during infection-mediated endothelial inflammation, we utilized human microvascular endothelial cells (HMVECs) with or without GPNMB knockdown (siGPNMB) and exposed them to heat-killed Escherichia coli (HKEC), one of the most common pathogens associated with sepsis. Silencing GPNMB altered the expression of 1,556 genes via RNA sequencing, affecting cytoskeleton function and the response to stimuli. When assessing the endothelial monolayer under basal conditions, siGPNMB cells displayed higher transendothelial electrical resistance (TEER), consistent with RNA sequencing pathway analysis, but exposure to HKEC resulted in increased barrier dysfunction compared to controls. Furthermore, compared to controls, assessments of viability, proliferation, and migration were compromised in siGPNMB cells following HKEC exposure. Exposure to HKEC decreased the oxygen consumption rate in controls and increased the extracellular acidification rate, but neither were changed in siGPNMB cells, indicating impaired metabolic adaptation and further corroborating aspects of the RNA sequencing data. Our findings demonstrate that GPNMB reduction hinders the endothelial response to infectious stimuli, resulting in decreased metabolic fluxes and a dysfunctional endothelium during infectious challenges.

overall_design: Total of 6 sample were analyzed, 3 TERT-immortalized dermal human microvascular endothelilal cells (HMVECs) treated for 72 hours with scrambled (control) siRNA and 3 TERT-immortalized dermal HMVECs treated with siRNA targeting glycoprotein nonmetastatic melanoma protein B (GPNMB)

first: Milene

middle: T

last: Fontes

first: Celia

last: Lamb

first: Allison

last: Pourquoi

first: Hong-Ngan

last: Nguyen

first: Sourav

last: Panja


title: Single-Cell Omics Analysis of Human Basophils Reveals Two Transcriptionally Distinct Populations

city: Solna

first: Joakim

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

summary: Single-omics technologies have been extensively used to study the heterogeneity of cell populations. However, human basophils are remarkably underrepresented in single-cell RNA-sequencing studies. Here, we used CITE-seq (single-cell RNA-sequencing with feature barcoding) to profile the basophil transcriptome, to detect cell surface epitopes, and to barcode specific cell populations.

overall_design:
We performed CITE-seq of low-density leukocytes and isolated basophils from the peripheral blood of 4 healthy donors. For the first dataset, side scatter (SSC) low leukocytes were sorted and mixed with SSClow Lin- CCR3+ FCεR1+ basophils. To generate the second dataset, we sorted SSClow Lin- CCR3+ FCεR1+ basophils and mixed them with SSClow Lin- CCR3+ FCεR1+ c-KIT+ basophils. To generate the third dataset, we MACS-enriched CCR3+ cells from low density leukocytes, producing 3 datasets from 2 donors in 2 indepedent experiments. To generate the fourth dataset, we repurposed the full-length amplified cDNA material used to produce the third dataset. Specifically, we performed long-read sequencing of 2 samples (1 library from each donor) using the Oxford Nanopore Technology.

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Please note that Swedish legislation and GDPR prevent unrestricted distribution of raw sequencing data and thus raw data is not provided.
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first: Sofia

last: Papavasileiou

first: Daryl

last: Boey


title: An in vitro methodology demonstrates the five steps of trained immunity in mice: implications on biomarker discovery, adaptive immune responses, mouse strains, sample cryopreservation and genetic ablation [ATAC-Seq]

first: BiNGS

last: Core

first: Maria

last: Gonzalez-Perez

first: Jana

last: Baranda

first: Leticia

last: Perez-Rodriguez

first: Patricia

last: Conde

first: Carlos

last: de la Calle-Fabregat

first: Marcos

last: Berges Buxeda

first: Alexander

last: Dimitrov

first: Javier

last: Arranz

first: Sergio

last: Rius-Rocabert

first: Alessia

last: Zotta

first: Ana

last: Dopazo

first: Nikita

last: Poddar

first: Xuedi

last: Wang

first: Estanislao

last: Nistal-Villán

first: Raphaël

last: Duivenvoorden

first: Joren

last: Madsen

first: David L.

last: Williams

first: Dan

last: Hasson

first: Daniel

last: Ojalvo-Lozano

first: Florent

last: Ginhoux

first: Luke A.J.

last: O'Neill

first: Jordi

last: Ochando


title: Investigation of transcriptomic signatures associated with sepsis risk in patients with infection

city: Budapest

first: Zsolt

last: Ronai

address: Ulloi u. 26.

