title: A forward genetics screen identifies modifiers of Rocaglate responsiveness

city: Montreal

first: Jerry

last: Pelletier

state: Qc

address: 3655 Promenade Sir William Olser

institute: McGill University

summary: Rocaglates are a class of eukaryotic translation initiation inhibitors that are being explored as chemotherapeutic agents. They function by targeting eukaryotic initiation factor (eIF) 4A, an RNA helicase critical for recruitment of the 40S ribosome (and associated factors) to mRNA templates. To appreciate how rocaglates could best be enabled in the clinic, an understanding of resistance mechanisms is important, as this could inform on strategies to bypass such events as well as responsive tumor types. In performing a forward genetics screen using a cDNA library, we identified FOXP3 to be a gene of interest. As FOXP3 is a known transcriptional regulator, understandings its impacts on the transcriptional landscape was a logical undertaking in elucidating the resistance mechanis. Here, we report on the RNAseq results in Hap1 cells overexpressing FOXP3 compared to a negative control cell line expressing GFP. We find that certain genes involved in response to drug, such as ABCB1 (P-glycoprotein), are potently upregulated in a FOXP3-overexpression setting.

overall_design: We performed RNA-Seq transcriptional profiling of Hap1 cells overexpressing FOXP3 or GFP cDNAs. Briefly, Hap1 CML cells were transduced with vectors encoding our genes of interest. Each cell line (5 x 10^6) was then seeded into 10 cm dishes and allowed to expand for 48 hours. Cells were then washed with PBS, and RNA was harvested using the Qiagen RNeasy Mini Kit with on-column DNase I digestion. Samples were then sent to the Institut de Recherches Cliniques de Montréal (IRCM) for library preparation and deep sequencing. RNA integrity was first assessed on Bioanalyzer RNA Pico chips, then strand-specific, barcoded libraries were prepared via cDNA production, PCR, and ribosomal RNA (rRNA) depletion. Deep sequencing was performed using the Illumina HiSeq 4000 platform with paired-end 50 reads at approximately 50 million reads per sample. Biological triplicates for both GFP- and FOXP3-expressing cells were obtained.

first: Leo

last: Shen

first: HanChen

last: Wang


title: Comparative transcriptome analysis of different root types in rice under salinity stress

status: Public on Sep 23 2021

city: Nagoya

first: Joyce

last: Cartagena

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

type: Expression profiling by high throughput sequencing

summary: Changes in the gene expression during exposure to salinity stress were compared among nodal roots, S-type lateral roots, and L-type lateral roots.

overall_design: Using RNA sequencing, key genes involved in lateral root development under salt stress conditions were identified.


title: Rat colonic tissue transcriptome with dietary intervention by freeze-dried baby spinach (10% w/w in AIN-93 diet)

status: Public on Sep 22 2021

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

country: USA

institute: Guangzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Polyposis in rat colon (Pirc) model harbors an Apc mutation and mimics human Familial Adenomatous Polyposis (FAP), allowing for intervention studies (e.g., PMID: 27706811, PMID: 30643017). RNA-sequencing of adenomatous polyps and normal colon identified genes altered by dietary spinach consumption.

overall_design: RNA-seq analyses of transcriptome from rat colon tumors and normal colon samples.

first: Ying-Shiuan

last: Chen

first: Wan

middle: M

last: Dashwood

first: Roderick


title: Transcriptome analysis of human pancreatic preadipocytes and in vitro differentiated adipocytes

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

summary: The aim of this study is to investigate the impact of the metabolic status on the transcriptome of isolated preadipocytes and in vitro differentiated adipocytes. We identified 38654 transcripts in pancreatic fat cells. We report that preadipocyte differentiation increased the abundance of mRNA levels of proteins related to adipogenesis and lipid metabolism. These changes in the transcriptome were absent or less pronounced in fat cells obtained from patients with prediabetes and type 2 diabetes. Meanwhile, mRNA levels of proteins involved in excellular matrix remodeling, angiogenesis and cytoskeleton organization were less abundant in adipocytes of all metabolic groups.

overall_design: Isolated preadipocytes and respective in vitro differentiated adipocytes from 12 different human donors stratified between non-diabetic, prediabetic and type 2 diabetic metabolic status.

first: S

last: Ullrich

first: M

middle: B

last: Oquendo

first: A

last: Dahl

last: Gauder


title: CircGLIS3 promotes high-grade glioma invasion via modulating Ezrin phosphorylation (microarray)

city: Guangzhou

first: Yan

state: Guangdong

address: Industrial Road No.253, Guangzhou, Guangdong, 510282, China

department: Department of Neurosurgery

country: China

institute: Zhujiang Hospital

summary: High-grade glioma is highly aggressive and malignant, resistant to combined therapies and easy to relapse. A better understanding of circRNA biological function in high-grade glioma might contribute to the therapeutic efficacy. Here, a circRNA merely up-regulated in high-grade glioma, circGLIS3 (hsa_circ_0002874, originating from exon 2 of GLIS3), was validated by microarray and qRT-PCR. Functional experiments uncovered that up-regulation of circGLIS3 promoted glioma cell migration and invasion, and showed aggressive characteristics in tumor-bearing mice. Fluorescence in situ hybridization, RNA pull-down, RNA immunoprecipitation and immunohistochemical staining showed that circGLIS3 could promoted Ezrin T567 phosphorylation. Further investigation showed that circGLIS3 could be excreted by glioma through exosomes and induced endothelial cells angiogenesis. This study indicates that circGLIS3 is up-regulated in high-grade glioma and contributes to the invasion and angiogenesis of glioma via promoting Ezrin T567 phosphorylation.

overall_design: circular RNA microarray analysis of human brain glioma samples.

first: Jiansheng

first: Yiquan

last: Ke


title: Ints11 is essential for normal function of hematopoietic stem/progenitor cells

city: San Antonio

first: Peng

last: Zhang

state: TX

address: 8403 Floyd Curl Drive

institute: UT Health San Antonio

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Next Generation Sequencing of Response to Mito-Tempo in Intestinal Mucosal Biopsies from Crohn's Disease patients

city: Aurora

first: Kibrom

middle: Meles

last: Alula

state: CO

department: Pediatrics

institute: University of Colorado Anschutz Medical Campus

summary: Purpose: The purpose of this study was to investigate the transcriptomic changes in active Crohn's disease biopsies driven by a mitochondrial-targeted drug (Mito-Tempo)

overall_design: Terminal ileal mucosal biopsies from active sites of Crohn's disease or non-IBD control patients were treated in an ex vivo culture system at 0.5 mg/g tissue Mito-Tempo or vehicle in a humidified environment at 37°C and 5% CO2 for 2 hr. Total RNA was isolated from patient biopsies and analyzed by RNA sequencing by Novogene.

first: Arianne

middle: L

last: Theiss


title: Smoking shifts Human Airway Epithelium Club Cells toward a Lesser Differentiated Population

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: The club cell, a small airway epithelial (SAE) secretory cell that uniquely expresses SCGB1A1, plays a central role in host defense in the human lung. Based on data demonstrating that ~50% of club cells express MUC5B, a secretory mucin critical for mucociliary clearance, we hypothesized that subpopulations of club cells with distinct functions may exist. To evaluate this, the SAE of normal nonsmokers and healthy cigarette smokers was sampled by bronchoscopy and brushing followed by single cell sequencing using Drop-seq technology. Subpopulations of SCGCB1A1+KRT5loMUC5AC- club cells were assessed by unsupervised clustering to evaluate club cell subpopulations. Immunostaining of SAE in lung sections, brushed SAE cells, and in vitro air-liquid interface culture was utilized to confirm the transcriptomic-based observations. Unsupervised clustering of SCGCB1A1+KRT5loMUC5AC‾ club cells in the SAE identified 3 unique club cell populations that differed by differentiation state and function, including: (1) progenitor; (2) proliferating; and (3) effector subpopulations. The progenitor club cell population was energetically active with high expression of mitochondrial and ribosomal proteins and the highest KRT5 levels vs other club cell populations. The proliferating population, defined by high expression of cyclins and proliferation markers, was the smallest, representing 2% of club cells. The effector club cell cluster expressed transcripts for host defense genes, xenobiotic metabo-lism, and barrier functions commonly associated with club cell function. Comparison of the club cell subpopulations in smokers vs nonsmokers demonstrated that the proportion of the club cell effector population was significantly decreased in smokers with a concomitant significant in-crease in the proliferating cell population. These observations provide novel insights into both the makeup of human SAE club cell subpopulations and smoking-induced changes in club cell biology.

overall_design: Single cell-RNAseq was used to compare the club cell subpopulations in smokers vs nonsmokers.

first: Michelle

middle: G

last: LeBlanc

first: Mahboubeh

middle: R

last: Rostami

last: Struclovici-Barel

first: Wu-lin

last: Zuo

first: Jason

last: Mezey

first: Sarah

last: O'Beirne

first: Robert

middle: J

last: Kaner

first: Philip

last: Leopold

first: Ronald

last: Crystal


title: Ints11 is essential for normal function of hematopoietic stem/progenitor cells [RNA-seq]

summary: To investigate the role of INTS11 in normal hematopoiesis, Ints11 conditional KO mouse model was generated. We purified the Lin-cKit+ cells from bone marrow of WT and Ints11 KO mice and studied the differentially expressed genes due to the Ints11 loss.

overall_design: RNA-seq for bone marrow Lin-cKit+ cells from WT (n=3) and Ints11 conditional KO (n=3) mice.

first: Feng-Chun

last: Yang

first: Pinpin

last: Sui


title: Transcriptomic analysis of glomeruli and kidney cortex  following podocyte-loss of Klf4

city: Philadelphia

first: Mark

last: Kahn

state: PA

address: 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania


title: Differential gene expression between immature and mature enterocyte like-Caco2 cells

city: Nantes

first: Aurelie

last: Thedrez

address: 8 quai Moncousu

country: France

institute: INSERM

summary: Human Caco2 intestinal cells represent an in vitro model of human enterocytes. These cells are able to acquire a phenotype of mature polarized enterocytes when they are maintained in transwell culture system for 2-3 weeks.The goal of this study was to analyze the differences in mRNA expression profiles between Caco2 cells at a early stage of their differentiation  (day 8) and at a more advanced stage of their differenciation (day 16) into absorptive enterocytes. A 3' Digital Gene expression (DGE) RNA sequencing  was performed to determine mRNA  expression profiles.

overall_design: 3' DGE RNA sequencing was performed on 4 samples of immature (day 8) and mature (day 16) enterocyte like-Caco2 cells.

first: Aurélie

first: Cédric

last: Le May


title: Transcriptomic analysis of kidney cortex following podocyte-loss of Klf4

summary: The goal of this study was to identify transcriptomic changes of mouse kidney cortex in mice with podocyte-specific deletion of Kruppel-like factor 4, a zinc-finger transcription factor.

overall_design: Two experimental groups were analyzed, with three replicates for each group.

