title: Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons [cortical]

city: Cambridge

first: Matthew

last: Leventhal

address: 77 Massachusetts Avenue

department: Computational and Systems Biology

institute: Massachusetts Institute of Technology

summary: Huntington’s Disease (HD) is caused by a CAG repeat expansion in the gene encoding Huntingtin (HTT). While normal HTT function appears impacted by the mutation, the specific pathways unique to CAG repeat expansion versus loss of normal function are unclear. To understand the impact of the CAG repeat expansion, we evaluated biological signatures of HTT knockout (HTT KO) versus those that occur from the CAG repeat expansion by applying multi-omics, live cell imaging, survival analysis and a novel feature- based pipeline to study cortical neurons (eCNs) derived from an isogenic human embryonic stem cell series (RUES2). HTT KO and the CAG repeat expansion influence developmental trajectories of eCNs, with opposing effects on the growth. Network analyses of differentially expressed genes and proteins associated with enriched epigenetic motifs identified subnetworks common to CAG repeat expansion and HTT KO that include neuronal differentiation, cell cycle regulation, and mechanisms related to transcriptional repression and may represent gain-of-function mechanisms that cannot be explained by HTT loss of function alone. A combination of dominant and loss-of-function mechanisms are likely involved in the aberrant neurodevelopmental and neurodegenerative features of HD that can help inform therapeutic strategies.

overall_design: We performed ATAC-seq and ChIP-seq in embryonic stem cell and ESC-derived cortical neuron models of Huntington's disease. In the ChIP-seq experiments we measured H3K27me3, H3K27Ac, H3K4me1 and H3K4me3 histone modifications. All measurements were performed in control cells, cells wtih HTT CAG repeat expansion (56CAG and 72CAG), and cells with HTT knockdown.

first: Jennifer

last: Stocksdale


title: Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons [ESC]

status: Public on May 05 2025

state: MA

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing


title: CCAAT/enhancer-binding proteins alpha and beta directly regulate ovulation and selectively regulate gene expression in granulosa cells by preovulatory stage- and dose-dependent mechanisms

city: Ithaca

first: Yi

last: Ren

address: 203 Morrison Hall

department: Animal Science

institute: Cornell University

type: Expression profiling by high throughput sequencing

summary: The preovulatory luteinizing hormone surge orchestrates complex cellular and molecular events leading to ovulation. CCAAT/enhancer-binding proteins alpha and beta (C/EBPα/β) are transcription factors acutely induced by the luteinizing hormone surge and crucial for ovulation and granulosa cell luteinization. However, biological processes and their regulatory mechanisms downstream of C/EBPα/β in the preovulatory ovary are not completely understood. To address this knowledge gap, we generated Cebpa/bfl/fl;Pgr-Cre mutants and compared them with Cebpa/bfl/fl;Cyp19a1-Cre mutant female mice. The Cebpa/bfl/fl;Cyp19a1-Cre mutants have undetectable levels of C/EBPα/β throughout preovulatory stages and no ovulation, aligning with previous reports, while Cebpa/bfl/fl;Pgr-Cre mutants presented gradual deletion of C/EBPα/β during late preovulatory stage and reduced ovulation rate. Comparison of these two models indicates that sustained expression of C/EBPα/β throughout preovulatory stages is necessary for successful ovulation. This provides a unique opportunity to interrogate gene regulatory mechanisms by C/EBPα/β during different preovulatory time windows and the impact of dysregulating C/EBPα/β on ovulation-associated biological processes. Our study revealed that C/EBPα/β regulate gene expression and distinct biological functions via preovulatory stage-, dose-, and/or potentially isoform ratio- dependent mechanisms. These findings shed new light on the intricate gene regulation mechanisms by C/EBPα/β downstream of the LH surge.

overall_design: To understand biological processes and their regulatory mechanisms downstream of C/EBPα/β in the preovulatory ovary, we we conducted Bulk RNA sequencing analysis on granulosa cells isolated from WT, Cebp-C, and Cebp-P mutants at 8 h and 12 h post-hCG.

first: Hanxue

last: Zhang

middle: A


title: Hypothermic machine perfusion alleviates DCD graft liver injury by inducing the expression of KLF2 and promoting macrophage efferocytosis

city: NanChang

first: Qi

last: Xiao

address: Nanchang University, 17 yongwai Zheng jie street, NanChang 33006, Jiangxi, China

country: China

institute: Department of Transplantation，The First Affiliated Hospital， Jiangxi Medical College，Nanchang University

summary: This study aims to investigate the protective effects and underlying mechanisms of hypothermic machine perfusion (HMP) on ischemia-reperfusion injury (IRI) in liver grafts from donation after cardiac death (DCD), with a specific focus on the regulation of KLF2 expression and its role in modulating macrophage efferocytosis.

overall_design: A DCD liver grafts model was established to evaluate the protective effects of HMP. KLF2 expression and macrophage efferocytosis were assessed in liver grafts. In vitro, human umbilical vein endothelial cells (HUVECs) were transfected to manipulate KLF2 expression and co-cultured with macrophages in a non-contact system to explore the endothelial–macrophage interaction. The efferocytosis agonist putrescine was administered in vivo to further assess its effect on DCD liver grafts. RNA sequencing (RNA-Seq) was conducted to analyze gene expression changes.

first: Qin

last: Deng


title: Myricone C, a novel neolignan from Myristica fragrans, induces ER stress-mediated apoptosis in gastric and colorectal cancer via ROCK inhibition

city: Gangneung

first: Myungsuk

last: Kim

state: Gangwon

address: 679 Saimdang-ro

country: South Korea

institute: Korea Institute of Science & Technology

summary: Gastric and colorectal cancers remain leading causes of cancer-related mortality worldwide, highlighting the need for novel therapeutic strategies. Here, we report the potent anticancer activity of myricone C (MyrC), a novel neolignan and diarylnonanoid derivative isolated from Myristica fragrans, as a potent anticancer agent against these malignancies in vitro and in vivo. MyrC exhibited significant cytotoxicity in human gastric and colorectal cancer cell lines (IC50 values: 2.1–9.8 µM). Mechanistic studies revealed that MyrC induces G1 phase cell cycle arrest (gastric cells), increases the apoptosis-associated sub-G1 fraction (colorectal cells), and triggers apoptosis. Comprehensive transcriptomic analysis (RNA-seq, GSEA), validated by targeted qPCR and Western blotting, demonstrated that MyrC robustly induces endoplasmic reticulum (ER) stress, activates the unfolded protein response (UPR) primarily via the PERK-eIF2α-ATF4-CHOP axis, and upregulates downstream pro-apoptotic signaling. Furthermore, in silico docking predicted, and in vitro kinase assays confirmed, that MyrC directly binds and potently inhibits ROCK1 and ROCK2 kinases (IC50 values: 206–247 nM), which are implicated in cancer progression and potentially influence ER stress responses. Importantly, MyrC significantly suppressed tumor growth in a gastric cancer xenograft model in vivo without overt toxicity. These findings establish MyrC as a promising therapeutic lead candidate for gastric and colorectal cancer.

overall_design: RNA-seq profiling of 23132/87 and SW48 cells treated with Myricone C at 0 µM and 10 µM for 48 hours

first: Ngoc Phung

last: Ly

first: Tam

middle: T

last: Le

first: Ngoc

middle: B

last: Nguyen

first: Ji Hoon

first: Hasun

first: Youngsic

last: Jeon

first: Young-Joo

first: Suk Woo

last: Kang

first: Dae-Geun

last: Song

first: Sang Hoon

last: Jung


title: Rtf1 HMD domain facilitates global histone H2B monoubiquitination and regulates morphogenesis and virulence in the meningitis-causing pathogen Cryptococcus neoformans

city: Zhengzhou

first: Youbao

last: Zhao

state: Henan

address: 218 Pingan Ave. Jinshui District

institute: Henan Agricultural University

summary: Rtf1 is generally considered to be a subunit of the Paf1 complex (Paf1C), which is a multifunctional protein complex involved in histone modification and RNA biosynthesis at multiple stages. Rtf1 is stably associated with the Paf1C in Saccharomyces cerevisiae, but not in other species including humans. Little is known about its function in human fungal pathogens. Here, we show that Rtf1 is required for facilitating H2B monoubiquitination (H2Bub1), and regulates fungal morphogenesis and pathogenicity in the meningitis-causing fungal pathogen Cryptococcus neoformans. Rtf1 is not tightly associated with the Paf1C, and its histone modification domain (HMD) is sufficient to promote H2Bub1 and the expression of genes related to fungal mating and filamentation. Moreover, Rtf1 HMD fully restores fungal morphogenesis and pathogenicity; however, it fails to restore defects of thermal tolerance and melanin production in the rtf1Δ strain background. The present study establishes a role for cryptococcal Rtf1 as a Paf1C-independent regulator in regulating fungal morphogenesis and pathogenicity, and highlights the function of HMD in facilitating global H2Bub1 in C. neoformans.

overall_design: RNA-seq profiling of WT, rtf1D, HMD, and Plus3 strains cultured on V8 media for 12 hours

first: Yixuan

last: Jiang

first: Ying

last: Liang

first: Jing


title: Atrophin-1 Antisense Oligonucleotide Provides Robust Protection from Pathology in a Fully Humanized DRPLA Model

city: Seattle

first: Robert

last: Bragg

state: Washington

address: 300 9th Ave

institute: University of Washington

summary: Dentatorubral-pallidoluysian atrophy (DRPLA) is a fatal neurodegenerative disease arising from a CAG repeat expansion in the atrophin-1 (ATN1) gene. Because DRPLA, like many repeat expansion disorders (REDs), arises predominantly from toxic gain-of-function mechanisms, we hypothesized that ATN1 knockdown would have therapeutic potential. To test this, we established the first fully-humanized mouse model of a RED, in which one allele of mouse Atn1 is completely replaced by human ATN1, including 112 pure CAG repeats. This novel approach to exploring RED biology provides significant advantages, notably the ability to test sequence-specific therapeutics targeting human sequences, even in introns and untranslated regions of pre-mRNA. We found that our model—the Atn1Q112/+ mouse—recapitulates key features of human DRPLA, including behavioral alterations, reduced brain size and aggregate accumulation. We treated Atn1Q112/+ mice with antisense oligonucleotides (ASOs) targeting mouse Atn1 (to probe for loss of function concerns), human ATN1, or a combination. Treatment with human, but not mouse, ATN1-targeting ASOs provides remarkable protection from a range of disease-related behavioral phenotypes, including aggregation of mutant ATN1 (mATN1), and marked rescue of transcriptional dysregulation in the cerebellum. These results have helped motivate an ongoing human clinical study of ASOs targeting ATN1 for DRPLA.

