title: Chromosome Architecture Impacts Virulence and Competitiveness in Agrobacterium tumefaciens C58

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Chromosome architecture plays a crucial role in bacterial adaptation, yet its direct impact remains unclear. Different bacterial species, and even strains within the same species, exhibit diverse chromosomal configurations, including a single circular or linear chromosome, two circular chromosomes, or a circular-linear combination. To investigate how these architectures shape bacterial behavior, we generated near-isogenic strains representing each configuration in Agrobacterium tumefaciens C58, an important soil bacterium widely used for plant genetic transformation. Strains with a single-chromosome architecture, whether linear or circular, exhibited faster growth, enhanced stress tolerance, and greater inter-strain competitiveness. In contrast, bipartite chromosome strains showed higher virulence gene expression and enhanced transient plant transformation efficiency, suggesting a pathogenic adaptation. Whole-transcriptome analysis revealed architecture-dependent gene expression patterns, underscoring the profound impact of chromosome organization on Agrobacterium fitness and virulence. These findings highlight how chromosome structure influences bacterial adaptation and shapes evolutionary trajectories.

overall_design: Hi-C and whole genome sequencing expriments were performed on wild type and mutants of Agrobacterium tumefaciens growing in minimal medium.


title: Epigenetic control and inheritance of rDNA arrays [2]

status: Public on Aug 25 2025

city: Kansas City

first: Tamara

last: Potapova

state: Missouri

country: USA

institute: Stowers Institute for Medical Research

type: Methylation profiling by high throughput sequencing

summary: Ribosomal RNA (rRNA) genes exist in multiple copies arranged in tandem arrays known as ribosomal DNA (rDNA). The total number of gene copies is variable, and the mechanisms buffering this copy number variation remain unresolved. We surveyed the number, distribution, and activity of rDNA arrays at the level of individual chromosomes across multiple human and primate genomes. Each individual possessed a unique fingerprint of copy number distribution and activity of rDNA arrays. In some cases, entire rDNA arrays were transcriptionally silent. Silent rDNA arrays showed reduced association with the nucleolus and decreased interchromosomal interactions, indicating that the nucleolar organizer function of rDNA depends on transcriptional activity. Methyl-sequencing of flow-sorted chromosomes, combined with long read sequencing, showed epigenetic modification of rDNA promoter and coding region by DNA methylation. Silent arrays were in a closed chromatin state, as indicated by the accessibility profiles derived from Fiber-seq. Removing DNA methylation restored the transcriptional activity of silent arrays. Array activity status remained stable through the iPS cell re-programming. Family trio analysis demonstrated that the inactive rDNA haplotype can be traced to one of the parental genomes, suggesting that the epigenetic state of rDNA arrays may be heritable. We propose that the dosage of rRNA genes is epigenetically regulated by DNA methylation, and these methylation patterns specify nucleolar organizer function and can propagate transgenerationally.

overall_design: Comparison of rDNA methylation levels between flow-sorted acrocentric chromosomes from chm13. Acrocentric chromosomes include chromosomes 13, 14, 15, 21, and 22. Activity markers show that the rDNA array in chromosome 22 is inactive in chm13. Flow sorting was performed twice to increase purity.

first: Matthew

last: Borchers

first: Paxton

last: Kostos

first: Sean

last: McKinney

first: Jeff

last: Haug

first: Andrea

last: Guarracino

first: Steven

last: Solar

first: Madelaine

last: Gogol

first: Graciela

last: Monfort Anez

first: Leonardo

last: Gomes de Lima

first: Yan

first: Kate

last: Hall

first: Sophie

last: Hoffman

first: Erik

last: Garrison

first: Adam

middle: M

last: Phillippy

first: Jennifer

middle: L

last: Gerton


title: Prolonged immune activation in post-acute sequelae of SARS-CoV-2: neutrophil dynamics and therapeutic insights

city: Daejeon

first: Suhee

last: Hwang

address: 55, Expo-ro, Yuseong-gu

department: Korea Virus Research Institute

country: South Korea

institute: Institue for Basic Science

type: Expression profiling by high throughput sequencing

summary: To comprehensively understand the mechanisms driving PASC, we utilized a Phodopus roborovskii hamster model to investigate the long-term effects of SARS-CoV-2 infection compared to Influenza A virus (IAV), showing impaired weight recovery, severe lung pathology, and significant neutrophil accumulation. At 30 dpi, single cell RNA sequencing of BALF, lung, and spleen revealed unique PASC gene signatures, with increased neutrophils and reduced macrophages indicating disrupted myeloid differentiation. Inhibition of neutrophil-driven inflammation reduced PASC symptoms.

overall_design: We utilized a Phodopus roborovskii hamster model to investigate the long-term effects of SARS-CoV-2 infection compared to Influenza A virus (IAV), showing impaired weight recovery, severe lung pathology, and significant neutrophil accumulation. We performed single-cell RNA sequencing on BALF, lung, spleen at 30dpi and histopathological examinations. Our analysis provide critical insights into PASC mechanisms.

first: Young Ki

last: Choi

first: Mina

last: Yu


title: Distinct roles for NF-κB in hematopoietic stem cells and the bone marrow milieu in promoting hematopoietic aging

city: Los Angeles

last: Chia

state: CA

address: 570 Boyer Hall

institute: UCLA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hematopoietic aging is characterized by chronic inflammation associated with myeloid bias, hematopoietic stem cell (HSC) accumulation, and functional HSC impairment. Yet it remains unclear how inflammation promotes aging phenotypes. Nuclear factor κB (NF-κB) both responds to and directs inflammation, and we present an experimental model of elevated NF-κB activity ("inhibitor of κB deficient" [IκB-]) to dissect its role in hematopoietic aging phenotypes. We find that while elevated NF-κB activity is not sufficient for HSC accumulation, HSC-autonomous NF-κB activity impairs their functionality, leading to reduced bone marrow reconstitution. In contrast, myeloid bias is driven by the IκB- proinflammatory bone marrow milieu, as observed functionally, epigenomically, and transcriptomically. A single-cell RNA sequencing (scRNA-seq) HSPC labeling framework enables comparisons with aged murine and human HSC datasets, documenting an association between HSC-intrinsic NF-κB activity and quiescence but not myeloid bias. These findings delineate separate regulatory mechanisms that underlie the three hallmarks of hematopoietic aging, suggesting that they are specifically and independently therapeutically targetable.

overall_design: CD45.1+ bone marrow was transplanted into young CD45.2 WT and IκB– recipient mice. After 13-15 weeks, donor LT-HSC, MPP2, MPP3 and MPP4 HSPC subsets were isolated from the bone marrow of the bilateral femur and tibia by flow sorting.

middle: J

first: Apeksha

last: Singh

first: Alexander

last: Hoffmann


title: Erroneous efferocytosis of live neutrophils during infection prevents the resolution of inflammation

city: Columbus

first: Juhi

last: Bagaitkar

address: 700 Childrens Dr

institute: Nationwide Childrens.org

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

overall_design: Refer to individual Series


title: Single Cell Profiling in the Sox10Dom Hirschsprung Mouse Implicates Hox Genes in Enteric Neuron Trajectory Allocation

city: Nashville

first: E Michelle

last: Southard-Smith

state: TN

address: 2215 Garland Ave,

department: Medicine, Genetic Medicine

institute: Vanderbilt University Medical Center

summary: Enteric nervous system (ENS) development requires migration, proliferation, and neuronal diversification of progenitors to achieve normal gastrointestinal motility. Sox10 deficits disrupt the ratios of mature enteric neuron subtypes. How Sox10 deficiency alters the proportions of neuronal subtypes is still being determined. Sox10's prominent expression in neural crest-derived enteric progenitors and lack of this gene in enteric neurons led us to investigate how Sox10 effects in early enteric progenitors could alter neuronal allocation. To explore this further, enteric progenitors, developing neurons, and enteric glia were isolated from Sox10+/+ and Sox10Dom/+ littermates at 15.5 days post-coitus based on dual Sox10-H2BVenus and Phox2b-H2BCerulean transgene expression for single-cell RNA sequencing (scRNA-seq). The data was processed in R to identify cell-specific markers, differentially expressed genes, biological processes associated with gene ontology, cell fate trajectories, and gene regulatory network activity between genotypes. Hybridization chain reaction (HCR) validated expression changes detected in scRNA-seq.

overall_design: Myenteric neurons and glia were isolated from Phox2b-CFP, Sox10-YFP fetal intestine expressing Sox10Dom/+ Or Sox10+/+. The whole fetal intestine was dissociated, and single cells were isolated via FACS for single-cell encapsulation using 10X encapsulation methods. DNA libraries were generated and processed for next-generation sequencing.

first: Justin

middle: A

last: Avila

first: Joseph

middle: T

last: Benthal

first: Michelle


title: SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [CUT&Tag]

city: Yokohama

first: Shinsuke

last: Ito

state: Kanagawa

address: 1-7-22 Suehirocho

department: IMS

country: Japan

institute: RIKEN

summary: Polycomb group (PcG) proteins are evolutionarily conserved repressors of developmental genes. Paradoxically, the same PcG proteins also play roles in gene activation via mechanisms that are not yet fully understood. Here, we found that S-phase kinase-associated protein 1A (SKP1A), an essential factor of SCF (SKP1A/CULLIN1/F-box) ubiquitin ligases and a subunit of the PCGF1 (Polycomb group RING finger protein 1) component of Polycomb repressive complex 1 (PCGF1-PRC1), mediates the link between PcG-dependent gene regulation and ubiquitin-dependent proteasomal degradation. By using differentiating mouse embryonic stem cells, we found that SKP1A removes EED, a core component of Polycomb repressive complex 2 (PRC2) that is bound to PcG target gene promoters, via proteasomal degradation, and it thereby sensitises these genes for subsequent activation. Furthermore, we show that SKP1A removes EED from the Meis2 promoter in the midbrain of developing mouse embryos, leading to Meis2 gene expression. In summary, we reveal here a previously unknown role of SKP1A in activating PcG-target genes via the proteasomal degradation of PRC2. This implies that SKP1A-containing PCGF1-PRC1 may confer reversibility on PcG-mediated gene silencing for robust spatiotemporal regulation of target genes.

overall_design: CUT&Tag analysis to investigate the localization of EED using Skp1a, Pcgf1 or Skp1a:Pcgf1  WT control and KO of embryonic midbrain or embryonic stem cell.

first: Takashi

last: Kondo

first: Takaho

last: Endo

first: Junichiro

last: Takano

first: Haruhiko

last: Koseki


title: Adult thymus-derived cMaf+RORγt+γδ T cells lack Scart2 chromatin accessibility and do not reach periphery

city: Hannover

first: Sarina

last: Ravens

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: T cell receptor (TCR) Vγ4+expressing γδT cells can be divided into IFN-γ and IL-17-producing effector T cell subsets. A bias towards γδ17 effector fate decisions is observed during early ontogeny. In contrast, the existence of Vγ4+γδ17 cells derived from adult thymus is still controversial. In the present work, we used a mouse model where T cells are exclusive generated within an adult thymus. Additionally, we employed single-cell chromatin state analysis from thymocytes of normal mice. A small, but considerable population of immatureCd24+Gzma+Vγ4 cells was found that exhibit molecular programs of γδ17 cells. These adult thymus-derived immatureCd24a+cMaf+Vγ4 cells secrete small amounts of IL-17A and IL-17F. Interestingly, do not reach the periphery under steady-state conditions. Furthermore,de novogenerated γδ17-like cells from adult thymus lack transcriptional activity of the Scart2 encoding gene, suggesting that Scart2 is a distinct trait of fetal γδT cell precursors. Together, this study provides valuable insights into developmental traits of Vγ4 cells during adulthood and raises the question on signals suppressing the full maturation and/or thymic export of γδ17-like cells within the adult thymus.