first: Jesse

middle: A

last: Pace

first: Yiqing

last: Guo

first: Chelsea

middle: C

last: Estrada

first: Sandeep

middle: K

last: Mallipattu


title: Dual RNA-seq transcriptome analysis of chicken caeca infected with Eimeria tenella

city: Utrecht

first: Arnar Kari

last: Sigurdarson Sandholt

address: Yalelaan 2

department: IRAS

country: Netherlands

institute: Utrecht University

summary: In order to elucidate the infection mechanisms of Eimeria tenella and the chicken immune response, chickens were infected with Eimeria tenella strain Hougton sporozoites. Samples were taken at 0, 1, 2, 3, 4 and 10 days post-infection and mRNA sequenced. A dual-RNA seq analysis was carried out, comparing the expression of infected chickens during each sampling time point with uninfected chickens and comparing E. tenella samples during the infection with a sample of pure sporozoites. The results show a variety of response signals in the chicken, both previously known and unknown, as well as a clear role for a variety of infection-related genes in E. tenella

overall_design: mRNA profiles of chicken caeca, both uninfected and infected with Eimeria tenella sporozoites

first: Arnar

last: Sandholt

first: Eva

last: Wattrang

first: Tobias

last: Lilja

first: Harri

last: Ahola

first: Anna

last: Lundén

first: Karin

last: Troell

first: Staffan

last: Svärd

last: Söderlund


title: Ints11 is essential for normal function of hematopoietic stem/progenitor cells [single-cell RNA-seq]

first: Peng

last: Zhang

summary: To investigate the role of INTS11 in normal hematopoiesis, Ints11 conditional KO mouse model was generated. We purified the cKit+ cells from bone marrow of WT and Ints11 KO mice and performed the single cell RNA-seq to study the molecular changes in each cell population.

overall_design: Single cell RNA-seq for bone marrow cKit+ cells from WT (n=2) and Ints11 conditional KO (n=2) mice.

first: Feng-Chun

last: Yang

first: Pinpin

last: Sui


title: Single-cell transcriptome of early hematopoiesis guides arterial endothelial-enhanced functional T cell generation from human PSCs

first: Xin

last: Li

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

summary: Human pluripotent stem cells (hPSCs) provide a powerful platform for studying the dynamic molecular network towards hematopoiesis. To date, a comprehensive roadmap at single-cell resolution for hPSC-derived hematopoietic differentiation has not been established. Here, we performed extensive single-cell transcriptomic analyses to map fate choices and gene expression programs during hematopoietic differentiation of hPSCs and identified strategies to improve the quantity and quality of hPSC-derived hematopoietic cells. By focusing specifically on cell populations and molecular events involved in endothelial-to-hematopoietic transition (EHT), the EHT was identified accompanying by a decline in aerobic metabolism and providing hypoxia in vitro enhances arterial and hematopoietic differentiation. Furthermore, arterial endothelial cells are validated as a critical regulator of definitive hematopoietic progenitor specification. Collectively, our study provides benchmark datasets to understand the origins of human hematopoiesis and presents an advance for guiding the generation of functional hematopietic cells in vitro for clinical applications.

overall_design: The study constructed the first hematopoietic landscape of hPSCs at the single-cell level and identify novel strategies for promoting definitive hematopoietic differentiation of hPSCs for applications in hematological biology.

first: Jun

last: Shen

first: Zack

first: Tao

last: Cheng


title: CG7379/ING1 in cancer progression. A study of migration and invasion in in vivo and in vitro epithelial systems

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

summary:
Metastasis is the leading cause of death for cancer patients. Consequently it is imperative that we improve our understanding of the molecular mechanisms that underlie progression of tumour growth towards malignancy. A large-scale genetic screen was carried out to identify genes that affect tumour progression in the living fly. This screen identified CG7379 as promoting cancer cell invasion when gene expression was knocked down in epithelial tumours in the dorsal thorax of the fly. The uncharacterised CG7379 Drosophila gene shows high homology with the human ING (inhibitor of growth) gene family. ING proteins are known to be involved in the control of cell proliferation, senescence and apoptosis. However, their potential role in cell migration and invasion is yet to be properly documented. Homeostasis of epithelial tissues relies on the control of cell polarity and architecture, and our results strongly suggest that CG7379 and ING1 play an important role in cell-cell junction integrity maintenance. The knockdown of both the Drosophila and human gene increases invasion in the living animal and in in vitro invasion assays respectively and gene knock-down led to severe disruption of cell-cell junction integrity.
We used Clariom™ S Assay arrays to detail the global programme of gene expression following ING1 KD to detect DEG involved in regulation of cell motility and cell-cell junction assembly and maintenance.

overall_design: In order to assess the role of ING1 in invasion, ING1 was transiently knocked down by siRNA in MCF-7 cells 48h prior to RNA extraction and hybridization on Affymetrix microarrays. 3 independent experiments were performed, each including un-treated cells, cells treated with mock siRNA and cells treated with ING1 siRNA. The microarray analysis was further conducted in triplicate for each sample.

first: Alexandra

middle: D

last: Rusu

first: Marcos

last: Castellanos Uribe


title: Regulation of gene expression in splenic cDC1 isolated from WT vs XCR1-/- miceNK cells orchestrate cDC1 migration to potentiate antiviral protective CD8+ T cell responses

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

summary: The expression of the XCR1 chemokine receptor univocally identifies all type 1 conventional dendritic cells (cDC1) throughout the body. The gene encoding its ligand, XCL1, is expressed constitutively by innate lymphoid cells such as natural killer (NK) cells. The evolutionary conservation of XCR1, XCL1 in vertebrates suggests that they play a critical, yet uncharacterized, role in immune responses. Here we showed using mouse cytomegalovirus (MCMV) infection, that the XCL1/XCR1 axis promoted the intra-splenic repositioning of cDC1 towards IFN--producing NK cells forming superclusters around infected cells. There, cDC1 and NK cells engaged into physical interactions enhancing their respective production of IL-12 and IFN-. This feed-forward mechanism also led to NK cell production of GM-CSF, which upregulated CCR7 on cDC1, instructing them to migrate into the T cell area for the priming of CD8+ T cells. In conclusion, we identified a novel mechanism through which NK cells boost the relay between innate and adaptive immunities by regulating the spatiotemporal functions of cDC1.

overall_design: C57BL/6J (WT)  and XCR1-/- mice were infected with MCMV and their spleens were harvested 1.5 days (36h) after infection: CD11c+ cells were first enriched from each splenocyte suspension, then cDC1 were FACS-sorted, and used for pangenomic gene expression profiling by microarrays. Sorted cDC1 from spleen of uninfected WT and XCR1-/- mice were used as controls.

first: Sonia

last: Ghilas

first: Marc

last: Ambrosini

first: Jean-Charles

last: Cancel

first: Marion

last: Massé

last: Dalod

first: Karine

last: Crozat


title: Ints11 is essential for normal function of hematopoietic stem/progenitor cells [ChIP-Seq]

summary: To investigate the role of INTS11 in normal hematopoiesis, Ints11 conditional KO mouse model was generated. We purified the Lin-cKit+ cells from bone marrow of WT and Ints11 KO mice and performed the ChIP-seq using different histone modifications to invesigate the gene regulation.

overall_design: ChIP-seq (H3K27me3 and H3K4me3) for bone marrow Lin-cKit+ cells from WT (n=2) and Ints11 conditional KO (n=2) mice.


title: Gene expression profile in failing heart with or without empafliglozin administration

city: Bunkyo-ku

first: Goro

last: Katsuumi

state: Tokyo

address: Hongo 2-1-1

institute: Juntendo University

summary: RNA-seq analysis to investigate gene expression profiles in cardiac tissue during pressure overload with or without Empafliglozin administration.

overall_design: Cardiac samples were harvested from C57BL/6Ncr mice  during pressure overload with or without empagliflozin treatment.

first: Masaaki

last: Nakao

first: Ippei

last: Shimizu

first: Tohru

last: Minamino


title: Aconitate decarboxylase 1 participates in the control of pulmonary Brucella infection in mice

status: Public on Sep 21 2021

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Brucellosis is one of the most widespread bacterial zoonoses worldwide. Here, our aim was to identify the effector mechanisms controlling the early stages of intranasal infection with Brucella in C57BL/6 mice. During the first 48 hours of infection, alveolar macrophages (AMs) are the main cells infected in the lungs. Using RNA sequencing, we identified the aconitate decarboxylase 1 gene (Acod1; also known as Immune responsive gene 1), as one of the genes most upregulated in murine AMs in response to B. melitensis infection at 24 hours post-infection. Upregulation of Acod1 was confirmed by RT-qPCR in lungs infected with B. melitensis and B. abortus. We observed that Acod1-/- C57BL/6 mice display a higher bacterial load in their lungs than wild-type (wt) mice following B. melitensis or B. abortus infection, demonstrating that Acod1 participates in the control of pulmonary Brucella infection. The ACOD1 enzyme is mostly produced in mitochondria of macrophages, and converts cis-aconitate, a metabolite in the Krebs cycle, into itaconate. Dimethyl itaconate (DMI), a chemically-modified membrane permeable form of itaconate, has a dose-dependent inhibitory effect on Brucella growth in vitro. Interestingly, modelling studies suggest the binding of itaconate into the binding site of isocitrate lyase. DMI does not inhibit multiplication of the isocitrate lyase deletion mutant ∆aceA B. abortus in vitro. Finally, we observed that, unlike the wt strain, the ∆aceA B. abortus strain multiplies similarly in wt and Acod1-/- C57BL/6 mice. These data suggest that bacterial isocitrate lyase might be a target of itaconate in AMs.

overall_design: Detection of genes differentially expressed before and after intranasal infection of mice with B. melitensis

first: Aurore

last: Demars

first: Armelle

last: Vitali

first: Audrey

last: Comein

first: Elodie

last: Carlier

last: Azouz

first: Stanislas

last: Goriely

first: Justine

last: Smout

first: Véronique

last: Flamand

first: Mégane

last: Van Gysel

first: Johan

last: Wouters

first: Jan

last: Abendroth

first: Thomas

last: E. Edwards

first: Arnaud

last: Machelart

first: Eik

last: Hoffmann

first: Priscille

last: Brodin

first: Xavier

last: De Bolle

first: Eric

last: Muraille


title: Gene expression analysis of Th-MYCN neuroblastoma tumours treated with CBL0137 and panobinostat

city: Randwick

first: Michelle

last: Haber

state: NSW

address: Lowy Cancer Research Centre, PO BOX 81

country: Australia

institute: Children's Cancer Institute

summary: The aim of this experiment is to identify the changes in gene expression induced by CBL0137, panobinostat and their combination

overall_design: The vehicle control, CBL0137, panobinostat, or the combination was given to homozygous Th-MYCN+/+ transgenic mice when spontaneous neuroblastomas developed to 5 mm in diameter in these mice. Three mice per group were included. CBL0137 was given intravenously at 40 mg/kg and panobinostat IP at 5 mg/kg one dose, and tumours were harvested 16 hours post treatment for RNA-seq.