department: Molecular Biology

country: Hungary

institute: Semmelweis University

summary: Sufficient immune response is responsible for eradicating pathogens and reestablishing tissue homeostasis. However, in certain patients, immune processes become dysregulated, leading to systemic inflammatory response syndrome (SIRS), which often results in life-threatening organ dysfunction. The phenomenon of outgrowing septic shock is associated with a mortality rate of up to 70–80%. The objective of the present data set is to facilitate the identification of transcriptomic signatures associated with the development of sepsis in patients with infection. A total of six patients were included in the study, with blood samples collected at various stages of the disease, ranging from severe septic conditions to periods of temporary improvement and recovery. Following RNA isolation, the mRNA and microRNA levels were determined by NGS. The dataset’s significance stems from the fact that more samples of the same patient were analyzed, ensuring that any observed alteration in the transcription levels is related to the change in medical condition.

overall_design: RNA-seq profiling (including mRNA and miRNA) of blood sample sets of patients with infection at the stage of severe sepsis, at temporary improvement and recovery.

first: Krisztina

last: Molnár

first: Katalin

last: Maricza

first: Zsuzsanna

last: Elek

first: Réka

last: Kovács-Nagy

first: Zsófia

last: Bánlaki

first: Eszter

last: Losoncz

first: Zoltán

last: Fülep

first: János

last: Kádas

first: Gergely

last: Keszler

last: Rónai


title: Heterochromatin spreading in cancer cells through HDAC7 mediated histone H3.3 landscape reprogramming

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1301 Morris Park Avenu

department: Computational and Systems Biology

institute: Albert Einstein College of Medicine

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

overall_design: Refer to individual Series


title: Disruption of the epigenetic regulator BAP1 drives chromatin remodeling leading to the emergence of cells with breast cancer stem cell properties and aberrant glycosylation [gRNA_MiSeq]

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

institute: IARC

summary: Epigenetic regulator genes are key in controlling cell identity and are frequently disrupted in breast cancers. However, specific epigenetic drivers (epidrivers) of mammary cell plasticity and their mechanistic contributions to this phenotype are poorly characterized. Here, we employed a CRISPR/Cas9 loss-of-function screening strategy to identify potential epidrivers of the emergence of mesenchymal breast cancer stem cell-like phenotypes in non-tumorigenic mammary cells. We unveiled that loss of the histone deubiquitinase BAP1 led to increased expression of breast cancer stem cell and several epithelial-to-mesenchymal transition markers accompanied by disrupted cell organization in mammary spheroids. In-depth characterization of epigenome and transcriptome changes following BAP1 loss revealed less permissive chromatin and downregulation in gene expression impacting programs that control cellular glycosylation, leading to decreased glycan abundance and complexity. BAP1 rescue restored the expression of several deregulated genes in a catalytic activity-dependent manner, suggesting that BAP1-mediated cell identity and glycosylation regulation are dependent on its histone deubiquitinase activity. Our results point to BAP1 as an epidriver of mammary cell plasticity and glycosylation aberrations, through the disruption of its histone modifying and gene expression regulation roles.

overall_design: To identify epigenetic regulators with potential driver roles in the acquistion of mesenchymal breast cancer stem cell markers, we have transduced two independent clones of MCF10A Cas9-expressing cells with a lentiviral gRNA library targeting 426 epigenetic regulator genes. Mesenchymal breast cancer stem cell-like populations were isolated by FACS based on CD24, CD44 and EpCAM marker expression. gRNAs were sequenced through MiSeq, and the enriched and depleted gRNAs were identified by comparing the mesenchymal breast cancer stem cell-like population with the bulk of cells on the day of sorting.

first: Mariana

last: Gomes da Silva Araujo

first: Aurélie

last: Sallé

first: Cyrille

last: Cuenin

first: Vincent

last: Cahais

first: Rita

last: Khoueiry


title: Expression data from B lymphoid precursors of EPO-exposed and PBS-exposed C57BL/6 mice

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
B lymphopoiesis, a critical process during hematopoiesis, is tightly regulated through the expression of specific gene sets. While exposure to erythropoietin (EPO) has been shown to negatively affect B lymphopoiesis in mice, its impact on transcriptional regulation remains poorly understood
Using microarrays, we analyzed gene expression in B lymphoid precursors from control wild-type (C57BL/6) mice and EPO-exposed mice. Our analysis revealed distinct classes of genes that were up-regulated or down-regulated during stress erythropoiesis

overall_design: B lymphoid precursors were FACS-sorted at successive stages of bone marrow lymphopoiesis (Pro-B, Pre-BI, Pre-BII-L, and Pre-BII-S) for RNA extraction and hybridization using Affymetrix microarrays

first: Salima

last: Hacein-Bey-Abina

first: Andrada

last: Chiron


title: Excitatory and inhibitory neurons accumulate distinct Ab plaques in mouse models of APP overexpression