overall_design: Mice were treated with ASO from 2 days to 9 weeks of age. We sequenced n=5 per genotype (WT or ATN1.Q112/+) treated with Saline, Mo_ASO, or Hu_ASO. Total N=30

first: Velvet

middle: L

last: Smith

first: Bereket

middle: Z

last: Gidi

middle: M

first: Jeffrey

last: Cantle

first: Aliza

last: Ben-Varon

first: Briana

last: Nobel

first: Silvia

last: Prades

first: Andrea

last: Compton

first: Julie

last: Greenfield

first: Joanna

last: Korecka-Roet

first: Tim

last: Yu

first: Vikram

last: Khurana

first: Holly

last: Kordasiewicz

first: Hien

first: Melissa

last: Barker-Haliski

first: Daniel

middle: D

last: Child

last: Carroll


title: The effect of BQ323636.1 overexpression on mRNA expression profile in breast cancer cells

city: Hong Kong

first: Ui-soon

last: Khoo

address: Queen Mary hospital

department: Pathology

country: Hong Kong

institute: University of Hong Kong

summary: BQ323636.1 (BQ), a truncated splice variant of NCOR2, promotes drug resistance in breast cancer by disrupting NCOR2’s repressor function through direct binding, leading to global gene expression changes. To elucidate its molecular impact, we established stable BQ-overexpressing breast cancer cell lines (MCF-7-BQ and ZR-75-BQ) and their controls (MCF-7 and ZR-75), performing RNA-sequencing to identify differentially expressed genes (DEGs) and associated pathways. The results revealed significant DEGs enriched in pathways linked to drug resistance and transcriptional regulation, highlighting BQ’s role in driving a drug-resistant phenotype. These findings provide critical insights into the mechanisms of BQ-mediated drug resistance, positioning BQ as a potential therapeutic target in breast cancer.

overall_design: PolyA-tail RNA sequencing of the controls (MCF-7 and ZR-75) and th ebQ overexpressing cells (MCF-7-BQ and ZR-75-BQ)

first: KHOO

last: Ui-soon

first: TSOI

last: Ho


title: The effect of LSM12 overexpression on NCI-H1703 cell line

city: Shenyang

first: Gang

last: Zhao

address: 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary: The aim of this study is to investigate the effect of high expression of LSM12 on transcriptome profile in NCI-H1703 cells

overall_design: Construction of NCI-H1703 stable cells overexpressing LSM12, followed by RNA-seq.

first: Lin

last: Wu

first: Fangyuan

last: Zhang

first: Huanhuan

last: Chen


title: 2,8-Dihydroxyadenine disrupts epithelial integrity and alters kidney cell phenotype in vitro

city: Reykjavík

first: Þórarinn

last: Guðjónsson

address: Læknagarður -  Lg-416

country: Iceland

institute: University of Iceland

summary: Adenine phosphoribosyltransferase (APRT) deficiency is an autosomal recessive disorder that causes accumulation of 2,8-dihydroxyadenine (DHA) in the urinary tract, leading to kidney stones and chronic kidney disease. Progression to end-stage kidney disease can occur without timely treatment. The xanthine oxidoreductase inhibitors, allopurinol and febuxostat, block DHA generation and halt or delay stone formation and disease progression. Some patients cannot tolerate these drugs, necessitating new therapeutic approaches. This study aimed to investigate how DHA influences structural and molecular changes in HK-2, HEK293, and MDCK kidney cells. DHA exposure reduced cell viability and impaired migration in all cell lines. Increased expression of the adhesion protein CD44 was observed in HEK293 and HK-2 cells, adjacent to DHA crystals. Transepithelial electrical resistance measurements of MDCK cells indicated reduced epithelial integrity following DHA exposure. RNA sequencing of DHA-treated HK-2 cells revealed gene expression changes, with upregulation of TNF-α and mTORC1 signaling and downregulation of epithelial–mesenchymal transition and oxidative phosphorylation. Functional enrichment analysis highlighted pathways related to cell cycle regulation, inflammation, and metabolic processes. These findings show that dose-dependent toxic effects of DHA toxicity interrupt cell migration and epithelial integrity. CD44 may contribute to crystal adhesion, making it a potential therapeutic target in DHA crystal nephropathy.

overall_design: RNA-seq profiling of HK-2 cells after 72 hours treatment with 60,120 and 240 ug/ml of  2,8-dihydroxyadenine suspended in media

first: Hildur Run

last: Helgudottir

first: Runolfur

last: Palsson

first: Vidar Orn

last: Edvardsson

first: Thorarinn

last: Gudjonsson


title: Impact of SLC39A9 knockdown in murine melanoma cells with Cdkn2a knockdown

city: Pittsburgh

first: Katherine

last: Aird

state: PA

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

summary: This dataset includes bulk RNA-Seq data from Yumm5.2 murine melanoma cells with Cdkn2a knockdown, either alone or in combination with Slc39a9 knockdown, cultured in vitro

overall_design: Yumm5.2 murine melanoma cells were infected with shRNAs targeting Cdkn2a (hairpins #1 and #2), either alone or in combination with shRNAs targeting Slc39a9 (hairpins #1 and #2). Cdkn2a-targeting shRNAs were cloned into the pLKO.1 vector expressing blasticidin resistance, while Slc39a9-targeting shRNAs were cloned into the pLKO.1 vector expressing puromycin resistance. Infected cells were selected with puromycin and blasticidin for 3 days, after which cells were harvested in Trizol for RNA isolation.

first: Raquel

last: Buj


title: Diverse Cell Types Establish a Pathogenic Immune Environment in Peripheral Neuropathy [bulk RNA-seq]

city: St. Louis

first: Julie

last: Choi

state: MO

address: 4370 Duncan Avenue

department: Genetics

institute: Washington University in St. Louis

summary: Neuroinflammation plays a complex and context-dependent role in many neurodegenerative diseases. We identified a key pathogenic function of macrophages in a mouse model of a rare human congenital neuropathy in which SARM1, the central executioner of axon degeneration, is activated by hypomorphic mutations in the axon survival factor NMNAT2. Macrophage depletion blocked and reversed neuropathic phenotypes in this sarmopathy model, revealing SARM1-dependent neuroimmune mechanisms as key drivers of disease pathogenesis. In this study, we investigated the impact of chronic subacute SARM1 activation on the peripheral nerve milieu using single cell/nucleus RNA-sequencing (sc/snRNA-seq). Our analyses reveal an expansion of immune cells (macrophages and T lymphocytes) and repair Schwann cells, as well as significant transcriptional alterations to a wide range of nerve-resident cell types. Notably, endoneurial fibroblasts show increased expression of chemokines (Ccl9, Cxcl5) and complement components (C3, C4b, C6) in response to chronic SARM1 activation, indicating enhanced immune cell recruitment and immune response regulation by non-immune nerve-resident cells. Analysis of CD45+ immune cells in sciatic nerves revealed an expansion of an Il1b+ macrophage subpopulation with increased expression of markers associated with phagocytosis and T cell activation/proliferation. We also found a significant increase in T cells in sarmopathic nerves. Remarkably, T cell depletion rescued motor phenotypes in the sarmopathy model. These findings delineate the significant changes chronic SARM1 activation induces in peripheral nerves and highlights the potential of immunomodulatory therapies for SARM1-dependent peripheral neurodegenerative disease.

overall_design: - Bulk RNA sequencing of WT and Nmnat2 V98M/R232Q;SARM1 KO mouse sciatic nerves at 2-3-month

first: Amy

last: Strickland

first: Caitlin

last: Dingwall

first: Aldrin

last: Yim

first: Joseph

last: Bloom

first: Aaron

last: DiAntonio

first: Jeffrey

last: Milbrandt


title: Base editing mediated correction of severe β0 IVS2-1 thalassemia mutations.

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: β-thalassemia is a highly prevalent monogenic recessive disease caused by mutations affecting the synthesis of the adult hemoglobin β-chains. Transplantation of autologous, genetically modified hematopoietic stem/progenitor cells (HSPCs) is an attractive therapeutic option. However, current gene therapy strategies based on the use of lentiviral vectors or CRISPR/Cas9 nuclease are not equally effective in all the patients and/or raise safety concerns. Base editing (BE), a new CRISPR/Cas9 derived genome editing tool, allows the effective introduction of point mutations at precise locations within the genome without generating double strand breaks. The two β0 mutations CD39 (CAG>TAG) and IVS2-1 (G>A) are among the most common and severe β-thalassemia mutations in the Mediterranean area and Middle East. We exploited the capacity of BE to correct these mutations in HSPCs from β-thalassemia patients. We demonstrated that red blood cells in vitro derived from edited HSPCs exhibited high β-globin levels and that the delayed erythroid differentiation typically observed in β-thalassemic cell cultures was corrected by our treatment. Finally, xenotransplantation experiments showed base editing in HSCs and correction of the β-thalassemic phenotype in vivo. Overall, our study provides in vitro and in vivo proof of efficacy of a BE approach to treat patients with prevalent and severe β-thalassemia mutations.

overall_design: Human sickle HSPCs  were transfected using an adenine base editor and a gRNA that corrects the IVS2-1  thalassemic mutation to evaluate potential off-targets. As control, each of the 3 donors was mock-transfected with TE buffer. Bulk RNAseq was performed at 48h to evaluate the impact of the editing procedure at the transcriptomic level.

first: Giulia

last: Hardouin

first: Annarita

last: Miccio


title: Identification of a VHL germline deletion in a family with Von Hippel-Lindau syndrome using MLPA-NGS

city: Shanghai

first: Chaoran

last: Xia

state: Shanghai

address: 800# Dong Chuan Road,  Shanghai, China

institute: Shanghai Jiaotong University

summary:
Gene chip analysis was performed using the Infinium OmniZhongHua-8 v1.3 BeadChip (Ilumina, Inc.). This method is used to detect ~240 CNV-affected genetic diseases/regions, including uniparental disomy and polyploidy.
To identify copy number and CNV variations on chromosome 3 and in the vicinity of VHL, compared to a new assay called MLPA-NGS, we analysed individual hybridizations conducted on  Infinium OmniZhongHua-8 v1.3 BeadChip (Ilumina, Inc.). Sample types included normal blood.

overall_design: The genotypes of the study samples were determined using Gene chip analysis. IMPUTE2 was utilized to impute supplementary autosomal single nucleotide polymorphisms (SNPs). The genotype assignments were grounded on the phase 3000 Genomes cosmopolitan reference panel.

first: Yongchen

last: Yang


title: Loss of the Maternal Effect Gene Nlrp2 Impairs Embryonic and Extra-Embryonic Development, Unveiling a Novel Cause of Congenital Anomalies

city: Houston

first: Michael

last: Jochum

state: TX

address: 1 Baylor Plaza

department: Obstetrics and Gynecology

institute: Baylor College of Medicine

summary: Maternal effect genes (MEGs) are expressed in the oocyte and early mammalian preimplantation embryo. Impaired MEG function can impact offspring development and health. We investigated the consequences of postimplantation embryonic and extra-embryonic development in mice with maternal loss-of-function of Nlrp2, an MEG that encodes a protein of the subcortical maternal complex (SCMC). We employed three mating schemes, wildtype (WT) x WT, maternal Nlrp2-knock-out (KO) x WT, and WT x paternal Nlrp2-KO, to study the embryonic and extraembryonic phenotypes at embryonic day 11.5. Concepti of maternal Nlrp2-KO matings have striking abnormalities, including aberrant yolk sac vasculature, lower embryo to yolk sac area ratios, increased embryo resorption, and embryos with variably severe craniofacial abnormalities, and congenital heart defects. The placentas have significant morphological abnormalities, particularly in the junctional zone and labyrinth layers. This indicates that Nlrp2 is important for trophoblast development and placental architecture, supported by significantly altered gene expression profiles in the placentas of pregnant Nlrp2-KO mice. Taken together, these findings highlight the importance of maternal Nlrp2 for embryonic and placental development, and for the first time confirm that inactivating maternal effect mutations can cause disrupted placental development along with congenital cardiac and other anomalies. In conclusion, maternal loss of Nlrp2 profoundly impacts mouse embryonic and extra-embryonic development, highlighting a new role of MEGs. These findings pave the way for future research into genetic mechanisms underlying congenital anomalies and developmental disorders.