first: Xiao

last: Lin

first: Somers

last: Klaartje

first: Mayoh

last: Chelsea

first: Murray

last: Jayne

first: Norris

last: Murray

first: Haber

last: Michelle


title: SNX18 inhibits melanoma migration by modulating the activation ratio of Cdc42 & RhoA [microarray]

city: Ramat Gan,

first: Maya

middle: Ramot

last: Goshen

address: Derech Sheba 2,

department: Clinical Microbiology and Immunology

country: Israel

institute: Tel Aviv University

summary:
To identify novel proteins that control melanoma development and progression, we integrated high-throughput proteomics, mRNA and miRNAs datasets from isogenic primary (WM115) and metastatic (WM266-4) melanoma cell-lines. We focused on differentially expressed proteins that had non-differential mRNA levels and were putatively targeted by a high number of miRNAs. SNX18, a sub-family member of sorting-nexins that participates in endocytosis and autophagy was down-regulated by 6-fold in WM266-4, and predicted to be targeted by 17 miRNAs. Over-expression of SNX18 in several melanoma cell-lines significantly reduced migration rate, while silencing of SNX18 resulted in the opposite effect. Notably, progression tissue microarrays demonstrated a trend for SNX18 downregulation in early metastasis. Luciferase assays confirmed the direct regulation of SNX18 by multiple miRNAs. Indeed, over-expression of these miRNAs repressed endogenous SNX18 expression at the protein but not mRNA level. Further, protein but not mRNA expression levels correlated with better overall survival as determined in a cohort of 48 metastatic melanoma patients and in the TCGA database. Mechanistically, SNX18-mediated reduced migration coincided with RhoA activation and Cdc42 inactivation. Both play a role, as RhoA inhibitor and constitutively activated Cdc42 mutants abrogated this effect. Moreover, phosphorylation-defective SNX18 mutants (S233A,S233D) migrated faster, with S233A inactivating RhoA and activating Cdc42, while S233D activated both. The downstream phosphorylation of the p38>MAPKAPK2>HSP27 signaling pathway was concordant. Both mutants were more abundant in the plasma membrane. Taken together, phosphorylation of S233 is crucial for SNX18 activation, but de-phosphorylation dynamics, which may occur at the membrane, is required for functional effect.
mRNA expression profile of primary (WM115) and metastatic (WM266-4) melanoma cell lines.

overall_design: A total of 3 biological replicates of WM115 and WM266-4 were compared.

first: Michal

last: Harel

first: Ettai

last: Markovits

first: Keren

last: Shapira

first: Erez

last: Baruch

first: Iris

last: Barshack

last: Besser

first: Jacob

last: Schachter

first: Rona

last: Ortenberg

first: Metsada

middle: P

last: Chor

first: Jasmine

last: Hirsch

first: Yoav

last: Henis

first: Tamar

last: Geiger

first: Gal

last: Markel


title: Mucosal melanomas of different anatomic sites share a common DNA methylation profile but show different patterns of genetic and epigenetic alterations

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

summary: Cutaneous, ocular and mucosal melanomas are histologically indistinguishable tumors that are driven by different spectrum of genetic alterations. With current methods, identification of the site of origin of a melanoma metastasis is challenging, in particular when the metastasis is the first tumor manifestation. Genome wide DNA methylation profiling has shown promise for the identification of the site of tumor origin in various settings. Here we explore the DNA methylation landscape of melanomas from different sites and analyze if different melanoma origins can be distinguished by their epigenetic profile.   We performed DNA methylation analysis, next generation DNA panel sequencing and copy number analysis of 82 non-cutaneous and 25 cutaneous melanoma samples. We further analyzed eight normal melanocyte cell culture preparations by DNA methylation profiling.  DNA methylation analysis clearly separated uveal melanomas from melanomas of other primary sites while mucosal, conjunctival and cutaneous melanomas were epigenetically almost identical. Still, we observed DNA methylation differences in cancer-related genes, such as low frequencies of RARB and CDKN2A promoter methylation in mucosal melanomas, while conjunctival melanomas frequently harbored APC promoter methylation. Furthermore, all investigated melanomas of the paranasal sinus showed loss of PTEN expression, mainly caused by promoter methylation. This was less frequently seen in melanomas of other sites.   Copy number analysis revealed recurrent amplifications in mucosal melanomas, including chromosome 4q, 5p, 11q and 12q. Most melanomas of the oral cavity showed gains of chromosome 5p with TERT amplification while 11q amplifications were enriched in melanomas of the nasal cavity.   Mucosal, conjunctival and cutaneous melanomas show a surprisingly similar DNA methylation profile and identification of the site of origin by DNA methylation testing is likely not feasible. Still, our study shows that there are DNA methylation differences on the gene level in known tumor drivers, related to the anatomical primary site.

overall_design: 25 cutaneous, 82 non-cutaneous malignant melanoma samples as well as eight normal melanocyte cell culture preparations were analyzed using the Illumina Infinium MethylationEPIC BeadChip

first: David

last: Capper


title: Transcription factor 4 controls positioning of cortical projection neurons through regulation of cell adhesion

status: Public on Sep 20 2021

city: Shanghai

first: Yunli

last: Xie

address: 131 Dong`an Road

department: Institutes of Brain Science

institute: Fudan University

summary: The establishment of neural circuits depends on precise neuronal positioning in the cortex, a tightly coordinated process of neuronal differentiation, migration and terminal localization. Deficit in this process is implicated in several psychiatric disorders. Here, we show that the transcription factor Tcf4 controls neuronal positioning during brain development. Tcf4-deficient neurons become mispositioned in clusters when their migration to the cortical plate is complete. We reveal that Tcf4 regulates the expression of cell adhesion molecules to control neuronal positioning. Furthermore, through in vivo extracellular electrophysiology, we show that neuronal functions are disrupted after the loss of Tcf4. TCF4 mutations are strongly associated with schizophrenia and cause Pitt-Hopkins syndrome, which is characterized by severe intellectual disability. Thus, our results not only reveal the importance of neuronal positioning in brain development and but also provide new insights into the potential mechanisms underlying neurological defects linked to TCF4 mutations.

overall_design: examine the gene expression change after loss of TCf4

first: Yandong

last: Zhang


title: Identifying Risk Factors for Secondary Infection Post-SARS-CoV-2 Infection

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

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

summary: The antibiotic catabolic process and myeloid cell homeostasis were activated while the T-cell response were relatively repressed in those with the risk of secondary infection.

overall_design:
RNA-seq analysis in the peripheral blood mononuclear cell isolated shortly from initial infection.

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: Jian

last: Chen

first: Mingquan

last: Guo


title: Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin [RNA-Seq]

city: Dallas

first: Jialiang

last: Wang

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Some cuboidal osteoblasts differentiate into bone-embedded, dendrite-bearing osteocytes through the poorly-understood process of osteocytogenesis. Here, we report that the transcription factor Sp7 plays an essential role in osteocytogenesis. Severe defects in bone integrity and osteocyte dendrite morphology are noted in mice lacking Sp7 at the stage of the osteoblast-to-osteocyte transition. In osteocytes, Sp7 controls expression of a neuronally-enriched gene network. Analysis of the osteocyte-specific Sp7 cistrome reveals distinct genomic binding motifs and target sites distinct from those in osteoblasts. Amongst osteocyte-specific Sp7 targets, the secreted peptide osteocrin rescues Sp7-deficient defects. Single-cell transcriptional profiling of cells undergoing osteocytogenesis identifies novel Sp7-dependent transitional cell types enriched in genes linked to human fracture risk. Finally, humans with an SP7 R316C mutation display osteocyte morphology defects similar to those observed in mouse models. These findings demonstrate that cuboidal osteoblasts use a neuronally-enriched Sp7/osteocrin gene expression program to differentiate into dendrite-bearing osteocytes.

overall_design: mRNA profiles of Sp7 knockdown, LacZ knockdown (control), Sp7 overexpress, GFP overexpress (control), Ostn overexpress, 3D and 2D culture libraries were generated by deep sequencing in duplicate. mRNA profiles of 3D and 2D culture MC3T3-E1 cells were generated by deep sequencing in duplicate.

middle: S

first: Marc

middle: N

last: Wein


title: Common Tumor Suppressive Signaling of Thyroid Hormone Receptor Beta in Breast and Thyroid Cancer Cells

city: Burlington

first: Frances

last: Carr

state: Vermont

address: 149 Beaumont Ave, HSRF 340

institute: University of Vermont

summary: The thyroid hormone receptor beta (TRβ) is a tumor suppressor in multiple types of solid tumors, most prominently in breast and thyroid cancer. An increased understanding of the molecular mechanisms by which TRβ abrogates tumorigenesis could aid in understanding the core tumor suppressive program that TRβ facilitates. Here, we introduce TRβ into the MDA-MB-468 basal-like breast cancer cell line and perform RNA-sequencing to determine changes in transcriptomic signaling. The TRβ expressing MDA-MB-468 cells exhibit a more epithelial character as determined by PCA-PAM50 score and through repression of mesenchymal cytokeratins. The epithelial to mesenchymal transition pathway is also significantly reduced. The MDA-MB-468 dataset was also compared to RNA sequencing results from the thyroid cancer line SW1736 to determine which genes are TRβ regulated across both tissue types. Stearate biosynthesis was revealed as upregulated from the shared gene set, a lipid which is known to repress breast tumorigenesis, as were chromatin remodeling pathways. These data provide novel insights into the molecular mechanisms by which TRβ suppresses breast tumorigenesis and suggests a common metabolic role in breast and thyroid cancer as well a role for TRβ in the maintenance of epithelial cellular identity.

overall_design: Transcriptomic analysis of breast cancer cells that stably overexpress TRβ and comparison with thyroid cancer cells that also overexpress TRβ (GSE150364).

first: Eric

last: Bolf

middle: E


title: Finding two synergized compounds from Chinese herbal medicine in rheumatoid arthritis therapy

city: Beijing

first: Xiaojuan

last: He

address: Dongzhimennei Nanxiaojie 16#

institute: China Academy of Chinese Medical Sciences

summary:
Purpose: To search candidate synergized compounds from Chinese herbal medicine used in RA therapy
Methods: Candidate synergized compounds were searched based on multi-information integrative approaches. In vivo experiment in collagen induced arthritis rat was then carried out to evaluate the efficacy and synergism of compounds combination treatment. RNA sequencing and IPA were used to investigate the synergized mechanism of combination treatment.
Results: We found a pair of compound combination which could alleviate the symptom of CIA rats. RNA sequencing and IPA analysis revealed that the synergistic mechanism of combination treatment was related to several canonical signaling pathways and key targets LTA, CD83 and SREBF1.
Conclusion: A pair of compound combination has been found. RNA sequencing and IPA analysis revealed that the synergistic mechanism of combination treatment was related to several canonical signaling pathways and key targets.