city: Houston

first: Jacob

middle: Michael

last: Dundee

address: 1 Baylor Plaza

department: Neuroscience

institute: Baylor College of Medicine

summary: Amyloid plaque heterogeneity is a hallmark of Alzheimer's disease (AD), yet the mechanisms governing plaque diversity and its relationship to disease progression remain poorly understood. Although both diffuse and neuritic plaques are present in AD brain tissue, we do not know how these distinct conformations arise or influence pathological outcomes. Here, we developed transgenic mouse models expressing identical APP constructs in either glutamatergic or GABAergic neurons to investigate how cellular context shapes amyloid pathology. This approach revealed that the cellular source of APP influences both the biochemical composition and structural characteristics of resulting Aβ deposits. APP expressed in GABAergic neurons generated exclusively diffuse plaques with elevated Aβ42/Aβ40 ratios that failed to induce gliosis, while glutamatergic expression produced primarily neuritic plaques surrounded by activated microglia. Differences in deposit characteristics appeared to arise from fundamental variations in APP processing between excitatory and inhibitory neurons. Moreover, only neuritic plaques generated by glutamatergic neurons caused behavioral deficits, while diffuse plaques from GABAergic neurons did not impair cognition despite substantial amyloid burden. These findings may provide new insight into the mechanisms underlying amyloid heterogeneity in AD and suggest that plaque conformation, rather than simply amyloid load, may influence cognitive trajectories. snRNA-seq revealed that microglia from the excitatory models showed many DAM genes were upregulated, which were absent in the inhibitory model. The data also revealed there were no changes in expression of key APP processing enzymes between excitatory or inhibitory neurons in each model.

overall_design: Single nucleus RNA sequencing (snRNA-seq) of frontal cortexes from CAMKII-, Vglut1-, or Gad2-driven APP transgenic mice at 6 mo, 9 mo, and 24 mo, respectively. Animal ages were chosen based on amyloid load. Each sample contained 2 animals.

first: Gabriella

last: Perez

first: Zoe

last: Lai

first: George

last: Edwards III

first: Shannon

last: Leahy

first: Chuangye

last: Qi

first: Yanyan

first: Ye-Jin

last: Park

first: Tzu-Chiao

last: Lu

first: Danish

last: Uddin

first: Rong

last: Zhao

first: Hui

last: Zheng

first: Hongjie

last: Li

first: Joanna

last: Jankowsky


title: Aged myeloid and mesenchymal cells develop unique senotypes

first: Chantal

last: McCabe

summary: Cellular senescence is a heterogeneous phenotype that has primarily been characterized in non-hematopoietic cells. The extent to which immune cells differ from mesenchymal cells in their senescence phenotype, or “senotype”, is unclear. Here, we applied single-cell transcriptomic and proteomic technologies with both global and cell-specific senolytic mouse models to test the extent to which cellular senescence occurs in immune cells in the bone marrow of aging mice and placed these findings in the context of aged bone mesenchymal cells. In the bone marrow, myeloid-lineage cells exhibited the highest expression of the senescence marker, p16, among all immune cell types, while also exhibiting high levels of inflammatory markers. Targeted clearance of p16+ myeloid cells in aged mice using the LysM-Cre x p16-LOX-ATTAC model reduced levels of senescence-associated markers in monocyte-lineage cells, yet only had minor effects on age-related bone loss in male mice, with no effect in females. In more detailed analyses, p16+ myeloid cells were only acutely cleared, being repopulated back to basal levels within a short time period. This led to a lack of long-lasting reduction in senescent cell burden, in contrast to when targeting bone mesenchymal cell types. In vitro, myeloid lineage cells failed to undergo growth arrest under genotoxic stress, potentially explaining their rapid repopulation in vivo . To further understand how DNA damage influences senescence in myeloid cells versus mesenchymal cells, we performed senescence induction using etoposide treatment on primary mouse bone marrow-derived macrophages (BMDMs) and mesenchymal bone marrow stromal cells (BMSCs) in side-by-side in vitro experiments. Although BMDMs upregulated mRNA transcripts for p16 and p21 in response to senescence induction, these increases were considerably lower in magnitude as compared to BMSCs. Furthermore, in contrast to BMSCs, BMDMs did not develop a transcriptional profile of senescence development. Collectively, our findings indicate that myeloid-lineage cells express the most robust features of senescence of all immune cells in the bone marrow but differ substantially in their senotype relative to mesenchymal cells in the aging skeleton. Specifically, while aged bone marrow myeloid cells express features of senescence, they do not possess the full senescent phenotype of aged mesenchymal cells. Thus, our findings point to fundamental differences in the senotypes of aged immune versus mesenchymal cells that warrants further investigation across tissues.

overall_design: The purpose of this study is to compare the transcriptomes of non-senescence (control) and senescent (using etoposide) primary mouse bone marrow-derived macrophages (BMDMs) versus mesenchymal bone marrow stromal cells (BMSCs) in vitro.

