title: CTCF acetylation at lysine 20 is required for early cardiac mesoderm differentiation from embryonic stem cells [RNA-Seq]

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

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

summary: In this study, we show that CTCF could be acetylated at lysine 20 (CTCF-K20) by CREB binding protein (CBP) and deacetylated by HDAC6, respectively. CTCF-K20 is required for CTCF interacting with CBP. CTCF point mutation at K20 has no effect on self-renewal but blocks mesoderm differentiation of mouse embryonic stem cells (mESCs).

overall_design: RNA-seq were performed in wild type and CTCF-K20R mESCs and differentiated EBs at day 4.

first: Shixin

last: Gong

first: Gongcheng

first: Hongjie

last: Yao


title: Gene expression profiling of wild type and BMPR1a deficient aTreg cells

status: Public on Oct 24 2022

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

country: USA

institute: Ohio State University

type: Expression profiling by high throughput sequencing

summary: The goal of this study was to compare transcriptome (RNA-seq) of adaptive Treg cells gegerated from Bone Morphogenic Protein Receptor 1a sufficient and deficient CD4+ T cells.

overall_design: Three replicas of wild type and BMPR-deficient aTreg cells were analyzed

first: Piotr

last: Kraj


title: CTCF acetylation at lysine 20 is required for early cardiac mesoderm differentiation from embryonic stem cells [ChIP-Seq]

country: China

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq experiments were performed in wild type and CTCF-K20R mESCs and differentiated EBs at day 4.


title: Time Restricted Feeding Mitigates Obesity Through Adipocyte Thermogenesis

city: Chicago

first: Nathan

last: Waldeck

state: IL

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

summary: In obesity, misalignment of feeding time with the light/dark environment results in disruption of peripheral circadian clocks. Conversely, restricting feeding to the active period mitigates metabolic syndrome through mechanisms that remain unknown. Here we show that adipocyte thermogenesis is essential for the healthful metabolic response to time restricted feeding. Genetic enhancement of adipocyte thermogenesis through ablation of Zfp423 attenuates obesity caused by circadian mistimed high fat diet feeding through a mechanism involving creatine metabolism. Circadian control of adipocyte creatine metabolism underlies timing of diet-induced thermogenesis, and enhancement of adipocyte circadian rhythms through overexpression of the clock activator Bmal1 ameliorates metabolic complications during diet induced obesity. These findings establish creatine mediated diet-induced thermogenesis as a bioenergetic mechanism driving metabolic benefits during time-restricted feeding.

overall_design: 36 ATAC-seq samples at 6 time points (3 replicates), 35 RNA-seq samples at 6 time points (3 replicates, 1 replicate missing BAT ZT17 RNA 3), 2 BMAL1 ChIP samples and 1 input ChIP sample.

first: Chelsea

last: Hepler

first: Joseph

last: Bass

first: Benjamin

last: Weidemann


title: CTCF acetylation at lysine 20 is required for early cardiac mesoderm differentiation from embryonic stem cells

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

overall_design: Refer to individual Series


title: Expression data comparing osimertinib-resistant H1975 and PC-9 cells, and cells that survive after treatment of those cells with a PAI-1 inhibitor

status: Public on Oct 21 2022

city: Hiroshima

first: Kentaro

last: Tokumo

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Molecular and Internal Medicine

country: Japan

institute: Hiroshima University

summary:
Even after osimertinib is administered to lung adenocarcinomas with EGFR mutations, there are a few cells which survive, and these tolerant cells are considered to be the source of later recurrence. We suspect that PAI-1 is involved in the regulation of these resistant cells and are currently investigating the role of PAI-1 in this process.
We used microarray analysis to explore mechanisms involving PAI-1 behind the tolerance to osimertinib in lung adenocarcinoma cells with EGFR mutations.

overall_design: H1975 cells or PC-9 cells surviving 1 week after treatment with 0.5 µM osimertinib (OR) and those cells treated with 100 μM of SK-216, a PAI-1 inhibitor (OR+SK100) were collected and RNA was extracted and hybridized on Affymetrix microarrays.

first: K


title: Genome-scale CRISPR screen identifies nucleotide metabolism as an actionable therapeutic vulnerability in diffuse large B-cell lymphoma  [CRISPR sgRNA]

status: Public on Oct 22 2022

city: Tabuk

first: Sael

middle: M

last: Alatawi

address: Duba Road

country: Saudi Arabia

institute: University of Tabuk

type: Non-coding RNA profiling by high throughput sequencing

summary: Myc dysregulation underpins lymphomagenesis in the Atm-null DLBCL model and confers dependence on nucleotide biosynthesis.MYC-driven DLBCL is sensitive to nucleotide depletion with combined mycophenolate mofetil and adavosertib in vitro and in vivo.

overall_design: A genome-scale CRISPR Cas9 dropout screen was performed on B-cells cell lines generated from ATM-null DLBCL cells using Mouse CRISPR Knockout Pooled Library (GeCKO v2)

first: Nicholas

last: Davies


title: CTCF acetylation at lysine 20 is required for early cardiac mesoderm differentiation from embryonic stem cells [BL-Hi-C]

overall_design: BL-Hi-C experiments were performed in wild type and CTCF-K20R EBs at day 4.

first: Rong

last: Guo


title: Functional significance of the SLC26A4 gene in silica-induced pulmonary toxicity

status: Public on Oct 23 2022

city: Morgantown

first: Christina

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

summary: Previous studies in our laboratory identified a correlation between silica-induced pulmonary toxicity and SLC26A4 transcript levels in the lungs of rats. To determine the role of the SLC26A4 gene product, pendrin (Pds) in silica-induced pulmonary toxicity, pendrin wild type (WT) and knockout (KO) mice were employed. All mice were exposed to either air or crystalline silica (15 mg/m3, 6 hours/day, 4 days) and pulmonary toxicity and lung gene expression profiles determined at post-exposure time intervals of 1-day, 3-months, and 9-months. Silica exposure resulted in the induction of pulmonary toxicity in both the WT and KO mouse strains, compared to corresponding air exposed controls.  However, there were significant differences (p<0.05) in the measured pulmonary toxicity parameters between silica exposed WT and KO groups being more severe in the WT compared with the KO mice. Significant differences in the gene expression profiles were also detected in the WT and KO mice in response to their exposure to crystalline silica.

overall_design: Lung gene expression profiles were determined by deep sequencing in mice at 1-day, 3-months, and 9-months following their exposure to air or crystalline silica. The number of lung RNA samples analyzed in each group of the mice is as follows: WT(Air) 1-day n=6; WT(Silica) 1-day n=6; KO(Air) 1-day n=6; KO(Silica) 1-day n=6; WT(Air) 3-Months n=6; WT(Silica) 3-Months n=6; KO(Air) 3-Months n=6; KO(Silica) 3-Months n=6; WT(AIR) 9-Months n=5; WT(Silica) 9-Months n=5; KO(Air) 9-Months n=6; KO(Silica) 9-Months n=6.

first: Tina

last: Sager

first: Pius

last: Joseph


title: The differential response of immunity and metabolism leads to differences in the resistance of Siganus oramin and Trachinotus blochii to Cryptocaryon irritans

city: Haikou

first: tian

last: jiang

address: 58 of Ren min Road

institute: Hainan University

summary: Numerous studies have demonstrated that the C. irritans can be efficiently propagated in the animal model golden pompano (Trachinotus blochii), especially in the process of intensive high-density culture, which causes large-scale infection and triggers bacterial invasion is a devastating blow to the golden pompano industry. This is in sharp contrast to the low sensitivity of S. oramin to C. irritans.

sample_organism:
Siganus canaliculatus
Trachinotus blochii

overall_design:
we simulated an experiment of artificially infecting C. irritans on S. oramin and T. blochii. RNA-seq was utilized to detect the transcripts in the gill of S. oramin and T. blochii at different times of infection, used the bioinformatics analysis of the pathways and compared the variations of all the involved differentially expressed genes (DEGs).
Please note that the identifiers in processed data (e.g. Sig_T000001, Trachinotus_GLEAN_10000138, etc.) are self-numbered in the transcriptome sequencing, and then these identifiers were annotated based on the genome (as included in two annotation files (Tra_gene.nr.xls  and  Sig_gene.nr.txt)).

first: Junlong

last: Sun

first: Jian

last: Luo


title: RNAseq carcinogen induced signatures in lung adenocarcinoma cell lines

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

summary: FVB, Balb/c, and C57BL/6 mice received the tobacco carcinogens urethane (Sigma Aldrich, U2500) intraperitoneally (1g/Kg in 100 μl phosphate-buffered saline) or diethylnitrosamine (200 mg/kg) (Sigma Aldrich, N0756). Carcinogen induced lung adenocarcinoma murine cell lines generation| Ten months post first carcinogen (urethane, DEN) exposure mice were sacrificed, lung tumours were dissected from surrounding healthy lung parenchyma under sterile conditions, were halved, one half was processed for histology and the other half was chopped into 1 mm pieces and seeded to cell culture dishes. Cells were cultured under standard conditions outlined below. When adenocarcinoma was diagnosed for a given tumour, its corresponding culture was passaged in vitro over a period of 18 months and 60 passages, whichever occurred first. After gene expression and mutational signature extraction, the signature were compared with human lung adenocarcinoma RNAseq results.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Compare differential gene expression between naïve mouse lung cells and mouse adenocarcinoma cell lines. Alignment of sequencing traces for exploration and visualization of transcripts alteration and single nucleotide variation.

first: M

middle: A

last: Pepe

first: G

first: N

middle: I

last: Kanellakis


title: Gene expression analysis of the hippocampus in Il18+/+ and Il18-/- with restraint stress

city: Nichinomiya

first: Kyosuke

last: Yamanishi

state: Hyogo

address: 1-1, Mukogawa

department: Neuropsychiatry

institute: Hyogo College of Medicine

summary: Interleukin-18 (IL-18) was one of the inflammatory cytokines and related to major depressive disorder (MDD) and dementia. We previously investigated IL-18 knockout (Il18−/−) mice developed impaired learning and memory, more anxiety, and less motivation comparing to Il18+/+ mice. In the Il18−/− mice with acute stress, both the immobility time in the forced swim test and the tail suspension test were decreased, even though no difference was observed in the Il18+/+ mice. To reveal the mechanism, RNA-Seq was performed.

overall_design: RNA-seq

first: Hisato

last: Matsunaga


title: Multiomic analysis reveals conservation of cancer associated fibroblast phenotypes across species and tissue of origin [scRNA-Seq]

