title: OsbHLH002-OSH1 module orchetrates the secondary cell wall formation in rice (RNA-Seq)

status: Public on Jul 31 2023

city: Hangzhou

first: Yang

last: lijia

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

summary:
To explore the in-depth mechanism of how OsbHLH002-OSH1 complex promotes SCW development
we performed the genome-wide transcriptomic profiles using the leaf sheaths of Osbhlh002-1, osh1-1 and the wild type.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Osbhlh002-1, osh1-1 and WT

first: Ying

last: Chen

first: Haoyue

last: Qi

first: Lijia

last: Yang

first: Shiyong

last: Song


title: Type 2 diabetes susceptibility gene GRK5 regulates physiological pancreatic β-cell proliferation via phosphorylation of HDAC5

city: Suita

first: Shugo

last: Sasaki

state: Osaka

address: 2-2 Yamadaoka, Suita-shi

department: Metabolic Medicine

country: Japan

institute: Osaka University

summary: Diabetes onset is accompanied with β-cell deficiency, and thus restoring functional β-cell mass is a promising therapy for those with diabetes. However, the mechanisms of β-cell mass regulation are not fully understood. Previously, we demonstrated that Sox4 is required for β-cell proliferation during prediabetes. Here, we report that Sox4 regulates β-cell mass through modulating expression of the type 2 susceptibility gene GRK5. Newly generated β-cell specific Grk5 knockout mice showed impaired glucose tolerance with reduced β-cell mass. In agreement with this phenotype, cell cycle inhibitor genes, Cdkn1a and Ccng1 were upregulated in Grk5 knockout islets. Furthermore, we found that Grk5 positively regulates β-cell mass through phosphorylation of HDAC5 and subsequent transcription of immediate early genes (IEGs) such as Nr4a1, Fosb, Junb, Arc, Egr1 and Srf. Together, these studies suggest GRK5 is linked to type 2 diabetes through regulation of β-cell mass. GRK5 could become a potential target of cell therapy to preserve functional β cells during the progression towards frank diabetes.

overall_design: Islet mRNA profiles of 18-week old β-cell specific Grk5 knockout (Pdx1-CreER; Grk5 flox/flox) and control (Grk5 flox/flox)) mice

first: Cuilan

last: Nian

first: Eric

middle: E

last: Xu

first: Daniel

middle: J

last: Pasula

first: Helena

last: Winata

first: Sanya

last: Grover

first: Dan

middle: S

last: Luciani

first: Francis

middle: C

last: Lynn


title: OsbHLH002-OSH1 module orchetrates the secondary cell wall formation in rice (ChIP-Seq)

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
To explore the in-depth mechanism of how OsbHLH002-OSH1 complex promotes SCW development
We performed chromatin immunoprecipitation sequencing (ChIP-seq) to investigate the genome-wide binding sites of OsbHLH002 using Osbhlh002-1 gOsbHLH002-3FLAG.


title: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice [NeuN+ hippocampal neurons]

city: Baltimore

first: Leandros

last: Boukas

address: 733 North Broadway

country: USA

institute: Johns Hopkins University

summary: Many Mendelian developmental disorders caused by coding variants in epigenetic regulators have now been discovered. Epigenetic regulators are broadly expressed, and each of these disorders typically exhibits phenotypic manifestations from many different organ systems. An open question is whether the chromatin disruption -- the root of the pathogenesis -- is similar in the different disease-relevant cell types. This is possible in principle, since all these cell-types are subject to effects from the same causative gene, that has the same kind of function (e.g. methylates histones) and is disrupted by the same germline variant. We focus on mouse models for Kabuki syndrome types 1 and 2, and find that the chromatin accessibility abnormalities in neurons are mostly distinct from those in B or T cells. This is not because the neuronal abnormalities occur at regulatory elements that are only active in neurons. Neurons, but not B or T cells, show preferential chromatin disruption at CpG islands and at regulatory elements linked to aging. A sensitive analysis reveals that the regions disrupted in B/T cells do exhibit chromatin accessibility changes in neurons, but these are very subtle and of uncertain functional significance. Finally, we identify a small set of regulatory elements disrupted in all three cell types. Our findings reveal the cellular-context-specific effect of variants in epigenetic regulators, and suggest that blood-derived episignatures may not be well-suited for understanding the mechanistic basis of neurodevelopment in Mendelian disorders of the epigenetic machinery.

overall_design: ATAC-seq in NeuN+ hippocampal neurons from the dentate gyrus in mouse models of Kabuki Syndrome 1, Kabuki Syndrome 2, and wild-type mice

first: Teresa

middle: R

last: Luperchio


title: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice [CD90.2+ T cells]

overall_design: ATAC-seq in CD90.2+ T cells in mouse models of Kabuki Syndrome 1, Kabuki Syndrome 2, and wild-type mice


title: Development of molecular indicators for adverse health responses of effluent exposure in caged longnose dace (Rhinichthys cataractae) in ACWA raceways

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

summary: The goal of this experiment was to assess transcriptomic responses in caged longnose dace (Rhinichthys cataractae) (LND) females and males exposed to 5% final effluent over time to identify potential transcriptomic markers that can be used as reliable indicators and that can further be explored in field-based ecotoxicogenomic studies in the Bow River. We used the Advancing Canadian Wastewater Assets (ACWA) artificial streams to cage LND for 28 days exposed to either 5% final effluent or control.

overall_design: Wild longnose dace (Rhinichthys cataractae; LND) were collected from an upstream reference site in the Bow River, Calgary, Alberta. Captured LND (376) were placed in minnow buckets subsequwntly deployed in six artificial raceways at the ACWA facility. Each cage was stocked with 20 LND males and females. Three out of six raceways contained Bow River water (control treatment) while the remaining three contained 5% Pine Creek final effluent mixed with Bow River water (exposure treatment). There were three cage replicates per each Bow River and Pine Creek raceway. Before the onset of the experiment, a subsample of 15 LND females and 16 males was processed immediately upon collection from the reference site in the Bow River, to establish baseline responses, and this marked day 0. A subset of these samaples were subjected to RNA sequencing (n = 10; 6 males + 4 females; group A). Caging exposure lasted 28 days; LND were sampled on day 7, 14, and 28 by randomly retrieving a cage replicate from each of the 6 raceways. Subsets of fish including both male and female LND from all sampling points were also subjected to RNA sequencing day 7 (n = 24; (6 males + 6 females) x 2 treatments; groups B and C), day 14 (n = 24;  (6 males + 6 females) x 2; treatments groups D and E) and day 28 (n = 24; (6 males + 6 females) x 2; treatments groups F and G).

first: Kelly

last: Munkittrick

first: Chris

first: Patricija

last: Marjan


title: Unveiling CNPY3 as an Innate Immune Effector and Therapeutic Target against Dengue Virus

city: Chongqing

first: Xiaoyan

last: Ding

address: No. 30, Gao Tan Yan Zheng Street， Shapingba District

institute: Army Medical University

summary: To explore the molecular mechanism of Cnpy3 in the treatment of DENVs infection,   transcriptome analysis was performed on the brains of suckling mice at two time points of DENVs infection after LNP-Cnpy3 treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for suckling mice brains after DENVs infection with LNP-Cnpy3 and LNP-empty  treatment.

first: Jiuxiang

last: He

first: Yuxin

last: Zhou

first: Jintao

last: Li


title: Causality of gut bacteria Klebsiella pneumoniae to hypertension development II

city: Beijing

first: Jing

state: Beijing

address: Beilishi Road 167, Xicheng District,

department: Department of Hypertension Center

institute: FuWai Hospital, National Center for Cardiovascular Diseases,  Peking Union Medical College & Chinese Academy of Medical Sciences

summary:
We conducted this study to investigate whether gut K.pn is a causal factor for HTN pathogenesis and the potential mechanism
Ttranscriptome changes of aorta were assessed by RNA-sequencing

overall_design: Transcriptome profiles of aorta from  mice receiving K.pn

first: Jun

last: Cai


title: RNA-Seq of PARPi-resistant ovarian cancer cells

city: Dresden

first: Jan

middle: Dominik

last: Kuhlmann

state: Saxony

address: Fetscherstraße 74

department: Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe

country: Germany

institute: Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden

summary: We have previously established an in vitro model of PARPi-resistant ovarian cancer by long-term exposure of UWB1.289 ovarian cancer cells (and their isogenic derivatives UWB1.289+BRCA1) to incrementally ascending olaparib concentrations. After finalizing this model, we performed RNA-seq, in order to identify differentially expressed transcript in the PARPi-resistant cells, with a focus on genes related to DNA-repair, multi-drug resistance and EMT. As a result, we show that the phenotype of PARPi resistance is associated with EMT-like traits and up-regulation of selective multi-drug related transcripts.

overall_design: UWB1.289  / UWB.1289+BRCA1 ovarian cancer cells and their isgenic PARPi-resistant derivatives (Olres-UWB1.289  / Olres-UWB.1289+BRCA1) were culturred under drug-free conditions and subjected to RNA-seq


title: Comparison of TCR, CAR, and CAR-like T-cells efficiency against the solid tumors

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

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

overall_design: Refer to individual Series


title: The tumor suppressive role of ANCO1 in early-stage triple-negative breast cancer [RNA-seq]

city: Washington

first: Meng

last: Yuan

state: DC

address: 3970 Reservoir Road NW

department: Lombardi Comprehensive Cancer Center

institute: Georgetown University

summary:
To understand the impact of ANCO1 reduction on gene expressions, we performed RNA-seq experiments in shANCO1 and shCTRL MCF10A and MCFDCIS cells  in 2D and 3D culture.
We report ANCO1 knockdown leads to altered gene expression profiles. Enriched gene sets including chr1q21.3 and mTORC1 signaling may be responsible for phenotypical changes in shANCO1 cell lines.

overall_design: RNA-seq experiments were performed in 2D- and 3D-cultured shANCO1 and shCTRL MCF10A and MCFDCIS cell lines to examine changes in transcriptome. At least two shANCO1 constructs targeting different regions of ANCO1 were used in each setting. Experiments were done in triplicates.

first: Megan

last: Barefoot

first: Marcel

middle: O

last: Schmidt

first: Ghada

middle: M

last: Sharif

first: Anna

middle: T

last: Riegel


title: AU565 small spheroids and capsules.

