title: Nasal DNA methylation differentiates severe from non-severe asthma in African-American (AA) children

city: Davis

first: Hong

last: Ji

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

summary:
Background: Asthma is highly heterogeneous and severity evaluation is key to asthma management. DNA methylation (DNAm) contributes to asthma pathogenesis. This study aimed to identify nasal epithelial DNAm differences between severe and non-severe asthmatic children and evaluate the impact of environmental exposures.
Methods: Thirty-three non-severe and 22 severe asthmatic African-American children were included in an epigenome-wide association study. Genome-wide nasal epithelial DNAm and gene expression were measured. CpG sites associated with asthma severity and environmental exposures and predictive of severe asthma were identified. DNAm was correlated with gene expression. Enrichment for transcription factor (TF) binding sites or histone modifications surrounding DNAm differences were determined.
Results: We identified 816 differentially methylated CpG positions (DMPs) and 10 differentially methylated regions (DMRs) associated with asthma severity. Three DMPs exhibited discriminatory ability for severe asthma. Intriguingly, six DMPs were simultaneously associated with asthma, allergic asthma, total IgE, environmental IgE, and FeNO in an independent cohort of children. 27 DMPs were associated with traffic-related air pollution or secondhand smoke. DNAm at 22 DMPs were altered by diesel particles or allergen in human bronchial epithelial cells. DNAm levels at 39 DMPs were correlated with mRNA expression. Proximal to 816 DMPs, three histone marks and several TFs involved in asthma pathogenesis were enriched.
Conclusions: Significant differences in nasal epithelial DNAm were observed between non-severe and severe asthma in African-American children, a subset of which may be useful to predict disease severity. These CpG sites are subject to the influences of environmental exposures and may regulate gene expression.

overall_design: Bisulfite converted DNA were hybridized to the Illumina Infinium HumanMethylation450 and EPIC beadchips

first: Xue

last: Zhang

first: Jocelyn

last: Biagini


title: HTR1D inhibitor GR127935 suppresses proliferation and migration of gastric cancer via cell cycle arrest and repression of EMT

status: Public on Apr 16 2022

city: shenzhen

first: xinghan

last: jin

address: No. 628, Zhenyuan Road, Xinhu street

country: China

institute: The seventh Affiliated Hospital of Sun Yat sen University

type: Expression profiling by high throughput sequencing

summary: The changes of gene expression of AGS and SGC7901 treated with GR127935(5 μM or 0 μM )

overall_design: 2 differrent cells(AGS and SGC7901) at 2 different drug concentrations(5 μM or 0 μM )

first: Xinghan

last: Jin

first: Huan

last: Li


title: Anti-CD37 radioimmunotherapy with 177Lu-NNV003 synergizes with the PARP inhibitor olaparib in treatment of non-Hodgkin’s lymphoma in vitro

status: Public on Apr 15 2022

city: Oslo

first: Ada

last: Repetto-Llamazares

state: Oslo

address: Kjelsåsveien 168B

department: R&D

country: Norway

institute: Nordic Nanovector ASA

summary: Background and purpose: PARP inhibitors have been shown to increase the efficacy of radiotherapy in preclinical models. Radioimmunotherapy results in selective radiation cytotoxicity of targeted tumour cells. Here we investigate the combined effect of anti-CD37 β-emitting 177Lu-NNV003 radioimmunotherapy and the PARP inhibitor olaparib, and gene expression profiles in CD37 positive non-Hodgkin’s lymphoma cell lines.  Materials and methods: The combined effect of 177Lu-NNV003 and olaparib was studied in seven cell lines using a fixed-ratio ray design, and combination index was calculated for each combination concentration. mRNA was extracted before and after treatment with the drug combination. After RNA-sequencing, hierarchical clustering was performed on basal gene expression profiles and on differentially expressed genes after combination treatment from baseline. Functional gene annotation analysis of significant differentially expressed genes after combination treatment was performed to identify enriched biological processes.  Results: The combination of olaparib and 177Lu-NNV003 was synergistic in four of seven cell lines, antagonistic in one and both synergistic and antagonistic in two, depending on the concentration ratio between olaparib and 177Lu-NNV003. Cells treated with the combination significantly overexpressed genes in the TP53 signalling pathway. However, cluster analysis did not identify gene clusters that correlate with the sensitivity of cells to single agent or combination treatment. Conclusion: The cytotoxic effect of the combination of the PARP inhibitor olaparib and the β-emitting radioimmunoconjugate 177Lu-NNV003 was synergistic in the majority of tested lymphoma cell lines.

overall_design: Seven Non-Hodgkin Lymphoma cell lines, treated with either 177Lu-NNV003, olaparib or the combination of both drugs. Baseline mRNA expression was also measured.

first: Marion

middle: M

last: Malenge

first: Astri

middle: F

last: Maaland

first: Sebastian

last: Patzke

first: Helen

last: Heyerdahl

first: Trond

last: Stokke

first: Anne

middle: H

last: Ree

first: Arne

last: Kolstad

first: Brian

last: Middelton

first: Marcel

last: Nijland

first: Lydia

last: Visser

first: Jostein

last: Dahle


title: Alox5 mediates survival of LSCs, and chemoresistance in AML via LTB4-BLTR signaling

status: Public on Apr 14 2022

city: New York

first: Christopher

middle: Y.

