title: Weight cycling impairs pancreatic insulin secretion but does not perturb whole-body insulin action in diet-induced obese mice

city: Nashville

first: Matthew

last: Cottam

state: TN

address: 2301 Vanderbilt Place

department: Surgical Sciences

institute: Vanderbilt University Medical Center

summary: In the setting of obesity and insulin resistance, glycemia is controlled in part by beta cell compensation and subsequent hyperinsulinemia. Weight loss improves glycemia and decreases hyperinsulinemia, whereas weight cycling worsens glycemic control. The mechanisms responsible for weight cycling-induced deterioration in glucose homeostasis are poorly understood. Thus, we aimed to pinpoint the main regulatory junctions at which weight cycling alters glucose homeostasis in mice. Using in vivo and ex vivo procedures we show that despite having worsened glucose tolerance, weight-cycled mice do not manifest impaired whole-body insulin action. Instead, weight cycling reduces insulin secretory capacity in vivo during clamped hyperglycemia and ex vivo in perifused islets. Islets from weight-cycled mice have reduced expression of drivers of b-cell identity (Mafa, Pdx1, Nkx6.1, Ucn3) and lower islet insulin content, compared to those from obese mice, suggesting inadequate transcriptional and posttranscriptional response to repeated nutrient overload. Collectively, these data support a model in which pancreatic plasticity is challenged in the face of large fluctuations in body weight resulting in a mismatch between glycemia and insulin secretion in mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for isolated pancreatic islets from obese and weight cycled mice.

first: Nathan

last: Winn

first: Monica

last: Bhanot

first: Heather

last: Caslin

first: Jamie

last: Garcia

first: Rafael

last: Arrojo e Drigo

first: Alyssa

last: Hasty


title: An overfeeding-induced obesity mouse model reveals necessity for Sin3a in postnatal peak β cell mass acquisition

status: Public on Nov 09 2022

city: Madrid

first: Alberto

last: Bartolomé

state: Madrid

address: Arturo Duperier 4

country: Spain

institute: Instituto de Investigaciones Biomédicas Alberto Sols (CSIC/UAM)

type: Expression profiling by high throughput sequencing

summary: The increase of functional β cell mass is paramount to maintain glucose homeostasis in the setting of systemic insulin resistance and/or augmented metabolic load. Understanding compensatory mechanisms that allow β cell mass adaptation may allow discovery of therapeutically actionable control nodes. In this study, we report the rapid and robust β cell hyperplasic effect in a mouse model of overfeeding-induced obesity (OIO) based on direct gastric caloric infusion. By performing RNA sequencing in islets isolated from OIO mice, we identified Sin3a as a novel transcriptional regulator of β cell mass adaptation. β cell-specific Sin3a knockout animals showed profound diabetes, due to defective acquisition of postnatal β cell mass. These findings reveal a novel regulatory pathway in β cell proliferation, and validate OIO as a model for discovery of other mechanistic determinants to β cell adaptation.

overall_design: RNA-seq of pancreatic islets from a mouse model of overfeeding.

first: Utpal

middle: B

last: Pajvani


title: Functional Characterization of lncRNA152 as an Angiogenesis-Inhibiting Tumor Suppressor in Triple-Negative Breast Cancers

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

summary: Long non-coding RNAs have been implicated in many of the hallmarks of cancer.  We previously annotated lncRNA152 (lnc152; a.k.a. DRAIC) and demonstrated its roles in proliferation, cell cycle progression, and regulation of the estrogen signaling pathway in breast cancer cells.  Herein, we found that lnc152 is highly upregulated in luminal breast cancers, but is downregulated in triple-negative breast cancers (TNBC).  Using a set of complementary experimental approaches, we found that knockdown of lnc152 promotes cell migration and invasion in luminal breast cancer cell lines.  In contrast, ectopic expression of lnc152 inhibits growth, migration, invasion, and angiogenesis in TNBC cell lines.  In xenograft studies in mice, lnc152 inhibited the growth and metastasis of TNBC cells.  Transcriptome analysis of the xenografts indicated that lnc152 downregulates genes regulating cancer-related phenotypes, including angiogenesis.  Using RNA-pull down assays coupled with LC-MS/MS analysis, we identified RBM47, a known tumor suppressor protein in breast cancer, as a lnc152-interacting protein.  We found that lnc152 suppresses the aggressive phenotypes of TNBC cells by regulating the expression of RBM47.  Collectively, our results demonstrate that lnc152 is an angiogenesis-inhibiting tumor suppressor that attenuates the aggressive cancer-related phenotypes found in TNBC.

overall_design: To investigate the in vivo impact of ectopic expression of lnc152 in TNBC, we performed a xenograft experiment using MDA-MB-231 cell line engineered for Dox-inducible overexpression of lnc152 or GFP mRNA as a control. At the end of the experiment, the mice were euthanized to collect the xenograft tissue. Using RNA-seq from xenograft tumor tissue, we evaluated the expression changes of mRNAs after ectopic expression of lnc152 in MDA-MB-231 cells compared to expression of GFP mRNA

first: Dae-Seok

last: Kim

first: Shrikanth

middle: S

last: Gadad

first: Rohit

last: Setlem

first: Kangsan

first: Srinivas

last: Malladi

first: Tim

middle: Y

last: Hou

first: Tulip

last: Nandu

first: Cristel

middle: V

last: Camacho

first: W

middle: L


title: BRD4 inhibitor GNE987 exerts anti-cancer effects by targeting C-Myc and S100A16 in Glioblastoma [ChIP-seq]

city: Suzhou

first: Gen

last: Li

state: Jiangsu

address: No. 92 Zhongnan Street

country: China

institute: Children's Hospital of Soochow University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Glioblastoma (GBM) in children is a relatively more common primary central nervous system tumor with a high degree of malignancy, high mortality, and complex surgical complete resection.. GNE987 is a newly developed von Hippel-Lindau tumor suppressor (VHL)-based pan-BET-targeting PROTAC, which can bind to the target proteins (BET proteins, including BRD2, BRD3, and BRD4) and recruit them to the ubiquitin/ proteasome system for degradation. However, the function of GNE987 has not been assessed in GBM cells so far. In the present study, ChIP-Seq analysis was performed to explore the effect of GNE987 on GBM cells.

overall_design: U87 cells were treated with  control (DMSO) or GNE987 for 48h, and then harvested for chip with H3K27Ac antibody.

first: Liya

last: Ma


title: The Mitochondrial RNA Granule is Necessary for Parkinsonism-Associated Metal Toxicity

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

summary: We report RNAseq profiles of human cell lines with deletions of the SLC30A10 gene or the PARK2 gene.

overall_design: We compare differential gene expression between control, SLC30A10 deletion and PARK2 deletion.

first: Victor

last: Faundez


title: Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee

city: London

first: Paul

last: Hurd

address: Mile End Road

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

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

overall_design: Refer to individual Series


title: Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [CAGEseq_MLLAF9-AML]

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: Genome-wide transcription factor binding profiles provide valuable insights into hematopoietic development and malignancies. Today, advanced computational methods exploit cis-regulatory information to predict complex gene regulatory networks controlled by transcription factors. However, these prediction methods still require large amounts of reference data or experimental expertise. Here, we present a low-requirement network-based computational framework that exploits bidirectional transcription marked regulatory elements to identify important transcription factors driving hematopoietic decision making. Using CAGE-seq we predicted TF binding and confirmed experimentally validated TF important in cell conversion strategies by exploiting bidirectional regions. Next, we applied our framework to predict driving transcription factors in induced normal erythropoiesis and early myelopoiesis, as well as in acute myeloid leukemia associated MLL-AF9-driven immortalisation. Our approach allowed the identification of experimentally validated as well as thus far unexplored transcription factors in these processes.

overall_design: Comparative CAGE transcription start sites (CTSS) expression profiling analysis of CAGE-seq data for primary CD14+ monocytes (FANTOM5 database) and MLL-AF9 AML.

first: B

middle: M

last: Heuts

first: S

middle: A

last: Apalategi

last: Frölich

last: Bergevoet

middle: N

last: van den Oever

middle: J

last: van Heeringen

last: van der Reijden

first: J

middle: H


title: Plasma exosomal microRNAs associated with metabolism as early predictor of gestational diabetes mellitus

city: Guangzhou

first: Bin

last: Liu

address: Guangzhou, 510080, PR China

department: Department of Obstetrics and Gynecology

institute: the First Affiliated Hospital of Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: The microRNA (miRNA) expression profile of plasma exosome in pregnant women complicated with gestational diabetes mellitus (GDM) has not been fully clarified. In this study, differentially expressed miRNAs in plasma exosomes were identified by high-throughput small RNA sequencing in 12 GDM and 12 normal glucose tolerance (NGT) pregnant women and validated in 102 GDM and 101 NGT pregnant women. A total of 22 exosomal miRNAs were found and five of them were verified by qRT-PCR. Exosomal miR-423-5p was upregulated, while miR-99a-5p, miR-192-5p, miR-148a-3p, and miR-122-5p were downregulated in pregnant women complicated with GDM.

overall_design: miRNA profiles in plasma exosomes derived from gestationla diabetes mellitus and normal glucose tolerance

first: Zhixin

last: Ye

first: Songzi

last: Wang

first: Xiaoqing

last: Huang

first: Peisong

last: Chen

first: Langhui

last: Deng

first: Shiqi

first: Suiwen

last: Lin

first: Zilian


title: The g3mclass is a practical software for multiclass classification on biomarkers

city: Philadelphia

first: Marina

last: Guvakova

state: PA

address: 380S University Avenue

department: Surgery

institute: University of Pennsylvania

type:
Expression profiling by array
Other

summary: The analytes qualified as biomarkers are potent tools to diagnose various diseases, monitor therapy responses, and design therapeutic interventions. The early assessment of the diverseness of human disease is essential for the speedy and cost-efficient implementation of personalized medicine. We developed g3mclass, the Gaussian mixture modeling software for molecular assay data classification. This software automates the validated multiclass classifier applicable to single analyte tests and multiplexing assays. The g3mclass achieves automation using the original semi-constrained expectation-maximization (EM) algorithm that allows inference from the test, control, and query data that human experts cannot interpret.  In this study, we used real-world clinical data and gene expression datasets (ERBB2, ESR1, PGR) to provide examples of how g3mclass may help overcome the problems of over-/underdiagnosis and equivocal results in diagnostic tests for breast cancer. We showed the g3mclass output’s accuracy, robustness, scalability, and interpretability. The user-friendly interface and free dissemination of this multi-platform software aim to ease its use by research laboratories, biomedical pharma, companion diagnostic developers, and healthcare regulators. Furthermore, the g3mclass automatic extracting information through probabilistic modeling is adaptable for blending with machine learning and artificial intelligence.