overall_design:
To characterize the variable in vivo embryological and placental consequences of maternal inactivation of Nlrp2. We performed detailed phenotypic characterization of embryos and placentas in pregnancies at E11.5 Nlrp2 females and performed bulk RNA seq on placentas to find altered gene transcriptions.
Maternal effect genes (MEGs) are expressed in the oocyte and early mammalian preimplantation embryo. Impaired MEG function can impact offspring development and health. We investigated the consequences of postimplantation embryonic and extra-embryonic deve

first: Momal

last: Sharif

first: Ignatia

last: Van den Veyver


title: The mechanism of gluconeogenic enzyme Pck1 in ulcerative colitis through regulation of Pla2g6-mediated lipid metabolism

city: Chengdu

first: Ming

last: Chen

state: Sichuan

address: No. 37, GuoXue Xiang, Chengdu, China

institute: West China Hospital of Sichuan University

summary: Metabolic dysregulation may serve as a pivotal driver of inflammatory bowel disease (IBD), with the crosstalk between metabolism and the immune system emerging as a critical research focus. Ulcerative colitis (UC) patients exhibit enhanced glycolysis but suppressed gluconeogenesis in the intestinal mucosa, yet the mechanistic links between these metabolic alterations and mucosal injury remain poorly defined. This study establishes phosphoenolpyruvate carboxykinase 1 (Pck1), a key rate-limiting enzyme in gluconeogenesis, as a central regulator of UC progression. We found Pck1 expression was significantly downregulated in colon tissues of UC patients and mice with DSS‑induced colitis. Utilizing an intestinal epithelial cell (IEC)-specific Pck1 knockout mouse model, we demonstrated for the first time that Pck1 deficiency exacerbates intestinal inflammation. Mechanistically, Pck1 depletion induces metabolic reprogramming that upregulates Pla2g6 expression, driving abnormal hydrolysis of phosphatidylcholine and phosphatidylethanolamine in IECs. Pharmacological inhibition of Pla2g6 ameliorated colitis in Pck1-deficient mice. These findings position Pck1 as a potential early diagnostic biomarker for UC and suggest that therapeutic targeting of the Pck1-Pla2g6 metabolic axis may yield novel strategies for UC management.

overall_design: RNA-Seq was performed on PCK1 intestinal epithelial cell-specific knockout mice and their littermate control mice after 7 days of DSS treatment.

first: Chengwei

last: Tang

first: Zhiyin

last: Huang


title: Transcriptome analysis of embryonic hearts from germline RBPMS knockout mutants

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: To investigate the function of RNA-binding protein with multiple splicing (RBPMS) in heart, we establish a germline RBPMS knockout mutant strain. RNA seq of neonatal (P1) hearts was performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for littermate control and RBPMS knock out hearts at neonatal stage.

first: Shan

last: Lin

first: Andre

last: Schneider

first: Stefan

last: Günther


title: Transcription factor binding divergence across maize inbred lines drives transcriptional and phenotypic variation

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

summary: We use DNA affinity purification-sequencing (DAP-seq) to map transcription factor binding events for 200 maize TFs belonging to 30 distinct families and heterodimer pairs in two distinct inbred lines historically used for maize hybrid plant production

overall_design: Genome-wide binding site data was generated for 200 maize transcription factors using DAP-seq in two maize inbred lines (B73 and Mo17).

first: Mary

last: Galli

first: Zongliang

first: Tara

last: Ghandour

first: Amina

last: Chaudhry

first: Jason

last: Gregory

first: Fan

last: Feng

first: Miaomiao

last: Li

first: Nathaniel

last: Schleif

first: Xuan

last: Zhang

first: Yinxin

last: Dong

first: Gaoyuan

last: Song

first: Justin

last: Walley

first: George

last: Chuck

first: Clint

last: Whipple

first: Heidi

last: Kaeppler

first: Shao-shan

middle: C


title: Affymetrix Axiom® Peanut 47K Genotyping Array

city: Qingdao

first: jing

last: xu

address: 126 Wannianquan Road

institute: Shandong Peanut Research Institute

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
The cultivated peanut, A. hypogaea L., is a critical oil and food crop worldwide. Decoding the genetic makeup behind natural variation in kernel oil and fatty acid concentrations is crucial for molecular breeding-based nutrient quantity and quality manipulation. Herein, we recognized 87 quantitative trait loci (QTLs) in 45 genomic regions for the concentrations of oil, oleic acid, and linoleic acid, as well as the oleic acid to linoleic acid (O/L) ratio via a genome-wide association study (GWAS) involving 499 peanut accessions. Eight QTLs clarified over 15% of the phenotypic variation in peanut accessions. Among the 45 potential genes significantly related to the 4 traits, only three genes displayed annotation to the fatty acid pathway. Furthermore, on the basis of pleiotropism or linkage data belonging to the identified singular QTLs, we generated a trait-locus axis to better elucidate the genetic background behind the observed oil and fatty acid concentration association. Together, our results provide strong evidence for the genetic mechanism behind oil biosynthesis in A. hypogaea L., facilitating future advances in multiple fatty acid component generation via pyramiding of desirable QTLs
This natural population consisting of 499 peanut accessions combined with high-density SNPs will provide a better choice for identifying peanut QTLs/genes in the future. Together, our results provide strong evidence for the genetic mechanism behind oil biosynthesis in peanut, facilitating future advances in multiple fatty acid component generation via pyramiding of desirable QTLs.

overall_design: Copy number analysis of Affymetrix 47K SNP arrays was performed for 499 peanut accessions. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from frozen leaf  samples.

first: Jing

last: Xu

first: Xiaoyuan

last: Chi


title: Fine particulate matter (PM2.5) induces microRNA-192–5p causing glomerular damage

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

institute: RWTH Aachen University Medical School

summary: To unravel changes in gene expression due to exposure to PM2.5, we performed bulk RNA-seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others, PM2.5 increased oxoglutarate alpha-ketoglutarate receptor 1a, nitric oxide synthase, arachidonate 5-lipoxygenase b, immunity-related GTPase family e1, sulfotransferase family 5A, and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore, protein tyrosine/serine/threonine phosphatase activity was decreased after exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation, inflammatory and immune response, leucocyte-mediated cytotoxicity, peptidase activator activity protein folding, and apoptotic signaling were upregulated after exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune-inflammatory and oxidative stress pathways and lipid and metabolic dysregulation.

overall_design: Zebrafish were mated at 28.5°C, and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hours post-fertilization (hpf) till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5-7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System (Promega, Madison, WI, USA), based on the manufacturer’s protocol.  The RNA quality of each sample was evaluated with a bioanalyzer, and only samples with an RNA Integrity Number (RIN) greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in-house protocol. Sequencing was carried out using paired-end reads of 150 base pairs on an Illumina Novaseq 6000 (Illumina, USA), yielding an average of 20 million reads per sample.

first: Janina

last: Müller-Deile


title: Time-course characterization of whole-transcriptome dynamics of HepG2/C3A spheroid and its toxicological implications

city: Gainesville

first: Chanhee

last: Kim

state: Florida

address: 2187 Mowry Road

department: Physiological sciences

institute: University of Florida

summary: Physiologically relevant in vitro models are a priority in predictive toxicology in order to replace and/or reduce animal experiments. The compromised toxicant metabolism of many immortalized human liver cell lines grown as monolayers as compared to in vivo metabolism limits their physiological relevance. However, recent efforts to culture liver cells in a 3D environment, such as spheroids, to better mimic the in vivo conditions, may enhance the toxicant metabolism of human liver cell lines.  In this study, we characterized the dynamic changes in the transcriptome of HepG2/C3A hepatocarcinoma cell spheroids maintained in a clinostat system (CelVivo) to gain insight into the metabolic capacity of this model as a function of spheroid size and culture time. We assessed morphological changes (size, necrotic core), cell health, and proliferation rate from initial spheroid seeding to 35 days of continuous culture in conjunction with a time-course (0, 3, 7, 10, 14, 21, 28 days) of the transcriptome (TempO-Seq, BioSpyder). The phenotypic characteristics of HepG2/C3A growing in spheroids was comparable to monolayer growth until ~Day 12 (Day 10-14) when a significant decrease in cell doubling rate was noted which was concurrent with down regulation of cell proliferation and cell cycle pathways over this time period. Principal Component Analysis and hierarchal clustering of the transcriptome data suggests that the Day 3, 7, and 10 spheroids are pronouncedly different from the Day 14, 21, and 28 spheroid in support of a biological transition time point during the long-term 3D spheroid cultures. Unexpectedly, the expression of genes encoding toxicant metabolism and transport rapidly increased during the early time points of spheroids to peak at Day 7 or Day 10 as compared to monolayer cultures with gradual decrease in expression with further culture, suggesting the most metabolically responsive time window for exposure studies. Overall, here we provide baseline information on the cellular and molecular characterization, with a particular focus on toxicant metabolic capacity dynamics and cell growth of HepG2/C3A 3D spheroid cultures over the time course.

overall_design: To investigate whole-transcriptome dynamics (changes) during formation and maintenance of 3D spheroid using HepG2/C3A human liver cell line, 2D monolayer and 3D spheroid (Day 3, Day 7, Day 10, Day 14, Day 21, Day 28, and  Day 28) samples cultured in ClinoStar system (CelVivo) were collected. Subsequently, those samples were processesd for TempO-Seq (BioSpyder), generating time-course whole-transcriptome data and subsequent downstream analyses.

first: Zhaohan

last: Zhu

first: Rhonda

last: Bacher

first: Christopher

last: Vulpe


title: Linderae Radix extract attenuates ulcerative colitis by inhibiting the JAK/STAT signaling pathway.

city: Hangzhou

first: Yingying

last: Wang

state: Zhejiang

address: No. 260, Baichuan Street, Fuyang District, Hangzhou City

institute: Zhejiang Chinese Medical University

summary: This study aimed to investigate the efficacy and the potential mechanism of LRWE against UC.

overall_design: Randomly, 3 mice from each of the NC group, MC group, and LRWE group (2.0 g/kg) were used to extract total RNA from colon tissues.

first: Weizhi

last: Lai

first: Xunjie

last: Zheng

first: Ke

last: Li

first: Yanhua

first: Xiaojun

last: Pang

first: Jianli

last: Gao

first: Zhaohuan

last: Lou


title: Dexamethasone-induced transcriptional patterns across different tissues

city: Krakow

first: Michal

last: Korostynski

state: malopolskie

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Maj Institute of Pharmacology PAS

summary: Glucocorticoids act in a highly coordinated manner on various tissues, causing discrete patterns of biological effects. In this study, we aimed to inspect this very sophisticated transcriptional machine by comparing gene expression changes in specific tissues after the administration of a prototypical GR (dexamethasone). We reevaluate the tissue-specific acute effects of dexamethasone on gene expression. We provide a resource summarizing the effects on gene expression of dexamethasone in multiple tissues in mice, as a model organism.

