title: Change in macrophages activation in tumour from GSKi pre-treated 4T1 cells 8 days or 14 post fatpad injection in Balb/c mice

status: Public on Jul 13 2022

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

institute: The Francis Crick Institute

summary: Cancer infiltrating macrophages from 4T1 cells pretreated with DMSO or GSKi (5 μM of GSK269962A (Axon, 1167)) for five days

overall_design: macrophages were isolated from enstablished tumours in Balb/c mice

first: Anna

last: Perdrix


title: miRNA Profiles in epithelial ovarian cancer patients

status: Public on Jul 14 2022

city: Jinan

first: Zhen

last: Zhang

address: jingshi 18877

country: China

institute: shandong academy of medical sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: The project aims to reveal the differentially expressed microRNAs in patients with ovarian cancer compared with normal controls.

overall_design: Three unpaired ovary tissues from ovarian cancer patients and controls were used.

first: Xia

last: Li


title: Change in Fibroblast activation in tumour from GSKi pre-treated 4T1 cells 8 days post fatpad injection in Balb/c mice

country: United Kingdom

type: Expression profiling by high throughput sequencing

summary: Cancer infiltrating fibroablas from 4T1 cells pretreated with DMSO or GSKi (5 μM of GSK269962A (Axon, 1167)) for five days

overall_design: Fibroblast were isolated from enstablished tumours in Balb/c mice


title: Expression data from autophagy-deficient keratinocytes and normal keratinocytes

city: Bunkyo-Ku

first: Ge

last: Peng

state: Tokyo

address: 2-1-1 Hongo

country: Japan

institute: Juntendo University Graduate School of Medicine

summary:
There is increasing evidence that autophagy contributes to the epidermal differentiation; however, the role of autophagy in epidermal tight junction (TJ) barrier remains unclear.
To evaluate the role of autophagy in the maintenance of skin TJ barrier, we knocked out autophagy in human primary keratinocytes by infecting cells with autophagy-related gene 3 (Atg3) C264S mutant adenovirus.

overall_design: A total of 4 samples were analyzed and data from autophagy-deficient keratinocytes and normal keratinocytes were compared.

first: Saya

last: Tsukamoto

first: Risa

last: Ikutama

first: Hai

middle: T

last: Nguyen

first: Yoshie

last: Umehara

first: Juan

middle: V

last: Trujillo-Paez

first: Hainan

last: Yue

first: Miho

last: Takahashi

first: Takasuke

last: Ogawa

first: Ryoma

last: Kishi

first: Mitsutoshi

last: Tominaga

first: Kenji

last: Takamori

first: Jiro

last: Kitaura

first: Shun

last: Kageyama

first: Masaaki

last: Komatsu

first: Ko

last: Okumura

first: Hideoki

first: Shigaku

last: Ikeda

first: François

last: Niyonsaba


title: APEX1-regulated alternative splicing of genes involve in lung cancer progression

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Alternative splicing (AS) is particularly relevant to cancer progression and apoptosis. Although previous studies have shown that the apurinic-apyrimidinic endonuclease-1 (APEX1) is involved in tumor progression, it is unclear whether APEX1 can regulate AS on cell proliferation and apoptosis of Non-small-cell lung cancer (NSCLC). We performed a comprehensive analysis of the APEX1 expression in 517 lung NSCLC samples from the TCGA (Cancer Genome Atlas) database, and selected two sets of cancer samples with differentially expression APEX1 to analyze potential APEX1-regulated alternative splicing events (ASEs). Functional analysis of the APEX1 in A549 cells were performed in vitro. The APEX1 was overexpression in A549 cell by gene transfection. We identified AS targets regulated by APEX1, analyzed the GO biological process and KEGG functional pathways, and validated APEX1-regulated ASEs detected by RNA-seq and RT-PCR in A549 cells, then in clinical NSCLC samples these results were verified. The expression of the APEX1 was up-regulated in NSCLC samples, and overexpression of the APEX1 resulted in cell proliferation reduction and apoptosis induction. AS of many genes regulated by the APEX1 were enrich in cancer-related functional pathways. Results from A549 cell model and clinical samples showed that the MAPK signaling pathway, the Wnt signaling pathway were shared among the top ten enriched GO processes and KEGG functional pathways. According to our research, the validated AS events regulated by APEX1 mostly located in genes encoding transcription regulation factor in various signaling pathways, including the AXIN1 (axis inhibition protein 1), GCNT2 (N-acetyl glucosaminyl transferase 2), SMAD3 (SMAD Family Member 3), CTBP2 (C-Terminal Binding Protein 2). In this study, we successfully applied RNA-seq technology to demonstrate APEX1 regulation of AS. Our results underline that APEX1 was efficiently up-regulated in NSCLC samples, while overexpression of the APEX1 in A549 cells resulted in proliferation reduction and apoptosis induction. We confirm that the APEX1 regulates the AS of many genes which involved in cancer proliferation and apoptosis functional pathways, such as the MAPK signaling pathway and the Wnt signaling pathway, leading to mediate lung cancer progression. We found that high expression of the APEX1 in NSCLC is an independent prognostic factor related to tumor progression. Therefore, the APEX1 can serve as a molecular marker or therapeutic target for NSCLC treatment.

overall_design: Alternative splicing analysis of APEX1 overexpression and control in A549 cells and lung adenocarcinoma

first: Li

last: Peng

first: Xujun

last: Ye


title: The dynamic reprogramming of H3K9me3 at hominoid-specific retrotransposons during early human development

city: GuangZhou

first: Hanwen

last: Yu

state: GuangDong

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-*Sen Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

institute: SUN YAT-SEN UNIVERSITY

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Reprogramming of H3K9me3-dependent heterochromatin is required for early development. How H3K9me3 is involved in early human development is, however, largely unclear. Here, we resolve the temporal landscape of H3K9me3 during human preimplantation development and its regulation for diverse hominoid-specific retrotransposons. At the 8-cell stage, H3K9me3 reprogramming at hominoid-specific retrotransposons termed SINE-VNTR-Alu (SVA) facilitates interaction between certain promoters and SVA-derived enhancers, facilitating the zygotic genome activation. In trophectoderm, de novo H3K9me3 domains prohibit pluripotent transcription factors from binding on hominoid-specific retrotransposons-derived regulatory elements for inner cell mass (ICM)-specific genes. H3K9me3 re-establishment at SVA elements in ICM is associated with higher transcription of DNA damage repair genes, compared to naïve human pluripotent stem cells. Our data demonstrate that species-specific reorganization of H3K9me3-dependent heterochromatin at hominoid-specific retrotransposons plays important roles during early human development, shedding light on how the epigenetic regulatory network for early development has evolved in mammals.

overall_design:
We investigated
1) H3K9me3 landscape on the genome of human preimplantation embryos using advanced ultra-low input ChIP-seq (AULIChIP-seq). AULIChIP-seq was performed in two biological replicates of human 4-cell embryo, 8-cel embryo, morula, inner cell mass (ICM) and trophectoderm (TE).
2) H3K9me3 or H3K27me3 landscape on the genome of hESCs and hTSCs using advanced ultra-low input ChIP-seq (AULIChIP-seq) or conventional ChIP-seq. AULIChIP-seq was performed in two biological replicates of hTSCs.
3) transcriptome of abnormal human embryos using SMART-seq2.
4) We investigated H3K9me3 landscape and gene expression of hESCs, prEpiSC and human preimplantation embryos in which the H3K9me3 modification were deposited on SVAs by epigenetic editing system (dCas9-KRAB).
5) genome of abnormal human embryos using WGS.

first: Manqi

first: Ruiqi

last: Li

first: Yuanlang

last: Hu

first: Jichang

last: Wang


title: RNA sequencing of RAI16 KO vs WT NIH3T3 cells

city: Shanghai

first: wen

address: 36 Yunxin Rd.

institute: Tongji University

summary:
RAI16 deficiency could protect cells against cell death induced by serum starvation. Furthermore, it was found that cell adhesion was enhanced in NIH3T3 RAI16 KO cells under serum starvation.
RAI16 deficiency could protect cells against cell death induced by serum starvation. Furthermore, it was found that cell adhesion was enhanced in NIH3T3 RAI16 KO cells under serum starvation.

overall_design: global expression analysis of RNA sequencing data to compare expression levels of RAI16 KO-NIH3T3 cells with Wt-NIH3T3 cells under serum starvation

first: Wen

last: WANG


title: In vitro biocompatibility of ZrO2 vs Y-TZP alloys on Saos-2 cells: influence of composition and surface topography

city: NANCY

first: Laëtitia

last: CHEZEAU

address: Campus Artem, 2 allée André Guinier

department: Institut Jean Lamour

country: France

institute: Université de Lorraine

summary: This study assess the biocompatibility of ZrO2 vs Y-TZP alloys on Saos-2 cells, through the combination of conventional toxicological assay, morphological observations and transcriptomic analysis performed on Saos-2 cells. The biocompatibility of ZrO2 alloys was evaluated in comparison with Y-TZP alloys, studying cell proliferation (WST-1) and cell morphology/adhesion (SEM) on human Saos-2 cell lines. Finally, an evaluation of gene expression was performed on Y-TZP alloys rough surface that seems more interesting regarding biocompatibility results.

overall_design: Changes in gene expression in Saos-2 cells (30 000 cells/mL, total of 180 000 cells for each experiment) incubated without (control) or with yttria zirconia discs with rough (Ra=1 µm) surface states for 96h, were measured. Four biological replicates were performed as controls : T1 ; T2 ; T3 ; T4. Four biological replicates were performed in Saos-2 cells exposed to Y-TZP rough surface discs : E1 ; E2 ; E3 ; E4. A total of 8 samples (microarrays) was used.

last: Chézeau

first: Alex

middle: P

last: Tchinda

first: Gaël

last: Pierson

first: Richard

last: Kouitat

first: Bertrand

middle: H

last: Rihn

first: Pierre

last: Bravetti


title: A multi-omics investigation into the mechanisms of hyper-virulence in Mycobacterium tuberculosis

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University (PolyU)

summary: The result validated the connections between mutations, gene expression and mycobacterial pathogenicity, and identified new possible virulence-associated pathways in M. tuberculosis.

overall_design: We profiled the genome-wide expression pattern for hyper-virulent (H112) and low-virulent strains (H54) during exponential growth in a nutrient-rich condition (7H9 medium) and a physiologically relevant multi-stress condition (NR medium) using RNA-sequencing and label-free quantitative proteomics.