overall_design:
We collected tissue lysates from the formalin-fixed paraffin-embedded sections from the human breast tissue (noncancerous, carcinoma in situ, invasive carcinoma) and analyzed the expression of several genes in samples by Affymetrix QuantiGene Plex 2.0 assay. Test tissue sample lysates were obtained from five tissue curls of 10-micron each.
Please note that each *txt (series supplementary) file contains raw data for multiple sasmples, as indicated in the corresponding sample title and description field (3 raw data txt files for all 251 samples).


title: Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework


title: unCTC: Unbiased characterisation of single circulating tumor cell transcriptomes [scRNA-seq]

city: New Delhi

first: Sarita

last: Poonia

state: Delhi

address: IIITD

department: Computational Biology

country: India

institute: IIITD

summary: The identification and characterisation of Circulating Tumour Cells (CTCs) is important to get insights into the biology of metastatic cancers, monitoring disease progression, and potential use in liquid biopsy-based personalised cancer treatment. The major limitation of CTC isolation is due to their heterogeneous nature, altered phenotype from primary tumour and availability in limited numbers. In the past years, several techniques have been developed to detect CTCs from peripheral blood, based on canonical markers. These methods are, however, prone to miss a larger set of CTCs due to variable or no expression of these markers. Furthermore, CTC enrichment processes are not free from White Blood Cell (WBC) contamination. Single cell RNA sequencing (scRNA-Seq) of CTCs provides a wealth of information about their tumors of origin as well as their fate. The first and most important roadblock encountered in CTC scRNA-Seq data analysis is confirmation of CTC capture. We present unCTC, an R software for unsupervised and semi-supervised characterisation of CTC transcriptomes, in contrast with WBCs. unCTC features various standard and novel computational/statistical modules for clustering, Copy Number Variation (CNV) inference, and marker based verification of the malignant phenotypes. Notably, we propose Deep Dictionary Learning using K-means clustering cost (DDLK) that robustly clusters scRNA-Seq profiles of CTCs and WBC contaminates to characterise heterogeneity among the concerned cell population. Interestingly, DDLK performs better as gene expression data is transformed into pathway enrichment profiles. To demonstrate the utility of unCTC, we produce scRNA-Seq profiles of breast CTCs enriched by the integrated ClearCell® FX/PolarisTM workflow that works on the principles of size selection and negative enrichment for CD45, a pan leukocyte marker.

overall_design: Profiling of 81 circulating tumor cells from six subjects with ER-/PR-/HER2-, ER+/PR+/HER2- and ER-/PR-/HER2+ hormone receptor status.

first: Debarka

last: Sengupta

first: Naveen

last: Ramalingam


title: Effects of matrine on gene expression of myeloid leukemia cells

city: Huizhou City

first: Wangjing

last: Zhong

state: Guangdong Province

address: No. 1, Xuebo Street, Huicheng District

institute: Huizhou Third People's Hospital

summary: To investigate the molecular mechanism of matrine's anti-myeloid leukemia effect, Acute myeloid leukemia cells HL-60 and U937 and chronic myeloid leukemia cells K562 were treated with 0.8mg/mL matrine for 30min and 24h, respectively. Then, RNA-Seq data before and after matrine treatment were used for gene expression profile analysis

overall_design: Comparative gene expression profile analysis of RNA-Seq data of myeloid leukemia cells before and after matrine treatment

first: Wang-jing

first: Fanfan

last: Yang

first: Lingdi

last: Ma


title: The role of UBE2T in breast cancer growth and progression

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

summary: Ubiquitin Conjugating Enzyme E2T (UBE2T) expression is elevated in many cancer types including Breast Cancer. Therefore, we analyzed the role of UBE2T in breast cancer. Genetic inhibition of UBE2T expression in breast cancer cell lines resulted in decreased proliferation, and increased cell death.

overall_design: T47D and MCF7 cells stably expressing two individual shRNAs against UBE2T were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina Hi-Seq 2500 platform, with three biological replicates for each sample.


title: Genome-wide DNA methylation profiles of endometrioid endometrial cancer tissue

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai

address: 35, Shinano-machi

department: Pathology

country: Japan

institute: Keio University School of Medicine

summary: Genome-wide DNA methylation screening was performed using the Infinium MethylationEPIC BeadChip in 49 fresh-frozen tissue samples and 31 formalin-fixed paraffin-embedded tissue samples obtained from surgically resected materials of patients with endometrioid endometrial cancer.

overall_design: Five-hundred-nanogram aliquots of DNA extracted from fresh frozen tissue samples were subjected to bisulfite conversion using an EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA). For FFPE tissue samples, 50 to 300-nanogram aliquots of DNA were used and DNA restoration was performed using an Illumina HD FFPE Restoration Kit (Illumina). DNA methylation status at 866,895 CpG loci was examined at single-CpG resolution using the Infinium MethylationEPIC BeadChip (Illumina). After hybridization, the specifically hybridized DNA was fluorescence-labeled by a single-base extension reaction and detected using an iScan reader (Illumina) in accordance with the manufacturer’s protocol. The data were then assembled using GenomeStudio methylation software (Illumina).

first: Eri

last: Arai


title: RNA sequencing of wild type and Thpo deficient hematopoietic stem cells

city: Shinjukuku

first: Ayako

last: Nakamura-Ishizu

state: Tokyo

address: 8-1 Kawadacho

institute: Tokyo Women's Medical University

summary: RNA sequencing was conducted on up to 5000 CD34-CD150+CD48-LSK cells from Thpo+/+ , Thpo-/-  along  with Thpo+/+ and Thpo-/- mice treated with 10 days of Thpo receptor agonist (Romiplostim)

overall_design: HiSeq4000 sequencing (Illumina) platform (150bp paired-end). Three samples from a single group were placed on single run to produce more than 8x107 reads per sample


title: Upregulation of BTN3A1 on CD14+ cells promotes Vγ9Vδ2 T cells activation in psoriasis vulgaris

city: Shanghai

first: Jiaqing

last: Zhou

address: Yixueyuan road No.138

institute: Fudan university

summary: Vγ9Vδ2 T cells play an important role in the development and progression of psoriasis vulgaris (PV), but how they promote skin inflammation and the molecular mechanisms underlying Vγ9Vδ2 T cell dysfunction are poorly understood. Here, we show that circulating Vγ9Vδ2 T cells are decreased and exhibit enhanced proliferation and increased production of IFN-γ and TNF-α in PV patients. Monocytes from PV patients express higher levels of the phosphoantigen sensor butyrophilin 3A1 (BTN3A1) than monocytes from healthy controls. Blockade of BTN3A1 suppresses Vγ9Vδ2 T cell activation and abolishes the difference in Vγ9Vδ2 T cell activation between PV patients and healthy controls. The CD14+ cells in PV skin lesions highly express BTN3A1 and juxtapose to Vδ2 T cells. In addition, IFN-γ induces the up-regulation of BTN3A1 on monocytes. Collectively, our results demonstrate a crucial role of BTN3A1 on monocytes in regulating Vγ9Vδ2 T cell activation and highlight BTN3A1 as a potential therapeutic target for psoriasis.

overall_design: Peripheral Vγ9Vδ2 T cells mRNA profiles of healthy controls (HC) and psoriasis vulgaris (PV)  patients

first: Jingjing

last: Zhang

first: Lu

last: Tao

first: Kexin

last: Peng

first: Qiaoan

first: Kexiang

last: Yan

first: Jing

last: Luan

first: Jiewen

last: Pan

first: Xiaohui

last: Su

first: Jiping

last: Sun

first: Zhenghua

first: Lei

last: Shen


title: Transcriptomic profiles of ivosidenib-sensitive and ivosidenib-resistant IDH1-mutated murine bone marrow cells

status: Public on Nov 08 2022

city: Toronto

first: AlexCH

last: Liu

state: Ontario

address: 101 College Street

department: Medical Biophysics

country: Canada

institute: University of Toronto

summary: To study the mechanism of resistance to ivosidenib, we developed a model of acquired drug resistance by treating ivosidenib-sensitive OCI-mIDH1/N cells continuously with ivosidenib in culture for a period of 2 months followed by a drug washout period. The resulting cell population (OCI-mIDH1/N-R cells) failed to differentiate upon ivosidenib treatment. We then performed RNA sequencing (RNA-seq) analysis of OCI-mIDH1/N and OCI-mIDH1/N-R cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ivosidenib-sensitive and ivosidenib-resistant IDH1-mutated murine bone marrow cells.

first: Alex

middle: C

first: Severine

last: Cathelin

first: Steven

last: Chan


title: Effect of SYK inhibition on gene expression during ivosidenib induced differentiation of IDH1-mutated murine bone marrow cells (OCI-mIDH1/N)

summary: To investigate the mechanisms by which SYK inhibition sensitizes OCI-mIDH1/N cells to ivosidenib, we performed RNA sequencing (RNA-seq) analysis of cells treated with DMSO (vehicle control), ivosidenib alone, fostamatinib alone, entospletinib alone, or the combination of ivosidenib with each of the two SYK inhibitors for 9 days.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for OCI-mIDH1/N cells treated with mutant IDH1 and SYK inhibitors.


title: Profile analysis of circRNAs in osteoblasts infected by Staphylococcus aureus

city: Soochow

first: zhihao

last: chen

address: china

institute: The Second Affiliated Hospital of Soochow University

summary: This study aims to compare differential expression circRNA between normal and Staphylococcus aureus infection in osteoblasts

overall_design: 6 samples were analyzed including 3 samples of control groups and Staphylococcus aureus infection group.

first: Mingxing

first: Zhihao

last: Chen


title: peripheral blood mononuclear cells (PBMCs) of pre- and post-treatment periodontitis patients and healthy donors by single-cell RNA profiling

city: Yangsan

first: Hansong

last: Lee

address: 49 Busandaehak-ro

country: South Korea

institute: Pusan National University

summary: The pathogenic determinants of chronic periodontitis leading to extra-oral comorbidity are unclear. This study was conducted to investigate the main determinants that correlate chronic periodontitis and systemic diseases via periodontitis-evoked molecular changes in immune cells resolved by therapy. Single-cell RNA sequencing using peripheral blood mononuclear cells was performed to compare the molecular and biological differences in immune cells of 4 pre- and 4 post-treatment patients and 4 healthy donors. Periodontal treatment was one-day full-arch scaling and root planning for full mouth disinfection. Altered expression of genes involved in the inflammatory response in the patients was compared with that in healthy donors following therapeutic intervention. The common representative genes across diverse cell types were investigated; those genes were associated with periodontitis-pathogenic bacterial systemic diseases. These important factors correlating chronic periodontitis and systemic inflammatory diseases at the single-cell level may serve as therapeutic targets.

overall_design: Single-cell RNA-seq analysis of peripheral blood mononuclear cells (PBMCs). samples: 4 healthy and paired pre- and post treatment samples from 4 periodontitis patients.