overall_design: CIA rats were treated with compound combination for 4 weeks. After sacrifice, the CD4+T lymphocytes from peripheral blood of rats were collected for further RNA sequencing.

first: Daogang

last: Guan

first: Aiping

last: Lu


title: Genome wide analysis of transcriptome modification after re-expression of PBRM1 WT and its BAH domain mutant in PBRM1 CRISPR-KO HEK293T cells.

city: Houston

first: Cheryl

last: Walker

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

institute: Baylor College of Medicine

summary: Purpose: To find out if cancer-associated mutation in BAH domain affects gene expression?  Method: We used PBRM1 CRISPR KO HEK293T cells and ectopically expressed GFP-PBRM1-WT, GFP-PBRM1 P1048R, GFP-PBRM1 T1202K and GFP-PBRM1 C1233W plasmid for 48 hours.  Result: We found that GFP-PBRM1 WT and GFP-PBRM1 T1202K mutant were identical in terms of gene expression. However, mutant P1048R and C1233W had very little difference in expression of only 15 (14 up- and 1 down) out of 10,160 genes.

overall_design: The cells were harvested after 48 hour of expression of WT and mutant PBRM1 and RNA was prepared for RNAseq analysis.

first: Coarfa

last: Cristian


title: Next Generation Sequencing Analysis of Bone Marrow Hematopoietic Progenitor Cells (HPC) and Leukemic Progenitors (LP) Transcriptomes

city: shanghai

first: hezhou

last: guo

address: Shanghai, P. R. China.  No. 197 Rui Jin Er Road

summary: Purpose: Next Generation Sequencing Analysis has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the transcriptomes between bone marrow HPC and LP sorted from early phase (E) and median phase (M) to find the changed genes in LP.

overall_design: mRNA profiles of HPC and LP sorted from E and M were generated by deep sequencing, in triplicate, using Illumina Hiseq 2000.

first: He-zhou

first: Jiang

last: Zhu


title: Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin [ChIP-Seq]

overall_design: Examination of Sp7 binding activity in mouse osteocyte-like cell line.


title: Transcriptomic analysis of glomeruli following podocyte-loss of Klf4

first: Mark

last: Kahn

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: The goal of this study was to identify transcriptomic changes of mouse glomeruli in mice with podocyte-specific deletion of Kruppel-like factor 4, a zinc-finger transcription factor.

overall_design: Two experimental groups were analyzed, with three replicates for each group.

first: Jesse

last: Pace

first: Yiqing

first: Chelsea

last: Estrada

first: Sandeep

last: Mallipattu


title: KAI1 functions as a negative regulator of angiogenesis

city: Suwon

first: Jae-Il

last: Choi

address: 164, World cup-ro, Yeongtong-gu

department: Pathology

country: South Korea

institute: Ajou University School of Medicine

summary: We sequenced mRNA from WT and Kai1 KO PVCs

overall_design: Examinantion of mRNA level in WT and Kai1 KO PVCs were generated by deep sequencing.

first: Jin

last: Hur

first: Hyo-Soo

last: Kim


title: Expression data from bone marrow stromal cells (CD45.1-Ter119-)

summary:
Recent studies suggest that bone marrow stromal cells are critical for forming a niche that maintains hematopoietic stem cells’ quiescence and adapt blood production to the organism’s needs. Alterations in the bone marrow niche are commonly observed in blood malignancies and directly contribute to the aberrant function of disease-initiating leukemic  stem cells.
We used microarrays to detail the global programme of stromal cells' gene expression during leukemic progression.

overall_design: Stromal cells were sorted form wild type mice or the leukemic recipients for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gradually changes of stromal cells’ gene expression during leukemic progression. To that end, we divide the leukemic progression in BM into four discrete phases: 1) the long latent phase when leukemic cells were nearly undetectable by routine flow cytometric assay; 2) the short early phase (E) in which leukemic proportion was between 1%-5%; 3) the medium phase (M) in which leukemic proportion was between 5-50%; and 4) the late phase (L) in which leukemic proportion was over 50%. Of note, the leukemic surpass soared up exponentially post-E phase

last: Guo


title: Importin α7 deficiency causes infertility in male mice by disrupting spermatogenesis

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Spermatogenesis, a fundamental process in male reproduction, is driven by an ordered series of events, which rely on the trafficking of specific proteins between nucleus and cytoplasm. The importin α family of proteins mediates movement of specific cargo proteins when bound to importin β. Importin α genes have distinct expression patterns in mouse testis, implying they may have unique roles during mammalian spermatogenesis. Here we use a loss-of-function approach to specifically determine the role of importin α7 (Kpna6) in spermatogenesis and male fertility. We show that ablation of importin α7 in male mice leads to infertility and has multiple cumulative effects on both germ cells and Sertoli cells culminating in oligozoospermia. Importin α7-deficient mice exhibit an impaired Sertoli cell function, including loss of Sertoli cells from the seminiferous epithelium and a compromised nuclear transport of the androgen receptor. Furthermore, our data demonstrate devastating defects in spermiogenesis that are accompanied by a disturbed histone-protamine-exchange in elongating spermatids, resulting in incomplete sperm maturation and a massive loss of sperms. Our work uncovers the essential role of importin α7 in spermatogenesis and hence in male fertility.

overall_design: The transcriptomes of testes obtained from Importin α7-/- and α7ΔIBB/ΔIBB mice was compared with those from C57Bl6/N by RNAseq in triplicate

last: Liu

first: Fatimunnisa

last: Qadri

first: Stefanie

last: Huegel

first: Gabin

last: Sihn

first: Ilya

last: Chuykin

first: Enno

last: Hartmann

first: Michael

last: Bader

first: Franziska

last: Rother


title: Expression signatures of long non-coding RNAs in Left ventricular Noncompaction

status: Public on Sep 19 2021

city: Nanchang

first: Qingshan

last: Tian

state: Jiangxi

address: 17 Yongwaizheng Street

department: Cardiology

institute: The First Affiliated Hospital of Nanchang University

summary: This result may predict some lncRNA as disease-specific biomarkers of LVNC, shed light on the development of LVNC diseases, and provide useful information for exploring potential therapeutic

overall_design: The blood samples of LVNC patients and healthy controls were obtained from May 2015 to October 2015 in the Department of Cardiology, this study compared the lncRNA and mRNA expression in the blood of 6 LVNC patients and tries to reveal the association of lncRNA with LVNC in the blood.

first: Hanxiao

last: Niu

first: Dingyang

last: Ta

first: Qing

last: Yang

first: Vikram

last: Norton

first: Yujing

last: Wu

first: Amit

last: Mati

first: Zhenzhong

last: Zheng

first: Hao


title: Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin [scRNA-Seq]

first: Jialiang

last: Wang

overall_design: Using single-cell RNA-seq to identify discrete populations of cells undergoing the osteoblast-to-osteocyte transition, and dramatic defects in this normal process in the absence of Sp7.

first: Marc

last: Wein


title: RNA-Sequencing quantitative analysis of transcriptomes changes between veh., and glutamate with or without P.edulis extracts treated mouse hippocampal HT-22 cells

city: Pathumwan

first: Shuqin

last: Cao

state: Bangkok

address: 154 Rama I Road Chula Soi 12

department: Allied Health Sciences

country: Thailand

institute: Chulalongkorn University

summary: Purpose: RNA-sequencing provides the system-based analysis of cellular pathways. The goals of this stude are to evaluate whether P.edulis attenuate glutamate-induced neurotoxicity via modify the expression of differenterly exprssed genes (DEGs) ant the relatives signaling pathways

overall_design: Methods: HT-22 cells mRNA samples from veh., glutamate with/without P.edulis pulp extract (FP) (100 μg/mL) or P. edulis peel extract (PP) (25 μg/mL) were used for transcriptomic analysis which performed by Beijing Genomics Institute (Hongkong).

first: Tewarit

last: Sarachana

first: Tewin

last: Tencomnao

first: Chalinee

last: Ronpirin


title: Single cell profiling of hemogenic endothelium and its surrounding niche in the mouse dorsal aorta

city: manchester

first: Muhammmad

middle: Zaki

last: Fadlullah Wilmot

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

summary: The first hematopoietic stem cells originate from hemogenic endothelium (HE), that trans-differentiate into the lumen to form hematopoietic clusters. The molecular mechanisms driving this transition are only poorly understood. Here, we performed single cell RNA-seq profiling of HE cells utilising a RUNX1 and GFI1 reporter mouse line.This allowed for a detailed characterisation of HE cells during endothelial-to-hematopoietic transition. Additionally we profiled the cells surrounding the dorsal aorta. These dataset present a comprehensive profile at single cell resolution of cells invovled in the endothelial-to-hematopoietic transition and the surrounding dorsal aorta niche.

overall_design:
Single cell RNA-seq of endothelium, hemogenic endothelium, cells undergoing endothelial-to-hematopoietic transition, and intra aortic hematopoietic clusters of E10.5 and E11.5. Surrounding mesenchymal cells of E10.5 were also profiled.

AGM of E10.5 and E11.5 embryos were dissected and scRNA-seq (Smart-seq2) was performed on phenotypically defined FACS populations. Utilizing the Gfi1/Gfi1b transgenic reporter mouse line, the following FACS population were sorted from E10.5 and E11.5 embryos; endothelial cells (FACS-ENDO, TER119-CD41-CD45-KIT-CDH5+GFI1-GFI1b-), hemogenic endothelium (FACS-HE, TER119-CD41-CD45-KIT-CDH5+GFI1+GFI1b-),  cells undergoing endothelial-to-hematopoietic transition (FACS-EHT, TER119-CD41+CD45-KIT+CDH5+GFI1+GFI1b-),  and intra-aortic hematopoietic clusters (FACS-IAHC, TER119-CD41+CD45-KIT+CDH5+GFI1+GFI1b+). Additionally, cells were isolated from E10.5 embryos utilising the Runx1b transgenic reporter to include hemogenic endothelium (FACS-HE, TER119-CD41-CD45-KIT-CDH5+RUNX1b+) and Runx1b+ mesenchymal cells surrounding the dorsal aorta (FACS-MES, TER119-CD41-CD45-KIT-CDH5-RUNX1b+). Finally, scRNA-seq was also performed on cells sorted based on ACE (CD143), encompassing endothelial cells (FACS_ENDO, TER119-CD41-CD45-KIT-CDH5+ACE-GFI1-), ACE positive cells (FACS-ACE_SinglePos, TER119-CD41-CD45-KIT-CDH5+ACE+GFI1-) and hemogenic endothelium (FACS-HE_DoublePos, TER119-CD41-CD45-KIT-CDH5+ACE+GFI1+).