first: Madison

last: Doolittle

first: Mitchell

last: Froemming

first: David

last: Monroe

first: Sundeep

last: Khosla


title: Disruption of the epigenetic regulator BAP1 drives chromatin remodeling leading to the emergence of cells with breast cancer stem cell properties and aberrant glycosylation [RNAseq_3D]

first: Zdenko

last: Herceg

overall_design: To assess changes in gene expression after BAP1 loss, we have generated BAP1 knockouts in MCF10A Cas9-expressing cells, and performed RNA-sequencing using two independent BAP1 knockout clones and Cas9-expressing control cells cultured as mammospheres, in duplicates.

first: Mariana

last: Gomes da Silva Araujo

first: Cyrille

last: Cuenin

first: Vincent

last: Cahais

first: Rita

last: Khoueiry


title: Disruption of the epigenetic regulator BAP1 drives chromatin remodeling leading to the emergence of cells with breast cancer stem cell properties and aberrant glycosylation [ChiPseq_2D]

overall_design: To assess the effect of BAP1 loss on the levels and distribution of H2AK119ub1, we have generated BAP1 knockouts in MCF10A Cas9-expressing cells, and performed ChIP-sequencing for this histone mark in MCF10A wildtype, MCF10A Cas9-expressing cells and two independent BAP1 knockout clones. Each library was sequenced twice to increase the number of reads.

first: Aurélie

last: Sallé

first: Claire

last: Renard

first: Caroline

last: Pires Poubel

first: Stéphane

last: Keita


title: Heterochromatin spreading in cancer cells through HDAC7 mediated histone H3.3 landscape reprogramming [RNA-seq]

first: Jorge

last: Fajardo

summary: Class IIa histone deacetylases (HDACs) are a family of enzymes that despite their name, do not have any measurable histone deacetylase activity but they function as multi-protein interaction hubs due to the presence of a prolonged N-terminal domain. Here we show that HDAC7, a member of the Class IIa HDAC family, is a chaperone for Histone H3.3 and, interacts with H3.3 and HIRA on chromatin. Specific inhibition of HDAC7 expression with subtype specific siRNAs results in inhibition of the interaction of H3.3 with HIRA, while the association of H3.3 with DAXX and H3K9me3 is significantly increased, resulting in H3.3 being deposited on H3K9me3+/DAPI+ heterochromatin nuclear foci with observed changes in RNA expression. This drives substantial alteration of cancer cell gene expression as well as inhibition of the stemness phenotype for cancer cells. To understand the genome wide effect on expression, we perform RNA-seq following HDAC7 knockdown.

overall_design:
We performed differential gene expression analysis in 2 patients dervied GSCs samples following siRNA knockdown of HDAC7
We compared sicontrol versus siHDAC7 samples using two different patients.

first: Ola

last: Hassan

first: Mattia

last: Pizzagalli

first: Owen

last: Leary

first: John

last: Zepecki

first: Laura

last: Jinxuan Wu

first: Daniel

last: Lee

first: Lindsey

last: Howard

first: Andras

last: Fiser

last: Karambizi

first: Nikos

last: Tapinos


title: Drug repurposing strategy reveals Cobimetinib as a promising disease-modifying drug for Osteoarthritis

city: Rotterdam

first: Gerjo

last: van osch

address: Dr. Molewaterplein 40

department: Orthopaedics and Sports Medicine

country: Netherlands

institute: Erasmus MC

summary: Osteoarthritis (OA) is a common disabling disease for which no effective pharmacological therapy exists. The progression of osteoarthritis is characterized by the loss of homeostasis in the cartilage. Since in the early stages of the disease, a phenotypic switch is seen in which articular chondrocytes become hypertrophic and promote degradation of the cartilage extracellular matrix, targeting this phenomenon might be the key to developing a disease-modifying osteoarthritis drug (DMOAD). In this study, the signature reversing principle combined with a drug repurposing strategy was used to accelerate the identiﬁcation and validation of potential DMOADs. Starting from single-cell transcriptomic analysis of patient-derived cartilage, we identified 6 drugs predicted to reduce chondrocyte hypertrophy. Subsequent in vitro evaluation in human chondrocytes and cartilage explants demonstrated that Cobimetinib, a MEK1/2 inhibitor, reduced chondrocyte hypertrophy-related and catabolic gene expression, such as SPP1, COL10A1, MMP13 and ADAMTS5, while promoting collagen type 2 and aggrecan gene expression. Finally, single-cell RNA sequencing performed on osteoarthritic cartilage explants exposed to Cobimetinib ex vivo confirmed the anti-hypertrophic effect of Cobimetinib on hypertrophy-related gene expression and additionally showed a deletion of chondrocytes with a fibrotic phenotype. This study is a proof of concept that omics data together with a drug repurposing strategy accelerate drug discovery in diseases like osteoarthritis and could quickly lead to many new therapeutic roles for safe and effective drugs.