last: Park

state: New York

address: 550 First Avenue

department: Pathology

country: USA

institute: New York University

summary: Acute myeloid leukemia (AML) is characterized by poor clinical outcomes due to high rates of relapse following induction chemotherapy. While many pathogenic drivers have been described in AML, our understanding of the molecular mechanisms mediating chemotherapy resistance remains poor, and initial management of AML continues to rely on standard induction chemotherapy for many patients. Given the importance of identifying new approaches to improve the efficiency of induction therapy in AML, we sought to identify resistance genes to induction therapy in AML and identified ALOX5 is a novel mediator of resistance to anthracycline based therapy.  ALOX5 mRNA is expressed at high levels in AML patient blasts in comparison to normal hematopoietic stem/progenitor cells (HSPCs) and ALOX5 mRNA and protein expression is increased in response to induction therapy. Genetic and pharmacologic perturbations of ALOX5 function in vitro and in vivo confirm that ALOX5 positively regulates the leukemogenic potential of AML LSCs, while ALOX5 loss does not significantly affect the function of normal HSPCs. ALOX5 mediates resistance to daunorubicin (DNR) and promotes AML cell survival and maintenance through its leukotriene (LT) synthetic capacity. Specifically, the ALOX5 dependent resistance phenotype depends on its ability to synthesize LTB4 and bind to the LTB receptor (BLTR). Overall, our studies reveal a previously unrecognized role of LT’s in AML pathogenesis and chemoresistance, and provide a potential novel strategy to enhance the therapeutic efficacy of induction chemotherapy in AML.

overall_design: Leukemic mice were generated by retroviral transduction of mouse HPSCs with the MLL-AF9 oncogene fusion following established protocol. Double FACS-sorted Lin-Sca-1+c-Kit+ cells (LSK) were isolated from the bone marrow of either C57BL/6J WT or Alox5-/- . Following retroviral transduction with MLL-AF9, GFP+ cells were transplanted into irradiated primary C57BL/6J recipients.

first: Sohini

last: Chakraborty

first: Iryna

last: Berezniuk

first: Alec

middle: W

last: Stranahan

middle: Y


title: mRNA profiling on GM-CSF knockout CART19 compared to wildtype CART19 and Ctrl gRNA CART19 produced from normal donors

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

summary: RNA sequencing was performed on three biological replicates of CART19 (GM-CSF wildtype), GM-CSF knockout CART19, and Ctrl gRNA CART19 produced from normal donors.

overall_design: T cells from normal donors were transduced with a replication-incompetent lentiviral vector expressing a second-generation chimeric antigen receptor (CAR) consisting of an anti-CD19 single chain variable fragment (FMC63) fused to 4-1BB and CD3ζ intracellular domains as previously described.  GM-CSF knockout CART19 were also transduced with CSF2 CRISPR Guide RNA in a pLentiCRISPR v2 backbone as previously described.  Ctrl gRNA CART19 were also transduced with non-targeting (Ctrl) guide RNA in a pLentiCRISPR v2 backbone as previously described. RNA was isolated on Day 8 of production.

first: Michelle

last: Cox

first: Claudia

last: Manriquez Roman


title: Derivation of cochlear organoids from human pluripotent stem cells reveals tight transcriptome-structure coupling during organogenesis

city: Indianapolis

first: Eri

last: Hashino

state: IN

address: 980 West Walnut Street

department: Otolaryngology—Head and Neck Surgery

institute: Indiana University School of Medicine

summary: A balance of morphogen gradients during embryogenesis is thought to determine the identity of inner ear end organs. We applied this developmental principle to aggregates of human pluripotent stem cells and found that modulations of Sonic Hedgehog and WNT signaling promote stem cell-derived otic progenitors to express ventral otic markers. Strikingly, these ventralized otic progenitors gave rise to hair cells with short hair bundles comprised of stereocilia arrayed in a geometry reminiscent of cochlear hair cells. Moreover, these ventralized hair cells expressed multiple markers defining outer or inner hair cells in the cochlea. These results reveal that early morphogenic signals are sufficient for not only establishing cochlear gene expression, but also defining structural properties pertaining to the cochlear sensory epithelium.

overall_design: Aggregates of hESCs were subject to 3 different culture conditions to induce otic tissue and hair cell development. 10X Chromium v3' v3 was used to sequence dissociated aggregates at three time points: day 20, day 80, and day 109. Three conditions were examined at day 20, and two conditions were examined at both day 80 and 109.

first: Stephen

middle: T

last: Moore

first: Takashi

last: Nakamura

first: Jing

last: Nie

first: Alexander

middle: J

last: Solivais

first: Yoshimoto

last: Ueda

first: V

middle: S

last: Reddy

first: Daniel

middle: R

last: Romano

first: Benjamin

last: Perrin

first: Rick

last: Nelson

first: Susan

last: Chuva de Sousa Lopes


title: lncSMaRT translational regulation of Spire1, a new player in muscle differentiation