first: Rahim

last: RAJWANI

first: Chala

last: GALATA

first: Pui-kin

last: SO

first: Kenneth

middle: S

last: LEUNG

first: Kingsley

middle: K

last: TAM

first: Sheeba

last: SHEHZAD

first: Timothy

last: Ng

last: ZHU

first: Annie

middle: W

last: LEE

first: Hiu

middle: Y

last: LAO

first: Chloe

last: CHAN

first: Jake

first: Lam-Kwong

first: Kin

middle: C

last: WONGd

first: Wing

last: YAM

first: Gilman

last: SIU


title: Transcriptome analysis of WT and lactoferrin knockout satellite cells grown for 4 days

city: Beijing

first: Xiong

last: Wang

address: No. 17, Qinghua East Road, Haidian District, Beijing

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

summary: Our phenotypic data suggest that lactoferrin knockdown reduces satellite cell proliferative capacity. The mouse muscle tissue was digested with collagenase, and satellite cells were obtained by flow sorting. We performed transcriptome analysis of wt and lactoferrin knockout cells grown for 4 days in vitro.

overall_design: We digested mouse muscle tissue by collagenase and flow-sorted Sca1 -/CD11b -/CD34 +/α7-integrin + satellite cells. After 4 days of in vitro growth, cells were harvested, added with 1 ml Trizol, snap-frozen in liquid nitrogen, and transported to GeneDenovo Biotechnology Co. Data were extracted and normalized according to the manufacturer’s standard protocol.


title: Arginine catabolism and polyamine biosynthesis pathway disparities within Francisella tularensis subpopulations

city: LINCOLN

first: Robert

middle: Bristow

last: Moore

state: NE

address: 1901 vine street

department: Biochemistry

country: USA

institute: University of Nebraska - Lincoln

summary:
Francisella tularensis is a highly infectious zoonotic pathogen with as few as 10 organisms causing tularemia, a disease that is fatal if untreated. Although F. tularensis subspecies tularensis (type A) and subspecies holarctica (type B) share over 99.5% average nucleotide identity, notable differences exist in genomic organization and pathogenicity. The type A clade has been further divided into subtypes A.I and A.II, with A.I strains being recognized as some of the most virulent bacterial pathogens known.
In this study, we report on major disparities that exist between the F. tularensis subpopulations in arginine catabolism and subsequent polyamine biosynthesis. The genes involved in these pathways include the speDEA and aguAB operons, along with metK. In the hypervirulent F. tularensis A.I clade, such as the A.I prototype strain SCHU S4, these genes were found to be intact and highly transcribed. In contrast, both subtype A.II and type B strains have a truncated speA gene, while the type B clade also has a disrupted aguA and truncated aguB. Ablation of the chromosomal speE gene that encodes a spermidine synthase reduced subtype A.I SCHU S4 growth rate, whereas the growth rate of type B LVS was enhanced. These results demonstrate that spermine synthase SpeE promotes faster replication in the F. tularensis A.I clade, whereas type B strains do not rely on this enzyme for fitness. Our ongoing studies on metabolism should provide a better understanding of the factors that contribute to F. tularensis pathogenicity.

sample_organism: Francisella tularensis subsp. tularensis

sample_organism: Francisella tularensis subsp. holarctica

overall_design: Comparative gene expression profiling analysis of RNA-Seq data for F. tularensis subtype A.I strains SCHU S4 and MA00-2987, subtype A.II strain WY96-3418, and type B LVS during mid-log growth in brain heart infusion (BHI) broth.

first: Marilynn

middle: A

last: Larson

first: Khalid

last: Sayood

first: Amirsalar

last: Mansouri

first: Tomas

last: Helikar


title: Flax rust effector transient expression in flax leaves RNA seq

city: Acton

first: Julian

last: Greenwood

state: ACT

address: Linnaeus Way

country: Australia

institute: Australian National University

summary: To investigate theinfluence of Flax rust effectors on gene expression when transiently overexpressed in flax leaves.

overall_design: Agrobacterium containing expression constructs for different flax rust effectors, or an empty vector control, were infiltrated into flax leaves of six week old plants. Infiltrated leaves were harvested at either 24 or 72 hours after infiltration.

first: Greenwood

last: Julian

first: McCombe

last: Carl

first: Akram

last: Ayesha


title: RNA-seq analysis in triple negative breast cancer cells after knocking down DDX18

city: Tianjin

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

summary: To assess the function of DDX18 in TNBCs, we performed transcriptome analysis through high-throughput RNA-Seq of control and DDX18 knockdown cells

overall_design: We knocked down DDX18 in MDA-MB-231 cells and performed the RNA-seq analysis in order to exam the transcriptome after DDX18 knockdown

first: Xianle

last: Shi

first: Xianhui

last: Ruan


title: Brain Region-Specific Gene expression in Exercise for a Mouse Model of Parkinson's Disease

first: Weifang

last: TONG

address: 1239 Siping Road, Yangpu District

institute: Tongji university

summary: Exercise plays an essential role in improving motor symptoms in Parkinson’s disease (PD), but the mechanism in the central nervous system remains obscure. We tested effects of 12-week treadmill exercise on a chronic 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse model of PD and observed a significant improvement in motor ability. Here we performed RNA-sequencing on 4 brain regions from control animals, MPTP-induced PD mice and MPTP-induced PD mice treated with exercise for 12 weeks.

overall_design: RNA-sequencing on 4 brain regions from control animals, MPTP-induced PD mice and MPTP-induced PD mice treated with exercise for 12 weeks were performed

last: Tong

first: Lingjing

last: Jin

first: Yi

middle: E

last: Sun

first: Siguang

last: Li

first: Kunshan

last: Zhang

first: Hongkai

last: Yao

first: Lixi

first: Yong

last: Hu

first: Jingxing

first: Yunping

last: Song

first: Qiang

last: Guan


title: Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer [ChIP-Seq]

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: University of Texas, MD Anderson Cancer Center

summary: We examined the pathways that are regulated by TDO2 in APC-deficient cancer cells by analyzing gene expression profiles of APC-WT and APC-KO MC38 cells that are transduced with inducible shTDO2 constructs. This study establishs that the TDO2-Kyn-AhR axis serves a critical role in promoting APC-deficient tumor growth via cancer cell autonomous (metabolism and proliferation) and non-autonomous mechanisms (tumor immunity).

overall_design: Comparison of ChIP-seq binding peaks for TCF4 on the promoters of TDO2 gene in APC-WT and APC-KO MC38 cells.

first: Rumi

last: Lee

first: Jiexi

first: Ronald

last: DePinho


title: A role for the mitogen-activated protein kinase kinase kinase 1 in epithelial wound healing

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: The mitogen-activated protein kinase kinase (MEK) kinase 1 (MEKK1), also known as MAP3K1, mediates activin B (ActB) signals required for eyelid epithelium morphogenesis during mouse fetal development. The present study investigates the role of MEKK1 in epithelial wound healing, another activin-regulated biological process. In a skin wound model, injury markedly stimulates MEKK1 expression and activity, which are in turn required for the expression of genes involved in extracellular matrix (ECM) homeostasis. MEKK1 ablation or down-regulation by interfering RNA significantly delays skin wound closure and impairs activation of Jun NH2-terminal kinases, induction of plasminogen activator inhibitor (PAI)-1, and restoration of cell-cell junctions of the wounded epidermis. Conversely, expression of wild-type MEKK1 accelerates reepithelialization of full-thickness skin and corneal debridement wounds by mechanisms involving epithelial cell migration, a cell function that is partially abolished by neutralizing antibodies for PAI-1 and metalloproteinase III. Our data suggest that MEKK1 transmits wound signals, leading to the transcriptional activation of genes involved in ECM homeostasis, epithelial cell migration, and wound reepithelialization.

overall_design: Hybridization was performed using 3 x wild type vs Map3k1 ko control, 3x wild type vs Map3k1 ko ActB, 3x  wild type ActB vs Map3k1 ko control and 3x wild type ActB vs Map3k1 ko ActB

first: Ying

last: Xia

first: Jingjing

last: Wang

first: Bo

last: Xiao

first: Maoxian

last: Deng


title: 3D chromatin organization involving MEIS1 factor in the cis-regulatory landscape of GJB2

city: Lausanne

first: Anaïs

last: LE NABEC

address: Station 19

country: Switzerland

institute: EPFL

summary: To study GJB2 gene regulation, we used Circular Chromosome Conformation Capture technique (4C) to analyse chromatin interactions inside DFNB1 locus.

overall_design: We used two viewpoints, GJB2 promoter and C3 enhancer, to detect chromatin interactions.

last: Le Nabec

first: Stéphanie

last: Moisan


title: Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer [array]

overall_design: Transcriptomic analysis of APC-intact and APC-deleted MC38 cell lines after inducible knockdown of TDO2.

last: Li


title: Genetic Encoding of an Esophageal Motor Circuit

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

summary: Motor control of the striated esophagus originates in the nucleus ambiguus (nAmb), a vagal motor nucleus which also contains upper airway motor neurons and parasympathetic preganglionic neurons for the heart and lungs. We disambiguate nAmb neurons based on their genome-wide expression profiles, efferent circuitry, and ability to control esophageal muscles. Our single-cell RNA-sequencing analysis predicts three molecularly distinct nAmb neuron subtypes and annotates them by subtype-specific marker genes: Crhr2, Vipr2, and Adcyap1. Mapping the axon projections of the nAmb neuron subtypes reveals that Crhr2nAmb neurons innervate the esophagus, raising the possibility that they control esophageal muscle function. Accordingly, focal optogenetic stimulation of cholinergic Crhr2+ fibers in the esophagus results in contractions. Activating Crhr2nAmb neurons has no effect on heart rate, a key parasympathetic function of the nAmb, whereas activating all nAmb neurons robustly suppresses heart rate. Together these results reveal a genetically defined circuit for motor control of the esophagus.

overall_design: Single-nuclei RNA-Seq (sNuc-Seq) analysis of 288 samples isolated from the nucleus ambiguus of 27 week old Chat-IRES-cre male mice (C57Bl6/j background) 4 weeks after injection of AAV-DIO-H2b-mCherry into the ventrolateral medulla.

first: Tatiana

last: Coverdell

first: Ruei-Jen

last: Abraham-Fan

first: Chen

first: Stephen

middle: B

last: Abbott

first: John

middle: N

last: Campbell


title: Chronically radiation-exposed survivor GBM cells display poor response to Chk1 inhibition.

city: Istanbul

first: Nareg

last: Pinarbasi-Degirmenci

address: Rumelifeneri Yolu

country: Turkey

institute: Koç University

summary: To investigate radiation response of reccurent glioblastoma models after radiotherapy, we have utilized clinically relevant radioresistant cell model. We have generated to radiation survivor GBM population from 1 cell line and 1 primary cell line. To investigate transcriptomic alterations we have performed RNA-seq to our both naive and IR survivor samples as triplicates.

overall_design: Examining transcriptomic alterations in radiation-survivor and naive GBM cells.

