title: Lipid metabolism genes in first trimester placenta

city: Boston

first: Perrie

last: O'Tierney-Ginn

address: 800 Washington Street

department: Mother Infant Research Institute

institute: Tufts Medical Center

summary: Placentas of obese women have low mitochondrial beta-oxidation of fatty acids (FA) and accumulate lipids in late pregnancy. This creates a lipotoxic environment, impairing placental efficiency. We assessed expression of key regulators of FA metabolism in first trimester placentas of lean and obese women. Expression of genes associated with FA oxidation (FAO; ACOX1, CPT2, AMPKα), FA uptake (LPL, LIPG, MFSD2A), FA synthesis (ACACA) and storage (PLIN2) were significantly reduced in placentas of obese compared to lean women. This effect was exacerbated in placentas of male fetuses. The PPARα pathway was enriched for placental genes impacted by obesity. These results demonstrate that obesity and hyperlipidemia impact placental FA metabolism as early as 7 weeks of pregnancy.

overall_design: First trimester placenta samples from lean (N=16) and obese (N=16) women were analyzed. Technical replicates were not included. Two samples from Lean and 3 from obese considered outliers, but .RCC files included.


title: Multiple tissue sequencing of WT and Scx-ko mice

status: Public on Oct 14 2022

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

country: China

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

summary: We used RNA sequencing and a gene knockout mice model to reveal the critical functions of Scx in multiple tissues.

overall_design: Multiple tissues of Wild type(WT) and Scx-/- limb cells derived from 3-week-old mice were sequenced using smart-seq2 based tehnique.

first: Hongwei

last: Ouyang

first: Junxin

last: Lin


title: A defect in endothelial autophagy occurs in patients with nonalcoholic steatohepatitis and promotes inflammation and fibrosis

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary:
Autophagy is a physiological process controlling endothelial homeostasis in vascular beds outside the liver. This study demonstrates that autophagy is defective in liver endothelial cells of patients with NASH and that this defect promotes liver inflammation and fibrosis at early stages of NASH, but also at advanced stages of chronic liver disease.
We used transcriptomic analysis to evaluate the global effect of autophagy deficiency in liver sinusoidal endothelial cells' (LSECs) gene expression

overall_design: LSECs were isolated from Atg5lox/lox and Atg5lox/lox;VE-cadherin-Cre mice fed a high fat diet for 2 weeks. RNA were extracted in TRIzol reagent. Microarray based whole transcriptome analysis was conducted, and Mouse ClariomS arrays were hybridized. Genes were considered significantly regulated when fold-change was ≥1.5 and uncorrected p-value ≤0.05. Hierarchical clustering was performed using hclust (R) with Euclidean distance and Ward agglomeration method.

first: Adel

last: Hammoutene

first: Louise

last: Biquard

first: Juliette

last: Lasselin

first: Marouane

last: Kheloufi

first: Marion

last: Tanguy

first: Anne-Clemence

last: Vion

first: Jules

last: Merian

first: Nathalie

last: Colnot

first: Xavier

last: Loyer

first: Alain

last: Tedgui

first: Patrice

last: Codogno

first: Sophie

last: Lotersztajn

first: Valérie

last: Paradis

first: Chantal

middle: M

last: Boulanger

first: Pierre-Emmanuel

last: Rautou


title: Endosperm and maternal-specific expression of EIN2 affects endosperm cellularization and seed size in Arabidopsis

status: Public on Oct 12 2022

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

country: USA

institute: The University of Texas at Austin

summary: Seed size is related to plant evolution and crop yield and is affected by genetic mutations, imprinting, and genome dosage. Imprinting is a widespread epigenetic phenomenon in mammals and flowering plants. ETHYLENE INSENSITIVE2 (EIN2) encodes a membrane protein that links the ethylene perception to transcriptional regulation. Interestingly, during seed development EIN2 is maternally-expressed in Arabidopsis and maize, but the role of EIN2 in seed development is unknown. Here we show that EIN2 is expressed specifically in the endosperm, and the maternal-specific EIN2 expression affects temporal regulation of endosperm cellularization. As a result, seed size increases in the genetic cross using the ein2 mutant as the maternal parent or in the ein2 mutant. The maternal-specific expression of EIN2 in the endosperm is controlled by DNA methylation but not by H3K27me3 or by ethylene and several ethylene pathway genes tested. RNA-seq analysis in the endosperm isolated by laser-capture microdissection show upregulation of many endosperm-expressed genes such as AGAMOUS-LIKEs (AGLs) in the ein2 mutant or when the maternal EIN2 allele is not expressed. EIN2 does not interact with DNA and may act through ETHYLENE INSENSITIVE3 (EIN3), a DNA binding protein present in sporophytic tissues, to activate target genes like AGLs, which in turn mediate temporal regulation of endosperm cellularization and seed size. These results provide mechanistic insights into endosperm and maternal-specific expression of EIN2 on endosperm cellularization and seed development, which could help improve seed production in plants and crops.

overall_design: Examination of transcripts (mRNA) in Arabidopsis thaliana endosperm at 6 DAP of reciprocal crosses between WT (Col-0) and ein2-5 mutant.

first: Atsumi

last: Ando

first: Ryan

middle: C

last: Kirkbride

first: Hong

last: Qiao

first: Z.

middle: J


title: Expression data from human lung epithelial A549 cells treated with DMEM containing 5.5 or 25 mM

status: Public on Oct 11 2022

city: Taipei

first: Ting-Jing

last: Shen

address: 10F, No. 250, Wu-Xing Street

country: Taiwan

institute: Taipei Medical University

summary:
Cells treated with DMEM containing 25 mM had higher cellular translation levels than that of cells treated with DMEM containing 5.5 mM .
We used microarrays to detail the global gene expression underlying hyperglycemic stress.

overall_design: A549 cells were treated with for DMEM containing 5.5 or 25 mM and then collected at 48 hours post-stimulation for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain global gene expression which related to hyperglycema. Two smaples (A549 cells treated with DMEM containing 5.5 mM glucose and A549 cells treated with DMEM containing 25 mM glucose) were analyzed for comparing the gene ecpression.

first: Jerry

last: Nien


title: DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development

status: Public on Oct 13 2022

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

type: Methylation profiling by genome tiling array

summary: To develop a better understanding of the biology underlying risk for CRC posed by germ line APC mutations we performed DNA methylation analysis of colon organoids derived from normal-appearing colons of FAP subjects (n=7) and matched healthy individuals (n=16). We identified a large number (n=358) of differentially methylated regions (DMRs) between colon organoids of FAP and healthy subjects, many of which were also identified in a comparison of tumor and normal adjacent tissue (NAT) in two independent, sporadic CRC tumor cohorts.

overall_design: Illumina EPIC array protocols were performed on 16 healthy and 7 FAP colon organoids derived from left colon at the time of colonoscopy.

first: Stephen

last: Eaton

first: Mourad

middle: W

last: Ali

first: Sarah

last: Plummer

first: Chris

middle: H

last: Dampier

first: Dan

last: Weisenberger

first: Steven

last: Powell

first: Graham

last: Casey


title: Loss of function of the nuclear envelope protein LEMD2 causes DNA damage-dependent cardiomyopathy

city: Dallas

first: Xurde

last: Menéndez Caravia

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Mutations in nuclear envelope proteins (NEPs) cause devastating genetic diseases, known as envelopathies, which primarily affect the heart and skeletal muscle. A mutation in the NEP LEMD2 causes severe cardiomyopathy in humans. However, the roles of LEMD2 in the heart and the pathological mechanisms responsible for its association with cardiac disease are unknown. To explore the mechanistic basis of this pathology, we generated mice carrying the human c.T38>G LEMD2 mutation. These mice phenocopied the human disease and developed severe dilated cardiomyopathy with extensive cardiac fibrosis leading to premature death. At the cellular level, LEMD2 mutant cardiomyocytes exhibited disorganization of the transcriptionally silent heterochromatin associated with the nuclear envelope. Moreover, mice with cardiac-specific deletion of LEMD2 also died shortly after birth due to heart abnormalities. LEMD2 mutant mice displayed aberrant cardiac gene expression and extensive DNA damage. The development of cardiac disease in both mouse models is linked to p53 activation. Together, our results reveal the essentiality of the nuclear envelope protein LEMD2 for genome stability and normal cardiac function.

overall_design: Adult and P1 hearts; different genotypes.

last: Caravia

first: Eric

middle: N

last: Olson


title: Yap1-mediated Flr1 expression reveals crosstalk between oxidative stress signaling and caffeine resistance in Saccharomyces cerevisiae

city: Seoul

first: Woo-Hyun

last: Chung

address: Samyangro 144-gil 33, Dobonggu

country: South Korea

institute: Duksung Women's University

summary: QuantSeq analysis to screen Yap1-dependent target genes for caffeine resistance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for strains: 50 mM caffeine-treated WT, yap1 deletion mutant, and Yap1 overexpression strain

first: Ji

middle: E

last: Choi

first: Seo-Hee

last: Heo


title: Multi-organ profiles of C fiber degenerated (KPCF) mice and respiratory syncytial virus (RSV)-infected KPCF mice

city: Chongqing Provence

first: Yu

last: He

address: No.136, Zhongshan 2nd Road, Yuzhong District

institute: Children's Hospital of Chongqing Medical University

summary: Stimulation of unmyelinated C-fibers is able to initiate host responses. In this study, we established the model of C fiber degenerated (KPCF) mice. KPCF mice were given  respiratory syncytial virus (RSV) infection. We aimed to figure out the role of C fibers in RSV infection.

overall_design: Lung, intestine, brain, and spleen tissues from six KCF mice (6 - 8 weeks old; three in KCF group and three in RSV-infected KCF group) were subjected to RNA sequencing

first: Zhili

last: Wang

last: Zang

first: Enmei

last: Liu


title: Multiregional single-cell transcriptomic analysis of liver cancer

city: Bethesda

first: Xin

middle: Wei

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary: Single-cell transcriptomic profiling of human liver tissues collected from hepatocellular carcinoma and intrahepatic cholangiocarcinoma patients. Samples were collected from multiple regions, including tumor core, tumor border and adjacent non-tumor tissue.

overall_design: A total of 34 samples were profiled

first: Xin-Wei


title: Breast cancer cells survive chemotherapy by activating robust, parallel programs of immune checkpoint expression

city: New Orleans

first: James

middle: G

last: Jackson

state: LA

address: 1430 Tulane

institute: Tulane

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Breast cancer cells that survive chemotherapy to cause relapse must avoid intrinsic and extrinsic mechanisms of cell death. Entry into senescence enables survival from mitotic catastrophe, apoptosis, and nutrient deprivation, but mechanisms used to evade immune mediated removal are unclear. We show here that human and mouse breast tumor cells that survive chemotherapy activate complex programs of immune modulation including clinically relevant checkpoints. scRNA-seq and cell imaging revealed distinct populations of cells in residual disease that have activated pathways related to either interferon signaling, typified by PD-L1 expression, or p53 signaling, typified by CD80 expression. In vivo, treatment of mammary tumors with chemotherapy followed by targeting of the PD-L1 and/or CD80 axes improved response, including complete eradication in some instances. Unfortunately, however, even combination strategies failed to fully eradicate the tumor in the majority of cases. Our findings reveal the formidable challenge of eliminating residual disease populated by senescent cells that express multiple redundant immune inhibitory pathways and suggest rational strategies are needed based on the specific checkpoint pathways expressed in residual disease.