overall_design: Sort Vγ4 γδT cells from thymus and peripheral lymph nodes of adult mice, then perform 5 'Single Cell V(D)J sequencing (10x genomics)

first: Tao

last: Yang


title: Imaging Studies of Local Responses of Prostate Cancer to Radiation Therapy

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary:
Patients receiving radiation therapy for prostate cancer received a multiparametric MRI and MRI/ultrasound-fusion targeted biopsy. Patients received a second mpMRI six months after radiation therapy.
The goal of this study was to generate gene expression profiles of prostate cancer tumor tissue prior to treatment, and compare the gene expression profiles of those patients based on imaging response or time to biochemical recurrence.

overall_design: FFPE blocks of biopsies targeted to MRI-visible lesions were sectioned onto glass slides, stained with H&E, and macrodissected. Tumor from the same MRI-visible lesion across different blocks were pooled.

first: Shana

middle: Y

last: Trostel

first: Elai

last: Davicioni

first: Houssein

last: Sater

first: Baris

last: Turkbey

middle: G

first: Deborah

middle: E

last: Citrin


title: Conserved small RNA networks link inflammation to pain signaling in mice and men

status: Public on Aug 24 2025

city: Jerusalem

first: Nimrod

last: Madrer

address: The Edmond J. Safra Campus, Guvat Ram

country: Israel

institute: The Hebrew University of Jerusalem

type: Non-coding RNA profiling by high throughput sequencing

summary: Inflammation may lead to pain, but the underlying mechanisms remain unclear. Here, we identify cooperating small non-coding RNA (sncRNA) signatures including microRNAs (miRs) and transfer RNA fragments (tRFs) that may drive inflammatory pain in both acute and chronic settings. Initiating lipopolysaccharide (LPS)-induced inflammation altered ganglion-specific, time-dependent miRs and tRFs in murine trigeminal (sensory) and superior cervical (sympathetic) ganglia. Indicating conserved pain-related regulatory elements, many of those changes overlapped with those observed in fibromyalgia syndrome (FMS) patient-derived blood cells and keratinocytes. Moreover, cross-species integrative analyses revealed two oppositely correlated sncRNA clusters whose expression ratios distinguished inflammatory from non-inflammatory states and increased during human nociceptor differentiation. Further suggesting functional roles in pain modulation, these pain-related sncRNAs targeted distinct long RNAs expressed in pain- and cholinergic-related states. Importantly, these sncRNAs and their associated transcripts were validated in datasets from both a murine spinal nerve injury model and synovium samples from osteoarthritis patients with varying pain intensities. Our findings reveal that specific miRs and tRFs act as conserved regulators of nociceptive signaling across species, tissues and pain modalities. Further, this work reveals new understanding of the molecular underpinnings of pain and highlights the notion that mammalian pain- and cholinergic-related sncRNAs actively contribute to the shift from inflammation to peripheral nervous system pain, including fibromyalgia pain.

overall_design: Short RNA-seq from mice trigeminal and super cervical ganglia taken 4 hours, 1 day or 1 week after exposure to LPS or saline

first: Estelle

middle: R

last: Bennett

first: Shani

last: Vaknine-Treidel

first: Menachem

last: Hanani

first: Hermona

last: Soreq


title: SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [RNA-seq]

first: Shinsuke

last: Ito

overall_design: ChIP-seq analysis to investigate the localization of EED using EED WT and KO of embryonic stem cell or embryoid body.

first: Takashi

last: Kondo

last: Enhdo


title: Effects of Pharmacological Polyploidization in Human iPSC-derived Cardiomyocytes

status: Public on Aug 23 2025

city: Durham

first: Nenad

last: Bursac

state: NC

address: 101 Science Dr. Rm. 1169

department: Biomedical Engineering

institute: Duke University

summary: Cell polyploidization, an increase in cellular DNA content without cytokinesis, is closely linked with aspects of cellular function in various tissues and is a defining characteristic of postnatal heart development in many species. However, investigation into how polyploidy affects cardiomyocytes (CMs) has been limited. Despite these challenges, CM polyploidy has been directly shown to attenuate proliferation in zebrafish CMs and diploid CM abundance correlates with recovery following coronary artery ligation in mice, highlighting the importance of understanding this biological process in CMs. In this study, we generated polyploid hiPSC-CMs via inhibition of Aurora Kinase B and found this results in increased cell size, reduced baseline cycling rates and responsiveness to mitogenic stimuli, affected the overall transcriptome and rates of transcription and translation, and altered CM Ca2+ handling. Our work suggests that CM polyploidy may not be just an outcome of CM maturation, but rather it serves a functional purpose. Further examination of the differences between diploid and polyploid hiPSC-CMs can expand our understanding of postnatal CM development and how polyploidy impacts CM growth and maturation.

overall_design: Human iPSC-derived cardiomyocytes were treated with either the small molecule AZD1152, which inhibits Aurora Kinase B (AURKBi, 100nM) or vehicle control, for 4d starting when the hiPSC-CMs were day 16-20 post initiation of differentiation. The CMs were then fed normally for 7d without drug, and collected for bulk RNA sequencing.

first: Strash

last: Nicholas

first: Patsy

last: Marisa

first: DeLuca

last: Sophia

first: Helfer

last: Abbigail

first: Jiang

last: Xixian

first: Wu

last: Tianyu

first: Bursac

last: Nenad


title: Single-cell DNA methylation analysis tool Amethyst resolves distinct non-CG methylation patterns in human astrocytes and oligodendrocytes

city: Portland

first: Lauren

last: Rylaarsdam

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Molecular & Medical Genetics

institute: Oregon Health & Science University

summary: Single-cell sequencing technologies have revolutionized biomedical research by enabling deconvolution of cell type-specific properties from heterogeneous tissue. While robust tools have been developed to handle bioinformatic challenges posed by single-cell RNA and ATAC data, options for emergent modalities such as methylation are much more limited, impeding the utility of results. Here we present Amethyst, a comprehensive R package for atlas-scale single-cell methylation sequencing data analysis. Amethyst begins with base-level methylation calls and enables clustering of distinct biological populations, cell type annotation, differentially methylated region calling, and interpretation of results - facilitating rapid data interaction in a local environment. We introduce the workflow using published single-cell methylation human peripheral blood mononuclear cell and human cortex data. We further apply Amethyst to an atlas-scale brain dataset and deconvolute non-CG methylation patterns in human astrocytes and oligodendrocytes, challenging the notion that this form of methylation is principally relevant to neurons in the brain. Tools such as Amethyst will increase accessibility to single-cell methylation data analysis, catalyzing research progress across diverse contexts.

overall_design: Single-cell methylation analysis was performed on human brain tissue and peripheral blood mononuclear cells.

first: Benjamin

last: Skubi

first: Ruth

last: Nichols

first: Brendan

last: O'Connell

first: Jack Henry

last: Kotnik

first: Stephen

last: Coleman

first: Gurkan

last: Yardimci

first: Andrew

last: Adey


title: ALKBH8-Mediated Codon-Specific Translation Promotes Colorectal Tumorigenesis

city: Hangzhou

first: Yu

last: Qian

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medicine

country: China

institute: Zhejiang University

summary: Reprogramming gene expression at the translational level drives intestinal tumorigenesis. Codon decoding during translation elongation relies on tRNA modifications, while their pathological relevance in colorectal cancer remains to be elucidated. Here, we show that AlkB homolog 8 (ALKBH8), a uridine 34 (U34) tRNA methyltransferase, is a direct target of Wnt/β-catenin and is upregulated in colorectal cancer. Genetic ablation of ALKBH8 inhibits the development of intestinal tumors in Apcmin/+, AOM/DSS, and xenograft models. Loss of ALKBH8 induces ribosome pausing at adenine-ending codons, impairing the translation elongation of mRNAs enriched with these codons. Specifically, ALKBH8 regulates the translation of KRAS proto-oncogene in a codon-dependent manner. Rescue experiments demonstrate that the methyltransferase activity of ALKBH8 is required for its translation-promoting function. Together, our findings reveal ALKBH8-dependent mRNA translation as a critical mediator of intestinal tumorigenesis, underscoring its potential as a promising target for colorectal cancer therapy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Examination of the translatome in HCT116 ALKBH8 knockout amd overexpressin cells compared to HCT116 WT cells using Ribo-Seq technology.Performed on intestinal tumor tissues from ApcMin/+ mice with or without Alkbh8 knockout to investigate the in vivo role of ALKBH8 in colorectal tumorigenesis.
Single-cell RNA sequencing was conducted in the AOM/DSS-induced colitis-associated colorectal cancer model to compare cellular heterogeneity and transcriptional alterations in Alkbh8 knockout versus control mice.

first: Canlan

last: Wu

first: Saisai

last: Wei

first: Xiangwei

last: Gao


title: scRNA-Seq of immune populations from nasal mucosa and lungs of C57BL/6 mice and BLT1 receptor deficient mice infected intranasally with MCMV K181 strain

status: Public on Aug 22 2025

city: Philadelphia

last: Springer

state: PA

address: 1020 Locust St

institute: Thomas Jefferson University

summary: We used a single cell sequencing approach using 10x Genomics scRNAseq to understand the transcriptional differences between immune populations from MCMV infected wildtype C57BL/6 mice and BLT1-/- mice. IFNy producing cells were similar between both experimental groups, however, BLT1-/- mice showed a reduced contribution of IFNy from CD8+T cells which was sublte in the nasal mucosa (NM) but obvious in the lungs. Comparison of T cell clusters showed that WT T cells had increased gene signatures associated with proliferation, integrin signaling, cytoskeleton regulation by Rho GTPases, T cell activation, and cytokine/chemokine signaling compared to BLT1-/- T cells, with this being true in CD8 clusters in the NM and both Cd4 and CD8 in the lungs.

overall_design: Following MCMV intranasal infection, immune cells from nasal mucosa and lungs were isolated by fluorescence-acitivated cell sorting (FACS) and analyzed using scRNA seq and CITEseq.

first: Christopher

last: Snyder


title: Profiling of Oestrogen Regulated RNA Binding Protein Landscape Identifies a Role for FXR1 in Endocrine Resistance

city: Hefei

first: yinzhong

last: shang

address: No.96, JinZhai Road Baohe District

department: Division of Life Sciences and Medicine

institute: University of Science and Technology of China

summary: Dysregulated oestrogen signaling plays a critical role in the development of endocrine resistance and bone metastasis of ER+ breast cancer. Screening of estrogen-regulated RNA-binding proteins by using iTRAQ technology identified that elevated expression of FXR1 is associated with anti-oestrogen resistance. FXR1 belongs to the fragile X mental retardation protein family and participates in RNA splicing, modification, localization, stability, and protein translation. To study the role of FXR1 in breast cancer, we performed RNA-seq assays in FXR1 knockdown and control cells.