first: Jiyoung

last: Joo

first: Yunhak

last: Kim

first: Hae-ryoun

last: Park


title: Targeting STAT5 signaling overcomes resistance to IDH inhibitors in acute myeloid leukemia through suppression of stemness


title: NK cell-derived exosomes enhance the anti-tumor effects against ovarian cancer by delivering chemotherapeutic drugs and reactivating NK cell functions

city: Guiyang

first: Heyong

last: Luo

address: Dongqing road

institute: Guizhou Medical University

summary: Global transcriptional analysis by RNA-seq was performed to understand the molecular mechanisms underlying the functional difference between NK cells, AS_NK cells and eNK-EXO treated NK cells.

overall_design: comparative gene expression profiling analysis of RNA-seq data for NK cells,AS_NK cells and eNK-EXO treated NK cells

first: Shiqi

last: Long


title: ESE1/AGR2 axis antagonizes TGF-β-induced epithelial-mesenchymal transition in pancreatic cancer

city: Wenzhou

first: Huijing

last: Xu

state: Zhejiang

address: Chashan University Park

institute: Wenzhou Medical unversity

summary: To investigate the function of ESE1 in the epithelial-mesenchymal, we established L3.6 cell lines in which  target gene has been knocked down by shRNA.We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at the same time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data forL3.6 cells and its knockdown derivatives (shESE1).

first: Hui-Jing

first: Jing

last: Bai

first: Ai-Ping

first: Ye

last: Tian

first: Xiao

last: Feng

first: Jie

last: Wang

first: Jin

last: Wu

first: Xu-Ru

last: Jin

first: Feng

last: Zhang

first: Mei-Yu

last: Quan

first: Chengshui

first: Kwang-youl

first: Jin-San


title: Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [ly6c]

city: rehovot

first: Coral

last: Halperin

address: Herzel 234

country: Israel

institute: Weizmann institute of sciences

summary: We performed RNA seq to charachterize the transcriptome of specific cancer associates fibroblasts (pCAFs)  sub-populations (Ly6c+ vs Ly6c- pCAFs)

overall_design: 4T1 cells  were injected orthotopcally into the mammary fat pad of balb\c mice, tumors were harvested and digested after reaching a size of 1 cm. Ly6c+ and Ly6c- pCAF were collected by  fluorescence-activated cell sorting (FACS) based on negative selection excluding EpCAM-, CD45-, and Ter119- and positive selection using PDPN. To subset the pCAFs we used anti-Ly6C antibody to separate between the negative and positive subsets.

first: Joschka

last: hey

first: Christoph

last: Plass

first: Ruth

last: Shouval


title: Exploring differentially expressed genes in hypothalamic (HT), pars tuberalis (PT) and pineal gland (PG) transcriptomes in different sexual behaviour phenotypes in rams using RNA-seq

city: Zaragoza

first: Kenza

last: Lakhssassi

state: Zaragoza

address: Av Montañana, 930,

institute: CITA

summary:
To understand the mechanisms of sexual behaviour in rams, transcriptomic sequencing technology was used to identify differentially expressed genes in key brain tissues
We then performed gene expression profiling analysis using data obtained from RNA-seq of hypothalamus (HT), pars tuberalis (PT) and pineal gland (PG) in rams with different sexual behaviours

overall_design:
The PT, HT and PG transcriptomes of 12 Rasa Aragonesa rams (6 sexually active (A) and 6 not active (NA) for each tissue) were generated by Novaseq 6000 platform
Identifcation of differentially expressed genes (DEGs) in the 3 studied tissues. The multifactorial design was used where the state (A or NA) was defined as the primary contrast condition and the tissue (PT, HT, and PG) as the secondary contrast condition

first: Jorge

last: Lacosta


title: PRMT3 drives glioblastoma progression by enhancing HIF1A and glycolytic metabolism

city: Cincinnati

first: Qing

middle: Richard

last: Lu

state: Ohio

address: 3333 Burnet Avenue

department: CBDI

institute: cincinnati children's hospital medical center

summary: To investigate the potential mechanisms underlying PRMT3 regulation of GBM growth, we performed RNA-seq transcriptomic profiling of U251 GBM cells treated with lenti-ShCtrl and shPRMT3.

overall_design: 2 Ctrl U251 GBM cells and 2 PRMT3-KD U251 GBM cells

first: Yunfei

last: Liao

middle: R


title: Whole-transcriptome analysis of hematopoietic progenitors in the cranial dura, femur, and skull

city: Beijing

first: Jijun

last: Yu

address: Taiping Road No.27

institute: Basic medical Research Institute

summary: Live Lin−/lowc-Kit+ singlets from the cranial dura, femur, and skull of adult mice were sorted for whole-transcriptome analysis.

overall_design: Leukocytes were mechanically isolated from the cranial dura, femur, and skull of ten 8 ~ 12-week-old C57BL/6 mice after intracardiac perfusion. Cells from the same compartment were mixed together and stained with DAPI and fluorescence-conjugated antibodies against c-Kit and lineage markers. Then DAPI−Lin−/lowc-Kit+ singlets were sorted and subjected to 10x Genomics single-cell RNA sequencing (scRNA-seq).

first: Jiyan

first: ChunXiao

last: Niu

first: Tao

last: Zou


title: Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [co-culture]

summary: We performed RNA seq to characterize the transcriptome of normal mammary fibroblasts (NMFs) co-cultured with 4T1 cancer cells for 3 and 5 days as well as mono-cultured NMFs.

overall_design: Fresh mammary fat pad tissue was extracted from 12-week-old female BALB/c mice and NMFs were isolated. The NMFs were cultured on a collagen layer for 1 week of recovery and then co-cultured with 4T1-GFP cancer cells for 3 and 5 days. NMF were isolated by FACS sorting using negative selection for GFP and positive selection for PDPN and RNA sequencing was preformed.


title: Novel prognostic implications of complement activation in the tumor microenvironment for de novo metastatic BRAF V600E mutant colorectal cancer

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary:
Prognosis of metastatic BRAF V600E mutant colorectal cancer (CRC) is poor, and the prognostic implications of immune contextures in the tumor microenvironment (TME) for CRC remain elusive.
Complement activation in the TME was significantly associated with poor OS and was correlated with TAM M2 in patients with de novo metastatic BRAF V600E mutant CRC.

overall_design: Gene expression profile

first: K

last: Chen

last: Yeh


title: Genome-wide maps of H3K79Me3 binding sites in ovarian cancer cell line OVCAR5 and expression profile of DOT1L knockdown OVCAR5 cells (ChIP-seq)

city: Chicago

first: Daniela

last: Matei

state: Illinois

address: 303 E Superior St

department: Ob-Gyn

institute: Northwestern University

summary: This study characterized the genome-wide binding of histone 3 lysine 79 tri-methylation and expression profile of DOT1L knockdown in OVCAR5 cells.

overall_design: Two datasets are included: 1) Examined transcriptome of OVCAR5 cells transduced DOT1L-targeting shRNA (shDOT1L) in OVCAR5 cells (in biological duplicates); 2) Determined the genome-wide bindng and occupancy profile of histone 3 lysine 79 tri-methylation in OVCAR5 cells by ChIP-seq

first: Yaqi

first: Yinu

last: Wang


title: Genome-wide maps of H3K79Me3 binding sites in ovarian cancer cell line OVCAR5 and expression profile of DOT1L knockdown OVCAR5 cells

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

overall_design: Refer to individual Series


title: Immortalized human choroid plexus endothelial cells enable an advanced endothelial-epithelial two-cell type in vitro model of the choroid plexus

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: We describe here the generation and characterization of immortalized HCPEnC (iHCPEnC) by ectopic expression of hTERT in primary cells using a lentiviral vector system without additional support by a viral oncogene. RNA sequencing (RNA-seq) analysis revealed that iHCPEnC retained an RNA expression profile very similar to the primary HCPEnC and different from that of other endothelial cell types as Human Brain Microvascular Endothelial Cells (HBMEC) and Human Umbilical Vein Endothelial Cells (HUVEC).

overall_design: Establishing an advanced co-culture model consisting of CP endothelial (iHCPEnC) and epithelial (HIBCPP) cells. Comparison of the gene expression of different endothelial cell lines.

first: Walter

last: Muranyi

first: Christian

last: Schwerk

first: Horst

last: Schroten


title: Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [RNA-Seq]

first: Coral

last: Halperin

summary: We preformed RNA seq to charachterize the transcriptome of cancer associates fibroblasts  (pCAF) compared to normal mammary fat pad fibroblasts (NMF)

overall_design: 4t1 cells  were injected orthotopcally into the mammary fat pad of balb\c mice, tumors were harvested and digested after reaching a size of 1 cm and pCAF were collected by  fluorescence-activated cell sorting (FACS) based on negative selection excluding EpCAM-, CD45-, and Ter119- and positive selection using PDPN. NMF were collected by harvsting the mammary fat pad of age matched Balb\c mice, and  facs sorting was performed with the above mentioned negative selection markers

first: Joschka

last: Hey

first: Christoph

last: Plass

first: Ruth

last: Scherz Shouval


title: Cancer cell-intrinsic XBP1 mediates immunosuppressive reprogramming of intratumoral myeloid cells by promoting cholesterol production

first: Likun

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: A hostile microenvironment in tumor tissues disrupts endoplasmic reticulum homeostasis and induces the unfolded protein response (UPR). A chronic UPR in both cancer cells and tumor-infiltrating leukocytes could facilitate evasion of immune surveillance. However, how the UPR in cancer cells cripples the anti-tumor immune response is unclear. Here, we demonstrate that, in cancer cells, the UPR component X-box binding protein 1 (XBP1) favors the synthesis and secretion of cholesterol, which activates myeloid-derived suppressor cells (MDSCs) and causes immunosuppression. Cholesterol is delivered in the form of small extracellular vesicle and internalized by MDSCs through macropinocytosis. Genetic or pharmacological depletion of XBP1 or reducing the tumor cholesterol content remarkably decreases MDSC abundance and triggers robust anti-tumor responses. Thus, our data unravel the cell non-autonomous role of XBP1/cholesterol signaling in the regulation of tumor growth and suggest its inhibition as a useful strategy for improving the efficacy of cancer immunotherapy.

overall_design: RNA-seq on subcutaneous MC38-OVA tumors in shNT and shXBP1 genotypes.