overall_design: scRNA-seq of CD45-positive immune cells and CD4/8-positive T-cells, ATAC-seq of mammary tumor cells, and RNA-seq of mammary tumor cells

first: Ashkan

last: Shahbandi


title: Transcriptomic insights into the role of the spleen in a mouse model of Wiskott-Aldrich Syndrome

city: shanghai

first: george

last: yue

address: Room 4B, the 3rd Building, No. 401, Caobao Road, Xuhui District, Shanghai, China, 200233

institute: Genergy Bio-technology (Shanghai) Co., Ltd

summary:
Wiskott-Aldrich syndrome (WAS) is a rare X-linked primary immunodeficiency characterized by microthrombocytopenia, eczema, recurrent infections, and increased incidence of autoimmune disorders and malignancies. WAS is caused by mutations in the was gene, which is expressed exclusively in hematopoietic cells, and the spleen plays an important role in hematopoiesis and red blood cell clearance. However, to date, detailed comparative analyses of the spleen between WASp-deficient (WAS-KO) mice and WT mice, particularly at the transcriptomic level, have not been reported. Here, we investigated the differences in the transcriptomes of spleen tissues of 10-week-old WAS-KO mice. Comparison of the gene expression profiles of WAS-KO and WT mice revealed 1964 differentially expressed genes (DEGs). Among these genes, 996 DEGs were upregulated, and 968 were downregulated in WAS-KO mice. To determine the functions of the DEGs, GO and KEGG enrichment analyses were performed for significantly upregulated and downregulated DEGs, respectively. The results showed that the levels of cell senescence and apoptosis-related genes were increased, that the antigen processing and presentation mechanisms involved in the immune response were damaged, and that signal transduction processes were impaired in the spleens of WAS-KO mice. Thus, was gene deletion may lead to anemia and hemolysis-related disease, mainly due to increased osmotic fragility of red blood cells, low hemoglobin, increased bilirubin levels and increased serum ferritin. These results indicate that senescence and apoptosis of blood cells also play an important role in the occurrence of WAS. However, most studies have focused only on the immune response. Therefore, the interesting findings of this paper can provide a stronger theoretical basis for further study and help improve the treatment of WAS.
We performed gene expression profiling analysis using data obtained from RNA-seq of 2 different group of WT and WAS-KO mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the spleen of WT mice and WAS-KO mice(Was -/- (129S6/SvEvTac-Wastm1Sbs/J) ).

first: Fangfang

last: Liang

first: Cheng

last: Peng


title: Global and gene-specific translational regulation in Escherichia coli across different conditions

city: Beijing

first: Di

last: Zhang

address: No.5 YiHeYuan Road, Haidian District

institute: Peking University

summary: How well mRNA transcript levels represent protein abundances has been a controversial issue. Particularly across different environments, correlations between mRNA and protein exhibit remarkable variability from gene to gene. Translational regulation is likely to be one of the key factors contributing to mismatches between mRNA level and protein abundance. Here, we quantified genome-wide transcriptome and relative translation efficiency (RTE) under 12 different conditions in Escherichia coli. By quantifying the mRNA-RTE correlation both across genes and across conditions, we uncovered a diversity of gene-specific translational regulations, cooperating with transcriptional regulations, in response to carbon (C), nitrogen (N), and phosphate (P) limitations. Intriguingly, we found that many genes regulating translation are themselves subject to translational regulation, suggesting possible direct feedbacks. Furthermore, we observed that genes with similar expression patterns share similar codon usage. Utilizing a random forest model, we confirmed that codon usage contributes to condition-dependent translational regulation. These findings broaden the understanding of translational regulation under environmental changes, and provide novel strategies for the control of translation in synthetic biology.

overall_design: Ribosome profiling and RNA-seq of E. coli cells under 12 different conditions

first: Sophia

last: Li

first: Zemer

last: Gitai

first: Ned

middle: S

last: Wingreen

first: Zhiyuan


title: Single cell RNA sequencing analysis of sorted pancreatic cells from normal and tumor-bearing pancreas

city: Charleston

first: Lu

last: Han

address: 86 Jonathan Lucas St

institute: Medical University of South Carolina

summary: We generated genetically engineered mouse models where the splanchnic mesenchyme descendents are labeled with tdTomato expression. We further combined the reporter system with genetic allels mutating Kras and p53 to obtain spontaneous pancreatic ductal adenocarcinoma formation. Both normal and tumor-bearing pancreata were dissociated and sorted into major cell types based on cell-surface markers and tdTomato expression. Sorted cells were then undergone 10X single cell RNA sequencing.

overall_design: Single cell RNA sequencing of sorted normal and tumor-bearing mouse pancreata

first: Gustavo

last: Leone

first: Michael

middle: T

last: Zimmermann

first: Angela

last: Mathison


title: Decreasing Wapl dosage partially corrects transcriptome phenotypes in Nipbl-/+ embryonic mouse brain

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

summary: Cohesin rings interact with DNA and modulate expression of thousands of genes. NIPBL loads cohesin onto chromosomes and WAPL takes it off. Heterozygous mutations in NIPBL lead to a developmental disorder called Cornelia de Lange syndrome. Nipbl heterozygous mice are a good model for this disease. Mutations in WAPL were not known to cause disease or gene expression changes in mammals. Here we show dysregulation of >1000 genes in Wapl-/+embryonic mouse brains. The patterns of dysregulation are highly similar in Wapl and Nipbl heterozygotes, suggesting that Wapl mutations may cause disease in humans. Since WAPL and NIPBL have opposite effects on cohesin’s association with DNA, we asked whether a heterozygous Wapl mutation could correct phenotypes seen in Nipbl heterozygous mice. In fact, both gene expression and embryonic growth are partially corrected. Our data are consistent with the view that cohesin dynamics play a key role in regulating gene expression.

overall_design: 21 embryonic brain samples: 5 WT, 7 Wapl deltas, 3 Nipbl deltas, 6 Wapl delta; Nipbl deltas

first: Connor

last: Kean

first: Christopher

last: Tracy

first: Matthew

last: Van Winkle

first: Claudia

last: Gebert

first: Jacob

last: Noeker

first: Anne

middle: L

last: Calof

first: Arthur

middle: D

last: Lander

first: Judith

middle: A

last: Kassis

first: Karl

last: Pfeifer


title: Single-cell analysis of skeletal muscle macrophages reveals age-associated functional subpopulations

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Tissue-resident macrophages represent a group of highly responsive innate immune cells that acquire diverse functions by polarizing towards distinct subgroups. The subgroups of macrophages that reside in skeletal muscle (SKM) and their changes during aging are not fully understood. By single-cell transcriptomic analysis, we found that mouse SKM macrophages comprise two large populations, Lyve1+ and Lyve1-. Lyve1+ macrophages expressed high levels of mRNAs encoding angiogenesis and tissue repair proteins, while Lyve1- macrophages expressed high levels of mRNAs encoding proteins with functions in translation, antigen presentation, and the proinflammatory response. SKM macrophages were further classified into four functional subgroups based on the expression levels of another cell surface marker MHCII: Lyve1+/MHCII-lo (similar to alternatively activated M2), Lyve1-/MHCII-hi (similar to classically activated M1), and two new subgroups, Lyve1+/MHCII-hi and Lyve1-/MHCII-lo, all displayed strong phagocytic capacities. Flow cytometric analysis validated the presence of the four macrophage subgroups in SKM. The new subgroup Lyve1+/MHCII-hi had traits of both M2 and M1 macrophages, while the other subgroup, Lyve1-/MHCII-lo, expressed high levels of mRNAs encoding cytotoxicity proteins. In old SKM, Lyve1+/MHCII-hi macrophages were less abundant and Lyve1-/MHCII-hi macrophages were more abundant. Furthermore, complementary unsupervised classification revealed the emergence of small clusters expressing proinflammatory markers including S100a8 and S100a9 mRNAs in aged SKM. In sum, our study has identified dynamically polarized mouse SKM macrophages and a shift toward a proinflammatory status during aging.

overall_design: Resident macrophages were isolated from mouse skeletal muscle from young and old C57BL/6JN mice by FACS. Single-cell libraries were prepared with 10x Genomics and sequenced with Illumina Nova-sequencer.

first: Linda

middle: K

last: Krasniewski

first: Papiya

last: Chakraborty

first: Chang

middle: Y

last: Cui

first: Krystyna

last: Mazan-Mamczarz

last: Dunn

first: Yulan

last: Piao

first: Jinshui

last: Fan

first: Changyou

last: Shi

first: Tonya

last: Wallace

first: Cuong

last: Nguyen

first: Isabelle

last: Rathbun

first: Rachel

last: Munk

first: Dimitrios

last: Tsitsipatis

first: Payel

last: Sen

first: Luigi

last: Ferrucci

first: Myriam

last: Gorospe


title: WT vs. NKR-P1B KO

city: Halifax

first: Andrew

middle: P.

last: Makrigiannis

state: ON

address: 5850 College Street, Room 7-C

department: Microbiology/Immunology

country: Canada

institute: Dalhousie University

summary: WT vs. NKR-P1B KO

overall_design: WT vs. NKR-P1B KO


title: Myeloid cell-derived proteases produce a proinflammatory form of IL-37 that signals via IL-36 receptor engagement

city: Dublin

first: Pavel

last: Davidovich

address: College Green

department: Genetics

country: Ireland

institute: Trinity College Dublin

summary: In order to compare gene expression signatures of IL-36β and IL-37, primary human keratinocytes were incubated with activated IL-36β and K53-IL-37 for 2h.

overall_design: Cells were harvested after 2h of treatment with cytokines and comparative gene-expression analysis was performed using RNA-sequence approach

first: Graeme

last: Sullivan

first: Seamus

last: Martin


title: Mitochondrial dysfunction induces ALK5-SMAD2-mediated hypovascularization and arteriovenous malformations in mouse retinas