overall_design:
Full-thickness 3mm cartilage biopsy punches taken from left over material from 3 OA patients recieving a total-knee arthroplasty were cultured for 24h in DMEM-LG supplemented with 1% ITS+, 50ug/ml gentamicin and 1.5ug/ml amphotericin B for calibration. After this, they were subjected for 6 days to a treatment with either 1000nM Cobimetinib or 0.01% DMSO as a vehicle control in DMEM-LG supplemented with 1% ITS+, 50ug/ml gentamicin and 1.5ug/ml amphotericin B. Subsequently, cartilage explants were subjected to a digestion protocol of 10mg/ml protease from streptomyces griseus for 45 minutes, followed by 4mg/ml collagenase B until everything was digested (~4.5hours). Donors were pooled per experimental condition. Samples were prepared using 10x genomics chemistry version 3' v3 and the resulting libraries were sequenced on a Novaseq6000 platform (Illumina, San Diego, CA, USA). Subsequently, FASTQ files were constructed using cellranger mkfastq (version 7.1.0) in combination with blc2fastq (version 2.20.0.422). The resulting FASTQ files were processed using cellranger count (version 7.1.0). The genome version used in processing was GRCh38. Cells were assigned to the correct sample present in the multiplexed pools using vireo (version 0.2.3) in combination with cellsnp-lite (version 1.2.3).
Raw data can be accessed through contacting the corresponding author: g.vanosch@erasmusmc.nl upon signing of a DTA.

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

last: Veldman

first: Mauricio

last: Ferrao Blanco

first: Gregory

last: van Beek

first: Remco

last: Hoogenboezem

first: Eric

last: Bindels

first: Andrea

last: Lolli

last: Farrell

last: van Osch


title: Disruption of the epigenetic regulator BAP1 drives chromatin remodeling leading to the emergence of cells with breast cancer stem cell properties and aberrant glycosylation [RNAseq_2D]

first: Zdenko

last: Herceg

overall_design: To assess changes in gene expression after BAP1 loss, we have generated BAP1 knockouts in MCF10A Cas9-expressing cells, and performed RNA-sequencing using two independent BAP1 knockout clones and Cas9-expressing control cells, in duplicates.

first: Mariana

last: Gomes da Silva Araujo

first: Cyrille

last: Cuenin

first: Vincent

last: Cahais

first: Rita

last: Khoueiry


title: ADAR1 Regulates SFTSV Replication by Modulating miRNA Expression

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

summary: RNA modification plays a crucial role in the regulation of various diseases and viral infections. ADAR1 (adenosine deaminase 1) is a key RNA editing enzyme that can convert adenosine (A) into the modified base inosine (I). This RNA modification has been confirmed to regulate the biological processes of various diseases and viruses. In our previous study on patients with thrombocytopenia syndrome, we conducted a longitudinal sampling study of transcriptomics and epigenetics (Nat. Commun., 2021, 12:5629). In this study, through the analysis of patient RNA-seq, we found that in patients infected with SFTSV, the expression of ADAR1 increased, and it gradually decreased with the recovery of the patients. By constructing cell models and conducting RNA sequencing analysis, we also obtained results similar to those from clinical samples. We found that ADAR1 knockdown promoted the replication of Bunyavirus (SFTSV), while overexpression inhibited virus replication. Further miRNA sequencing analysis revealed that after ADAR1 knockdown, some miRNAs with differential expression were produced, and the target genes of these differentially expressed miRNAs were closely related to neutrophil-mediated immune signaling pathways. These differentially expressed miRNAs may be due to ADAR1 editing the adenosine (A) in the double-stranded region of miRNA precursors to inosine (I), thereby changing the structure of dsRNA and making it difficult for Drosha or Dicer to obtain, thereby reducing the production of miRNAs. Considering these phenomena, we speculate that in the ADAR1 knockdown state, the changes in miRNA expression levels lead to the downregulation of genes involved in neutrophil-mediated immune signaling pathways, potentially causing neutrophil-mediated immune function impairment, thereby enhancing SFTSV replication. These findings provide new insights into the role of ADAR1 in SFTSV replication and immune signaling pathways, and provide a theoretical basis for the development of treatment strategies targeting ADAR1.

overall_design: This study shows that ADAR1 expression increases during SFTSV infection and decreases as patients recover. Knockdown of ADAR1 promotes SFTSV replication, while its overexpression inhibits it. Further analysis reveals that ADAR1 knockdown alters miRNA expression, affecting neutrophil-mediated immune signaling pathways. This suggests ADAR1 edits miRNA precursors, impacting miRNA production and immune function, thereby enhancing SFTSV replication. These findings offer new insights into ADAR1's role in viral replication and immune regulation, providing a foundation for developing ADAR1-targeted therapies.