overall_design: The microarray experiment was performed in nine tissues (adrenal cortex, perigonadal adipose tissue, hypothalamus, liver, kidney, anterior thigh muscle, pituitary gland, spleen, and lungs) from adult male C57BL/6 mice using whole-genome microarrays. The animals that received DEX 10 mg/kg i.p. four hours before tissue collection. For each tissue, 4-6 samples (each representing RNA pooled from two animals) were hybridized with Illumina MouseWG-6 v2 BeadChip arrays.

first: Marcin

last: Piechota


title: SMAD2 linker phosphorylation impacts TGF beta 1-dependent gene expression in A549 cells

city: Borstel

first: Doerte

last: Nitschkowski

address: Parkallee 1-40

department: Histology

institute: Research Center Borstel

summary: We investigated the impact of SMAD2 linker phosphorylation (pSMAD2L) on TGF-beta 1 signaling in A549 cells. Data has been published in the British Journal of Cancer under the title “SMAD2 linker phosphorylation influences overall survival, proliferation, TGFβ1-dependent gene expression, and pluripotency-related proteins in NSCLC”.

overall_design: We generated A549 cells constitutively lacking pSMAD2L (A549Lsub) by substituting three serine residues to alanine within the linker domain of SMAD2 (S245A/S250A/S255A). For comparison, we stimulated wild-type and A549Lsub cells with human TGF-beta 1 for 48 hours. Three individual tests were carried out for each stimulation.

first: Dörte

first: Sebastian

last: Marwitz

first: Torsten

last: Goldmann

first: Holger

last: Heine

first: Tim

last: Vierbuchen


title: Evidence for a lipofibroblast-to-Cthrc1pos myofibroblast reversible switch during the development and resolution of lung fibrosis in old mice

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Idiopathic pulmonary fibrosis (IPF) is frequently diagnosed in elderly men. IPF is characterized by irreversible accumulation of excessive extracellular matrix components by activated myofibroblasts (aMYFs) leading to lung failure. Lineage tracing of alpha smooth muscle actin-positive (ACTA2+) cells in the context of bleomycin-induced pulmonary fibrosis in young mice has shown that activated myofibroblasts (aMYFs) are heterogeneous population. However, aMYFs heterogeneity and as well as their fate during fibrosis resolution in aged mice is still studied. Tg(Acta2-CreERT2), tdTomatoflox, 52-56 week-old mice were used to identify Acta2+ cells following bleomycin treatment (Bleo-Tam condition). At the peak of fibrosis formation (day 14) as well as during resolution (days 30 and 60), the origin and fate of Acta2+ cells converging on the aMYF/Cthrc1+ myofibroblast lineage were examined using scRNA-seq.  Our findings demonstrate that at the peak of fibrosis day 14, aMYF/Cthrc1+ cells significantly recruited. Four subclusters within aMYF/Cthrc1+ exhibit distinct pro-fibrotic vs pro-alveologenic characteristics. During fibrosis formation and resolution, alveolar fibroblasts with a strong LIF-like signature are primarily responsible for the origin and fate of aMYFs. Finally, our findings indicate that a LIF-to-aMYF reversible switch is observed during the development and resolution of fibrosis in both young and old mice.

overall_design: Tg(Acta2-CreERT2), tdTomatoflox, 52-56 weeks old mice were used to identify Acta2+ cells following bleomycin treatment (Bleo-Tam condition), at the peak of fibrosis formation (day 14) as well as during resolution (days 30 and 60).

first: Arun

last: Lingampally

first: Saverio

last: Bellusci


title: TIPE regulates TGFB2 expression and induces extracellular M2 polarization in CRC

city: Fuzhou

first: Kun

last: Zhang

address: Dadao Street 190

department: General Surgery

institute: Fuzhou First General Hospital affliated with Fujian Medical University

summary: Abstract Background: M2 macrophages (M2) play a crucial role in the development of colorectal cancer (CRC). The elevated expression of TIPE in CRC is closely associated with CRC progression; however, the impact of TIPE on M2 polarization remains unclear.  Methods: IHC, WB, flow cytometry, qPCR, and IF were used to verify the promoting effect of TIPE on M2 polarization in specimens and in vitro co-culture models. RNA-seq, ELISA, and WB were used to identify the secreted proteins regulated by TIPE and the underlying mechanism. CCK-8 assay, wound healing assay, and transwell invasion assay were used to verify the effect of M2 on CRC. In vivo experiments were used to identify the promoting effect of TIPE on M2 polarization.  Results: In this study, we first demonstrated that the abnormal overexpression of TIPE in CRC promotes M2 polarization and is correlated with a poor prognosis for CRC patients. We then found that TIPE activates the P38 MAPK signaling pathway in CRC to regulate TGFΒ2 secretion and, furthermore, induces M2 macrophage polarization. In subcutaneous and lung xenograft models of CRC in nude mice, we found that TIPE regulates TGFΒ2 secretion from human CRC to promote M2 polarization of murine macrophages.  Conclusion: These results indicate that TIPE is a potent oncogene for inducing M2 polarization. It is suggested that all cancers with high TIPE expression need to be alert to the production and infiltration of M2 macrophages, which provides a new perspective for cancer treatment.

overall_design: The SW480 human colon cancer cell line was obtained from the Typical Culture Cell Bank of the Chinese Academy of Sciences in Shanghai, China. The cells were maintained in DMEM supplemented with 10% fetal bovine serum, 100IU/ml penicillin, and 100μg/ml streptomycin. Lentivirus was utilized for transfection of empty or TIPE overexpressed plasmids into SW480 cells, resulting in the creation of a TIPE overexpressed group (SW480OE) and an unloaded control group (SW480V). Transfection efficiency was assessed using western blot and qPCR techniques. The cells were incubated in a complete medium supplemented with puromycin (2µg/ml) for a minimum of two weeks prior to RNA-seq analysis.

first: Qiang

last: Zhu

first: Shiying

first: Changxiu

last: Yan

first: Zeyang

last: Lin

first: Shuaishuai

first: Haoyang

first: Yuhan

last: Ye

first: Zhongchen

last: Liu

first: Guohong

last: Zhuang


title: GPS2 and HDAC3 ChIP-Seq and RNA-Seq in GPS2-KO MCF-7

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

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

overall_design: Refer to individual Series


title: GPS2 and HDAC3 ChIP-Seq in GPS2-KO MCF-7 [ChIP-Seq]

summary: Within the nucleus, G-Protein Pathway Suppressor 2 (GPS2) was first recognized as a component of the core NCoR/SMRT corepressor complex. This is a multi-protein complex that functions as a corepressor for a variety of transcription factors, including nuclear receptors, and promotes the deacetylation of histones on target regulatory regions via its main catalytic unit, the histone deacetylase HDAC3. Based on this association, GPS2 was initially characterized as a transcriptional corepressor, with transcriptomic analysis of various KO/KD models confirming its role in contributing to the repression of inflammatory genes targeted by the NCoR/SMRT complex. To address this knowledge gap, we asked whether GPS2's dual role in transcription could be attributed to the stabilization of distinct chromatin remodeling factors, with the hypothesis that stabilization of other enzymes may, in turn, affect post-transcriptional modification of histone marks in different directions. In particular, we investigated whether GPS2 presence in the NCoR/SMRT complex may prevent HDAC3 ubiquitination. Our results confirmed that lack of GPS2 leads to aberrant HDAC3 ubiquitination and its dismissal for its target genes.

overall_design: GPS2 and HDAC3 ChIP-Seq in wild-type MCF-7 and in GPS2-depleted cells. GPS2 depletion was carried out using the CRISPR-Cas9 genome editing system with sgRNAs targeting the exons 2 and 6 of the human GPS2 gene sequence.

first: Santina

last: Cutrupi

first: Michele

last: De Bortoli

first: Valentina

last: Perissi


title: Structural basis for nucleolin recognition of MYC promoter G-quadruplex

city: Changsha

first: Kewei

last: Zheng

address: Lushan Road

department: School of Biomedical Sciences

institute: Hunan University

summary: The MYC oncogene promoter G-quadruplex (MycG4) regulates transcription and is a prevalent G4 locus in immortal cells. Nucleolin, a major MycG4-binding protein, exhibits greater affinity for MycG4 than for nucleolin recognition element (NRE) RNA. Nucleolin's four RNA binding domains (RBDs) are essential for high-affinity MycG4 binding. We present the 2.6-angstrom crystal structure of the nucleolin-MycG4 complex, revealing a folded parallel three-tetrad G-quadruplex with two coordinating potassium ions (K+), interacting with RBD1, RBD2, and Linker12 through its 6-nucleotide (nt) central loop and 5' flanking region. RBD3 and RBD4 bind MycG4's 1-nt loops as demonstrated by nuclear magnetic resonance (NMR). Cleavage under targets and tagmentation sequencing confirmed nucleolin's binding to MycG4 in cells. Our results revealed a G4 conformation-based recognition by a regulating protein through multivalent interactions, suggesting that G4s are nucleolin's primary cellular substrates, indicating G4 epigenetic transcriptional regulation and helping G4-targeted drug discovery.

overall_design: Cleavage under targets and tagmentation (CUT&Tag) for G4 and NCL in HeLa-S3 cells.

first: Luying

last: Chen

first: Danzhou

last: Yang


title: Discrete placental gene expression signatures of diabetes during pregnancy

first: Michael

last: Jochum

summary: BACKGROUND: Although gestational diabetes affects up to 10% of all pregnancies, there is ambiguity as to whether the disease subtype classifications are biologically significant at the maternal-fetal interface, or more reflective of an extended spectrum of normal pregnancy endocrine physiology.  OBJECTIVE: Bulk RNA-sequencing (RNA-seq), single-cell RNA-sequencing (scRNA-seq), and spatial transcriptomics have been integrated to reveal gene signatures of disease in subsets of cells and microenvironments. We aimed to combine these high-resolution technologies with rigorous classification of diabetes subtypes in pregnancy. We hypothesized that differences between pre-existing and gestational diabetes subtypes would be associated with altered gene expression profiles in specific placental cell populations.  STUDY DESIGN: In a two-phase case-cohort design, we clinically validated gestational diabetes mellitus type 1 (GDMA1), GDMA2, and type 2 diabetes (T2DM) cases within a cohort of placentae and compared them to healthy controls by bulk RNA-seq (n=54). Quantitative analysis with RT-qPCR of presumptive genes of significant interest were undertaken in an independent and non-overlapping validation cohort of similarly well-characterized cases and controls (n=122). Additional integrated analyses of term placenta single-cell, single-nuclei, and spatial transcriptomics data to determine the cellular subpopulations and niches that aligned with the GDMA1, GDMA2, and T2DM gene expression signatures.  RESULTS: Dimension reduction of the bulk RNA-seq data revealed that the most common source of placental gene expression variation was diabetic disease subtype. Relative to controls, we found 2,052 unique significantly differentially expressed transcripts (-2<Log2(fold-change)>2 threshold; q<0.05 Wald Test) among GDMA1 placental specimens, 267 among GDMA2, and 1,520 among T2DM. Several candidate marker genes (CSH1, PER1, PIK3CB, FOXO1, EGFR, IL2RB, SOD3, DOCK5, and SOGA1) were validated in an independent and non-overlapping validation cohort (q<0.05 Tukey). Functional enrichment revealed the pathways and genes most impacted for each diabetes subtype, and degree of proximal similarity to other subclassifications. Surprisingly, GDMA1 and T2DM were more proximal by virtue of increased expression of chromatin remodeling and epigenetic regulation genes, while albumin was the top marker for GDMA2 with increased expression of genes in the wound healing pathway. Assessment of these gene signatures in the single-cell, single-nuclei, and spatial transcriptomics data revealed expression of these genes were highly variable by placental cell and microarchitecture type. For example, at the cellular and spatial (e.g., microarchitectural) levels, distinguishing features were observed in  in extravillous trophoblasts (GDMA1) and macrophages (GDMA2). Lastly, we utilized these data to generate machine learning models to predict participants diabetes status and observed greater proximity of placental gene expression among GDMA1 and T2DM participants relative to GDMA2.  CONCLUSION: Consistent with their distinct risks of perinatal outcomes, placentae from GDMA1, GDMA2, and T2DM affected pregnancies harbor gene signatures which can be further distinguished by placental microarchitecture and cellular subtypes.