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Although mitochondrial activity is critical for angiogenesis, its mechanism is not entirely clear. Here, we investigate the angiogenic functions of three separate nuclear genes that encode for mitochondrial proteins, including mitochondrial transcriptional factor (TFAM), respiratory complex IV component (COX10), and a mitochondrial redox protein thioredoxin 2 (TRX2), which are responsible for distinct mitochondrial functions. We aim to investigate if mitochondrial activities regulate common endothelial cell (EC) signaling pathways during angiogenesis. The silencing of Tfam, Cox10, or Trx2 in an in vitro 3D sprouting assay attenuates EC sprouting, which correlated with reduced EC proliferation but not with ROS generation or EC apoptosis. Mice with an inducible deletion of Tfam, Cox10, or Trx2 exhibit retarded retinal vessel growth without penetration into the deep plexi at early ages (P5-P12). The three mutant mice develop arteriovenous malformations (AVM) with microaneurysm formation in the microvessels at advanced ages (P12-P30); the hypovasculature and microaneurysm phenotypes resemble that of aged human retinas and human primitive retinal vascular abnormalities such as Coats’ disease, Leber’s military aneurysms and familial exudative vitreoretinopathy. Single-cell RNA-seq analyses of retinal ECs suggest that the three mutant mice have common EC clusters with reduced gene expressions in anion transporters, actin organization, extracellular matrix, and angiogenesis. These EC clusters also have increased gene expressions in endothelial-mesenchymal transition and arterial markers, correlating with enhanced TGFbR signaling in Tfam, Cox10, or Trx2-deficient mice. Importantly, pharmacological blockade by TGFbR inhibitors attenuated retinal vessel growth retardation and AVM formation in all three mutant mice. Our study demonstrates that mitochondrial dysfunction induces TGF-b receptor-mediated arteriovenous malformations and microaneurysm formation in mouse retinas, and provide a novel model and therapeutic intervention for human primitive retinal vascular abnormalities, which are characterized by retinal vascular malformations and are associated with many pathological complications such as diabetes and hypertension that can result in vision loss.

overall_design: Single-cell transcriptome profiles of retina endothelial cells with mitochondrial gene KO

first: Jenny

last: Zhou

first: Yoshiaki

last: Tanaka

first: Sameet

last: Mehta

first: Haifeng

last: Zhang

first: Guilin

last: Wang

last: Lopez-Giraldez


title: Culture media composition influences patient-derived organoids ability to predict therapeutic response in gastrointestinal cancers

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

summary:
In this study, we have generated patient-derived organoids (PDOs) from primary and metastatic lesions of gastrointestinal cancers, including pancreatic ductal adenocarcinoma, colorectal adenocarcinoma, and cholangiocarcinoma and evaluated their ability to predict donor tumor drug response. Specifically, we examined individual PDO responses to therapeutic agents with the observed clinical responses of donor patients to the same treatments and demonstrated an approximately 80% concordance rate. Importantly, we found a profound influence of culture media in PDOs phenotypes, we observed a significant difference in response to common PDAC chemotherapies, distinct morphologies, and transcriptomes between media in the same PDOs. These studies demonstrate the important role of culture media when using PDOs to inform patient care and predict response across a spectrum of GI cancers.
We compared transcriptome data from pancreatic ductal adenocarcinoma patient-derived organoids in two media (WNT and PaTOM).

overall_design: mRNA was extracted patient-derived PDAC organoids and RNA profiles were created using Illumina HiSeq 4000.

first: Tara

last: Hogenson

first: Merhi

last: Toruner

first: Cheng

first: Martin

last: Fernandez Zapico


title: Transcriptome profiling of over-expression of GC0643 in HGC-27 cancer cells

city: Shanghai

first: Yingyan

last: Yu

address: No. 197 Ruijin Second Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: To investigate the molecular biological function of GC0643, we enforced GC0643 overexpression in HGC-27 cell lines.

overall_design: RNA-Seq was performed for cell lines with GC0643 overexpression or without on three replicates respectively.

first: Chaochun

last: Wei


title: Association of RNASET2 Gene Polymorphisms with Decreased Expression and Clinical Characteristics of Severity in Crohn’s Disease

city: Los Angeles

first: Rivkah

last: Gonsky

state: California

address: 8700 Beverly Blvd. Davis Building, Room D4062

department: Gastroenterology/IBIRI

institute: Cedars-Sinai

summary: Background & Aims Variants in the tumor necrosis factor superfamily member 15 gene (TNFSF15, also called TL1A) have been associated with risk for inflammatory bowel diseases (IBD). TL1A affects expression of multiple cytokines to promote mucosal inflammation. Little is known about the TL1A-response pathways that regulate cytokine expression. We investigated T-cell gene expression patterns to determine the mechanisms by which TL1A regulates cytokine production, and whether these associate with outcomes of patients with Crohn’s disease (CD).Methods Peripheral T cells isolated from normal donors were cultured with TL1A. We performed gene expression profile analysis, by RNA sequencing, of subsets of interferon gamma (IFNG)-producing and non-producing cells, purified by flow cytometry. Unsupervised hierarchical clustering analysis was used to identify gene expression differences between these subsets. Ribonuclease T2 gene (RNASET2) expression and methylation were assessed by quantitative trait loci analyses. Clinical characteristics of patients (complications, resistance to therapy, recurrence time) were associated with single nucleotide polymorphisms in RNASET2. We performed motif screening to identify polymorphisms that disrupt transcription factor binding sites. Levels of RNASET2 were knocked down with small interfering RNA in CD4+ T cells and the effect on protein expression was determined by proteomic analysis and cytokine production. Cell aggregation was measured by flow cytometry. ResultsWe identified 764 genes with at least a 2-fold difference in TL1A-mediated expression between IFNG-secreting and non-secreting T cells (P<1 × 10−5). Many of these genes were located near IBD susceptibility variants. RNASET2 was the only IBD risk-associated gene with greater than 5-fold downregulation in the IFNG-secreting subset. RNASET2 disease risk variants were associated with decreased expression in peripheral and mucosal tissues and DNA hypermethylation in CD patients requiring surgical intervention. RNASET2 disease risk variants were associated in CD patients with more complicated disease or resistance to therapy, defined in part by failed response to treatment, increased length of intestinal resection, shorter time to repeat surgery, and high Rutgeerts score (>2) in post-operative endoscopy. The RNASET2 variant rs2149092 was predicted to disrupt a consensus binding site for the transcription factor ETS within an enhancer region. Expression of RNASET2 correlated with expression of ETS. RNASET2 knockdown in T cells increased expression of IFNG and ICAM1 and induced T cells aggregation. A blocking antibody against LFA1, disrupting the LFA1-ICAM1 interaction, reduced T-cell production of IFNG. Conclusions We identified decreased expression of RNASET2 as a component of TL1A-mediated increase in production of IFNG and as a potential biomarker for patients with severe CD. Further study of the role of RNASET2 in regulating mucosal inflammation may lead to development of novel therapeutic targets.

overall_design: CD3+ T-cells were purified from blood from Crohn Disease patients. We performed gene expression profile analysis, by RNA sequencing, of subsets of interferon gamma (IFNG)-producing and non-producing cells, purified by flow cytometry. Unsupervised hierarchical clustering analysis was used to identify gene expression differences between these subsets.

first: Phillip

last: Fleshner

first: Richard

last: Deem

first: Eva

last: Biener-Ramanujan

first: Dalin

first: Alka

last: Potdar

first: Janine

last: Bilsborough

first: Shaohong

last: Yang

first: Dermot

middle: P

last: McGovern

first: Stephan

middle: R

last: Targan


title: RNA Sequencing of HEK293T cells expressing a Dual-specificity Aptamer that specifically increases O-GlcNAcylation on beta-catenin when EZH2 was knocked-down

first: Yi

last: Zhu

address: 511 WBSB, 725 N. Wolfe St.

department: Biological Chemistry

institute: Johns Hopkins University, School of Medicine

summary: O-GlcNAc is a dynamic post-translational modification on thousands of intracellular proteins, it regulates protein functions and is involved in many metabolic diseases. Using a dual-specificity aptamer, we targeted the O-GlcNAc transferase (OGT) to endogenous β-catenin and specifically increased O-GlcNAcylation of β-catenin. To study how O-GlcNAcylation of β-catenin regulates the transcriptome, we performed RNA sequencing on HEK293T cells expressing individual (Ctrl.) or dual-specificity aptamers. This dataset is from the control experiment in which EZH2 was knocked-down with a shRNA in all samples.

overall_design: 12 samples from 4 groups of HEK293T cells were analyzed: cells expressing Ctrl (T1 ∙ bc339) or Dual-specificity (3JB8F+12) aptamers were exposed to Wnt- or Wnt+ medium. Each group contains 3 replicates. Cells in all replicates stably expressed a shRNA that targets EZH2.

first: Gerald

last: Hart


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Tight control of cell fate choices is crucial for normal development. Here we show that lamin A/C plays a key role in chromatin organization in embryonic stem cells (ESCs), which safeguards naïve pluripotency and ensures proper cell fate choices during cardiogenesis. We find major changes in chromatin compaction and localization of cardiac genes already in Lmna−/−ESCs resulting in precocious activation of a transcriptional program promoting cardiomyocyte versus endothelial cell fate, accompanied by premature cardiomyocyte differentiation, cell cycle withdrawal, and abnormal contractility. Gata4 is activated by lamin A/C loss and Gata4 silencing or haploinsufficiency rescues the aberrant cardiovascular cell fate choices induced by lamin A/C deficiency. Importantly, we observe divergent functions of lamin A/C in naïve pluripotent stem cells and cardiomyocytes, which has distinct contributions to the transcriptional alterations of patients with LMNA-associated cardiomyopathy. Thus, disruption of lamin A/C-dependent chromatin architecture in ESCs is a primary event in LMNA loss-of-function cardiomyopathy.

overall_design: Refer to individual Series


title: Transcriptome of anthers from both the ZmCCT-active and non-transgenic control plants.

first: Wang

last: Zi

address: NO2 Yuanmingyuan West Road, Haidian

department: ational Maize Improvement Center  of China

institute: China Agricultural University

summary: To ascertain whether ZmCCT is involved in the development of anther.

overall_design: RNA sequencing (RNA-seq) was performed using anthers of ZmCCT10 transgenic and control plants spanning three anther developmental stages (S3-4, S5-6 and S7)

first: Zi

last: Wang


title: CUT&RUN Sequencing of EZH2 binding sites in HEK293T cells expressing a Dual-specificity Aptamer that specifically increases O-GlcNAcylation on beta-catenin, when beta-catein was knocked-down

summary: O-GlcNAc is a dynamic post-translational modification on thousands of intracellular proteins, it regulates protein functions and is involved in many metabolic diseases. Using a dual-specificity aptamer, we targeted the O-GlcNAc transferase (OGT) to endogenous β-catenin and specifically increased O-GlcNAcylation of β-catenin. We found that O-GlcNAc on β-catenin promoted its interaction with EZH2 regardless of the Wnt signaling status. To study how this interaction regulates the distribution of EZH2 on the genome, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) on HEK293T cells expressing individual (Ctrl.) or dual-specificity aptamers, under Wnt - and Wnt + conditions. This is a control experiment in beta-catenin knockdown cells.

overall_design: 12 samples from 4 groups of HEK293T cells were analyzed: cells expressing Ctrl (T1 ∙ bc339) or Dual-specificity (3JB8F+12) aptamers were exposed to Wnt- or Wnt+ medium. Each group contains 3 replicates. Cells in all replicates stably expressed a shRNA that targets beta-catenin.


title: Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner II

status: Public on Oct 10 2022

city: Bonn

first: Rayk

last: Behrendt

state: North Rhine-Westphalia

address: Venusberg-Campus 1, 53127 Bonn

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: Universitätsklinikum Bonn

summary:
Loss of SAMHD1 causes chronic activaiton of the MDA5/MAVS dsRNA sensing pathway, only when cGAS/STING signaling is intact.
Peritoneal macrophages from  mutant and control mice were isolated by FACS.  Total RNA was subjected to next generation mRNA sequencing.