overall_design: We treated MCF-7 cells expressing empty vector or FXR1 shRNA, respectively. we next performed RNA extraction and sequenced on Illumina HiSeq (Homo sapiens).

first: Yinzhong

last: Shang

first: Tao

last: Zhu


title: Interplay between Genetic Variation and Nutrition Challenge Controls Hepatic Diurnal Rhythms [ChIA-PET]

city: Houston

first: Dongyin

last: Guan

state: TX

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

summary: Variation in diurnal rhythms contributes to the risk of multiple diseases, yet the genomic and epigenomic basis remains largely unknown. Here, we show that SNPs in enhancer and promoter regions genome-wide contribute to variations in human diurnal rhythms. Differential rhythmic gene expression and physiological responses to diet-induced obesity in mice with different genetic backgrounds are linked to time-dependent enhancer-promoter interactions (EPI) regulated by cis-regulatory SNPs and transcription factors (TFs) like ESRRγ. Hepatocyte-specific Esrrγ knockout alters rhythmic processes in liver, including triglyceride synthesis and lipid droplet formation, across mouse strains. Moreover, motifs of ESRRγ and other lipid metabolism-related TFs are enriched in individual-specific EPIs harboring SNPs to control rhythmic genes in patients with MAFLD. SNPs located in these sites are correlated with hepatic metabolic traits. Thus, SNPs and TFs interdependently form the genomic and epigenomic basis for diurnal rhythm variation, contributing to disease risk.

overall_design: ChIA-PET-sequencing using anti-H3K27ac and anti-ESRRg antibody  in livers from normal chow and high-fat diet fed mice with C57BL/6J and 129S1/SvImJ genetic background.

first: Zhou

last: Dishu

first: Chen

last: Ying

first: Liu

last: Panpan

first: Guan

last: Dongyin


title: iCB elicits ABA-responsive gene expression in Arabidopsis thaliana seedlings

city: Valencia

first: Pedro

middle: L.

last: Rodriguez

state: Valencia

address: C/ Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP

summary: To compare the genome-wide transcriptional effect of ABA and iCB in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 10 uM iCB-treated plants. Differential gene expression analysis between mock- and ABA-treated or iCB-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iCB upregulated and downregulated genes represent almost all the ABA-responsive genes, which reflects the activation of PYL1-like and PYL4-like and PYL8-like ABA receptors in tomato seedlings.

overall_design:
A. thaliana seedlings (3 d.a.g.) were transferred from plates to flashes with 3 ml of liquid Murashige and Skoog (MS medium) for 7 days in a growth chamber at 22ºC under long-day conditions (16 h light/8 h dark). Before treatment, the medium was refreshed and supplemented with either 0.1% DMSO (mock) or 10 μM ABA or 10 µM iCB. Samples were collected after 3 hours of incubation, and the experiment was conducted with three independent biological replicates.
We performed genome-wide expression profiling analysis using data obtained from RNA-seq of the three biological replicates
Comparative analysis of transcriptional profiles using RNA-seq data for mock, iCB or ABA treatments in Arabidopsis thaliana (Col-0, wildtype genotype)

first: Jonatan

last: Illescas-Miranda

first: Mar

last: Bono

first: Javier

last: Forment


title: Interplay between Genetic Variation and Nutrition Challenge Controls Hepatic Diurnal Rhythms [RNA-seq]

overall_design: RNA-sequencing in livers from normal chow and high-fat diet fed mice with C57BL/6J and 129S1/SvImJ genetic background, and high-fat diet fed control and hepatocyte-specific Esrrg knockout mice


title: Developmental Programming: Differing impact of prenatal testosterone and prenatal bisphenol-A -treatment on hepatic methylome in female sheep

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

summary:
Steroid hormones play a crucial role in pregnancy and fetal development, influencing
metabolism, inflammation, and immune responses. Excessive prenatal exposure to
steroids or environmental chemicals like bisphenol A can disrupt offspring's
metabolism. This study examines how prenatal exposure to testosterone and BPA
affects the liver's DNA methylome, which is critical for long-term health.

overall_design: Whole genome bisulfite sequencing of liver tissue from two cohorts of Suffolk sheep: one exposed prenatally with testosterone (5 treated and 5 controls), and the other prenatally exposed to BPA (4 treated and 4 controls).

first: John

middle: F

last: Dou

first: Soundara

middle: V

last: Thangaraj

first: Yiran

last: Zhou

first: Vasantha

last: Padmanabhan


title: Erroneous efferocytosis of live neutrophils during infection prevents the resolution of inflammation [RNAseq_single_species]

first: Juhi

last: Bagaitkar

summary: Here, we show that neutrophils infected with the bacterial pathogenPorphyromonas gingivalis (Pg) are internalized alive by macrophages in a manner that bypasses all known efferocytic receptor-ligand interactions. Live cell uptake was mediated by the proteolysis of neutrophil granule proteins by the Pg protease RgpB. Subsequent translocation and recognition of these RgpB-generated efferocytic ligands by macrophage complement receptor 3 (CR3) receptors led to the internalization of live neutrophils by macrophages. Contrary to the immunosuppression induced by apoptotic cells, efferocytosis of live neutrophils was highly inflammatory. Thus, our data show a novel immune subversion strategy employed by a bacterial pathogen that utilizes a previously unknown receptor-ligand interaction for the efferocytosis of live cells and consequently dysregulates the resolution of inflammation.

overall_design: To examine the consequences of atypical (live neutrophil) efferocytosis in vivo. We fluorescently labeled CD45.1 bone marrow neutrophils, then treated with bacterial protease (RgpB) or induced apoptosis. We injected RgpB treated live neutrophils (gLN) or apoptotic neutrophils (AN) into the inflammed peritoneum of CD45.2 mice. 4 h following injection, we collected peritoneal cells by lavage and sorted for macrophage populations that were positive for fluorescently labeled BMN or macrophage populations that were negative for BMN (control macrophages). We collected peritoneal exudate macrophages (PEMs) from the inflammed peritoneum of CD45.2 mice (no BMN injection) and resident peritoneal macrophages (RPM) from peritoneal cavities of naive CD45.2 mice. We profiled gene expression in efferocytosing macrophages vs control macrophages in gLN vs AN injected mice in order to characterize macrophage transcription and polarization during live cell efferocytosis.

first: Kelley

last: Cooper

first: Marina

last: Terekhova

first: Barbara

last: Potempa

first: Ana

last: D'Aubeterre

first: Carlos

last: Rodriguez-Hernandez

first: Jerome

last: Timbol

first: Si

last: Chen

first: Shunying

last: Jin

first: Antoine

last: Dufour

first: Maxim

last: Artyomov

first: Jan


title: Click-code-seq mapping of oxidized guanines in cells exposed to DNMT1 inhibitor GSK-3484862. Click-code-seq mapping of oxidized guanines and abasic sites in plasmids with site-specific DNA modifications.

city: Zurich

first: Shana

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: By relating the numbers of oxidized guanines in different sequence contexts to the abundance of these contexts in the human genome, we observed that the probability of guanine to be or remain oxidized is low if this guanine is preceded by cytosine (CpG sites) compared to other nucleotides. As CpG sites are substrates of epigenetic cytosine methylation, we investigated the influence of cytosine methylation status on guanine oxidation level in CpG sites. For this, we exposed HAP1 and U2OS cells for three days to GSK-3484862, a novel DNA methyltransferase 1 (DNMT1) inhibitor causing the degradation of this enzyme within 24 hours and having low cellular toxicity. Using Infinium MethylationEPIC v2.0 array, we observed a drastic hypomethylation after the exposure in both cell lines such that the peak of highly methylated CpG sites (beta values 0.8–1) found in vehicle (DMSO) exposed cells is absent in GSK-3484862-exposed cells. In contrast, the oxidation level of guanines in the CpG sites profiled by the array did not change in response to the inhibitor and was virtually constant across CpG sites with different methylation levels. In addition, on the level of all CpG sites in the genome, guanine-oxidation did not differ between DMSO and GSK-3484862 exposures. Thus, in CpG sites, guanine oxidation level likely does not depend on cytosine methylation status. As a control for the click-code-seq protocol, we successfully called 8-oxoG incorporated at specific sites in a plasmid (~25 fmol) that was mixed with ~28-times bigger amount of the unmodified vector. As a control for click-code-seq detection of abasic sites, we inserted uracils in a plasmid, converted them to abasic sites by uracil-DNA glycosylase (UDG) and successfully called them in the expected locations.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: Single-nucleotide-resolution genome-wide mapping click-code-seq of guanine oxidation in HAP1 or U2OS wild-type cells exposed to GSK-3484862 or DMSO (vehicle), with each cell line - exposure condition in 3 biological replicates. Single-nucleotide-resolution genome-wide mapping click-code-seq of guanine oxidation in a plasmid with site-specific 8-oxoguanine insertion and a plasmid vector without the insertion; FPG was used to recognize guanine oxidation in plasmid DNA. Single-nucleotide-resolution genome-wide mapping click-code-seq of abasic sites in a plasmid with site-specific uracil insertion and a plasmid vector without the insertion; UDG was used to convert uracils to abasic sites in plasmid DNA.

first: Vakil

last: Takhaveev

first: Navnit

middle: K

last: Singh


title: Interplay between Genetic Variation and Nutrition Challenge Controls Hepatic Diurnal Rhythms [ChIP-seq]

first: Dongyin

last: Guan

overall_design: ChIP-sequencing using anti-ESRRg antibody  in livers from normal chow and high-fat diet fed mice with C57BL/6J and 129S1/SvImJ genetic background.

first: Zhou

last: Dishu

first: Chen

last: Ying

first: Liu

last: Panpan

first: Guan

last: Dongyin


title: Epigenetic dysregulation in aged muscle stem cells drives mesenchymal progenitor expansion via IL-6 and Spp1 signaling [CUT&Run]

first: Stephen

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Sarcopenia, the age-related decline in muscle mass, strength, and function, is characterized by impaired muscle homeostasis, reduced regenerative potential of muscle stem cells (MuSCs), and increased fibrosis. Here, we report that aged MuSCs can autonomously instruct fibro-adipogenic progenitors (FAPs) to proliferate and acquire a fibrogenic phenotype, independent of other cell types. Both the Polycomb-deficient Ezh2-/- mouse model and aged mice exhibited defective regeneration, FAP expansion, fibrosis, and elevated secretion of interleukin 6 (IL-6) and Spp1/Osteopontin by MuSCs. In aged MuSCs, reduction of the histone H3K27me3 repressive mark at the Nfbk1 gene correlated with its increased expression, enhanced chromatin recruitment to the IL6 and Spp1 genes, leading to their activation. Pharmacological inhibition of IL-6 and Spp1 signaling in co-culture systems or in aged mice reduced FAP proliferation and muscle fibrosis. These findings indicate that epigenetic dysregulation of aged MuSCs contributes to aged-related muscle fibrosis.

overall_design: To investigate the mechanism underlying the increased activation of IL-6 and Spp1 signaling in aged MuSCs, we compared genomewide distribution of the epiegenetic repressive mark H3K27me3 in adult and aged MuSCs by CUT&RUN.