last: Degirmenci

first: Ilknur

last: Erdem

first: Vuslat

last: Akcay

first: Ugur

last: Selek

first: Yasemin

last: Bolukbasi

first: Tugba

last: Bagci-Onder


title: Chronic exposure to waterpipe smoke elicits immunomodulatory and carcinogenic effects in the lung II

first: Humam

last: Kadara

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Previous reports showed that cigarette smoke elicits various molecular and immune changes in the lung. Very little is known of the effects of the chronic consumption of other forms of tobacco, such as waterpipe smoke (WPS), on lung pathobiology. Here, we studied the effects of chronic exposure to WPS versus control air on lungs of tumor-prone mice by RNA-sequencing (RNA-Seq). We find that WPS elicits immunomodulatory changes in the lung that are pertinent to carcinogenesis.

overall_design: WPS or control air (one-hour whole-body exposure session per day for five days per week) for 20 weeks (n = 10 each group). Mice were then followed up for another five months after which lungs were studied by RNA-Seq.

first: Ansam

last: Sinjab

first: Zahraa

last: Rahal


title: Peripheral blood circRNA expression profiles and circRNA-related functions in children with autism spectrum disorder: A preliminary analysis based on circRNA chips

city: Wuxi City

first: Ziyun

last: Zhou

state: Jiangsu Province

address: No. 299, Qingyang Road, Liangxi District

institute: The Affiliated Wuxi Children’s Hospital of Nanjing Medical University, Wuxi, China.

summary: The incidence rate of autism spectrum disorder (ASD) is increasing year by year. Apart from some knowledge of the clinical manifestations of ASD, there has been no significant progress in the study of its pathogenesis and biomarkers. To find biomarkers for early clinical diagnosis, we analyzed the expression profiles of circRNAs in peripheral blood of ASD children. After preliminary screening, among the 160985 circRNA sequences obtained, 461 differentially expressed circRNAs were identified, including 270 up-regulated ones and 146 down-regulated ones. The expression difference of 2 randomly selected circRNAs was verified by qPCR. Gene ontology (GO) and Kyoto Encyclopedia of genes and genomes (KEGG) pathway databases were used for enrichment analysis of biological functions. Dysregulated circRNAs were found abundant in biological functions related to synaptic structure, morphological development, and nervous system development. Pathway analysis suggested that extracellular matrix (ECM) receptor interaction, which is associated with synaptic plasticity and behavior, might be related to ASD. Our circRNA-microRNA interaction analysis showed that most circRNAs had multiple microRNAs binding sites, including miR-146, which might contribute to neuroinflammation of ASD. Our results show that some circRNAs are differently expressed in children with ASD and may take a part in the disease process. The differentially expressed circRNAs in peripheral blood have the potential to serve as biomarkers for early clinical screening of ASD.

overall_design: CircRNA microarray analysis of 8 samples, including 4 from ASD group and 4 from TD group. ASD stands for autism spectrum disorder group and TD stands for typical developmental group.

first: Lei

last: Wang

first: Ping

last: Guan

first: Ying

last: Xu

first: Ruixuan

last: Zheng

first: Yan

last: Yang

first: Lili

last: Zhang


title: Emergence of Resistance to MTI-101 Selects for Favorable MET Phenotype in Lung Cancer

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: MTI-101 is a first-in-class novel cyclic peptide shown to have anti-tumor activity in both multiple myeloma and castrate-resistant prostate in vivo cancer models. These data suggest the potential for a broad spectrum of anti-cancer activity for this class of compounds.  To further delineate determinants of sensitivity and resistance that were not dependent on oncogenic drivers, two isogenic drug resistant cell lines were generated with chronic exposure to MTI-101 in a non-small cell lung cancer (NSCLC) PC-9 (EGFR driven) and a small cell lung cancer (SCLC) H446 (PTEN deleted and c-MYC amplified).  Using the isogenic cell line systems coupled with RNA-SEQ, the top enriched GSEA hallmark was downregulation of genes that contribute to epithelial to mesenchymal transition (EMT), a finding that was consistent in both acquired MTI-101 selected resistant cell lines.  The RNA-SEQ data correlated with predicted changes in the phenotype, including significant decreased invasion in Matrigel and changes of EMT markers (E-Cadherin, Vimentin and Twist) at the protein level.  Furthermore, in the EGFR driven PC-9 cell line, selection for resistance towards MTI-101 resulted in collateral sensitivity toward EGFR inhibitors.  To determine the stability of the MET phenotype, cells were removed from drug and tested for invasion and drug resistance every month. These data indicated that the mesenchymal to epithelial transition (MET) phenotype and genotype was stable for a minimum of six months.  MTI-101 treatment in PC-9 and H446 cells showed synergistic activity with the standard of care agents Erlotinib, Osimertinib, and Cisplatin when used in combination in PC-9 and H446 cells, respectively.  Finally, in vivo data indicates that MTI-101 treatment selects for increased E-Cadherin and decreased Vimentin in H446.  In addition, treatment with MTI-101 decreased incidence of bone metastasis in the PC-9 in vivo model.  Together, these data indicate that MTI-101 treatment could be used as a tool to delay  the emergence of metastatic disease for the treatment of lung cancer.

overall_design: MTI-101 resistant cell lines were developed with chronic exposure to MTI-101 over a 6-month period starting with parentel cell lines PC-9 and H446. We also removed MTI-101 drug pressure for the resistant PC-9 line for a time course up to six months. We applied RNA-Seq to each of the cell lines to profile genome-wide expression.

first: Clark

last: Jones

first: Sebastian

last: Dziadowicz

first: Samuel

last: Suite

first: Ashley

last: Eby

first: Lori

last: Hazlehurst


title: Chronic exposure to waterpipe smoke elicits immunomodulatory and carcinogenic effects in the lung

summary: Previous reports showed that cigarette smoke exposed normal-appearing airways in phenotypically lung cancer-free smokers carry alterations that are characteristic of tumors – suggestive of an airway field of injury. Very little is known of the effects of the chronic consumption of other forms of tobacco, such as waterpipe smoke (WPS), on lung pathobiology. Here we studied normal-appearing airway brushings from waterpipe smokers and those who were not exposed to WPS. We find that WPS elicits a molecular field of injury with gene programs that are pertinent to lung carcinogenesis.

overall_design: Bronchial epithelial brushings from normal-appearing airways were acquired from lung cancer-free and eligible patients during diagnostic bronchoscopy. We performed RNA-sequencing of bronchial airway epithelial brushings from five individuals who never smoked waterpipe and from four waterpipe smokers who smoked at least 100 waterpipes in their lifetime, including during the 12-month period prior to enrollment.


title: RNA-Sequencing based analysis of bovine endometrium during the maternal recognition of pregnancy

city: Honolulu

first: Vedbar

last: Khadka

state: HI

address: 651 IIalo Street

institute: JABSOM Bioinformatics Core, University of Hawaii

summary:
Purpose: Perform RNA-seq study on bovine endometrial tissues during the peri-implantation period (Day16-17 of gestation) to reveal important genes and biological pathways required for conceptus growth and development
Methods:RNA sequencing was done using Illumina NextSeq500. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was not found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. Cleaned reads were aligned against the bovine reference genome (Bos_taurus.ARS-UCD1.2) using HiSAT2. The resulting SAM files were sorted, converted to BAM files using SAMtools. Read counts mapped to bovine gene models were generated using htseq-count script from HTSeq package. Bioconductor DESeq2 was used to get the differentially expressed genes among pregnant vs. non-pregnant (P vs. NP), pregnant vs. cyclic (P vs. C), and non-pregnant vs. cyclic (NP vs. C) groups.
Conclusions: The study demonstrated that the presence of conceptus at Day 15-17 of gestation affects the endometrial gene expression related to endometrial remodeling, immune response, nutrients and ion transporters, and relevant signaling pathways in the caruncular region of bovine endometrium during the maternal recognition of pregnancy.

overall_design: There are 4 Cyclic, 4 Pregnant, 4 Non-Pregnant samples. Differential gene expression between each group (pregnant vs. non-pregnant, pregnant vs. cyclic, and non-pregnant vs. cyclic) are compared.

first: Birendra

last: Mishra

first: Bindu

last: Adhikari


title: Exploration of the transcriptional regulation network of the differentiation of porcine endothelial cells (ECs)

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

summary: To investigate the transcriptional regulation network of the differentiation of porcine ECs, we induced differentiation of porcine iPSCs into ECs using an efficient protocol we previously estabulished. We then performed gene expression profiling analysis using data obtained from RNA-seq of cells at different stages of differentiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cells at different stages of differentiation was performed. Three biological replicates for each condition have been done.

first: Yu


title: IGFBP3 contributes to cell migration and proliferation in an endophytic tongue squamous cell carcinoma cell line

city: Bunkyo-ku

first: Atsushi

last: Kaida

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

summary: We previously found that IGFBP3 mRNA levels are higher in endophytic-type human tongue squamous cell carcinoma (TSCC) that is more invasive and more prone to metastasis than exophytic and superficial types. To investigate the roles of IGFBP-3 in SAS cells that express a fluorescent ubiquitination-based cell-cycle indicator (Fucci).

overall_design: SAS cells expressing Fucci were treated with siRNA for 48 and 72 h. The RNA was extracted from IGFBP3-knockdown and control cells for RNA-Seq.

first: Esther

last: Ng

first: Hitomi

last: Nojima

first: Masahiko

last: Miura


title: RNA-seq analysis of combination effect of H3B-6527 and Lenvatinib treatment in the Hep3B in vivo model

city: cambridge

first: Kun

last: Yu

state: ma

address: 300 Technology Square City

institute: H3 BIOMEDICINE, INC.

summary: To investigate the underlying mechanism of the enhanced combination effect of H3B-6527 and Lenvatinib, we conducted RNA-seq analysis of Hep3B cell line xenograft tumors following treatment of tumor bearing mice with one dose of H3B-6527 or Lenvatinib as single agents or in combination. Principal component analysis and hierarchical clustering of differentially expressed genes (differentially expressed genes with adjusted p value < 0.05) showed two largely separated groups in which vehicle and Lenvatinib samples are close to each other whereas the H3B-6527 and the combination samples show similar pattern (Fig. 4A and 4B), suggesting Lenvatinib at 10mg/kg does not drastically alter transcriptional profiles of tumor cells. We then performed pathway enrichment analysis of differentially expressed genes, which showed bile acid metabolism as the top upregulated pathway in H3B-6527 single-agent group, a well-known selective effect to the FGFR4 signaling pathway (Fig. 4C). E2F targets and MYC targets scored as the top downregulated pathways; an effect that is common among many receptor tyrosine kinases including FGFR4. Combination of H3B-6527 and Lenvatinib showed significant upregulation of hypoxia and glycolysis pathways, consistent with anti-angiogenic effect resulting in lack of oxygen and nutrients in tumor microenvironment (Fig. 4C). Moreover, the combination groups showed stronger effects on E2F targets as compared with the single agent groups, and explains the increased antitumor activity observed in efficacy experiments (Fig. 4D). In summary, the RNAseq analysis provided direct mechanistic evidence for the combined anti-angiogenic and anti-tumorigenic effects resulting in enhanced efficacy.