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary: AU565 HER2+  breast cancer cells were each grown into aggregates using two fabrication approaches, (1) liquid overlay with a low (8,000 cell) seeding density, and (2) via microencapsulation with subsequent microcapsule processing. Upon sample maturation, RNA from these samples was extracted and sequenced to help identify differences in model gene expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Cassandra

last: Roberge

first: Margarida

last: Barroso

first: Christopher

last: James


title: The role of PTENα in brain

first: Yue

last: Yin

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

summary: In contrast to the ubiquitous expression profile of PTEN, PTENα is predominantly expressed in brain. To study the biological function of PTENα in brain, we employed LCMV to induce murine viral encephalitis model. Through single cell RNA sequencing, we revealed the immunological function of PTENα during viral infection in the brain.

overall_design: The cortex from infected wild-type and Ptenα-specific deficient mice on day 7 after intracranial injection of LCMV-Cl13 were isolated and dissociated. Cells were pooled by 10x Genomics platform.

first: Zeliang

last: Yang

first: Xin

last: Zhang

first: Dan

last: Lu


title: Single cell RNA-seq for bone marrow mononuclear cells from CAR-T therapy received DLBCL patient

first: Yuzhuo

address: Zheng Yutong Building room D311

institute: Tsinghua University

summary: To investigate whether metoprolol treatment could affect immune cells population and proinflammatory gene expression in  bone marrow mononuclear cells from CAR-T therapy received DLBCL patient

overall_design: Mononuclear cells were isolated before and after metoprolol treatmetn from bone marrow of CAR-T therapy received DLBCL patient by Ficoll gradients, and isolated cells were frozen for preservation and sent out for scRNA-seq library construction by using 10x genomics platform.


title: Effects of BPA, BPAF, and BPS on Endochondral Ossification and on the Transcriptome of Ex Vivo Murine Limb Bud Cultures

city: MONTRÉAL

first: Barbara

last: Hales

state: QC

address: 3655 Promenade Sir-William-Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University


title: Screening for differentially expressed circRNAs in ischemic stroke by RNA sequencing

city: shijiazhuang

first: haibin

last: li

address: 102 Youyi Bei Dajie, Shijiazhuang, Hebei 050000

institute: The Third Hospital of Hebei Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Acute coronary syndrome (ACS) is one of the most serious cardiovascular diseases. Percutaneous coronary intervention (PCI) combined with stent implantation improves outcomes in patients with ACS. However, the treatment of in-stent restenosis in ACS patients remains a major clinical challenge. In this study, RNA library construction and high-throughput sequencing were performed. The DEmRNA-DElncRNA co-expression analysis showed that there were 19 DElncRNA-DEmRNA relationship pairs (including 15 DEmRNA, 3 DElncRNA) in the PCI_NR/PCI_Re and NC/PCI_Re intersection group and 993 DElncRNA-DEmRNA relationship pairs (including 74 DEmRNA, 19 DElncRNA) in the NC/ACS and ACS/PCI_NR intersection group. We selected genes in the top 10 of differential expression and those involved in the co-expression of lncRNA-mRNA for diagnostic analysis. The area under curve (AUC) of PDZK1IP1, PROK2 and LAMP3 were greater than 0.7, which were 0.747, 0.769 and 0.725, respectively. It is indicated that PDZK1IP1, PROK2 and LAMP3 may as the potential diagnostic gene biomarkers in ACS.

overall_design: The cohort subjected to RNA-Seq consisted of 3 patients with ACS, 3 patients with PCI_non-restenosis (PCI_NR), 3 patients with PCI_restenosis (PCI_Re) and 3 normal controls (NC). The expression of mRNA and lncRNA in blood samples.

first: Haibin

last: Li


title: ChIP-Seq for nuclear GAPDH in ex-vivo cortical microglia from LPS treated mice

first: Adriana

last: Ramos

address: 600 North Wolfe Street

summary: We report the genome wide map for the peaks of occupancy of nuclear GAPDH in cortical microglia from mice treated with LPS.

overall_design: Examination of the transcriptional targets that GAPDH can have when it translocates to the nucleus under stress situations

first: Akira

last: Sawa

first: Corina

last: Antonescu

first: Liliana

last: Florea


title: Human healthy mononuclear blood cells

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary: Healthy mononuclear cells from periferal blood (PB), mobilized peripheral blood (MPB) or bone marrow (BM) of healthy adult donors.

overall_design: Healthy mononuclear cells were obtained from periferal blood (PB), mobilized peripheral blood (MPB) or bone marrow (BM) of healthy adult donors. RNA was purified from healthy MNCs.

first: Allison

last: Boyd

first: Luca

last: Orlando

first: Zoya

last: Shapovalova


title: Transcriptome analysis of control (y w) and Paip1 mutant third instar larval wing imaginal discs

first: Wanzhong

last: Ge

state: Zhejiang

address: Yuhangtang Road 866

summary: We report the genome-wide RNA profiling of  third instar larval wing imaginal discs upon Paip1 mutation

overall_design: mRNA expression profiles of two replicates of control (y w) and two replicates of Paip1 mutant third instar larval wing imaginal discs


title: RNA-seq of human colorectal cancer cells in presence and absence of ZEB1

city: Barcelona

first: Antonio

last: Postigo

address: Villarroel 170

department: Oncology and Hematology

country: Spain

institute: IDIBAPS

summary: Characterize the gene expression profile with RNA-seq using Illumina HiSeq2000 of Ls174T and RKO1 CRC cell lines in presence of siRNA against control and ZEB1

overall_design: RNA sequencing of total RNA from Ls174T and RKO1 colorectal cancer cells in presence of siRNA against control and ZEB1

first: E

last: Sánchez-Tilló

first: A

first: Anna

last: Esteve-Codina


title: Murine conditional Cxadr (CAR) knockout using an Mx1-Cre system

status: Public on Jul 30 2023

city: Vienna

first: Lukas

last: Kazianka

address: Währinger Gürtel 18-20

department: Medicine I, Div. of Hematology

country: Austria

institute: Medical University of Vienna

summary: In addition to a series of in vitro experiments characterizing the role of Coxsackie-Adenovirus Receptor (CAR) in erythropoiesis (GSE147963), in vivo proof of concecpt was obtained from an Mx1-Cre Cxadrfl/fl conditional knockout mouse model. After poly I:C injection (400µg on 3 consecutive days) to induce Cxadr deletion mice were observed for up to 10 months to study changes in erythropoiesis. After development of anemia, mice were sacrificed and myeloid BM progenitors sorted. RNA of purified populations was used for RNA-seq to study molecular effector mechanisms.

overall_design: 4 mice per group (Mx1-Cre+ Cxadrfl/fl experimental mice vs. Mx1-Cre- Cxadrfl/fl controls); CMP, GMP, MEP and LSK progenitor populations were sorted for each mouse

first: Carmen

last: Schweicker

first: Christiane

last: Agreiter


title: Aldolase A Accelerates Cancer Progression by Modulating mRNA Translation and Protein Biosynthesis via Noncanonical Mechanisms

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

summary: We provide robust and intensive evidence highlighting a close cooperative mechanistic interaction between ALDOA and IGF2BP1 that fine-tunes mRNA translation and enhances liver cancer progression. Moreover, specifically targeting ALDOA with GalNAc-conjugated siRNA shows promising anti-HCC effect in vivo. our findings uncover a previously unappreciated function of ALDOA in modulating mRNA translation and highlight the potential of targeting ALDOA as a prospective therapeutic strategy in HCC.

overall_design: RNA immunoprecipitation followed by sequencing (RIP-seq) was performed using antibody against IGF2BP1 to identify the targeted transcripts enriched by IGF2BP1 in HuH-7 cells. m6A-RNA immunoprecipitation followed by sequencing (MeRIP-seq) was performed to identify the m6A sites across mRNA in HuH-7 cells.

first: Junjiao

last: Song

first: Zhiao

last: Chen


title: WT vs IFN-gamma treated bulk RNA-seq libraries of HSCs

city: Houston

first: Bailee

last: Kain

state: Texas

address: 1102 Bates Avenue

institute: Baylor College of Medicine

summary: Purpose: to determine changes in RNA expression in WT vs BST2 KO mice following 24 hour treatment of IFNg. We were particularly interested in performing pathway analysis using GSEA.

overall_design: HSC (Lineage- c-Kit+ CD150+ CD48- CD34-) were sorted using a Sony cell sorter, SH800. 5,000-11,000 HSCs were isolated from each mouse and RNA was isolated using RNeasy kit (Qiagen, Cat#74004). RNA-sequencing library was generated using SMARTer® Stranded Total RNA-Seq Kit V3 (Takara Bio USA). The sequencing was performed using Illumina NovaSeq SP with a paired-end sequencing length of 10bp.

first: Marcus

last: Florez

first: Katherine

last: King


title: MeVa2.1.dOVA is a novel immune-refractory cell line to study tumor immune resistance [exome-seq]

city: Amsterdam

first: PETROS

last: DIMITRIADIS

email: p.dimitriadis@nki.nl, d.rao@nki.nl

state: Noord-Holland

address: Plesmanlaan 121

country: Netherlands

institute: NETHERLANDS CANCER INSTITUTE - NKI

summary: Pre-clinical model to study tumor immune resistance are essential. To this end, we generated cell lines from tumors induced on BrafV600E Pten-/- mice. The cell lines have been characterized to evaluate the tumor growth in vivo and response to immunotherapies. In addition, we have also chaacterised the DNA expression profile of the cell lines.

overall_design: Cell lines were left untreated and harvested for DNA sequencing analysis.

first: Blank

last: Christian

first: Dimitriadis

last: Petros

first: Rao

last: Disha

first: Lacroix

last: Ruben


title: MeVa2.1.dOVA is a novel immune-refractory cell line to study tumor immune resistance [RNA-seq]

summary: Pre-clinical model to study tumor immune resistance are essential. To this end, we generated cell lines from tumors induced on BrafV600E Pten-/- mice. The cell lines have been characterized to evaluate the tumor growth in vivo and response to immunotherapies. In addition, we have also chaacterised the baseline RNA expression profile of the cell lines.

overall_design: Cell lines were left untreated and harvested for RNA sequencing analysis. Three replicates of each cell line were analysed.


title: RNA-seq experiment of wild-type (WT) and pif4 mutant seedlings grown for 3 days in darkness and exposed or not to heat stress for 3 hours.

city: Cerdanyola del Vallès

first: Guiomar

last: Martín

state: Barcelona

address: Vall Moronta

institute: Centre for Research in Agricultural Genomics

summary: Transcriptome profiles of wild-type (WT), pif4-101, and transgenic plants expressing the coding region of PIF4 under the control of its endogenous promoter (H71 and H76; pif4-101 mutant background) grown for 3 days in the dark at 22ºC and then, for 3 additional hours, exposed or not to heat stress (37ºC).

overall_design: Triplicate biological samples were analyzed.

first: Paula

last: Duque


title: Gene expression in B breve SW1107E in the presence of media containing lactose, BMO and 3SL as carbon sources

city: Davis

first: David

middle: A

last: Mills

state: CA

address: One Shields ave

department: Dept. of Food Science and Technology

institute: University of California Davis

summary: Bifidobacterium species in the infant gut can metabolize intact human milk oligosaccrides. There is species varation in the types of the olgosaccharides that can bedigested by Bifidobacterium species. B. breve strains have shown digestion of LNT and LNnT oligoscchrides. The objective of te current study was idetification of B. breve strains that can digest sialylated oligosacchrides. The currnet study was designed to idetify the genes that show upregulation when grown in lactose, 3'-siallylactose and Bovine Milk Oligosaccharides

overall_design: Three biological replicates each of B. breve SW1107E grown on three treatments - 2%Lactose, 2%-3'-SL and 2'-BMO. Samples were collected at midlog phase of growth in RNA protect and RNA was extracted.