first: Giulia

last: Riparini

first: Morgan

last: Mackenzie

first: Faiza

last: Naz

first: Kan

last: Jiang

first: Anshu

last: Deewan

first: Brittany

last: Dulek

first: Shamima

last: Islam

first: Kyung Dae

last: Ko

first: Wanxia

last: Tsai

first: Massimo

last: Gadina

first: Stefania

last: Dell'Orso

first: Vittorio

last: Sartorelli


title: Erroneous efferocytosis of live neutrophils during infection prevents the resolution of inflammation [RNAseq_dual_species]

first: Juhi

last: Bagaitkar

overall_design: To examine the consequences of live neutrophil efferocytosis in vivo using a dual species model. We depleted C57BL6/J mice of their endogenous neutrophil populations (anti-Ly6G), then induced peritonitis. Human peripheral neutrophils were treated with bacterial protease (RgpB) or apoptosis was induced. RgpB-treated neutrophils (gLN) or apoptotic neutrophils (AN) were injected into the inflammed peritoneum. 4 h or 24 h after injection, peritoneal cell populations were collected by lavage and sorted to obtain a pure macrophage population. Peritoneal exudate macrophages (PEM) were obtained from the inflammed peritoneum of mice that did not receive an adoptive transfer of neutrophils. Isotype control (iso ctrl) indicates PEMs obtained from the inflammed peritoneum that were not neutrophil depleted. We profiled differential gene expression in macrophages from gLN vs AN injected mice to determine how live cell efferocytosis effects macrophage polarization.

first: Kelley

last: Cooper

first: Marina

last: Terekhova

first: Barbara

last: Potempa

first: Ana

last: D'Aubeterre

first: Carlos

last: Rodriguez-Hernandez

first: Jerome

last: Timbol

first: Si

last: Chen

first: Shunying

last: Jin

first: Antoine

last: Dufour

first: Maxim

last: Artyomov

first: Jan


title: Thyroid Hormone Promotes Fetal Neurogenesis [CosMx]

city: Chicago

first: Federico

last: Salas-Lucia

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: The University of Chicago

summary: Maternal low thyroxine (T4) serum levels during the first trimester of pregnancy correlate with cerebral cortex volume and mental development of the progeny, but why neural cells during early fetal brain development are vulnerable to maternal T4 levels remains unknown. In this study, using iPSCs obtained from a boy with a loss-of-function mutation in MCT8—a transporter previously identified as critical for thyroid hormone uptake and action in neural cells—we demonstrate that thyroid hormones induce transcriptional changes that promote the progression of human neural precursor cells along the dorsal projection trajectory. Consistent with these findings, single-cell, spatial, and bulk transcriptomics from MCT8-deficient cerebral organoids and cultures of human neural precursor cells underscore the necessity for optimal thyroid hormone levels for these cells to differentiate into neurons. The controlled intracellular activation of T4 signaling occurs through the transient expression of the enzyme type 2 deiodinase, which converts T4 into its active form, T3, alongside the coordinated expression of thyroid hormone nuclear receptors. The intracellular activation of T4 in NPCs results in transcriptional changes important for their division mode and cell cycle progression. Thus, T4 is essential for fetal neurogenesis, highlighting the importance of adequate treatment for mothers with hypothyroidism.

overall_design: Spatial transcriptomic data of two slides of control (CS01ictr) and MCT8-deficient (CS58iMCT8) cortical organoids after 50 days in culture

first: Sergio

last: Escamilla

first: Amanda

last: Charest

first: Hanzi

last: Jiang

first: Randy

last: Stout

first: Antonio

middle: C

last: Bianco


title: DNA methylation profiling of cells exposed to DNMT1 inhibitor GSK-3484862 or DMSO (vehicle)

first: Shana

last: Sturla

type: Methylation profiling by genome tiling array

summary: By relating the numbers of oxidized guanines in different sequence contexts to the abundance of these contexts in the human genome, we observed that the probability of guanine to be or remain oxidized is low if this guanine is preceded by cytosine (CpG sites) compared to other nucleotides. As CpG sites are substrates of epigenetic cytosine methylation, we investigated the influence of cytosine methylation status on guanine oxidation level in CpG sites. For this, we exposed HAP1 and U2OS cells for three days to GSK-3484862, a novel DNA methyltransferase 1 (DNMT1) inhibitor causing the degradation of this enzyme within 24 hours and having low cellular toxicity. Using Infinium MethylationEPIC v2.0 array, we observed a drastic hypomethylation after the exposure in both cell lines such that the peak of highly methylated CpG sites (beta values 0.8–1) found in vehicle (DMSO) exposed cells is absent in GSK-3484862-exposed cells. In contrast, the oxidation level of guanines in the CpG sites profiled by the array did not change in response to the inhibitor and was virtually constant across CpG sites with different methylation levels. In addition, on the level of all CpG sites in the genome, guanine-oxidation did not differ between DMSO and GSK-3484862 exposures. Thus, in CpG sites, guanine oxidation level likely does not depend on cytosine methylation status.

overall_design: We performed DNA methylation profiling with Infinium MethylationEPIC v2.0 array in HAP1 and U2OS wild-type cells exposed to GSK-3484862 or DMSO (vehicle), with each cell line - exposure condition in 3 biological replicates.

first: Vakil

last: Takhaveev

first: Navnit

last: Singh


title: Integrative morpho-physiological and transcriptomic insights into wheat responses to combined drought, heat, and elevated CO₂ under future climate conditions

city: Brno

first: Zbynek

last: Milec

address: Belidla 986

country: Czech Republic

institute: Global Change Research Institute

summary: Climate change is anticipated to exacerbate environmental stressors such as drought, elevated temperatures, and increased CO2 levels, posing a significant threat to crop productivity. We investigated the morpho-physiological acclimation and transcriptional responses of hexaploid wheat (Triticum aestivum L.) under both single and combined stress conditions. Wheat plants were subjected to drought (D), elevated temperature (eT), and elevated CO2 (eC) individually, as well as in double (eT+D, eC+D, eC+eT) and triple (eC+eT+D) stress combinations. Our findings reveal that the eT+D combination resulted in the most severe reductions in growth and yield, while elevated CO2      cccccpartially mitigated these effects by enhancing biomass production and water-use efficiency. Transcriptomic analyses identified key regulatory networks, including specific protein-coding genes, transcription factor (TF) families, and potential marker genes associated with stress adaptation. Overall, this study provides new insights into the complex genetic and physiological mechanisms underlying wheat resilience to multifactorial environmental stress. These findings highlight valuable molecular targets for breeding strategies aimed at improving wheat tolerance to climate change-induced stress conditions

overall_design: RNAseq data from winter bread wheat Alana. Plants were grown under different regimes: D - drought, T - elevated temperature (up to 31°C), C - elevated CO2 concentration (700 ppm) and their mutual combinations: C+T, T+D, C+D, C+T+D. Samples were collected from the 3rd and 4th leaf on the main tiller at the stage GS61.

first: Kashif

last: Nawaz

first: Swati

last: Puranik

first: Anna

last: Nowicka

first: Martin

last: Kovacik

first: Hana

last: Findurova

first: Barbora

last: Vesela

first: Kojo

last: Kwakye Ofori-Amanfo

first: Ales

last: Pecinka

first: Otmar

last: Urban

first: Karel

last: Klem

first: Pranav

last: Pankaj Sahu


title: IceQream: Quantitative chromosome accessibility analysis using physical TF models

city: Rehovot

first: Amos

last: Tanay

address: Herzl

institute: Weizmann Institute of Science

summary: Single-cell mapping of chromosomal accessibility patterns has recently led to improved predictive modelling of epigenomic activity from sequence. However, quantitative models explaining the epigenome using directly interpretable components are still lacking. Here we develop IceQream (IQ), a modelling strategy and inference algorithm for regressing accessibility from sequences using physical models of transcription factor (TF) binding. IQ uses spatial integration of sequences over a range of TF-DNA affinities and localization relative to the target locus. It infers TF effective concentrations as latent variables that activate or repress regulatory elements in a non-linear fashion. These are supplemented with synergistic and antagonistic pairwise interactions between TFs. Analysis of both human and mouse data shows that IQ derives similar, and in some cases, better performance compared to state-of-the-art deep neural network models. IQ provides an essential mechanistic and explicable baseline for further developments toward understanding gene and genome regulation from sequence.

overall_design: Single nuclei were extracted from mouse embryos harvested from timed pregnant Hsd:ICR (CD-1) females at embryonic days E6.5-E7.5. Nuclei isolation was performed using a modified low cell input protocol with lysis buffer containing 10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20, 0.1% Nonident P40 substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, and RNase inhibitor. Single-cell ATAC and gene expression libraries were prepared using the 10X Genomics Multiome platform with Chromium Next GEM Chip J and sequenced on an Illumina NovaSeq 6000 instrument.

first: Saifeng

last: Cheng

first: Roni

last: Stok

first: Akhiad

last: Bercovich

first: Aviezer

last: Lifshitz

first: Michal

last: Eldar

first: Yonatan

last: Stelzer


title: Linear ubiquitination prevents lipodystrophy and obesity-associated metabolic syndrome

city: Stuttgart

first: Nieves

last: Peltzer

address: Allmandring 31

department: Institute of Biomedical Genetics

institute: Universität Stuttgart

summary: Adipocyte hypertrophy during obesity triggers chronic inflammation, leading to metabolic disorders. However, the role of adipocyte-specific inflammatory signalling in metabolic syndrome remains unclear. The linear ubiquitin chain assembly complex, LUBAC, is an E3-ligase that generates non-degradative linear ubiquitination (Lin-Ub). LUBAC regulates NF-κB/MAPK-driven inflammation and prevents cell death triggered by immune receptors like TNF-receptor-1. Here we show that mice lacking HOIP, LUBAC’s catalytic subunit, in adipocytes (HoipA-KO) display lipodystrophy and heightened susceptibility to obesity-induced metabolic syndrome, particularly Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD). Mechanistically, loss of HOIP attenuates TNF-induced NF-κB activation and promotes cell death in human adipocytes. Inhibiting caspase-8-mediated cell death is sufficient to prevent lipodystrophy and MASLD in HoipA-KO obese mice. Importantly, HOIP expression in adipose tissue positively correlates with metabolic fitness in obese individuals. Overall, our findings reveal a fundamental developmental role for Lin-Ub in adipocytes by mitigating cell death-driven adipose tissue inflammation and protecting against obesity-related metabolic

overall_design: Bulk RNAseq extraction from liver of male, 24 weeks old mice; Hoip fl/fl AdipoQ.Cre+(HoipA-KO) or Hoip fl/fl AdipoQ.Cre- (WT control) fed for 16 weeks with 14% Control Diet (CD) or 60% High Fat Diet (HFD)