first: Muhammad

middle: H

last: Fadlullah

first: Wen

last: Neo

first: Roshana

last: Thambyrajah

first: Syed

last: Baker

first: Valerie

last: Kouskoff

first: Magnus

last: Rattray

first: Georges

last: Lacaud


title: DNA damage-p53/p21 response contributes to ependymal cell development

city: PARIS

first: nathalie

last: spassky

address: 46 rue d'ULM

institute: IBENS

summary: Multiciliated Ependymal Cells and Adult Neural Stem Cells are components of the adult neurogenic niche, essential for brain homeostasis. These cells share a common glial cell lineage regulated by the Geminin family members Geminin and GemC1/Mcidas. Ependymal precursors require GemC1/Mcidas expression to massively amplify centrioles and become multiciliated cells. Here we show that GemC1-dependent differentiation occurs mostly in cycling Radial Glial Cells, in which a DNA damage response, including replicative stress and dysfunctional telomeres, arrests the cell cycle after the G1/S restriction point due to the activation of the p53-p21 pathway, which contributes to centriole amplification. Telomerase expression in Radial Glial Cells impairs ependymal differentiation and favors the Neural Stem Cell fate.

overall_design: Study how GemC1 trigger multiciliated cell fate

first: Gonzalo

last: Ortiz-Álvarez

first: Aurélien

last: Fortoul

first: Ayush

last: Srivastava

first: Matthieu

last: Moreau

first: Benoit

last: Bouloudi

first: Marion

last: Faucourt

first: Mathieu

last: Bahin

first: Franck

last: Toledo

first: Corinne

last: Blugeon

first: Marielle

last: Breau

first: Auguste

last: Genovesio

first: Vincent

last: Géli

first: Frédéric

last: Causeret

first: Alice

last: Meunier

first: Nathalie

last: Spassky


title: Chronic Kidney Disease in a Murine Model of non-Alcoholic Steatohepatitis (NASH)

city: New York

first: Chengguo

last: Wei

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary:
Non-alcoholic steatohepatitis (NASH) is a severe form of non-alcoholic fatty liver disease  (NAFLD) that underlies a growing prevalence of cirrhosis and liver cancer worldwide.  Clinical studies suggest that NASH is an independent risk factor for chronic kidney  disease (CKD), but models and mechanisms linking these two diseases are lacking. Here,  we have characterized the renal function, histological features, and transcriptomic profile  in a well-validated murine NASH model generated by feeding a western diet (WD), with  high contents of fat, fructose, and cholesterol, combined with a low dose of weekly IP  carbon tetrachloride (CCl4).
NASH mice developed significant glomerulosclerosis, tubular  epithelial cell injury, and interstitial fibrosis at an intermediate stage (12 weeks). Animals  with advanced NASH (24 weeks) displayed renal dysfunction, proteinuria, and renal  fibrosis characterized by increased collagen deposition as tubulointerstitial fibrosis,  tubular atrophy, and inflammatory cell infiltration. Mice treated with a low dose of CCl4  alone did not develop renal injury, thereby excluding the possibility of CCl4-induced  nephrotoxicity. Transcriptomic analysis of kidney cortices revealed differentially  expressed genes (DEGs) that were highly enriched in mitochondrial dysfunction, ATP  synthesis, and oxidative stress at the intermediate stage (12 weeks) and dysregulation of  the immune response, lipid metabolic process, and insulin signaling pathways at the late  stage (24 weeks). NRF-mediated oxidative stress pathway, Sirtuin signaling, and AMPK  pathways were also highly enriched. Our results confirm a causative role of NASH in the  development of CKD and reveal potential mechanisms of NASH-induced kidney injury.  These findings establish valuable model to study the pathogenesis of NASH-associated CKD, an important feature of fatty liver disease that has been largely overlooked, yet has  clinical and prognostic importance.

overall_design:
Control mice for 12 weeks (mice were fed with normal diet and corn oil for 12 weeks)
NASH mice for 12 weeks (mice were treated with WD and CCl4 for 12 weeks)
Control mice at 24 weeks (mice were fed with normal diet and corn oil)
NASH mice at 24 weeks (mice were treated with WD and CCl4)
RNA-seq profilin of kidney cortices

first: Xuezhu

last: Li

first: Dipankar

last: Bhattacharya

first: Scott

last: Friedman

first: John

last: He


title: Postprandial blood glucose and triglyceride metabolism govern bone marrow stem cell transcriptional regulation, premature aging and rejuvenation.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: The number of circulating endothelial progenitor cells (EPCs) predicts future development of atherosclerotic cardiovascular disease (ASCVD) and is reduced in patients with type 2 diabetes (T2DM) or impaired glucose tolerance (IGT). Recent studies revealed the contribution of tight control of glycolysis and mitochondrial oxidative phosphorylation (OXPHOS), as well as fatty acid oxidation in the regulation of stem cell behavior. In this study, we show that how dysregulated glucose and triglyceride metabolism in T2DM/IGT affects the homeostasis of EPCs, i.e. bone marrow stem/progenitor cells (BMSCs).   In our clinical study, consistent with previous reports, the patients with IGT or T2DM showed reduced level of circulating EPCs, as compared normal glucose tolerance. On the other hand, fasting or postprandial hypertriglyceridemia (hTG) itself did not affect the level of circulating EPCs. However, further analysis using single and multiple regression analyses strongly suggested that, in the presence of postprandial hTG, postprandial hyperglycemia exerts devastating effect on EPC homeostasis. We therefore carried out the proof of concept study in mice. Our experimental study revealed that repetitive glucose+lipid (G+L) spikes, but not repetitive glucose (G) spikes or lipid (L) spikes, rapidly upregulated p53 in BMSCs and induced premature aging phenotype of bone marrow cells, i.e. the impairment of BMSC quiescence and function, and myeloid-biased differentiation. Subsequent analysis implicated that p53-mediated augmentation of mitochondrial OXPHOS plays pivotal role for the impairment of BMSC quiescence and function. On the other hand, it is still not clear how repetitive G+L injection induced myeloid-biased differentiation. Because cell-fate decisions are executed by transcription factors in response to extracellular signals, and the best-known function of p53 is as a transcription factor, we asked to what extent repetitive glucose spikes and repetitive glucose+TG spikes affect transcriptional regulation in LSK cells.

overall_design: We obtained LSK cells from G injected mice (G-LSK cells), GL injected mice (GL-LSK cells) and respective PBS injected control mice (cont-LSK cells), and carried out RNA sequence analysis (n = 2, for each).

first: Masayoshi

last: Iwasaki

first: Ichiro

last: Shiojima


title: RNA-sequencing explores the transcriptional profile of Wild Type and DYRK1B transgenic hearts

first: Lingfang

last: Zhuang

address: 197 Rui Jin Road II

department: Department of Vascular & Cardiology

summary: Here, we investigates the effects of dual-specificity tyrosine-regulated kinase 1B (DYRK1B) on mitochondrial bioenergetics, cardiac hypertrophy, and heart failure.We engineered DYRK1B transgenic and the effects of DYRK1B and its downstream mediators were subsequently elucidated using RNA-seq analysis. In this dataset, we inquire the transcriptional profile of WT and DYRK1B transgenic hearts at 3-day and 8-week old.

overall_design: A total of twelve samples was analyzed. The 3-day old WT (n = 3) and DYRK1B-Tg (n = 3) hearts, 8-week old WT (n = 3) and DYRK1B-Tg ( n = 3) were included in final RNA-sequencing analysis. After genotyping, the hearts were collected and immediately frozen in liquid nitrogen for further analysis. Total RNA was extracted using TRIzol Reagent, reverse-transcribed, and amplified according to the standard procedures. Sequencing libraries were constructed using the BGISEQ-500 platform (BGI, Wuhan, China).

first: Kangni

last: Jia

first: Zhigang

first: Jiaxin

last: Zhao

first: Jian

last: Hu

first: Hang

last: Zhang

first: Qin

last: Fan

first: Chunkai

last: Huang

first: Hongyang

last: Xie

first: Lin

last: Lu

first: Weifeng

last: Shen

first: Guang

last: Ning

first: Jiqiu

last: Wang

first: Kang

last: Chen

first: Xiaoxiang

last: Yan


title: Construction of Synthetic Nanobody Library in Mammalian Cells by dsDNA-Based Strategies

city: Tianjin

first: Shuai

last: Li

state: Tianjin

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

summary: A nanobody is an antibody fragment consisting of a single monomeric variable antigen-binding domain. Mammalian cells are ideal platforms for identifying nanobodies targeting hard-to-display transmembrane proteins and nanobodies that function as modulators of cellular phenotypes. However, the introduction of a high-diversity nanobody library into mammalian cells is challenging. We have developed two novel methods for constructing a nanobody library in mammalian cells. Complementarity-determining region (CDR) random sequences were first incorporated into upstream and downstream dsDNAs by PCR. In the first method, named dsDNA-HR, upstream and downstream dsDNAs containing an identical overlapping sequence were co-transfected into cultured mammalian cells for intracellular homologous recombination that resulted in the formation of an intact nanobody library expression cassette. In the second method, named in vitro ligation, we generated full-length nanobody expression dsDNAs via ligation of restriction digested upstream and downstream dsDNAs. The obtained full-length dsDNAs were transfected into mammalian cells for nanobody library expression. Using both methods, we generated over a million unique nanobody sequences, as revealed by high-throughput sequencing. Single-cell sequencing was employed to resolve the diversity of the dsDNA-HR nanobody library. We also identified a small molecule, Nocodazole, which could enhance the efficacy of dsDNA-HR.

overall_design: Construction of nanobody libraries in mammalian cells: Two novel methods for the construction of nanobody libraries in mammalian cells, called dsDNA-HR and in vitro ligation, were developed. Both methods generated over a million unique nanobody sequences as revealed by high-throughput sequencing.

first: Yanjie


title: Genome-wide analysis of gene expression by LSD1 overexpression or inhibiting by ORY1001 with or without irradiation in MDA-MB-231 breast cancer cells

first: Junyun

state: Beijing

address: NO.1 Beichen West Road, Chaoyang District

department: CAS Key Laboratory of Genomic and Precision Medicine

institute: Beijing Institute of Genomics

summary: Analysis of LSD1 regulation after DNA damage at gene expression level.We supposed that LSD1 is involved in Double Strand DNA repair, alterated LSD1 expression with transfection vector or LSD1 inhibtor in MDA-MB-231, and finally found LSD1 promted DNA damage reponse after IR treatment.

overall_design: Total RNA obtained from MDA-MB-231 cells with six groups:WTIR-,WTIR+,OE+IR-,OE+IR+,ORY1001+IR-,ORY1001+IR+,IR represents exposed with ionization radiation (IR) treatment, WT represents control without any treatment, OE represents LSD1 overexpression (OE) with transfected LSD1 vector, ORY1001 represents treatment with LSD1 inhibitor ORY1001.

first: Yingli

last: Sun


title: Effects of a Uty gene trap on the transcriptomic profile of mouse cardiac left ventricles in response to castration