overall_design: Rayk, Behrendt

first: Tina

last: Schumann

first: Andreas

last: Dahl

first: Mohamad

last: Mayo


title: Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner (Set II)

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


title: CUT&RUN Sequencing of EZH2 binding sites in HEK293T cells expressing a Dual-specificity Aptamer that specifically increases O-GlcNAcylation on beta-catenin when O-GlcNAc transferase was inhibited

summary: O-GlcNAc is a dynamic post-translational modification on thousands of intracellular proteins, it regulates protein functions and is involved in many metabolic diseases. Using a dual-specificity aptamer, we targeted the O-GlcNAc transferase (OGT) to endogenous β-catenin and specifically increased O-GlcNAcylation of β-catenin. We found that O-GlcNAc on β-catenin promoted its interaction with EZH2 regardless of the Wnt signaling status. To study how this interaction regulates the distribution of EZH2 on the genome, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) on HEK293T cells expressing individual (Ctrl.) or dual-specificity aptamers, under Wnt - and Wnt + conditions. This is a control experiment in which all samples were treated with the OGT inhibitor Ac5S.

overall_design: 12 samples from 4 groups of HEK293T cells were analyzed: cells expressing Ctrl (T1 ∙ bc339) or Dual-specificity (3JB8F+12) aptamers were exposed to Wnt- or Wnt+ medium. Each group contains 3 replicates. Cells in all replicates were treated with an OGT inhibitor (Ac5S).


title: Loss of tetraspanin-7 expression reduces pancreatic beta-cell exocytosis Ca2+ sensitivity but has limited effect on systemic metabolism [human]

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

summary: Background: Tetraspanin-7 (Tspan7) is an islet autoantigen involved in autoimmune type 1 diabetes and known to regulate beta-cell L-type Ca2+ channel activity. However, the role of Tspan7 in pancreatic beta-cell function is not yet fully understood. Methods: Histological analyses were conducted using immunostaining. Whole-body metabolism was tested using glucose tolerance test. Islet hormone secretion was quantified using static batch incubation or dynamic perifusion. Beta-cell transmembrane currents, electrical activity and exocytosis were measured using whole-cell patch-clamping and capacitance measurements. Gene expression was studied using mRNA-sequencing and quantitative PCR. Results: Tspan7 is expressed in insulin-containing granules of pancreatic beta-cells. Tspan7-knockout mice (Tspan7 y/- mouse) exhibit reduced body weight and ad libitum plasma glucose but normal glucose tolerance. Tspan7y/- islets have normal insulin content and glucose- or tolbutamide-stimulated insulin secretion. Depolarisation-triggered Ca2+ current was enhanced in Tspan7y/- beta-cells, but beta-cell electrical activity and depolarisation-evoked exocytosis were unchanged suggesting that exocytosis was less sensitive to Ca2+. TSPAN7 knockdown (KD) in human pseudo-islets led to a significant reduction in high K+-stimulated insulin secretion. Transcriptomic analyses show that TSPAN7 KD in human pseudo-islets correlated with changes in genes involved in hormone secretion, apoptosis and ER stress. Consistent with rodent beta-cells, exocytotic Ca2+ sensitivity was reduced in a human beta cell line (EndoC-H1) following Tspan7 KD. Conclusion: Tspan7 is involved in the regulation of Ca2+-dependent exocytosis in beta-cells. Its function is more significant in human beta-cells than their rodent counterparts

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human pseudoislet cells with control and TSPAN7 shRNA.

first: Kerry

last: McLaughlin

first: Quan

last: Zhang


title: Alteration of the N6-methyladenosine Epitranscriptome Profile in Synthetic Phthalate-treated Human Induced Pluripotent Stem Cell-Derived Endothelial Cells [RNA-seq]

city: Chicago

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois

summary:
Background: This study aims to characterize the N6-methyladensosine epitranscriptomic profile induced by mono(2-ethylhexyl) phthalate (MEHP) exposure using a human-induced pluripotent stem cell-derived endothelial cell model.
Methods: A multi-omic approach was employed by performing RNA sequencing in parallel with an m6A-specific microarray to identify mRNAs, lncRNAs, and miRNAs affected by MEHP exposure.
Results: An integrative multi-omic analysis identified relevant biological features affected by MEHP, while functional assays provided a phenotypic characterization of these effects. Transcripts regulated by the epitranscriptome were validated with qPCR and Me-RIP.
Conclusion: Our findings offer important information regarding the alterations occurring within the m6A epitranscriptome and the gene expression changes which occur in response to treatment with a synthetic phthalate in hiPSC-ECs and may be an important resource for future research.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three lines of hiPSC-EC treated with either DMSO or 120 µM MEHP for 72 hours.

first: Sang

last: Ong


title: Alteration of the N6-methyladenosine Epitranscriptome Profile in Synthetic Phthalate-treated Human Induced Pluripotent Stem Cell-Derived Endothelial Cells [array]

type:
Expression profiling by array
Non-coding RNA profiling by array
Other


title: HDAC5 regulates arachidonic acid metabolism via cPLA2

city: Wuhan

first: Haixin

last: Yu

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We performed HDAC5 knockdown in pancreatic cancer cells along with RNA sequencing. The result helped us to verify that HDAC5 regulates GATA1 dependent cPLA2 expression and arachidonic acid metabolism.

overall_design: RNA sequencing in PANC-1 cell line with shControl or shHDAC5

first: H

first: Y

last: Zhou


title: TREM2 Drives Microglia Response to Amyloid-β via SYK-dependent and -independent Paths [DAP12KI scRNA-seq]

city: St. Louis

first: Vincent

last: Peng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine in St. Louis

summary: Genetic studies have highlighted microglia as pivotal in orchestrating Alzheimer’s disease (AD). Microglia that adhere to Aβ plaques acquire a transcriptional signature, “diseaseassociated microglia” (DAM), which largely emanates from the TREM2-DAP12 receptor complex that transmits intracellular signals through the protein tyrosine kinase SYK. The human TREM2R47H variant associated with high AD risk fails to activate microglia via SYK. We found that SYK-deficient microglia cannot encase Aβ plaques, accelerating brain pathology and behavioral deficits. SYK deficiency impaired the PI3K-AKT-GSK3β-mTOR pathway, incapacitating anabolic support required for attaining the DAM profile. However, SYK-deficient microglia proliferated and advanced to an Apoe-expressing prodromal stage of DAM; this pathway relied on the adaptor DAP10, which also binds TREM2. Thus, microglial responses to Aβ involve non-redundant SYK- and DAP10-pathways. Systemic administration of an antibody against CLEC7A, a receptor that directly activates SYK, rescued microglia activation in mice expressing the TREM2R47H allele, unveiling new options for AD immunotherapy.

overall_design: Compare the transcriptomes of CD45+ cells of KΔY75 5XFAD mice with that of WT 5XFAD mice

first: Yingyue

first: Shoutang


title: Tn-Seq Survival Profiling

city: NY

first: Saeed

last: Tavazoie

address: 1150 St Nicholas

institute: Columbia University

summary: A Tn5 transposon insertion library generated in a thyA- strain was selected in thymidine-free media and insertions were mapped and sequenced at different time points to look for changes in survival caused by gene disruptions

overall_design: The library was thawed and pre-grown for 2h in high thymidine, washed twice in 1x phosphate buffered saline (PBS), and placed in thymidine-free media. Samples were collected at three time points during the selection: “Start”, “0h”, and “3h”.

first: Alexandra

last: Ketcham

first: Peter

last: Freddolino


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function[RNA-seq_ESC]

first: Gergana

last: Dobreva

overall_design: Conrol and Lmna KO E14 Tg(Nkx2-5-EmGFP)  mESCs  were maintained on mitomycin treated mouse embryonic fibroblasts (MEF) in DMEM high glucose  supplemented with 15% fetal bovine serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 4.5 mg/ml D-glucose, 1% penicillin-streptomycin and 1000 U/ml leukemia inhibitory factor and collected for RNA-seq.

first: Yinuo

first: Julio

last: Cordero

first: Adel

last: Elsherbiny

first: Linda

last: Kessler


title: Thymidine starvation

summary: The transcriptome profiling experiment mapped and quantified RNA extracted from three experimental conditions in the evolved and parental strains in the MDS42 background

overall_design: Three samples were taken for each strain: a high thymidine sample 2h into growth, a sample 30 minutes into thymidine starvation, and a control was washed twice similar to the starved sample but placed back into high thymidine and collected after 30 minutes.


title: Structure and functional mapping of the KRAB-KAP1 repressor complex [KAP1_ChIP-seq]

city: Lund

first: Ninoslav

last: Pandiloski

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary: We used ChIP-seq to assess how abolition of KRAB binding by KAP1 (through structure-guided mutations in the KAP1-KRAB binding interface) changed the distribution of KAP1 on chromatin genome-wide.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for KAP1 in three different conditions [KAP1-KO, WTcomp (KAP1-KO cells complemented with a wild type KAP1), and CCmutComp (KO cells complemented with a KAP1-coiled coil mutant)]. Experiments were performed in HEK293T cells (n=2 for each condition).

first: Christopher

last: Douse


title: Structure and functional mapping of the KRAB-KAP1 repressor complex


title: NFATC1's role in AhBMSCs

city: Chengdu

first: Fanyuan

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology


title: BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking CLU+ CAF expression with HSF1 signaling

city: Rehovot

first: Ruth

last: Scherz-Shouval

state: Rehovot

address: Herzl 234

country: Israel

institute: Weizmann institute of science


title: Tyrosine phosphorylation controlled poly(A) polymerase I activity regulates general stress response in bacteria

city: Trivandrum

first: Rakesh

last: Laishram

state: Kerala

address: Thycaud P O, Poojappura

department: Cardiovascular and Diabetes Biology Group

institute: Rajiv Gandhi Centre for Biotechnology(RGCB)

summary: We did Genome wide RNA seq analysis between wild type MG1655 cells and mutant of bacterial poly(A) polymerase I (MG-pcnB null mutant). We show that pcnB-null mutation widely stabilises stress response mRNAs (>30%) and imparts cellular tolerance to multiple stresses.

overall_design: E.coli K-12 MG 1655 cells and MG-pcnB null mutant cells  were grown up to OD600=0.5 and isolated total RNA. rRNA depleted samples were used further for cDNA library preparation and analysis

first: Nimmy

last: Francis


title: Structure and functional mapping of the KRAB-KAP1 repressor complex [KAP1_CUT&RUN-seq]

summary: We used CUT&RUN to assess how abolition of KRAB binding by KAP1 (through structure-guided mutations in the KAP1-KRAB binding interface) changed the distribution of H3K9me3 epigenetic mark genome-wide.