overall_design: 4 study groups including Vehicle, H3B-6527, Lenvatinib and H3B-6527+Lenvatinib. 3 tumor samples collected for each group for RNAseq analysis

first: Xuesong

last: Zhao

first: Jaya

middle: J

last: Joshi

first: Daniel

last: Aird

first: Craig

last: Karr

first: Chia-Ling

last: Huang

first: Federico

last: Colombo

first: Milena

last: Virrankoski

first: Sudeep

last: Prajapati

first: Anand

last: Selvaraj


title: PCBP-1 regulates the transcription and alternative splicing of inflammation and ubiquitination-related genes in Parkinson’s disease model

city: Urumqi

first: Aishanjiang

last: Yusufujiang

address: Tianchi road 91

department: Neurology

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

summary: In this study, we cloned and constitutively overexpressed PCBP-1 in rat PC12 cells. RNA-seq was performed to analyze PCBP-1-regulated differentially expressed genes (DEGs) and alternative splicing events (ASEs) between control and PCBP1-overexpressed cells. GO and KEGG pathway analyses were performed to identify functional DEGs and alternatively spliced genes. Consequently, we validated PCBP-1-regulated genes using RT-qPCR.Overexpression of PCBP-1 widely regulated the ASE and expression of genes enriched in neuroinflammation and protein ubiquitination, which were also associated with PD pathogenesis. Moreover, RT-qPCR assay verified the PCBP-1-modulated expression of neuroinflammatory genes, like LCN-2, and alternative splicing (AS) of ubiquitination-related gene WWP-2

overall_design: Detecting the expression level of differential genes and alternative splicing after PCBP1 overexpression in PC12 cells by RNA-seq

first: Hongyan


title: High intensity aerobic exercise suppresses cancer growth by regulating skeletal muscle-derived oncogenes and tumor suppressors (Gastrocnemius)

city: Gyeongsan

first: Hyunseok

last: Jee

state: Gyeongbuk

address: 280, Daehak-ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea

country: South Korea

institute: Yeungnam University

summary: High intensity aerobic exercise (90% of the maximum heart rate) can effectively suppress cancer proliferation in vivo. However, the molecular effect of aerobic exercise and its relevance to cancer prevention remains uninvestigated. The mRNA-sequencing technique (mRNA-seq) can provide a genome-wide depiction of gene expression changes by aerobic exercise. Mice with colorectal cancer were subjected to high intensity aerobic exercise, and mRNA-seq analysis was performed on heart, lung, and skeletal muscle tissues to analyze the molecular effects of the exercise in a genome-wide manner. The skeletal muscle-derived genes with exercise-dependent differential expressions were further evaluated for their effects on colorectal cancer cell viability. Regular and high intensity aerobic physical activity in the mice produced positive results in comprehensive parameters (i.e., food intake, weight, and survival rate) compared to those in the control groups (healthy and cancer with no exercise). A heatmap of differentially expressed genes revealed markedly different expression patterns between these groups. RNA-seq analysis of 23,282 skeletal muscle-derived genes identified a number of anticancer effector genes. Knockdown and overexpression of selected anticancer genes significantly repressed CT26 proliferation by 20% (p<0.05). Our finding based on the aerobic exercise cancer mouses model suggest that the high intensity exercise resulted in a global change in gene expression patterns, particularly those that affect cancer cell viability.

overall_design:
Examination of 4 group (i.e., Blue, Green, Pink, and Yellow, each 10 samples of mice)
E - Exercise
T - Tumor

first: Yoosik

last: Kim


title: Bioinformatics analysis of miRNAs and mRNAs network-Xuefu Zhuyu Decoction Exerts Neuroprotection of Traumatic Brain Injury Mice Trough Modulation of MAPK signaling pathway

city: Changsha

first: Xi

middle: Yu

last: Zhou

state: Hunan Province

address: No. 72 Xiangya Road, Changsha City, Hunan Province

institute: Xiangya Stomatological Hospital

summary: Xuefu Zhuyu decoction (XFZYD) is used to treat traumatic brain injury (TBI). XFZYD-based therapies have achieved good clinical outcomes in TBI. However, the underlying mechanisms of XFZYD in TBI remedy remains unclear. The study aimed to identify critical miRNAs and putative mechanisms associated with XFYZD through comprehensive bioinformatics analysis. We established a controlled cortical impact (CCI) mice model and treated the mice with XFZYD. The high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) confirmed the quality of XFZYD. The modified neurological severity score (mNSS) and Morris water maze (MWM) tests indicated that XFZYD improved the neurological deficit (P < 0.05) and cognitive function (P < 0.01). Histological analysis validated the establishment of the CCI model and the treatment effect of XFZYD. HE staining displayed that the pathological degree in the XFZYD-treated group was prominently reduced. The transcriptomic data was generated using microRNA sequencing (miRNA-seq) of the hippocampus. According to cluster analysis, the TBI group clustered together was distinct from the XFZYD group. Sixteen differentially expressed (5 upregulated; 11 downregulated) miRNAs were detected between TBI and XFZYD. The reliability of the sequencing data was confirmed by qRT-PCR. Three miRNAs (mmu-miR-142a-5p, mmu-miR-183-5p, mmu-miR-96-5p) were distinctively expressed in the XFZYD compared with the TBI and consisted of the sequencing results. Bioinformatics analysis suggested that the MAPK signaling pathway contributes to TBI pathophysiology and XFZYD treatment. The present research provides an adequate fundament for further knowing the pathologic and prognostic process of TBI and supplies deep insights into the therapeutic effects of XFZYD.

overall_design: Hippocampus miRNA profiles of 14-day old TBI and XFYZD-treated mice

first: Yang

last: Wang

first: Tao

last: Tang

first: Zhaoyu

last: Yang


title: Trans regulatory evolution of a young microRNA during Drosophila spermatogenesis

city: Guangzhou

first: Yumei

state: Guangdong

address: Haizhu District Xingangxi Road No. 135

institute: Sun Yat-sen University

summary: Both cis and trans regulatory evolution underlies phenotypic innovation and diversification. However, how the nascent trans regulators escape negative pleiotropy, which may constrain their evolution and contribution to adaptation, remain unclear. Here, we compare the testis transcriptomes at single-cyst level between knockout lines of miRNA-983, an adaptively evolving young miRNA, in D. melanogaster and D. simulans, and the replacement line of dme-miR-983 with dsi-miR-983 in D. melanogaster. By distinguishing context effects and miR-983 effects in the framework of cis and trans regulation of gene expression, we demonstrate that miR-983 contributes to interspecific expression divergence in spite of its antagonism with context effects which is often predominant. Gain and loss of miR-983 effects involve distinct gene sets featured in different phases of spermatogenesis, which may help minimize pleiotropy. The magnitude of miR-983 effects is negatively associated with the variability of target gene expression dynamics during spermatogenesis. Moreover, knocking out dme-miR-983 in D. melanogaster affects sperm length and sperm competitive ability, which can be rescued partially by dsi-miR-983. Our results provide empirical evidence for the resolution of negative pleiotropy, and also have broad evolutionary implications for the biological function of trans regulators.

sample_organism:
Drosophila melanogaster
Drosophila simulans

overall_design: mRNA profiles of testes and spermatogenic single cysts for miR-983 related strains (wild types, knockout strains and interspecific gene replacement line) in two sibling species, Drosophila melanogaster and Drosophila simulans

first: Tian


title: Pericyte-derived extracellular vesicle-mimetic nanovesicles ameliorates erectile dysfunction through Lipocalin 2 in the diabetic mice

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

summary: Diabetes mellitus is one of the main causes of erectile dysfunction (ED). Due to neurovascular dysfunction, men with diabetic ED do not respond well to oral phosphodiesterase 5 inhibitors. Pericyte-derived extracellular vesicles-mimetic nanovesicles (PC-NVs) are known to play a role in promoting nerve regeneration in a mouse model of cavernous nerve injury. Here, we report that administration of PC-NVs can effectively promote penile angiogenesis and neural regeneration, thereby improving erectile function under diabetic conditions. We found that PC-NVs can induce endothelial proliferation, migration, and reduce cell apoptosis under diabetic conditions. In addition, PC-NVs induce neural regeneration in STZ-induced diabetic mice in vivo and ex vivo MPG or DRG explants under high-glucose conditions. We found that Lipocalin 2 (Lcn2) is a new target of PC-NVs in this process, indicating that PC-NVs exert their angiogenesis and nerve regeneration effects by activating MAP kinase, PI3K/Akt and suppressing P53 signaling pathway in an Lcn2-dependent manner under diabetic conditions. Our findings provide new conclusive evidence that PC-NVs mediate neurovascular regeneration and erectile function recovery under diabetic conditions through an Lcn2-dependent mechanism. Local administration of PC-NVs may be a promising treatment strategy for the treatment of diabetic ED.

overall_design: HG+HBS (high glucose+HBS), and HG+PC-NVs (high glucose+PC-NVs)

first: Guo

last: Yin

first: Limanjaya

last: Anita

first: Ji-Kan

last: Ryu

first: Jun-Kyu

last: Suh


title: High intensity aerobic exercise suppresses cancer growth by regulating skeletal muscle-derived oncogenes and tumor suppressors (Heart)


title: mRNA expression profiling (QuantSeq3' mRNA) analysis of human glioblastoma cell line U87MG treated with ID Family (ID1, ID2, ID3, and ID4) overexpression

city: Seoul

first: Sang-Hun

last: Choi

address: Anamro 145

department: Biotechnology

institute: Korea University

summary: To understand the changes in the expression of genes in U87MG cells due to ID Family, we analyzed the transcriptome of U87MG cells overexpressing ID Family. As a result, we identify differentially expressed genes patterns so that the signaling mechanism regulated by ID Family in GBM and changes in cells were observed. These mRNA expression profiling analysis results enable an understanding of the signaling mechanism by ID Family in GBM.

overall_design: Transcriptome of U87MG treated with control vector (GFP) and treated with ID Family (ID1, ID2, ID3, and ID4) overexpression vector

first: Seon

last: Lee

first: Hyunggee


title: Transcriptome analysis of long non-coding RNA Smyca knockdown in breast cancer cells

city: Taipei

first: Ruey-Hwa

last: Chen

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: Gene expression profiles of Smyca or Control shRNA expressing MDA-MB 231 cells were generated by Illumna RNA sequencing.

first: Hsin-Yi


title: Knockdown of 15-bp Deletion-type BRAF mRNA Represses Growth of Pancreatic Ductal Adenocarcinoma Cells

city: Tokyo

first: Yoshiaki

last: Kobayashi

address: 2-11-16 Yayoi, Bunkyo-ku

institute: The University of Tokyo

summary: To investigate effects of siRNA with 2'-O-methyl (2'-Ome) modifications on genome-wide off-targetat, we analyzed gene expression profile of HeLa cells transfected by their siRNAs.