overall_design:
Bulk RNA-seq analysis.
In a two-phase case-cohort design, we clinically validated gestational diabetes mellitus type 1 (GDMA1), GDMA2, and type 2 diabetes (T2DM) cases within a cohort of placentae and compared them to healthy controls by bulk RNA-seq (n=54).

first: Kjersti

last: Aagaard

first: Enrico

last: Barrozo


title: GPS2 and HDAC3 RNA-Seq in GPS2-KO MCF-7 [RNA-Seq]

overall_design: Total RNA-Seq was performed in a biological triplicate of wild-type MCF-7 and in GPS2-depleted cells.


title: SMAD2 linker phosphorylation impacts gene expression in A549 cells

first: Doerte

last: Nitschkowski

summary: We investigated the impact of SMAD2 linker phosphorylation (pSMAD2L) on gene expression in A549 cells. Data has been published in the British Journal of Cancer under the title “SMAD2 linker phosphorylation influences overall survival, proliferation, TGFβ1-dependent gene expression, and pluripotency-related proteins in NSCLC”.

overall_design: We generated A549 cells constitutively lacking pSMAD2L (A549Lsub) by substituting three serine residues to alanine within the linker domain of SMAD2 (S245A/S250A/S255A). For comparison, wild-type and A549Lsub cells were harvested and analyzed after 48 hours. Three individual experiments were performed.

first: Dörte

first: Sebastian

last: Marwitz

first: Torsten

last: Goldmann

first: Holger

last: Heine

first: Tim

last: Vierbuchen


title: Glycolysis inhibition by 2-Deoxy-D-Glucose sustains a distinct cell pluripotency state in human pluripotency stem cells

city: macau

first: Chengcheng

last: SONG

address: universtiy of macau

department: fhs

country: Macau

institute: university of macau

summary: To investigate the TGFb pathway regulation on glycolysis in hPSCs, we processed glycolysis inhibition (2DG) treamtent in E7 medium (E8-TGFb) for 24h with or without multiple proteins of TGFb pathway in H1. Nodal, Activin A and TGFb were used for treatment with or without 2DG.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of H1 cells following 2DG treatment with or without Nodal, Activin A and TGFb.

last: Song

first: Guokai


title: Shining Light on Regulatory Networks Integrating Nitrogen Use and Photosynthesis

city: Urbana

first: Matthew

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

institute: USDA

summary: Nitrogen and light availability are well-known to influence photosynthesis, having both individual and synergistic effects. However, the regulatory interactions between these signaling pathways, especially the transcription factors that perceive and integrate these cues remain to be elucidated. Arabidopsis grown in a matrix of nitrogen and light treatments exhibited distinct physiological and transcriptomic responses. Notably, the effect of nitrogen dose on biomass, nitrogen use efficiency, carbon:nitrogen ratio, and gene expression was highly dependent on light intensity. Genes differentially expressed across the treatments were enriched for photosynthetic processes, including pentose-phosphate cycle, light-harvesting and chlorophyll biosynthesis. We identified bZIP and MYB-related family transcription factors as key regulators of photosynthesis, nitrogen assimilation, and light response using gene regulatory network analysis. The transcription factors unveiled in this study have the potential to unlock new strategies for enhancing photosynthetic activity and nutrient-use efficiency in plants.

overall_design: Leaf discs were collected from Arabidopsis grown under different nitrogen and light treatments (4 nitrogen doses and 3 light levels). Eight replicates were collected for each treatment, along with biomass, photosynthetic parameters (chlorophyll fluorescence), pigment content and elemental composition.

first: Kithmee

last: de Silva


title: Study of the Role of Pomegranate Juice Ellagitannins in the Modulation of Inflammation in Inflammatory Bowel Disease

city: Parma

first: Ilaria

last: Minato

address: Parco Area delle Scienze 23/a

institute: Università di Parma

summary: Aim of this study was to explore the effect of 12-week pomegranate-juice consumption on the global transcriptional profile in individuals with inflammatory bowel disease (IBD) in clinical remission.

overall_design: Transcriptomic response was measured in circulating peripheral blood mononuclear cells (PBMCs) at baseline (t0) and after 12 weeks (t1) of intervention with pomegranate juice (seven IBD patients) or placebo (three IBD patients)

first: Francesca

last: Danesi

first: Eleonora

last: Derlindati

first: Enrica

last: Rotondo

first: Barbara

last: Montanini


title: Base editing mediated correction of severe β0 thalassemia mutations

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

institute: University of Padova

summary: β-thalassemia is a highly prevalent monogenic recessive disease caused by mutations affecting the synthesis of the adult hemoglobin β-chains. Transplantation of autologous, genetically modified hematopoietic stem/progenitor cells (HSPCs) is an attractive therapeutic option. However, current gene therapy strategies based on the use of lentiviral vectors or CRISPR/Cas9 nuclease are not equally effective in all the patients and/or raise safety concerns. Base editing (BE), a new CRISPR/Cas9 derived genome editing tool, allows the effective introduction of point mutations at precise locations within the genome without generating double strand breaks. The two β0 mutations CD39 (CAG>TAG) and IVS2-1 (G>A) are among the most common and severe β-thalassemia mutations in the Mediterranean area and Middle East. We exploited the capacity of BE to correct these mutations in HSPCs from β-thalassemia patients. We demonstrated that red blood cells in vitro derived from edited HSPCs exhibited high β-globin levels and that the delayed erythroid differentiation typically observed in β-thalassemic cell cultures was corrected by our treatment. Finally, xenotransplantation experiments showed base editing in HSCs and correction of the β-thalassemic phenotype in vivo. Overall, our study provides in vitro and in vivo proof of efficacy of a BE approach to treat patients with prevalent and severe β-thalassemia mutations.

overall_design: Human beta-thalassemia HSPCs carrying the CD39 mutation were transfected using an adenine base editor to correct the CD39 mutation. As control, each of the 3 donors was mock-transfected with TE buffer. Bulk RNAseq was performed at 48h to evaluate the impact of the editing procedure at the transcriptomic level.

first: Giulia

last: Hardouin

first: Annarita

last: Miccio


title: Trabectedin and olaparib combination primes cellular immunotherapy with HLA-independent killer lymphocytes against sarcoma preclinical models through the cGAS-STING pathway

first: Giulio

last: Ferrero

summary:
Background. Advanced sarcomas have a severe prognosis, limited therapeutic options, and are seldom sensitive to immunotherapy with checkpoint inhibitors. Novel strategies are urgently needed.
Methods. We set up a preclinical approach for testing the combination of chemotherapy (trabectedin) and PARP1 inhibitor (olaparib) to potentiate the HLA-independent cellular immunotherapy with natural killer (NK) or cytokine-induced killer (CIK) lymphocytes. The NK/CIK activators NKG2DLs were studied by qRT-PCR and flow cytometry. Drug-induced transcriptomic events were studied by RNA sequencing and the activation of the cytosolic DNA sensing pathway (cGAS-STING-IRF3-IFNβ) was explored. Focusing on the putative cancer stem cell (CSCs) subpopulation, OCT4 marker was evaluated. IRF3 silencing experiments were done to investigate the role of the cGAS-STING pathway in the control of NKG2DLs. NK/CIK killing activity on both bulk and OCT4-positive cells was tested by viability assay and flow cytometry, respectively.
Results. We obtained the enhancement of NK/CIK activity against sarcoma cell lines through an integrated approach based on the combination of trabectedin and olaparib. These drugs upregulated the NKG2DL expression at both mRNA and protein level by inducing the genotoxicity pathway (WP4286) and repressing the cellular response to DNA damage stimulus (GO:0006974). The drug treatment significantly increased the cytosolic DNA content and consequently activated the cGAS-STING-IRF3 pathway and IFNβ production. These molecular events significantly enhanced the antitumor activity of NK and CIK against drug-pretreated sarcoma cells. The OCT4-positive cell fraction was enriched after chemotherapy. Noteworthy, NK/CIK cells efficiently killed both the drug-surviving bulk and CSC subpopulation.
Conclusions. Trabectedin+olaparib treatment followed by NK/CIK-based immunotherapy is a promising therapeutic strategy against sarcomas, deserving further investigations.

overall_design: Duplicate total RNA-Seq of HT-1080, DMR, S018 cell lines treated with Trabectedin (PharmaMar, Madrid, Spain) and olaparib (Biosynth Carbosynth, Staad, Switzerland) alone, in combination, or untreated.

first: Giorgia

last: Giordano

first: Federica

last: Capozzi

first: Alessandra

last: Merlini

first: Cristina

last: Tucciarello

first: Shahab

last: Majidi

last: Mesiano

first: Erika

last: Fiorino

first: Elisa

last: Prola

last: Galvagno

first: Annamaria

last: Massa

first: Maria

last: Centomo

first: Silvia

last: Brusco

first: Valeria

last: Leuci

first: Santina

last: Cutrupi

first: Michele

last: De Bortoli

first: Massimo

last: Aglietta

first: Lorenzo

last: D’Ambrosio

first: Dario

last: Sangiolo

first: Giovanni

last: Grignani

first: Ymera

last: Pignochino


title: Role of SLC15A3 in pulmonary fibrosis

first: Jun

last: Luo

state: State...

address: College of Pharmaceutical Sciences, Zhejiang University， Hangzhou, Zhejiang P. R. China 31005

institute: Zhejiang University

summary: The oligopeptide/histidine transporter SLC15A3 (PHT2) belongs to the solute carrier protein 15 family and is mainly expressed in the membrane of lysosomes and endosomes in monocytes/macrophages. Macrophages are a key immune cell population in the development of pulmonary fibrosis. In order to examine the role of SLC15A3 in pulmonary fibrosis, we build bleomycin (BLM)-induced mouse model in wild-type (WT) mice and the Slc15a3 knockout(Slc15a3-/-) mice.

overall_design: Wild-type (WT) mice and the Slc15a3 knockout(Slc15a3-/-) mice were intratracheally administered BLM (2 mg/kg) in 50 μl normal saline on day 0. Mice administered with the same volume of normal saline served as controls. The mice were euthanized on day 21 following BLM/radiation challenge to analyze pulmonary fibrosis.