first: Zaili

last: Yang

first: Yazhen

last: Huo

first: Shixin

last: Zhou

first: Jingya

last: Guo

first: Xiaotu

last: Ma

last: Li

first: Congli

last: Fan


title: Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [WGBS]

type: Methylation profiling by high throughput sequencing

summary: We preformed whole-genome bisulfite sequencing to charachterize the DNA methylation landscape of cancer associates fibroblasts  (pCAF) compared to normal mammary fat pad fibroblasts (NMF)

last: hey

last: Shouval


title: Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma


title: Genome-wide maps of H3K79Me3 binding sites in ovarian cancer cell line OVCAR5 and expression profile of DOT1L knockdown OVCAR5 cells (RNA-seq)

first: Daniela

last: Matei

first: Yaqi

last: Zhang

last: Wang


title: (ChIP-seq) USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: patrick G Johnston Centre for Cancer research

institute: Queen's University Belfast

summary: Ubiquitin-specific protease 7 (USP7) has been implicated in cancer progression and neurodevelopment. However, its molecular targets remain poorly characterized. We combined quantitative proteomics, transcriptomics, and epigenomics to define the core USP7 network. Our multi-omics analysis reveals USP7 as a control hub that links genome regulation, tumor suppression, and histone H2A ubiquitylation (H2AK119ub1) by noncanonical Polycomb-repressive complexes (ncPRC1s). USP7 strongly stabilizes ncPRC1.6 and, to a lesser extent, ncPRC1.1. Moreover, USP7 represses expression of AUTS2, which suppresses H2A ubiquitylation by ncPRC1.3/5. Collectively, these USP7 activities promote the genomic deposition of H2AK119ub1 by ncPRC1, especially at transcriptionally repressed loci. Notably, USP7-dependent changes in H2AK119ub1 levels are uncoupled from H3K27me3. Even complete loss of the PRC1 catalytic core and H2AK119ub1 has only a limited effect on H3K27me3. Besides defining the USP7 regulome, our results reveal that H2AK119ub1 dosage is largely disconnected from H3K27me3.

overall_design:
ChIP-seq analysis of H3K27me3 and H2AK119Ub in RING1A/B-DKO HAP1 cells
contributor: Erasmus Genomics CTU

first: Ayestha

last: Sijm

first: Jan

last: van der Knaap

first: Joyce

middle: W

last: van der Meer

first: Gillian

middle: E

last: Chalkley

first: Karel

last: Bezstarosti

first: Dick

last: Dekkers

first: Wouter

last: Doff

first: Zeliha

last: Ozgur

first: Wilfred

middle: F

last: van IJcken

first: Jeroen

last: Demmers

first: C

middle: P

last: Verrijzer


first: Jiyan

address: 27 Taiping Road

institute: Beijing Institute of Basic Medical Sciences

summary: Over 8000 high-qualified CD45IV-DAPI-CD45+ dura cells were sorted for single cell RNA sequencing; 13 cell populations were identified, Including T cells, B cells ,NK cells, monocytes, erythroid cells, and progenitors.

overall_design: Single cell RNA sequencing of dura leukocytes from four 8 ~ 12-week-old wild type (WT) mice

first: ChunXiao

last: Niu

first: Jijun

last: Yu

first: Tao

last: Zou


title: (RNA-seq) USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3

overall_design:
RNA-seq analysis of wild-type or USP7-KO DLD1 cells. DOX treatment for 1, 3, or 9 days was carried out to rescue USP7 expression.
contributor: Erasmus Genomics CTU


title: SFB-driven regulation in small intestinal epithelial cells during infection

first: Theresa

last: Alenghat

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Expression in intestinal epithelial cells from intestine of germ-free and segmented filamentous bacteria (SFB)-monoassociated mice during infection. Intestinal epithelial cells were harvested from the terminal ileum of germ-free or SFB mice infected with Citrobacter rodentium for 6 days. RNA was isolated using RNeasy Kit (Qiagen). Sequencing was performed using the Illumina HiSeq2500. Reads were mapped to the mm10 genome using Bowtie.

overall_design: Characterization of differential expression in intestinal epithelial cells from Citrobacter rodentium-infected GF and SFB-monocolonized mice

first: Vivienne

last: Woo


first: Yaser

last: Atlasi

overall_design:
ChIP-seq analysis of H3K27me3 and H2AK119Ub in USP7-KO-DOX-USP7 DLD1 cells.
contributor: Erasmus Genomics CTU

first: Ayestha


title: Newborn pig uterus gene expression changes in response to lactocrine insufficiency from birth

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: Maternal effects on offspring phenotype do not end at birth. Bioactive factors are transmitted from mother to nursing offspring through colostrum, which is known as lactocrine programming. The lactocrine hypothesis posits that disruption of lactocrine signaling from birth will have both short- and long-term effects on the postnatal developmental program with lasting consequences. Previous research established that lactocrine insufficiency from birth in pigs, indicated by reduced serum immunoglobulin immunocrit (iCrit) ratios in nursing piglets on the day of birth (postnatal day 0, PND0), altered the postnatal uterine developmental program and reduced lifetime fecundity in adult, neonatally lactocrine insufficient females. To determine the effects of lactocrine insufficiency on uterine development in the rapid growth phase, we performed RNA sequencing in six high-low iCrit pairs in PND14 gilt littermates. High-quality RNA-seq reads were mapped to the porcine reference genome, and the expression levels were quantified in the uterus transcriptome. We identified 148 (1.1% of expressed genes) differentially expressed genes (DEGs) between the high and low iCrit groups at P < 0.05, including the the FOXA2 gene, which was known to be downregulated in low-iCrit uterus samples. Gene ontology analysis reveals that immune-related functions, including the complement pathways are up-regulated in the low iCrit group.

overall_design: Crossbred gilts, born and maintained at the US Meat Animal Research Center (Clay Center, NE), were assigned to low (n=6) or high (n=6) iCrit groups based on iCrit ratio values determined on PND0. To characterize lactocrine effects on the PND14 uterine transcriptome in low/high iCrit  gilts, 6 pairs of low and high iCrit gilts from the same litters were euthanized and uterus samples were collected on PND14, following by RNA extraction, stranded mRNAseq library construction and sequencing.

first: Frank

last: Bartol


title: Continuous gene expression profile of leaf of rice grown under field conditions

city: Tsukuba

first: Hinako

last: Takehisa

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences (NIAS)

summary: A continuous gene expression profiling of leaves at regular interval was performed to understand the changes of transcriptional program and physiological state of the rice plant under two different field conditions.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: For continuous gene expression profile of leaf, the uppermost fully-expanded leaf in the main stem was sampled at 10:00-12:00 AM at regular intervals of about 7 days encompassing 10 different growth stages during a normal rice growing season.

first: Yutaka

last: Sato


title: SFB-driven epigenetic regulation in small intestinal epithelial cells

summary: H3K27Ac enrichment in intestinal epithelial cells from intestine of germ-free and segmented filamentous bacteria (SFB)-monoassociated mice. Intestinal epithelial cells were harvested from the terminal ileum of germ-free or SFB mice. Chromatin immunoprecipitation was performed with anti-H3K27Ac. Sequencing was performed using the Illumina HiSeq2500. Reads were mapped to the mm10 genome using Bowtie.

overall_design: Characterization of  histone acetylation in intestinal epithelial cells from GF and SFB-monocolonized mice


title: Early-life starvation affects phosphatidylcholine metabolism and eicosanoid signaling in adults to cause pathology

city: New York

first: James

middle: Matthew

last: Jordan

state: NY

department: Medicine

institute: Weill Cornell Medical College, Cornell University


title: mRNA-seq analysis of early adult C. elegans fatty acid synthesis mutant following extended L1 arrest

summary: Early-life malnutrition increases adult disease risk in humans, but the causal changes in gene regulation, signaling, and metabolism are unclear. In the roundworm Caenorhabditis elegans, early-life starvation causes well-fed larvae to develop germline tumors and other gonad abnormalities as adults. Furthermore, reduced insulin/IGF signaling (IIS) during larval development suppresses these starvation-induced abnormalities. How early-life starvation and IIS affect adult pathology is unknown. We show that early-life starvation has pervasive effects on adult gene expression that are largely reversed by reduced IIS following recovery from starvation. Early-life starvation increases adult fatty-acid synthetase fasn-1 expression in daf-2 IIS receptor-dependent fashion, and fasn-1/FASN promotes starvation-induced abnormalities. Lipidomic analysis reveals increased levels of phosphatidylcholine in adults subjected to early-life starvation, and supplementation with unsaturated phosphatidylcholine during development suppresses starvation-induced abnormalities. Genetic analysis of fatty-acid desaturases reveals positive and negative effects of desaturation on development of starvation-induced abnormalities. In particular, the delta 3 fatty-acid desaturase fat-1 and the delta 5 fatty-acid desaturase fat-4 inhibit and promote development of abnormalities, respectively. fat-4 is epistatic to fat-1, suggesting that arachidonic acid, or lipids that contain it, promotes development of starvation-induced abnormalities. This work shows that early-life starvation and IIS converge on regulation of adult lipid metabolism, affecting stem-cell proliferation, tumor formation, and additional adult pathologies.

overall_design: Two conditions (starved wild type (N2) and starved fasn-1(g14) mutants) with two biological replicates per condition.

first: Jingxian

last: Chen

first: Rojin

last: Chitrakar

first: L

last: Baugh


title: Loss of neuronal Tet2 enhances hippocampal-dependent cognitive function

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

summary: DNA methylation has emerged as a critical modulator of neuronal plasticity and cognitive function. Notwithstanding, the role of enzymes that demethylate DNA remain to be fully explored. Here, we report that loss of ten-eleven translocation methylcytosine dioxygenase 2 (Tet2), which catalyzes oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), in adult neurons enhances cognitive function. In the adult mouse hippocampus, we detected an enrichment of Tet2 in neurons. Viral-mediated neuronal overexpression and RNA interference of Tet2 altered dendritic complexity and synaptic-plasticity-related gene expression in vitro. Overexpression of neuronal Tet2 in adult hippocampus, and loss of Tet2 in adult glutamatergic neurons, resulted in differential hydroxymethylation associated with genes involved in synaptic transmission. Functionally, overexpression of neuronal Tet2 impaired hippocampal-dependent memory, while loss of neuronal Tet2 enhanced memory. Ultimately, these data identify neuronal Tet2 as a molecular target to boost cognitive function.

overall_design: RNA sequencing of hippocampal neuronal nuclei isolated from CamKIIaCreERT2;Tet2fl/fl mice vs WT Tet2fl/fl. RNA sequencing of E17 primary neuron cultures infected with lentivirus against luciferase or Tet2 (Samples 8-19).

first: Karishma

last: Pratt

first: Jeremy

last: Shea

first: Saul

last: Villeda


title: mRNA-seq analysis of early adult C. elegans following extended L1 arrest with reduced insulin/insulin-like signaling

summary: We characterized the effects of early-life starvation and reduced insulin/insulin-like signaling (IIS) during larval development on adult gene expression using mRNA-seq of whole worms. In our two-factor design, 'starved' worms were cultured without food (E. coli) in L1 arrest for eight days, and 'control' worms were starved overnight for synchronization. Both populations of worms were fed ad libitum with either empty vector (EV; negative control) or daf-2/InsR RNAi food (reduced IIS). RNAi was used rather than a daf-2 mutant so that the results would not be confounded by daf-2 function during L1 arrest, instead disrupting daf-2 only after starvation in fed, developing larvae. Upon reaching adulthood, animals were collected for transcript profiling.