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 Pine Ave West

department: Institut de recherches cliniques de Montréal (IRCM)

country: Canada

institute: Université de Montréal

summary: Previous results from the laboratory showed that the genetic make up of chromosome Y modulated the effects of castration on the transcriptome of mouse cardiac left ventricles.  To test the effect of the chromosome Y Uty locus, the current study tests how castration affects the transcriptomes of cardiac left ventricles from adult male carrying a Uty gene trap (KO) in comparison to wild-type (WT)couterparts.

overall_design: Frozen left ventricles were obtained from adult mice that were either UtyGt(XS0378)Wtsi (which carries a gene trap within the 4th intron of the Uty gene) or their wild-type counterparts from the isogenic strain C57BL/6.Y<129P2> adult mice.  Animals had previously been either sham-operated (S) or castrated (C) at about 10 days of age.


title: STRAP is involved in mutated Apc-induced stemness and tumorigenesis in colon cancer

city: Birmingham

first: Pran

last: Datta

state: AL

address: 1824 6th Ave S

institute: University of Alabama at Birmingham

summary: To identify pathways mediating the effects of Strap in colon cancer development, we established the mRNA expression proﬁles of intestinal adenomas that formed in ApcMin/+ mice with and without Strap deletion.

overall_design: Colon adenoma mRNA profiles of 110-day old ApcMin and ApcMin StrapIEKO mice

first: Trung

last: Vu


title: Intestinal macrophage mRNA sequencing of patients with colonic inflammatory bowel disease and a cohort of healthy controls

city: Southampton

first: Tilman

last: Sanchez-Elsner

state: Hampshire

address: Southampton General Hospital, Tremona Road

institute: University of Southampton

summary: The objective of this study was to investigate the role of intestinal macrophages in inflammatory bowel disease.  A prospective observational study was completed. Gut biopsies from patients with Ulcerative Colitis, Crohn’s Disease and Healthy donors were harvested.  Using Fluorescence-activated cell sorting a purified CD14+/CD163+ intestinal macrophage population was isolated. RNA extracted and amplified from this population of macrophages was subjected to RNA-sequencing and bioinformatically analysed. The most relevant candidates were validated with RT-qPCR and immunohistochemistry. Intestinal macrophages in UC and CD patients show a strong reprograming with over 1200 and 800 dysregulated genes, respectively. UC and CD intestinal macrophages showed an activated M1 inflammation associated to the attraction and activation of inflammatory T-cells and a Th1 immune response. Interestingly, macrophages from CD also showed a significant activation of M2 genes, associated with a Th2 response. Mirroring clinical observations, CD (but not UC) macrophages showed enrichment of expression of fibrotic and granuloma genes. Both UC and CD macrophages are down-regulating genes engaged in drug/xenobiotics metabolism roles key for IBD therapy (such as TPMT). Key genes such as MMP12 (fibrosis), CXCL9 (T-cell attraction) and CD40 (T-cell activation) were confirmed by RT-qPCR and also at the protein level by immunohistochemistry.

overall_design: This study evaluated mRNA expression in 28 human macrophage samples from three disease groups: ulcerative colitis, Crohn’s disease, and healthy controls.


title: Gene expression in radio-sensitive or -resistant breast cancer cells

status: Public on Sep 18 2021

city: Gyeongju

first: soyoung

last: Kim

address: Dongdae-ro 123

department: Department of Pharmacology

institute: Dongguk university

summary:
During radiotherapy most cancer cells are removed, but some cells are not. These remained cancer cells become resistant to radiotherapy and lead to cancer recurrence. Radioresistnat cancer cells show different gene expression profile than radiosensitive tumor cells. Among the genes distinctly up or down-changed in expression level, some are associated with development of radioresistance.
We used microarrays to select multiple genes showing distinct change in expression level for seeking genes that contribute to the develpoment of radioresistance in breast cancer cells during radiotherapy.

overall_design: We selected 3 kinds of cell lines with different radiosensitivity for RNA extraction and hybridization on Affymetrix microarrays. To that end, parental SK-BR-3 cells were irradiated with 4 Gy twice a week and then cultured until survived cells recoved. The same cycle of irradiation were repeated until cells exhited distinct radioresistance. We tested cells' sensitivity to radiation by colony forming assay. Finally, SK-BR-3, Pre-SR, and SR cells were selected as radiosensitive, mild radioresistance and distinct radioresistant cells, respectively.

first: Yun-Suk

last: Kwon

first: Min-Gu

last: Lee

first: Jun-Young

last: Baek

first: Hyunsoo

last: Jang

first: Soyoung


title: Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin

city: Dallas

first: Jialiang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Investigating the AZDR1208 resistance in HSB-2 cells

city: Tucson

first: James

middle: Teak

last: Lim

state: AZ

address: 1515 N Campbell Ave Room 4951

institute: University of Arizona

summary: The study uses RNA sequencing to profile AZD1208 resistant (AZDR) vs AZD1208 sensitive HSB-2 cells. PIM inhibitor treatment decreases leukemia burden in early T-cell precursor acute lymphoblastic leukemias (ETP-ALL) both in vitro and in vivo. However, prolonged treatment of ETP-ALL with PIM kinase inhibitors results in PIM inhibitor resistance. The analysis revealed that the HOXA9, mTOR, MYC, NF-B, and PI3K-AKT pathways were activated in PIM inhibitor resistant ETP-ALL

overall_design: PIM inhibitor resistance in HSB-2 cells was induced by growing the cells in the presence of increasing doses of AZD1208 over a 4 month period until resulting cell populations were able to maintain their growth at 1 µM AZD1208.  RNA sequencing was utilized to define differentially expressed genes.

first: Sathish

last: Padi

first: Andrew

last: Kraft


title: Systems-level Responses to Salinity and Temperature Variations in the Marine Bacterium Vibrio natriegens

city: Washington

first: Sophie

middle: M

last: Colston

state: DC

address: 4555 Overlook Ave SW

department: CBMSE

institute: Naval Research Laboratory

summary: Vibrio natriegens strain ATCC 14048 is a salt marsh isolate with a notably rapid growth rate that has garnered considerable interest for biotechnological applications. We used systems-level tools (i.e. metabolomics, transcriptomics, proteomics) to characterize its physiological response to different salinities and temperatures that are relevant not only to its natural environment but also to planned scalable culturing processes. We found organic osmolyte synthesis and membrane transporters were most responsive to changes in salinity. The osmolytes glutamate, glutamine and ectoine responded to salinity across temperature treatments. However, when media was supplemented with choline, glycine betaine appeared to replace ectoine. These results provide a baseline data set for metabolic activity under a variety of conditions that will influence future basic and applied V. natriegens research.

overall_design: Vibrio natriegens strain ATCC 14048 was grown in a modified minimal medium at three different temperatures and in three different salinities. Cells were collected for RNA, metabolite and protein extractions.

first: Winifred

last: Johnson

first: Erin

last: Kelly

first: Janna

last: Schultzhaus

first: Scott

last: Dean

first: Gregory

last: Ellis

first: Elliot

last: Gerlach

first: Katherine

middle: L

last: Akingbade

first: W

last: Hervey

first: Dagmar

last: Leary

first: Gary

last: Vora


title: New insight into the radioresistance in breast cancer identify a dual function of miR-122 as tumor suppressor and oncomiR

city: Ciudad de México

first: Isidro

middle: Xavier

last: Pérez-Añorve

state: Cuajimalpa

address: Vasco de Quiroga 487, Santa Fe

department: Posgrado en Ciencias Naturales e Ingeniería

country: Mexico

institute: Universidad AUtónoma Metropolitana Unidad Cuajimalpa

summary:
Through the use of antagomiR-122, the knockdown of miR-122 was achieved with an efficiency of 70% in the cell line MCF-7RR with phenotype of acquired resistance to ionizing radiation.
To evaluate the transcriptomic landscape resulting from knockdown of miR-122 of radioresistant breast cancer cells MCF-7RR. These assays showed the modulation of genes enrichment in RAS-MAPK and TNFR signaling pathways, inflammatory response and regulation of transcription.

overall_design: expression profile of genes from MCF-7RR cell line silenced by antagomir-122 (MCF7-122_1 and MCF7-122_2) versus MCF-7RR control without transfection (MCF-7RR_1 and MCF-7RR_2) using the Affymetrix Human Transcriptome Array 1.0 platform Array data was processed by Transcriptome Analysis Console (TAC).

middle: X

last: Perez-Añorve

first: Claudia

last: Gonzalez-De la Rosa

first: Ernesto

last: Soto-Reyes

first: Fredy

middle: O

last: Beltran-Anaya

first: Oscar

last: Del Moral-Hernandez

first: Marisol

last: Salgado-Albarran

last: Angeles-Zaragoza

first: Juan

last: Gonzalez-Barrios

first: Daniel

last: Landero-Huerta

first: Margarita

last: Chavez-Saldaña

first: Alejandro

last: Garcia-Carranca

first: Nicolas

last: Villegas-Sepulveda

first: Elena

last: Arechaga-Ocampo


title: Crotamiton derivative JM03 extends lifespan and improves 1 oxidative and hypertonic stress resistance in Caenorhabditis 2 elegans via inhibiting OSM-9

status: Public on Sep 17 2021

city: Shanghai

first: Liu

last: Wenwen

address: 130 Meilong Road

institute: East China University of Science and Technology

summary: While screening our in-house 1,072 marketed drugs for their ability to extend the lifespan using Caenorhabditis elegans (C. elegans) as an animal model, crotamiton (N-ethyl-o-crotonotoluidide) showed anti-aging activity and was selected for further structural optimization. After replacing the ortho-methyl of crotamiton with ortho-fluoro, crotamiton derivative JM03 was obtained and showed better activity in terms of lifespan-extension and stress resistance than crotamiton. It was further explored that JM03 extended the lifespan of C. elegans through osmotic avoidance abnormal-9 (OSM-9). Besides, JM03 improves the ability of nematode to resist oxidative stress and hypertonic stress through OSM-9, but not osm-9/capsaicin receptor related-2 (OCR-2). Then the inhibition of OSM-9 by JM03 reduces the aggregation of Q35 in C. elegans via upregulating the genes associated with proteostasis. SKN-1 signaling was also found to be activated after JM03 treatment, which might contribute to proteostasis, stress resistance and lifespan extension. In summary, this study explored a new small molecule derived from crotamiton, which has efficient anti-oxidative, anti-hypertonic and anti-aging effects, and could further lead to promising application prospects.

overall_design: Examination of JM03-treated and control group in C. elegans by RNA-seq, in triplicate

first: Bao

last: Keting

first: Feng

last: Jiali

first: Hu

last: Zelan

first: Li

last: Jian


title: Human colorectal tumor tissue: Tumor vs. histologically normal tissue

city: Beijing

first: Tianqi

last: Liu

address: Fucheng street

institute: Peking University

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

summary: Transcriptional profiling of human colorectal cancer tissues comparing control from histologically normal tissue samples adjacent to the tumors. High throughput bioluminescence imaging, and PET were performed. The overall goal was to determine the differential expression of lncRNA and mRNA between tumor and match normal samples.