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

institute: Stanford University

summary: Cancer associated fibroblasts (CAFs) are integral to the solid tumor microenvironment. Once thought to be a relatively uniform population of matrix-producing cells, the arrival of single cell RNA sequencing has revealed diverse CAF phenotypes. Here, we further probe CAF heterogeneity with a comprehensive multiome approach. Using paired, same-cell chromatin accessibility and transcriptome analysis, we provide an integrated analysis of CAF subpopulations over a complex spatial transcriptomic and proteomic landscape to identify three superclusters – steady state-like (SSL), mechanoresponsive (MR) and immunomodulatory (IM) CAFs. These superclusters are recapitulated across multiple tissue types and species. Selective disruption of underlying mechanical force or immune checkpoint inhibition therapy results in shifts in CAF subpopulation distributions and impacts tumor growth. As such, the balance among CAF superclusters may have considerable translational implications. Collectively, this research expands our understanding of CAF biology, identifying regulatory pathways in CAF differentiation and elucidating novel therapeutic targets in a species- and tumor-agnostic manner.

overall_design: scRNA-seq of unsorted cells from tumor samples from mouse breast, human breast, and human pancreas cancer using the 10X genomics platform

first: Deshka

middle: S

last: Foster

first: Daniel

last: Delitto


title: Effect of IL-1α/TNFα/C1q Cocktail on gene expression of astrocytes

city: Shanghai

first: Chang

last: Liu

address: 1954 Hua Shan Road

department: School of Biomedical Engineering

institute: Shanghai Jiao Tong University

summary: To investigate the gene expression difference between resting astrocytes and C3d+ reactive astrocytes.

overall_design: Astrocytes were isolated from P0 C57BL/6 mice and were treated with IL-1α/TNFα/C1q Cocktail to acquire a C3d+ reactive phenotype. Comparative gene expression profiling analysis of RNA-seq data for resting astrocytes (no treatment) and C3d+ reactive astrocytes, each group has 4 separate duplications.

first: Shiyu

last: Deng

first: Guo-Yuan

last: Yang

first: Yaohui

last: Tang


title: CTCF acetylation at lysine 20 is required for early cardiac mesoderm differentiation from embryonic stem cells [ATAC-Seq]

first: gongcheng

last: Hu

overall_design: ATAC-seq experiments were performed in wild type and CTCF-K20R EBs at day 4.

first: Shixin

last: Gong

first: Gongcheng

first: Hongjie

last: Yao


title: Multiomic analysis reveals conservation of cancer associated fibroblast phenotypes across species and tissue of origin [scATAC-seq]

overall_design: scATAC-seq of unsorted cells from tumor samples from endogenous mouse breast cancer using the 10X genomics platform


title: RNA-seq from the hearts of 7-day-old mice that underwent apical resection and anti-arrhythmic drug treatment

city: Guangzhou

first: Jing

last: Tan

address: No.74 Zhongshan Rd II

department: Department of Biochemistry, Zhongshan Medical School

institute: Sun Yat-sen University

summary:
Background: As a biological pump, the heart needs to consume a substantial amount of energy to maintain sustained beating. Myocardial energy metabolism was recently reported to be related to the loss of proliferative capacity in cardiomyocytes (CMs). However, the intrinsic relationship between beating rate and proliferation in CMs and whether energy metabolism can regulate this relationship is not known. In this study, we found that limited heart rate reserve (HRR) induced CM proliferation under physiological conditions and promoted cardiac regenerative repair after myocardial injury. However, the role of HRR in regulating CM proliferation and damaged heart repair has not been explored.
Results: We found that the control and isoproterenol groups had more similar transcriptional profiles that clearly differed from those of the five groups treated with each anti-arrhythmic drug and thus were clustered together. With Gene Ontology (GO) analysis, we found that genes that commonly showed upregulated expression in various HRR drug-treated cells were related to proliferation and metabolic regulation, including the cell cycle process, heart process, and nucleoside triphosphate metabolic process, with a particular upregulation of the expression of glucose metabolic genes.

overall_design: 1-day-old neonatal mice that underwent apical resection were injected subcutaneously with anti-arrhythmic drugs (amiodarone, metoprolol, propranolol, lidocaine, ivabradine) or isoproterenol for seven consecutive days.

first: Weibin

last: Cai


title: RNAseq for mettl4 mutant in long-day condition

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

institute: Fudan University

summary: METTL4 belongs to a subclade of MT-A70 family members of methyltransferase (MTase) proteins and has been shown to mediate N6-adenosine methylation for both RNA and DNA in diverse eukaryotes. Here, we analysed differentially expressed genes and different alternatively splicing genes compared to the mutant and wild-type by RNA-seq, we found that METTL4 can regulate pre-mRNA alternative splicing.

overall_design: 2 geneotype (wild-type and mettl4-1) with 2 replicates

first: Aiwu

last: Dong

first: Qiang

last: Luo

first: Kangxi

last: Du


title: A novel membrane-bound IL-2 for NK cell immunotherapy

city: Chengdu

first: Qi

last: Xiong

address: Ke-yuan Road 4, No. 1, Gao-peng Street

department: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy

institute: Sichuan university

summary: Transcriptional profiling of mbIL2 activated NK-92 cells compared to recombinant human IL2 activated NK-92 cells.

overall_design: Two-condition experiment, mbIL2 activated NK-92 cells and recombinant human IL2 activated NK-92 cells. Biological replicates, 3 mbIL2 activated NK-92 cells and 3 recombinant human IL2 activated NK-92 cells independently grown and harvested.

first: Hongxin


title: Low-Dose Carbon Monoxide Inhibits Cancer Metastasis

city: New York

first: Nancy

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Analysis of pathways regulated by low-dose CO at the mRNA expression levels in two human breast cancer cell lines.

overall_design: Total RNA was extracted from actively growing MDA-MB-231 and MCF7 cell lines in the presence or absence of 250 ppm CO for 16 hours.

first: Yi-Chieh Nancy

middle: N

first: George

last: Zhang


title: 3D Osteogenesis using human iPS cells

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: We developed methods that reproduce the osteogenesis process using human iPS cells and addressed gene expression dynamics in the differentiation by single cell RNA-sequencing.

overall_design: We constructed a 3D culture system with type I collagen gel, and observed migration of the cells into the gel matrix. We collected two samples: (i) cells migrated into the matrix, and (ii) whole cells including both cells on the surface of the gel matrix and cells migrated into the matrix. We compared the two samples to analyze gene expression traits related to the differentiation.

first: Shunsuke

last: Kawai

first: Junya

last: Toguchida

first: Satooko

last: Sakamoto


title: Gene Expression Profile of BORA control and overexpressed tumors

city: Barcelona

first: Alfonso

last: Parrilla

address: Paseo Vall Hebron (VHIR)

country: Spain

institute: Vall Hebron Research Institute (VHIR)

summary: Gene Expression profile of xenograft tumors generated with SK-OV-3 pIND_EV (Empty vector) cells and SK-OV-3 pIND_BORA (Bora overexpressing) cells.

overall_design: Transcriptome expression profile of quatriplicate experimental samples for SK-OV-3 xenograft tumors with EV (empty vector) and BORA overexpressing vector using the Affymetrix microarray platform and the Genechip Human Gene 1.0 ST Array.

first: Marta

last: Barber

first: Anna

last: Santamaria


title: Tumor Stemness Score to Estimate Epithelial-to-Mesenchymal Transition (EMT) and Cancer Stem Cells (CSCs) Characterization and to Predict the Prognosis and Immunotherapy Response in Bladder Urothelial Carcinoma

city: Beijing

first: Yanlong

address: 10th Tieyi Road, Haidian District

institute: Beijing Shijitan Hospital

summary:
Background: The relationships between cancer stem cells (CSCs), epithelial-to-mesenchymal transition (EMT), and the tumor microenvironment (TME) in bladder urothelial carcinoma (BLCA) remain unclear.
Methods: We first constructed tumor stemness (TS) score using principal component analysis to quantify tumor stemness in BLCA. Then, we evaluated the clinical value of the TS score for predicting the response to tumor immunotherapy using immunotherapy cohorts. Finally, we built an EMT cell model by treating T24 cells with TGF-β and validated the relationship between the TS score and the EMT process in tumors by real-time quantitative PCR, cell invasion assays, and RNA-seq.
Results: A TS scoring system was established with 61 TS-related genes to quantify the TS. The prognostic value of the TS score was then confirmed in multiple independent cohorts. A high TS score was associated with high EMT activity, CSC characteristics, high stromal cell content, high TP53 mutation rate, poor prognosis, and high tumor immunotherapy tolerance.
Conclusion: The TS score provides an index for EMT and CSC research and helps clinicians develop treatment plans and predict outcomes for patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T24 cells with or without TGF-β treatment for 48h

first: Yong

last: Yan


title: Phellgoen (PH), aerenchymatous phellem (AP), and cortex (CO) specific microarray analysis in soybean

city: Nagoya

first: Hirokazu

last: Takahashi

state: Aichi

address: Furo-cho, Chikusa

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary: AP and phellogen gene expressions were compared with the cortex using microarrays. These tissues were isolated by laser capture microdissection (LCM).

overall_design: 3 different tissues experiment, PH vs CO, AP vs CO. Biological replicates: 6  replicates.

first: Mikio

last: Nakazono


title: Transcriptome analysis after TINCR knockdown

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

summary: In order to study the mechanism of TINCR affecting development of HCC, TINCR in liver cancer stem cells was knocked down. RNA-seq was employed to explore the potential target genes and signaling pathways.

overall_design: RNA profiles of  test and control samples were generated by deep sequencing

first: Junli

last: Ma

first: Jing

last: Shi

first: Cao

last: Guo

first: Yang

last: Li


title: Innate immune genes up-regulated during infectious bursal disease virus infection in chicken embryos

city: Botucatu

first: Bruno

middle: Evaristo de Almeida

last: Fantinatti

state: São Paulo

address: Prof Antonio Celso Wagner Zanin

department: Morphology

country: Brazil

institute: Unesp

summary: Next generation sequencind applied to understanding bursal disease virus infection response in chicken embryos

overall_design: Embryos transcriptome sequencing: 1, 2, 3, 5 and 7 days post infection

first: Gabriela

last: Nascimento

first: Leonardo

middle: C

last: Caserta

middle: E

first: Ana

last: Barnabé

first: Raíssa

last: Beck

first: Ligia

middle: P

last: Cuccato

last: Moraes

first: Taís

middle: F

last: Cruz

first: João

last: Junior

first: Muhammad

last: Munir

first: Clarice

middle: W

last: Arns


title: Multiomic analysis reveals conservation of cancer associated fibroblast phenotypes across species and tissue of origin [spatial trascriptomics]

first: Michael

last: Januszyk

overall_design: spatial transcriptomics data from mouse endogeneous breast tumors using the 10X Genomics Visium platform

first: Deshka

last: Foster

first: Daniel

last: Delitto


title: Mammalian oocytes store mRNAs in a mitochondria-associated membraneless compartment

city: Göttingen

first: Shiya

last: Cheng

address: Am Fassberg 11

department: Meiosis

institute: Max Planck Institute for Multidisciplinary Sciences

summary: To investigate the transcriptomic profile of Zar1 -/- oocytes

overall_design: Expression profiling through RNA sequencing

first: Gerrit

last: Altmeppen

first: Sarah

last: Penir

first: Melina

last: Schuh


title: DNA methyltransferases are complementary in maintaining DNA methylation in embryonic stem cells

first: zhen

last: Xu

address: Mid Huaxia road 393

institute: ShanghaiTech university

type: Methylation profiling by high throughput sequencing

summary: To investigate the cooperative function DNMTs in the maintenance of DNA methylation at the ICRs, we established mutant ES clones lacking three major DNA methyltransferases (DNMTs).