first: Saumya

last: Wickramasinghe


title: Bone marrow mononuclear cells

first: Yuzhuo

last: Yang

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

overall_design: Refer to individual Series


title: Integrative genomic analyses identify lncRNA regulatory networks across pediatric leukemias and solid tumors

city: Philadelphia

first: Sharon

last: Diskin

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Long non-coding RNAs (lncRNAs) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curated RNA sequencing data for 1,044 pediatric leukemia and extra-cranial solid tumors and integrated paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. A total of 2,657 lncRNAs were robustly expressed across six pediatric cancers, including 1,142 exhibiting histotype-elevated expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multi-dimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell-type specific transcription factors further implicated distinct histotype-elevated and developmental lncRNAs. Integration of these analyses prioritized lncRNAs for experimental validation, and silencing of TBX2-AS1, the top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming the computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies.

overall_design:
In order to investigate the function of the TBX2 and TBX2-AS1 genes in neuroblastoma, we used siRNAs to knockdown their expression in the neuroblastoma cell line, NLF.
We then performed gene expression profiling using RNA-seq after cells were treated with siRNA for 48 hours.
Comparative gene expression profiling analysis of RNA-seq data for NLF cells treated with non targeting control, siTBX2, and siTBX2-AS1.

first: Apexa

last: Modi

first: Karina

last: Conkrite


title: Corticosteroid treatment during sepsis influences hippocampal function in survivors

city: Ann Arbor

first: Joanna

last: Spencer-Segal

address: 205 Zina Pitcher PI

department: Michigan Neuroscience Institute

institute: University of Michgan

summary: Millions of sepsis survivors annually face long-term neuropsychiatric sequelae of their illness. Corticosteroids are frequently administered in sepsis, and their use affects neuropsychiatric outcomes, but the mechanisms are unknown. We used the cecal ligation and puncture method to induce acute infection in mice and test the hypothesis that corticosteroid treatment during illness has long-term effects on hippocampal function. Functional phenotyping and hippocampal RNA-sequencing were performed in the same survivor mice to identify underlying mechanisms of behavioral and neuroendocrine outcomes. Long-term CLP survivors exhibited anxiety-like behavior, increased central hypothalamic-pituitary-adrenal (HPA) axis activity, and persistent systemic and neuro-inflammation. The relationship between gene expression and behavior suggested a protective role for inflammation and oxidative metabolism after CLP. Corticosterone treatment during illness had distinct effects on hippocampal function in survivors, including object memory impairment. The long-term behavioral effects of corticosterone treatment were associated with persistent downregulation of activity-dependent gene expression in the hippocampus. The results suggest that corticosteroid treatment for sepsis influences hippocampal function in survivors via long-lasting changes to basal hippocampal activity. Neural activity, inflammation, and oxidative metabolism should be explored as future treatment targets to modify neuropsychiatric outcomes in sepsis survivors.

overall_design:
Overall Design: C57/Bl6 mice used in this experiment were obtained from Jackson Laboratories and were aged 8-9 weeks old. They were housed 5 per cage on ventilated racks with a controlled light:dark cycle, temperature, and humidity. Food and water were available ad libitum. Mice were moved into the housing rooms and left undisturbed to acclimate to the environment for at least one week before starting experiments. A total of 80 mice were initially used in this experiment in two different cohorts. Each cohort consisted of 40 mice, 20 male and 20 female mice. Mice were assigned to one of four experimental groups based on a preliminary measure of locomotor activity such that each group had similar average locomotion. Within each cohort, therefore, there were 5 male and 5 female mice per group. Mice either received a cecal ligation and puncture (CLP) surgery or a sham control surgery (SHAM). Mice were given either a dose of 13 mg/kg of corticosterone or vehicle control subcutaneously for five days following surgery. Only mice from the first cohort, animal IDs 368-407, were used to obtain hippocampal samples. This cohort started with 40 mice, 20 male and 20 female mice. Following surgery, 2 female mice died resulting in a final n=38. The mice that died included one female from the CLP+saline group and one female from the CLP+cort group. Both mice died 3 days post-surgery. This resulted in the following distribution of animals among the four groups for behavioral tests and tissue collection:
SHAM+saline: 5 males, 5 females
SHAM+cort: 5 males, 5 females
CLP+saline: 5 males, 4 females
CLP+cort: 5 males, 4 females
Beginning 15 days after CLP or SHAM surgery, mice underwent the following behavioral procedures prior to collection of hippocampal for RNA-sequencing on day 21: open field test (day 15), novel object recognition (day 16), and elevated zero maze (17).
Euthanasia and Dissection: Mice were sacrificed at baseline in the morning 21 days post-surgery and 3 days post-testing for behavior by rapid decapitation. Trunk blood was collected and the brain was removed from skull and placed onto an inverted glass petri dish in ice. The brain was cut into two hemispheres and the entire hippocampus was then dissected out of one hemisphere and cut into dorsal and ventral halves. The same was repeated for the second hemisphere. Each mouse’s dorsal hippocampal samples (2/mouse) or ventral hippocampal samples (2/mouse) were then placed into the bottom of 1.5 mL sterile Eppendorf tubes and SNAPfrozen on dry ice. Samples were stored at -80 degrees C until use for RNA extraction. Only one sample was not able to be obtained, and that was for mouse #390 ventral hippocampus (female, CLP+saline). For three mice, only one of two ventral hippocampal samples were obtained: #381 (male, CLP+cort), #402 (female, CLP+cort), and #404 (female, SHAM+cort). Dorsal hippocampus collection for those mice was completely successful.

middle: L

first: Huzefa

last: Khalil

first: Swapnil

last: Gavade

first: Klaudia

last: Laborc

first: Savannah

last: Kounelis


title: Immunotranscriptomic Study of Human anti-GD2 CAR T-cells

first: Roman

last: Perik-Zavodskii

address: Yadrincevskaya 14

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

summary: In this work, we compared the expression profiles of Anti-GD2- transduced T-cells with Anti-GD2-transduced T-cells co-cultured with SK-Mel-37.

overall_design: We profiled total RNA from the anti-GD2-transduced TCR T-cells on NanoString Sprint Platform using Immunology V2 panel.


title: Targeting Clic1 for the Treatment of Obesity: A Novel Therapeutic Strategy to Reduce Food Intake and Body Weight

city: La Jolla

first: Olivia

last: Osborn

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

summary: Overconsumption of energy-rich food is a key driver of the obesity epidemic. However, the neural circuits that regulate food overconsumption are highly complex and many molecular components of these circuits remain unknown.  Our recent studies attribute a novel role of Clic1 as a driver of food intake and overconsumption. Clic1 is expressed in the arcuate nucleus of the hypothalamus and expression specifically increases in Agrp/Npy neurons in the fasted state. Importantly, Clic1 exists in two forms and fasting induces a transformation from the predominant soluble enzymatic form to the membrane-associated ion channel form.  Clic1KO mice eat significantly less and have a lower body weight than WT littermates when either fed chow or high fat diet.  Furthermore, pharmacological inhibition of Clic1 inhibition results in suppression of food intake and promotes highly efficacious weight loss in obese mice.

overall_design: Randomized controlled study

first: Rizaldy

last: Zapata

first: Chanond

last: Nasamran

first: Daisy

last: Chillin-Fuentes


title: Ratiometric Inclusion of Fibroblasts Promotes Both Castration-resistant and Androgen-dependent Tumorigenic Progression in Engineered Prostate Cancer Tissues

city: Auburn University

first: Elizabeth

last: Lipke

state: AL

address: 212 Ross Hall

institute: Auburn University

summary: To investigate the ratiometric role of fibroblasts in prostate cancer (PCa) progression, this work establishes a matrix-inclusive, three-dimensional engineered prostate cancer tissue (EPCaT) model that enables direct coculture of neuroendocrine-variant castration-resistant (CPRC-ne) or androgen-dependent (ADPC) PCa cells with tumor-supporting stromal cell types. Results show that the inclusion of fibroblasts within CRPC-ne and ADPC EPCaTs drives PCa aggression through significant matrix remodeling and increased proliferative cell populations. Interestingly, this is observed to a much greater degree in EPCaTs formed with a small number of fibroblasts relative to the number of PCa cells. Fibroblast coculture also results in ADPC behavior more similar to the aggressive CRPC-ne condition, suggesting fibroblasts play a role in elevating PCa disease state and may contribute to the ADPC to CRPC-ne switch. Bulk transcriptomic analyses additionally elucidate fibroblast-driven enrichment of hallmark gene sets associated with tumorigenic progression. Finally, the EPCaT model clinical relevancy is probed through a comparison to the Cancer Genome Atlas (TCGA) PCa patient cohort; notably, similar gene set enrichment is observed between EPCaT models and the patient primary tumor transcriptome. Taken together, study results demonstrate the potential of the EPCaT model to serve as a PCa-mimetic tool in future therapeutic development efforts.

overall_design: Bulk RNAseq analysis of our CRPC and ADPC mono- and coculture EPCaTs on Day 15 of in vitro coculture (RNA isolated from n > 2 EPCaTs).

first: Nicole

last: Habbit

first: Michael

middle: W

last: Greene

first: Balabhaskar

last: Prabhakarpandian

first: Robert

middle: D

last: Arnold


title: The tumor suppressive role of ANCO1 in early-stage triple negative breast cancer [ChIP-seq]

first: Meng

last: Yuan

address: 3970 Reservoir Road NW

institute: Georgetown University

summary:
To examine the impact of ANCO1 reduction on H3K27Ac modification and its association with gene expression changes, we performed ChIP-seq experiments in shANCO1 and control MCF10A and MCFDCIS cells.
We report ANCO1 knockdown causes global changes to H3K27Ac pattern and enhances accessibility of breast cancer enhancers. Altered H3K27Ac signal is associated with gene expression changes.

overall_design: ANCO1 knockdown MCF10A and MCFDCIS cells were generated with lentiviral infection. ChIP-seq experiments were performed in shANCO1 and shCTRL cell lines to examine H3K27Ac engagement in the genome. Experiments were done in triplicates. Immunoprecipitated samples were normalized to respective input controls.

first: Megan

last: Barefoot

first: Moray

last: Campbell

first: Marcel

last: Schmidt

first: Ghada

last: Sharif

first: Anna

last: Riegel


title: The tumor suppressive role of ANCO1 in early-stage triple negative breast cancer


title: RUNX2 regulates gene expression in mature chondrocytes

city: Toronto

first: Zoe

last: Gillespie

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

summary: The vertebrate skeleton is mostly composed of three specific cell types: immature chondrocytes (IMM), mature (hypertrophic) chondrocytes (MAT), and osteoblasts (OST). These three cell types are distinct, but they also share the expression of many genes. This overlapping gene expression can be attributed to two transcription factors, SOX9 and RUNX2, which operate near the top of hierarchy of the gene regulatory network (GRN) underlying IMM, MAT, and OST. Sox9 drives IMM differentiation, whereas Runx2 regulates OST differentiation. Importantly, MAT do not form without the function of either Sox9 or Runx2, but little is known about mechanisms of GRN regulation in MAT.  During MAT differentiation, the expression of Runx2 increases, and many genes regulated by this transcription such as Spp1, Mef2c, Ibsp, and Alpl are activated. To understand regulatory control of gene expression in mature chondrocytes, ChIP-seq experiments were performed using the mouse chondrogenic cell line ATDC5. These experiments identified in vitro RUNX2 binding sites at different stages of chondrogenesis. RUNX2 appeared to bind in most genes enriched in MAT at both day 3 of differentiation.  The ChIP-seq analyses presented here verified the molecular mechanisms predicted here to regulate transcription of the many genomic loci in MAT, proving more insight into regulatory control during cartilage maturation.