overall_design:
Two-condition experiment, Tumor vs. Normal Control. Biological replicates: 9 normal tissue control replicates, 9 colorectal tumor samples.
Please note that the experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed as single channel. Thus each raw data file contains raw data for both tumor [C] and normal tissue [N] samples, and is linked to the corresponding tumor tissue sample records.


title: RNA-Seq  of wild type and short telomere E12.5 PGCs

city: tianjin

first: nannan

last: zhao

state: --- Select a state ---

address: nankai

institute: nankai university

summary: We aimed to investigate if the short telomere could have an effect on the cell fate decision in the PGCs

overall_design: The E12.5 PGCs of the short telomere and wild type both in male and female.

first: Lin

first: Chenglei

last: Tian

first: Dai

last: Heng

first: Nannan

last: Zhao


title: Determine MARCH1-dependent molecular differences in dendritic cells that carry allergen from the lungs to the draining lymph nodes

city: San Francisco

first: Carlos

middle: Andres

last: Castellanos

state: CA

address: 513 Parnassus Ave, HSE-201

department: Microbiology & Immunology

institute: University of California, San Francisco

summary: MARCH1-/- mice have a deficit in TH2 cell development in the mediastinal LN to HDM allergens. Pulmonary DCs that capture allergens and migrate to mediastinal lymph node have been implicated in driving TH2 cell polarization. We then investigated whether MARCH1 is involved in transcriptional reprograming of migratory DCs, which has been suggested to condition the DCs to drive TH2 cell development. To do this, we performed single cell RNA sequencing  through the 10X Chromium platform of allergen-carrying WT or MARCH1-/- DCs in the LNs of mice.

overall_design: HDM+ WT DCs or HDM+ MARCH1-/- DCs were enriched from the medLNs of CD45.1/.1 Zbtb46GFP :CD45.2/.2 Zbtb46GFP MARCH1-/- mixed BM chimeric mice (24h after oropharyngeal aspiration) and the DCs were sorted using a FACS Aria. Immediately post-sorting, cells were run on the 10X Chromium (10X Genomics) and then through library preparation by the Institute for Human Genetics at UCSF following the recommended protocol for the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry). Libraries were run on the NovaSeq 6000 for Illumina sequencing. Post-processing and quality control were performed by the Genomics Core Facility at the Institute for Human Genetics at UCSF using the 10X Cell Ranger package (Cell Ranger Version 3.0.2, 10X Genomics). Primary assessment with this software for WT DC sample reported 2,441 cell-barcodes with 7,651 median unique molecular identifiers (UMIs, transcripts) per cell and 2,004 median genes per cell sequenced to 61.4% sequencing saturation with 48,559 mean reads per cell. Primary assessment with this software for MARCH1-/- DC sample reported 681 cell-barcodes with 6,309 median unique transcripts per cell and 1,774 median genes per cell sequenced to 73.1% sequencing saturation with 202,410 mean reads per cell.

first: Jeoung-Sook

last: Shin

first: Andrew

last: Schroeder


title: Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis [RNA-seq]

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

summary: Inflammation is a major risk factor for pancreatic ductal adenocarcinoma (PDAC). When occurring in the context of pancreatitis, mutations of KRAS accelerate tumor development. We discovered that long after its complete resolution, a transient inflammatory event primes pancreatic epithelial cells to subsequent transformation by oncogenic KRAS. Upon recovery from acute inflammation, epithelial cells of the pancreas display an enduring adaptive response associated with sustained transcriptional and epigenetic reprogramming. Such adaptation enables the prompt reactivation of acinar-to-ductal metaplasia (ADM) upon subsequent inflammatory events, thus efficiently limiting tissue damage via rapid decrease of zymogen production. We propose that since activating mutations of KRAS maintain an irreversible ADM, they may be beneficial and under strong positive selection in the context of recurrent pancreatitis.

overall_design: Pancreatic spheroids were derived from untreated as well as post caerulein-treated C57BL/6J wild-type mice. Total RNA from pancreatic spheroid was processed for multiparallel sequencing.

first: E

last: Del Poggetto

first: I

last: Ho

first: C

first: G

last: Natoli

first: A

last: Viale


title: RNA-seq analysis of lung tissues of Dnah9 and WT mice

city: SHANGHAI

first: XIANGYU

last: ZHOU

state: SHANGHAI

address: Shanghai First Maternity and Infant Hospital

institute: Tongji University

summary: We reported the RNA-seq analysis on lung tissues of 2 Dnah9 knockout mice and their WT and Hez littermates. (N=4)

overall_design: Examination the differentiation expressed genes (DEGs) caused by Dnah9 knockout in lung tissues of mice

first: Xiangyu

last: Zhou

first: Libing

last: Shen


title: Studies of autophagy pathway during submergence in Arabidopsis thaliana

city: guangzhou

first: mk

last: yang

address: wushan

institute: scau

summary: Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In Arabidopsis thaliana, submergence induces the transcription of autophagy-related (ATG) genes and the formation of autophagosomes. To study the role of autophagy during submergence, we performed transcriptome analysis with atg5, an autophagy-defective mutant, under submergence conditions. Our data showed that submergence changed the expression profile of DEG in the atg5 versus wild-type.

overall_design: Whole Arabidopsis plants (4-week-old) were gently submerged at depths of 10 cm beneath the water surface under normal light/dark cycle condition. Plant samples for microarray were collected after 0 h or 48 h submergence treatment.

first: Liang

last: Chen

first: MingKang

last: Yang


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Two Kinds of Chenopodium quinoa Transcriptomes

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

summary: We generated 95.37 Gb of high-quality sequencing data (~7.95 Gb per sample). The analysis showed differences of transcriptomes between the common white sweet quinoa and the yellow bitter quinoa. We identified numerous differentially expressed genes that exhibited distinct expression patterns. These genes have known or potential roles in taste of quinoa fruit.Therefore, we are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to the accumulation of bitter saponins in C. quinoa fruits.

overall_design: Two kinds of quinoa (the common white sweet quinoa and the yellow bitter quinoa) flowers and fruits mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq4000.


title: DNA-protein Crosslinking Sequencing for Genome-wide Mapping of Thymidine Glycol

city: Riverside

first: feng

last: tang

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

summary: Thymidine glycol (Tg) is the most prevalent form of oxidatively induced pyrimidine lesion in DNA. Tg can arise from direct oxidation of thymidine in DNA. In addition, 5-methyl-2¢-deoxycytidine (5-mdC) can be oxidized to 5-mdC glycol and its subsequent deamination also yields Tg. However, its distribution in the human genome remains unknown. Here, we presented a DNA-protein cross-linking sequencing (DPC-Seq) method for genome-wide mapping of Tg in human cells. Our approach is capitalized on the specificity of a DNA glycosylase, i.e., NTHL1, for the covalent labeling, as well as DPC pulldown, SDS-PAGE fractionation, and membrane transfer for highly efficient and selective enrichment of Tg-bearing DNA. By employing DPC-Seq, we detected thousands of Tg sites in HEK293T cells and the isogenic NTHL1 and NEIL1 double knock out cell lines. We found that Tg is depleted in genomic regions associated with active transcription, but enriched at the nucleosome-binding sites, especially at heterochromatin sites. Collectively, our approach allows for comprehensive analysis of Tg in the human genome and provides a robust tool for future functional studies of Tg in DNA. It can be envisaged that the method can be adapted for mapping other modified nucleosides in genomic DNA in the future.

overall_design:
The method is capitalized on the NTHL1-mediated removal of thymine glycol, covalent binding of the ensuing abasic site with the Lys residue at its active site, reduction to stabilize the resulting Schiff base, and a two-step procedure for the highly selective enrichment of DNA-NTHL1 cross-link for subsequent library construction and next-generation sequencing analysis.
By employing DPC-Seq, we detected thousands of Tg sites in HEK293T cells and the isogenic NTHL1 and NEIL1 double knock out cell lines.

first: Feng

last: Tang

first: Yinsheng

last: Wang


title: TRIM33 binding in hematopoietic cell lines and effects of TRIM33 deletion on RNA PolII occupancy during activation of primary macrophages

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

institute: cea

summary: To get insight into lineage-specific TRIM33 functions, TRIM33 ChIP-seq was carried out in non-differentiated erythroid (MEL NI), differentiated erythroid (MEL I), immature myeloid (32D). In addition, we compared the genome-wide profiles of RNA PolII occupancy between wild-type bone marrow-derived macrophages (BMDM) and Trim33-/- BMDM activated with LPS.

overall_design: Chromatin immunoprecipitations of TRIM33 and RNA PolII followed by multiparallel sequencing performed in hematopoietic cell lines and murine bone marrow-derived macrophages (BMDM).

first: Federica

last: Ferri

first: Paul

last: Romeo


title: Primary mediastinal large B-cell lymphoma is hallmarked by large-scale copy-neutral loss of heterozygosity

status: Public on Sep 16 2021

city: Leuven

first: Nicolas

last: Dierckxsens

address: ON I Herestraat 49

department: Human Genetics

institute: KULeuven

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

summary: Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. It is unknown whether copy-neutral loss of heterozygosity (CN-LOH) contributes to the pathogenesis of this tumor. To get insight into the CN-LOH landscape of PMBL, we performed  Single Nucleotide Polymorphism array (SNPa) analysis of two PMBL-derived cell lines and 33 primary tumors. The study uncovered large-scale CN-LOH lesions in both cell lines and 90.9% (30/33) of primary tumors. The latter cases showed 133 CN-LOH stretches of size >25Mb which affected up to 14 chromosomes per case (mean of 4.4).  Involvement of chromosomal segments was predominant (81.2%), which, in a heterozygous diploid context, suggests the implication of B-cell specific crossover events. Further analysis indicated that the CN-LOH lesions were triggered by one or two consecutive molecular hits. Notably, CN-LOH segments were non-randomly clustered on chromosome 6p (60%), 15 (37.2%) and 17q (40%). Preliminary whole-exome sequencing data yielded coincidence of these lesions with mutations in MHC I and histon-related genes (6p21), B2M (15q15) and GNA13 (17q23), respectively. We hypothesize that CN-LOH-associated hits occurred early during lymphomagenesis, following mutagenesis but preceding genomic gains. Screening of the cohort of 2,658 cancer whole-genomes revealed that the CN-LOH landscape in PMBL is unique and distinguishes this tumor from other malignancies. Altogether, CN-LOH lesions rank as the most frequent genetic defect identified so far in this disease and the CN-LOH landscape suggest a hitherto undescribed mitotic recombinational driver. The aberrations affect the expression of key driver genes and functionally alternate genomic deletions which are infrequent in PMBL.