overall_design:
We performed WGBS for a series of D1911 mouse embryonic stem cells: wildtype (WT),DNMT1 knockout,UHRF1 knockout, DNMT3A and DNMT3B double knockout (DKO), DNMT triple knockout (TKO),
We perform WGS with the 129SvEv maouse tail DNA.

first: Zhen

first: Yu

last: Zhang

first: Yuhan

last: Liu

first: Xiajun

last: Li


title: RNAseq analysis of brown adipose tissue (BAT) and thyroid of new-born lambs, subjected to short-term cold exposure, reveals signs of early whitening of BAT

status: Public on Oct 20 2022

city: Palmerston North

first: Andrea

last: Grana

address: Tennent Drive

country: New Zealand

institute: Massey University

summary:
An RNA-seq approach was utilized to characterise the transcriptome of brown adipose tissue and thyroid tissue in new-born Romney lambs after a short exposure (2 days) to cold conditions.
This study provides an in-depth expression network of the main characters involved in thermogenesis and fat whitening mechanisms that take place in the new-born lamb.

overall_design: RNAseq of isolated RNA from brown adipose tissue and thyroid tissue of 15 new-born Romney lambs, exposed to cold (4°C, n=6) or ambient conditions (20-22°C, n=6) for two days. A control group was utilized as baseline for analysis (n=3), where tissues were collected at around 24 h after lambing.

last: Graña-Baumgartner

first: Venkata

middle: R

last: Dukkipati

first: Paul

last: Kenyon

first: Hugh

last: Blair

first: Nicolás

last: López-Villalobos

first: Patrick

middle: J

last: Biggs


title: Serum exosome miRNA expression profile in patients with cholangiocarcinoma(CCA) and common bile duct stones(CBDS)

city: Jinan

first: Shu

middle: Li

last: zhuang

state: China/Shandong

address: Department of General Surgery, Qilu Hospital, Shandong University, 107, Jinan Culture Road, Jinan, 250012, China.

department: Qilu Hospital

institute: Shandong University

summary: Cholangiocarcinoma (CCA) is a type of highly aggressive cancer arising from the biliary system. Through serum exosome miRNA sequencing, we screened out the  differentially expressed miRNA in patients with cholangiocarcinoma(CCA) and common bile duct stones(CBDS).

overall_design: Serum exosome miRNA expression profiling was dected by high throughput sequencing.

first: Zongli

first: Yunfei

first: Lizhuang

last: Shu


title: Impact of two and three dose COVID-19 vaccination schedule on transcriptional, humoral and T cell immune response in previously heavily treated, single agent treated and naïve CLL patients

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: This study investigates the innate immune response to COVID-19 mRNA and vector-based vaccines in 15 patients with chronic lymphocytic leukemia (CLL). It assessed the innate and adaptive immune response of CLL patients after booster vaccination and generated a comprehensive transcriptome (mRNA-seq) analysis of peripheral blood mononuclear cells (PBMCs). Specifically, this investigation on a ‘3-dose’ cohort of heavily pretreated CLL patients, who had tested seronegative following a two-dose homologous vaccination (either BNT162b2 or ChAdOx1) and had received a third heterologous dose. A ‘2-dose’ cohort encompassed treatment-naïve or minimal pretreated CLL patients, who showed a serological immune response after the first vaccination and had received a second dose. Bulk mRNA-seq was conducted on PBMCs harvested prior to the vaccination and at days 2 and 7 post vaccination. The innate immune response observed in all patients was independent of the IgG antibody response. Expression of interferon-regulated genetic pathways was induced within two days after vaccination.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) from chronic lymphocytic leukemia (CLL) patients who had received the BNT162b2 or ChAdOx1 vaccine.

first: HyeKyung


title: JAK2V617F-dependent clonal hematopoiesis drives vascular resident macrophages toward a pathogenic phenotype and promotes dissecting aortic aneurysm

city: Paris

first: Hafid

last: Ait-Oufella

address: 56, Rue Leblanc

country: France

institute: Inserm

summary: In order to understand the mechanisms responsible for lethal JAK2V617F-dependent aortic disease, we performed RNA sequencing in the aorta of 7-week old Jak2V617F HC-EC and control Jak2WT mice

overall_design: Bulk aorta RNA-seq analysis from 7-week old mice with a JAK2V617F mutation or their wild-type littermates.

first: Rida

last: Al-Rifai

first: Marc

last: Diedisheim


title: Rapid gene content turnover on the germline-restricted chromosome in songbirds

city: Prague

first: Jakub

last: Ridl

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

summary: We compared assembled germline-restricted chromosmomes (GRCs) from two closely related songbird species (Luscinia megarhynchos and Luscinia luscinia) including the expression analysis of GRC genes

sample_organism:
Luscinia megarhynchos
Luscinia luscinia

platform_organism:
Luscinia megarhynchos
Luscinia luscinia

overall_design: The comparisson of expressed GRC genes from two nightingale species using mRNA-seq data

first: Stephen

last: Schlebusch

first: Radka

last: Reifova


title: The synthetic opioid fentanyl increases HIV replication and chemokine co-receptor expression in lymphocyte cell lines

city: Cincinnati

first: Janani

last: Madhuravasal Krishnan

state: Ohio

address: 3230 Eden Ave

department: Internal Medicine

institute: University of Cincinnati

summary: Fentanyl enhanced expression of CXCR4 and CCR5 protein levels and viral expression in a dose-dependent manner in multiple HIV-susceptible and HIV-infected cell lines. Multiple genes associated with apoptosis, antiviral / interferon response, chemokine. signaling, and NFκB signaling were differentially regulated by fentanyl. Thus fentanyl impacts HIV replication and chemokine co-receptor expression in HIV-susceptible and HIV-infected lymphocyte cell lines suggesting that opioid use may increase the likelihood of transmission to others and accelerate disease progression.

overall_design: ACH-2 cells were analyzed in presence and abscenece of fentanyl. Cells were treated with 100ng of fentanyl for 24 hours. ACH-2 cells without fentanyl treatment is considered as control. Both control and test were performed in replicates. Total RNA was extracted from both fentanyl-treated and untreated ACH-2 cells miRNA Isolation Kit

first: Rebekah

last: Karns

first: Jason

last: Blackard


title: Whole-genome sequencing of Extrachromosomal circular DNA (eccDNA) of cerebrospinal fluid of Medulloblastoma

first: LiXin

last: Ma

address: Haidian District

department: Neurosurgery

institute: Sanbo Brain Hospital

summary: Background: Medulloblastoma (MB) is one of the malignant tumors of the central nervous system (CNS) with a poor prognosis and lack of effective detection. Extrachromosomal circular DNA (eccDNA) has been reported to be closely related to CNS tumors. However, there is still a gap in eccDNA of MB.Methods: Genomic features of eccDNAs were identified in MB tissues and matched cerebrospinal fluid (CSF) using a circle-map, compared with normal. The nucleotides on both sides of the eccDNAs breakpoint were analyzed to investigate the mechanisms of eccDNAs formation. Bioinformatics analysis combined with the GEO database identified reliable features of eccDNA-related genes in MB. Lasso Cox regression model, univariate and multivariate Cox regression analysis, time-dependent ROC, and Kaplan–Meier curve were used to assess the potential diagnostic and prognostic value of the Hub genes.Results: 35179 eccDNAs were identified, with the majority less than 1000 base pairs (bp). The distribution of eccDNAs on the genome was closely related to gene density. EccDNAs in CSF exhibited phase parallelism with matched MB tissues and were shown differently in tumors and normal. Ten core genes were identified in combination with GEO and showed reliable diagnostic and prognostic value in independent datasets through univariate and multivariate Cox regression. Nomogram included Hub-gene signatures was established and showed clinical benefit.Conclusions: This study described the characteristics and formation mechanism of eccDNAs in MB and CSF. The role of eccDNA in MB was revealed, and eccDNA-associated hub genes in CSF could be used as diagnostic and prognostic biomarkers for MB.

overall_design: Comparative gene expression profiling analysis by whole genome sequencing of Extrachromosomal circular DNA (eccDNA) data for Medulloblastoma (MB)-derived tissue samples and cerebrospinal fluid (CSF) samples as well as normal brain tissue samples and CSF samples.

first: Yi

last: Zhu


title: ATAC-seq of progenitors and neurons from human brain organoids

city: Vienna

first: Jaydeep

last: Sidhaye

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

summary: During development of the human cerebral cortex, multipotent neural progenitors generate excitatory neurons and glial cells. This process is faithfully recapitulated in brain organoids.  By using telencephalic brain organoids grown using a dual reporter cell line to isolate neural progenitors and neurons we generated a cell type and developmental stage-specific ATAC-seq dataset.

overall_design: To investigate progenitor and neuron-specific chromatin accessibilty, we generated a dual reporter H9 hESC line that enables sorting of neural progenitors and neurons. To label neural progenitors, we replaced the stop codon of one allele of the pan-neural progenitor marker gene SOX2 with P2A-EGFP. On the other hand, to label neurons, we inserted dTomato driven by human Synapsin1 (hSYN1) promoter in the AAVS1 safe harbor locus. Using this reporter line, we generated telencephalon brain organoids enriched in dorsal telencephalon tissue and isolated EGFP+, dTomato+ cells across different stages of organoid development (Days 40, 60, 90 and 120) . We isolated nuceli from these cells and performed ATAC-seq

first: Jürgen

last: Knoblich


title: mouse prostate and urethra Visium analysis

city: SEATTLE

first: Li

last: Xin

state: WA

address: 850 Republican Street Rm N326

department: Department of Urology

institute: University of Washington

summary: We performed spatial RNA-Seq of prostate and urethra tissues from C57Bl/6 wild type mice. Downstream analyses demonstrated that Foxf2 is highly expressed in the mouse proximal prostate as compaired to the distal ducts.

overall_design: This experiment is to define gene expression in mouse prostate and urethra using the Visium platform.

first: Mary

last: Regier

first: Deyong

last: Jia

first: Oh-Joon

last: Kwon


title: The superenhancer binding factor Med1 is broadly required for optimally expressing and hypermutating IgH genes as well as for terminating their expression through locus suicide recombination