overall_design: ChIPseq for RUNX2 and H3K4me3 in ATDC5 cells at 3 time points of differentiation (day 0, day 3, day 10)

first: Christopher

last: Eskiw

first: Brian

last: Eames

first: Patsy

last: Gomez


title: Insight into integrated control of pituitary function revealed through analysis of Musashi target mRNAs

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

summary: The anterior pituitary is comprised of distinct cell types that each secrete specific hormones to control a variety of biological processes including growth, metabolism, reproduction and stress responses.  The anterior pituitary shows a remarkable level of cell type plasticity that allows shifts in hormone producing populations to meet organismal demands.  Pituitary cell plasticity is tightly regulated and both deficiency in cell plasticity and excessive cell plasticity are associated with common pituitary pathologies.  The molecular mechanisms underlying this plasticity are not well characterized but recent work has implicated the stem cell determinants and sequence-specific mRNA binding proteins of the Musashi family as regulators of adult pituitary hormone production.  In this study we have sought to identify the full range of Musashi target mRNAs in the adult mouse pituitary.  Using Musashi RNA immunoprecipitation we identify a cohort of 1192 mRNAs that show specific Musashi binding.  These include mRNAs restricted to discrete hormone-producing cell lineages as well as mRNAs associated with stem and progenitor cells.  The processes influenced by the proteins encoded by the Musashi-associated mRNAs include cellular homeostasis, protein trafficking and secretion, unfolded protein response, endocrine processes and female pregnancy.  Functional analysis of validated mRNA regulatory 3' untranslated regions (3’ UTRs) reveals UTR-specific positive or negative control by the Musashi proteins within the same cellular context.  Together, our findings indicate a broad role for Musashi proteins in the control of pituitary function.

overall_design: RIP-seq

first: Jewel

last: Banik

first: Alicja

last: Urbaniak

first: Ana

last: Silva Moriera

first: Katherine

last: Bronson

first: Sophia

last: Tomlinson

first: Alex

last: Lagrasse

first: Linda

last: Hardy

first: Stephanie

last: Byrum

first: Ania

last: Wilczynska

first: Angela

last: Odle

first: Melanie

last: MacNicol

first: Gwen

middle: V

last: Childs

first: Angus


title: AVEN is an indirectly druggable mediator of neuroblastoma cell tumorigenicity and chemotherapy resistance [RNA-seq]

city: Berlin

first: Hedwig

middle: Elisabeth

last: Deubzer

state: Berlin

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charite - University Hospital Berlin

summary: Approximately half of children diagnosed with neuroblastoma have aggressive high-risk disease, against which current multimodal therapy has little success. New targets for therapeutic intervention are urgently needed. In a systems approach, we combined time-resolved mRNA-Seq with miRNA profiling in a model of neuroblastoma differentiation treated with or without the clinically approved histone deacetylase inhibitor, panobinostat. Treatment most strongly regulated miR-630, which strongly downregulated AVEN, an inhibitor of apoptosis. Here we characterized AVEN for the first time in neuroblastoma pathogenesis, disclosed its epigenetic regulation and discovered correlations between AVEN expression and resistance to chemotherapy. High-level AVEN expression in 649 primary neuroblastomas negatively correlated with patient survival. Stably enforcing AVEN expression in BE(2)-C cells markedly promoted growth as subcutaneous xenografts in mice, while CRISP/Cas9-mediated AVEN knockout in BE(2)-C cells substantially reduced xenograft growth and enhances the efficacy of systemic doxorubicin treatment. Cell-based assays, flow cytometric cell cycle analyses and SILAC experiments demonstrate that AVEN is required for neuroblastoma proliferation.

overall_design: Panobinostat induced gene expression in human neuroblastoma BE(2)-C cells, treated with 5 nM, 10 nM or 15 nM for 6 h and 12 h.

first: Sebastian

last: Pfeil

first: Inás

middle: I

last: Sahly

first: Annika

last: Winkler

last: Sprüssel

first: Jasmin

last: Wuenschel

first: Daniela

last: Tiburtius

first: Matthias

last: Ziehm

first: Christoph

last: Bartenhagen

first: Patrick

last: Hundsdörfer

last: Selbach

first: Angelika

last: Eggert

first: Marco

last: Lodrini


title: Transcriptome and translatome of killing supernatant cultured human monocytes

city: Beijing

first: Yuzhuo

last: Yang

address: Zheng Yutong Building room D311

institute: Tsinghua University

summary: To investigate whether metoprolol treatment could affect the transcriptome and translatome of killing supernatant cultured human monocytes

overall_design: PBMC were isolated from buffy coat of healthy blood donors by Ficoll gradients, and CD14+ monocytes were isolated from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec). CD14+ monocytes were cultured with killing supernatant  for 5 days and treated with metoprolol or PBS prophylactically or conditionally and then were sent for both ribo-seq and RNA-seq

first: Gang

last: Xu


title: Network analyses of single cell-based digital twins for individualized treatment of antigen induced arthritis in mice.

city: Linköping

first: Sandra

last: Lilja

address: Sandbäcksgatan 7

department: BKV

country: Sweden

institute: Linköping University

summary: Computational treatment of digital twins of individual patients has been proposed as a strategy to personalize treatment. Systematic solutions are though currently lacking for inflammatory diseases. Here, we propose a strategy (scDrugPrio) that creates scRNA-seq based multicellular disease models that incorporate the key biological and pharmacological properties such as gene interactions within and between cell types, varying gene expression levels between cells and individuals, and inhibitory or enhancing drug effects. scDrugPrio was constructed based on joint scRNA-seq data from a mouse model of antigen induced arthritis. It was and validated by improved precision/recall for known drug targets and in vitro studies of predicted but yet unknown drug targets. When applied to human multiple sclerosis and Crohn’s disease, scDrugPrio was able to stratify predicted treatments based on interindividual variations. We hence propose scDrugPrio as a solution to personalize treatment by projecting network-based drug screening to digital twins of individual patients on cellulome-, genome-and drugome-wide scales.

overall_design: After pre-sensitization to mBSA, antigen induced arthritis (AIA) was triggered in 8 weeks old, female 129/Sve mice (N = 5) by intra-articular injection of methylated bovine serum (mBSA) in the left knee joint. The left knee joint of the healthy control mice (N = 4) was injected with phosphate-buffered saline (PBS,20 μL). One week after triggering, the mice were sacrificed. Successful AIA was ensured among the sick mice by immunohistochemistry and the whole left joint was prepared for scRNA-seq.

first: Samuel

last: Schäfer

first: Martin

last: Smelik

first: Desiré

last: Eklund

first: Xinxiu

last: Li

first: Oleg

last: Sysoev

first: Huan

last: Zhang

first: Yelin

last: Zhao

first: István

last: Kovács

first: Mika

last: Gustafsson

first: Danuta

last: Gawel

first: Hui

last: Wang

first: Mikael

last: Benson


title: Effects of Vhl deletion in Dmp1-expressing cells alterering gene expression of megakaryocyte-erythroid progenitor cells (MEPs)

city: Merced

first: Betsabel

last: Chicana

address: 5200 Lake Rd

institute: University of California Merced

summary: In recent years, general hypoxia-inducible factor (HIF)-prolyl hydroxylase (PHD) enzyme inhibitors have been developed for the treatment of anemia due to renal disease and osteoporosis. However, it remains a challenge to target the HIF signaling pathway without dysregulating the skeletal and hematopoietic system. Here, we examined the effects of Vhl deletion in bone by performing longitudinal analyses of VhlcKO mice at 3, 6, 10, and 24 weeks of age, where at 10 and 24 weeks of age, high bone mass and splenomegaly are present. Using flow cytometry, we observed increased frequency (%) of CD71loTER119hiFSClo orthochromatophilic erythroblasts and reticulocytes in 10- and 24-week-old VhlcKO bone marrow (BM), which correlated with elevated erythropoietin levels in the BM and increased number of red blood cells in circulation. The absolute numbers of myeloerythroid progenitors (MEPs) in the BM were significantly reduced at 24 weeks. Bulk RNA-Seq of the MEPs showed upregulation of Epas1 (Hif1a) and Efnb2 (Hif2a) in VhlcKO MEPs, consistent with a response to hypoxia, and genes involved in erythrocyte development, actin filament organization, and response to glucose.Additionally, histological analysis of VhlcKO spleens revealed red pulp hyperplasia and the presence of megakaryocytes, both of which are features of extramedullary hematopoiesis (EMH). EMH in the spleen was correlated with the presence of mature stress erythroid progenitors, suggesting that stress erythropoiesis is occurring to compensate for the BM microenvironmental irregularities. Our studies implicate that HIF-driven alterations in skeletal homeostasis can accelerate erythropoiesis.

overall_design: To explore the cell extrinsic effects of Vhl deletion in Dmp1+ bone cells (VhlcKO) have on megakaryocyte-erythroid progenitor cells (MEPs). We sorted MEPs from mice whole bone marrow from control and VhlcKO mice and performed gene expression profiling analysis.

first: Jennifer

last: Manilay

first: Janna

last: Emery

first: Aimy

last: Sebastian


title: Next Generation Sequencing Facilitates Quantitative Analysis of BALB/C mice skin Transcriptomes

status: Public on Jul 29 2023

city: Tianjin

first: Chunqiu

address: NO 94 Weijin Road

institute: Nankai University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived skin transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Skin mRNA profiles of 8-week old BALB/C mice were generated by deep sequencing, in triplicate.

first: Yin

last: Jiang


title: Integrated proteogenomic analysis of medulloblastoma progression (DNA methylation)

city: Goyang

first: Seong-min

last: Park

address: Ilsan-ro

country: South Korea

institute: NCC

type: Methylation profiling by genome tiling array

summary: Medulloblastoma is a malignant pediatric brain cancer, whose primary tumors are representatively classified into four molecular subgroups, WNT, SHH, Group 3 and 4. Although the molecular characters have been known well, conventional chemotherapy and radiotherapy after surgery have been used for the treatment to young children, which cause harmful side effects to their chronic health conditions. Moreover, the patients frequently suffer from recurrence and have shown poor prognosis following relapse. Here, we characterized the five layers of molecular profiles and identified potential therapeutic targets of medulloblastoma by performing multi-omics-based analysis including mass spectrometric proteome analysis. The proteome-added integrated analyses characterized new subtypes which showed specific protein functions, such as cell cycle (SHHa), EMT (G4a) and neuronal (G4b and SHHb) functions. Based on the kinase-substrate relations of phospho-proteome, we found the kinase-centered functional modularity of each subtype. These features were significantly associated with clinical features, such as recurrence and progression, and informed us the therapeutic options. Thus, we suggest that our data and analysis would support molecular basis and clinically applicable targets for precision diagnostics and therapeutics of medulloblastoma.