first: Shaoqing

last: Han

first: Yafen

last: Wang


title: Androgen receptor splice variant expression and prostate cancer recurrence after salvage therapy

city: Charlestown

first: Keisuke

last: Otani

address: 149 13th Street, Rm 4406

department: Radiation Oncology

institute: Massachusetts General Hospital

summary: Radiotherapy (RT) with or without androgen deprivation therapy (ADT) is standard salvage therapy for men with local or biochemical recurrence of prostate cancer after prostatectomy, but there is an unmet need for biomarkers to identify potential non-responders. We hypothesized that androgen receptor splice variants (ARVs) are detectable in primary prostate cancer and may modulate response to salvage RT+ADT. We identified a retrospective cohort of prostate cancer patients treated with prostatectomy followed by salvage RT + ADT, and we performed targeted RNA-seq of archival formalin-fixed paraffin-embedded prostatectomy samples to comprehensively characterize the landscape of ARVs.

overall_design: We performed targeted RNA-seq using a custom library of >3000 primers spanning all AR exons and introns. 43 prostatectomy samples from the salvage RT+ADT patient cohort were sequenced.  6 additional prostatectomy specimens from a separate cohort of localized prostate cancer patients and 7 tumor samples from another cohort of metastatic prostate cancer patients were also sequenced using the same methodology.

first: David

middle: J

last: Konieczkowski

last: Miyamoto


title: Heterochromatin spreading in cancer cells through HDAC7 mediated histone H3.3 landscape reprogramming [ChIP-seq]

first: Jorge

last: Fajardo

summary: Specific inhibition of HDAC7 expression with subtype specific siRNAs results in inhibition of the interaction of H3.3 with HIRA, while the association of H3.3 with DAXX and H3K9me3 is significantly increased, resulting in H3.3 being deposited on H3K9me3+/DAPI+ heterochromatin nuclear foci with observed changes in RNA expression. Inhibition of HDAC7 triggers a significant increase of heterochromatin marks H3K9me3 and H3K27me3, global heterochromatin spreading in cancer cells, and reprogramming of the H3.3 chromatin landscape. We performed H3K9me3 chip-seq in glioma stem cells following HDAC7 knockdown in order to identify specific sites of heterochromatin spreading and/or increased occupancy.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K9me3  in control and HDAC7 KD glioma stem cells.

first: Ola

last: Hassan

first: Mattia

last: Pizzagalli

first: Owen

last: Leary

first: John

last: Zepecki

first: Laura

last: Jinxuan Wu

first: Daniel

last: Lee

first: Lindsey

last: Howard

first: Andras

last: Fiser

last: Karambizi

first: Nikos

last: Tapinos


title: GATA4 Ubiquitinated by CRL4B complex to stimulated Lysosome and promote Ovarian cancer EMT process [RNA-seq]

city: Chongqing

first: Xin

last: Yin

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing medical university

summary: GATA4 has emerged as a prominent transcription active factor for cardiomyogenesis and carcinogenesis. Ovarian cancer is a lethal cancer for women due to the hard diagnosis and easy metastasis. However, the role of GATA4 in breast cancer metastasis remains poorly understood. Here, we indicated that GATA4 was decreased in ovarian cancer and associated with excessive lysosome function and epithelial-mesenchymal transition (EMT). Mechanically, GATA4 was ubiquitinated by CUL4B, a submit of Cullin-Ring E3 ligase (CRL) complexes, and decreased the histone H3K27 acetylation. In vivo, knock down GATA4 was facilitated the proliferation and metastasis of SKOV3. Genome-wide analysis of the transcriptional target of the GATA4 and GATA4/CUL4B complex identified a cohort of genes including TRM22 and KLK15 that are potential involved in lysosome and EMT. These results suggest that GATA4 as a tumor suppressor to impair the lysosome acid environment and promote ovarian cancer metastasis in vivo and vitro through ubiquitin degradation system initiated by CRL4B complex. Our study supporting the tumor suppression role of GATA4, implied the pursuit of GATA4 as a therapeutic target for cancer intervention.

overall_design: To investagate the function of GATA4 in regulation of ovarian cancer, we overexpression GATA4 in ovaria cancer cell line SOKV3 and find the potential key differential genes and signaling pathway

first: Junlin

last: He


title: GATA4 Ubiquitinated by CRL4B complex to stimulated Lysosome and promote Ovarian cancer EMT process [ChIP-seq]

summary: GATA4 has emerged as a prominent transcription active factor for cardiomyogenesis and carcinogenesis. Ovarian cancer is a lethal cancer for women due to the hard diagnosis and easy metastasis. However, the role of GATA4 in breast cancer metastasis remains poorly understood. Here, we indicated that GATA4 was decreased in ovarian cancer and associated with excessive lysosome function and epithelial-mesenchymal transition (EMT). Mechanically, GATA4 was ubiquitinated by CUL4B, a submit of Cullin-Ring E3 ligase (CRL) complexes, and decreased the histone H3K27 acetylation. In vivo, knock down GATA4 was facilitated the proliferation and metastasis of SKOV3. RNA-seq and CUT&Tag ChIP-seq of the transcriptional target of the GATA4 and GATA4/CUL4B complex identified a cohort of genes including TRM22 and KLK15 that are potential involved in lysosome and EMT. These results suggest that GATA4 as a tumor suppressor to impair the lysosome acid environment and promote ovarian cancer metastasis in vivo and vitro through ubiquitin degradation system initiated by CRL4B complex. Our study supporting the tumor suppression role of GATA4, implied the pursuit of GATA4 as a therapeutic target for cancer intervention.