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Assembly, expression and maturation of the Immunoglobulin heavy (IgH) chain repertoire necessitates long-range 3D-interactions under regulation by the IgH locus Eµ and 3’ regulatory region (3’RR) super-enhancers. In progenitors, Eµ instrumentally supports VDJ recombination notably towards distal VH genes. In mature cells, the 3’RR first boosts the production of membrane-type IgH transcripts. It later attracts Activation-induced cytidine deaminase at three specific locations: VDJ genes undergoing somatic hypermutation (SHM), switch regions undergoing class switch recombination (CSR), and the 3’RR itself during locus suicide recombination (LSR). In plasma cells devoted to abundant Ig secretion, a late long-range effect is to promote high IgH transcription. The Mediator subunit Med1, which binds super-enhancers and has increased activity after phosphorylation by ERK, was previously attributed a role restricted to class-switched cells. We now show its broader impact on IgH expression, both by promoting recombination of distal VH genes in progenitors and by later supporting SHM. Med1-dependence also marks all long-range functions of the 3’RR, including not only intra- but also trans-chromosomal CSR, LSR, optimal BCR expression and the transcriptional boost featured by plasma cells. Altogether, Med1 appears as a major and specific actor of all the long-range tasks effected by the IgH locus super-enhancers beyond transcription.

overall_design: 3 or 4 RNA-seq point was realized per genotypes (3 for wt and 4 for mutant) from in vitro activated (LPS + IL4) splenic B cells

first: M

last: Cogné

first: S

last: Le Noir

first: F

last: Boyer

first: B

last: Hervé


title: Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance

city: Worcester

first: Robin

last: Ganesan

state: MA

address: 368 Plantation Street

department: Microbiology and Physiological Systems

institute: UMass Chan Medical School

summary: Upf1, Upf2, and Upf3 are the central regulators of nonsense-mediated mRNA decay (NMD), the eukaryotic mRNA quality control pathway generally triggered when a premature termination codon is recognized by the ribosome. The NMD-related functions of the Upf proteins likely commence while these factors are ribosome-associated, but little is known of the timing of their ribosome binding, their specificity for ribosomes translating NMD substrates, or the nature and role of any ribosome:Upf complexes. Here, we have elucidated details of the ribosome-associated steps of NMD. By combining yeast genetics with selective ribosome profiling and co-sedimentation analyses of polysomes with wild-type and mutant Upf proteins, our approaches have identified distinct states of ribosome:Upf association. All three Upf factors manifest progressive polysome association as mRNA translation proceeds, but these events appear to be preceded by formation of a Upf1:80S complex as mRNAs initiate translation. This complex is likely executing an early mRNA surveillance function.

overall_design: We have employed selective profiling of ribosomes bound by FLAG-tagged NMD factors Upf1, Upf2, or Upf3, and of ribosomes from strains harboring NMD-altering mutations. Ribosome profiling libraries were prepared from both total and immunopurified ribosomes in duplicate or triplicate.  RNAseq libraries were prepared from cell lysates of the same strains. High throughput sequencing was performed using Illumina NextSeq500 or HiSeq4000.  The size and transcript location of ribosome protected fragments with respect to  transcript coding regions, 5' and 3'UTRs, and start or stop codons from both NMD and non-NMD substrates was determined.

first: Kotchaphorn

last: Mangkalaphiban

first: Richard

last: Baker

first: Feng

last: He

first: Allan

last: Jacobson


title: Transcriptome and proteome analysis revealed tyrosine oxidation involved in the periostracum formation of the green mussel Perna viridis (Linnaeus)

first: Maoguo

last: Luo

address: Haidian District, Beijing Zhongguancun South Street, 5th

institute: Beijing Institute of Technology

summary: Mollusk secretes a periostracum layer prior to the underlying calcified shell. This organic membrane serves as the first line of protection and primary template for shell orchestration. However, the chemical composition and formation mechanism of the periostracum layer is largely unknown. In this study, we applied transcriptomic, proteomics, physical and chemical analysis to unravel the mysteries of the periostracum formation in the green mussel Perna viridis (Linnaeus). Scanning electron microscopy examination and FTIR analysis showed that the periostracum layer was a multilayered organic membrane composed of polysaccharides, lipids and proteins. Interestingly, proteomic study identified components enriched in tyrosine and some enzymes evolved in tyrosine oxidation, indicating that tyrosine oxidation might play an important role in the periostracum formation. Moreover, comparative transcriptomics suggested that tyrosine-rich proteins were intensively synthesize in the periostracum groove. After being secreted, the periostracum proteins were gradually tanned by oxidation in the sea water, and the level of crosslink increased significantly as revealed by the ATR-FTIR. Our present study sheds light on the chemical composition and putative tanning mechanism of the periostracum layer in bivalve mollusk.

overall_design: Mature and healthy mussel individuals were collected from the coast of Zhuhai city in China. Animals with shell length around 6-7 cm were selected for subsequent analysis. The shell valves were opened by cutting the adductor muscles with a scalpel. Tissues of the periostracum groove (PG) and submarginal zone (SZ) were cut and placed in 1.5 mL Eppendorf tube. Each sample contained tissues from six animals, and three biological replicates were set in the RNA- seq.

first: Jingliang

last: Huang


title: Hepatocyte nuclear factor 1β gene regulation in E14.5 ureteric bud cells

city: Minneapolis

first: Annie

last: Shao

state: Minnesota

address: 420 Washington Ave SE

department: Medicine

institute: University of Minnesota

summary: HNF-1β mutations are one of the most common single-gene mutations that underlie kidney developmental disease. Hepatocyte nuclear factor 1β (HNF-1β) is essential for kidney development, but its functions in ureteric bud (UB) branching morphogenesis are incompletely understood. We isolated E14.5 UB cells using fluorescence-activated cell sorting, and performed RNA-sequencing to compare gene expression in wild-type and HNF-1β deficient UB cells. 1632 genes have significantly lower expression in the HNF-1β deficient UB cells and 2223 genes have significantly higher expression in HNF-1β deficient UB cells.

overall_design: RNA-sequencing (RNA-seq) to compare gene expression in wild-type and HNF-1β deficient E14.5 ureteric bud cells

first: Micah

middle: D

last: Gearhart

first: Juan

last: Abrahantes

first: Peter

last: Igarashi


title: Reversal of Cancer Gene Expression Identifies Repurposed Drugs for Diffuse Intrinsic Pontine Glioma

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 15 Michigan ST NE

department: Department of Pediatrics and Human Development

institute: Michigan State University

summary: Diffuse Intrinsic Pontine Glioma (DIPG) is an aggressive incurable pediatric brainstem cancer. Due to its inoperable tumor location and resistance to conventional chemotherapy agents such as temozolomide, radiotherapy is the current standard treatment. This study aimed to identify potential therapeutic agents for DIPG treatment using a computational drug screening pipeline.   We hypothesized that drugs that can reverse a disease gene signature can be potential drug candidates for that disease. Because of lack of normal brain samples as control for creating disease signature, we implemented a deep learning autoencoder to select reference control samples. Using a systematic computational approach with publicly available gene expression databases for DIPG signature and gene expression data of pre and post drug treated cancer cell lines, we identified drug hits with potential to reverse a DIPG gene signature to one that matches normal tissue background. We then tested the identified drugs at their IC50 concentration for 24 hours on patient-derived DIPG4 cell lines.        Overall Design: mRNA profiles of DIPG4 cell lines treated with Triptolide (TPL), Triamterene(TRIAM), Mycophenolate mofetil (MMF) and DMSO as control

overall_design: We setup three sets of experiments with DMSO, TPL, TRIAM and MMF treated DIPG4 cells. RNA was extracted using the RNeasy plus mini kit (Qiagen).  Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit; prepared libraries were quality controlled and quantified using a Qubit and Labchip Bioanalyzer. Libraries were pooled and run on a Illumina NovaSeq 6000 instrument. Sequencing was performed by 2 × 150 bp paired-end read format.

first: Guisheng

last: Zhao

first: Patrick

last: Newbury

first: Evagene

last: Chekalin

first: William

last: Zheng

first: Benjamin

last: Glicksberg

first: Anita

last: Wen

first: Shreya

last: Paithankar

first: Takahiro

last: Sasaki

first: Yukitomo

last: Ishi

last: Sui

first: Rintaro

last: Hashizume

first: Theodore

last: Nicolaides


title: Stromal FOXF2 suppresses prostate cancer progression and metastasis by enhancing antitumor immunity

first: Li

last: Xin

summary: We performed single cell RNA-Seq of FACS-isolated CD45+ leukocytes and Lin-CD24- prostate stromal cells  from Col1a2-TRAMP(Control) group and Col1a2-Foxf2-TRAMP group. Unsupervised clustering analysis on integrated single-cell datasets revealed an increased CD8+ T cell frequency and activity and a decreased Macrophage and MDSC activity in the Col1a2-Foxf2-TRAMP mice. The analysis in TRAMP mice revealed two major subpopulations that represented the myofibroblastic CAF (myCAF) and inflammatory CAF (iCAF). The percentage of myCAF increased by 15% in the Col1a2-Foxf2-TRAMP mice, suggesting that Foxf2 induced a shift toward the myCAF phenotype. On the other hand, the overall CAF gene signature score defined by the average expression of 30 CAF-associated genes on a single cell level was slightly but significantly reduced in the Col1a2-Foxf2-TRAMP mice.

overall_design: Sorted Prostate Stroma and Immune cells in Col1a2-TRAMP(Control) and Col1a2-Foxf2-TRAMP

first: Deyong

last: Jia

first: Mary

last: Regier

first: Oh-Joon

last: Kwon


title: RNA_Seq analysis of localization along animal-vegetal axis of axolotl (Ambystoma mexicanum)

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

summary: Asymmetrical localization of biomolecules inside the egg, results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs, of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However, our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal-vegetal axis of mature eggs of four diverse models, Xenopus laevis, Danio rerio, Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO-Seq. Surprisingly, we revealed RNAs that code for many known important genes such as germ layer determinants, germ plasm factors and members of key signalling pathways, are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model.

overall_design: Total RNA  was extracted using TriReagent. The concentration of RNA was measured using a spectrophotometer (Nanodrop 2000, Thermo Scientific), and the quality of RNA was assessed using a Fragment Analyzer (AATI, High Sensitivity RNA analysis kit). RNA profiles were generated using RNA-Sequencing in 4 replicates (each divided into five segments).