overall_design: DNA methylation (Illumina 850k EPIC array) data among five platform omics data of primary and recurrent medulloblastoma tumor tissues (genome, transcriptome, methylome, global proteome, phosphoproteome)

first: Kyung-Hee

last: Kim

first: Jong

middle: H

last: Yoon

first: Seung

last: Choi

first: Sung-Hye

first: Seung-Ki

middle: B


title: Circadian disruptions and time-of-day-dependent memory deficiency with long noncoding RNA expression profiling changes in Presenilin1/2 conditional knockout mice

city: Shanghai

first: Youwen

last: Si

address: North Zhongshan Road Campus: 3663 N. Zhongshan Rd., Shanghai

institute: East China Normal University

summary:
Alzheimer’s disease (AD) patients exhibit sleep and circadian disturbances before cognitive decline, and these disruptions worsen with disease severity. However, the molecular mechanisms of sleep and circadian disruptions in AD patients are poorly understood.
In this study, we investigated the sleep pattern and circadian rhythms in Presenilin-1/2 conditional knockout mice (DKO mice). Assessment of EEG and EMG recording showed that DKO mice exhibit sleep disorders from 2 months of age that worsen at the age of 6 months. The actogram of wheel running activity of DKO mice manifested movement splitting both in Dark and Light phases during the 24-hour light/dark cycle compared to WT mice. Notably, DKO mice also displayed increased NREM sleep time during the dark phase compared to WT mice at the age of two months; however, REM sleep showed no change in either WT or DKO littermates in the dark phase. When sleep and wakefulness were examined at the age of 6 months, the DKO mice showed increased wakefulness time and decreased total time spent in NREM and REM sleep. Analysis of the circadian modulation of memory revealed that the recall for contextual fear memory trained at ZT2 in WT mice was greater at ZT2 than at ZT14; however, the DKO mice had the same freezing responses with respect to both ZT2 and ZT14.
Long noncoding RNAs (lncRNAs) are typically defined as transcripts longer than 200 nucleotides, and they have rhythmic expression in mammals. However, no study has investigated rhythmic lncRNA expression in Alzheimer’s disease so we applied RNA-seq technology to profile the expression of lncRNAs in the hippocampus of DKO mice in the light (resting) phase and dark (active) phase. Furthermore, we performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the biological process, cell component and molecular function of these differentially expressed lncRNAs (DE-lncRNAs).
These results provide a useful resource for studying lncRNAs in circadian disruptions in Alzheimer’s disease.

overall_design: Mice were deeply anesthetized with sodium pentobarbital (30 mg/kg) and sacrificed at 9 a.m. or 9 p.m. The hippocampal tissues were rapidly removed on ice and then transported into liquid nitrogen followed by storage at -80℃ prior to RNA extraction. RNA extraction and RNA-seq were performed by Shanghai OE Biotech Co., Ltd.

first: Bo

last: Meng


title: To investigate the role of CXCL4 in activation of macrophages in vitro and in vivo

city: New York

first: David

last: Oliver

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: CXCL4 activates myeloid cells and augments endosomal TLR responses contributing to the pathogenesis of inflammatory and fibrotic diseases. However, the underlying mechanisms are not well defined because the receptor(s) that mediates CXCL4 inflammatory responses is not known and downstream signaling pathways leading to gene induction are not well characterized. Here we report that CXCL4 activates inflammatory and tissue repair/fibrotic gene expression in human primary macrophages ex vivo and regulates macrophage skin infiltration and promotes skin wound healing in vivo.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In vitro experiment, human CD14+ monocytes were harvested from PBMCs and cultured with 20 ng/ml M-CSF overnight. The cells were then stimulated with 10 ug/ml CXCL4 for 1 h and 3 h. The cells were then harvested for RNA-seq. In vivo experiment, skin wound from WT littermates and Cxcl4-/- mice were harvested. Two to three wounds in each genotype were pooled together and digested. Then macrophages in the cell suspension were sorted based on Ly6C and F4/80 expression. The sorted cells were used for RNA-seq to investigate how CXCL4 affect macrophage activation in vivo.

first: Chao

last: Yang

first: Ruoxi

last: Yuan

first: Max

last: Chao

first: Franck

last: Barrat

first: Lionel

last: Ivashkiv


title: RNA-Seq analyses in bta-miR-484 transfected adipocyte

city: Yinchuan

first: Mengli

address: No. 489, Helan Mountain West Road, Xixia District, Yinchuan City, Ningxia

institute: Ningxia University

summary: To elucidate the role of bta-miR-484 in adipocytes. we compared expression profiles of mRNAs in control and bta-miR-484 overexpressed adipocytes by RNA se-quencing. A total of 51 up-regulated genes and 77 down-regulated genes were detected in adipocytes overexpressing bta-miR-484. GO annotation showed that differ-entially expressed genes (DEGs） enrichment positive regulation of glycogen biosynthetic process, positive regulation of glucose import and other biological processes. COG classification found that DEGs are rich in Amino acid transport and metabolism, Posttranslational modification, protein turnover, chaperones, Secondary metabolites bio-synthesis, transport and catabolism, General function prediction only, Signal transduc-tion mechanisms, and other items. KEGG enrichment analysis showed that DEGs were enriched in apoptosis, AMPK signaling pathway, calcium signaling pathway, Ras signaling pathway, MAPK signaling pathway, Wnt signaling pathway, PI3K-Akt signaling pathway, adipocyto-kine signaling pathway, insulin secretion , PPAR signaling pathway, etc.

overall_design: Adipocytes were isolated from bovine subcutaneous fat. One group was transfected with bta-miR-484 agomir, and the other group was transfected with bta-miR-484 agomir NC. Adipocytes transfected for 48h were collected for RNA extraction and analysis.

first: Xiaoqian

last: Gao

first: Chunli

last: Hu

first: Shuzhe

last: Wang

first: Hui

last: Sheng

first: Yun

last: Ma


title: Tiam1 methylation by NSD2 promotes Rac1 signaling activation and cancer metastasis II

city: Wuhan

first: da

last: song

state: Hubei

address: Jiefang Avenue 1095

department: tongji hospital

institute: huazhong university of science and technology

summary: Metastasis is the key cause of failure of cancer therapy or mortality, but targeting metastatic seeding and colonization remains an unresolved challenge. Here, we report a novel molecular event in cancer metastasis mediated by NSD2/Rac1 signaling and provide a detailed mechanistic investigation of cancer metastasis. We found that NSD2, a histone methyltransferase responsible for di-methylating histone 3 at lysine 36, was overexpressed in metastatic tumors, and overexpressed NSD2 enhanced tumor metastasis both in vitro and in vivo. We further investigated that NSD2 promoted tumor metastasis by activating the Rac1 signaling pathway. Mechanistically, NSD2 methylated Tiam1, a guanine nucleotide exchange factor that facilitates GDP-Rac1 to GTP-Rac1 transition at K724. We demonstrated that Tiam1 K724 methylation plays a crucial role in Tiam1 activation and GDP-Rac1 to GTP-Rac1 transition. Specifically, we identified that Tiam1 K724 methylation could be a predictive factor in cancer prognosis, and we demonstrated that pharmacological blocking of Tiam1 K724 methylation by employing a transmembrane peptide inhibited tumor metastasis both in vitro and in vivo. Thus, NSD2-methylated Tiam1 promoted Rac1 signaling activation and cancer metastasis, which might provide novel insights into tumor metastasis inhibition.

overall_design: To explore which key genes are involved in tumor metastasis, we performed RNA-seq screening in paired primary and liver metastasis specimens of colon cancer (CRC), CRC cell line SW620, and specific liver metastasis cell line SW620L1

first: Da

last: Song

first: Fuqing

first: Junbo

first: Guihua


title: LH/hCG regulation of circular RNA in mural granulosa cells during the periovulatory period in mice

status: Public on Jul 28 2023

city: Kansas city

first: praveen Chakravarthi

last: Veera raghavulu

state: Kansas

address: 3915 Booth Street, Apt 10

department: Cell Biology and Physiology

institute: University of Kansas Medical Center

summary:
To investigate the role of circular RNA in the granulosa cells at two different stages of gonadotropin stimulation
RNA was isolated from ovarian granulosa cells followed by highthroughput sequencing and circRNA anlaysis

overall_design: Granulosa cells were isolated 46 hours after PMSG injection and 4h after hCG injection (PMSG primed mice) were used for RNA isolation and high through put sequencing

first: Wei

last: Ting

first: Praveen

last: Veera Raghavulu

first: Lane

last: Christenson


title: Transcriptional response of USA300 MRSA to coculture with EGM139 Desemzia incerta

city: Philadelphia

first: Monica

last: Wei

address: 421 Curie Blvd, BRB II/III 1046

department: Department of Dermatology

institute: University of Pennsylvania

summary: We wished to examine the effect that coculture with Desemzia incerta  would have on the  S. aureus transcriptional profile. We have previously shown D. incerta to have antimicrobial activity against S. aureus.  We used a transwell coculture system to separate the two bacterial cultures.  Transcriptional profiling revealed downregulated of genes in the arc operon, the pur operon, the mnh family proteins, and cap family proteins and upregulations in the arg operon and the ahp opeorn.  Subsequent biological follow-up revealed decrease in S. aureus  biofiom formation after D. incerta co-culture.

overall_design: EGM139 D. incerta and USA300 Rosenbach MRSA were cocultured in a Corning 12 well transwell system as described in Wei et al.  S. aureus RNA was extracted from the lower well using the ZymoResearch DirecZol RNA-Purification Kit.  Sequencing was performed by SeqCenter.  4 replicates of S. aureus cocultured with D. incerta or TSB control were used

first: Simon

last: Knight

first: Elizabeth

last: Grice


title: Production of highly uniform midbrain organoids from human pluripotent stem cells

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

institute: KIST (Korea Institute of Science and Technology)

summary: Brain organoids have been considered as an advanced platform for in vitro disease modeling and drug screening, but numerous roadblocks exist, such as lack of large-scale production technology and lengthy protocols with multiple manipulation steps, impeding the industrial translation of brain organoid technology. Here we describe the high-speed and large-scale production of midbrain organoids using a high-throughput screening-compatible platform within 30 days. Micro midbrain organoids (µMOs) exhibit a highly uniform morphology and gene expression pattern with minimal variability. Notably, µMOs show dramatically accelerated maturation, resulting in the generation of functional µMOs within only 30 days of differentiation. Furthermore, individual µMOs display highly consistent responsiveness to neurotoxin, suggesting their usefulness as an in vitro high-throughput drug toxicity screening platform. Collectively, our data indicates that µMO technology could represent an advanced and robust platform for in vitro disease modeling and drug screening for human neuronal diseases.

overall_design: To establisj high-speed and large-scale production method of midbrain organoids from hPSCs, we have throughly set up a novel methods for producing highly uniform midbrain organoids, namely micro midbrain organoids, from hPSC.