overall_design: To investagate the target genes of GATA4 and CUL4B in regulation of ovarian cancer, CUT&Tag ChIP-seq for GATA4 and CUL4B was performed in SKOV3 cells


title: Disruption of the epigenetic regulator BAP1 drives chromatin remodeling leading to the emergence of cells with breast cancer stem cell properties and aberrant glycosylation [ATACseq_3D]

city: Lyon

first: Zdenko

last: Herceg

overall_design: To assess changes in chromatin accessibility after BAP1 loss, we have generated BAP1 knockouts in MCF10A Cas9-expressing cells, and performed ATAC-sequencing using two independent BAP1 knockout clones and Cas9-expressing control cells cultured as mammospheres, in duplicates.

first: Mariana

last: Gomes da Silva Araujo

first: Cyrille

last: Cuenin

first: Vincent

last: Cahais

first: Claire

last: Renard

first: Caroline

last: Pires Poubel

first: Stéphane

last: Keita

first: Rita

last: Khoueiry


title: A DUF630 and 632 Domains-containing Protein, ZmNRL1, Acts as a Positive Regulator of Nitrogen Stress Response in Maize

city: Guangzhou

first: Chunyan

last: Zheng

address: Wushan Street

institute: South China Agricultural University

summary: Nitrogen (N) is a key macronutrient whose availability often determines maize growth and productivity. Improving nitrogen use efficiency (NUE) is critical to increase maize yield while reducing N input, and more importantly, alleviating environmental pollution. However, only a few genes have been exploited for maize NUE improvement thus far. Here, we evaluate NUE-related traits in 296 maize inbred lines. A total of 87 genetic variants, resolved to a total of 44 candidate genes, were found to associated with NUE-related traits through a genome-wide association study. We further found that the natural variations in ZmNRL1, encoding a DUF630 and DUF632 domains-containing protein, strongly associated with chlorophyll content under N starvation. Loss of ZmNRL1 function causes accelerated leaf senescence and reduces biomass, nitrate content and nitrate reductase activity under N limitation, while overexpression of ZmNRL1 enhanced N stress tolerance. Comparative transcriptome analysis revealed that ZmNRL1 has a broad impact on the expression of many N utilization and signaling genes. Furthermore, heterologous expression of ZmNRL1 in Arabidopsis also improved the growth and yield under N-limiting conditions. Thus, ZmNRL1 plays a key role in regulating maize adaptation to N limitation and could be a potential target for breeding high-yield maize with enhanced NUE.

overall_design: For maize RNA-seq analysis, 10-day-old maize seedlings were treated with modified Hoagland solutions supplemented with 15 mM NO3- or 0.15 mM NO3- for 48 hours and roots were harvested for total RNA isolated. A total of 18 cDNA libraries of six samples (WT+N, ZmNRL1-OE+N, zmnrl1-mu+N, WT–N, ZmNRL1-OE–N and zmnrl1-m–N) with three repeats were constructed and sequenced.

first: Hanjie

last: Li

last: Luo

first: Faqiang


title: Single-cell sequencing reveal transcriptional cell lineage heterogeneity in extracranial arteriovenous malformation

city: Shanghai

first: Yi

last: Sun

address: Zhizaoju Road 639

department: Department of Interventional Therapy, Multidisciplinary Team of Vascular Anomalies

institute: Shanghai Ninth People’s hospital, Shanghai Jiao Tong University, Shanghai, PR China