first: Viktoriia

last: Iegorova

first: Pavel

last: Abaffy

first: Ravindra

last: Naraine

last: Sindelka


title: Major differences in transcriptional alterations in dorsal root ganglia between spinal cord injury and peripheral neuropathic pain models

city: Monterrey

first: Raquel

last: Cuevas Diaz Duran

address: Av Morones Prieto No. 3000, Colonia Los Doctores

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tecnologico de Monterrey

summary: Chronic, often intractable pain is caused by neuropathic conditions such as peripheral nerve injury (PNI) and spinal cord injury (SCI). These conditions are associated with alterations in gene and protein expression correlated with functional changes in somatosensory neurons having cell bodies in dorsal root ganglia (DRGs). Most studies of DRG transcriptional alterations have utilized PNI models where axotomy-induced changes important for regeneration may overshadow changes that drive neuropathic pain. Both PNI and SCI produce DRG neuron hyperexcitability linked to pain, but contusive SCI produces little peripheral axotomy or peripheral nerve inflammation. Thus, comparison of transcriptional signatures of DRGs across PNI and SCI models may highlight pain-associated transcriptional alterations that don’t depend on peripheral axotomy and associated effects such as peripheral Wallerian degeneration. Data from our rat thoracic SCI experiments were combined with meta-analysis of whole-DRG RNA-seq datasets from prominent rat PNI models. Striking differences were found between transcriptional responses to PNI and SCI, especially in regeneration-associated genes and long noncoding RNAs. Many transcriptomic changes after SCI were also found after corresponding sham surgery, indicating they were caused by injury to surrounding tissue rather than to the spinal cord itself. Another unexpected finding was of few transcriptomic similarities between any rat neuropathic pain model and the only reported transcriptional analysis of human DRGs linked to neuropathic pain. These findings show that DRGs exhibit complex transcriptional responses to central and peripheral neural and tissue injury. Although few genes in DRG cells show similar changes in gene expression across all these painful conditions, the few widely shared transcriptional alterations promise novel insights into fundamental mechanisms within DRGs that can drive neuropathic pain.

overall_design: Comparative gene expression profiling analysis of RNA-seq data generated from lumbar and thoracic dorsal root ganglia (DRG) samples excised bilaterally below spinal level T11 under three conditions: Naïve, Sham, and spinal cord injury (SCI). We used three biological replicates of each experimental group.

last: Cuevas-Diaz Duran

first: Carmen

last: Dessauer

first: Jiaqian

last: Wu

first: Edgar

last: Walters


title: Hepatocyte nuclear factor 1β binding in E14.5 kidney

first: Annie

last: Shao

summary: HNF-1β mutations are one of the most common single-gene mutations that underlie kidney developmental disease. Hepatocyte nuclear factor 1β (HNF-1β) is essential for kidney development, but its functions in kidney development are incompletely understood. We identified 8284 HNF-1β binding sites using ChIP-sequencing. The majority of these peaks map to promoter (26%), intron (34%) or distal intergenic regions (37.4%) of the mouse genome. 61% of peaks map to protein coding genes, 12% map to long-noncoding RNAs, and 2% map to miRNAs.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HNF-1β in embryonic day 14.5 mouse kidneys

first: Micah

last: Gearhart

first: Peter

last: Igarashi


title: CD47 blocking antibody confers exercise effects by activating AMPK and improving mitochondrial energetics of skeletal muscle

city: Shanghai

first: Xiangyi

last: Chen

address: No. 1239, Siping Road, Shanghai, China

institute: Weida Li

summary: We report transcript profiles from skeletal muscle tissues of CD47-/-, wild-type sedentary and exercise group mice that exercise continuously for 8 weeks, 6 days a week, at a speed of 15 m/min for 1 hour per day. We found that the transcripts of CD47-/- mice were more similar to exercise mice.

overall_design: For the mouse dataset, skeletal muscle tissue was taken for RNA-Seq analysis after overnight starvation treatment of sedentary WT, CD47-/- and exercise mice under a normal diet.

first: Yajuan

last: Su

first: Weida

last: Li


title: Gastric and esophagogastric junction adenocarcinoma with infrequent hypermethylation show poor prognosis

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: Background  Gastric cancer (GC) was characterized by unique DNA methylation epigenotypes (MEs). Still, MEs, including adenocarcinoma of the esophagogastric junction (AEG) and background non-neoplastic columnar mucosae (NM), are yet to be clarified.   Methods  We analyzed genome-wide DNA MEs of AEG, GC, and background NM using Infinium 450k beadarray, followed by quantitative pyrosequencing validation. Large-scale data of the Cancer Genome Atlas (TCGA) were additionally reviewed.   Results  Unsupervised two-way hierarchical clustering using Infinium data of 21 AEG, 30 GC, and 11 NM showed four DNA MEs: extremely high-ME (E-HME), high-ME (HME), low-ME (LME), and extremely low-ME (E-LME). The promoter methylation levels were validated by pyrosequencing in 146 samples. Although almost normal mucosae were clustered into E-LME, gastric or esophagogastric junction mucosae with chronic inflammatory change due to either Helicobacter pylori infection or reflux esophagitis were clustered together into LME, which suggested that the inflammation status determined DNA MEs regardless of the causes. Three cases of Barrett’s-related adenocarcinoma were all clustered into HME. Among 94 patients whose tumors can be clustered into one of four MEs, 11 patients with E-LME cancers showed significantly shorter overall survival than the other MEs, even in multivariate Cox regression estimate. TCGA data also showed enrichment of AEG in HME and a poorer prognosis of E-LME.  Conclusions  E-LME cases, newly confirmed in this study, would be a unique aggressive subtype not associated with the elevation of DNA methylation levels caused by inflammation. LME could be acquired via chronic inflammation independent of the causes, and AEG frequently showed HME.

overall_design: Bisulphite converted DNA from the 56 samples were hybridised to the Infinium HumanMethylation450 BeadChip.

first: Masayuki

last: Urabe

first: Keisuke

last: Matsusaka

first: Tetsuo

last: Ushiku

first: Bahityar

last: Rahmutulla

first: Hiroharu

last: Yamashita

first: Yasuyuki

last: Seto

first: Masashi

last: Fukayama

first: Atsushi

last: Kaneda


title: Expression data from intestinal epithelial cells of  hindlimb unloading (HU) and control mice

city: Beijing

first: Junxiu

last: Shi

address: Xueyuan Road No. 38

department: Immunology

institute: Peking University Health Science Center

summary:
Commensal bacteria can manipulate the proliferation, differentiation, and survival of intestinal epithelial cells. Hindlimb unloading alters the composition and structure of the microbial community.
To further characterize the epithelial changes, we performed a genome-wide microarray analysis of colon epithelium isolated from HU and control mice.

overall_design: Transcriptional profiling was determined in 6 samples of isolated colonic epithelial cells (3 replicates from HU and 3 from control mice), using Affymetrix 430 2.0 GeneChip arrays.

first: Qing

last: Ge


title: RNA_Seq analysis of localization along animal-vegetal axis of Danio rerio

first: Radek

last: Šindelka

overall_design:
We performed cryosectioning of oocytes along the animal-vegetal axis (first developmental axis, section A (first animal) to section E (last vegetal), followed by RNA-Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization.
Total RNA was extracted using Qiagen (Microkit) column based isolation. The concentration of RNA was measured using a spectrophotometer (Nanodrop 2000, Thermo Scientific), and the quality of RNA was assessed using a Fragment Analyzer (AATI, High Sensitivity RNA analysis kit). RNA profiles were generated using RNA-Sequencing in 4 replicates (each divided into five segments).

first: Ravindra

last: Naraine

first: Pavel

last: Abaffy

last: Sindelka


title: FOXG1 drives transcriptomic networks to specify principal neuron subtypes during the development of the medial pallium

status: Public on Oct 19 2022

city: Nanjing

first: Ru

last: Ba

state: Jiangsu

address: Southeast University

institute: Southeast University

summary: The medial pallium (MP) is the major forebrain region underlying learning and memory, spatial navigation, and emotion; however, the mechanisms underlying the specification of its principal neuron subtypes remain largely unexplored. Here, by postmitotic deletion of FOXG1 (a transcription factor linked to autism and FOXG1 syndrome) and single-cell RNA sequencing, we found that FOXG1 controls the specification of upper-layer retrosplenial cortical pyramidal neurons (RSC-PyNs (UL)), subiculum PyNs (SubC-PyNs), CA1-PyNs, CA3-PyNs and dentate gyrus granule cells (DG-GCs) in the mouse MP. We uncovered subtype-specific and subtype-shared FOXG1-regulated transcriptomic networks orchestrating MP neuron specification.

overall_design: we conducted scRNA-seq of 27198 cells sampled from the medial pallium of Foxg1fl/fl and Nex-Cre; Foxg1fl/fl  mice at E17.5

first: Lin

last: Yang

first: Chunjie

last: Zhao


title: Mod(mdg4) variants repress telomeric retrotransposon Het-A by blocking subtelomeric enhancers

city: Shinjuku-ku

first: Chikara

last: Takeuchi

state: Tokyo

address: 35 Shinanomachi

department: Molecular biology

institute: Keio University

summary: Telomeres in Drosophila are composed of sequential non-LTR retrotransposons: Het-A, TART, TAHRE. Although their expression is highly dynamic, molecular mechanism governing these retrotransposons is poorly understood. Here, we show that specific splice variants of Mod(mdg4) act as repressors of Het-A by blocking subtelomeric enhancers in ovarian somatic cells. We found that a variant, Mod(mdg4)-N, can repress Het-A expression most efficiently among variants. Mod(mdg4)-N mutant flies show elevated Het-A expression and female sterility. Further investigation revealed that Mod(mdg4)-N-binding subtelomeric sequences exhibit enhancer-blocking activity, and recruitment of RNA polymerase II (Pol II) on subtelomeres by Mod(mdg4)-N is essential for this enhancer-blocking. Moreover, Mod(mdg4)-N functions to form chromatin boundaries of higher-order chromatin conformation but this mechanism is independent with its Pol II recruitment activity observed at telomeres/subtelomeres. This study provides an unexpected link between enhancer-blocking and telomere regulation, and two different molecular mechanisms exhibited by an insulator protein to orchestrate precise gene expression.

overall_design: Micro-C XL, RNA levels and Pol II occupancy in OSC depleted of Mod(mdg4).Localization of Ty1-tagged Mod(mdg4) isoforms. RNA levels in Mod(mdg4)-N mutant ovaries.

first: Yuka

last: Iwasaki

first: Haruhiko

last: Siomi


title: Transcriptome Analysis of Particulate Matter 2.5-Induced Ab-normal Effects on Human Sebocytes

city: Yongin-si

first: Hye-Won

state: Gyeonggi-do

address: 20, Yonggu-daero 1916beon-gil, Giheung-gu

country: South Korea

institute: Research and Innovation Center, AMOREPACIFIC

summary:
To investigate the effect of PM2.5 on sebocyte, we treated PM2.5 on SZ95 seboccyte and perfomed transcriptome analysis.
We examined the role of PM2.5 via identification of differentially expressed genes, functional enrichment and canonical pathway analysis, upstream regulator analysis, and disease and bio-logical function analysis through mRNA sequencing. Xenobiotic and lipid metabolism, inflam-mation, oxidative stress, and cell barrier damage-related pathways were enriched; additionally, PM2.5 altered steroid hormone biosynthesis and retinol metabolism-related pathways.

overall_design: Examination of total RNA from SZ95 sebocytes treated with PM2.5 and control.

first: Hyung-Jun

last: Kim


title: The synthetic opioid fentanyl increases HIV replication and chemokine co-receptor expression in lymphocyte cell lines