overall_design: Total RNAs were extracted from HeLa cells transfected by unmodified or 2'-O-methyl (2'-Ome) modified siRNA and performed microarray analysis.

first: Kumiko

last: Ui-Tei


title: RNA sequencing analysis of human glioblastoma cell line U87MG treated with LMO2 overexpression.

summary: To understand the changes in the expression of genes in U87MG cells due to LMO2, we analyzed the transcriptome of U87MG cells overexpressing LMO2. As a result, we identify differentially expressed genes patterns so that the signaling mechanism regulated by LMO2 in GBM and changes in cells were observed. These RNA sequencing analysis results enable an understanding of the signaling mechanism by LMO2 in GBM.

overall_design: Transcriptome of U87MG treated with control vector and treated with LMO2 overexpression vector

first: Cheol

middle: G

last: Park


title: The effects of Korean Red Ginseng on Di-(2-ethylhexyl) phthalate-induced inflammatory response in endometrial cancer cells

first: Heewon

last: Song

address: 209, Neungdong-ro, Gwangjin-gu

institute: Sejong Univ

summary: Di-(2-ethylhexyl) phthalate (DEHP) is the most common endocrine disrupting chemical used as a plasticizer. DEHP is associated with the development of endometrium-related diseases through the induction of inflammation. The major therapeutic approaches against endometrial cancer and endometriosis involve the suppression of inflammatory response. Korean red ginseng (KRG) is a natural product with anti-inflammatory and anti-carcinogenic effects. Thus, the purpose of this study is to investigate the effects of KRG on DEHP-induced inflammatory response in endometrial cancer Ishikawa cells.

overall_design: Ishikawa cells were pre-treated with KRG for 1 h and treated with DEHP for 8 h.

first: Ji

last: Won

first: Jeonggeun

first: Hee

middle: D

last: Han

first: YoungJoo


title: Human Mesenchymal Stem Cell-derived Knee Joint-on-a-Chip for Disease Modeling and Drug Testing

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Diseases of the knee joint such as osteoarthritis affect all joint elements. A human cell-derived ex vivo model capable of simulating intraarticular tissue crosstalk is desirable for studying etiologies/pathogenesis of joint diseases and testing potential therapeutics. Herein we generated a human mesenchymal stem cell-derived microphysiological joint-on-a-chip system (microJoint), in which engineered osteochondral, synovial, and adipose tissues were integrated into a microfluidics-enabled bioreactor. This novel design facilitated different tissues communicating while still maintaining their respective phenotypes. The microJoint exhibited physiologically relevant changes when exposed to interleukin-1β mediated inflammation, which were similar to observations in joint diseases in humans. The potential of the microJoint in predicting in vivo efficacy of drug treatment was confirmed by testing the “therapeutic effect” of the nonsteroidal anti-inflammatory drug, naproxen, as well as four other potential disease-modifying osteoarthritis drugs. The data demonstrate that the microJoint recapitulates complex tissue interactions, thus providing a robust model for the study of joint pathology and the development of novel therapeutic interventions.

overall_design:
mRNA profiles of 3 types of microtissues engineered from human mesenchymal stem cells and cultured in a microfluidic device that mimics healthy and inflamed human knee joint

MicroTissues used in this study:
AD: engineered adipose tissue
FT: engineered fibrous tissue
OC-O: osseous (bone) component of the engineered osteochondral tissue
OC-C: chondral (cartilage) component of the engineered osteochondral tissue

first: Zhong

last: Li

first: Zixuan

last: Lin

first: Silvia

first: Haruyo

last: Yagi

first: Xiurui

last: Zhang

first: Lauren

last: Yocum

first: Monica

last: Romero-Lopez

first: Claire

last: Rhee

first: Benjamen

last: O’Donnell

first: Eileen

first: Tingjun

last: Hao

first: Meagan

last: Makarcyzk

first: Kek

last: Goh

first: Peter

last: Alexander

first: Bhushan

last: Mahadik

first: John

last: Fisher

first: Stuart

last: Goodman

first: Bruce

last: Bunnell

first: Rocky

last: Tuan

first: Hang


title: Transcriptional regulation of liver lipotoxicity in non-alcoholic steatohepatitis

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

institute: University of Basel

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptional regulation of liver lipotoxicity in non-alcoholic steatohepatitis [ATAC-seq]

summary: Non-alcoholic fatty liver disease is continuum of disorders among which non-alcoholic steatohepatitis (NASH) is particularly associated with a negative prognosis. Hepatocyte lipotoxicity is one of the main pathogenic factors of liver fibrosis and NASH. However, the molecular mechanisms regulating this process are poorly understood. Here, we integrated transcriptomic and chromatin accessibility analyses from human liver and mouse hepatocytes to identify lipotoxicity-sensitive transcription factors. We found that several transcription factors that were activated in liver from NASH patients and by mouse hepatocyte lipotoxicity. Notably, the gene expression linked to lipotoxicity closely correlated with transcriptional patters in fibrosis progression in NASH patients. Collectively, our findings uncovered novel molecular insights into lipotoxicity-induced NASH.

overall_design: Liver tissue was obtained from healthy subjects and NASH patients suffering from obesity and diabetes. In addition, lipotoxicity was investigated in FL83B mouse hepatocytes that were stimulated with bovine serum albumin (BSA) or BSA conjugated with the saturated fatty acid palmitate (PAL) for 24 h. RNA-seq and ATAC-seq was performed with human liver tissue and mouse hepatocytes following PAL stimulation.

first: Christoph

last: Handschin


title: Transcriptional regulation of liver lipotoxicity in non-alcoholic steatohepatitis [RNA-seq]


title: The effects of compression load to the trunk on lipid metabolism in an inactive phase

city: Kawasaki

first: kousuke

last: shimada

state: Kanagawa

address: 3-25-13 Tonomachi

department: Group for Food Functionality Assessment

institute: Kanagawa Institute of Industrial Science and Technology

summary: Hepatic gene expression of compression loading mice were analyzed using DNA microarray. The compression load to trunk affected on  gene expression related to carbohydrate metabolism, lipid metabolism and the immune system.

overall_design: We made the adjustable compression clothes for mice and, ten-weeks-C57BL/6N male mice were attached to adjustable compression clothes, and were divided into two groups (compression group or non-compression group which only wore the clothes). 8hr after compression load to trunk to compression group, we performed transcriptome analysis in liver tissue to investigate the functional mechanism of compression loading.

first: Kousuke

last: SHIMADA

first: Masakatu

last: NOHARA

first: Fumika

last: SHINOZAKI

first: Midori

last: TATSUDA

first: Takayuki

last: WATANABE

first: Asuka

last: KAMEI

first: Keiko

last: ABE


title: 10x single cell sequencing for primary neurons transcriptomes after sevoflurane exposure

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: We thus isolated cortex from mice, with or without sevoflurane exposure, and performed single cell sequencing. Single cell sequencing is a innovative experimental procedures which allows the identification of various subsets of cells in the neverous system after sevoflurane exposure. Isolated cells were concentrated to 1000 cells/uL and approximately 17,000 cells were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which led to expected mRNA barcoding of 10,000 single-cells for each sample. Seurat package was used for cell normalization and regression. Sevoflurane and control groups were aligned and combined using Seurat. Using t-distributed stochastic neighbor embedding (tSNE), 13 cluters of cells were visualized. Cells were assigned to various clusters based on strong expression of specific genes.

overall_design: Examination of 2 different exposure in primary neurons

first: Lei

last: Zhang


title: Krüppel-like factor 2 controls IgA plasma cell compartmentalization and IgA responses

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

country: Germany

institute: Universitätsklinikum Erlangen

summary:
Krüppel-like factor 2 (KLF2) is a potent regulator of lymphocyte differentiation, activation and migration. However, its functional role in adaptive and humoral immunity remains elusive. Therefore, by using mice with a B cell-specific deletion of KLF2, we investigated plasma cell differentiation and antibody responses. We revealed that the deletion of KLF2 resulted in perturbed IgA plasma cell compartmentalization, characterized by the absence of IgA plasma cells in the bone marrow, their reductions in the spleen, the blood and the lamina propria of the colon and the small intestine, concomitant with their accumulation and retention in mesenteric lymph nodes and Peyer’s patches. Most intriguingly, secretory IgA in the intestinal lumen was almost absent, dimeric serum IgA was drastically reduced and antigen-specific IgA responses to soluble Salmonella flagellin were blunted in KLF2-deficient mice.
Perturbance of IgA plasma cell localization was caused by deregulation of CCR9, Integrin chains αM, α4, β7, and sphingosine-1-phosphate receptors. Hence, KLF2 not only orchestrates the localization of IgA plasma cells by fine-tuning chemokine receptors and adhesion molecules but also controls IgA responses to Salmonella flagellin.

overall_design: RNASeq of sorted mesenteric lymph node P1 IgA plasma cells (CD138+ TACI+ IgA+ CD19+ B220+)  from mb1cre(+/-) and mb1cre(+/-);Klf2(fl/fl) mice

first: Sebastian

middle: R

last: Schulz

first: Jens

last: Wittner

first: Wolfgang

last: Schuh


title: Transcriptional profiling identifies white matter changes in eNOS+/- mice I

status: Public on Jul 12 2022

city: Charlestown

first: Mahesh Chandra

last: Kodali

institute: Massachusetts General Hospital / Harvard Medical School

summary: To elucidate the effects of eNOS deficiency at the transcriptional level, we performed RNA-seq on white matter and grey matter regions dissected from the brains of eNOS+/+ and eNOS+/- mice

overall_design: RNA seq was done on the White matter and grey matter regions dissected from the brains of eNOS+/+ and eNOS+/- mice

first: Francesca-fang

last: Liao

first: Zhengjun

last: Wang


title: Transcriptional profiling identifies white matter changes in eNOS+/- mice


title: Mapping of clonal lineages across developmental stages in human neural differentiation

city: Shanghai

first: Zhiwen

last: You

address: 320 Yueyang Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

summary: The cell lineages across developmental stages remains to be elucidated. We developed single-cell split barcoding (SISBAR) to allow clonally tracking single-cell transcriptomes across stages in an in vitro model of human ventral midbrain-hindbrain differentiation. We developed “potential-spective” and “origin-spective” analysis to interrogate the cross-stage lineage relationships, and mapped a multi-level clonal lineage landscape depicting the whole differentiation process. We uncovered many previously uncharacterized converging and diverging trajectories. We demonstrated that a transcriptome-defined cell type can arise from distinct lineages that leave molecular imprints on their progenies, and the multi-lineage fates of a progenitor cell type represent the collective results of distinct rather than similar clonal fates of individual progenitors, each with distinct molecular signatures. Specifically, we uncovered a ventral midbrain progenitor cluster as the common clonal origin of midbrain dopaminergic (mDA) neurons, midbrain glutamatergic neurons, and vascular and leptomeningeal cells, and identified surface markers that can predict its lineage fate after transplantation and improve graft outcomes.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We developed SISBAR method, which integrated virus-mediated cellular barcoding, clonal splitting, and scRNA-seq, to investigate the lineage relationships among cells across developmental stages in hPSC-based neural differentiation. SISBAR works by genetically labelling each progenitor cell with a unique viral barcode at an earlier differentiation stage, followed by limited cell division, and then randomly splitting the cells into two parts. Half of the cells are immediately subjected to scRNA-seq and viral barcode recovery, and the remaining cells are allowed to continue differentiating to a later stage, followed by scRNA-seq and viral barcode recovery. We designed three successive but independent labelling experiments to investigate the lineage relationships between stage I-II (Exp #1), stage II-III (Exp #2), and stage III-IV (Exp #3), respectively.