first: Ximena

last: Hildebrant

first: Önay

last: Veli

first: Armel

last: Hyoubi

first: Julia

last: Zinngrebe

first: Ali

last: Abdallah

first: Julian

last: Rodefeld

first: Anne

last: Hoffmann

first: Liane

last: Gardeweg

first: Oyku

last: Kaya

first: Elena

last: Wagner

first: Andreas

last: Lindhorst

first: Matea

last: Poggenberg

first: Yuan

last: Wang

first: Joëlle

last: Dimmler

first: Jutta

last: Schillings

first: Pegi

last: Koci

first: Francesca

last: Bonechi

first: Lucas

last: Valdez Capuccino

first: Christine

last: Kiefer

first: Konstantinos

last: Kelepouras

first: Adhideb

last: Ghosh

first: Falko

last: Noé

first: Christian

last: Wolfrum

first: Michael

last: Singer

first: Tom

last: Luedde

first: Aslihan

last: Yavas

first: Gianmaria

last: Liccardi

first: Ahmed

last: Ghallab

first: Jan

last: Hengsler

first: Phillipp

last: Antczak

last: Gericke

first: Holger

last: Winkels

first: Matthias

last: Blüher

first: Henning

last: Walczak

first: Alessandro

last: Annibaldi

first: Pamela

last: Fischer-Posovszky


title: Conserved and distinct expression of circular RNAs in commercially used Marek’s disease vaccine viruses

city: Namur

first: Camille

last: Ponsard

state: Namur

address: Rue de Bruxelles, 61

department: Veterinary Medecine

country: Belgium

institute: Unamur

summary: Circular RNAs (circRNAs) are covalently closed RNA molecules, supporting a wide diversity of functions. While aberrant circRNA expression stands as a recognized hallmark of cancer development, our attention has turned to investigate their role in viral infections, specifically Mardivirus Gallidalpha 2 (GaHV-2, MDV) infection. In a previous study focused on the virulent GaHV-2, RB-1B strain, we extensively cataloged circRNAs produced from virulence genes, notably from the MEQ-vIL-8 locus and the Latency Associated Transcripts (LATs) gene. Building upon this groundwork, our current investigation uncovers novel loci expressing viral circRNAs in distinct stages of GaHV-2 infection. Furthermore, we extend our focus to viral circRNA signatures in three commonly used MDV vaccines, the avirulent GaHV-2 (CVI988- Rispens strain), non-oncogenic Mardivirus Gallidalpha 3 (GaHV-3), and non-oncogenic Mardivirus Meleagridalpha 1 (MeHV-1) commercially called Herpesvirus of Turkey (HVT). In these vaccine viruses, we identified viral circRNA expression from a locus antisense to the immediate early ICP4 gene a conserved feature across the three species. This region has been characterized herein for the first time in term of candidate LATs exons and introns for GaHV-3 and MeHV-1. Potential LATs circRNAs were then deeply analyzed and we observed both similarities and distinctions when compared to those of the virulent GaHV-2. Another conserved gene, encoding the DNA packaging protein, was identified as a source of circRNAs in all three species. Eventually, different levels of circRNAs expression were found from the meq locus between virulent and avirulent GaHV-2 strains. Our findings highlight a conserved pattern of viral derived circRNA expression in these related avian alphaherpesviruses. This conservation underscores the potential significance of these transcripts in completing the viral cycle and facilitating viral spread.

overall_design:
To identify circRNAs expression from three viruses used in Marek's Disease vaccination program, we used in vitro  lytic infection of ESCDL-1 cells with GaHV-2 CVI-988 (Acc. n° DQ530348), GaHV-3 SB-1(Acc. n° NC_002577), and MeHV-1 FC-126 (Acc. n° NC_002641) viral strains .
We extracted RNAs from the infected cell lines and treated them with RNase R before sending them for paired-end RNA sequencing at Novogene.
We processed the data through vCircTrappist to identify candidate circRNAs.

first: Alexis

middle: S

last: Chasseur

first: Pierre

last: Lombard

first: Béatrice

last: Danneels

last: Letellier

last: Kheimar

first: Yu

last: You

first: Caroline

last: Denesvre

first: Benedikt

middle: B

last: Kaufer

first: Damien

last: Coupeau

first: Benoît

last: Muylkens


title: RNAs expression analyses in commercially used Marek’s disease vaccine viruses to identify their Latency associated transcripts splicing patterns

overall_design:
To identify Latency associated transcripts splicing pattern from three viruses used in Marek's Disease vaccination program, we used in vitro  lytic infection of ESCDL-1 cells with GaHV-2 CVI-988 (Acc. n° DQ530348), GaHV-3 SB-1(Acc. n° NC_002577), and MeHV-1 FC-126 (Acc. n° NC_002641) viral strains .
We extracted RNAs from the infected cell lines and send them for paired-end RNA sequencing at Novogene.
We processed the data through vCircTrappist to identify spliced RNAs (sense and antisense).

first: Ahmed


title: A molecular circuit regulates fate plasticity in emerging and adult AT2 cells [ATAC-seq]

city: Rochester

first: Douglas

middle: Glenn

last: Brownfield

state: MN

address: 200 First St. SW

institute: Mayo Clinic

summary: Alveolar AT1 and AT2 cells are vital for gas exchange in the lung and become compromised in several common and deadly diseases. While the signals driving differentiation of either cell type have been identified, it remains unclear when and how fate plasticity is regulated in the emerging and adult alveolar epithelium. Here we show AT2s first emerge as singletons at zones between the proximal stalks and distal tips of the embryonic lung that quickly extrude and can traverse the interstitium to connect with nearby epithelium, a process we term interlumenal junctioning. Throughout the late embryonic and early perinatal period, we find that a window of AT2 fate plasticity exists that is closed by the bZIP transcription factor C/EBPα, mediated by its transcriptional suppression of the Notch signaling regulator DLK1. C/EBPα acts on Dlk1 at a novel regulatory site. Further, both Dlk1 and Cebpa are regulated by the polycomb repressive complex (PRC2), and together constitute a novel incoherent feedforward loop that generates a Dlk1 pulse upon downregulation of PRC2. We propose these form a “pulse generator” circuit capable of generating a timed activation of Notch signaling, resulting in a “salt and pepper” pattern of AT1 and AT2 fate. Following injury in the adult lung, we found that C/EBPα downregulation is required for re-accessing AT2 fate plasticity and is mediated by the dominant negative C/EBP family member CHOP. Finally, we observe Cebpa loss also activates a “defender” AT2 state enriched in interferon-stimulated antipathogenic gene expression that is distinct from its reparative state and propose AT2s toggle between these states following infection to robustly protect and repair alveoli.

overall_design: Bulk ATACseq of lineage label AT2s of wildtype and Cebpa floxed in perinatal day (day 11-25)

first: Amitoj

last: Sawhney

first: Junming

last: Cai

first: Liu

last: Wang

first: Zong

last: Wei


title: An autochthonous model of lung cancer in the Naked Mole-Rat (Heterocephalus glaber)

city: Tampa

first: Joseph

last: Kissil

state: FL

address: 12902 Magnolia Dr

department: Molecular Oncology

institute: H Lee Moffitt Cancer Center and Research Institute

summary: There is growing interest in understanding the mechanisms underlying differences in cancer incidence among species. The naked mole-rat (NMR) is often referenced as “cancer-resistant” and prior studies focused on identifying mechanisms explaining this. However, efforts to assess this in vivo have been limited. Herein, we provide evidence that the NMR presents as a novel autochthonous model of lung tumor initiation, driven by an introduction of the oncogenic Eml4-Alk fusion protein using CRISPR-mediated genome editing. While in mice the inversion alone is sufficient to drive tumorigenesis, the inversion alone was insufficient to drive tumorigenesis in the NMR lung and tumor development required additional losses of the tumor suppressors p53 and pRb. Our findings suggest that the proposed “resistance” of the NMR to the development of cancer may reflect tumor initiation mechanisms that are likely to be comparable to the mechanisms present in human cells.

overall_design: We utilized deep sequencing of NMR Rb and p53 in order to detect what mutations were introduced into the NMR lung tissue. To do this, we performed laser capture microscopy on 3 different NMR lungs to obtain specific lung tumor areas as well as non-cancerous regions. We amplified regions surrounding the CRISPR sites and sequenced them using the Illumina Nextera XT kit following the manufacturer?s protocol. Briefly, following the quality control screening of 100ng of each amplicon on a 1% agarose gel, both amplicons for each sample were pooled equimolar and 1ng of input DNA was used for the Nextera tagmentation reaction, followed by PCR amplification and sample indexing. The libraries were purified, quantitated with the Qubit Fluorometer, and screened on the Agilent TapeStation 4200 using the TapeStation High-Sensitivity D1000 Screen Tape . The final libraries were normalized, denatured, and sequenced on the Illumina MiSeq sequencer using a Nano flow cell to generate approximately 20,000 150-base read pairs per sample.

first: Alyssa

last: Shepard

first: Daniel

last: Lester

first: Dongliang

last: Du

middle: L


title: Y665F variant of mouse STAT5b protects against acute kidney injury through transcriptomic shifts in renal gene expression

city: Bethesda

first: Jakub

last: Jankowski

address: 8 Center DR.

department: NIDDK

institute: NIH

summary: The impact of single nucleotide polymorphisms (SNP) on physiology is often underestimated. One amino acid change can result in a variety of phenotypes apparent only in response to disease or injury. Even known pathogenic SNPs have widespread effects that are currently unaccounted for. In this study, we investigated the impact of the known activating and pathogenic STAT5bY665F mutation in a renal injury context in mice carrying this variant. Using ischemia-reperfusion model of acute kidney injury, immunohistochemistry, RNA-seq and ChIP-seq, we establish the protective role of STAT5b activation in renal epithelium and showcase the shifts in transcriptomic landscape in a tissue not associated with the usual human phenotype of the STAT5bY665F mutation. Our data indicate new links between the JAK/STAT pathway and known kidney injury markers, contribute to the understanding of the sexual dimorphism of renal disease, and provide new potential targets for JAK inhibitor- and amino acid transport modulation-based therapies.

overall_design: Bulk RNA-seq was used to investigate the effects of Statb5 Y665F SNP on renal gene expression at the baseline and in 30’ bilateral renal ischemia model at the 24h timepoint, in male and female mice.


title: New Cell lines Expanding the Diversity of Ewing Sarcoma Models – WXS Data

city: Essen

first: Maximilian

last: Kerkhoff

address: Hufelandstrasse 55

department: Pediatrics III

institute: University Hospital Essen

summary: Ewings sarcoma (EwS) is a highly aggressive, malignant, solid tumor of childhood and adolescence. Most EwS develop in bone, while it originates from connective, adipose or muscle tissue less frequently. We report the establishment of new human EwS cell lines, all of which carry a t(11;22) (q24;q12) translocation generating the oncogenic transcription factor EWSR1::FLI1. Sequencing of the chimeric mRNAs indicated genomic DNA breakpoints localized in intron 8 of the EWSR1 gene and 3 different introns of translocation partner gene FLI1. While three EwS cell lines carry the EWSR1::FLI1 fusions of ex7/ex6 (type I) or ex7/ex5 (type II), the EWSR1::FLI1 fusion variant ex7/ex7 (type IV) is described for the first time in a continuous EwS model. The cell lines presented genomic, epigenomic and transcriptomic stability over a period of six months, though some variations in the chromosomal aberrations were observed in one cell line. The transcriptional variation within the novel EwS cell line panel might have been influenced by the EWSR1::FLI1 fusion type and TP53 mutations. Furthermore, the TP53 mutational status seemed to have the biggest impact on drug sensitivity profiles. The new EwS models presented here may help to identify small molecule inhibitors that act directly on EWSR1::FLI1 fusion proteins or uncover other genetic vulnerabilities of the altered epigenome and transcriptome in EwS, which would contribute to a better understanding of Ewing sarcoma tumorigenesis.