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

summary: The illicit use of synthetic opioids such as fentanyl has led to a serious public health crisis in the United States.  People with opioid use disorder are more likely to contract infections such as HIV and viral hepatitis.  While several drugs of abuse are known to enhance viral replication and to suppress immunologic responses, the effects of synthetic opioids on HIV pathogenesis have not been investigated thoroughly.  Thus, we examined the impact of fentanyl on HIV-susceptible and HIV-infected cell types and chemokine receptor expression in vitro.    TZM-bl and HIV-infected lymphocyte cells were incubated with fentanyl at concentrations of 1 ng, 100 ng, and 10 ug.  Expression levels of the CXCR4 and CCR5 chemokine receptors were measured in cell lysates, and HIV p24 antigen was quantified in culture supernatants by ELISA.  HIV proviral DNA was quantified in cells using SYBR RT-PCR targeting the pol gene.  Cell viability in the presence of drug was detected by the MTT Cell Proliferation Assay.  RNA-seq and miRNAseq was performed to characterize cellular gene regulation in the presence of fentanyl.    Fentanyl enhanced expression of CXCR4 and CCR5 protein levels in a dose-dependent manner in HIV-susceptible and HIV-infected cells.  Similarly, fentanyl induced viral expression in HIV-exposed TZM-bl cells and in multiple HIV-infected lymphocyte cell lines.  Multiple genes associated with apoptosis, antiviral / interferon response, chemokine signaling, and NFκB signaling were differentially regulated by fentanyl.     These data demonstrate that the synthetic opioid fentanyl impacts HIV replication and chemokine co-receptor expression in HIV-susceptible and HIV-infected cells.  Increased virus levels also suggest that opioid use may increase the likelihood of transmission to others and accelerate disease progression.

overall_design: ACH-2 cells were analyzed in presence and abscenece of fentanyl. Cells were treated with 100ng of fentanyl for 24 hours. ACH-2 cells without fentanyl treatment is considered as control. Both control and test were performed in replicates. Total RNA was extracted from both fentanyl-treated and untreated ACH-2 cells miRNA Isolation Kit

first: Janani

last: Krishnan

first: Jason

last: Blackard


title: IL1β-dependent extravasation of pre-existing lung-restricted autoantibodies activates complement to promote primary graft dysfunction

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

summary: Pre-existing lung restricted autoantibodies (LRA) are associated with a higher incidence of primary graft dysfunction (PGD) although it remains unclear whether LRA can drive its pathogenesis. In syngeneic murine left lung transplant recipients, pre-existing LRA worsened graft dysfunction, which was evident by impaired gas exchange, increased pulmonary edema, and activation of damage-associated pathways in lung epithelial cells. LRA-mediated injury was distinct from ischemia-reperfusion injury since deletion of donor non-classical monocytes as well as host neutrophils could not prevent graft dysfunction in LRA-pretreated recipients. Whole LRA IgG molecule was necessary for lung injury which was mediated by the classical and alternative complement pathways and reversed by complement inhibition. However, deletion of Fc receptors in donor macrophages or mannose-binding lectin proteins failed to rescue lung function. LRA- mediated injury was localized to the transplanted lung and dependent on IL1β-mediated permeabilization of pulmonary vascular endothelium which allowed extravasation of antibodies. Genetic deletion or pharmacological inhibition of IL1R in the donor lungs prevented LRA-induced graft injury. In humans, pre-existing LRA was an independent risk factor for severe PGD and could be treated with plasmapheresis and complement blockade. We conclude that pre-existing LRA can compound ischemia-reperfusion injury to worsen PGD for which complement inhibition may be effective.

overall_design: Single-cell suspensions from 24 hours post-transplant allografts from isotype or LRA treated mice .

first: Wenbin

first: Emily

last: Cerier

first: Félix

middle: L

last: Núñez-Santana

first: Qiang

last: Wu

first: Chitaru

last: Kurihara

first: Xianpeng

last: Liu

first: Haiying

last: Sun

first: Emilia

last: Lecuona

first: Ankit

last: Bharat


title: sRNA sequencing of mature and developing gonads during protandrous changes in the Asian seabass

city: Veszprém

first: László

last: Orbán

address: Egyetem u. 10

department: Department of Animal Sciences

country: Hungary

institute: University of Pannonia

summary:
Purpose: sRNA-sequencing of mature and intermediate gonadal tissue in order to identify the differential expression of miRNAs during male to female (i.e. protandrous) sex transition

Methods: Total RNA was extracted and sRNA was purified. cDNA libraries were constructed using a high definition adapter protocol (Xu et al. 2015). 50 bp sequencing was performed on Illumina's HiSeq 2500 at the Earlham Institute, Norwich, UK. Sequenced data was trimmed for adapters and filtered to remove very short and low complexity sequences. miRBase animal miRNA precursor sequences were mapped against the Asian seabass genome in order to generate a set of putative miRNA precursors. Putative precursor molecules with aligning mature miRBase miRNA(s) and forming a valid pre-miRNA hairpin structure were annotated as valid precursor miRNAs.  Novel precursor and mature miRNAs were annotated using a combination of published algorithms and manual checking to ensure consistency with canonical miRNA biogenesis criteria. The alignment of sequenced reads against a non-redundant miRNA precursor set was used to determine raw read counts of mature miRNAs. Differential expression analysis was performed in order to identify differentially expressed mature miRNAs between conditions.

Results: We detect 156, 71, 122, 151, 171 and 155 differentially expressed miRNA for the testis -> T1/T2, T1/T2 -> T3/T4, T3/T4 -> ovary, testis -> T3/T4, T1/T2 -> ovary and the testis->ovary comparisons respectively

Conclusions: There is substantial differential expression of miRNAs at every stage of gonadal change in the Asian seabass during the sex transition process

overall_design:
sRNA-sequencing of Asian seabass testis, ovary and the T1,T2,T3 and T4 intermediate stages

Raw data are unavailable for this series due to file loss.

first: Darrell

last: Green

first: Thomas

last: Bradley

first: Shubha

last: Vij

first: Jolly

middle: M

last: Saju

first: Kathiresan

last: Purushotaman

first: Simon

last: Moxon

first: Tamas

last: Dalmay


title: Transcriptional profiling of striatum in METH self-administered rats [miRNA]

city: Daegu

first: Taekwon

last: Son

address: 61, Cheomdan-ro, Dong-gu

department: Korea Brain Bank

institute: Korea Brain Research Institute

summary: This study aimed to identify changes in novel miRNAs and their target genes during METH self-administration and investigate their roles in METH-induced locomotion. RNA sequencing analysis revealed that mir-183-5p was upregulated in the striatum of METH self-administered rats, and target gene prediction revealed that the glucocorticoid receptor (GR) gene, Nr3c1, was a potential target gene for mir-183-5p. We confirmed that single and repeated METH administrations increased METH-induced locomotion and plasma corticosterone levels in rats.

overall_design: miRNA expression profiling of the striatum of rats following treatment with methamphetamine or saline.

first: Sang-Hoon

last: Song

first: Won-Jun

last: Jang

first: Sooyeun

last: Lee

first: Chul-Ho

last: Jeong


title: Disulfiram/Copper induces immunogenic cell death via NPL4 in hepatocellular carcinoma

city: Hang Zhou

first: xingxing

last: gao

state: Zhejiang

address: qingchun road

institute: zhejiang university

summary: Some chemotherapeutic agents have been found to enhance the antitumor immunity by inducing immunogenic cell death (ICD). The combination of disulfiram (DSF) and copper (Cu) has demonstrated anti-tumor effects in a range of malignancies including hepatocellular carcinoma (HCC). However, the potential of DSF/Cu as an ICD inducer and whether it could enhance the efficacy of immune checkpoint blockade in HCC remains unknown. Here, we showed that DSF/Cu-treated HCC cells exhibited characteristics of ICD in vitro, such as calreticulin (CRT) exposure, ATP secretion, high mobility group box 1 (HMGB1) release. DSF/Cu treated HCC cells elicited significant immune memory in a vaccination assay. DSF/Cu treatment promoted dendritic cell activation and maturation. The combination of DSF/Cu and CD47 blockade further facilitated DC maturation and subsequently enhanced CD8+ T cell cytotoxicity. Mechanically, DSF/Cu promoted the nuclear accumulation and aggregation of nuclear protein localization protein 4 (NPL4) to inhibit the ubiquitin-proteasome system, thus induced endoplasmic reticulum (ER) stress. Inhibition of NPL4 induced ICD-associated damage-associated molecular patterns. Collectively, our findings demonstrated that DSF/Cu induced ICD-mediated immune activation in HCC and enhanced the efficacy of CD47 blockade.

overall_design: HCCLM3  cells were treated with DSF/Cu in a concentration of 0.2μM for 24h or transfected with siRNA-NC or NPL4 siRNA-1 for 48h.

first: Xingxing

last: Gao


title: Impaired TIGIT expression on B cells drives circulating follicular helper T cell expansion in multiple sclerosis

city: New Haven

first: Hiromitsu

last: Asashima

state: CT

address: 300George St

institute: Yele School of Medicine

summary: B cell depletion in patients with relapsing remitting multiple sclerosis (RRMS) markedly prevents new MRI lesions and disease activity, suggesting the hypothesis that altered B cell function leads to the activation of T cells driving disease pathogenesis. Here, we performed comprehensive analyses of memory B cells from patients with MS and healthy age-matched controls stimulated with CD40L and IL-21, modeling the help of follicular helper T cells (Tfh cells), and found a differential gene expression signature in multiple B cell pathways. Most striking was impaired TIGIT expression on MS-derived B cells mediated by dysregulation of the transcription factor TCF4. Activated circulating Tfh cells (cTfh cells) expressed CD155, the ligand of TIGIT, and TIGIT on B cells revealed their capacity to suppress the proliferation of IL-17-producing cTfh cells via TIGIT/CD155 axis. Finally, CCR6+ cTfh cells were significantly increased in MS and their frequency was inversely correlated with that of TIGIT+ B cells. Together, these data suggest that the dysregulation of negative feedback loops between TIGIT+ memory B cells and cTfh cells in MS drive the activated immune system in the disease.

overall_design: memory B cell profiles of patients with multiple sclerosis and healthy donors in multiple conditions (A) treated with CD40L+IL-21, B) CD40L or CD40L+IL-4 treated, C) TIGIT+, IL-10+ B cells )

first: Pierre-Paul

last: Axisa

first: David

last: Hafler


title: Transcriptional profiling of striatum in METH self-administered rats [mRNA]

overall_design: Gene expression profiling of the striatum of rats following treatment with methamphetamine or saline.


title: Memory phase-specific genes identified by CrebB-target DamID in the Mushroom Bodies

city: Fribourg

first: Noemi

last: Sgammeglia

address: Chemin du Musee 10

country: Switzerland

institute: University of Fribourg

summary: The formation of long-term memories requires changes in the transcriptional program and de novo protein synthesis. One of the critical regulators for long-term memory (LTM) formation and maintenance is the transcription factor CREB. Genetic studies have dissected the requirement of CREB activity within memory circuits, however less is known about the genetic mechanisms acting downstream of CREB and how they may contribute defining LTM phases. To better understand the downstream mechanisms, we here used a targeted DamID approach (TaDa). We generated a CREB-Dam fusion protein using the fruit fly Drosophila melanogaster as model. Expressing CREB-Dam in the mushroom bodies (MBs), a brain center implicated in olfactory memory formation, we identified genes that are differentially expressed between paired and unpaired appetitive training paradigm. Of those genes we selected candidates for an RNAi screen in which we identified genes causing increased or decreased LTM.