overall_design: Comparative H3K9me3 enirchment analysis of CUT&RUN-seq data for HEK293T cells and its derivatives [KAP1-KO, WTcomp (KAP1-KO cells complemented with a wild type KAP1), and CCmutComp (KO cells complemented with a KAP1-coiled coil mutant)]. Experiments were performed on HEK293T cells (n=2 for each condition)


title: RNAseqencing of wild type (WT) and Ripk3-/- (KO) AML-12 cells in the presence (PA) of absence (C)  of 125 µM palmitate-bovine serum albumin for 24 h

city: Paris

first: Jeremie

last: Gautheron

address: 27 rue chaligny

institute: Sorbonne Universite - Centre de Recherche Saint-Antoine

summary:
Purpose: Necroptosis as been implicated in various deseases. The goal of this study is to invastigate the impact of RIPK3 in the lipid metabolism of hepatic cells.
Methods: AML-12 cells invalidated or not for RIPK3 were exposed to free fatty acid and the  mRNA profiles of wild type (WT) or knockout (RIPK3-KO) AML-12 cells control (C) or exposed to palmitic acid (PA) were generated by deep sequencing, in 5 copies, using Illumina NOVAseq 6000 plateform. Differential expression analysis between two conditions/groups (five biological replicates per condition) was performed using DESeq2 R package. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. qRT–PCR validation was performed using SYBR Green assays
Results: The DEGs were clustered using a hierarchical clustering algorithm, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis unveiled that transcripts associated with OXPHOS and thermogenesis were markedly upregulated in unchallenged Ripk3-/- hepatocytes compared with WT cells an effect that was aggravated by the PA treatment. Similarly, gene ontology enrichment analysis showed that mitochondria respiration-related proteins were overrepresented among the cellular components that were upregulated in Ripk3-/- hepatocytes compared with WT cells
Conclusions: The absence of Ripk3 impacts on hepatocyte transcriptomic profile, increasing the expression of genes implicated in mitochondria bioenergetics and function, rescuing mitochondria respiration after free fatty acid overload.

first: Julie

last: Magusto

first: Carine

last: Beaupere


title: Effects of NMDAR on mouse hippocampal neuron (HT22) mRNA and lncRNA expression during hypoxia/reoxygenation injury

city: Changchun

first: Qiwei

last: Yang

state: Jilin

address: Ziqiang Street No.218

institute: Jilin University

summary: To investigate the changes of the transcriptome in neuronal cells under the condition of NMDAR hypofunction and H/R injury, we compared the changes of mRNA and lncRNA expression levels in mouse hippocampal neuron HT22 cell with or without NMDAR knockdown and H/R stimulation by RNA sequencing.

overall_design: Comparative mRNA and lncRNA expression profiling analysis of RNA-seq data for mouse hippocampal neuron HT22 cell with or without NMDAR knockdown and H/R stimulation.

first: Jinting

last: He


title: Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner I

first: Rayk

last: Behrendt

first: Tina

last: Schumann

first: Andreas

last: Dahl

first: Mohamad

last: Mayo


title: Loss of tetraspanin-7 expression reduces pancreatic beta-cell exocytosis Ca2+ sensitivity but has limited effect on systemic metabolism

first: Sumeet

last: Singh

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: RNAseq analysis of the herbicide propyzamide on a pre-clinical model of IBD on Antigen induced Mouse T Cells

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Studying the effects of propyzamide on Inflammtory Bowel Disease on Antigen induced Mouse T Cells

overall_design: In total there are 24 samples: 8 samples are collected at none stimulated stage, 8 samples are collected at 3 hours after CD3 antigen stimulation and 8 samples are collected at 24 hours after CD3 antigen stimulation.

first: Liliana

middle: M

last: Sanmarco

first: Francisco

middle: J

last: Quintana


title: Loss of tetraspanin-7 expression reduces pancreatic beta-cell exocytosis Ca2+ sensitivity but has limited effect on systemic metabolism [mouse]

summary: Background: Tetraspanin-7 (Tspan7) is an islet autoantigen involved in autoimmune type 1 diabetes and known to regulate beta-cell L-type Ca2+ channel activity. However, the role of Tspan7 in pancreatic beta-cell function is not yet fully understood. Methods: Histological analyses were conducted using immunostaining. Whole-body metabolism was tested using glucose tolerance test. Islet hormone secretion was quantified using static batch incubation or dynamic perifusion. Beta-cell transmembrane currents, electrical activity and exocytosis were measured using whole-cell patch-clamping and capacitance measurements. Gene expression was studied using mRNA-sequencing and quantitative PCR. Results: Tspan7 is expressed in insulin-containing granules of pancreatic beta-cells. Tspan7-knockout mice (Tspan7 y/- mouse) exhibit reduced body weight and ad libitum plasma glucose but normal glucose tolerance. Tspan7y/- islets have normal insulin content and glucose- or tolbutamide-stimulated insulin secretion. Depolarisation-triggered Ca2+ current was enhanced in Tspan7y/- beta-cells, but beta-cell electrical activity and depolarisation-evoked exocytosis were unchanged suggesting that exocytosis was less sensitive to Ca2+. TSPAN7 knockdown (KD) in human pseudo-islets led to a significant reduction in high K+-stimulated insulin secretion. Transcriptomic analyses show that TSPAN7 KD in human pseudo-islets correlated with changes in genes involved in hormone secretion, apoptosis and ER stress. Consistent with rodent beta-cells, exocytotic Ca2+ sensitivity was reduced in a human beta cell line (EndoC-bH1) following Tspan7 KD. Conclusion: Tspan7 is involved in the regulation of Ca2+-dependent exocytosis in beta-cells. Its function is more significant in human beta-cells than their rodent counterparts

overall_design: Comparative gene expression profiling analysis of RNA-seq data for pancreatic islet from WT and TSPAN7-KD mouse.

first: Kerry

last: McLaughlin

first: Quan

last: Zhang


title: TREM2 Drives Microglia Response to Amyloid-β via SYK-dependent and -independent Paths

first: Vincent

last: Peng

overall_design: Refer to individual Series


title: BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking CLU+ CAF expression with HSF1 signaling (PSC)

first: Ruth

last: Scherz-Shouval

summary: Cancer-associated fibroblasts (CAFs) give rise to desmoplastic stroma, which supports tumor progression and metastasis, and comprises up to 90% of the tumor mass in pancreatic cancer. Recent work by us and others has shown that CAFs are transcriptionally rewired by adjacent cancer cells to form heterogeneous subtypes. Whether this rewiring is differentially affected by different driver mutations in cancer cells is largely unknown. Here we address this question by dissecting and comparing the stromal landscape of BRCA-mutated and BRCA Wild-type (WT) pancreatic ductal adenocarcinoma (PDAC). We comprehensively analyze PDAC samples from a cohort of 42 patients by laser-capture microdissection, RNA-sequencing and multiplexed immunofluorescence, revealing different CAF subtype compositions in germline BRCA-mutated vs. BRCA-WT tumors. In particular, we detect an increase in a subset of Clusterin (CLU)-positive CAFs in BRCA-mutated tumors. Using cancer organoids, co-cultures and in-vivo models we show that loss of BRCA function in cancer cells leads to a transcriptional shift of pancreatic stellate cells from myofibroblastic into immune-regulatory CLU+ CAFs. This process is mediated through activation of heat-shock factor 1 (HSF1), the transcriptional regulator of Clu. Our findings unravel a new dimension of stromal heterogeneity, influenced by germline mutations in cancer cells, with direct translational implications for clinical research.

overall_design: Pancreatic stellate cells (PSCs) were cultured in matrigel growth factor reduced (GFR) with growth medium for 4 days. The media was then replaced to KPC organoid-shBRCA2 or KPC organoid -shControl conditioned medium (CM), or with PSC own conditioned medium as control for 4 days. The cells were harvested and RNA-sequencing was performed.

first: Lee

last: Shaashua

first: Meirav

last: Pevsner-Fischer

first: Gil

last: Friedman

first: Yaniv

last: Stein

first: Oshrat

last: Levi-Galibov

first: Aviad

last: Ben-Shmuel

first: Debra

last: Barki

first: Shimrit

last: Mayer


title: BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking CLU+ CAF expression with HSF1 signaling (KPC)

overall_design: KPC-shBrca2 or KPC-shControl cells were seeded in 6-wells and cultured in growth medium. The cells were then stained with propidium iodide (PI, 1:1000) and then 10,000 PI- cells were FACS sorted into 40 ul of lysis/binding buffer ( Thermo-Fisher scientific ), and mRNA was isolated using Dynabeads oligo (dT).


title: Murine Allogeneic CAR-T Cells Integrated Before or Early After Posttransplant Cyclophosphamide Exert Anti-Tumor Effects

status: Public on Oct 09 2022

city: Bethesda

first: Margaret

last: Cam

address: 9000 Rockville Pike

institute: NCI

summary: The direct integration of chimeric-antigen-receptor (CAR) T cell with allogeneic hematopoietic cell transplantation (allo-HCT) carries the risk of graft-versus-host disease (GVHD) induction by allogeneic CAR-T cells. Based on our past experiments, it has been shown that post-transplantation cyclophosphamide (PTCy) prevents GVHD induction by other cell infusions after T-cell-replete MHC-haploidentical murine allo-HCT models. In this study, we investigated whether CAR-T cells, given in a similar manner in the same MHC-haploidentical murine allo-HCT model, could safely exert anti-tumor effects. We showed that anti-CD19 CAR-T cells administered early after (day +5 of transplant) or prior to (day 0 of transplant) PTCy for allo-HCT cleared leukemia without toxicity or GVHD exacerbation. Using next generation single-cell RNA sequencing approaches, we demonstrated that in comparison to CAR-T cells infused early after PTCy (day +5), CAR-T cells infused prior to PTCy (day 0) exhibited transcriptional changes consistent with increased CD4+ T-cell activation and CD8+ T-cell cytotoxicity.

overall_design: Next-generation sequencing approaches on a large data set enabled the identification of transcription factors associated with increased CD4 activation and CD8 cytotoxicity in CAR-T cells administered on mice prior to PTCy transplantation.