first: Luyue

first: Wu

last: Wei

first: Yuejun

last: Chen


title: Identification of RNAs regulated by oligoribonuclease

city: Miami

first: Chaitanya

last: Jain

state: FL

address: 1011 NW 15th St

department: Biochemistry and Molecular Biology

institute: University Of Miami

summary: The effect of Oligoribonuclease inactivation on RNA abundance was measured

overall_design: To identify RNAs regulated by oligoribonuclease, I created a temperature sensitive mutant and isolated RNA after temperature shift. The abundance of different RNAs in the wild-type and mutant strains was determined using RNA-Seq.


title: Dysregulation of cell envelope homeostasis in Staphylococcus aureus exposed to solvated lignin

city: Gainesville

first: Kelly

last: Rice

address: 1355 Museum Drive

institute: University of Florida

summary: Lignin is an aromatic plant cell wall polymer that facilitates water transport through the vasculature of plants. Although lignin’s ability to reduce bacterial growth been previously reported, it’s hydrophobicity complicates the ability to examine its biological effects on living cells in aqueous growth media. We recently described the ability to solvate lignin in Good’s buffers with neutral pH, a breakthrough that has allowed examination of lignin’s antimicrobial effects against the human pathogen Staphylococcus aureus. We previously showed that lignin damages the S. aureus cell membrane, causes increased cell clustering, and inhibits growth synergistically with tunicamycin, a teichoic acid synthesis inhibitor. In this current study, additional experiments were performed to better understand the physiological and transcriptomic responses of S. aureus to lignin. Intriguingly, lignin restored the susceptibility of genetically resistant S. aureus isolates to β-lactam antibiotics, dysregulated intracellular pH, and impaired normal cell division. Additionally, RNAseq analysis of lignin-treated cultures revealed a number of gene expression changes related to cell envelope, cell wall physiology, fatty acid metabolism and stress resistance. Altogether, these results represent the first comprehensive analysis of lignin’s antibacterial activity against S. aureus that provide clarity in deciphering the mechanisms of lignin’s antibacterial activity, while supporting the notion that lignin has potential to be repurposed for biomedical applications.

overall_design: Examination of solvated lignin on S. aureus global gene expression at 20 minutes and 2 hours post-treatment, in aerobic Tryptic Soy Broth (TSB) cultures


title: SMAD4 plays acritical role in CD8 T cell cytotoxic function

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University


title: Expression analysis of mice hepatic NMuLi cells treated LNA gapmer ASO containing  nucleobase modification

first: Takao

last: Inoue

address: 3-25-26, Tonomachi

department: Division of Molecular Target and Gene Therapy Products

institute: National Institute of Health Sciences

summary:
Antisense oligonucleotide (ASO) has the potential to induce hybridization-dependent effects by inadvertent binding of ASOs to RNA with sequences similar to that of the target RNA. In the present study, we examined the effects of the nucleobase derivatives introduced into the gapmer ASOs on gene expression.
We performed microarray analysis using NMuLi cells (mouse liver-derived cells) treated with  LNA gapmer ASO containing  nucleobase modification.

overall_design: The NMuLi cells were seeded in 12-well plates (n = 4/group) and transfected with the LNA-gapmer ASOs using Lipofectamine® 2000 according to the manufacturer’s protocol.Cells treated with transfection reagent in the absence of ASO were used as a control. After a further 24 h,  total RNA was isolated.

first: Tokuyuki

last: Yoshida


title: SMAD4 plays acritical role in CD8 T cell cytotoxic function [ChIP-seq]

summary: Transforming growth factor-beta (TGF-β) restrains cytotoxic immune response to maintain self-tolerance and to promote tumor immune evasion. Yet how SMAD4, a central transcription factor component of TGF-β signaling, regulates CD8+ T cell function remains unclear. Here we have demonstrated SMAD4 played a critical role in promoting CD8+ T cell activation and cytotoxic function. SMAD4-mediated transcriptional regulation of CD8+ T cell activation and cytotoxicity is regulated by T-cell receptor (TCR) signaling pathway rather than TGF-β signaling pathway. We described a new mechanism that in TCR-mediated intracellular signal propagation, SMAD4 markedly translocated into the nucleus, upregulated genes that encoding TCR complex subunits and cytotoxic molecules in CD8+ T cells, reinforced the TCR-activation signals through a positive feedback loop. And in this signaling, SMAD4 is phosphorylated by ERK at Ser367 residue. Our study thus demonstrates an essential role of SMAD4 in promoting CD8+ T cell mediated cytotoxic immune responses.

overall_design: SMAD4 ChIP-seq of in vitro activated CD8 T cells

first: Xinwei

last: Liu

first: Xiaohong

last: Zhao


title: Time makes histone H3 modifications drift

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

summary: To disclose the epigenetic drift of time passing, we determined the genome-wide distributions of mono- and tri-methylated lysine 4 and acetylated and tri-methylated lysine 27 of histone H3 in the livers of healthy 3, 6 and 12 months old C57BL/6 mice. The comparison of different age profiles of histone H3 marks revealed global redistribution of histone H3 modifications with time, in particular in intergenic regions and near transcription start sites, as well as altered correlation between the profiles of different histone modifications. Moreover, feeding mice with caloric restriction diet, a treatment known to retard aging, preserved younger state of histone H3 in these genomic regions.

overall_design: Examination of 4 different histone modifications in Formalin-Fixed Paraffin-Embedded (FFPE) liver tissue specimens from 31 mice, at different age and diet conditions.

first: Roman

last: Hillje

first: Lucilla

last: Luzi

first: Stefano

last: Amatori

first: Giuseppe

last: Persico

first: Francesca

last: Casciaro

first: Mirco

last: Fanelli

first: Pier

last: Pelicci

first: Marco

last: Giorgio


title: Analysis of PMK-1 p38 MAPK and PMK-1(D327E) Caspase Cleavage Resistant Mutant and Effect of DAF-16 (FOXO) Mutants on Gene Regulation in C. elegans

city: Dallas

first: Benjamin

last: Weaver

address: 6001 Forest Park Rd

department: Pharmacology

institute: University of Texas Southwestern Medical Center

summary: We identified genes inversely regulated by pmk-1 null mutation and pmk-1(D327E). We also identified genes working through daf-16, working around daf-16 and working independent of daf-16

overall_design: We analyzed total mRNA at the late L4 stage for wild type, pmk-1(km25), pmk-1(D327E), daf-16(m26), daf-16(mgDf50), daf-16(m26);pmk-1(km25) double mutant, daf-16(m26);pmk-1(D327E) double mutant, daf-16(mgDf50);pmk-1(km25) double mutant, and daf-16(mgDf50);pmk-1(D327E) double mutant.   wild type, pmk-1(km25), pmk-1(D327E) had three biological replicates.  Remainder had two biological replicates.

first: B

middle: P

first: Y

first: W

last: Yuan


title: Gene expression profile at single cell level of the lung tissue of the septic mice

status: Public on Jul 11 2022

city: wuhan

first: Fuquan

last: Wang

address: Institute of Anesthesia and Critical Care, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277, Jiefang Avenue, Wuhan 430022, China

institute: wuhan union hospital

summary: Single-cell sequencing of mouse lung tissue from the Sham group, CLP group, CLP+Maresin1 and the CLP-48h group.

overall_design: We used the Cecal ligation and puncture (CLP), the most commonly used method to induce polymicrobial sepsis, to construct the mouse model of septic lung injury.  The mice in Sham group , CLP group,CLP+Maresin1 group were sacrificed 24 hours after operation, while the CLP-48h group were sacrificed at 48 hours after operation.The mice in the CLP+Maresin1 group were administered 1 ng of Maresin1 via the tail vein. The lung tissue samples were collected for subsequent testing and analysis.  Three sham group specimens, three CLP specimens,  three CLP-48h specimens and three CLP+Maresin1 group specimens were mixed for single-cell RNA sequencing. The prepared single cell suspensions was subjected to Magnetic-activated cell sorting (MACS) using Miltenyi mouse CD45 magnetic beads according to the manufacturer's recommendations. The CD45- and CD45+ cell suspensions were mixed 1:1 for single-cell sequencing.

first: Shanglong

last: Yao


title: Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins

city: University

first: Zhiqiang

last: Pan

state: MS

address: 1558 University Ave

institute: USDA-ARS-NPURU

summary:
BCKGROUND: Citral is a phytochemical monoterpene aldehyde that has been reported to be phytotoxic to a number of plant species. When treated in a solution, citral was phytotoxic to barnyard grass, wild oat, redroot pigweed, ribwort, lettuce, and barley, but not active on soybean, rice, maize, wheat, field bindweed, or common purslane. To investigate the mechanism of citral phytotoxicity in plant, we performed transcriptome analysis experiments using the model plant Arabidopsis.
RESULTS: The concentration of citral that inhibited growth by 50% (202 μM) down regulated transcription of 9156 and 5541 genes in roots and shoots, respectively, at the p ≤ 0.001 level after 1 h.  Only 56 and 62 genes in roots and shoots, respectively, were upregulated. In the roots, these effects dissipated after 3 and 6 h, but similar effects began again at 12 and continued until 24 h.  In the shoots, the down regulation increased at 3 h (6239 genes downregulated, vs. 66 upregulated) with the effect decreasing at from 6 to 24 h, with only 1 gene downregulated at 24 h. Of all genes affected in roots at 1 h and shoots at 3 h (times of greatest effect), 6.5 and 9.2 %, respectively, of affected genes were for DNA and RNA binding functions.  Genes for single strand DNA binding proteins (SSBP) WHY1, WHY 2 and WHY3 were strongly downregulated in the shoot up until 12 h after citral exposure.
CONCLUSIONS: Molecular docking analysis suggests a potential binding model of citral with the single-strand binding proteins (SSBPs) WHY1, WHY2, and WHY3, as well as with other transcription factors such as MYC-2, ANAC, and SCR-SHR.  Such an effect could account for the profound and unusual effects on down-regulation of gene transcription.

overall_design: Arabidopsis seedlings (14 days-old) were treated with citral at IC50 concentration (202 µM). After treatment, plants were incubated for 0, 1, 3, 6, 12 and 24 h. Three replicate samples were collected from control plants (0.1% EtOH) and treated plants for each time point.