overall_design: Comparative gene profiling of targeted DamID-derived sequencing in Drosophila melanogaster. Triplicates of two types of sample (Dam-CrebB vs Dam-Only) are treated in three different conditions (paired, unpaired and naives).

first: Yves

last: Widmer

first: Jenifer

last: Kaldun

first: Cornelia

last: Fritsch

first: Rémy

last: Bruggmann

middle: G

last: Sprecher


title: Pax3 loss of function delays tumor progression in kRAS-induced zebrafish rhabdomyosarcoma models

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

institute: Navarrabiomed - Fundacion Migues Servet

summary: Rhabdomyosarcoma is a soft tissue cancer that arises in skeletal muscle due to mutations in myogenic progenitors that lead to ineffective differentiation and malignant transformation. The transcription factors Pax3 and Pax7 and their down-stream target genes are tightly linked with the fusion positive alveolar subtype, whereas the RAS pathway is usually involved in the embryonic, non-fusion variant. Here, we analyse the role of Pax3 in a non-fusion context, by linking alterations in gene expression in pax3a/pax3b double mutant zebrafish with tumour progression in kRAS-induced rhabdomyosarcoma tumours. Several genes in the RAS signalling pathway, including MAPK signalling pathway, were significantly down-regulated in pax3a/pax3b double mutant zebrafish. Onset and progression of rhabdomyosarcoma tumours were also delayed in the pax3a/pax3b double mutant zebrafish indicating that Pax3 transcription factors have an unappreciated role in mediating malignancy also in non-fusion rhabdomyosarcoma.

overall_design: Zebrafish embryos from wild type and pax3a-/-(umu5); pax3b-/-(umu6) homozygous double mutants were collected at 42 hpf for RNA preparation. A total of six samples, two triplicates each, were included in RNA sequencing. poly-A selection libraries were prepared, pooled and sequenced on a 1/4th NovaSeq600 S4 lane, with 2x150bp reads

first: Abraha

last: Kahsay

first: Eva

last: Rodriguez-Marquez

first: Andreas

last: Hörnblad

first: Jonas

last: von Hosften


title: Transcriptional profiling of striatum in METH self-administered rats

first: Taekwon

last: Son

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

overall_design: Refer to individual Series


title: The effects of YTHDC1 on islet β-cell function

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary:
The goal of this study is to investigate how YTHDC1 regulates islet β-cell function.
Our study represents the first detailed analysis of islet transcriptomes from Ythdc1flox/flox and Ythdc1-βKO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 2869 genes were downregulated and 2825 genes were upregulated in the pancreatic islets of Ythdc1-βKO mice.

overall_design:
mRNA profiles in pancreatic islets of Ythdc1flox/flox and Ythdc1-βKO mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).
Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from pancreatic islets of Ythdc1flox/flox and Ythdc1-βKO mice at 7 weeks old. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome (GRCm38/mm10) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.

first: Xinzhi

last: Li

first: Ying

last: Yang


title: tRNA-derived Small RNAs and their Potential Roles in the Therapeutic Heterogeneity of Sacubitril/valsartan in Heart Failure Patients after Acute Myocardial Infarction

city: Ningbo

first: Jia

last: Su

state: China

address: Liuting Street No.59

institute: Ningbo No. 1 Hospital

summary: Background: It has been reported that sacubitril/valsartan can improve cardiac function in acute myocardial infarction (AMI) patients complicated by heart failure (HF). However, a number of patients cannot be treated successfully; this phenomenon is called sacubitril/valsartan resistance (SVR), and the mechanisms remain unclear.  Methods:In our present research, the expression profiles of tRNA-derived small RNAs (tsRNAs) in SVR along with NSVR patients were determined by RNA sequencing. Through bioinformatics, qRT–PCR, and cell-based experiments, we identified SVR-related tsRNAs and confirmed their diagnostic value, predicted their targeted genes, and explored the enriched signal pathways as well as regulatory roles of tsRNAs in SVR.  Results:Our research indicated that 36 tsRNAs were upregulated and that 21 tsRNAs were downregulated in SVR. Among these tsRNAs, the expression of tRF-59:76-Tyr-GTA-2-M3 and tRF-60:76-Val-AAC-1-M5 was upregulated, while the expression of tRF-1:29-Gly-GCC-1 was downregulated in the group of SVR. Receiver operating characteristic (ROC) curve analysis demonstrated that these three tsRNAs were potential biomarkers of the therapeutic heterogeneity of sacubitril/valsartan. Moreover, tRF-60:76-Val-AAC-1-M5 might target Tnfrsf10b and Bcl2l1 to influence the observed therapeutic heterogeneity through the lipid and atherosclerosis signaling pathways.  Conclusions:Hence, tsRNA might play a vital role in SVR. These discoveries provide new insights for the mechanistic investigation of responsiveness to sacubitril/valsartan.

first: Ji

last: Cheng

first: Yingchu

last: Hu


title: Transcriptommic profiling of hematopoietic progenitor cells following PCGF1 loss [RNA-Seq]

city: Yokohama-shi

first: Junichiro

last: Takano

state: Kanagawa-kwn

department: IMS

institute: RIKEN

summary: Polycomb proteins are epigenetic regulators important for cell fate decision and maintenance. Here we show that PCGF1, one of components of Polycomb repressive complex (PRC) 1 is important for the differentiation of hematopoietic stem/progenitor cells (HSPCs) towards lymphoid lineage. The deletion of Pcgf1 in HSPCs lead to severe defects in B cell development with an expansion of myeloid progenitors. The blockade of B cell differentiation occurred at the lymphoid-primed multipotent progenitor (LMPP) stage. Chromatin immunoprecipitation followed by DNA sequencing analysis of normal LMPP-like cells demonstrated that PCGF1 colocalized with RING1A/B and PRC2. Upon deletion of Pcgf1, we found dramatic decline of H3K27me3 levels, resulting in de-repression of target genes. Strikingly, the occupancy of RING1A/B, PRC2 and monoubiquitination of histone H2A at lysin 119 on the target loci was not affected. These results demonstrate that the PCGF1 safeguards the immune system development by directly regulating the PRC2-mediated H3K27me3 levels.

overall_design: RNA-seq analysis  in Pcgf1 -/- and control hematopoietic progenitor cells

first: J

first: T

last: Ikawa

first: H

last: Koseki


title: Inducible deletion of Raptor and mTOR from adult skeletal muscle impairs muscle contractility and relaxation

city: Padova

first: Bert

last: Blaauw

address: Via Ugo Bassi 58/b

department: Department of Biomedical Sciences

country: Italy

institute: University of Padova

summary: Skeletal muscle weakness has been associated with different pathological conditions, including sarcopenia and muscular dystrophy, and is accompanied by altered mTOR signaling. Here we wanted to better elucidate the functional role of mTOR on muscle contractility. Most loss of function studies for mTOR signaling have used the drug rapamycin to inhibit some of the signaling downstream of mTOR. However, as rapamycin does not completely inhibit all mTOR signaling, we generated a double k.o. for mTOR and for the scaffold protein of mTORC1, Raptor, in skeletal muscle. We found that dk.o. mice results in a more severe phenotype compared to Raptor or mTOR deletion alone. Indeed, they display muscle weakness, increased fiber denervation, and a slower muscle relaxation following tetanic stimulation. This is accompanied by a shift towards slow-twitch fibers and changes in the expression levels of calcium-related genes, like Serca1 and Casq1. Indeed, dk.o. mice show a decrease in calcium decay kinetics after tetanus in vivo, suggestive of a reduced calcium reuptake. In addition, RNA sequencing analysis revealed that many downregulated genes are linked to sarcomere organization, like Tcap and Fhod3. These results suggest a key role for mTOR signaling in maintaining a proper fiber relaxation in skeletal muscle.

overall_design: Inducible, muscle-specific Raptor knockout mice were generated crossing mice expressing Raptor gene between two LoxP sites with mice carrying Cre recombinase fused to a mutated estrogen receptor domain under the control of human skeletal actin promoter. Inducible, muscle-specific Raptor mTOR double knockout mice were generated crossing HSA-Cre-Raptorfl/fl mice with mTORfl/fl mice. Tamoxifen-induced Cre LoxP recombination was activated by oral administration of tamoxifen-containing chow (Tam400/Cre-estrogen receptor, Harlan), for 7 weeks. For long-term treatment muscles were collected 7 months from the beginning of the treatment. RNA-seq was carried out on gastrocnemius muscles of wild-type, Raptor k.o. and Raptor mTOR dk.o. mice, with the contrast of interest being wt v dk.o. and k.o. v dk.o..

first: Martina

last: Baraldo


title: Therapeutic Delivery of Targeted Nanoparticle Cannabinoid Equivalents

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

country: Australia

institute: University of Sydney

summary: Nanoparticles and nano delivery systems are continuously being refined and developed as means of treating numerous human diseases by site-specific, and target-oriented delivery of medicines.  The nanoparticles can carry therapeutic cargo or be medicinal themselves by virtue of their constitutional structural components. Here we report the ability of synthetic N-acylethanolamides, linoleoylethanolamide (LEA) and oleoylethanolamide (OEA), with endocannabinoid-like activity, to form spherical colloidal nanoparticles that when conjugated with tissue specific homing molecules, can localise to specific areas of the body, and reduce inflammation. The opportunities to mediate pharmacological effects of endocannabinoids at targeted sites provides a novel drug delivery system with increased medicinal potential to treat many diseases in many areas of medicine.

overall_design: Four experimental groups, each with 3 sample replicates were used in this study. Experimental groups included: RA_UT, RA_TNF, RA_NP, RA_TNF_NP. Differential expression was performed between each group.

first: Nicholas

last: Manolios


title: The transcriptional coactivator Eya1 exerts transcriptional repressive activity by interacting with REST corepressors and DNA recognition sequences to maintain nephron progenitor identity [ChIP-seq]