overall_design: Whole Exome Sequencing of the C-ES series of Ewing sarcoma cell lines (C-ES-I, C-ES-M, C-ES-P and C-ES-Y).

first: Christiane

last: Schaefer

first: Wilhelm

last: Dirks

first: Dawid

last: Krzeciesa

last: Bretschneider

first: Pauline

last: Plaumann

first: Wiebke

last: Guder

first: Arne

last: Streitbürger

first: Sonja

last: Herter

first: Heike

last: Peterziel

first: Ina

last: Oehme

first: Felina

last: Zahnow

first: Thomas

last: Grünewald

first: Uta

last: Dirksen


title: New Cell lines Expanding the Diversity of Ewing Sarcoma Models

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

overall_design: Refer to individual Series


title: Gut microbe-derived metabolites drive psoriatic inflammation via modulation of skin Th17 cells

city: Beijing

first: Chenliang

last: Wang

state: Beijing

address: Medical Science Building, Room D307, Tsinghua University

institute: Tsinghua University

summary: The maintenance of tissue-specific chronic inflammation results from the interplay of genetic and unidentified environmental factors. Here, we describe an immunoregulatory role for an environmentally driven microbial metabolite in Card14E138A/+-induced spontaneous psoriasis. Through metabolite screening, we demonstrate chronic skin inflammation is accompanied by alterations microbial metabolite. Notably, depletion of gut, not skin, microbes alleviates disease symptoms. We further identify indoxyl sulfate (I3S), a bacteriogenic metabolite, as a key driver of psoriatic inflammation and confirm that gut-resident indole-producing microbiota mediate this process. Mechanistically, indole-producing microbiota promote host I3S biothsynthesis via a metabolic relay, and I3S potentiates skin inflammation by reshaping chromatin accessibility in skin Th17 cells through AHR signaling. In human psoriasis cohorts, serum I3S levels correlate with disease severit. In summary, our study uncovers a mechanistic link between gut microbial factors and type 3 skin inflammation, highlighting targeting gut microbiota as a strategy for mitigating skin inflammation.

overall_design: Bulk RNAseq was performed to reveal that ABX module skin inflammation, allowing a comparison to the genes signature of ABX and WAT treatment. ATACseq and Bulk RNAseq were performed to reveal that I3S module Th17 cell. Previously published methods and those not used in the main Figs. are described in Supplementary Methods.

first: Xin

last: Lin


title: Distinct molecular processes mediate donor-derived cell-free DNA release from kidney transplants in different disease states.

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

country: Canada

institute: University of Alberta

summary:
Background: Among all biopsies in the Trifecta kidney study (ClinicalTrials.gov #NCT04239703), elevated plasma dd-cfDNA correlated most strongly with molecular antibody-mediated rejection (ABMR) (JASN 33:387, 2022), but was also elevated in other states: T cell-mediated rejection (TCMR), acute kidney injury (AKI), and some apparently normal biopsies. The present study aimed to define the molecular correlates of plasma dd-cfDNA within specific states.
Results: In all 604 biopsies, dd-cfDNA was elevated in ABMR, TCMR, and AKI. Within ABMR biopsies, dd-cfDNA correlated with ABMR activity and stage. Within AKI, the correlations reflected acute parenchymal injury, including cell cycling. Within biopsies classified as NRNI, dd-cfDNA still correlated significantly with rejection- and injury-related genes. TCMR activity (e.g., the TCMRProb classifier) correlated with dd-cfDNA, but within TCMR biopsies, top gene correlations were complex and not the top TCMR-selective genes.
Conclusions. In kidney transplants, elevated plasma dd-cfDNA is associated with three distinct molecular states in the donor tissue: ABMR, recent parenchymal injury, including cell cycling, and TCMR, potentially complicated by parenchymal disruption. Moreover, subtle rejection- and injury-related changes in the donor tissue can contribute to dd-cfDNA elevations in transplants considered to have no rejection or injury.

overall_design: Methods: Dd-cfDNA was measured by the ProsperaTM test. Molecular rejection and injury states were defined using the Molecular Microscope® system. We studied the correlation between dd-cfDNA and the expression of genes, transcript sets, and classifier scores within specific disease states, and compared ABMR, TCMR, and AKI to biopsies with no molecular rejection or injury (NRNI).


title: New Cell lines Expanding the Diversity of Ewing Sarcoma Models – WGS Data

last: Kerkhoff

overall_design: Whole Genome Sequencing of the C-ES series of Ewing sarcoma cell lines (C-ES-I, C-ES-M, C-ES-P and C-ES-Y).


title: New Cell lines Expanding the Diversity of Ewing Sarcoma Models – Affymetrix Data

summary: Ewings sarcoma (EwS) is a highly aggressive, malignant, solid tumor of childhood and adolescence. Most EwS develop in bone, while it originates from connective, adipose or muscle tissue less frequently. We report the establishment of new human EwS cell lines, all of which carry a t(11;22) (q24;q12) translocation generating the oncogenic transcription factor EWSR1::FLI1. Sequencing of the chimeric mRNAs indicated genomic DNA breakpoints localized in intron 8 of the EWSR1 gene and 3 different introns of translocation partner gene FLI1. While three EwS cell lines carry the EWSR1::FLI1 fusions of ex7/ex6 (type I) or ex7/ex5 (type II), the EWSR1::FLI1 fusion variant ex7/ex7 (type IV) is described for the first time in a continuous EwS model. The cell lines presented genomic, epigenomic and transcriptomic stability over a period of six months, though some variations in the chromosomal aberrations were observed in one cell line. Transcriptome and epigenome were stable over time and there was only little variation between the novel EwS cell lines. The TP53 mutational status seemed to have the biggest impact on drug sensitivity profiles. The new EwS models presented here may help to identify small molecule inhibitors that act directly on EWSR1::FLI1 fusion proteins or uncover other genetic vulnerabilities of the altered epigenome and transcriptome in EwS, which would contribute to a better understanding of Ewing sarcoma tumorigenesis.

overall_design: Analysis of gene expression in the C-ES series of Ewing sarcoma cell lines (C-ES-I, C-ES-M, C-ES-P and C-ES-Y) at early and later passages. STA-ET-1 and SK-N-MC were included as controls.

last: Schaefer


title: Chronic Oxaliplatin Treatment Resembles Human CIPN Behavior in Mice and Leads to Activation of TXNIP Pathway

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

summary: Oxaliplatin is a platinum-based alkylating chemotherapeutic agent used for cancer treatment. Long-term neurotoxicity with oxaliplatin is one of the most devastating adverse effects in patients treated with oxaliplatin. At the high accumulative dosage, the negative effect of oxaliplatin on the becomes evident and is linked to a growing number of clinical reports. The aim of this study was to determine the potential mechanisms of chronic oxaliplatin treatment. C57BL/6 male mice were treated with intraperitoneal oxaliplatin (0 and 10 mg/kg) once a week for eight weeks which is the human equivalent dosage. During the treatment, mice were followed with the measurement of physiological parameters, electron microscopy of the sciatic nerve, NCV, histology and RNA sequencing of the DRG. Oxaliplatin replicated clinically significant spontaneous and evoked pain behaviors in our mouse model and induced strong changes in redox and inflammatory profile in DRG. Histological post-mortem evaluation of the sciatic nerves identified strong effects on mitochondria. KEGG analysis, non-negative matrix factorization, and correlation analysis on the differentially expressed genes (DEGs) in DRG pointed to the potential role of thioredoxin interacting protein (TXNIP) in regulating oxidative stress pathways. Up-regulation of TXNIP in DRG was verified through qPCR, western blotting, and immunohistochemistry and connected to the upstream and downstream pathways. Overall, the results provided insights into the pathophysiology and the mechanism of CIPN with oxaliplatin and highlighted potential drug targets for treatments.

overall_design: After 8 weeks of oxaliplatin treatment, mice DRGs were collected and total RNA was extracted. There were 10 RNA samples, 5 from control and 5 from oxaliplatin group passed the integrity threshold (larger than 8) and were used for RNA sequencing. Differentially expressed genes between control and oxaliplatin-treated mice were identified with Partek software to study the effects of oxaliplatin on gene expression profile in mice DRG.

first: Junwei

last: Du

first: Leland

last: Sudlow

first: Kiana

last: Shahverdi

first: Haiyin

last: Zhou

first: Yameng

last: Xu

first: Amulya

last: Joseph

first: David

last: Wozeniak

first: Lara

last: Crock

first: Dan

last: Hunter

first: Judith

last: Golden

first: Shamim

last: Mollah

first: Mattew

last: Wood


title: New Cell lines Expanding the Diversity of Ewing Sarcoma Models - methylation

first: Maximilian

overall_design: Analysis of DNA methylation in the C-ES series of Ewing sarcoma cell lines (C-ES-I, C-ES-M, C-ES-P and C-ES-Y) at early and later passages.

first: Christiane

first: Wilhelm

last: Dirks

first: Dawid

last: Krzeciesa

last: Bretschneider

first: Pauline

last: Plaumann

first: Wiebke

last: Guder

first: Arne

last: Streitbürger

first: Sonja

last: Herter

first: Heike

last: Peterziel

first: Ina

last: Oehme

first: Felina

last: Zahnow

first: Thomas

last: Grünewald

first: Uta

last: Dirksen


title: Genomic DNA methylation profile in peripheral blood of children with Congenital biliary dilatation

city: Shenzhen

first: feng

last: qi

address: No.7019 Yitian Road, Futian District

institute: Shen zhen Children’s Hospital

summary: Congenital biliary dilatation (CBD) is a relatively rare biliary tract disease. It is a prevalent congenital biliary disease in children. CBD mainly affects in infants and children, with a higher prevalence in females. To investigate the DNA methylation patterns in children with CBD and in healthy children, we performed a comparative analysis of the genome‐wide DNA methylation profiles of whole blood samples from patients with CBD child and from healthy children using the Illumina Infinium Human Methylation 850k BeadChip. Bioinformatics statistical analysis revealed that 5,863 genes with differential DNA methylation between the two groups correlated to a total of 24,230 methylated sites.Of these differential methylation sites, 831,3 were hypermethylated and 15,917 were hypomethylated in comparison to the methylation status of those sites in the control samples. Differentially methylated regions (DMRs) between the CBD cases and the control group was significant difference in DMR_1~DMR_54. Furthermore, T cell receptor signaling pathways represented accounted for an important percentage of the differentially methylated genes. Abnormalities in the DNA methylation pattern identified in the peripheral blood of CBD patients may play an important  role in the development of CBD and warrant further investigation.

overall_design: This study aims to investigate the DNA methylation patterns in a specific population. Samples were derived from peripheral blood cells collected from consenting adult volunteers. DNA was extracted and prepared for high-throughput methylation analysis using the Illumina Infinium MethylationEPIC BeadChip platform. Sequencing was performed on the Illumina Infinium platform, with raw data (.idat format) preprocessed using Illumina's Methylation Module and further analyzed with custom scripts.