first: Christopher

last: Kanakry

first: Maggie

first: Michael

last: Patterson

first: Shanzay

last: Khan

first: Natalia

last: Nunes

first: Rochelle

last: Flecter

first: Jing

middle: H

last: Bian


title: BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking CLU+ CAF expression with HSF1 signaling (CAF)

first: Ruth

overall_design: CAFs were collected for bulk RNA-seq as follows: 2-3 weeks following KPC shControl or KPC shBrca2 orthotropic injection into the pancreas the mice were sacrificed, PDAC tumors were excised, digested into single cells and suspended in MACS buffer. The cell suspension was depleted of CD45+ and EpCAM+ cells using manganic beads. The CAF-enriched flow through was then stained for FACS sorting with the following antibodies: CD45-FITC, CD31-FITC, EpCAM-FITC, PDPN-APC, and Ghost Dye-violet 450 for detection of live cells. To collect CAFs, the following gating strategy was applied: CD45-/CD31-/EpCAM-/PDPN+


title: Effects of Intravitreal Injection of Human CD34+ Bone Marrow Stem Cells in a Murine Model of Diabetic Retinopathy

city: Davis

first: Zeljka

last: Smit-McBride

state: CA

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

institute: University of California, Davis Eye Center

summary:
Human CD34+ stem cells are mobilized from bone marrow to sites of tissue ischemia and play an important role in tissue revascularization. This study used a murine model to test the hypothesis that intravitreal injection of human CD34+ stem cells harvested from bone marrow (BMSCs) can have protective effects in eyes with diabetic retinopathy. Streptozotocin-induced diabetic mice (C57BL/6J) were used as a model for diabetic retinopathy. Subcutaneous implantation of Alzet pump, loaded with Tacrolimus and Rapamycin, 5 days prior to intravitreal injection provided continuous systemic immunosuppression for the study duration to avoid rejection of human cells. Human CD34+ BMSCs were harvested from the mononuclear cell fraction of bone marrow from a healthy donor using magnetic beads. The CD34+ cells were labeled with enhanced green fluorescent protein (EGFP) using a lentiviral vector. The right eye of each mouse received an intravitreal injection of 50,000 EGFP-labeled CD34+ BMSCs or phosphate buffered saline (PBS). Simultaneous multimodal in vivo retinal imaging system consisting of fluorescent scanning laser ophthalmoscopy (enabling fluorescein angiography), optical coherence tomography (OCT) and OCT angiography was used to confirm the development of diabetic retinopathy and study the in vivo migration of the EGFP-labeled CD34+ BMSCs in the vitreous and retina following intravitreal injection.
After imaging, the mice were euthanized, and the eyes were removed for immunohistochemistry. In addition, microarray analysis of the retina and retinal flat mount analysis of retinal vasculature were performed. The development of retinal microvascular changes consistent with diabetic retinopathy was visualized using fluorescein angiography and OCT angiography between 5 and 6 months after induction of diabetes in all diabetic mice. These retinal microvascular changes include areas of capillary nonperfusion and late leakage of fluorescein dye. Multimodal in vivo imaging and immunohistochemistry identified EGFP-labeled cells in the superficial retina and along retinal vasculature at 1 and 4 weeks following intravitreal cell injection. Microarray analysis showed changes in expression of 162 murine retinal genes following intravitreal CD34+ BMSC injection when compared to PBS-injected control. The major molecular pathways affected by intravitreal CD34+ BMSC injection in the murine retina included pathways implicated in the pathogenesis of diabetic retinopathy including Toll-like receptor, MAP kinase, oxidative stress, cellular development, assembly and organization pathways. At 4 weeks following intravitreal injection, retinal flat mount analysis showed preservation of the retinal vasculature in eyes injected with CD34+ BMSCs when compared to PBS-injected control. The study findings support the hypothesis that intravitreal injection of human CD34+ BMSCs results in retinal homing and  integration of these human cells with preservation of the retinal vasculature in murine eyes with diabetic retinopathy.

first: Amirfarbod

last: Yazdanyar

first: Pengfei

last: Zhang

first: Christian

last: Dolf

first: Whitney

last: Cary

first: Jan

last: Nolta

first: Robert

last: Zawadzki

first: Nicholas

last: Marsh-Armstrong

first: Susanna

last: Park


title: NAP1L5 is required for translation activation during cardiomyocyte hypertrophy

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

summary: Pathological growth of cardiomyocytes during hypertrophy is characterized by excess protein synthesis; however, the regulatory mechanism remains largely unknown. Using a neonatal rat ventricular myocyte (NRVMs) model, here we find that the expression of nucleosome assembly protein 1 like 5 (Nap1l5) is upregulated in phenylephrine (PE)-induced hypertrophy. Knockdown of Nap1l5 expression by siRNA significantly blocks cell size enlargement and pathological gene induction after PE treatment. In contrast, Adenovirus-mediated Nap1l5 overexpression significantly aggravates the pro-hypertrophic effects of PE on NRVMs. RNA-seq analysis reveals that Nap1l5 knockdown reverses the pro-hypertrophic transcriptome reprogramming after PE treatment. Whereas immune response is dominantly enriched in the upregulated genes, oxidative phosphorylation, cardiac muscle contraction and ribosome related pathways are remarkably enriched in the down-regulated genes. Although PRC2 and PRC1 are involved in Nap1l5-mediated gene regulation, Nap1l5 does not directly alter the levels of global histone methylations. However, puromycin incorporation assay shows that Nap1l5 is both necessary and sufficient to drive the increased protein synthesis rate in cardiomyocyte hypertrophy. This is attributable to a direct regulation of ribosome assembly by Nap1l5. Our findings demonstrate a previously unrecognized role of Nap1l5 in translation control during cardiac hypertrophy.

overall_design: NRVMs were first transfected with siNap1l5 or siNeg, then treated with PE for 36h after 12h of transfection. NRVMs were used to extracted RNA according to the manufacturer's instructions. Transcriptome sequencing of RNA was completed by Beijing Genomics Institution (BGI). Three independent biological replicate samples were sequenced for each group.

first: Ningning

last: Guo

first: Di

last: Zheng

first: Jiaxin

last: Sun

first: Jian

last: Lv

first: Shun

first: Yu

last: Fang

first: Zhenyi

last: Zhao

first: Sai

last: Zeng

first: Qiuxiao

first: Jingjing

last: Tong


title: Stage- and cell type-specific requirements of ikzf1 during hematopoietic differentiation in zebrafish [it325]

status: Public on Oct 08 2022

city: Freiburg

first: Thomas

last: Boehm

address: Stuebeweg 51

department: Developmental Immunology

institute: Max Planck Institute for Immunobiology and Epigenetics

summary: The characterisation of two zebrafish ikzf1 mutant lines missing the two C-terminal zinc fingers only and both part of the DNA  binding domain plus the C-terminal zinc fingers respectively gives insight into the specific roles of these elements during zebrafish hematopoiesis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for zebrafish mutant lines IT325 (allele no. t24980) and CRISPR ikzf1 (allele no. fr105) vs. wt siblings

first: Isabell

last: Hess

first: S

last: Sagar

first: Connor

last: O'Meara

first: Dominic

last: Grün

first: Michael

last: Schorpp


title: TREM2 Drives Microglia Response to Amyloid-β via SYK-dependent and -independent Paths [SYK and TREM2 scRNA-seq]

first: Vincent

last: Peng

overall_design: 6-month old female 3 Syk fl/fl, 3 Cx3cr1-creER Syk fl/fl, 3 Syk fl/fl 5XFAD, 3 Cx3cr1-creER Syk fl/fl 5XFAD mice, 2 Trem2 WT 5XFAD, and 3 Trem2 KO 5XFAD mice.

first: Shoutang

first: Marco

last: Colonna


title: KW-2449 and VPA exert therapeutic effects on human neurons and cerebral organoids derived from MECP2-null hESCs

city: Beijing

first: Zhongze

last: Yan

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, CAS

summary: To gain a deeper insight into roles of MECP2 in hESCs derived organoids, we performed RNA-seq to analyze the transcriptome changes after MECP2 deletion in hESCs-derived organoids.

overall_design: Total RNA was extracted from WT and MECP2-KO organoids treated after KW-2449 or VPA，and generated by deep sequencing, in two biological replicates, using novaseq 6000.

first: Ya-Jie

last: Xu

first: Zhong-Ze


title: RNAseq analysis of the herbicide propyzamide on a pre-clinical model of IBD on Mouse using single cell RNA-Seq I

first: Zhaorong

last: Li

summary: Studying the effects of CEBPB knockouts on T Cells and Dendritic Cells using single cell RNA-Seq

overall_design: In total there are 15 samples: 9 wild type samples, 2 CEBPB knockout dendritic cells samples and 4 CEBPB knockout T Cells samples

first: Liliana

last: Sanmarco

first: Francisco

last: Quintana


title: RNAseq analysis of the herbicide propyzamide on a pre-clinical model of IBD on Danio rerio model

summary: Studying the effects of propyzamide on Inflammtory Bowel Disease on Danio rerio model

overall_design: In total there are 48 samples: 24 Naïve samples and 24 TNBS induced samples. Out of the 24 Naïve and TNBS samples each set consists of 12 samples of Myeloid Cells and 12 samples of Lymphoid Cells. For each set of Lymphoid and Myeloid Cells there are 4 Control treatment, 4 Propyzamide (20 uM) and 4 Propyzamide (1 uM) treatment.


title: In vivo expression of mutant Samd9l collaborates with inflammation to induce bone marrow failure

city: Memphis

first: Jeffery

last: Klco

state: Tennessee

address: 262 Danny Thomas Place, D4047B

department: Pathology

institute: St Jude Children's Research Hospital

summary: SAMD9 and SAMD9L germline mutations have recently emerged as a new class of predispositions to pediatric myeloid neoplasms. Patients commonly have hypocellular bone marrows and a greater risk of developing clonal chromosome 7 deletions. We recently demonstrated that expressing SAMD9/SAMD9L mutations in hematopoietic cells suppresses their proliferation and induces apoptosis. Here we generated a mouse model that conditionally expresses mutant Samd9l to assess the in vivo impact on hematopoiesis. We showed that mutant Samd9l cells are less fit relative to wild-type counterparts, which is exacerbated by inflammatory stimuli, and ultimately leads to marrow hypocellularity. Genomic and phenotypic analyses recapitulated many of the hematopoietic cellular phenotypes observed in patients with germline SAMD9 or SAMD9L mutations, including lymphopenia, and pinpointed TGF-b  as a potential causative and targetable networkpathway. Further, we observed non-random genetic deletion of the mutant Samd9l locus on mouse chromosome 6, mimicking the pathologic features observed in patients.

overall_design: For experiment 1, WBM cells were extratced from 3-month old Samd9l-KO, Samd9l-Wt and Samd9l-Mut mice (n=1 per group). For Experiment 2, Samd9l-Wt and Samd9l-Mut mice were treated with vehicle or pI:pC twice a week for 4 weeks (n=1 per group). WBM was then extracted and Lineage-cKit+ cells were sorted to run 10x csRNA-seq.

first: Sherif

last: Abdelhamed

first: Chandra

last: Rolle

first: Virginia

last: Valentine

first: Laura

last: Janke

first: Melvin

middle: E

last: Thomas III

last: Walsh

first: Marcus

first: Tamara

last: Westover

first: Huiyun

last: Wu

first: Stanley

last: Pounds

first: Masayuki

last: Umeda

first: Jason

last: Schwartz

first: Jing

last: Ma


title: In vivo expression of mutant Samd9l collaborates with inflammation to induce bone marrow failure. [RNA-Seq]

overall_design: RNA-seq was performed on Lin-cKit+ sorted BM cells.

first: Michael


title: Targeted RNA-sequencing of aged archival formalin-fixed paraffin-embedded tissue samples