first: Ping

last: Li

first: Huidi

last: Jiang

first: Yuqing

last: Wang


title: Transcriptome analysis of cardiac specific depletion of RBPMS and RBPMS2 embryonic hearts [sch4_rnaseq]

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

summary: To investigate the function of RNA-binding protein with multiple splicing (RBPMS) family, RBPMS and RBPMS2, in heart, we establish two RBPMS/2 double knock out mutant strains using cardiomyocyte specific Cre delete strains. Xenopus laevis light chain 2 (XMLC2) promoter CRE mice (Breckenridge et al., 2007) were crossed to RBPMSflox/flox / RBPMS2flox/flox animals to generate the RBPMS/2flox/flox / XMLC2-Cre mice line. In a parallel approach, we crossbred RBPMSflox/flox / RBPMS2flox/flox mice with animals carrying alpha myosin-heavy chain (Myh6) Cre (αMyHC-Cre) (Agah et al., 1997), resulting in the RBPMS/2flox/flox / aMyHC-Cre line. RNA seq of E11.5 (XML-Cre) and E16.5 (αMyHC-Cre) embryonic hearts was performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for littermate control and cardiomyocyte specific double knock out of RBPMS/2 hearts at embryonic stage.

first: Shan

last: Lin

first: André

last: Schneider

first: Stefan

last: Guenther


title: Transcriptome analysis of cardiac specific depletion of RBPMS and RBPMS2 embryonic hearts [sch7_rnaseq]


title: Transcriptome analysis of cardiac specific depletion of RBPMS and RBPMS2 embryonic hearts


title: gene expression of KYSE410 cells  with control or treatment of 50 ng/mL CCL22

city: beijing

first: di

last: zhao

address: 52 Fucheng Road, Haidian District, Beijing

institute: beijng cancer hospital

summary:
KYSE410 cells were treated with  50 ng/mL CCL22, and KYSE410 cells were collected for gene expression analysis using Agilent SurePrint G3 Human Gene Expression v3 (8×60K) Microarray.
Investigation of the critical gene of KYSE410 cells treated by  50 ng/mL CCL22.

overall_design: We designed this experiment to screen for gene whose expressions are effected by  50 ng/mL CCL22 treatment.

first: Jie

last: Chen

first: Qimin

last: Zhan


title: Conditional Overexpression of Serpine2 Promotes Hair Cell Regeneration from Lgr5+ Progenitors in the Neonatal Mouse Cochlea

status: Public on May 04 2025

city: Nanjing, Jiangsu Province, China

first: Jiheng

last: Wu

address: No.371 Heyan Road, Qixia District

institute: Southeast University

summary: Neonatal cochlear Lgr5+ progenitors can regenerate hair cells (HCs), and this process is regulated by several genes and signaling pathways. However, this regeneration ability is limited, and whether additional genes are involved in this process remains unknown. Serpine2 was shown to participate in regulating proliferation and differentiation of cochlear Lgr5+ progenitors in our previous in vitro study. Here, we explored the expression pattern and in vivo roles of Serpine2 in HC regeneration by constructing transgenic mice in which Serpine2 is conditionally overexpressed in cochlear Lgr5+ progenitors. We found that Serpine2 is expressed in the mouse cochlea after birth with a downward trend as the mice aged. In addition, Serpine2 conditional overexpression in vivo in Lgr5+ progenitors of neonatal mice cochlea resulted in an increase number of ectopic HCs in a dose-dependent manner. And Serpine2 knockdown ex vivo and in vivo can inhibit HC regeneration. EdU assay and lineage tracing assay demonstrated that these ectopic HCs likely originated from Lgr5+ progenitors through direct trans-differentiation rather than through mitotic regeneration. Moreover, snRNA-seq analysis and RT-qPCR results revealed that Serpine2 cOE likely induces HC regeneration via inhibiting sonic hedgehog (SHH) signal pathway and inducing Atoh1 and Pou4f3 transcription factor. In brief, our data indicate that Serpine2 plays a pivotal role in HC regeneration from Lgr5+ progenitors in the neonatal mouse cochlea, and this suggests a new avenue for future research into HC regeneration.

overall_design: snRNA-seq was performed using 19 cochleae from Serpine2loxp/loxp (control) and 20 cochleae from Lgr5EGFP-CreER/+Serpine2loxp/loxp (Serpine2 cOE) mice at P7, after tamoxifen injection at P1, with cochlear basement membrane pooled per group. Purified nuclei were diluted to 700–1200 nuclei/μl for 10× Genomics Chromium. Library preparation followed the 10× Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol, and sequencing was performed on the Illumina NovaSeq 6000 system. Gene expression was aligned using the GRCm39 reference genome and quantified with the 10× Cell Ranger v3 pipeline (version 8.0.1).

first: Hairong

last: Xiao

first: Lixuan

last: Huang

first: Ying

last: Ma

first: Leilei

first: Yanqin

first: Zixuan

last: Ye

first: Xin

last: Tan

first: Xujun

last: Tang

first: Wei

last: Tong

first: Mingchen

last: Dai

first: Yintao

first: Xia

last: Sheng

first: Renjie

last: Chai

first: Shasha

last: Zhang


title: Genomic effects of an EP4-receptor agonist in airway epithelia

city: Calgary

first: Radhika

last: Joshi

state: Alberta

address: 3300 Hospital Drive NW

department: Department of Physiology and Pharmacology

country: Canada

institute: University of Calgary

summary: It has been proposed that inhaled EP4-receptor agonists could represent an alternative class of bronchodilators for the treatment of asthma that are as effective as β2-adrenoceptor agonists. However, the genomic impact of such drugs is often overlooked despite being potentially deleterious to respiratory health. Herein, we used mRNA-seq to compare the genomic impact of ONO-AE1-329 (an EP4-receptor agonist) and vilanterol (a β2-adrenoceptor agonist) in BEAS-2B human airway epithelial cells. We also determined if an increase in cAMP mediated by different GPCRs promoted distinct transcriptional signatures by expanding this enquiry to include the adenosine A2B- and I-prostanoid receptor agonists, Bay-60-6583 and taprostene, respectively. Maximally-effective concentrations of ONO-AE1-329 and vilanterol significantly regulated (q ≤ 0.05; ≥1.5-/≤0.67-fold) 232 and 320 genes, respectively of which 217 were shared. Spearman analysis showed these gene expression changes to be highly rank order correlated indicating that the functional overlap between the two interventions should be considerable. Unexpectedly, the genomic effects of ONO-AE1-329, vilanterol, Bay 60-6583 and taprostene were also highly rank order correlated. This finding raises the prospect that cAMP generated by any GPCR would initiate the same transcriptional program. Nevertheless, relative to vilanterol, ONO-AE1-329 typically behaved as a partial agonist with a potency and intrinsic activity that varied across transcripts. Collectively, this investigation demonstrated that each ONO-AE1-329-regulated gene differs in sensitivity to cAMP and is defined by a unique receptor occupancy-response relationship. Moreover, if this relatively modest genomic response in BEAS-2B cells is reproduced in vivo, then inhaled EP4-receptor agonists could represent a safer class of bronchodilators.

overall_design: Confluent BEAS-2B cells were treated for two hours with vehicle, RNO (1 µM), a maximal concentration of ONO-AE1-329 (1 µM), two sub-maximal concentrations of ONO-AE1-329 (0.1 nM and 1 nM), a maximal concentration of Vilanterol (100 nM) and their combination with RNO (ONO0.1 + RNO, ONO1 + RNO, ONO1000 + RNO, Vil100 + RNO). Total RNA was extracted, quantified, processed into mRNA libraries, and sequenced across two high-throughput sequencing kits on a NextSeq 500 instrument (Illumina). Samples from 4 replicates were submitted for sequencing.

first: Mark

last: Giembycz


title: Angptl5 restricts primitive hematopoiesis by modulating retinoic acid signaling in zebrafish

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

summary: Purpose: Characterization of cell types in angptl5Δ10/Δ10 zebrafish. Methods: The angptl5Δ10/Δ10 embryos were raised in 0.3× Danieau Buffer and harvested at 16 hpf. Collected samples were digested with trypsin into single cell suspension for single cell sequencing. Libraries were constructed with  a Chromium Single Cell 3′v3 Reagent Kit (10x Genomics) according to the manufacturer’s protocol for 7350 cell recovery.Sequencing was performed with Illumina Novaseq 6000 according to the manufacturer’s instructions (Illumina). Results:  Global amplification of myeloid and erythroid progenitors in angptl5Δ10/Δ10 embryos. Conclusions: Angptl5 regulated primitive hematopoiesis in zebrafish.

overall_design: Collected samples of angptl5Δ10/Δ10 embryos at 16 hpf were digested with trypsin into single cell suspension for  scRNA-seq.

first: Jing

last: Mo

last: Cheng

first: Yang

last: Dong


title: Transcription factor OsWRKY11 induces rice heading at low concentrations but inhibits rice heading at high concentrations

city: Kunming

first: Lirong

last: Zhao

state: Yunnan

address: No.88 Xuefu Road

department: Xishuangbanna Tropical Botanical Garden

institute: Chinese Academy of Sciences

summary: To identify direct targets of OsWRKY11, we performed DNA affinity purification sequencing (DAP-seq).

overall_design: The OsWRKY11-Halo protein and GFP-Halo were synthesized in vitro, and a genomic DNA library (200~800 bp) was derived from of Oryza sativa seedling. The SYZ samples were obtained by performing the DAP reaction of the OsWRKY11-Halo protein with the DNA library, while DDZ was obtained by DAP reaction of the GFP-Halo protein with the DNA library. GFP-Halo was used as a control.

first: Yunwei

last: Liu

first: Houping

last: Wang

first: Diqiu

last: Yu


title: Diet-induced obesity dysregulates rapid epigenetic response to hypoxia in macrophages (RNA-Seq)

city: Syracuse

first: Norifumi

last: Urao

state: New York

address: 750 E. Adams St.

department: Pharmacology

institute: SUNY Upstate Medical University

summary: Macrophages play important roles in tissue homeostasis and tissue healing process. The response to hypoxic environment is a trigger to induce key signaling pathways in macrophages. Functions of macrophages are dysregulated in metabolic diseases such as diabetes and obesity resulting in poor tissue healing. Epigenetic status including histone modification in macrophages is regulated by hypoxia. However, whether and how obesity influences histone modification under hypoxia is unknown. Using chromatin immunoprecipitation-sequencing (ChIP-seq), RNA-seq on mouse bone marrow-derived macrophages, we sought to determine whether hypoxia alters histone 3-lysine 4 trimethylation (H3K4me3) and gene expression profile in macrophages and how obesity influences H3K4me3 enrichment on the genome in hypoxia-dependent and -independent manner.

overall_design: Gene expression profile analysis of RNA-seq data for bone marrow-derived macrophages (BMDMs) cultured from C57B6/J mice fed a high-fat diet or a normal-fat diet.