first: Xuerui

last: Yao

first: Ji

last: Kang

first: Kee-Pyo

last: Kim

first: Hyogeun

last: Shin

first: Zhe-Long

last: Jin

first: Hao

last: Guo

first: Yong-Nan

last: Xu

first: Ying-Hua

last: Li

first: Sai

last: Hali

first: Jeongwoo

last: Kwon

first: Hyeonwoo

last: La

first: Yong-June

first: Lin

first: Kwonho

last: Hong

first: Qilong

last: Cao

first: Il-Joo

last: Cho

first: Nam-Hyung

first: Dong

last: Han


title: Serological microRNAs as biomarkers for the diagnosis of adolescent tuberculosis infection in pleura

city: Foshan

first: He

middle: Yan

last: Bin

state: GUANGDONG

address: Sino-European Center A, 2 Lingnan Avenue South, Shunde, Foshan, Guangdong, China

institute: BCBIO

summary: We used human miRNA arrays to explore the miRNA expression profile in pulmonary tuberculosis patients (PTB), pulmonary with pleural tuberculosis patients (PPLTB) and non-tuberculous pleurisy patients (NTP).

overall_design: Biological replicates, PPLTB:4 patients PBMC sample, PTB : 4 patients PBMC samples. NTP: 4 patients PBMC sample.

first: Yanbin

last: He

first: Yu

last: Chen


title: CD47 promotes peripheral T cell survival by preventing dendritic cell–mediated T cell necroptosis

city: Kobe

first: Yasuyuki

last: Saito

state: Hyogo

address: 7-5-1, Kusunoki-cho, Chuo-ku

department: Biochemistry and Molecular Biology, Division of Molecular and Cellular Signaling

institute: Kobe University Graduate School of Medicine

summary: Conventional dendritic cells (cDCs) are required for peripheral T cell homeostasis in lymphoid organs, but the molecular mechanism underlying this requirement has remained unclear. We here show that T cell–specific CD47-deficient (Cd47ΔT) mice have a markedly reduced number of T cells in peripheral tissues. Direct interaction of CD47-deficient T cells with cDCs resulted in activation of the latter cells, which in turn induced necroptosis of the former cells. The deficiency and cell death of T cells in Cd47ΔT mice required expression of CD47 or its receptor SIRPα (signal regulatory protein α) on cDCs. The development of CD4+ T helper cell–dependent contact hypersensitivity and inhibition of tumor growth by cytotoxic CD8+ T cells were both markedly impaired in Cd47ΔT mice. CD47 on T cells thus likely prevents their necroptotic cell death initiated by cDCs and thereby promotes T cell survival and function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T cells and cDC2s isolated from spleen of Cd47f/f mice and Cd47ΔT mice.

first: Satomi

last: Komori

first: Taichi

last: Nishimura

first: Datu

last: Respatika

first: Hitomi

last: Endoh

first: Hiroki

last: Yoshida

first: Risa

last: Sugihara

first: Rie

last: Iida-Norita

first: Tania

last: Afroj

first: Tomoko

last: Takai

first: Okechi

middle: S

last: Oduori

first: Eriko

last: Nitta

first: Takenori

last: Kotani

first: Yoji

last: Murata

first: Yoriaki

last: Kaneko

first: Ryo

first: Hiroshi

last: Ohnishi

first: Takashi

last: Matozaki


title: RNA externalized by neutrophil extracellular traps promotes inflammatory pathways in endothelial cells

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Abstract.  Objectives: Neutrophil extracellular traps (NETs) are extracellular lattices composed of nucleic material bound to neutrophil granule proteins. NETs may play pathogenic roles in development and severity of autoimmune diseases such as systemic lupus erythematosus (SLE), at least in part, through induction of type I interferon (IFN) responses via externalization of oxidized immunostimulatory DNA. A distinct subset of SLE proinflammatory neutrophils (low density granulocytes; LDGs) displays enhanced ability to form proinflammatory NETs that damage the vasculature.  We assessed whether NET-bound RNA can contribute to inflammatory responses in endothelial cells and the pathways that mediate this effect.  Methods:  Expression of newly-synthesized RNA was quantified if healthy control and lupus NETs. The ability of endothelial cells to take up NET-bound RNA and downstream induction of type I IFN responses was quantified. RNAs present in NETs were sequenced and  specific small RNAs were tested for induction of endothelial type I IFN pathways.  Results: NETs extruded newly-synthesized RNA that was internalized by endothelial cells and this was enhanced when NET nucleic acids were oxidized, particularly in lupus LDG NETs. Internalization of NET-bound total RNA by endothelial cells was dependent on endosomal TLRs and the actin cytoskeleton and induced type I IFN stimulated genes (ISGs). This ISG induction was dependent on NET-associated miR-let7b, a small RNA expressed at higher levels in LDG NETs, which acted as a TLR7 agonist.   Conclusion:  These results highlight underappreciated roles for small RNAs externalized in NETs in the induction of proinflammatory responses in vascular cells, with implications to lupus vasculopathy.

overall_design: This dataset includes a total of 12 individual samples. This study sought to characterize and sequence small RNA in NETs from normal-dense neutrophils of SLE patients (n=5), a low-dense granulocyte from SLE (n=1), and healthy control normal-dense neutrophils (n=6).

first: L

middle: P

last: Blanco

first: X

last: Wang

first: P

last: Carlucci

first: J

middle: J

last: Torres-Ruiz

last: Romo-Tena

first: H

first: M

last: Hafner

last: Kaplan


title: Effects of BPA, BPAF, and BPS on Endochondral Ossification and on the Transcriptome of Ex Vivo Murine Limb Bud Cultures III

city: MONTRÉAL

first: Barbara

last: Hales

state: QC

address: 3655 Promenade Sir-William-Osler

department: Pharmacology and Therapeutics

institute: McGill University

summary: We report the results of treatment of embryonic limbs with bisphenol S. RNA sequencing was performed to measure differential expression as a result of exposure to BPS compared to DMSO treated control limbs.

overall_design: Forelimb buds were collected from gestation day 13 CD1 mouse embryos and were cultured for 3, 24, or 48 hours in the presence of either vehicle (DMSO), 10 μM, or 50 μM BPS; n = 5.

first: Bernard

last: Robaire

first: Lama

last: Iskandarani

first: Tessa

last: McHattie


title: Effects of BPA, BPAF, and BPS on Endochondral Ossification and on the Transcriptome of Ex Vivo Murine Limb Bud Cultures II

summary: We report the results of treatment of embryonic limbs with bisphenol AF. RNA sequencing was performed to measure differential expression as a result of exposure to BPAF compared to DMSO treated control limbs.

overall_design: Forelimb buds were collected from gestation day 13 CD1 mouse embryos and were cultured for 3, 24, or 48 hours in the presence of either vehicle (DMSO), 1 μM, or 5 μM BPAF; n = 5.


title: Skeletal muscle transcriptional adaptions to hypoxia and maximal exercise

city: Montreal

first: R. Thomas

last: Jagoe

state: Quebec

address: Jewish General Hospital, 3755 Cote Ste Catherine

summary: Hypoxic conditions and maximal exercise provide related but distinct energetic stresses for muscle tissue and induce different adaptations in skeletal muscle in mammals.  High swim performance fish, including Danio Rerio (Zebrafish), are well-able to tolerate both hypoxia and fast swimming.  Expression profiling was performed using microarrays to compare and contrast the adaptations to sustained hypoxia and repeated near maximal exercise in skeletal muscle of adult wild-type Zebrafish.

overall_design: Four conditions were studied: control (a) normoxia  (20kPa O2) + spontaneous swimming; (b) normoxia (20kPa O2) and high swim exercise (35 cm/sec) for 6hrs per 24 hrs; (c) hypoxia (6kPa O2) +  high swim exercise (30 cm/sec) for 6hrs per 24hrs; (d) hypoxia (4kPa O2) + low swim exercise (7 cm/s).  Fish were kept under test conditions for 5 days in a shoal of up to 8.  Total RNA was extracted from post-anal muscle block from each fish and equal quantities of high-quality RNA from 2-3 fish from each experiment were pooled.  16 pooled samples were formed and applied to separate arrays representing 4 independent experimental replicates of each of the 4 experimental conditions.

first: R


title: Effect of RPS3 Serine 149 mutation on gene expression in hiPSC-derived cardiomyocytes during Ang II administration

first: Saiyang

last: Xie

address: Jiefang Road 238

institute: Wuhan university

summary: Angiotensin II (Ang II) treatment contributes to hypertrophic growth and mitochondrial dysfunction in hiPSC-derived cardiomyocytes. Here, we report enhanced RPS3 phosphorylation at serine 149 in nuclear compartment and abnormal mitochondrial biogenesis during Ang II incubation. Furthermore, RPS3 S149 mutation attenuated Ang II induced cardiomyocyte hypertrophy and improved mitochondrial biogenesis and dysfunction. Mechanistically, RPS3 Ser149 mutation promoted mitochondrial RNA stabilization and blunt Ang II induced mitochodnrial RNA alternative splicing for degradation, by which RPS3 dephosphorylation restored mitochondrial complex assembly in cardiomyocytes.

overall_design: To evaluate function of RPS3 Serine 149 mutation in Ang II induced cardiomyocyte hypertrophy, we generated hiPSC with or without RPS3 serine 149 mutation and induced hiPSC to differentiate into cardiomyosytes following Ang II treatment.

first: Qizhu

last: Tang


title: Loss of TP53 cooperates with c-MET overexpression to drive hepatocarcinogenesis

city: Xi'an

first: Yi

last: Zhou

state: Shaanxi

address: 277# Yanta West Road

institute: The First Affiliated Hospital of Xi'an Jiaotong university

summary: We found that concomitant deletion of Trp53 and overexpression of c-MET (c-MET/sgp53) in the mouse liver led to HCC formation in vivo.  Subsequently, a stably passaged cell line derived from a c-MET/sgp53 HCC were generated. We then performed gene expression profiling analysis using data obtained from RNA-seq of the c-MET/sgp53 HCC cell line. Wild-type FVB/N mouse liver were used as control.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the mouse HCC cell line (derived from c-MET/sgp53 mouse HCC) and wild-type FVB/N mouse liver.

first: Guofei

last: Cui

first: Hongwei

last: Xu

first: Doris

last: Yang

first: Joanne

last: Chu

first: Zheng

last: Zhang

first: Lihui

first: Jingxiao

first: Meijuan

last: Wan

first: Diego

middle: F

last: Calvisi

first: Shumei

last: Lin

first: Xin

last: Chen

first: Haichuan


title: Effects of BPA, BPAF, and BPS on Endochondral Ossification and on the Transcriptome of Ex Vivo Murine Limb Bud Cultures I

first: Barbara

last: Hales

summary: We report the results of treatment of embryonic limbs with bisphenols A. RNA sequencing was performed to measure differential expression as a result of exposure compared to DMSO treated control limbs.

overall_design: Forelimb buds were collected from gestation day 13 CD1 mouse embryos and were cultured for 3, 24, or 48 hours in the presence of either vehicle (DMSO) or, 10 μM, or 50 μM BPA; n = 5.