first: Elisa

last: Graña

first: Carla

last: Díaz-Tielas

first: Adela

middle: M

last: Sánchez-Moreiras

first: Manuel

last: Reigosa

first: María

last: Celeiro

first: Ruben

last: Abagyan

first: Marta

last: Teijeira

first: Stephen

middle: O

last: Duke


title: Next Generation Sequencing to check the enrichment of RIPK1/BAF on chromatin, RIPK1-dependent chromatin state and RIPK1-dependent transcriptome during inflammatory responses.

city: Boston

first: Wanjin

last: Li

state: Massachusetts

address: 240 longwood Ave

department: Cell Biology

institute: Harvard Medical School

summary: RIPK1 is a master regulator of multiple cell death pathways, including apoptosis and necroptosis, and inflammation. Multiple RIPK1 inhibitors have been advanced into human clinical trials as new therapeutics for human inflammatory and neurodegenerative diseases, including ALS and AD. However, while the mechanism of cytosolic RIPK1 in control of cell death has been extensively investigated, how the activation of RIPK1 may promote transcription of proinflammatory cytokines is unclear as a nuclear function of RIPK1 has not been explored, nor is it clear if and how RIPK1 kinase activity may directly mediate inflammation independent of cell death. Here we show that nuclear RIPK1 is recruited by specific transcription factors and binds to the BAF complex on active enhancers and promoters marked by H3K4me1 and H3K27ac. Nuclear RIPK1 mediates the phosphorylation of SMARCC2, a key component of the BAF complex, to promote chromatin remodeling and the transcription of specific proinflammatory genes. Our results suggest that RIPK1 kinase serves a transcriptional coregulator in nucleus that can transmit extracellular stimuli to BAF complex to modulate the chromatin accessibility and directly regulate the transcription of specific genes involved in mediating inflammatory responses.

overall_design:
Chromatin acessibility and transcriptiome in RIPK1D325A/D325A; RIPK3-/- MEFs were analyzed.
p-S166-RIPK1, SMARCC2, BRG1 enrichiment on chromatin in RIPK1D325A/D325A; RIPK3-/- MEFs treated with TNF for 2h, 4h were analyzed.
p-S166-RIPK1, SMARCC2, BRG1 enrichiment on chromatin in spinal cords from ALS mouse model and human patients were analyzed.


title: Inflammatory gene expression associated with advanced myelofibrosis

city: Cambridge

first: David

last: Mooney

address: 58 Oxford Street

institute: Harvard University

summary: Myelofibrosis (MF) is a progressive, bone marrow (BM) malignancy associated with monocytosis, and is believed to promote the pathological remodelling of the extracellular matrix. Here, we show that the pathologic grading of MF was associated with inflammatory gene expression in primary patient samples.

overall_design: The pathology archives at Brigham & Women’s Hospital (BWH) and Massachusetts General Hospital (MGH) was queried to identify patients with myelofibrosis on bone marrow biopsy obtained between 2005 and 2016. Patients diagnosed with myelodysplastic syndrome/MPN overlap disease and those who had progressed to acute leukemia, received treatment with chemotherapeutic agents for prior cancer diagnoses, or had undergone stem cell transplantation were excluded. Histologic review and fibrosis grading were performed by W.W., R.P.H. and O.P. based on consensus, using the 2016 WHO Revised Classification of Myeloid Neoplasms. The study was conducted in accordance with the principles set forth by the Declaration of Helsinki and the requirement for informed consent was waived by the institutional review board.

first: Kyle

middle: H

last: Vining

first: Waihay

last: Wong


title: SMAD4 plays acritical role in CD8 T cell cytotoxic function [RNA-seq]

first: Chen

last: Dong

overall_design: RNA-seq of OVA+ CD8 TILs from WT and Smad4-KO E.G7 tumor bearing mice

first: Xinwei

last: Liu

first: Xiaohong

last: Zhao


title: Effect of gut microbiota colonizing on gene expression in the porcine hypothalamus

city: Rongchang

first: Renli

last: Qi

address: Changlong Road 51#

institute: Chongqing Academy of Animal Science

summary:
To investigate the impact of gut microbiota deleting and colonizing on hypothalamic health and function, the tissue samples from the germ-free (GF) pigs and the GF pigs colonized gut microbiota (CG) are used to perform whole RNA-seq for gene expression analysis
We then performed long RNAs and small RNAs expression profiling analysis using data obtained from the RNA-seq of 3 different hypothalamus samples from the two groups of pigs

overall_design: Comparative gene expression profiling analysis of RNA-seq data in the hypothalamus for the germ free (GF) pigs and the pigs with gut microbiota

first: Xiaoyu

last: Qiu

first: Jing

last: Sun

last: Wang

first: Zuohua


title: White matter damage as a consequence of vascular dysfunction in a spontaneous mouse model of chronic mild hypoperfusion with eNOS deficiency

city: MEMPHIS

first: Zhengjun

state: TN

address: 71 S Manassas Street

institute: University of Tennessee Health Science Center

summary: Vascular cognitive impairment and dementia (VCID) is the second most common form of dementia after Alzheimer’s disease (AD). Currently, the mechanistic insights into the evolution and progression of VCID remain elusive. White matter change represents an invariant feature. Compelling clinical neuroimaging and pathological evidence suggest a link between white matter changes and neurodegeneration. Our prior study detected hypoperfused lesions in mice with partial deficiency of endothelial nitric oxide (eNOS) at very young age, precisely matching to those hypoperfused areas identified in preclinical AD patients. White matter tracts are particularly susceptible to the vascular damage induced by chronic hypoperfusion. Using immunohistochemistry, we detected severe demyelination in the middle aged eNOS-deficient mice. The demyelinated areas were confined to cortical and subcortical areas including the corpus callosum and hippocampus. The intensity of demyelination correlated with behavioral deficits of gait and associative recognition memory performances. By Evans blue angiography, we detected blood-brain barrier (BBB) leakage as another early pathological change affecting frontal and parietal cortex in eNOS-deficient mic. Sodium nitrate fortified drinking water provided to young and middle aged eNOS-deficient mice completely prevented non-perfusion, BBB leakage, and white matter pathology, indicating that impaired endothelium-derived NO signaling may have caused these pathological events. Furthermore, genome-wide transcriptomic analysis revealed altered gene clusters most related to mitochondrial respiratory pathways selectively in the white matter of young eNOS-deficient mice. Using eNOS-deficient mice, we identified BBB breakdown and hypoperfusion as the two earliest pathological events, resulting from insufficient vascular NO signaling. We speculate that the compromised BBB and mild chronic hypoperfusion trigger vascular damage, along with oxidative stress and astrogliosis, accounting for the white matter pathological changes in the eNOS-deficient mouse model. We conclude that eNOS-deficient mice represent an ideal spontaneous evolving model for studying the earliest events leading to spontaneous white matter changes, which will be instrumental to future therapeutic testing of drug candidates and for targeting novel/specific vascular mechanisms contributing to VCID and AD.

overall_design: Bend3 treated with rBMP4 for 8 hr

first: Mahesh

last: Kodali

first: Francesca-Fang

last: Liao


title: Propionate axis in infancy small intestinal eosinophils

city: Yokohama

first: Hiroshi

last: Ohno

address: 1-7-22 Suehiro-cho

institute: RIKEN Center for Integrative Medical Sciences

summary: Evidence has accumulated that gut microbiota and its metabolites, in particular, a short chain fatty acid propionate, are significant contributors to the pathogenesis of a variety of diseases, although little is known regarding its impact on pediatric bronchial asthma, one of the most common allergic diseases in childhood. This study aimed to elucidate whether, and if so how, intestinal propionate during lactation is involved in the development of BA. In order to perform a bias-free and comprehensive genetic screening of intestinal eosinophils, we next performed RNA sequencing analysis on SILP eosinophils sorted from offspring mice of mothers fed with propionate-containing water or control water

overall_design: Comparative gene expression profiling analysis of RNA-seq data for small intestine eosinophils.

first: Takashi

last: Ito

first: Hirosh


title: Comparative RNA-sequencing of Brachypodium distachyon wild-type and bdmute mature leaf zones

city: Bern

first: Michael

last: Raissig

address: Altenbergrain 12

department: Institute of Plant Sciences

institute: University of Bern

summary: Comparative RNA-sequencing of the mature leaf zones in Brachypodium distachyon wild type and bdmute mutants that do not form stomatal subsidiary cells was performed. The aim was to identify genes relevant for subsidiary cell function in B. distachyon.

overall_design: 25 mature zones (25-30mm from base of 2nd leaves) were analyzed per replicate and genotype. 3 replicates per genotype were sequenced, WT1, WT2, WT5 and sid1, sid2, sid5. WT corresponds to the reference genotype and sid (=bdmute) corresponds to the mutant genotype.

middle: T

first: Dominique

last: Bergmann


title: The protective effect of edaravone on TDP-43 plus oxidative stress-induced neurotoxicity in neuronal cells: Analysis of its neuroprotective mechanisms using RNA sequencing

first: Aki

last: Soejima-Kusunoki

address: 1000, Kamoshida-cho, Aoba-ku

institute: Mitsubishi Tanabe Pharma Corporation

summary: Edaravone is a free-radical scavenger drug that was recently approved for the treatment of amyo-trophic lateral sclerosis (ALS), a neurodegenerative disease. A pathological hallmark of ALS is the accumulation of ubiquitinated or phosphorylated aggregates of the 43-kDa transactive response DNA binding protein (TDP-43) within the cytoplasm of motor neurons. This study revealed the efficacy of edaravone in preventing neuronal cell death in a TDP-43 proteinopathy model and analyzed the molecular changes associated with the neuroprotection. The viability of the neuronal cells expressing TDP-43 was reduced by oxidative stress, and edaravone (≥10 μmol/L) protected in a concentration-dependent manner against the neurotoxic insult. Differential gene expression analysis revealed changes among pathways related to nuclear erythroid 2-related-factor (Nrf2)-mediated oxidative stress response in cells expressing TDP-43. In edaravone-treated cells express-ing TDP-43, significant changes in gene expression were also identified among Nrf2-oxidative re-sponse, unfolded protein response, and autophagy pathways. In addition, the expression of genes belonging to phosphatidylinositol metabolism pathways was modified. These findings suggest that the neuroprotective effect of edaravone involves the prevention of TDP-43 misfolding and en-hanced clearance of pathological TDP-43 in TDP-43 proteinopathy.

overall_design: RNA-seq experiment was designed as follows: Control (Group 1); Eda (edaravone) (Group 2); TDP43+EA (ethacrynic acid) (Group 3); and TDP43+EA+Eda (Group 4). According to this study design, cells pellets were sampled from the four groups in triplicate (N=3) and further processed for RNA sequencing.