first: Qi

last: Feng

first: Chenyao

last: Wang

first: Yuelan

last: Zheng

first: Yan


title: Treatment of LNCaP prostate cancer cells with EGF and NRG

status: Public on Aug 21 2025

first: Adam

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B

institute: National Cancer Institute

summary: Gene expression signatures are routinely used to infer pathway activity. In this project, we stimulated LNCaP prostate cancer cells with growth factors to derive gene expression sigantures indicative of pathway activation.

overall_design: Differential gene expression in the LNCaP cell lines treated with FBS, charcoal stripped serum (CSS) and stimulated with either EGF or NRG for 5m, 1h, or 4h.


title: tRNA-overlapping long non-coding RNAs loci repress codon-biased genes

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: The functions of most long non-coding RNAs (lncRNAs) are not known. Here, we define a group of ‘tRNA-Overlapping LncRNA’ (tROL) genes that are upregulated during in vitro cartilage development. Deletions of tROLs result in changes in the expression of codon-biased genes, where downregulated genes are enriched in codons corresponding to tRNAs overlapping disrupted tROLs. tROL loci are located in gene-dense regions and interact extensively between chromosomes, and tROL whole-gene deletions result in the upregulation of significantly overlapping subsets of genes in the vicinity of tROL loci. Inhibiting the lncRNA transcription and degrading the lncRNA transcripts of a tROL gene downregulates tRNA expression. Taken together, the results suggest that tROL loci coalesce and are dependent on each other’s transcription to repress genes in spatial proximity and to activate tRNA expression. Our investigation thus provides insight into a previously uncharacterized role for tROLs as a regulatory bridge between the non-coding and coding genomes.

overall_design:
To investigate lncRNAs during in vitro cartilage development, we differentiated primary human mesenchymal stem cells (MSCs) into chondrocytes over 14 days. We then performed gene expression profiling analysis of data from RNA-seq of MSCs from two donors (female and male), differentiated in replicate, at 5 time points.
To investigate the function of the tROL LINC00324 in cartilage development, we generated two isogenic deletions (KOs) in C-28/I2 chondrocytes. We then performed gene expression profiling analysis of data from RNA-seq of WT and LINC00324 KO clones.
To investigate the function of additional tROLs and their interdependence, we generated two isogenic deletions (KOs) for the tROLs LINC00324, LINC01962, ENSG00000284607, and ENSG00000287264 in HEK-293 cells. We then performed gene expression profiling analysis of data from RNA-seq of WT and tROL KO clones.

first: Sameen

last: Ahmed

first: Jacob

last: Fine

first: Jordan

middle: J

last: Chalmers

first: Katerina

last: Kiriakopulos

first: Lindsay

last: Clarke

first: Carla

last: Casanova Suárez

first: Katty

last: Soleimanpour

first: Winona

last: Oliveros

first: Kate

last: Delfosse

first: Milad

last: Mokhtaridoost

first: Cassandra

last: Wong

first: Anne-Claude

last: Gingras

first: Brian

last: Ciruna

first: Marc

last: Fabian

first: Benjamin

last: Blencowe


title: Aged muscle stem cells epigenetically drive the expansion of mesenchymal progenitors [bulk RNA-Seq]

first: Stephen

last: Brooks

summary: Sarcopenia, the age-related loss of muscle mass and strength, is characterized by impaired muscle repair and increased deposition of fibrotic tissue. Yet, the specific role of individual cell types in the development of fibrosis remains poorly defined. Here, we report that aged muscle stem cells (MuSCs) directly instruct fibro-adipogenic progenitors (FAPs) to proliferate and adopt a fibrogenic phenotype. Polycomb Ezh2-/- or aged mice exhibited regenerative defects, FAP expansion, fibrosis, and elevated levels of MuSC-secreted interleukin 6 (IL-6) and Spp1/Osteopontin.  In aged MuSCs, H3K27me3 erosion at the NF-kB gene correlated with increased expression and enhanced chromatin recruitment at the IL-6 and Spp1 genes, leading to their activation. Blocking IL-6 and Spp1 signaling in co-cultures of aged MuSC and FAPs, or aged mice, reduced FAP proliferation and muscle fibrosis. In summary, our results indicate that aged MuSCs instruct FAPs to proliferate and acquire a fibrogenic phenotype through a mechanism involving epigenetically-mediated derepression of NF-kB and increased activation of IL-6 and Spp1- both of which are potential pharmacological targets.

overall_design: To investiate the role of Polycomb Repressive Complex 2 (PRC2) methyltransferase Ezh2 in adult MuSCs, we generated a tamoxifen inducible iEzh2fl/fl mouse model by crossing Pax7 locus (Pax7creER) with mice bearing floxed Ezh2 alleles (Ezh2fl/fl). MuSCs and FAPs from either control or Ezh2-/- mice were FACS-isolated at 3 and 7 days post injury, and RNA was extracted and processed for RNAsequencing.

first: Giulia

last: Riparini

first: Morgan

last: Mackenzie

first: Faiza

last: Naz

first: Anshu

last: Deewan

first: Brittany

last: Dulek

first: Shamima

last: Islam

first: Kyung Dae

last: Ko

first: Wanxia

last: Tsai

first: Massimo

last: Gadina

first: Stefania

last: Dell'Orso

first: Vittorio

last: Sartorelli


title: RNA binding proteins in cancer spliceome [Tumor RNA-Seq]

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: We aimed to study the contribution of RNA binding proteins in shaping the highly divergent cancer spliceome

overall_design: RNA-seq data from tumor tissue with the normal expression and with shRNA knockdown of PTB and with shRNA knockdown of PKM2. 3 batches of each kind.

first: Yuxin

last: Li

first: Yi

last: Zhang


title: Aged muscle stem cells epigenetically drive the expansion of mesenchymal progenitors [single cell RNA-Seq]

address: 50 SOUTH DR, RM 1140

institute: NIAMS/NIH

overall_design: Two single cell experiments are included. For the first study, FAPs were isolate from mouse muscle tissue in both Control and iEZh2-/- mice, 7 days post injury, and single cell RNAseq analysis was performed. In the second study (coculture experiments), Control or iEzh2-/- MuSCs FACS-isolated from 7 dpi mice were co-cultured with control PDGFR⍺EGFP FAPs, also isolated from 7 dpi mice. The cells were cocultured for 72 hrs and performed scRNAseq.

first: Riparini

last: Giulia

first: Mackenzie

last: Morgan

first: Naz

last: Faiza

first: Brooks

last: Stephen

first: Deewan

last: Anshu

first: Dulek

last: Brittany

first: Islam

last: Shamima

first: DaeKo

last: Kyung

first: Tsai

last: Wanxia

first: Gadina

last: Massimo

first: Dell'Orso

last: Stefania

first: Sartorelli

last: Vittorio


title: Multilayer regulation underlies the functional precision and evolutionary potential of the olfactory system

city: Lausanne

first: Richard

last: Benton

address: Route Cantonale

institute: University of Lausanne

summary: Sensory neurons must be reproducibly specified to permit accurate neural representation of external signals but also able to change during evolution. We studied this paradox in the Drosophila olfactory system by establishing a single-cell transcriptomic atlas of all developing antennal sensory lineages, including latent neural populations that normally undergo programmed cell death (PCD). This atlas reveals that transcriptional control is robust, but imperfect, in defining selective sensory receptor expression. A second layer of precision is afforded by the intersection of expression of functionally-interacting receptor subunits. A third layer is defined by stereotyped PCD patterning, which masks promiscuous receptor expression in neurons fated to die and removes “empty” neurons lacking receptors. Like receptor choice, PCD is under lineage-specific transcriptional control; promiscuity in this regulation leads to previously-unappreciated heterogeneity in neuronal numbers. Thus functional precision in the mature olfactory system belies developmental noise that might facilitate the evolution of sensory pathways

overall_design: 10-15 virgin peb-Gal4 females were placed in vials with 5-10 UAS-unc84:GFP or UAS-p35,UAS-un84:GFP males for 5 days, after which adults were removed. White pupae (corresponding to 0 h after puparium formation (APF)) were carefully transferred to fresh vials and aged for 18, 24, 30, 36, 42, 48, 56, 64, 72 or 80 additional hours. Developing antennae from aged pupae were dissected in ice cold Schneider’s medium and immediately transferred to 1.8 ml Eppendorf tubes containing 100 µl Schneider’s medium, flash-frozen in liquid nitrogen and stored at -80°C. The numbers of antennae dissected in control (peb-Gal4/+,UAS-unc84:GFP/+) and PCD-blocked (peb-Gal4/+,UAS-p35/+,UAS-unc84:GFP/+) genotypes are as follows (time-point in h APF (n antennae control / n antennae PCD-blocked): 18 (49 / 57), 24 (72 / 52), 30 (67 / 56), 36 (52 / 51), 42 (45 / 48), 48 (45 / 55), 56 (59 / 49), 64 (48 / 60), 72 (54 / 62) and 80 (47 / 53).  Samples were thawed on dry ice and nuclear suspensions prepared as described (Li et al., 2022; McLaughlin et al., 2021). Suspensions from “early” (18/24/30 h APF), “mid” (36/42/48 h APF) and “late” (56/64/72/80 h APF) developmental time points were pooled together, with the exception of time point 80 h APF in the control genotype, which was pooled with mid time points. This latter pooling reflected the initial experimental design, but 80 h APF control cells could be effectively re-classified in the late time point for all subsequent analyses. After addition of Hoechst 33342 (Thermo Fisher Scientific, 62249), samples were loaded into a FACSAria flow cytometer. For each pooled sample, 2 ´ 20,000 GFP-positive nuclei were sorted (20,000 for early nuclei in PCD-blocked condition), which were immediately loaded onto the Chromium Next GEM Chip (10x Genomics)

first: Jérôme

last: Mermet

first: Steeve

last: Cruchet

first: Asfa

last: Borbora

first: Daehan

last: Lee

first: Phing Chian

last: Chai

first: Andre

last: Jang

first: Karen

last: Menuz


title: Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology [CRISPR Screen]

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

summary: Overall, the LNCaP line has served as a remarkably versatile PC model, though the molecular characteristics of several important substrains have not been established nor compared in a systematic manner.  In this study, we used genome-scale approaches to characterize the genomic and transcriptomic features of the parental LNCaP_FGC line, and a spectrum of 12 derivative models that have been deployed for studies of PC.  These studies provide insights into the biochemical features that endow PC with the potential to resist AR-directed therapy and identify features that may underlie the metastatic and treatment resistant phenotypes observed in patients. An important but under-appreciated feature of LNCaP concerns the remarkable heterogeneity of the original LNCaP isolate and the current LNCaP_FGC line which was never subjected to clonal selection. This feature, coupled with the inherent DNA mismatch repair deficiency and genomic instability, has produced a remarkable spectrum of sublines that have provided important insights into PC pathobiology, but also challenge reproducibility and the accurate interpretation of experimental findings.

overall_design: CRISPR Screen of LNCaP_FGC Using the Brunello Library

first: Arnab

last: Bose

first: Armand

last: Bankhead III

first: Michael

last: Yang

first: Ilsa

last: Coleman

first: Rabeya

last: Bilkis

first: Wanting

last: Han

first: Jared

middle: M

last: Jucas

first: Dapei

last: Li

first: Thomas

last: Persse

first: Patty

last: Galipeau

last: Haffner

first: Gavin

last: Ha

first: Peter

last: Nelson


title: Photosynthetic bacterium Rhodobacter alkalitolerans strain JA916T, Jul 25 '25

city: Hyderabad

first: Rajagopal

last: Subramanyam

state: Telangana

address: School of Life Sciences Building UoH

department: Plant Sciences

country: India

institute: University of Hyderabad

summary:
The study is done to compare the impact of high light on the photosynthetic bacterium Rhodobacter alkalitolerans strain JA916T when grown in high pH and neutral pH. After the analysis we found several photosynthetic and cell division transcripts to be differentially expressed. These transcripts were majorly from the bacteriochlorophyll and carotenoid biosynthesis pathway. Reaction center transcripts were also found to be highly upregulated in nhpH conditions. Similary cell division transcripts were also found to be highly upregulated in high light conditions. Further for detailed study the publication can be referred.