overall_design: 4 conditions (control-EV, control-daf-2 RNAi, starved-EV, and starved-daf-2 RNAi) with 3 biological replicates per condition.

first: Amy

middle: K

last: Webster


title: RNA-seq reveals the immuno-modulation of exosomes in Zhikong scallop Chlamys farreri

city: Qingdao

first: Mengqiang

state: Shandong

address: Nanhai Road

institute: The Institute of Oceanology, Chinese Academy of Science

summary: As marine invertebrates, scallops lack adaptive immunity and employ innate immunity as the front line and almost the solo defense mechanism to protect them against invaders. Accumulating research achievements demonstrated that exosomes could act as innate immune effectors that contribute to host defense mechanism. To better understand the immune functions of exosomes in Chlamys farreri, mRNA profiles of hemocytes from scallops injected with PBS, with normal exosomes and LPS stimulating exosomes, respectively, were generated by deep sequencing, in triplicate.

overall_design: Hemocytes mRNA profiles of scallops injected with PBS, with normal exosomes and LPS stimulating exosomes, respectively, were generated by deep sequencing, in triplicate, using Illumina Novaseq™ 6000.


title: Identification of drugs in leukaemia differentiation therapy by network pharmacology

city: Sinagpore

first: Eleni

middle: G.

last: Christodoulou

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: Acute leukaemias differ from their normal haematopoietic counterparts in their inability to differentiate. This phenomenon is thought to be the result of aberrant transcriptional reprogramming involving transcription factors (TFs). Here we leveraged on Mogrify, a network-based algorithm for predicting reprogramming factors, to identify TFs and their gene regulatory networks that drive ATRA-induced differentiation of the acute promyelocytic leukaemia (APL) cell line NB4. We further integrated the detected TF regulatory networks with the Connectivity Map (CMAP) repository and recovered small molecule compounds which induce similar transcriptional changes. Our method outperformed standard approaches, retrieving ATRA as the top hit. Of the other drug hits, dimaprit and mebendazole enhanced ATRA-mediated differentiation in both parental NB4 and ATRA-resistant NB4-MR2 cells. Thus, we provide a proof-of-principle of our network-based computational platform for drug discovery and repositioning in leukaemia differentiation therapy, which can be extended to other dysregulated disease states.

overall_design: 33 NB4 APL samples consisting of No Treatment(basal=3), ATRA (treatment=15) and DMSO (control=15) conditions in 5 time points 4h, 12h, 24h, 72h and 120h in 3 biological replicates. Each biological replicate was further subjected to paired-end RNA-Seq in 2 technical replicates.

middle: G

first: Lin

last: Lee

first: Kian

first: Enrico

last: Giuseppe Petretto

first: Owen

last: Llewllyn Rackham

first: Sin

middle: T

last: Ong

first: Pavithra

last: Shyamsunder

first: Bei

first: Tsz

last: Fung

first: Wai Eric

last: So

first: Gee

last: Wong


title: Circulating lncRNAs NONHSAT054669.2 and ENST00000525337 can be used as early biomarkers of gestational diabetes mellitus

status: Public on Nov 07 2022

city: Jinan

first: lina

last: wang

address: North Park Street 247

institute: Second Hospital of Shandong University

summary:
This study aimed to identify key circulating long non-coding RNAs (lncRNAs) as novel biomarkers for diagnosis of GDM at the early stages. First, lncRNA microarray analysis was conducted for plasma samples of GDM women before delivery and 48 h after delivery. The expression of differentially expressed lncRNAs in clinical samples at different trimesters was randomly validated by quantitative PCR. Moreover, the correlation between lncRNA expression and oral glucose tolerance test (OGTT) level in GDM women during the second trimester was analyzed, and the diagnostic value of key lncRNAs for GDM during different trimesters was evaluated by receiver operating characteristic (ROC) curve.
The plasma level of NONHSAT054669.2 and ENST00000525337 may be used as novel diagnostic biomarkers for early diagnosis of GDM.

overall_design: We performed lncRNA microarray analysis of plasma samples from 3 pregnant women with GDM before delivery and 48 hours after delivery to identify key lncrnas associated with GDM

first: Lina

last: Wang


title: ILC2 promote type 2 immunity in myeloid and epithelial cells of the lung (scRNAseq)

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: ILC2 contribute to tissue immunity by secreting large amounts of cytokines upon activation. However, their role in steady state tissue homeostasis remains incompletely explored. We tested the impact of ILC2 on tissue immunity in steady state the lungs by scRNA sequencing of myeloid and epithelial cells from mice specifically lacking ILC2 (Nmur1-Cre Id2 fl/fl). Transcripts typically associated with type 2 immunity were reduced in ILC2-deficient mice, indicating a non-redundant role of ILC2 for type 2 tissue immunity that cannot be compensated by other cell types. These findings highlight the importance of ILC2 for balancing tissue homeostasis in the healthy murine lung.

overall_design: Sequencing of RNA was performed from flow cytometry-sorted epithelial (CD45lo/- EpCAM+ ) and myeloid cells (CD45+ (CD11b+ and/or CD11c+)) from the lung of Nmur1-Cre Id2fl/fl mice and littermate controls, using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit.

first: Katja

last: Jarick

first: Frederik

last: Heinrich

first: Gabriela

middle: M

last: Guerra

first: Mir-Farzin

last: Mashreghi

first: Christoph

middle: S

last: Klose


title: Reemergence of pathogenic, autoantibody-producing B-cell clones in myasthenia gravis following B-cell depletion therapy.

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

institute: Yale University

summary: Myasthenia gravis (MG) is an autoantibody-mediated autoimmune disorder of the neuromuscular junction. Some patients with MG have pathogenic mAbs that recognize muscle-specific tyrosine kinase (MuSK). Patients respond well to CD20-mediated B-cell depletion therapy (BCDT); most achieve complete stable remission. However, relapse often occurs. To further understand the immunomechanisms underlying relapse we sought to study autoantibody-producing B-cells over the course of BCDT. We developed a monomeric fluorescently labelled antigen to enrich for MuSK-specific B-cells, which was validated with a novel Nalm6 cell line engineered to express a human MuSK autoantibody as B-cell receptor. We found that MuSK-specific B-cells are rare within the circulation (<3 per 10 million cells). From two MuSK-specific B-cells isolated from two distinct patients, we generated human recombinant MuSK mAbs. The autoantibodies originated from plasmablasts, used the IgG4 subclass, recognized the Ig1-like domain of MuSK and showed pathogenic capacity using an in vitro AChR clustering assay. Persistent clones of the mAbs were identified through B-cell repertoire tracing. Clonal variants of 2E6 were detected at several timepoints spanning more than five years months and reemerged after BCDT-mediated remission, appearing several months prior to relapse. These results indicate that a reservoir of rare pathogenic MuSK autoantibody-expressing B cell clones survive BCDT, then reemerge prior to manifestation of clinical relapse. This study provides both a mechanistic understanding of MuSK MG relapse and a valuable candidate biomarker for relapse prediction.

overall_design: Samples from eight subjects were studied. Four subjects had the MuSK subtype of myastenia gravis, four were healthy cotrols. Samples underwent bulk BCR sequencing, as well as scRNA-seq and scBCR sequencing.

first: Miriam

middle: L

last: Fichtner

first: Kenneth

middle: B

last: Hoehn

first: Kevin

last: O'Connor


title: Effect of Protein Kinase C-epsilon knockout on atrial tissue gene-expression in old mice.

city: Tampa

first: Sami

last: Noujaim

state: FL

address: 12901 Bruce B Downs Blvd

department: Molecular Pharmacology and Physiology

institute: University of South Florida

summary: We conducted RNAseq on old PKCε KO vs old WT mouse atrial samples to identify pathways contributing to reduced inducibility and duration of AF in the old KO compared to old WT mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three biological replicates of old PKCe-KO mice vs. three biological replicates of old WT mouse controls.

first: Jenna

last: Oberstaller

first: Justin

last: Gibbons

first: Mengmeng

last: Chang

first: Kirin

middle: D

last: Gada

first: Bojjibabu

last: Chidipi

first: Athanasios

last: Tsalatsanis

first: Elizabeth

last: Remily-Wood

first: Diomedes

last: Logothetis


title: Effect of overexpressing Il-25 mediated the regulatory gene expression in the absence or presence of EV71 infection in HeLa cells

city: Nanjing

first: Jing

last: Wu

address: Han Kou road 22#

institute: Nanjing University

summary: To investigate IL-25 in the regulation of antivral immunity, we established Il-25 stably expressing cell lines in which each target gene has been regulated by IL-25 overexpression.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of HeLa cells and IL-25 overexpressing HeLa cells in the uninfected and infected with EV71,respectively .
Comparative gene expression profiling analysis of RNA-seq data for IL-25_V and WT_V.

first: Deyan

last: Chen

first: Zhiwei


title: Modeling gene × environment interactions in PTSD using human neurons reveals diagnosis-specific glucocorticoid-induced gene expression

first: Carina

middle: of

last: Seah

state: New York

address: 1 Gustave L Levy Pl Fl 1

institute: Icahn School of Medicine at Mount Sinai

summary: Post-traumatic stress disorder (PTSD) can develop following severe trauma, but the extent to which genetic and environmental risk factors contribute to individual clinical outcomes is unknown. Here, we compared transcriptional responses to hydrocortisone exposure in human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons and peripheral blood mononuclear cells (PBMCs) from combat veterans with PTSD (n = 19 hiPSC and n = 20 PBMC donors) and controls (n = 20 hiPSC and n = 20 PBMC donors). In neurons only, we observed diagnosis-specific glucocorticoid-induced changes in gene expression corresponding with PTSD-specific transcriptomic patterns found in human postmortem brains. We observed glucocorticoid hypersensitivity in PTSD neurons, and identified genes that contribute to this PTSD-dependent glucocorticoid response. We find evidence of a coregulated network of transcription factors that mediates glucocorticoid hyper-responsivity in PTSD. These findings suggest that induced neurons represent a platform for examining the molecular mechanisms underlying PTSD, identifying biomarkers of stress response, and conducting drug screening to identify new therapeutics.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NGN2-neurons and PBMCs from PTSD case or control donors treated with glucocorticoids (hydrocortisone and dexamethasone, respectively)


title: Chip-on-ChEPseq analysis of RAD21 cohesin subunit cleaved by separase in a human cancer cell line

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

summary: The goal of the study was to map the epigenomic positions of proteolyzed RAD21 human protein in mitotic DLD-1 cells with proprietary antibodies against the neo-epitope (RAD21*) generated by cleavage with separase. The study involved chromatin IP analyzed by high-throughput sequencing analysis using immortalized human cancer cells.

overall_design: DLD-1 (ATCC® CCL-221™) cells were grown at standard conditions and synchronized using double thymidine block protocol. The cells synchronously progressing through mitosis were collected at equal intervals in order to capture anaphase cells.