first: Bernard

first: Lama

first: Tessa


title: Microarray expression data from bone marrow monocytes and myeloid progenitors

city: St. Louis

first: Kevin

middle: William

last: O'Connor

state: MO

address: 4925 Children's Place

department: Pathology and Immunology

institute: Washington University in St. Louis

summary:
Ly6Clo monocytes are a myeloid subset that specializes in the surveillance of vascular endothelium.  Ly6Clo monocytes have been shown to derive from Ly6Chi monocytes.  Notch2 signaling has been implicated as a trigger for Ly6Clo monocyte development, but the basis for this effect is unclear.  Here, we examined the impact of Notch2 signaling of myeloid progenitors on the development of Ly6Clo monocytes in vitro.  Notch2 signaling induced by delta-like ligand 1 (DLL1) efficiently induced the transition of Ly6Chi TremL4– monocytes into Ly6Clo TremL4+ monocytes.  We further discovered two additional transcriptional requirements for development of Ly6Clo monocytes.  Deletion of Bcl6 from myeloid progenitors abrogated development of Ly6Clo monocyte development.  IRF2 was also required for Ly6Clo monocyte development in a cell-intrinsic manner.  DLL1-induced in vitro transition into Ly6Clo TremL4+ monocytes required IRF2 but unexpectedly could occur in the absence of Nur77 or Bcl6.  These results imply a transcriptional hierarchy for these factors in controlling Ly6Clo monocyte development.
This experiment compare RNA expression profiles between nonclassical monocytes and various cell types involved in their development.

overall_design: Monocyte-dendritic cell progenitors, common dendritic cell progenitors, common monocyte progenitors, classical monocytes, and nonclassical monocytes were collected from the bone marrow of WT C57Bl/6 mice and sorted to >95% purity on a FacsAria Fusion.

first: Carlos

middle: G

last: Briseno


title: Single-cell RNAseq of mesenteric adipose tissue from Crohn's disease patients and healthy controls

city: Guangzhou

first: Fengfei

last: Wu

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District, Guangzhou, Guangdong, China

department: Department of Gastroenterology

institute: Nanfang   Hospital, Southern Medical University

summary: As a hallmark of Crohn's disease (CD)，creeping fat (CF) is intimately related to intestinal fibrosis and postoperative recurrence. It is defined as expansion of mesenteric adipose tissue envelops the diseased intestinal segment. Compared with the healthy controls, CF has enriched functions related to adipogenesis and immune response.

overall_design: Single-cell RNA-seq analysis of stromal vascular fraction (SVF) isolated from the mesenteric fat tissue (MAT) of patients undergoing bowel resection. Creeping fat from Crohn's disease patients (n=6), CD-MAT from the same patients (n=3) and healthy MAT from ileal controls (n=2).

first: Fangting

first: Fang

first: Lan

last: Bai


title: MeVa2.1.dOVA is a novel immune-refractory cell line to study tumor immune resistance

city: Amsterdam

first: PETROS

last: DIMITRIADIS

state: Noord-Holland

address: Plesmanlaan 121

institute: NETHERLANDS CANCER INSTITUTE - NKI

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

overall_design: Refer to individual Series


title: Transcriptome analysis of kidneys of cisplatin (CP)-induced AKI model

city: Jinhua

first: Weiqiang

state: Zhejiang

address: Shangcheng street N1

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

summary: In the cisplatin (CP)-induced AKI model group, the mice were administered CP and DXZ.

overall_design: In the cisplatin (CP)-induced AKI model group, the mice (6-8-week male C57BL/6J mice) were administered CP (20 mg/kg) via the tail vein.  DXZ (40 mg/kg) was administered via the tail vein 30 minutes prior to and every 24 hours after CP injection for 3 days. RNA-Seq detected  different expression gene that were differentially expressed in the two groups.


title: The genome-wide targeting of H3K18la in H1299 cells

city: Shijiazhuang

first: Lingxiao

last: Xing

state: Hebei

address: No.361 East Zhongshan Road

institute: Hebei Medical University

summary: L-lactate was reported as a precursor that can label and stimulate histone lysine-N-L-lactylation (Kla), which represents a new epigenetic mark affecting gene expression directly via histone PTMs under conditions of high glycolysis, such as the Warburg effect. To investigate the genome-wide targeting of H3K18la, we performed ChIP-seq in H1299 cells using anti-H3K18la antibody. 50.6% of the H3K18la binding sites displayed enrichment close to -1kb promoter of genes.  More importantly, our ChIP-seq data showed that H3K18la is enriched in many genes that related with replication processes, highlighted the importance of histone Kla involved in DNA replication.

overall_design: Human NSCLC cell line H1299, including anti-H3K18la and IgG group.


title: PU.1 enforces quiescence and limits hematopoietic stem cell expansion during inflammatory stress

status: Public on Jul 27 2023

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: Hematopoietic stem cells (HSCs) are capable of entering the cell cycle to replenish the blood system in response to inflammatory cues; however, excessive proliferation in response to chronic inflammation can lead to either HSC attrition or expansion. The mechanism(s) that limit HSC proliferation and expansion triggered by inflammatory signals are poorly defined. Here, we show that long-term HSCs (HSCLT) rapidly repress protein synthesis and cell cycle genes following treatment with the proinflammatory cytokine interleukin (IL)-1. This gene program is associated with activation of the transcription factor PU.1 and direct PU.1 binding at repressed target genes. Notably, PU.1 is required to repress cell cycle and protein synthesis genes, and IL-1 exposure triggers aberrant protein synthesis and cell cycle activity in PU.1-deficient HSCs. These features are associated with expansion of phenotypic PU.1-deficient HSCs. Thus, we identify a PU.1-dependent mechanism triggered by innate immune stimulation that limits HSC proliferation and pool size. These findings provide insight into how HSCs maintain homeostasis during inflammatory stress.

overall_design: ChIP-seq for PU.1 in LSK Flk2- CD150+ HSPC with whole cell extract controls

first: Robert

last: Welner

first: Eric

middle: M

last: Pietras


title: Widespread priming of transcriptional regulatory elements by incipient accessibility or Pol II pause in early embryos of the sea urchin Strongylocentrotus purpuratus

city: Staten Island

first: Cesar

last: Arenas-Mena

address: 2800 Victory Boulevard

department: Biology

institute: CSI CUNY


title: AVEN is an indirectly druggable mediator of neuroblastoma cell tumorigenicity and chemotherapy resistance

city: Berlin

first: Hedwig

last: Deubzer

address: Augustenburger Platz 1

institute: Charite - University Hospital Berlin


title: Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

type: Methylation profiling by high throughput sequencing

summary: The molecular mechanisms controlling the transition from meiotic arrest (germinal vesicle stage) to meiotic resumption (germinal vesicle breakdown stage) in mammalian oocytes have not been fully elucidated. Single-cell omics technology provides a new opportunity to decipher the early molecular events of oocyte maturation in mammals. Here we focused on analyzing oocytes that are collected from antral follicles of porcine puberty ovary. We used single-cell M&T-seq technology to analyze the nuclear DNA methylome and cytoplasmic transcriptome in parallel for 62 oocytes. We developed a package of pipelines for single-cell methylomics analysis, namely methyConcerto, to specifically and comprehensively characterize the methylation state and allele-specific methylation events for a single cell. We also performed 10X Genomics single-cell transcriptomic analyses to explore the bi-directional cell-cell communications within antral follicles. We characterized the gene expression and DNA methylation programs of individual oocytes in porcine antral follicle, thereby enabled defining two distinct types of oocytes, one of which is significantly more poised for maturation. Significantly differentially expressed or allele-specifically methylated genes were enriched in “RNA metabolism”, “oocyte meiosis” important signaling pathways, e.g., HIF-1/Ras/mTOR/Phospholipase D/ErbB signaling pathways etc. These results are in concert with the cellular communication results. We further confirmed Insulin Receptor Substrate-1 (IRS-1) in insulin signaling pathway is a key regulator of germinal vesicle stage oocyte maturation by in vitro maturation experiments. Our study provides new insights into the regulatory mechanisms between meiotic arrest and meiotic resumption in mammalian oocytes. We also provide a new analytical package for future single-cell methylomics study.

overall_design: Here, we analyzed oocytes that are collected from five antral follicular stages of pubertal ovaries. We used single-cell M&T-seq technology that analyze the nuclear DNA methylome and cytoplasmic transcriptome in parallel for 62 oocytes. We also performed scRNA-seq of somatic cells within antral follicles, to explore the bi-directional interactions and reveal the role of granulosa cells in oocyte maturation. At last, in vitro maturation experiments were performed to verify the key regulators in oocyte maturation.

first: Xiaolong

last: Yuan

first: Yance

last: Feng

first: Yuhan

last: Tian

first: Junwen

last: Wang

first: Yao

last: Jiang

first: Dou

last: He

first: Jiaqi

last: Li

first: Fei


title: AVEN is an indirectly druggable mediator of neuroblastoma cell tumorigenicity and chemotherapy resistance [microarray]

summary: Approximately half of children diagnosed with neuroblastoma have aggressive high-risk disease, against which current multimodal therapy has little success. New targets for therapeutic intervention are urgently needed. In a systems approach, we combined time-resolved mRNA-Seq with miRNA profiling in a model of neuroblastoma differentiation treated with or without the clinically approved histone deacetylase inhibitor, panobinostat. Treatment most strongly regulated miR-630, which strongly downregulated AVEN, an inhibitor of apoptosis. Here we characterized AVEN for the first time in neuroblastoma pathogenesis, disclosed its epigenetic regulation and discovered correlations between AVEN expression and resistance to chemotherapy. High-level AVEN expression in 649 primary neuroblastomas negatively correlated with patient survival. Stably enforcing AVEN expression in BE(2)-C cells markedly promoted growth as subcutaneous xenografts in mice, while CRISP/Cas9-mediated AVEN knockout in BE(2)-C cells substantially reduced xenograft growth and enhances the efficacy of systemic doxorubicin treatment. Cell-based assays, flow cytometric cell cycle analyses and SILAC experiments demonstrate that AVEN is required for neuroblastoma proliferation.

overall_design: Panobinostat induced miRNA gene expression in human neuroblastoma BE(2)-C cells, treated with 5 nM, 10 nM or 15 nM for 24 h. Two independent experiments were performed

first: Sebastian

last: Pfeil

first: Inás

last: Sahly

first: Annika

last: Winkler

last: Sprüssel

first: Jasmin

last: Wuenschel

first: Daniela

last: Tiburtius

first: Matthias

last: Ziehm

first: Christoph

last: Bartenhagen

first: Patrick

last: Hundsdörfer

last: Selbach

first: Angelika

last: Eggert

first: Marco

last: Lodrini

middle: E


first: Epigenomics

last: Gao

first: Xiaolong

last: Yuan

last: Chen

first: Yance

last: Feng

last: Tian


title: Total RNA from cell lines (JurkatLAG+PD1+ and Raji-PDL1)  treated with anti-PD1 antibody (MK3475) and/ or anti-LAG3  antibody (MK4280) was sequenced.