summary: Extracranial arteriovenous malformations (eAVMs) are rare congenital vascular anomalies consisting of abnormal artery-vein bypass with no intervening capillary network and can lead to disability and death.  In this study, an integration of two cutting-edge technologies, single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), was applied to uncover the underlying pathophysiology of eAVMs. Patient-matched eAVM tissue samples and normal tissue control data were analyzed. We identified different cell states of endothelial cells (ECs), perivascular cells and immune cells in eAVMs and characterized their spatial distributions with multiple immunofluorescence staining (mIF), immunostaining and spatial transcriptomics. Dysregulated cell-to-cell interactions among ECs, perivascular cells and immune cells that are associated with disease progression were cataloged. By performing scRNA-seq on 117,360 individual cells, we identified 14 transcriptomically defined cell lineages from eAVMs. We uncovered the presence of MAFB+ nidus ECs. Moreover, mesenchymal activation was observed in ECs, characterized by high expression of POSTN or FN1 and the upregulation of the NOTCH and TGF-β pathways. mIF and ST verified the location of MAFB+ nidus ECs and mesenchymal activation of eAVM ECs. We identified transcriptional variation within perivascular cells and the presence of smooth muscle–like pericytes in eAVMs. Ligand‒receptor-based cell‒cell interaction analysis indicated that Nd ECs might specifically communicate with perivascular cells through the MDK, VEGF, SEMA3 and ANGPT pathways, and this cellular crosstalk was supported by colocalization analysis of spatial transcriptomics. In addition, we found that hypoxia plays an important role in the development of eAVMs, and hyperbaric oxygen therapy (HBOT) was used to treat one large pelvic eAVM. Thus, correcting the hypoxic microenvironment could be a promising therapeutic strategy.

overall_design: To generate an overview of the molecular information within eAVMs at the single-cell level, we performed scRNA-seq on nine samples of eAVMs receiving a confirmatory histopathologic evaluation from a board-certified dermatopathologist and two nonlesional tissue sample controls

first: Ren

last: Cai


title: A Spatiotemporal Atlas of Cerebrovascular Development in Zebrafish: From Vasculatures to Cells and Molecules

city: Zhan Jiang

first: Xiaoyu

state: Guangdong

address: 57 People's Avenue

institute: Affiliated Hospital of Guangdong Medical University

summary: The cerebrovascular system plays a pivotal role in brain development and the maintenance of its functions. Although several single-cell transcriptomic studies have delineated the molecular profiles of brain vasculature, integrating these data into a coherent multiscale understanding across molecular, cellular, and vascular network architecture remains a fundamental challenge. Here, we present a comprehensive spatiotemporal atlas of zebrafish cerebrovascular development that bridges these scales by combining in situ sequencing with three-dimensional (3D) vascular network reconstruction. Our quantitative 3D analysis revealed region-specific cerebrovascular growth dynamics at 3, 6, and 11 days post-fertilization. Through single-cell RNA sequencing, we identified endothelial cell (EC) subtypes at these stages and validated their molecular signatures and cross-species conservation during vascular development. Spatial transcriptomics further demonstrated that capillary ECs are the predominant vascular subtype within intracranial vessels, showing progressive enrichment in mesencephalic/metencephalic regions. Importantly, we identified three previously uncharacterized genes (slc16a1a, zgc:158423, and si:ch73-86n18.1) that critically contribute to blood-brain barrier integrity. Our study systematically deciphers the molecular profile of ECs during development, establishing a foundational framework for understanding the dynamic landscape of cerebrovascular development.

overall_design: Endothelial-specific Tg(kdrl:eGFP) transgenic zebrafish line was used to isolate the brain endothelial cells by flow cytometry at 3, 6, and 11 dpf, and then performed  10x Genomics scRNA-seq on the sorted cells with 3' labelling strategy.


title: CRISPR activation screen identifies GNAO1 as a driver of glioblastoma cell differentiation

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

summary: Inducing tumor cell differentiation is a potential strategy for treating malignant cancers, including glioma. Here we perform a genome-scale CRISPR activation screen and identify that G Protein Subunit Alpha O1 (GNAO1) as a critical regulator of glioma cell differentiation. GNAO1 overexpression in combination with a small molecular inhibitor cocktail, including CHIR99021, SB431542, RepSox, and Y27632, markedly promotes neuronal differentiation of glioblastoma cells. GNAO1 is high expressed in normal neuronal tissues but low expressed in gliomas. High expression of GNAO1 is correlated with a better prognosis. GNAO1 overexpression decreases cell proliferation, cell migration, and orthotopic GBM tumor xenograft growth. GNAO1 overexpression activates neuronal differentiation pathways by down-regulation of transcript factor HES1, a key mediator of neuronal differentiation. GNAO1 recruits TRIM21 and increases TRIM21-mediated ubiquitination and degradation of CREB, leading to decreased p300-mediated H3K27ac levels of HES1 promoter and HES1 downregulation. In addition, GNAO1 mRNA stability is regulated by METTL3-regulated N6-methyladenosine (m6A). Overexpression of GNAO1 enhances glioblastoma response to Temozolomide (TMZ) and extends the survivals of animals bearing orthotopic GBM xenograft tumors. Our finding suggests that inducing neuronal differentiation of glioblastoma cells by engineering GNAO1 overexpression is a potential therapy strategy, which not only reduces tumor cell proliferation but also enhances tumor cell response to chemotherapy.

overall_design: To understand why GNAO1 is important for glioma cell differentiation, we performed transcriptome analysis in GSC R83/WT and GSC R83/GNAO1 cells using RNA-seq.

first: Bowen