first: Kentaro

last: Takahashi


title: The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development

city: Barcelona

first: Maria

middle: Pia

last: Cosma

address: Dr Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Centre for Genomic Regulation

summary: Embryo size, specification, and homeostasis are regulated by a complex gene regulatory and signalling network. Reverse engineering of a mouse embryonic stem cell (ESC) regulatory network and its interrogation with gene expression signatures of Wnt-activated ESC clones identified NKX1-2 as a novel master regulator of pre-implantation embryo development. Nkx1-2 inhibition resulted in reduction of nascent RNA synthesis, downregulation of genes regulating ribosome biogenesis, RNA translation and transport, and in severe alteration of nucleolus structure, with exclusion of RNA polymerase I from nucleoli. In turn, these dysfunctions lead to chromosome missegregation in 2-cell to 4-cell embryo stages, severe decrease of blastomere number, alteration of tight junctions, and lack of microlumens coarsening. Taken together, these changes impair the blastocoel expansion–collapse cycle and embryo cavitation, leading to altered lineage specification and developmental arrest.

overall_design: scRNA-Seq of morpholino injected mouse morula and blastocyst embryos

first: Shoma

last: Nakagawa

first: Davide

last: Carnevali

first: Xiangtian

last: Tan

middle: P


title: PIKfyve inhibition synergizes with Cisplatin to provoke antitumor immunogenicity in melanoma by alleviating lysosomal degradation of STING

city: Shanghai

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

summary: Immune checkpoint blockade (ICB) has obtained significant progress in treating multiple types of cancers, but its overall response rate and therapeutic efficacies are not yet satisfactory. To fulfil such needs, identification of combinational approach to enhance the therapeutic efficacies of ICB is highly demanded. The activation of cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling is critical to elicit the antitumor innate immune responses and a promising target to develop combinational immunotherapy. Accordingly, the application of STING agonist exhibits potent antitumor functions in preclinical models and is currently tested in clinical trials. However, deregulation of cGAS-STING is frequently observed in cancers and substantially attenuates the efficacies of treatments by harnessing cGAS-STING signaling. Hence, the underlying mechanisms of maintaining intracellular homeostasis of cGAS-STING need to be elucidated. Here we report the identification of PIKfyve as a negative regulator of cGAS-STING signaling. Inhibition of PIKfyve by kinase inhibitor YM201636 or genetic ablation markedly provokes the expression of cGAS-STING downstream IFN-stimulated genes (ISGs) and reschedules the antitumor microenvironment by recruiting CD8+ T lymphocytes. In melanoma models, PIKfyve inhibition confers sensitivity to the combinational therapy of cisplatin and anti-PD1, leading to a durable treatment response. Mechanistically, PIKfyve interacts with STING to promote its lysosomal degradation. These results highlight the importance of maintaining STING homeostasis as a direction to augment the efficacies of combinational immunotherapies

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MUM2B cells were treated with DMSO, 0.5uM YM201636,1uM Cisplatin or 0.5uM YM201636+1uM Cisplatin for 72 hours. Total RNA was extracted and then sent for RNA sequencing. In vivo experiments, tumor bearing mice were treated with YM201636 or vehicle by oral administration. Comparative gene expression profiling analysis of RNA-seq data for mouse tumors.

first: Jianfeng

last: Shen

first: Jie

last: He


title: Rhinovirus-induced gene expression patterns that distinguish between neutrophilic asthma and other asthma inflammatory phenotypes in human peripheral blood mononuclear cells

city: Woolloongabba

last: Xi

state: QLD

address: 37 Kent St

country: Australia

institute: University of Queensland Diamantina Institute

summary:
Objective: The aim of the current study was to use circulating immune cells to define gene expression patterns that best distinguish between different asthma phenotypes. We hypothesised that analysing gene expression patterns in unstimulated cells would be of limited value, and that variations in gene expression patterns would be most apparent in the setting of RV stimulation.
Methods: Peripheral blood mononuclear cells samples from adults with persistent asthma of different inflammatory subtypes were stimulated with RV in vitro with RNA sequencing and bioinformatics used to define gene expression patterns.
Results: RV-induced changes in gene expression differed markedly between neutrophilic asthma (NA) and other asthma phenotypes. Expression of many anti-viral immune pathways and their regulators genes was down regulated in NA compared to the other phenotypes, accompanied by enhanced expression of chemokine genes, proinflammatory cytokines and Y chromosome linked genes. These changes were detected in circulating, bone marrow-derived immune cells and were most apparent in RV-stimulated rather than resting cells.

overall_design: Examination of rhinovirus stimulated gene expression pattern in human peripheral blood mononuclear cells that obtained from people with different asthma subtypes

first: Valentine

last: Murigneux

first: Jodie

last: Simpson

first: Chris

last: Grainge

first: Melanie

last: Carroll

first: John

middle: W

last: Upham


title: DNA methyltransferase 1 modulates mitochondrial function through bridging m5C RNA methylation

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effect of PPAR γ agonist on gene expression changes in RBL-2H3 cells

first: Weihua

last: Wang

address: 150 Jimo Road

department: Otolaryngology-Head & Neck Surgergy

institute: School of Medicine, Tongji University

summary: To identify the key genes participating in the regulation of mast cell activation, we profiled the expression patterns of mRNAs associated with PPAR γ agonist,pioglitazone (PIO), treatment in RBL-2H3 cells.

overall_design: RBL-2H3 cells were treated without or with PIO (10uM) for 6 h. Then,transcriptome sequencing was performed to compare the gene expression profiling between the two groups.

first: Yu

first: Suyu

last: Ruan

first: Xiaoqing

last: Rui


title: Vagal neuroimmune axis modulates heart failure by limiting monocyte-derived inflammatory CCRL2 macrophage

status: Public on May 03 2025

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Autonomic neuronal dysfunction is associated with heart failure (HF). Here, we report that targeted vagal nerve stimulation (VNS) using optogenetics attenuates cardiac remodelling and HF induced by pressure overload. Unbiased approaches revealed that VNS decreased the proportion of the Ccrl2+ macrophage subset, which derived from myeloid monocytes and exhibited a distinct tumour necrosis factor-alpha (TNFα)-responsive, pro-hypertrophic, and profibrotic signature. Elimination of Ccrl2+ macrophages prevented cardiac remodelling and HF. Functional characterisation by Ccrl2+ macrophage-specific overexpression or global genetic loss of α7 nicotinic acetylcholine receptor (α7nAChR) highlighted its crucial contribution to VNS-mediated cardioprotection. Mechanistically, activation of α7nAChR inhibited the TNFα responsiveness through upregulated expression of the transcription factor NRF2. Cardiac Ccrl2+ macrophages and TNFα-responsive proteins were positively correlated with cardiac remodelling and dysfunction in humans. Finally, an α7nAChR agonist effectively blocked the development of HF. These results suggest that the vagal neuroimmune axis modulates heart failure and is a promising target for treatment.

overall_design: To explore this phenomenon, we isolated four macrophage subsets from the hearts of Ctrl-TAC mice and performed bulk transcriptome profiling.


title: Vagal neuroimmune axis modulates heart failure by limiting monocyte-derived inflammatory CCRL2 macrophage [2]

overall_design: We confirmed the function of Ccrl2+ macrophages through in vitro co-culture of primary cardiomyocytes (CMs) and cardiac fibroblasts (CFs) with Ccrl2+ macrophages or Ccrl2- macrophages


title: Tissue factor pathway inhibitor promotes the migration, proliferation and colonization of MSCs by regulating CXCL12/CXCR4 signaling pathway

first: Miao

last: Li

address: 180 Fenglin Road

institute: Zhongshan Hospital, Fudan University

summary: MSCs (mesenchymal stem cells) can promote the structural and functional recovery of lung injury, but most of MSCs do not retain in the injury sites. TFPI (tissue factor pathway inhibitors) can promote stem/progenitor cell migration and homing. The objective of this study was to explore investigate the feasibility and efficacy of TFPI combined therapy with MSCs to alleviate lung injury and the possible mechanism. rhTFPI or (and) MSCs were administered via tail vein to LPS-induced ALI mice. Lung H&E, coagulation function, TFPI, TNF-α, IL-1β, CXCL12 and CXCR4 in BALF and plasma, 7-day survival rate, and colonization of MSC in lung were observed. Transmembrane migration assay, CCK-8 and EdU assay were used to determine the migration, viability and proliferation of MSCs. RNA sequencing was performed to find differentially expressed genes. The lentivirus transfection technique was used to infect MSCs to overexpession and knockdown TFPI of MSCs. The data demonstrated that rhTFPI could promote cell viability, proliferation and migration of MSCs to improve lung injury. RNA sequence indicated that CXCL12 was in top 40 DEGs and up-regulated after the combination treatment of rhTFPI and MSCs. LPS dampened TFPI, CXCL12/CXCR4 levels in a dose- and time- dependent manner, but can restored by rhTFPI. The level of TFPI expressed by MSCs affected the levels of CXCL12/CXCR4 in MSCs, and migration, proliferation and colonization of MSCs. The results indicated that TFPI may promote the migration, proliferation and colonization of MSCs by regulating CXCL12/CXCR4 signaling pathway.

overall_design: Fresh lung tissue was prepared and added Trizol for lysis and total RNA extraction. mRNA library was prepared, and sequencing was conducted using VAHTS Universal V6 RNA-seq Library Prep Kit. Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). GO and KEGG pathway enrichment analysis of DEGs were performed to screen the significant enriched term using R (v3.2.0). Protein-protein interaction (PPI) analysis was performed for target genes.

first: Yuanlin

last: Song

first: Linlin


title: Ablation of Id1 Reduces Clonal Hematopoiesis, Genomic Instability and Delays Leukemia in Mice with Tet2 Loss of Function [RNA-seq]

city: Frederick

first: Shweta

last: Singh

state: Maryland

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

institute: National Cancer Institute

summary: Hematopoietic malignancies emerge through the gradual acquisition of genetic mutations within hematopoietic stem and progenitor cells (HSPCs). Mutations that occur early in disease progression impart a selective growth advantage to HSPCs, which allows them to expand and contribute to a substantial percentage of mature blood cells. This increased expansion is termed clonal hematopoiesis (CH) and is a preleukemic phase associated with an increased risk of developing leukemia. Inhibitor of DNA binding 1 (ID1) protein is a transcriptional regulator of proliferation/differentiation of neuronal, muscle, and other cells, and is frequently overexpressed in cancer. Id1 is expressed at low levels in normal HSCs and is induced by growth factors and other mediators of inflammatory stress and promotes HSPC proliferation. HSCs that lack Id1 (Id1-/-) show reduced cycling/activation and are protected from exhaustion under chronic stress including bone marrow transplantation (BMT), genotoxic and inflammatory stress, and aging. Since chronic inflammation is associated with the progression of hematopoietic malignancies, reducing Id1 expression during CH may be therapeutic. Mutations in TET2 are frequently observed in patients with CH, and Tet2-/- mice show CH. ID1 is upregulated in HSPCs from patients with TET2 mutations and Tet2-/- mice. Genetic ablation of Id1 in Tet2-/- HSPCs reduces HSPC expansion/self-renewal/CH, extramedullary hematopoiesis, myeloid skewing, genetic instability and delays the onset of disease. Mechanistically, p16 expression, senescence and apoptosis were increased and proliferation decreased in Tet2-/-; Id1-/- HSPCs. Thus, ID1 may represent a potential therapeutic target to reduce CH and delay the onset of leukemia.

overall_design: RNA-seq.  Donor Lin- ckit+ cells were sort purified from the bone marrow cells of competitive bone marrow transplantation recipient mice (WT, Tet2 KO, Id1 KO, Tet2 KO + Id1KO).