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: Eya1 is critical for specifying and maintaining nephron progenitor cells (NPCs). It belongs to a protein family known as phosphatase-transcriptional activator but without intrinsic DNA-binding activity. However, the Eya1-centered network and the spectrum of its interaction partners are underexplored. Here, we combined transcriptomic, genomic and proteomic approaches to characterize gene regulation by Eya1 in the NPCs. We identified Eya1 target genes, genomic binding sites, and partner proteins. Eya1 binds preferentially to promoter sequences and interacts with general transcription factors (TFs), RNA polymerases, different types of TFs, and DNA replication/repair proteins. Intriguingly, we identified REST-binding motifs in 76% of Eya1-binding sites without H3K27ac-deposition, which were present in many Eya1 target genes upregulated in Eya1-deficient NPCs. Eya1 copurified REST-interacting proteins, including chromatin-remodeling factors with ATPase or helicase activity, histone deacetylase/lysine demethylase, and corepressors. Coimmunoprecipitation validated complex formation between Eya1, Hdac1 and Cdyl in kidneys. Thus, these results suggest that through interactions with chromatin-remodeling factors, Eya1 may modify chromatin structure to facilitate the assembly of regulatory complexes that regulate transcription positively or negatively. These findings provide a mechanistic basis for how Eya1 functions as a multifunction protein by cooperating with protein partners in various fundamental biological processes to maintain the cellular state of NPCs.

overall_design: Mouse kidneys from Eya1 embryos

first: Jun

first: Chunming

first: Jinshu

last: Xu

first: Ting

last: Zhang

first: Pin-Xian


title: RNA-sequencing profiling of mRNAs in A549 cells with TIF1γ overexpression or TAF15 knockdown

city: Suzhou

first: Zhiyue

address: 199 Ren'ai Road

country: China

institute: Soochow University

summary: To investigate the target gene regulated by TIF1γ and TAF15, we established stable TIF1γ-overexpressing and TAF15-silencing A549 cells separately, and total RNA was extracted and subjected to RNA sequencing analysis. Following that, differentially expressed genes were employed for further investigation.

overall_design: The stable TIF1γ-overexpressing and TAF15-silencing A549 cells were established by the lentiviral system containing TIF1γ stable expression vector (TIF1γ) or the shRNA expression vector for decreasing TAF15 expression (sh-TAF15). The cells infected with corresponding empty vectors were used as a negative control (vector, sh-NC). Three biological replicates were included in each group.

first: Hong-Tao


title: The transcriptional coactivator Eya1 exerts transcriptional repressive activity by interacting with REST corepressors and DNA recognition sequences to maintain nephron progenitor identity [RNA-seq]

overall_design: Mouse kidneys from Wt and Eya1 conditional knockout embryos


title: DNMT and EZH2 inhibitors synergize for gene activation in hepatocellular carcinoma cells.

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

type: Methylation profiling by genome tiling array


title: Gene regulation by PCGF1 in hematopoietic progenitor cells [ChIP and MNaseSeq]

first: Junichiro

country: Japan

overall_design: ChIP MNaseSeq


title: DNMT and EZH2 inhibitors synergize for gene activation in hepatocellular carcinoma cells [RNA-seq]

summary: Hepatocellular carcinoma (HCC) is the most common primary liver malignancy with cases increasing dramatically in the USA. Developing more effective targeted therapies for HCC is an urgent need. The FDA-approved DNA methyltransferase inhibitors (DNMTis) 5-azacytidine (5-aza-CR, Vidaza) and 5-aza-2’-deoxycytidine (5-aza-CdR, Decitabine) represented the first clinical breakthrough to target aberrant cancer epigenomes. However, the clinical efficacies of DNMTis are still limited, in part due to an “epigenetic switch” mechanism, in which a large group of genes demethylated by DNMTi treatment remain silenced by Polycomb Repressive Complex 2 (PRC2) occupancy. Overexpression of PRC2 subunits, especially EZH2, is correlated with poor patient survivor in HCC. In this study, we tested the combination of 5-Aza-CdR and the EZH2 inhibitor (EZH2i) GSK-126 in human HCC cell lines (SNU398, HepG2, and SNU475) on DNA methylation, nucleosome accessibility, and gene expression profiles. Compared with single agent treatments, all cell lines showed increased sensitivity after receiving both drugs concomitant with prolonged anti-proliferative changes and sustained reactivation of nascently silenced genes. The increased number of up-regulated genes, including tumor suppressors, were correlated with prolonged anti-proliferation effects and nucleosome accessibility but negatively correlated with gene promoter DNA methylation. Detailed epigenome analyses reveal a mechanistic rationale in which the combination treatment of 5-aza-CdR with an EZH2 inhibitor (EZH2i) activates demethylated promoters that are repressed by PRC2 occupancy. Furthermore, about 13.6% to 31% of genes down-regulated by DNA methylation in primary HCC tumors can be reactivated through this combination treatment scheme in vitro. Finally, combination treatment also exacerbates viral mimicry activation as well as leukocyte, lymphocyte and T cell mediated immunity, while most those genes or pathways were downregulated in over 50% of primary HCC tumors in TCGA dataset. Conclusion: we have linked the anti-tumor effects of DNMTi and EZH2i combination treatments to detailed epigenetic alterations in HCC cells, identified potential therapeutic targets and provided a rationale for combination treatment efficacy in HCC patients.

overall_design: Examination of total RNA expressed after treatment with vehicle control, EZH2i, decitabine and combination of the two in HepG2, SNU398 and SNU475 cells.

first: Minmin

last: Liu

first: Gangning

last: Liang


title: The transcriptional coactivator Eya1 exerts transcriptional repressive activity by interacting with REST corepressors and DNA recognition sequences to maintain nephron progenitor identity


title: RORb modulates a gene program that is protective against articular cartilage damage

city: Jupiter, FL 33458

first: Gogce

middle: Ceren

last: Crynen

state: Florida

address: 130 Scripps Way

department: Bioinformatics and Statistics Core

institute: UF Scripps Biomedical Research

summary: Osteoarthritis (OA) is the most prevalent chronic joint disease which increases in frequency with age eventually impacting most people over the age of 65.  OA is the leading cause of disability and impaired mobility, yet the pathogenesis of OA remains unclear. Treatments have focused mainly on pain relief and reducing joint swelling. Currently there are no effective treatments to slow the progression of the disease and to prevent irreversible loss of cartilage. Here we demonstrate that stable expression of RORb in cultured cells results in alteration of a gene program that is supportive of chondrogenesis and is protective against development of OA. Specifically, we determined that RORb regulates the balance of FGFRs signaling on FGFR1/FGFR3 that ERK1/2-MAPK signaling was suppressed by FGFR1(cartilage destruction) and AKT signaling was enhanced by FGFR3 (cartilage protection). These results suggest a critical role for RORb in chondrogenesis and suggest that identification of mechanisms that control the expression of RORb in chondrocytes could lead to the development of disease modifying therapies for the treatment of OA

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RORb function in osteoarthritis

first: Mi

last: Chang

first: Patrick

last: Griffin


title: DNMT and EZH2 inhibitors synergize for gene activation in hepatocellular carcinoma cells [methylation array]

overall_design: Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium Human MethylationEpic Beadchip


title: Actions of WNT family member 5A to regulate developmental competence of the bovine preimplantation embryo

city: Gainesville

middle: James

last: Hansen

state: FL

address: 2250 SW Shealy Drive

department: Animal Sciences

institute: University of Florida

summary: WNT5A, one of the most abundant cell-signaling ligands expressed in the endometrium, appears to be an important regulator of early development because it can act on the preimplantation bovine embryo through a ROCK-dependent pathway to improve competence to develop to the blastocyst stage and increase number of cells in the inner cell mass.

overall_design: Transcriptomic analyses of bovine embryos at the morula stage treated with WNT5A and control

first: Surawich

last: Jeesuk

last: Ortega

first: Briana

last: Hawryluk

first: Tracy

last: Scheffler


title: Ambient RNA analysis of single-nuclei RNA-Seq data from the frontal cortex of C57BL/6J mice

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center

summary: Contamination of ambient RNA was found in single-nuclei RNA-Seq data of mouse frontal cortex. CellBender plus subcluster cleaning selectively removed ambient RNA signature from glial cell types.

overall_design: P56 wildtype mice were harvested rostral part of the frontal cortex which is corresponding to the cortex part of Coronal level 22-36 in Allen Brain Atlas: Reference Atlas, Version 2 (2011), and extracted single nuclei for sequencing.

first: Joseph

middle: S

last: Takahashi

first: Yuxiang

first: Ashwinikumar

last: Kulkarni

first: Miles

last: Fontenot


title: SGLT2 inhibitors suppress epithelial-mesenchymal transition in diabetic podocyte via downregulating IGF1R/PI3K pathway

city: Zhengzhou

first: Ruixue

last: Guo

state: Henan

address: No. 1 of Jianshe East Road

department: Nephrology

institute: the First Affiliated Hospital of Zhengzhou University

summary:
Purpose:Renal injury with the loss of podocyte was characteristic pathology of diabetic nephropathy (DN) and correlated with increased albuminuria. Many studies have found the nephroprotective effect of the novel inhibitors of sodium-glucose cotransporter 2 (SGLT2-is), like Dapagliflozin, delaying the progression of DN. However, the underlying mechanisms of SGLT2 associated with podocyte injury are still not fully elucidated.
Methods: Through mRNA sequencing, streptozotocin-induced and Dapagliflozin-intraperitoneal injection mice models were established to explore potential mechanism between Dapagliflozin and renal phenotype. And all changes referring this observed pathway were proven repeatedly in podocyte.
Results: Here, we generated the streptozotocin-induced DN models and found the accumulation of nephrotoxin and pathological lesions of the kidney, including interstitial inflammatory infiltration, mesangial expansion and glomerular sclerosis, while low expression of SGLT2 mitigated these injuries in Dapagliflozin-treated mice. Moreover, mRNA expression profile in these treated models determined the significance of insulin-like growth factor-1 receptor (IGF1R)/PI3K regulatory axis in glomerular injury. Particularly, SGLT2-is inhibited the increase of mesenchymal marker, α-SMA and the decrease of podocyte marker, nephrin at the gene or protein level. KEGG analysis also showed the enrichment of phosphatidylinositol signaling system and TGF-β/smad pathway. In parallel, the protein level of IGF1R, phosphorylated PI3K, and α-SMA were increased in high-glucose stimulated human podocyte, and reduced in Dapagliflozin (50nM and 100nM) or OSI-906 (inhibitor of IGF1R, 60nM) used groups. Notably, combination of the two inhibitors produced an accumulative effect in the protection of podocyte integrity. Mechanistically, IGF1 or IGF2 could bind to IGF1 receptors to mediate the epithelial-mesenchymal transition (EMT) of diabetic podocyte in response to the upregulation of SGLT2. Indeed, we enrolled the urine and plasma samples from a cohort consisting of 13 healthy people, and a cohort of 19 patients with DN using SGLT2-inhibitors (n=9) or not (n=10). Compared with pure DN patients, Elisa results suggested an increased circulation and excretion level of IGF1/2 in SGLT2-is used DN cohort.
Conclusions: Taken together, our study reported the key role of SGLT2/IGF1R/PI3K signaling in regulating podocyte EMT. Modulating the IGF1R expression may provide a novel idea for DN therapy.

overall_design: Renocortical  mRNA profiles of healthy mice (n=6),  Dapagliflozin-used (n=6) and non-Dapagliflozin-used (n=6) diabetic mice.

first: Rui

middle: X

first: Jin

last: Shang