city: South San Fransisco

first: Shree

last: Bhagwat

address: 213 E Grand Ave

institute: Merck & Co., Inc., Kenilworth, NJ, USA

summary: A previously established bioassay using Jurkat cells overexpressing PD1 and Lag3 allowed for assessment of simultaneous blockade of PD1 and LAG3 pathways in an in-vitro setting and demonstrated that an antibody cocktail increased IL-2 levels 5-fold better than single agent treatment. To gain understanding of signal transduction events RNA-Seq analysis of cell pellets individually treated with LAG3 or PD1 antibodies was used to reveal modest immune activation however, 5-fold more genes were upregulated upon combination treatment. There were increases in costimulatory genes like CD28, CD5, CD6 as well as other intracellular signaling molecules like LCP2 and ITK. Given the role of ERK in immune activation of T cells, pERK levels of Jurkat cells in the assay were evaluated, indicating that ERK phosphorylation was impacted on PD1 and LAG3 engagement with their ligands and this could be reversed by antibody blockade. A small molecule phosphatase inhibitor NSC87877, when combined with the PD1 antibody, could phenocopy the effect of combining PD1 and LAG3 blocking antibodies. CD28 has a recognized role in PD1 signaling but the impact on LAG3 signaling remains unknown. CD28 knockout cells demonstrated an overall muted IL-2 response but retained combination benefit in terms of IL-2 production in the context of LAG3 and PD1 co-blockade versus individual antibody treatments. Taken together, these observations provide new insights on the impact of LAG3 and PD1 co-blockade and provides additional support for ongoing immunotherapy clinical trials that combine PD1 and LAG3 antibodies.

overall_design: Total RNA from  the co-culture assay (JurkatLAG+PD1+ and Raji-PDL1)  treated with anti-PD1 antibody (MK3475) and/ or anti-LAG3  antibody (MK4280) was sequenced.

first: Bhagyashree

first: Aarron

last: Willingham

first: Rene

last: de Waal Malefyt


title: Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation [ATAC-seq]

first: Cesar

last: Arenas-Mena

summary: Transcriptional regulatory elements (TREs) are the primary nodes of the gene regulatory networks that control development.   TREs are identified by PRO-seq and their accessibility by ATAC-seq during sea urchin embryonic development and differentiation.  Our analysis identifies surprisingly early accessibility in 4-cell cleavage embryo TREs that is not necessarily followed by subsequent transcription, and an excess of ATAC-seq peaks transcriptionally disengaged during the stages analyzed.  Embryonic accessibility shifts are driven by transcriptionally engaged TREs, and PRO-seq transcriptional differences at TREs provide more contrast among embryonic stages than ATAC-seq accessibility differences.  TRE accessibility reaches a maximum around the 20-hour late blastula, which coincides with major embryo regionalizations. At the same time, a large number of distal TREs become transcriptionally disengaged, in support of an early Pol II primed model for developmental gene regulation that eventually resolves in transcriptional activation or silencing.  A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during early embryogenesis.

overall_design: Chromatin accesibility during early embryogenesis is characterized by ATAC-seq or OmniATAC and transcriptional engagement by PRO-seq or qPROseq. All reads are mapped to the Sp5.0 version of the Strongylocentrotus purpuratus genome.


title: Acute mental tress-induced modulation of aortic endothelial cells in mice

city: Munich

first: Hendrik

last: Sager

address: Lazarettstr. 36

department: Klinik für Herz- und Kreislauferkrankungen

institute: Deutsches Herzzentrum München

summary: Mental stress is a substantial contributor to human disease initiation and progression, including cardiovascular pathologies. However, the underlying mechanisms remain largely unclear. Here, we show in mice that acute mental stress enhances influx of leukocytes into atherosclerotic plaques through modulation of endothelial cells. Specifically, acute stress increases adhesion molecule expression and chemokines release through locally derived norepinephrine.

overall_design: Here, we tested whether acute mental stress activates endothelial cells and consequently promotes influx of leukocytes in mice. We applied acute mental stress to ApoE mice for each 3 h on 3 consecutive days and excised aortae afterwards. To get a broader understanding which phenotypic changes endothelial cells undergo in response to acute stress, we FACS (fluorescence-activated cell sorting) isolated aortic endothelial cells from stressed vs. non-stressed mice and subjected them to RNA sequencing.

first: Julia

last: Hinterdobler


title: Genome-wide binding sites of MCM6 in Plasmodium falciparum

city: New Delhi

first: Shashank

last: Shekhar

state: New Delhi

address: JNU Campus

department: Special Centre for Molecular Medicine

country: India

institute: Jawaharlal Nehru University

summary: Genome-wide ChIP-sequencing analysis of PfMCM6 was carried out in trophozoite stage parasites using PfMCM6 antibodies. We have observed that PfMCM6 is highly enriched at the exon regions. Moreover, PfMCM6 was also found in promoter-TSS, transcription termination site (TTS), and intergenic regions in minimal proportion. This study shed some light on PfMCM6 binding sites in Plasmodium falciparum genome.

overall_design: Examination of PfMCM6 binding sites in trophozoite stage of Plasmodium falciparum.

first: Suman

last: Kumar Dhar

first: A

last: Krishnamachari

first: Sunita

last: Verma


title: Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity [ChIP-seq]

city: London

first: Sara

last: Rohban

state: London

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: To investigate the role of catalytic subunit of the Integrator complex, INTS11, during the transcription cycle, we established U2OS cell line in which INTS11 has been knock down by siRNA.

overall_design: We performed total RNAPII ChIP-seq on siCtrl- and siINTS11-transfected cells at 48h post transfection in duplicates.

first: Mahmoud

middle: R

last: Rafiee

first: Jernej

last: Ule

first: Nicholas

last: Luscombe


title: Rescue of insulin receptor condensates in insulin resistant cells

city: Cambridge

first: Charalampos

last: Lazaris

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: Insulin resistance is accompanied by chronic hyperinsulinemia and is associated with type 2 diabetes and other metabolic syndromes in a substantial portion of the population. The risk factors and features of insulin resistance have been thoroughly described but its mechanistic triggers are still under study. Here we consider a condensate model for insulin receptor (IR) function in normal conditions and when dysregulated in chronic hyperinsulinemia-induced insulin resistance. We find that IR is incorporated into liquid-like condensates at the plasma membrane, in the cytoplasm and in the nucleus of liver cells, and provide evidence for insulin-dependent IR function in condensates. Insulin stimulation promotes further incorporation of IR into these dynamic condensates in insulin sensitive cells, which form and dissolve on short, sub-minute time-scales. In contrast, insulin stimulation does not promote further incorporation of IR into condensates in insulin resistant cells, where IR molecules within condensates exhibit less dynamic behavior. Metformin treatment of insulin resistant cells rescues IR condensate dynamics and insulin responsiveness. Insulin resistant cells experience high levels of oxidative stress, which causes reduced condensate dynamics, and treatment of these cells with metformin reduces ROS levels and returns condensates to their normal dynamic behavior.  The condensate model we propose can account for features of normal and dysregulated insulin response and has implications for improved therapeutic approaches to insulin resistance.

overall_design: RNA-seq time series after treating HepG2 cells with insulin. In the case of ChIP-seq, insulin receptor ChIP-seq was performed in HepG2 cells after double fixation

first: Alessandra

last: Dall'Agnese

first: Jesse

last: Platt


title: Bcl6, Irf2 and Notch2 promote nonclassical monocyte development [RNA-seq]

first: Kevin

last: O'Connor

summary: Ly6Clo monocytes are a myeloid subset that specializes in the surveillance of vascular endothelium.  Ly6Clo monocytes have been shown to derive from Ly6Chi monocytes.  Notch2 signaling has been implicated as a trigger for Ly6Clo monocyte development, but the basis for this effect is unclear.  Here, we examined the impact of Notch2 signaling of myeloid progenitors on the development of Ly6Clo monocytes in vitro.  Notch2 signaling induced by delta-like ligand 1 (DLL1) efficiently induced the transition of Ly6Chi TremL4– monocytes into Ly6Clo TremL4+ monocytes.  We further discovered two additional transcriptional requirements for development of Ly6Clo monocytes.  Deletion of Bcl6 from myeloid progenitors abrogated development of Ly6Clo monocyte development.  IRF2 was also required for Ly6Clo monocyte development in a cell-intrinsic manner.  DLL1-induced in vitro transition into Ly6Clo TremL4+ monocytes required IRF2 but unexpectedly could occur in the absence of Nur77 or Bcl6.  These results imply a transcriptional hierarchy for these factors in controlling Ly6Clo monocyte development.

overall_design: Comparison of RNA expression in cMoPs and Ly6C+ classical monocytes which were cocultured with either OP9 or OP9-DLL1 cells for 6 hours.

middle: W

first: Kenneth

last: Murphy


title: High expression of adrenal cortisol synthases is acquired after intrauterine inflammation in periviable sheep fetuses

city: Sendai, Miyagi

first: Shinichi

last: Sato

address: 1-1 Seiryo-machi, Aoba-ku

institute: Tohoku University Hospital

summary:
To clarify the effects of endotoxin-induced intrauterine inflammation on the HPA axis of periviable sheep fetuses, fetal sheep (0.63 term) were divided into two groups: (1) the endotoxin group, in which the endotoxin was injected into the amniotic fluid and (2) the control group, in which the saline solution was injected instead.
Gene expression levels in the fetal adrenal glands of each group were analyzed by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for fetal adrenal glands in the endotoxin and control groups.

first: Shimpei

last: Watanabe

first: Yuya

last: Saito

first: Aika

last: Takanashi

first: Hideyuki

last: Ikeda

first: Yoshie

last: Sakurai

first: Shouta

last: Koshinami

first: Yusaku

last: Kumagai

first: Haruo

last: Usuda

first: Takushi

last: Hanita

first: Atsuo

last: Kikuchi

first: Masatoshi


title: A regulatory circuit for maintenance and regeneration of root patterning

city: Pozuelo de Alarcon

first: Miguel

middle: Angel

last: Moreno-Risueno

state: Madrid

department: Biotechnology

institute: Center for Plant Biotechnology and Genomics

summary: We directed expression of BLUEJAY, JACKDAW and SCARECROW through the UAS promoter in the J0571 line and performed cell sorting followed by microarray experiments to identify differentially expressed genes.

overall_design: Three independent replicates were processed for each control (J0571) and experimental (BLJ-J0571, JKD-J0571 and SCR-J0571).  Seedlings were grown for 5 days and root tips were collected. J0571 and J0571-UAS-BIRDS sorted fluorecent cells were harvested for RNA extraction.

first: Rosangela

last: Sozzani

first: Philip

middle: N

last: Benfey


title: Inhibiting LCN2 can suppress the development of NSCLC by promoting ferroptosis

city: Nanjing

first: Shuwen

last: Cheng

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

summary: Ferroptosis, a recently discovered form of regulated cell death, has been closely linked to tumor progression. However, the underlying mechanism of ferroptosis in non-small cell lung cancer (NSCLC) remains unclear. In this study, we conducted transcriptome sequencing on NSCLC samples.  Overall, our study suggests that suppressing LCN2 can effectively inhibit the development of NSCLC by promoting ferroptosis

overall_design: collect tumor and paratumor tissue of 3 NSCLC patients and perform RNA-seq.

first: Zhongjun

last: Pan


title: Bcl6, Irf2 and Notch2 promote nonclassical monocyte development

city: St. Louis

first: Kevin

last: O'Connor

institute: Washington University in St. Louis