first: Tanmoy

last: Sarkar

first: Kristbjorn

middle: O

last: Gudmundsson

first: Jonathan

middle: R

last: Keller


title: Nuclear cholesterol regulates nuclear size and DNA damage responses in the tumor hierarchy

city: Pittsburgh

first: Tingting

last: Duan

state: PA

address: 5117 Centre Avenue

institute: University of Pittsburgh

summary: Normal stem cells undergo morphologic, epigenetic, and metabolic changes during cellular differentiation. Here, we report that glioblastoma stem cells (GSCs) display smaller nuclear size than differentiated progeny. Leveraging differential gene expression and proteomics to discover potential mediators of nuclear size regulation, we found that GSCs are enriched for a nuclear lamina-localized sterol reductase, Lamin B Receptor (LBR). LBR bridges two functions, genome organization and cholesterol synthesis, of which nuclear cholesterol synthesis mediates LBR regulation of GSC nuclear size. Targeting LBR increased nuclear size and decreased GSC viability and tumor initiation. Mass spectrometry defined an LBR interactome in GSCs with mediators of DNA damage repair (DDR) and R-loop resolution, including DEAD-Box Helicase 5 (DDX5). Consistently, targeting LBR induced double-strand DNA breaks (DSBs) and P53-dependent DDR. Genetic LBR loss reduced DDX5 expression and increased R-loops; pharmacologic LBR sterol reductase inhibition phenocopied LBR loss, increasing R-loops and DSBs with synergy with irradiation to inhibit GSC survival. Together, we propose that LBR regulates nuclear cholesterol synthesis, which contributes to the small GSC nuclear sizes and promotes efficient DNA damage repair.

overall_design: To understand mechanims underlying LBR requirements in GSCs, we profiled gene expression upon LBR loss in two independent GSC lines, each with two independent shRNAs targeting LBR


title: RNA m6A reader IGF2BP3 promotes metastasis of triple-negative breast cancer via SLIT2 repression (MeRIP-Seq)

city: xi'an

first: tongtong

last: jiang

address: changle western load

institute: Fourth Military Medical University

summary: Triple-negative breast cancer (TNBC) is a group of fatal malignancies characterized by high metastatic capacity, the underlying mechanisms of which remain largely elusive. We found here that insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3), but not other members of the IGF2BP family, is highly expressed in breast cancer and correlated clinically with TNBC metastasis and patient prognosis. IGF2BP3 promotes the migration and invasion capabilities of TNBC cells dependent upon cellular RNA N6-methyladenosine (m6A) modification. Mechanistically, IGF2BP3 binds to and unstabilizes m6A-methylated mRNA of the extracellular matrix glycoprotein, SLIT2, impairs its downstream signaling via the cognate receptor ROBO1, and consequently derepresses the canonical oncogenic PI3K/AKT and MEK/ERK pathways. These findings shed light into the regulatory network of distal metastasis and provide rationale for targeting the m6A machinery in the treatment of TNBC

overall_design: RIP-seq analysis of m6A-IP versus input in MDA-MB-231 cells

first: Tongtong

last: Jiang

first: Lintao

last: Jia


title: Transcriptome-based analysis of early post-mortem formation of pale, soft, and exudative (PSE) pork

city: urumqi

first: Zequan

last: Xu

address: Line 311, Nongda East Road

institute: Xinjiang agriculture university

summary: The goals of this study was to analyze of differences gene expression between PSE and normal pork in postmortem by transcriptome profiling ,using BGISEQ500 platform.We measured the pH of the longissimus lumborum to screen for PSE and NO (normal) carcasses (PSE: pH ≤ 6.0, normal: pH > 6.0) at postmortem using a pH metre (Testo 205, Testo, Inc., PA, USA).Our study found 97.56% of the sequencing reads had quality scores at the Q20 level (99% base calling accuracy) and 89.93% had quality scores at the Q30 level (99.9% base calling accuracy).Approximately 92.58% of the clean reads were mapped to the reference genome. There were 326 differentially expressed genes (DEGs) in the longissimus lumborum between normal and PSE pork, with 197 upregulated and 129 downregulated genes. Additionally, 324 DEGs were identified in the semimembranosus between normal and PSE carcasses, with 176 upregulated and 148 downregulated genes. There were 1022 DEGs between longissimus lumborum and semimembranosus in the normal carcasses, with 878 upregulated and 144 downregulated genes in the semimembranosus. Additionally, there were 1011 DEGs between longissimus lumborum and semimembranosus in PSE carcasses, with 823 upregulated and 188 downregulated genes.we compared the DEGs between longissimus lumborum and semimembranosus in PSE carcasses with those of normal carcasses and found 74 commonly downregulated and 430 commonly upregulated genes. Five genes showed the opposite expression trends, including BGI_novel_G000027, LOC110261743, BGI_novel_G000053, HSPA6, and BGI_novel_G000051.

overall_design: Longissimus lumborum and semimembranosus mRNA profiles in postmortem PSE and (NO) normal carcasses

first: Zirong

first: Yonggang

last: Shao

first: Heng


title: Transcriptomic establish of pig macrophage polarization signatures and potential applications for pig health and disease

city: Chengdu

first: Jing

address: huimin road 211

institute: Sichuan Agricultural University

summary: Macrophages are the main effector cells of inflammatory response and play an important role in the initiation and regression of inflammation. Macrophages are derived from monocytes which are differentiated into M1 macrophages (classically activated macrophages) or M2 macrophages (selectively activated macrophages) in response to different external stimuli, distinguished by the differential expression of cytokines, cell surface markers, and chemokines. In vitro macrophages are crucial models for understanding the regulatory mechanism of immune response and the establishment of infection models, ultimately, for the diagnosis or treatment of a variety of diseases. Porcine is the most important agricultural animal and one of the most valuable animal models for preclinical studies, but no unified method for porcine macrophage isolation and differentiation at present, neither a systematic study compared the porcine macrophage obtained by different methods. In this study, we used two strategies to induce porcine BMDM into M1 and two strategies to induce porcine BMDM into M2 macrophages. Subsequently, we compared the transcriptomic profile of BMDM treated with different induction methods by RNA-seq. The DEG analysis showed that porcine M1 macrophage and porcine M2 macrophage obtained have consistent gene signatures as mouse and human macrophages, respectively. We also observed differences in transcriptional levels in macrophages induced by different methods. We obtained the transcriptome sequencing data of macrophages infected by different pathogens from GEO and analyzed them quantitatively. We performed GSEA analysis on macrophages infected with different pathogens and porcine bone marrow-derived macrophages (BMDM). We found that the enrichment pathways of macrophages obtained by different induction methods and macrophages infected by different pathogens were different. Our study provided a framework to guide the interrogation of macrophage phenotypes in the context of health and disease. The approach described here could be used to propose new biomarkers for diagnosis in diverse clinical settings including porcine reproductive and respiratory syndrome virus (PRRSV), African swine fever virus (ASFV), and Toxoplasma gondii.

overall_design: We used different methods to induce and differentiate porcine bone marrow-derived macrophages, and obtained M1 macrophages and M2 macrophages induced by two methods. We compared the transcriptome differences of macrophages induced by different methods by RNA-seq. We performed Pearson's analysis, PCA analysis, edger difference analysis, pathway enrichment analysis and PPI pathway enrichment analysis. We also compared different diseases with our induced differentiated macrophages for GSEA analysis.

first: Teng

last: Yuan


title: RNA-Seq from SCs after exercise

city: Hong Kong

first: Feng

last: Yang

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

summary: RNA seq of Freshly isolated satellite cells from wild type mice after volunteer exercise (VE), endurance exercise (EE) and non-exercise Ctrl (NE)

overall_design: RNA-Seq was perpormed in freshly isolated SCs from wild type mice after 21das VE, 10days EE or NE

first: Huating

last: Wang

first: Suyang

last: Zhang

first: Yile

last: Huang

first: Yingzhe

last: Ding


title: H3 Acetylation promotes H2A.Z incorporation into chromatin through SWR1 recruitment to stimulate expression.

status: Public on May 02 2025

city: Xianyang

first: Mingming

last: Zhao

address: Taicheng Road,Yangling District

institute: Northwest A&F University China

summary: Following DNA replication, canonical H2A in eukaryotes is frequently replaced by histone variants, such as the conserved H2A.Z. Chromatin remodelers like the SWR1 complex facilitate this process, substituting the H2A histone with H2A.Z in an ATP-dependent manner. However, the precise mechanisms that recruit SWR1 to specific loci remain partially studied. In this study, we investigate the role of H3 acetylation in mediating the incorporation of H2A.Z into the chromatin to promote gene expression. Our results show that artificially induced hyperacetylation is associated with higher levels of H2A.Z and a decrease in H2A.W (HTA6 and HTA7). This phenomenon is also observed in histone deacetylases HDA6 and HDA9 defective backgrounds. Moreover, H2A.Z is required for the phenotype observed in hda6-1 and hda9-1

overall_design: ChIP-seq of H2A.Z、H3K9K14Ac、H3K18Ac in Columbia-0(WT) and hda6-1 mutant background; ChIP-seq of H2A.Z、H3K9K14Ac、H3K27Ac in Columbia-0(WT) and hda9-1 mutant.ChIP-seq of  H2A、H2A.X in Columbia-0(WT) background;ChIP-seq of HTA67 in Columbia-0(WT) and h2az-5 mutant background.ChIP-seq of H3、H3K9K14Ac、H3K27Ac、H2A.Z、HTA67、HTA12 in Columbia-0(WT) and Columbia after TSA treatment. Plants used for ChIP-Seq and TSA treatments were grown in MS media supplemented with 1% sucrose under long-day photoperiod and ~21°C. In all cases, seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

first: Yafei

first: Israel

last: Ausin

first: Han

first: Min

last: Liu

first: Wenshuo

first: Junjie


title: Disruption of DNA methylation underpins the neuroinflammation induced by targeted CNS radiotherapy

city: London

first: James

middle: Gervase

last: Nicholson

state: London

address: 4 Newark St,

department: Blizzard Institute

country: United Kingdom

institute: QMUL

summary: Although targeted radiotherapy (RT) is integral to the increasing survival of cancer patients, it has significant side-effects, the cellular and molecular mechanisms of which are not fully understood. During RT epigenetic changes occur in neoplastic tissue, but few studies have assessed these in non-neoplastic tissue and results are highly variable. Using bulk DNA methylation and RNA sequencing as well as spatial transcriptomics (ST) in a unique cohort of patient tissue samples, we show distinct differences in DNA methylation patterns in irradiated brain tissue, whilst ST characterisation identifies specific micro-environmental niches present after irradiation and highlights neuropeptides that could be propagating neuroinflammation. We also show that in a cerebral organoid (CO) model of early changes in neurons after irradiation there are similar DNA methylation alterations and disruption of the DNA methylation machinery, suggesting that early but persistent epigenetic dysregulation plays a role in neurotoxicity. We provide a link between radiotherapy induced neuroinflammation and disruption of DNA methylation for the first time and suggest possible driving mechanisms for this chronic neuroinflammation.

overall_design: scRNAseq of Cerebral organoids derived from two cell lines (NSC19 or NSC61), collected 1 day after irradiation with 24 Gy, as well as sham controls (0 Gy).

first: Thomas

last: Millner

middle: G

first: Pratistha

last: Panday

first: Silvia

last: Marino