first: AbdelHalim

last: Boukaba

first: Jian

last: Liu

first: Cheng

first: Jierong

last: Liang

first: Qiongfang


title: USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3

first: Yaser

last: Atlasi

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

overall_design: Refer to individual Series


title: Next Generation Sequencing  Analysis of primary rat lung fibroblast transcriptomes

city: Ulm

first: Manfred

last: Frick

address: Albert-Einstein Allee 11

country: Cote d'Ivoire

institute: University of Ulm

summary: Purpose: We report the application of single-molecule-based sequencing technology for high-throughput profiling of primary rat lung fibroblast cultured on 3-5 kPa PDMS compared to plastic over a 14-day timecourse.

overall_design: Methods: mRNA of primary fibroblasts were generated by deep sequencing, in triplicates or quadruplicates, using Illumina HiSeq2000. Sequenced read quality was checked with FastQC v0.11.2. Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment. The gene expression profiles were quantified using Cufflinks software version 2.2.

first: Julia

last: Nemeth

last: Groß

first: Karsten

last: Quast


title: 10x single cell RNA sequencing of intratumoral OTI T cells with Snx9 KO vs intergenic controls

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: 10x 3' scRNA-seq analysis of intratumoral OTIs 13 days post adoptive transfer into C57BL/6 mice harboring a subcutaneous MC38-OVA tumor.

overall_design: purified sorted OTI T cells from tumors of 5 mice per condition (intergenic and Snx9 KO) were pooled into 2 pools. cells were then indexes using a 10x 3' kit and then libraries were constructed for sequencing on an Illumina NovaSeq 6000

first: Marcel

last: Trefny

first: Alfred

last: Zippelius

first: Julien

last: Roux

first: Marina

last: Natoli

first: Nicole

last: Kirchhammer


title: Single-nucleus transcriptomic atlas of spinal cord neuron in human

city: Chengdu

first: Donghang

last: Zhang

state: Sichuan

address: No.37, guoxue lane, wuhou district, chengdu city, sichuan province

institute: West China Hospital of Sichuan University

summary: Despite the recognized importance of the spinal cord in sensory processing, motor behaviors, and/or neural diseases, the underlying organization of neuronal clusters remain elusive. Recently, several studies have attempted to define the neuronal types and functional heterogeneity in the spinal cord using single-cell and/or single-nucleus RNA-sequencing in various animal models. However, molecular evidence of neuronal heterogeneity in the human spinal cord has not yet been established. Here, we sought to classify spinal cord neurons from human donors using high-throughput single-nucleus RNA-sequencing. The functional heterogeneity among the identified cell types and signaling pathways that connect neuronal subtypes were explored. Moreover, we compared the transcriptional patterns obtained in human samples with previously published single-cell transcriptomic profiles of the mouse spinal cord. As a result, we generated the first comprehensive transcriptomic atlas of human spinal cord neurons and defined 18 neuronal clusters. In addition to identifying new and functionally distinct neuronal subtypes, our results also provide novel marker genes for previously described neuronal types. The comparison with mouse transcriptomic profiles revealed an overall similarity in the cellular composition of the spinal cord between the two species, while simultaneously highlighting some degree of heterogeneity. In summary, these results illustrate the complexity and diversity of neuronal types in the human spinal cord and provide an important resource for future research to explore the molecular mechanisms underlying spinal cord physiology and diseases.

overall_design: Single-nucleus transcriptomic profiles of spinal cord neuron in 2 human donors

first: Yiyong

last: Wei

first: Jin

first: Hongjun

last: Chen

last: Li

first: Tao

last: Zhu

last: Zhou


title: Targeting SNX9 rescues CD28-mediated T cell exhaustion for cancer immunotherapy - Targeted Pooled CRISPR Screen for T cell Exhaustion

summary: Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. To explore new pathways for reinvigoration of anti-tumor immune functions, we developed a human ex vivo exhaustion model by repetitive antigenic stimulation of primary CD8 T cells. This results in T cells that resemble patient-derived T cells in tumors on a phenotypic and transcriptional level. A pooled targeted CRISPR screen was performed on ex vivo exhausted T cells. The readout was elevated CD107a degranulation after repetitive stimulation (CD107a+ vs CD107- cells after 4h co-culture with peptide loaded tumor cells).

overall_design: CD8+ T cells from five healthy donor PBMCs were used in two batches to generate NY-ESO-1 specific T cells by lentiviral transduction and co-transduced with a lentiviral gRNA-Cas9 library. The library targeted 32 genes selected by analysis of mRNA expression of ex vivo exhausted T cells and published exhaustion gene sets. Additionally 20 guides against regions without known gene functions (intergenic) were used as controls. After repetitive stimulation for 12 days (4 rounds of stimulations of 3 days each), the cells were co-cultured with NY-ESO-1 peptide loaded T2 tumor cells in presence of anti-CD107a antibody. After 4h co-culture the cells were sorted for CD107a+ or CD107a- cells (both CD8+ DAPI-). The cells were lysed and genomic DNA extracted. gRNAs were amplified from the genomic DNA and sequenced to measure gRNA enrichment in one of the cell fractions.


title: Transcriptional programs dictating Schwann cell transformation in MPNST [Dropseq scRNAseq]

city: CINCINNATI

first: Lai Man

middle: (Natalie)

last: Wu

address: 3333 Burnet Avenue, MLC7013,Lu lab, T6.525

institute: CCHMC

summary: We used single-cell RNAseq to profile early and advanced mouse MPNST tumors, as well as human neurofibroma and MPNST. Our work defines the stage-specific kinetics of transcriptomics, cellular heterogeneity, and tumor cell fate decisions in murine and human MPNSTs.

overall_design: Single-cell mRNA profiles of 10 neurofibromas and 4 MPNSTs were generated on the 10X Genomics platform and sequenced by NovaSeq 6000 (Illumina). Single-cell mRNA profiles of Three pooled early (1.5 mo) and two advanced (4 mo)  mouse Lats1/2-def sciatic nerve tumors were generated by Dropseq platform. Two mouse early and two advanced paraspinal tumors; two early and two advanced dermal tumors; one NF1-mutant and two NPE (Nf1 fl/fl; P53 fl/fl; Eed fl/fl; Dhh-Cre) sciatic nerves were generated on the Dropseq platform, and sequenced on NextSeq 500 (Illumina). The datasets also include 1 scATACseq each of an advanced mouse MPNST paraspinal tumor and human NF and MPNST. Droplet based scATAC-seq on peripheral nerve tumors from 16-week-old mouse MPNST, human benign NF and MPNST. Tumor cells were profiled for chromatin accessibility changes. Bulk RNA-seq of 8 NF and 9 MPNSTs were included.

first: Lai

first: Qing

middle: R

last: Lu


title: RNA-Seq of Nothobranchius furzeri brain of male and female with an age of 39-108 days post hatch (dph).

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: A vast body of studies is available that describes age-dependent gene expression in relationship to aging in a number of different model species. These data were obtained from animals kept in conditions with reduced environmental challenges, abundant food and deprivation of natural sensory stimulation. Here we compared wild- and captive-aging in the short-lived turquoise killifish (Nothobranchius furzeri). These fish inhabit temporary ponds in the African savannah and when the ponds are flooded eggs hatch synchronously enabling a precise timing of the population age. We collected brains for wild fish of different ages and quantified the global age-dependent regulation of transcripts using RNAseq. A major difference between captive and wild population is that wild population reach larger sizes and cease their growth rapidly, enabling the analysis of age-dependent gene expression without the confounding effect of adult brain growth.We found that the majority of differentially-expressed genes show the same direction of regulation in wild- and captive-population. However, a number of genes were regulated in opposite direction. Genes down-regulated in the wild and up-regulated in captivity were enriched for terms related to neuronal communication. Genes up-regulated in the wild and down-regulated in captive conditions were up-regulated in terms related to DNA replication. Finally, the rate of age-dependent gene regulation was higher in the wild animals suggesting a phenomenon of accelerated aging.

overall_design: 24 samples: 39 dph (4 male + 4 female), 73 dph  (4 male + 4 female), 108 dph  (4 male + 4 female)

first: Mario

last: Baumgart

first: Mariateresa

last: Mazzetto

first: Martin

last: Reichard

first: Alessandro

last: Cellerino


title: RNAseq of ex vivo exhausted human antigen-specific T cells

first: DBM Bioinformatics

last: Core Facility

summary: Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. To explore new pathways for reinvigoration of anti-tumor immune functions, we developed a human ex vivo exhaustion model by repetitive antigenic stimulation of primary CD8 T cells. This results in T cells that resemble patient-derived T cells in tumors on a phenotypic and transcriptional level.

overall_design:
Four human healhy donor CD8+ T cells  were isolated, transduced with an NY-ESO-1 TCR lentivirus construct, stimulated in four different conditions (Trested, Ttumor, Tex, Teff) with T2 tumor cells and specific peptides over 12 days. Cells were then sorted for TCR Vbeta 13.1+ (NY-ESO-1 TCR) CD8+ CD3+ CD56- CD4- DAPI- cells.
-----------------------------------
Authors state "raw data are not available due to lack of patient consent".

first: Marcel

last: Trefny

first: Alfred

last: Zippelius


title: Transcriptional programs dictating Schwann cell transformation in MPNST

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptional programs dictating Schwann cell transformation in MPNST [bulk RNA-seq]


city: Montpellier

first: Jacques

last: Colinge

address: 208, avenue des Apothicaires

country: France

institute: Inserm

summary: Cancer cells and fibroblasts from 6 metastases obtained from 5 different patients were submitted to single-cell sequencing on the 10xGenomics platform. These data revealed different subpopulations of cancer-associated fibroblasts (CAF) and their ligand-receptor interactions with cancer cells.

overall_design: Single-cell sequencing of colorectal cancer liver metastases cancer cells and fibroblasts.

first: Andrei

last: Turtoi


title: Transcriptional programs dictating Schwann cell transformation in MPNST [scATACseq]


title: Transcriptional programs dictating Schwann cell transformation in MPNST [10X scRNA-seq]


title: Epigenome of an adult Paralvinella palmiformis body wall

status: Public on Nov 06 2022

city: Montreal

first: Maeva

last: Perez

state: Qc

address: 1375 Avenue Thérèse-Lavoie-Roux

institute: Université de Montréal

summary: 5mCpG methylation for Paralvinella palmiformis

overall_design: Methylation data was obtained from Oxford Nanopore reads.

first: Bernard

last: Angers

first: Oluchi

last: Aroh

first: Yannan

last: Sun

first: Yi

last: Lan

first: Pei-Yuan

last: Qian


title: Epigenome of an adult Paraescarpia echinospica vestimentum

summary: 5mCpG methylation for Paraescarpia echinospica.


title: Dual T cell– and B cell–intrinsic deficiency in humans [CD4+ T cell SubSeries]

city: Doha

first: Nico

last: Marr

address: Education City

country: Qatar

institute: Hamad Bin Khalifa University

summary: Human RLTPR deficiency is a combined immunodeficiency affecting the CD28-responsive pathway in T cells and the BCR-responsive pathway in B cells. This SubSeries contains high throughput gene expression data from primary CD4+ T cells of patients with RLTPR deficiency and controls.

overall_design: Primary CD4+ T cells from three patients and 4 unrelated controls were stimulated for two hours with PMA, CD40L or IgM.

first: Taushif

last: Khan

first: Tanwir

last: Habib

first: Andrea

last: Guennoun

first: Romain

last: Levy

first: Anne

last: Puel

first: Jean-Laurent

last: Casanova


title: Transcriptome analysis of ovules offers early developmental clues after fertilization in Cicer arietinum L.