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

summary: Formalin-fixed paraffin-embedded (FFPE) samples are the only remaining biological archive for many toxicological and clinical studies, yet their use in genomics has been limited due to variability in RNA quality from formalin fixation. Older FFPE samples, which often have highly degraded RNA, pose a particularly difficult technical challenge. Recent developments in probe-based targeted sequencing technologies show promise in addressing this issue, while also being more cost effective than traditional RNA-sequencing (RNA-seq) methods. In the current study, we evaluated dose-dependent transcriptional changes from paired frozen and archival FFPE liver samples stored for over 20 years using targeted resequencing (TempO-Seq) and whole-genome RNA-seq methods. Samples were originally collected from male mice exposed to a reference chemical (dichloroacetic acid, DCA) at 0, 198, 313 and 427 mg/kg-day, (n=6/dose) by drinking water for 6 days. TempO-Seq showed high overlap in differentially expressed genes (DEGs) between matched FFPE and flash-frozen (FROZ) samples and concordance in fold-changes across the highest two dose levels of DCA vs. control (R2 ≥ 0.94). Similarly, high concordance in fold-changes was observed between TempO-Seq FFPE and RNA-seq FROZ results (R2 ≥ 0.92). Only 28 DEGs or fewer were identified in RNA-seq FFPE samples. Modeling of DCA-dependent changes in gene sets identified benchmark doses from TempO-Seq FROZ and FFPE samples that were within 1.4-fold of RNA-seq FROZ samples (93.9 mg/kg-d), whereas RNA-seq FFPE samples were 3.3-fold higher (310.3 mg/kg-d). This work demonstrates that targeted sequencing may provide a more robust method for quantifying gene expression profiles from aged archival FFPE samples.

overall_design: Gene expression from paired frozen (FROZ) and formalin-fixed paraffin-embedded (FFPE) liver samples collected in 1994 from mice exposed to 0, 198, 313, and 427 mg/kg-d DCA via drinking water (n=6/dose/preservation) using the TempO-seq platform.

first: Susan

last: Hester

last: Cannizzo

first: Charles

last: Wood


title: Gene expression by CREB5 overexpression in LNCaP cells

city: Jinan

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

summary: The aim of this research was to confirm the regulatory effect of CREB5 on gene expression in the development of prostate cancer.

overall_design: In this research, there were two samples examed including sample of  control cells (PcDNA3-1) and sample of CREB5 overexpression cells (pCREB5).

first: Xueli

last: Wang

first: Bo

last: Han


title: RNAseq analysis of the herbicide propyzamide on a pre-clinical model of IBD on Mouse using single cell RNA-Seq II

first: Zhaorong

last: Li

summary: Studying the effects of propyzamide on Inflammtory Bowel Disease on Mouse using single cell RNA-Seq

overall_design: In total there are 4 samples. Lili_1_5 is the Naïve Condition sample treated with Vehicle, Lili_6_10 is the colitis sample treated by Vehicle, Lili_11_15 is the Naïve Condition sample treated with Propyzamide and Lili_16_20 is the colitis sample treated by Propyzamide.

first: Liliana

last: Sanmarco

first: Francisco

last: Quintana


title: Blood transcripts from female Japanese quail given LPS injection or saline

city: Orange

first: Patricia

middle: C

last: Lopes

address: 450 N Center St

department: Biological Sciences

institute: Chapman University

summary: The aim of this experiment was to test how female Japanese quail respond to being housed with sick (LPS treated) relative to control males. LPS injected females were also tested.

overall_design: Adult female Japanese quail received either saline or LPS injection. All animals were allowed to interact with males for 3 h. Half of the saline injected birds were exposed to LPS injected males and the other half to control males. A blood sample was collected from the brachial vein at the end of the 3h. Blood was spun down and plasma and red blood were separated. RNA was extracted from red blood portion.


title: Change in whole-blood microRNA profile during the worsening and recovery process of cerebral infarction, a human study

city: Bunkyo-ku

first: Tomiko

last: Asakura

state: Tokyo

department: Applied Biological Chemistry Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

summary:
Circulating miRNA species are becoming promising symptom markers for various diseases including cardiovascular diseases. However, studies on their role in the recovery processes are few especially concerning cerebral infarction. We compared whole blood miRNA profiles between cerebral infarction patients (P-group) and the subjects with no symptom (C-group), and also between P-group and treated patients (T-group).
A Total of 64 miRNAs were found to be differentially expressed between C and P-groups. Of 64 miRNAs, the expression levels of 2 miRNAs correlated with hypertension. A total of 155 miRNAs were differentially expressed between P- and T-group. There were 5 common miRNAs among the 64 and 155 miRNAs identified. Importantly, these 5 common miRNAs were inversely regulated in each comparison (e.g., C < P > T).

overall_design: Cerebral infarction patients (P-group n=23) and the subjects with no symptom (C-group n=22), and also between P-group and treated patients (T-group n=7), and the miRNA expression in the whole blood was compared between the three group.

first: Abe

last: Arata

first: Tanaka

last: Mayui

first: Yasuoka

last: Akihito

first: Saito

last: Yoshikazu

first: Okada

last: Shinji

first: Mishina

last: Masahiro

last: Keiko

first: Kimura

last: Kazumi

first: Asakura

last: Tomiko


title: Expression data from NexCre:Atg7 conditional knockout mice brain

status: Public on Oct 07 2022

city: Tsukuba

first: Fuminori

last: Tsuruta

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary:
Transcriptome analysis of NesCre:Atg7 conditional knockout mice.
Autophagy plays an important role in regulating protein metabolism and tissue homeostasis. Recent studies have reported that neural stem cell-specific Atg7 knockout mice (NesCre:Atg7f/f cKO mice) exhibit neonatal lethal due to severe neurodegeneration. However, the precise mechanisms of how neuronal fate is regulated by the autophagic pathway have not been elucidated. Here, we performed microarray experiments to analyze the changes in gene expression patterns in NesCre:Atg7 cKO mice. As a result, we could find a lot of candidate genes changed by Atg7 deficiency.

overall_design: Brains were collected from either WT or Atg7 cKO mice for RNA extraction and hybridization on Affymetrix microarray.


title: RNA-seq of NFATC1's role in AhBMSCs

city: Chengdu

first: Fanyuan

last: Yu

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

summary: We report the application of RNA sequencing technology for high-throughput profiling of gene expression in NFATC1 knockdown (siNFATC1) or inactivation (FK506 treatment) adult human bone marrow mesenchymal stem cells (AhBMSCs).To knockdown NFATC1 in AhBMSCs we transfected cells with NFATC1 specific siRNAs and the scrambled RNAs were ste as controls. To block NFATC1 activation we used 20μM FK506 and its control was DMSO. AhBMSCs are derived from a 24-year-old healthy male human donor. Total mRNA was collected using TRIzol ® (Invitrogen, CA, USA) solution. Then all the extraction procedures were conducted according to manufacture’s instructions for RNA extraction from homogenized tissues.  After quality checks they were subjected to the high-throughput RNA-sequencing. Every group consists of 3 replicates which were from 3 independent experimental repeats.

overall_design: Examination of RNA expression in AhBMSCs after NFATC1 knockdown or FK506 treatment respectively.

first: Feifei


title: Gastrodin ameliorates the lipopolysaccharide-induced neuroinflammation in mice by downregulating miR-107-3p

city: Xuzhou

first: Hui

state: Jiangsu

address: No.209, Tongshan Road, Huangshan Street

department: School of Life Sciences

institute: Xuzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: To further elucidate the role of miRNAs, HTS was used to screen differential miRNAs. Mice hippocampus from the saline group, the LPS group, and the LPS+GAS group were removed to analyze using HTS.

overall_design: Comparative genomic expression profiling of microRNA sequencing data from mice hippocampal tissues and their treatment groups with drugs (Saline, LPS, Gastrodin)

first: Yanyan

last: Fu


title: ChIP-seq of NFATC1's role in AhBMSCs

address: No.14, 3rd Section, Ren Min Nan Rd

summary: We report the application of ChIP sequencing technology for high-throughput profiling of target-gene of NFATC1 in NFATC1 knockdown (NFATC1 RNAi) or widetype control (NC) adult human bone marrow mesenchymal stem cells (AhBMSCs).To knockdown NFATC1 in AhBMSCs we transfected cells with NFATC1 specific siRNAs and the scrambled (SCR) RNAs were ste as controls. AhBMSCs are derived from a 24-year-old healthy male human donor. 48h-post siNFATC1 or negative control siRNA transfection, AhBMSCs were subjected to ChIP sample preparation, respectively using Chromatin-Prep-Kit (MM_NF-17-10461, Millipore, CA, USA) for Chromatin dissection and HiSens-Chromatin-Immunoprecipitation-Kit (MM_NF-17-375, Millipore, CA, USA) for immunoprecipitation according to instruction manuals. Briefly, cells were fixed using 1% formaldehyde for 1min at room temperature to crosslink chromatin. Adding 125mM glycine to stop crosslinking. Then cells were washed w/ cold PBS twice and then lysed using lysis buffer supplemented with protease inhibitors cocktails, followed by centrifuged to obtain cell lysates in according to the manual. After cell lysis, purified nuclei were collected and then incubated with nuclease to get mononucleosomes. After sample preparation soluble chromatin was precleared by SCW washing buffer and subjected to immunoprecipitation as described in manufacture’s protocols. For immunoprecipitation, 1-2µg of antibody of anti-NFATC1 (Novus, Cat#NB300-620) was added. After immunoprecipitation, chromatin was washed, eluted, reverse-crosslinked and digested. Finally purified DNA was subjected to the high-throughput ChIP-sequencing (Novogene, China) after quality check. The data was analyzed by Novogene Inc (China). Every group consists of 3 replicates which were from 3 independent experimental repeats.

overall_design: Examination of target-genes which are trancript directly via NFATC1 in AhBMSCs.

last: Li


title: Stage- and cell type-specific requirements of ikzf1 during hematopoietic differentiation in zebrafish [ikaros]

first: Thomas

last: Boehm

first: Isabell

last: Hess

first: S

last: Sagar

first: Connor

last: O'Meara

first: Dominic

last: Grün

first: Michael

last: Schorpp


title: Single-cell profiling of complex plant responses to Pseudomonas syringae infection

city: Berkeley

first: Benjamin

middle: Jeremy

last: Cole

address: 1, Cyclotron Road

institute: DOE-Joint Genome Institute

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

overall_design: Refer to individual Series


title: Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti–PD-1 Immunotherapy in Endometrial Carcinoma

city: New Haven

first: Tai

last: Michaels

state: CT

address: P.O. Box 208011, 300 Cedar Street

department: Immunobiology

institute: Yale School of Medicine

summary: Responses to immune checkpoint blockade (ICB) are variable among mismatch repair-deficient (MMRd) cancers. We completed a phase 2 clinical trial of the PD-1 inhibitor pembrolizumab in 24 patients with MMRd endometrial cancer (NCT02899793). Patients with mutational MMRd tumors (6 patients) had higher response rates and longer survival than those with epigenetic MMRd tumors (18 patients). Mutation burden was higher in tumors with mutational MMRd compared to epigenetic MMRd; however, within each category of MMRd, mutation burden was not associated with ICB response. Notably, JAK1 mutations did not confer resistance to pembrolizumab. Longitudinal single-cell RNA-seq of circulating immune cells revealed contrasting modes of anti-tumor immunity against mutational and epigenetic MMRd cancers. Whereas effector CD8+ T cell responses correlated with regression of mutational MMRd tumors, highly active CD16+ NK cells were associated with ICB-responsive epigenetic MMRd tumors. These data highlight the interplay between tumor-intrinsic and extrinsic factors that influence ICB response.