This study is to be published in the article titled as " Integration of transcriptomics and metabolomics for understanding the global responses to neutral pH and high pH under high light in photosynthetic bacterium Rhodobacter alkalitolerans strain JA916T".

overall_design: The photosynthetic bacterium was grown in control light condition (30 micor mole photons/m2/s) and in treated high light condition (500 micor mole photons/m2/s) at neutral and alkaline pH conditions.

first: Mohammad

last: Zamal

first: Sureshbabu

last: Marriboina

first: Vijay

last: Lavudiya

first: Gunasekaran

last: Xavier

first: Aprajita

last: Kumari

first: Kapuganti

last: Gupta

first: Chintalapati

last: Ramana

first: Subramanyam

last: Rajagopal


title: Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology [ChIP-Seq]

first: Brian

last: Hanratty

overall_design: ChIP-Seq of LNCaP Sublines using AR antibody ab108341

first: Arnab

last: Bose

first: Armand

last: Bankhead III

first: Michael

last: Yang

first: Ilsa

last: Coleman

first: Rabeya

last: Bilkis

last: Han


title: CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts [ATAC-seq]

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

institute: Stowers Institute for Medical Research

summary: The Maternal-to-Zygotic transition (MZT) is a reprograming process encompassing zygotic genome activation (ZGA) and the clearance of maternally-provided mRNAs. While some factors regulating MZT have been identified, there are thousands of maternal RNAs whose function has not been ascribed yet. Here, we have performed a proof-of-principle CRISPR-RfxCas13d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT. Bckdk mRNA knockdown caused epiboly defects, ZGA deregulation, H3K27ac reduction and a partial impairment of miR-430 processing. Phospho-proteomic analysis revealed that Phf10 (Baf45a), a chromatin remodeling factor, is less phosphorylated upon Bckdk depletion. Further, phf10 mRNA knockdown also altered ZGA and Phf10 constitutively phosphorylated rescued the developmental defects after bckdk mRNA depletion. Altogether, our results demonstrate the competence of CRISPR-RfxCas13d screenings to uncover new regulators of early vertebrate development and shed light on the post-translational control of MZT mediated by protein phosphorylation.

overall_design: ATAC-seq assays in embryos injected only with RfxCas13d protein and embryos injected with RfxCas13d protein a mix of 2 gRNAs targeting bckdk mRNA (Bckdk KD)


title: Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology

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

WGS data for this study is available at: PRJNA1219540

overall_design: Refer to individual Series


title: Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology (ATAC-Seq)

overall_design: ATAC-Seq of LNCaP Sublines using OMNI-ATACseq protocol

first: Wanting

first: Jared

last: Jucas

first: Dapei

last: Li

first: Thomas

last: Persse

first: Patty

last: Galipeau

last: Haffner

first: Gavin

last: Ha

first: Peter

last: Nelson


title: RNA sequencing human melanoma, glioblastoma and pancreatic adenocarcinoma cell lines

city: Brussels

first: Sandra

last: Tuyaerts

address: Laarbeeklaan 103

department: Translational Oncology Research Centre

institute: Vrije Universiteit Brussel

summary: Bulk RNA sequencing was performed on commercially available melanoma, glioblastoma and pancreatic adenocarcinoma cells lines. The RNA expression data were then correlated to the effect of a newly developed oncolytic virus on the growth of the cell lines.

overall_design: RNA seq profiling of wildtype 624-mel, 938-mel, U87, LN229, BXPC3, ASPC1, Capan-1, SW1990, PaTu8988t, SUIT2 and MiaPaca-2 cells

first: Latoya

last: Stevens

first: Xenia

last: Geeraerts

first: Bart

last: Neyns


title: Melanocyte differentiation and mechanosensation are differentially modulated by distinct extracellular matrix proteins

city: Homburg

first: Carole

last: Luthold

state: Saarland

address: Kirrberger Straße

institute: Saarland University

summary: Dysfunctions in melanocytes can lead to pigmentation disorders, such as albinism, or contribute to the development of melanoma, the most aggressive form of skin cancer. Epidermal melanocytes typically interact with the collagen IV-rich basement membrane, but upon injury or in pathological conditions, they can encounter environments rich in collagen I or fibronectin. While alterations in ECM composition and stiffness are known to impact cell behavior, the specific roles of each of these cues for melanocyte functions remain unclear. To explore the impact of these extrinsic cues, we here exposed murine melanocytes to different ECM proteins as well as varying substrate stiffnesses. This study identified MITF, a key regulator of melanocyte differentiation and function, as an ECM- and mechanosensitive transcription factor. We further revealed that distinct ECM proteins and substrate stiffness engage a FAK/MEK/ERK/MITF signaling axis to control melanocyte functions. Exposure of melanocytes to collagen I restricted FAK and ERK activation, promoting high nuclear MITF levels associated with melanocyte proliferation and differentiation. Conversely, fibronectin elicited elevated FAK and ERK activation, leading to low nuclear MITF, correlating with a dedifferentiated and motile phenotype. Consistent with these observations, RNA sequencing revealed that COL I supports a differentiated gene expression program, whereas FN induces a neural crest-like and dedifferentiated transcriptomic signature. Importantly, inhibiting MEK or ERK activity in melanocytes cultured on fibronectin led to increased MITF nuclear localization, and enhanced melanogenesis. Additionally, we uncovered that melanocyte mechanoresponses differ depending on the specific ECM environment. Together, these findings reveal a synergistic effect of extrinsic cues on melanocyte function, with a context-dependent MITF regulation downstream of ERK, offering new perspectives for our understanding of melanocyte-related pathologies.

overall_design: RNA-seq-based gene expression profiling of immortalized murine melanocytes (iMCs) cultured on type I collagen, type IV collagen, or fibronectin. Cells were harvested 24 hours after plating, and RNA was extracted from three independent biological replicates per condition.

first: Marie

last: Didion

first: Vanessa

last: Rácz

first: Emilio

last: Benedum

first: Ann-Kathrin

last: Bukhart

first: Nina

last: Demmerle

first: Evelyn

last: Wirth

first: Gubesh

last: Gunaratnam

first: Sudharshini

last: Thangamurugan

first: Volkhard

last: Helms

first: Markus

last: Bishoff

first: Annika

last: Ridzal

last: Iden


title: Aged muscle stem cells epigenetically drive the expansion of mesenchymal progenitors

first: Stephen

last: Brooks

state: MD

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


title: The ribonuclease DISL-2 mediates piRNA degradation in C. elegans

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

summary: The PIWI/piRNA pathway serves as a conserved RNA-directed immune mechanism that suppresses transposons and promotes fertility. The biogenesis of piRNAs has been extensively investigated since their discovery, yet the mechanisms governing piRNA degradation remain poorly understood. This study determines the half-lives of thousands of C. elegans piRNAs, revealing a broad range from less than 1 hour to over 20 hours. Notably, piRNAs with 3' terminal uridines are degraded faster than those with 3' guanines or cytosines, suggesting that 3' uridines induce nucleolytic degradation. We identify DISL-2, a 3' to 5' exoribonuclease, as a key enzyme responsible for degrading piRNAs with templated 3' uridines as well as non-templated 3' uridines added by Poly(U) polymerase PUP-1. Furthermore, DISL-2 acts as a quality control factor to target piRNAs that are improperly processed at their 3' ends. Together, our findings advance the understanding of piRNA homeostasis by determining piRNA half-lives and identifying factors involved piRNA decay.

overall_design:
Analysis of piRNA half-lives measured by depletion of piRNA transcription factor TOFU-5. Analysis of piRNAs in disl-2 and pup-1 genetically null mutants compared to that in wild-type.
mRNA sequencing of disl-2 mutants compared to that in wild-type. RNAs were isolated from gravid adult animals, subjected to high-throughput RNA sequencing anda analyzed.

first: Benjamin

last: Pastore

first: Hannah

last: Hertz


title: ZMYND11 Functions in Bimodal Regulation of Latent Genes and Brain-like Splicing to Safeguard Corticogenesis [CUT&RUN]

city: Cincinnati

first: Jason

last: Tchieu

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: While the identification of pathogenic variants linked to neurodevelopmental (NDD) and autism spectrum disorders (ASD) has advanced rapidly, the mechanisms underlying these genetic risks remain unclear. Here, we leveraged a human pluripotent stem cell model to uncover the neurodevelopmental consequences of mutations in ZMYND11, a newly implicated risk gene. ZMYND11, known for its tumor suppressor function, encodes a histone-reader that recognizes sites of transcriptional elongation and acts as a co-repressor. Our findings reveal that ZMYND11 deficient cortical neural stem cells exhibit upregulation expression of latent developmental pathways, leading to impaired production of secondary neural progenitors and neurons. In addition to its chromatin-related functions, we found ZMYND11 orchestrates a brain specific isoform switch that affects migration and proliferation of cortical neural stem cells. We further demonstrated that brain specificity is likely to involve the activity of the splicing regulator RBFOX2. Finally, we extended our findings to 10 additional lines with different chromatin-related NDD/ASD risk factors and identified a subset displaying similar activation of developmental pathways and splicing dysregulation, which could partially be rescued by leveraging the transcriptional repression and splicing coordination of ZMYND11. Collectively, our work highlights the critical role of ZMYND11 in regulating developmental signals and alternative splicing, offering novel insights into the molecular pathology of ZMYND11-associated NDDs. Moreover, these findings suggest broader convergence with other genetic risk factors for NDD/ASD, presenting potential therapeutic avenues for intervention.

overall_design: To investigate how ZMYND11 regulates gene expression in neurodevelopment, we performed CUT&RUN seq on WT d18 neural stem cells for ZMYND11, H3K36me3, H3K27me3 and IgG control, on ZMYND11 mutant neural stem cells for ZMYND11 and on FLAG-ZMYND11 overexpressed neural stem cells for FLAG, ZMYND11 and IgG control.

first: Xuyao

last: Chang


title: Multiomic assessments of LNCaP and derived cell strains reveal determinants of prostate cancer pathobiology (RNA-Seq)

first: Brian

last: Hanratty

overall_design: RNA sequencing of LNCaP-FGC and 12 LNCaP sublines using Illumina stranded mRNA TruSeq Library prep and sequenced on Illumina NovaSeq 6000.

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last: Bose

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last: Bilkis

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