first: Kinya

last: Okada

first: Ryuta

last: Sito

first: Kazuhiro

last: Watabe


title: Single-cell transcriptomic analysis of honeybee brains identifies vitellogenin as caste differentiation-related factor

city: Kunming

first: Liangliang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

institute: Yunnan University

summary: The honeybee (Apis mellifera) is a well-known eusocial insect. In honeybee colonies, thousands of sterile workers, including nurse and forager bees, perform various tasks within or outside the hive, respectively. The queen is the only fertile female and is responsible for reproduction. The queen and workers share similar genomes, but occupy different caste statuses. We established single-cell transcriptomic atlases of brains from queens and worker subcastes, and identified five major cell groups: Kenyon, optic lobe, olfactory projection, glial, and hemocyte cells. By dividing Kenyon and glial cells into multiple subtypes based on credible markers, we observed that vitellogenin (vg) was highly expressed in specific glial-cell subtypes in brains of queens. Knockdown of vg at the early larval stage significantly suppressed the development into adult queens. We demonstrate vg expression as a "molecular signature" for the queen caste, and suggest involvement of vg in regulating caste differentiation.

overall_design: single-cell transcriptomic atlases of honeybee brains from three castes (nurses, foragers, and queens)

first: Dahua

last: Chen

first: Wenxin

last: Zhang


title: Stable CDK12 knock-out ovarian cancer cells do not show an increased sensitivity to cisplatin and PARP inhibitor treatment

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

summary: We stabily knock-out CDK12 in A2780 cell line and performed RNA-Seq profiling comparing WT and KO conditions.

first: Giovanna

last: Damia

first: Francesco

last: Bertoni


title: HMGA2 project, CRISPR screen

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: sgRNA whole genome library sequencing in OCI-AML5-Cas9 EKO library cells overexpressing HMGA-YFP or control YFP vectors. The goal of this experiment is to identify synthetic lethal and synthetic rescue sgRNAs with regard to HMGA2 overexpression in AML.

overall_design: OCI-AML5-Cas9 EKO library cells were infected with HMGA-YFP or control YFP vectors for 3 days and then treated with DOX for 7 days to induce Cas9 expression. Cells were further expanded for 7 days before DNA extraction. ID sequences of the sgRNAs were amplified by PCR and sequenced.

first: Céline

last: Moison

first: Jalila

last: Chagraoui

first: Jean-Francois

last: Spinella

first: Tara

last: Macrae


title: Transcriptome analysis of methionine restriction or CRISPR knockout of AHCY or MAT2A in Rael cells

first: Rui

last: Guo

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

summary: RNAseq was used to identify host and viral transcriptome changes in methionine restricted Rael cells or Rael cells expressing control, AHCY or MAT2A sgRNAs.

overall_design: For methionine restriction, Rael cells were washed with PBS and then cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.01mM L-methionine for 3 days.  Control cells were cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.1mM L-methionine for 3 days. Control or  methionine restricted cells were then subjected to RNAseq analysis. For CRISPR KO, Rael cells expressing control, AHCY, or MAT2A sgRNAs were subjected to the RNAseq analysis.

first: Benjamin

last: Gewurz


title: Transcriptome analysis of methionine restriction and folate metabolism inhibitor SHIN1 treatment in P3HR-1 cells

summary: RNAseq was used to identify host and viral transcriptome changes in methionine restricted or SHIN1 treated P3HR-1 cells.

overall_design: For methionine restriction, P3HR-1 cells were washed with PBS and then cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.01mM L-methionine for 3 days.  Control cells were cultured in methionine free RPMI-1640 media supplemented with 10% dialyzed FBS and 0.1mM L-methionine for 3 days. Control or  methionine restricted cells were then subjected to RNAseq analysis. For SHIN1 treatment, P3HR-1 cells were treated with 10uM SHIN1 for 3 days. 1mM sodium formate was used to rescue the SHIN1 effects.


title: Epigenetic Landscape of Pediatric Ependymoma Recurrence

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

type: Methylation profiling by high throughput sequencing

summary: Pediatric ependymoma has relatively low frequencies of DNA mutations, which suggest that epigenetics may drive tumors. However, the epigenetic mechanisms for recurrent ependymoma are still poorly understood. Here, we performed longitudinal and comprehensive DNA methylation and gene expression analysis for recurrent pediatric ependymoma tumors from 10 patients, total 46 DNA methylomes (including primary tumors and matched recurrent tumors; normal pediatric brain tissues and PDOX tumors). Both RELA and PFA tumors maintained the subtype DNA methylation signatures during repeated relapses.  We further identified the potential DNA methylation predictors, drivers and boosters and their potential regulated genes for recurrent ependymoma tumors. Increased DNA methylation levels within H3K4me1 enriched regions indicates disturbed functions of LSD1 gene in recurrent ependymoma tumors. Combining novel LSD1 inhibitor SYC-836 with radiation (XRT) significantly prolonged animal survival times in PDOX models of recurrent PFA ependymoma. Our PDOX models provide a unique platform for preclinical testing drugs and development of new therapy for pediatric recurrent ependymoma.

overall_design: DNA methylation and RNAseq analysis on pediatric Ependymoma recurrent tumors

first: Sibo

last: Zhao

first: XiaoNan


title: RNA-seq analysis of hepatocellular carcinoma

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 1610

department: Biostatistics and Data Science

institute: Tulane University School of Public Health and Tropical Medicine

summary: Dysregulation of genes and associated mRNAs plays critical roles in the etiology and progression of hepatocellular carcinoma (HCC). Previous transcriptomic studies of HCC have been largely focused on Asian populations based on microarray platforms. Next generation-based RNA sequencing has provided an unparalleled power and opportunities to comprehensively characterize HCC at the whole transcriptome level.

overall_design: Seventeen fresh frozen HCC samples with paired non-neoplastic liver from Caucasian patients undergoing liver resection or transplant were used for RNA-seq analysis. Pair-wise differential expression analysis was performed on the RNA-seq data to identify genes, pathways and functional terms differentially regulated in HCC vs. non-neoplastic tissues.

first: Liu

last: Yao-Zhong

last: Yongjun


title: Overlap Between Pediatric Nodal Marginal Zone Lymphoma (PNMZL) and Pediatric-Type Follicular Lymphoma (PTFL) : Morphological and Molecular Analysis (CytoScan)

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

type: Genome variation profiling by genome tiling array

summary: Pediatric nodal marginal zone lymphoma (PNMZL) is an unusual and poorly understood primary B-cell nodal neoplasms. Patients are predominantly young males presenting with localized disease. The tumor shows overlapping morphological features with pediatric-type follicular lympgoma. The  alterations involved in the pathogenesis of PNMZL are not known.

overall_design: The aim of this study was to perform a complete genetic characterization of PNMZL. Fifty-two cases (47 males and 5 females; mean age: 17.5 years, range 5-48) were analyzed by copy number (CN) array and next-generation sequencing analyses as whole-exome sequencing and targeted sequencing investigating the state of genes associated with close related entities like adult NMZL, pediatric-type and adult follicular lymphoma.

first: Julia

last: Salmeron-Villalobos

first: Leticia

last: Quintanilla-Martinez


title: Next-generation sequencing reveals miRNA expression profiles of endometrial cancer cells

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

summary: Abundantly expressed oncogenic miRNAs in endometrial cancer cells are identified by next-generation sequencing.

overall_design: miRNA expression profiles of endometrial cancer cells, HEC-1A and Ishikawa, were generated by sequencing using Solexa Ga2x.

first: Chiujung

last: Yang

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: RNAseq of mouse colon epithelial cell fraction in Lingo3, and WT mice

city: Philadelphia

first: De'Broski

last: Herbert

address: 3900 Spruce Street

department: Pathobiology

institute: University of Pennsylvania

summary: The purpose of this experiment is to deep sequence transcripts in WT mice and mice lacking Lingo3, and compare gene expression in the epithelial cells of the colon between wild type and mutant mice. Colon tissue was isolated from each mouse, and epithelial cells were removed from the colon by washing the tissue with 5 mM EDTA + 2.5 mM DTT solution.

overall_design: wild type and Lingo3 mutant mice, 3 replicates for each condition, 6 samples total

first: Kelly

last: Zullo

first: Annabel

last: Ferguson


title: Overlap Between Pediatric Nodal Marginal Zone Lymphoma (PNMZL) and Pediatric-Type Follicular Lymphoma (PTFL) : Morphological and Molecular Analysis

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

platform_organism:
Homo sapiens
Capra hircus
Mus musculus
Cavia porcellus
Ignicoccus hospitalis

overall_design: Refer to individual Series


title: Long Non-Coding RNA and mRNA profiling using High-throughput RNA sequencing in pseudorabies virus type II infected cells

city: Hangzhou

first: Kailun

last: Zhang

address: Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang

institute: Zhejiang University

summary: Pseudorabies, an acute infectious disease caused by pseudorabies virus (PRV), has caused enormous economic losses to the breeding industry in many countries worldwide. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) may play important roles in the antiviral responses. However, little is known about the identification and functions of swine lncRNAs in cellular antiviral responses against PRV II. In this study, we detected the expression profiles of host lncRNAs and mRNAs from PRV-DX, a wild-type (WT) strain of PRV II, and its attenuated gE-TK- PRV-DX infected cells by high-throughput RNA sequencing. Finally, we identified differentially expressed (DE) 664 lncRNAs and DE 7,199 mRNAs from PRV-DX infected cells, and 654 DE lncRNAs and DE 7,149 mRNAs from gE-TK- PRV-DX infected cells when compared to MOCK infected cells, respectively, especially including 469 common DE lncRNAs and 5836 DE mRNAs. Besides 276 DE lncRNAs and 2,272 DE mRNAs between PRV-DX and gE-TK- PRV-DX infected cells were identified. The potential functions of the significant DE lncRNAs were involved in interleukin secretion, axon extension and metabolic process based on the Gene ontology and Kyoto Encyclopedia of Genes and Genomes databases. Taken together, results highlighted the potentials of lncRNA as targets for antiviral therapy and enriched the current knowledge of the mechanisms underlying the interaction between PRV II and its host cells.

overall_design: Examine the different of mRNA and lncRNA expression profiles in PRV-DX, gE-TK-PRV-DX or MOCK infected cells.

first: Yulan

last: Jin

first: Jiyong

last: Zhou


title: The unique establishment  of histone H3 lysine 4 mono-methylation pattern on the promoter regions in early embryo development

status: Public on Jul 10 2022

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road

department: School of life science and technology

institute: Tongji University

overall_design: Histone H3 lysine 4 methylation on promoter regions plays essential roles in transcriptional regulation in mouse early embryo development. Here, we presented the first genome-wide map of H3K4me1 in mouse pre-implantation embryos and observed a unique establishment process of H3K4me1 pattern on promoter regions, which is strongly correlated with active transcription and the broad H3K4me3 domain formation. We further demonstrate that the histone methyltransferase ASH2L contributes to forming the H3K4me1 DIP pattern on the promoter regions in mouse pre-implantation embryos.