overall_design: Longitudinal single cell RNA-seq and TCR-seq of PBMCs from endometrial cancer patients undergoing PD-1 immunotherapy

first: Ryan

last: Chow

first: Stefania

last: Bellone

first: Tobias

last: Hartwich

first: Elena

last: Bonazzoli

first: Akiko

last: Iwasaki

first: Eric

last: Song

first: Alessandro

last: Santin


title: Microglial BV2-derived exosomal microRNA sequencing in heatstroke

city: Guangzhou

first: Jie

last: Zhu

state: Guangdong

address: 111 Liuhua Road, Yuexiu District

institute: General Hospital of Southern Theater Command of PLA

summary:
We performed exosomal microRNA sequencing on BV2 in heatstroke, to shed light on the expression and function changes of microglia in heatstroke.
We then performed gene expression profiling analysis using data obtained from microRNA-seq of 2 groups.

overall_design: Culture dishes containing BV2 cells in 37℃ cell incubator for 2h as a control group, and the experimental group are maintained in 42℃ for 2h, and then rewarmed in 37℃ for 12h.Extraction of BV2-derived exosomes by ultracentrifugation. Exosomal RNA Extraction TRIzol reagent is used to extract the RNA from exosomes. Illumina HiSeqTM 2500 is applied for sequencing, with a data volume of 20 M reads per sample.The total RNA or purified sRNA fragment of the sample is extracted. The 3'-end and 5'-end junctions are ligated, reverse transcribed into cDNA, and then amplified by PCR.During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

first: Yahong

last: Chen


title: MLL3 Loss Drives Metastasis by Promoting a Hybrid Epithelial-Mesenchymal Transition State [ATAC-seq]

city: Bronx

first: Jihong

last: Cui

state: NY

address: 1301 Morris Park Avenue, Room 108/114

institute: Albert einstein college of medicine

summary:
Phenotypic plasticity associated with the hybrid epithelial-mesenchymal transition (EMT) state is crucial to metastatic seeding and outgrowth.
We showed that deletion of the epigenetic regulator MLL3, a tumor suppressor frequently altered in human cancer, promoted the acquisition of the hybrid EMT state in both epithelial and mesenchymal breast cancer cells by facilitating EMT and MET, distinct from other known EMT regulators mediating unidirectional changes.
MLL3 deletion greatly increased metastasis by enhancing metastatic outgrowth during colonization. Mechanistically, MLL3 loss led to IFNγ signaling upregulation, which contributes to the induction of hybrid EMT cells and the enhanced metastatic capacity.

overall_design: We treated the WT and MLL3-mutant MDA-MB-231 cells with  forskolin for 14 days and used flow cytometry to isolate CD44+CD104high hybrid EMT and CD44+CD104low mesenchymal tumor cells.  ATAC-Seq was performed using sorted cells in 2 replicates.

first: Wenjun

last: Guo


title: Effect of Mll3 deletion in MCF7 cells

summary:
MLL3 inactivation mutations occurs frequently in human breast cancer. To understand the function of MLL3 inactivation, we compared the gene expression profiles of the vector control (WT) and Mll3-knockout MCF7 cells generated by CRISPR-CAS9.
Affymetrix human Gene 2.0ST arrays were used for microarray.

overall_design: To investigate the effect of MLL3 loss-of-function mutations on tumor cells, we deleted Mll3 in MCF7 cells with a lentiviral CRISPR vector. Total RNA was extracted from wild type (WT) and Mll3-Knockout MCF7 cells,  and used for microarray analysis.


title: Stage- and cell type-specific requirements of ikzf1 during hematopoietic differentiation in zebrafish

first: Thomas

last: Boehm


title: Single-cell profiling of complex plant responses to Pseudomonas syringae infection [bulk RNA-seq]

summary: Plant response to pathogen infection varies within a leaf, yet this heterogeneity is not well resolved. We exposed Arabidopsis to Pseudomonas syringae or mock treatment and profiled the transcriptomes of 11,000 individual cells using single-cell RNA sequencing. Integrative analysis of cell populations from Pseudomonas and mock inoculated leaves identified five distinct pathogen responsive cell clusters exhibiting transcriptional responses ranging from immunity to susceptibility. Pseudotime analyses through pathogen infection revealed a continuum of disease progression from an immune to susceptible state. Confocal imaging of promoter reporter lines for pathogen responsive cell clusters visualized immune activated cell clusters surrounding substomatal cavities colonized by bacteria, suggesting immune clusters are sites of early pathogen invasion. Susceptibility cell clusters exhibited more general localization and were highly induced at later stages of infection. Overall, our work uncovers cellular heterogeneity within an infected leaf and provides unique insight into plant differential response to infection at a single-cell level.

overall_design: 4-week old Arabidopsis thaliana leaves syringe-infiltrated with Pseudomonas syringae pv. tomato DC3000 or a mock treatment for 24 hours. After treatment, cells (Protoplasts) were isolated from leaf tissue using a tape-sandwich method to enrich for the mesophyll layer. In parallel, whole leaf tissue was also isolated. RNA was then extracted from protoplast preparations and whole leaf tissue, and processed for RNA sequencing. Three biological replicates for mock- and DC3000-treated whole leaves were prepared, and one replicate of protoplasts derived from mock- and DC3000-treated leaves were also processed.

first: Signe

last: Lolle

first: Brian

last: Kvitko

first: Gitta

last: Coaker


title: MLL3 Loss Drives Metastasis by Promoting a Hybrid Epithelial-Mesenchymal Transition State [ChIP-seq histone marker]

summary:
Phenotypic plasticity associated with the hybrid epithelial-mesenchymal transition (EMT) state is crucial to metastatic seeding and outgrowth. However, the mechanisms controlling the induction of hybrid EMT remain poorly defined.
We showed that deletion of the epigenetic regulator MLL3, a tumor suppressor frequently altered in human cancer, promoted the acquisition of the hybrid EMT state in both epithelial and mesenchymal breast cancer cells by facilitating EMT and MET, distinct from other known EMT regulators mediating unidirectional changes. Consequently, MLL3 deletion greatly increased metastasis by enhancing metastatic outgrowth during colonization. Mechanistically, MLL3 loss led to IFNγ signaling upregulation, which contributes to the induction of hybrid EMT cells and the enhanced metastatic capacity.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K27ac, H3K4me1 and H3K4me3 in MLL3-WT and Mut MDA-MB-231 cells.

first: Chi

last: Zhang


title: MLL3 Loss Drives Metastasis by Promoting a Hybrid Epithelial-Mesenchymal Transition State [RNA-seq EM vs M]

summary:
Loss of MLL3 facilitates mesenchymal cells to acquire a mesenchymal/epithelial hybrid state during metastatic colonization.
The MET occurring in distant metastases is likely driven by stromal signals in the metastatic niche. One signaling pathway that promotes the MET is the activation of protein kinase A (PKA). The MET hybrid cells can be identified as CD44+CD104+/high.
Forskolin treatment generated significantly more CD44+CD104high hybrid cells in MLL3-mutant cells than the WT MDA-MB-231 cells. While both WT and MLL3-mutant CD44+CD104high hybrid EMT cells showed significantly increased lung metastatic ability than the counterpart CD44+CD104low mesenchymal cells, the MLL3-mutant hybrid cells showed a much greater metastasis-initiating ability than the WT hybrid cells.
Here we reported the gene expression profiles of CD44+CD104high E/M hybird and CD44+CD104-/low mesenchymal cell populations sorted from Foskolin-treated, WT MDA-MB-231 cells.

overall_design: We treated the WT and MLL3-mutant MDA-MB-231 cells with the PKA activator forskolin for 14 days and used flow cytometry to isolate CD44+CD104high hybrid EMT and CD44+CD104low mesenchymal tumor cells. RNA was isolated from these populations and RNA-seq was preformed for comparison the gene expression.


title: Bioengineered pancreas-liver crosstalk in a microfluidic co-culture chip identifies human metabolic response signatures in prediabetic hyperglycemia

city: Stockholm

first: Volker

last: Lauschke

address: Solnavägen 9

institute: Karolinska Institutet

summary: Aberrant glucose homeostasis is the most common metabolic disturbance affecting 1 in 10 adults worldwide. Prediabetic hyperglycemia due to dysfunctional interactions between different human tissues, including pancreas and liver, constitutes the largest risk factor for the development of type 2 diabetes. However, this early stage of metabolic disease has received relatively little attention. Microphysiological tissue models that emulate tissue crosstalk offer emerging opportunities to study metabolic interactions. Here, a novel modular multi-tissue organ-on-a-chip device is presented that allows for integrated and reciprocal communication between different 3D primary human tissue cultures. We achieved precisely controlled heterologous perfusion of each tissue chamber through a microfluidic single “synthetic heart” pneumatic actuation unit connected to multiple tissue chambers via specific configuration of microchannel resistances. On-chip co-culture experiments of organotypic primary human liver spheroids and intact primary human islets demonstrate insulin secretion and hepatic insulin response dynamics at physiological timescales upon glucose challenge. Integration of transcriptomic analyses with promoter motif activity data of 503 transcription factors reveals tissue-specific interacting molecular networks that underlie β-cell stress in prediabetic hyperglycemia. Interestingly, liver and islet cultures showed surprising counter-regulation of transcriptional programs, emphasizing the power of microphysiological co-culture to elucidate the systems biology of metabolic crosstalk.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary human pancreatic islets and primary human hepatic cells

first: Reza

middle: Z

last: Shafagh

first: Sonia

last: Youhanna

first: Jibbe

last: Keulen

first: Joanne

middle: X

last: Shen

first: Nayere

last: Taebnia

first: Lena

last: Preiss

first: Kathrin

last: Klein

first: Florian

last: Büttner

first: Mikael

last: Bergqvist

first: Wouter

last: van der Wijngaart


title: REST overexpression in mice causes deficits in spontaneous locomotion

city: Houston

first: Bin

last: Liu

state: TX

address: 1515 Holcombe BLVD

department: epigenetics and molecular carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: Overexpression of REST has been implicated in brain tumors, ischemic insults, epilepsy, and movement disorders such as Huntington’s disease. However, owing to the lack of a conditional REST overexpression animal model, the mechanism of action of REST overexpression in these disorders has not been established in vivo. We created a REST overexpression mouse model using the human REST (hREST) gene. Our results using these mice confirm that hREST expression parallels endogenous REST expression in embryonic mouse brains. Further analyses indicate that REST represses the dopamine receptor 2 (Drd2) gene, which encodes a critical nigrostriatal receptor involved in regulating movement, in vivo. Overexpression of REST using Drd2-Cre in adult mice results in increased REST and decreased DRD2 expression in the striatum, a major site of DRD2 expression, and phenocopies the spontaneous locomotion deficits seen upon global DRD2 deletion or specific DRD2 deletion from indirect-pathway medium spiny neurons. Thus, our studies using this mouse model not only reveal a new function of REST in regulating spontaneous locomotion but also suggest that REST overexpression in DRD2-expressing cells results in spontaneous locomotion deficits.

overall_design:
RNA profiling of a REST overexpression mouse model using the human REST (hREST) gene.
*** Submitter declares that raw data files are no longer available. ***

first: Sadhan

last: Majumder