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

summary: Chickpea (Cicer arietinum L.) seeds are valued for their nutritional scores and limited information on the molecular mechanisms of chickpea fertilization and seed development is available. In the current work, comparative transcriptome analysis was performed on two different stages of chickpea ovules (pre- and post-fertilization) to identify key regulatory transcripts. Two-staged transcriptome sequencing was generated and over 208 million reads were mapped to quantify transcript abundance during fertilization events. Mapping to the reference genome showed that the majority (92.88%) of high-quality illumina reads were aligned to the chickpea genome. Reference-guided genome and transcriptome assembly yielded a total of 28,783 genes. Of these, 3399 genes were differentially expressed after the fertilization event. These involve up-regulated genes including LOC101500970, LOC101506539 and down-regulated genes LOC101493897, LOC101491695 and so on. Transcription factor families including UDP-glucuronyltransferase, NAC transcription factor, heat shock transcription factor, and auxin-responsive transcription factor were also found to be activated after fertilization. Activation of these genes and transcription factors results in the accumulation of carbohydrates and proteins by enhancing their trafficking and biosynthesis. Total 17 differentially expressed genes, were randomly selected for qRT-PCR for validation of transcriptome analysis and showed statistically significant correlations with the transcriptome data. Our findings provide insights into the regulatory mechanisms underlying changes in fertilized chickpea ovules. This work may come closer to a comprehensive understanding of the mechanisms that initiate developmental events in chickpea seeds.

overall_design: Total RNA was isolated pre- and post-fertilization ovules from chickpea using TRI-reagent. RNA-Seq library was generated on illumina platform.Sequencing of library was done on illumine Nextera 500 sequencing platform.

first: R

last: Singh

last: Shankar

first: S

last: Yadav

first: V

last: Kumar


title: An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model

city: New York

first: Ignacio

last: Hernandez-Morato

address: 180 Fort Washington Ave. 8th floor. Room 860

department: Otolaryngology-Head And Neck Surgery

institute: Columbia University

summary: Challenges related to high-quality RNA extraction from post-mortem tissue have limited RNA-sequencing (RNA-seq) application in certain skeletal muscle groups, including the intrinsic laryngeal muscles (ILMs). The present study identified critical factors contributing to substandard RNA extraction from the ILMs and established a suitable method that permitted high-throughput analysis. Here, standard techniques for tissue processing were adapted, and an effective means to control confounding effects during specimen preparation was determined. The experimental procedure consistently provided sufficient intact total RNA (N = 68) and RIN ranging between 7.0 and 8.6, which was unprecedented using standard RNA purification protocols. This study confirmed the reproducibility of the workflow through repeated trials at different postnatal time points and across the distinctive ILMs. High-throughput diagnostics from 90 RNA samples indicated no sequencing alignment scores below 70%, validating the extraction strategy. Significant differences between the standard and experimental conditions suggest circumvented challenges and broad applicability to other skeletal muscles. This investigation remains ongoing given the prospect of therapeutic insights to voice, swallowing, and airway disorders. The present methodology supports pioneering global transcriptome investigations in the larynx previously unfounded in literature.

overall_design: Gene expression analysis of the rat larynx muscles (PCA, LTA, and MTA) based on age (P15, adult), sex, side (left, right) and muscle type (denoted, PCA, LTA, and MTA)

first: Kemfack

last: Angela M

first: Hernandez-Morato

last: Ignacio

first: Moayedi

last: Yalda

first: Pitman

last: Michael J


title: The Groucho/Tle coregulators are essential for early thymic progenitors and T-cell lineage specification [ATAC-seq]

city: Xi'an

first: Xiaoke

last: Ma

state: Shaanxi

address: No.2 South TaiBai Road

institute: Xidian University

summary: The goal of this study is to determine the functional requirements for Groucho/Tle coregulators in early stages of T cell development. By ablating three mammalian homologues, Tle1, Tle3, and Tle4 genes, we found that Tle1/3/4 are essential for repressing non-T cell lineage potential in early thymic progenitors, and therefore pivotal for T-cell lineage specification.

overall_design: Genome-wide mapping of chromatin accessibility profiles in WT and Tle134-deficient DN1 cells.

first: Hai-Hui

last: Xue

first: Xin

last: Zhao


title: The Groucho/Tle coregulators are essential for early thymic progenitors and T-cell lineage specification [RNA-seq]

overall_design: Genome-wide mapping of transcriptomic profiles in WT and Tle134-deficient DN1 cells.


city: Taichung

first: Shih-Chieh

last: Hung

address: No.6, Hsueh-Shih Road., North Dist.

department: Drug Development Center, Institute of New Drug Development

institute: China Medical University

summary: As obesity has becoming an urged issue nowadays, delineation of the mechanisms of WAT tissue white-browning and beige adipose origin are of important topic. By the use of snRNA-seq, we can outline LepR cells play important role in the white-browning process and investigate the mechanisms participate at different white-browning treatments.

overall_design: snRNA-seq of Lepr-cre; Tomato inWAT at different white-browning treatments comparing to non-treated (control) inWAT.

first: Yu-Ting

last: Yen

first: May

last: Chien


title: Gene expression profile at the single-cell level of Neurog3 derived tomato cells from Neurog3Cre and Neurog3Cre-FoxO1 f/f (NFKO) of the small intestine

first: Wen

last: Du

address: 1150 ST NICHOLAS AVE

summary: To discover cells with mixed enteroendocrine/Paneth/goblet features arising from Neurog3+ progenitors in WT and NFKO mice, we used single-cell RNA sequencing (scRNA-seq) to analyze the diversity of Neurog3 derived cells in the small intestine.

overall_design: Intestinal Neurog3 derived epithelial cells from the Neurog3Cre; Rosa26tdtomato and Neurog3Cre-FoxO1 f/f; Rosa26tdtomato mice were isolated by fluorescence-activated cell sorting (FACS) according to the presence or absence of tomato signal and analyzed using scRNAseq.

first: Junqiang

last: Wang

first: Domenico

last: Accili


title: The Groucho/Tle coregulators are essential for early thymic progenitors and T-cell lineage specification

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

overall_design: Refer to individual Series


title: The Groucho/Tle coregulators are essential for early thymic progenitors and T-cell lineage specification [Cut&Run]

overall_design: Genome-wide mapping of Tle3 binding profiles in WT DN1 cells


title: Gene expression of Neurog3 derived small intestine cells from Neurog3Cre-FoxO1 f/f (NFKO) mice

summary: To investigate the characteristics of CD24 subdivied Neurog3-derived (Tomato+) cells: CD24neg/Ngn3Tomato+, CD24+/Ngn3Tomato+ and NgnTomato3neg

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  Neurog3 derived CD24neg/Tomato+, CD24+/Tomato+ and Tomato neg cells population


title: Hedgehog Interaction Protein Acts in the Habenula to Regulate Nicotine Intake

first: Stephanie

last: Caligiuri

address: 1 Gustave L. Levy Place,, Box 1662

institute: Icahn School of Medicine

summary: Medial habenular (mHb) cholinergic neurons that project to the interpeduncular nucleus (IPn) regulate aversive behavioral responses to nicotine that protect against tobacco addiction. Little is known about the nicotine-evoked cellular or molecular adaptations in these neurons that influence the development of the smoking habit. Using in vivo calcium imaging and single-cell RNA sequencing, we show that a dose of nicotine that stimulates mHb neural activity evokes robust transcriptional plasticity in neuronal and non-neuronal cells in the mHb, including upregulated expression of Hedgehog-interacting protein (HHIP) in putative cholinergic neurons. Allelic variation in HHIP confers risk for smoking-related diseases including chronic obstructive pulmonary disease and lung cancer, but underlying mechanisms of action are unclear. Using Translating Ribosome Affinity Purification (TRAP) sequencing and RNAscope, we confirmed that Hhip transcripts are highly enriched in mHb cholinergic neurons. HHIP mutant mice exhibit hundreds of differentially expressed transcripts in the mHb and perturbed transcriptional responses to nicotine. Moreover, acute in vivo CRISPR/Cas9-mediated genomic cleavage of mHb Hhip attenuated noxious responses to nicotine and increased intravenous nicotine self-administration behavior in mice. In vitro knockdown of Hhip reduces intracellular calcium release to nicotine and increases Gli activity. These findings suggest that HHIP acts in the mHb to regulate nicotine intake and that HHIP alleles may increase vulnerability to smoking-related diseases by modulating mHb signaling and enhancing the addictive properties of tobacco.

overall_design: HHIP mutant x WT. Saline x Nicotine. Medial Habenular tissue.

first: Paul

last: Kenny

first: Robert

last: Sebra

first: Kristin

last: Beaumont


title: Genome-wide investigation of transcriptional regulation in malaria sporozoite [RNA-Seq]

status: Public on Nov 05 2022

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

summary: Sporozoite is the stage in which malaria parasites initially infect the vertebrate host. Elucidation of gene regulation in this stage will promote the investigation of mechanisms of liver infection by this parasite and contribute to development of strategies for preventing the malaria transmission. AP2-Sp is a transcription factor essential for formation of sporozoites or sporogony, which take place in oocysts on the midgut of infected mosquitoes. To understand the role of this transcription factor in the transcriptional regulatory system of this stage we performed ChIP-seq analysis using whole mosquito midguts containing late oocysts as start materials and explore its target genes genome-widely. Target genes were composed of 640 genes, which encompassed various functional categories and were contained genes involved in distinct processes parasites pass through in this stage, from sporogony to development into the liver stage. Furthermore, RNA-seq analysis showed that these genes constituted majority of the genes highly expressed in in this stage.  These results suggested that this TF determines basal pattern of gene expression of this stage by targeting a broad range of genes directly.

overall_design: Plasmodium berghei transcriptomes were analyzed in oocyst/oocyst sporozoites and salivary gland sporozoites.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Tsubasa

last: Nishi

first: Yuho

last: Murata


title: Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2, Glis1, Essrb and Sall4 [RNA-seq]