overall_design: 33 primary tumor samples and two cell lines

first: Stefania

last: Tuveri

first: Koen

last: Debackere

first: Lukas

last: Marcelis

first: Jonas

last: Demeulemeester

first: Eftychia

last: Dimitriadou

first: Daan

last: Dierickx

first: Pierre

last: Lefesvre

first: Karen

last: Dereadt

first: Carlos

last: Graux

first: Lucienne

last: Michaux

first: Jan

last: Cools

first: Thomas

last: Tousseyn

first: Joris

middle: R

last: Vermeesch

first: Iwona

last: Wlodarska


title: Function of Arabidopsis PUB2 and PUB4 in plant immunity

city: HONG KONG

first: Huan

last: ZHONG

state: HONG KONG

address: T1012 CHA CHI-MING SCIENCE TOWER

department: BIOLOGY

country: Hong Kong

institute: HKBU

summary: Plants recognize and respond to pathogens relying on pattern recognition receptors (PRRs) which usually are receptor like kinases (RLKs) or receptor like proteins (RLPs). Upon binding to conserved structures or molecules, the so-called pathogen-associated molecular patterns (PAMPs), in pathogens, PRRs form complex with coreceptors and activate pattern triggered immunity (PTI). Here, we show that two U-box type E3 ligases (PUBs), PUB2 and PUB4, play important roles in PTI responses and disease resistance in Arabidopsis.

overall_design: Transcriptome sequencing of pub2/4 double mutant and wild-type of Arabidopsis

first: Yiping

last: Wang

first: Yingying

last: Wu

last: Zhong

first: Yiji

last: Xia


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and artificial sweeteners-stressed Acinetobacter baylyi ADP1 and pWH1266 plasmid Transcriptomes

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type Acinetobacter baylyi ADP1 and Pwh1266 plasmid, and their mRNA response under the exposure of four artificial sweeteners, including saccharin, sucralose, aspartame, and acesulfame potassium. 3 mg/L of each sweetener was used to treat the mixture of bacteria cell and plasmid. The group without dosing any artificial sweeteners was the control group. Each sample was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these four artificial sweeteners on the transcriptional levels can be revealed. Illumina HiSeq 2500 was applied. The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the Acinetobacter baylyi ADP1 reference genome (NC_005966) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell culture. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

overall_design: Bacterial mRNA profile of wild-type Acinetobacter baylyi ADP1 in response to 3 mg/L artificial sweeteners for 2 hours, bacteria and plasmid without dosing artificial sweeteners are the control group, in triplicate, using Illumina HiSeq 2500

first: Zhigang

last: Yu

first: Yue

first: Likai

last: Mao


title: Identification of UNC1999-responsive gene signatures in NK92MI cells

status: Public on Sep 15 2021

city: Tianjin

first: Yang

last: Li

address: Anshan Road No.154

institute: Tianjin Medical University General Hospital

summary: We performed second-generation high-throughput sequencing analysis of UNC1999-treated and control NK92MI cells to identified UNC1999-responsive gene signatures.

overall_design: NK92MI cells were cultured in the presence of DMSO or 10μM UNC1999 for 48h.

first: Xi

first: Minghang


title: Effects of exercise on the expression of long non-coding RNAs in the bone of mice with osteoporosis

city: shanghai

first: Jianmin

state: Yangpu District

address: No 399 changhai street

institute: shanghai university of sport

summary: To further the mechanism of exercise prevent and treatment osteoporosis,we have employed a microarray of lncRNA to detect the expression  of lncRNA in bone of osteoporosis mice after exercise

overall_design: 12-weeks C57BL/6 mice received a sham operation or bilateral ovariectomy, and the exercise treatment groups were subjected to 9 weeks of treadmill running exercise in 4 weeks of the operation was done

first: Jun

last: Zou


title: Pig backfat miRNA profiling

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary:
Purpose: Analysis of the effect of different fats and amonut of cDDGS in the feedstuff on miRNA expression in porcine backfat
Methods: miRNA-seq analysis was performed on backfat samples collected from 24 male and female crossbred fatteners originating from sows (Polish Landrace × White Large Polish) mated with a boar (Duroc × Pietrain) divided into four dietary groups: 7-cDDGS+rapeseed oil (group I), n=6 (+cDDGS+rapeseed oil -group II), n= 6 (+cDDGS+beeftallow -group III),n=5 (+cDDGS+coconut oil -group IV). The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). 100 single-end cycle sequencing was performed on the HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). MicroRNA differentially expressed between dietary groups were identified with the DESeq2 software.
Results: The comparison of miRNA profiles between dietary groups showed The highest number of miRNAs with altered expression was identified in the comparison of animals fed the diet containing cDDGS and coconut oil (group IV)  with animals from the –cDDGS + rapeseed oil (group I)  (37 miRNA, p adjusted <0.01). Moreover, in comparison between the group IV  and groups III and II , 29 (12 upregulated and 17 downregulated in +cDDGS+coconut oil group) and 28 (10 upregulated and 18 downregulated in +cDDGS+coconut oil group)  miRNAs were identified, respectively (p adjusted <0.1)
Conclusions: Obtained results suggest that coconut oil  induces changes in miRNA profile of backfat in pigs.

overall_design: MicroRNA next generation sequencing of 24 pig backfat samples collected from  castrated males and females was performed using Illumina HiScan SQ.

first: Maria

last: Oczkowicz


title: The long noncoding RNA H19 regulates tumor plasticity in neuroendocrine prostate cancer [ChIP-seq]

city: Tucson

first: Ritu

last: Pandey

state: Arizona

address: 1515 N Campbell Ave.,

department: Cellular and Molecular Medicine, Arizona Cancer Center

institute: University of Arizona

summary: To determine the functional epigenetic landscape of changes induced by H19, ChIP-seq was performed on H3K27me3 and H3K4me3 in V16D CRPC cells transduced with H19 (to induce NEtD) versus V16D CRPC control cells.  Comaparison of genome-wide maps of chromatin state in V16D CRPC cells with and without H19 overexpression.

overall_design: Examination of 2 different histone modifications, H3K4Me3 and H3K27Me3 in V16D CRPC cells with and without H19 overexpression.

first: Neha

last: Singh

first: Andrew

last: Kraft


title: RNA-seq of limmmunocompetent mice in response to  Aspergillus fumigatus conidia and hyphae

city: Nanjing

first: Yingzhi

last: Luo

address: Meiyuan street

institute: Jinling Hospital

summary: We bulit a pulmonary aspergillosis model in immunocompetent mice.  Mice were inoculated intratracheally with 50 μL suspension of conidia , hyphal fragments or normal saline, respectively, after anesthesia.  Lungs from were harvested and ground for RNA extraction 24 hours after fungal inoculation. The  result of RNA-seq indicated both conidia and hyphae can activate  a series of  immunologically relevant pathways and these pathways were much more strongly activated by hyphae. Hyphae  could promote Th2 cell differentiation and suppress Th1 cell differentiation. Both hyphae and conidia could activate Th17 cell differentiation.

overall_design: RNA profile of pulmonary aspergillosis in response to different states of A. fumigatus

first: Lin

last: deng

first: Fang

last: Liu

first: Jie

last: Xu

first: Qingtao

last: Kong

first: Yi

last: Shi

first: Hong

last: Sang


title: Screening of the targeted mRNAs of ER-anchored PARN by transcriptome sequencing.

first: Yong-Bin

last: Yan

address: Tsinghua University

department: School of Life Sciences

institute: Tsinghua University

summary: The goals of this study are to identify the potential targets and then elucidate the function of ER-anchored PARN. After overexpressing the empty vector, PARN(wild type) or D28A(the enzyme-dead mutant of PARN) in HEK-293T cell respectively and the following fractionation of the cytosol and ER fraction, we performed the high-throughput RNA sequencing for each fraction. After comparing the abundance of detected transcripts in different samples we found ER-anchored PARN only affects a small subset of mRNAs in HEK-293T cell.

overall_design: HEK-293T mRNA profiles of cytosol and ER fraction after overexpressing pcDNA3.1(N- flag,empty vector),flag-PARN and flag-PARN-D28A

first: Yongbin

first: Tianli

last: Duan


title: Expression profile alteration of lncRNA and their target genes in patients with aortic dissection

city: Fuzhou

first: yunnan

last: Hu

state: Fujian

address: Xinquan Road No. 29

institute: fujian medical university union hospital

summary: Aortic dissection (AD) is a cardiovascular emergency resulted from blood flows into vessel wall, with high mortality in early stage. Due to the vital pathological mechanism for AD occurrence has not been clarified, and no effective ways to prevent and diagnose AD’s process. In this study, we determine the lncRNA expression profile in aortic dissection group and control group. The key lncRNAs were screen out by using microarray analysis in defferent group.

overall_design: The experiment is divided into two groups: HT as control group, AD as study group. Then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar).

first: Yun-nan

first: Sheng

last: Chen

first: Liang-wan


title: Identification of TGF-β regulated lncRNAs in GBM cells using microarray screen

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To identify TGF-β regulated lncRNAs in glioblastoma, we performed a genome-wide microarray screen in T98G glioma cells. T98G cells were treated with 10 ng/ml TGF-β (24h) and differentially expressed lncRNAs were identified using microarray in comparison with control cells.

overall_design: Agilent Human Whole Genome 8x60k Microarray: AMADID: 72363: Control T98G cells - 3 replicates (C1, C2, C3) and TGF-β treated T98G cells (T1, T2, T3)

first: Vivek

last: Sharma

first: Bakhya

last: Shree


title: Inflammatory response of iPSC- and PBMC-derived macrophages in contact with S. aureus Newman strain

city: Hannover

first: Anna

last: Rafiei Hashtchin

state: Niedersachsen

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Medical School Hannover

summary: Whole transcriptome analysis of iMφ compared to monocyte-derived macrophages indicates a more profound upregulation of inflammatory genes early after infection and faster normalization 24 hours post-infection.

overall_design: In total 12 samples were analyzed in this experiment, and it was performed in duplicate; 6x iPSC-macrophages sample and 6x PBMC-macrophages

first: Nico

last: Lachmann

last: Rafiei


title: Brd4 regulates the homeostasis of CD8+ T-lymphocytes and their proliferation in response to antigen stimulation.

city: 广州

first: Peng

middle: zhi

last: lin

address: 74 Zhongshan 2 Rd

department: zhongshan school of medicine

institute: Sun-Yat sen university

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

overall_design: Refer to individual Series


title: NRF2 Integrates Metabolic, Epigenetic and Oncogenic Regulation in Driving Liver Cancer Progression

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

country: USA

institute: Augusta University

summary: The expression of NRF2 was activated in human hepatocellular carcinoma. In current study, we observed that in hepatic carcinogen diethylnitrosamine induced liver tumor mouse model, NRF2 knockout mouse developed less liver tumor incidence than wild type mouse. To reveal the detailed mechanism, RNA-seq experiment was conducted to compare gene transcriptome profiles of NRF2 WT and KO mice during HCC progression.

overall_design: Comparison of liver tissue/tumor transcriptome in NRF2 WT (3 samples) and NRF2 KO mice (3 samples) at 2-day (2D),  4-week (4W) and 36-week (36W) post-DEN treatment.

first: Caixia

last: Xi

first: Junfeng

last: Pan

first: Nahid

last: Mivechi