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

summary: Reprogramming somatic cells to pluripotency represents a paradigm for cell fate determination. A binary logic of closing and opening chromatin provides  a simple way to understand iPSC reprogramming driven by both Yamanaka factors or chemicals.  Here we apply this logic to the design a four  factor combination, Jdp2, Glis1, Essrb and Sall4 (4F), that reprogram MEFs to chimera competent iPSCs efficiently.  RNA- and ATAC-seq reveal differences between JGES and 7F induced pluripotency, 7IP and JGES IP, in transcriptomic and chromatin accessibility dynamics(CAD). Sall4 emerges as a dominant force that can close and open chromatin with the help of Jdp2 and Glis1 in resetting somatic chromatin to a pluripotent state. These results reveal a previously unknown path between somatic and pluripotent states, open a door for cell fate control.

overall_design: In total, we collected 10  cell samples in reprogramming D0, D1, D3,D5 and D7 from 2 independent expriments. mRNA Library sequencing done with NextSeq500.

first: Bo


title: Compare gene expression profile of Ins2 Tomato positive and negetive cells from cultured gut organoids or Ins2 Tomato positive pancreatic beta cells

summary: To investigate the characteristics of Ins2 expression cells from cultured gut organoids

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RipcreTomato+ cells from islets and drug treated mice gut organoids


title: Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2, Glis1, Essrb and Sall4 [scRNA-seq]

summary: Reprogramming somatic cells to pluripotency has revolutionized our understanding of cell fate control. Yet, most of that knowledge has been predicated on a single system powered by Oct4, Sox2, Klf4 and Myc.  Here we describe two four factor sets capable of reprogramming mouse embryonic fibroblasts (MEFs) to pluripoten-cy. We first developed Jdp2, Glis1, Essrb and Sall4 or JGES that can mediate ro-bust reprogramming by orchestrating a unique chromatin accessibility dynamics involving loci encoding genes for mitochondrial respiration and meiosis/germ cell development. Single cell sequencing further reveals early Sox2+ intermediates as well as late neuron-, hematoendothelial-, mesoderm-, visceral endoderm- and plu-ripotent-like fates.   Along a fate continuum, we show distinct transitions of differen-tially expressed genes marked by a critical crossover point.  Among genes sus-tained after the point, we identify Zfp296, Etv5, Sall1 and Tfap2c or ZEST that can reprogram MEFs to pluripotency. Our study suggests that the JGES and ZEST sys-tem may allow deeper understanding of cell fate control.

overall_design: Single cell RNA-seq profiles of 8 JGES reprogamming samples which were collected every 24 hours. Sequencing was proformed by  HiSeqX10.

first: He


title: Role of YAP/TAZ in KGN human granulosa cell line [Clariom_S_Human]

status: Public on Nov 04 2022

city: Eiheiji

first: Tetsuya

last: Mizutani

state: Fukui

address: 4-1-1 Kenjojima

institute: Fukui Prefectural University

summary:
To identify the YAP/TAZ target genes in granulosa cells, DNA microarray experiments were performed in KGN cells where YAP/TAZ were knocked down.
The effect of the presence or absence of 8Br-cAMP, an intracellular second messenger of FSH, was also investigated in KGN cells.

overall_design: Observation of gene expression changes in KGN cells after treatmet with siRNAs targeting YAP/TAZ using microarray.


title: Nasal administration of anti-CD3 monoclonal antibody (Foralumab) modulates effector CD8+ T cell function and induces a regulatory response in T cells in human subjects

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

overall_design: Immune cell populations are isolated from the PBMC from 5 different patients and single cell RNA-Seq is used to study them.

first: Clare

last: Baecher-Allan

first: Howard

last: Weiner


title: Gene Changes Following in vitro Alectinib Treatment in EML4-ALK Murine NSCLC Cells

city: Aurora

first: Emily

last: Kleczko

state: Colorado

institute: University of Colorado Anschutz Medical Campus

summary: First line treatment for EML4-ALK fusion-positive lung cancer patient is the use of an ALK tyrosine kinase inhibitor (TKI), such as alectinib. While most patients initially respond to this therapy, many patients often develop relapse, and efficacious therapies for patients with relapse disease are limited.  To study EML4-ALK fusion-positive lung cancer, novel murine lung cancer cell lines were generated from C57BL/6 mice using an intratracheally injected Adeno-virus that contains Cas9 and guide RNAs for the EML4-ALK translocation, which leads to the development of lung tumors. Cell lines were derived from these tumors. In an effort to better understand how cells respond to alectinib, we treated EML4-ALK-positive murine cell lines (EA1, EA2, and EA3 cells) in vitro for 1-7 days with either 100nM alectinib or DMSO-control.  At each time point, RNA was isolated from each condition.  RNA was submitted to RNA-seq.  Differential analysis on the RNA-seq data was performed to determine and track gene changes over time between control and treated cells. These data will allow us to better develop novel therapeutics to use in conjunction with alectinib when treating EML4-ALK fusion-positive patients.

overall_design: Cells were treated with 100nM alectinib or DMSO-control for 1, 2, 3, 5, and/or 7 days.  RNA was isolated and submitted to RNA-seq.

first: Trista

last: Hinz

first: Daniel

middle: J

last: Sisler

first: Teresa

last: Nguyen

first: Lynn

middle: E

last: Heasley


title: the natural product erianin induces melanoma apoptosis by targeting GSK3α-NF-κB pathway

city: Shanghai

first: Sipeng

last: Zuo

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary: Erianin has been reported to play key roles in suppressing a wide variety of tumors. Howbeit, the mechanism underlying the erianin in anti-carcinogenesis remains to be fully addressed. Half-maximal inhibitory concentration (IC50) was detected to determine the influence of erianin on melanoma in vitro. Subcutaneous xenografts were established to observe the effect of erianin on the proliferation of melanoma cells in vivo. Transcriptome screening was performed to identify the meaningful target. Molecular docking and western blot were performed to verified the GSK3α-NF-κB cascade reaction. We reported the finding of Erianin as an efficient inhibitor of melanoma. Erianin selectively inhibited the growth of melanoma cells, rather than normal human melanocyte cell line. Specifically, erianin downregulated the cellular GSK3α-NF-κB pathway to induce melanoma cell apoptosis. Collectively, we initially proved that erianin inhibited melanoma effectively, which was caused by inactivation of GSK3α-NF-κB signaling inducing melanoma cells apoptosis. Thus, the study implies that erianin provides a novel therapeutic strategy for melanoma therapy.

overall_design: RNA-seq for two melanoma cell lines (A375 and MEL-290)

first: Lin

first: Rui

first: Linna

last: Lu


title: antitumor effect of berberine from perspective of gene expression

city: Hangzhou

first: Chenxiao

last: Ye

address: Puyan street

institute: zhejiang chinese medical university

summary: to explore the pro-carcinogenic property of high-fat diet in AOM/DSS induced CRC mice model and to fathom how berberine inhibits the formation of adenocarcinoma induced by high-fat diet.

overall_design: We then performed gene expression profiling analysis using tissue from chow diet, high-fat diet and berberine group.

first: Haitao

last: Chen


title: Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity [ChIP-Seq]

city: Paris

first: David

last: Bikard

address: 28 rue du Dr Roux

institute: Institut Pasteur

summary: Over the last decade, gene-silencing mediated by dCas9 binding to transcribed regions or their promoters, a strategy referred to as CRISPRi, has emerged as a powerful tool in bacterial genetics. While this strategy has already been broadly adopted, several studies have reported experimental setups in which dCas9 expression was toxic. In particular, guide RNAs that share specific PAM-proximal sequence motifs were shown to be toxic to E. coli. Here we demonstrate that this toxicity is caused by off-target binding of dCas9 to the promoter of essential genes. Silencing of off-target genes can occur with as little as 4nt of identity between the PAM-proximal sequence and the off-target position. This phenomenon only occurs in some promoter sequences but does not appear to be constrained to any specific PAM-proximal sequence. Accordingly, screens performed in various strains of E. coli and related species shows that the nature of toxic guide RNAs changes together with the evolution of the sequence of off-target positions. These results highlight the importance of relying on several guide RNAs targeting the same gene when performing CRISPRi experiments in bacteria in order to avoid any possible confounding results due to off-target binding.

overall_design: ChIP-seq was performed using a FLAG-tagged dCas9 in the presence of guide RNAs with the AGGAA or ACCCA toxic seed sequences, as well as a control guide RNA targeting the lacZ gene.

first: Lun

last: Cui

first: Theophile

last: Grebert


title: Studies on a hydrocephalus-causing mutation on Trim71 [RNA-seq]

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: We studies on how a hydrocephalus-causing mutation (R783H) on mouse Trim71 alters transcriptomes in mouse embryonic stem cells

overall_design: Transcriptomes from the WT and the R783H mutant Trim71 mESCs were surveyed by the standard poly(A) selected RNA-seq

first: Qiuying

last: Liu

first: Mariah

last: Novak

first: Rachel

last: Pepin

first: Xiaoli

first: Shaojie

last: Zhang


title: Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2, Glis1, Essrb and Sall4 [ATAC-seq]

city: Guangzhou

first: Jing

overall_design: In total, we collected 5 reprogramming samples from D0, D1, D3,D5 and D7 and  the data sequenced by illumina nextseq 500.

first: Bo

last: Wang


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham


title: Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2, Glis1, Essrb and Sall4


title: RNA Immunoprecipitation(RIP)-seq of BUD31 in the mouse reproductive system

city: jinan

first: Junchao

last: Qin

address: 44 Wenhua Xi Road

institute: Shandong University

summary: The testis is the organ with the most transcriptome diversity and alternative splicing (AS) is considered to be the most important source. However, the physiological role of AS in spermatogenesis is poorly understood. Here, we report that spliceosome component BUD31 is a prominent AS regulator in early stage of spermatogenesis in mice. Bud31 expression in the testis is initiated soon after birth. Conditional knock out of Bud31 in germ cells in Vasa-Cre mice led to loss of spermatogonial stem cells (SSCs) and to infertility. We further demonstrate that BUD31was required for both SSC pool maintenance and initiation of spermatogenesis. Mechanistically, BUD31 regulates the alternative splicing of multiple genes involved in cell cycle checkpoint and cell differentiation. In particular, we identified CDK2 as a direct splicing target of BUD31 through integrative analysis of SMART-seq and RIP-seq data. Knockout of BUD31 results in the intron retention as well as exon skipping of CDK2, which led to decrease in CDK2 expression. Our findings highlight the significance of BUD31 and its regulated AS in SSC self-renewal and differentiation.

overall_design: The assay was performed in the mouse Germ cells with BUD31anti-BUD31 antibody.10% of total RNA was used as input.

first: Tao

last: Huang

first: Zixiang

first: Zhaojian

first: Hongbin


title: RNA sequencing (RNA-SEQ) of BUD31 knockout by cre-loxp in the mouse reproductive system

overall_design: Spermatogonial stem cells （SSCs）mRNA profiles of 4-day old wild type (WT) and Bud31-vKO mice; Primary mouse testis cells RNA Immunoprecipitation (RIP) profiles of 14-day old wild type (WT)