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

summary: Total RNA of DHX36 RIP experiment in Human differentiating myoblasts at DM1 was extracted and subjected to unstranded paired end library prep and sequencing. DHX36 is an ATP-dependent helicase of the DEAH family that is known to be involved in unwinding of G-Quadruplex structures, regulating mRNA metabolism and translation. We demonstrated that mouse DHX36 and the lncRNA lnc-SMaRT are involved in muscle differentiation by translationally regulating G-Quadruplex containing mRNAs (Mlx and Spire1). Here, we characterize the human DHX36 interactome in differentiating myoblasts in order to find out a lnc-SMaRT analogous gene.

overall_design: INPUT, DHX36 IP and IgG samples were collected from human myoblasts at day 1 of differentiation

first: Scalzitti

last: Silvia

first: Setti

last: Adriano

first: Colantoni

last: Alessio

first: Lisi

last: Michela

first: Mariani

last: Davide

first: Martone

last: Julie


title: TNFR2/14-3-3ε signaling complex instructs macrophage plasticity in inflammation and autoimmunity

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

summary: To elucidate the molecular mechanisms by which 14-3-3ε and PGRN regulates macrophage plasticity, we performed unbiased RNA-seq on BMDMs isolated from WT, PGRN-/- and 14-3-3ε-/- mice stimulated with pro-inflammatory LPS/IFNγ or anti-inflammatory IL-4.

overall_design: mRNA frofiles of WT, PGRN-/- and 14-3-3e-/- BMDMs polarized to M1 or M2 macrophages

first: Wenyu

last: Fu

first: Wenhuo

last: Hu

first: Chuanju

last: Liu


title: ADAPTATION AND RESPONSE OF KOBRESIA LITTLEDALEI TO COLD STRESS

city: Wuhan

first: Zhou

last: Jian

address: Wuhan China

institute: AJBK

summary: This study presents an integrated transcriptome sequencing to identify how Kobresia littledalei plants mount their responses and initiate acclimation against cold stress. Several significant DEGs and metabolic responses were categorized.  By execution of BLAST analysis of the all genes against selected protein databases like Nr, Swiss-Prot, KEGG and COG, we got functional annotations and classifications. The large number of transcriptomic sequences and their functional annotations provide sufficient resources for future molecular studies. Moreover, information on the KEGG metabolic pathways and transcription factors will facilitate the discovery of other cold resistant genes. Importantly, our findings herein further the general understanding of Kobresia plants adaptation and responses to cold stress through the molecular mechanisms involved in signal regulation and cold resistance.

overall_design: Kobresia plants (Kobresia littledalei) were randomly picked from natural field grounds in Tibet and afterwards transplanted into a nursery bed for recovery. The grass patches were grown in pots for 7 days in a 25℃ greenhouse. Thereafter, the grass pots were sub-divided into 6 batches and moved to a -5℃ cryogenic treatment room; where each grass pot (Kli-0 to Kli5) was exposed to different cold treatment timelines.Kli-0, Kli-1, Kli-2, Kli-3, Kli-4, Kli-5 were treated for 0 hour, 0.5 hours, 4 hours, 12 hours, 24 hours, 48 hours respectively.All treatments were performed in triplicates.Total RNA from each sample were extracted and sequenced.

first: Guangpeng

last: Qu

first: Yuhong

last: Bao


title: Ectopic expression of long noncoding RNA AI662270 led to differential gene expression in mouse mesangial cell line SV40 MES13

status: Public on Apr 13 2022

city: Nanjing

first: Yuhui

last: Zang

address: 163 Xianlin Road

institute: Nanjing University

summary: We generated the SV40 MES13 subline stably expressing long noncoding RNA AI662270 and performed transcriptome RNA sequence.

overall_design: Total RNA was extracted from SV40 MES13 subline cells with TRIzol reagent. The RNA purity and integrity were analyzed with the Agilent Bioanalyzer 2100 (Agilent). The mRNA was purified from total RNA after removal of rRNA and sequenced on an Illumina Hiseq2000 system.

first: Yanyan

last: Sun

first: Junfeng

last: Zhang


title: Single-cell analysis reveals gene expression profiles and cell types in wooden breast myopathy

city: Changsha

first: Kelang

last: Kang

state: Hunan

address: No.1 Nongda Road, Furong District, Changsha, China

institute: Hunan Agriculture University

summary: Wooden Breast (WB) is a novel myopathy affecting the pectoralis major muscle of modern broiler chickens. We selected pectoralis fillet samples, a normal(healthy) fillet and a WB fillet.

overall_design: Normal fillets and severe WB fillets  were dissociated with enzymatic digestion with collagenase I for 30 minutes at a concentration of 0.15 g per 100 mL. Then single-cell suspension were obtained by passing the dissociated cell suspensions through a 40 μm cell strainer. All isolated cells were applied to magnetic bead separation method to remove dead cells. Then trypan blue (Thermo Fisher Scientific, waltham, MA, USA) and Automated Cell Counter (TC 20TM, BIO-RED Inc., CA, USA) were used to evaluate the viability of filtrated single cells. Noteworthy, the lipid cells were excluded. Following counting, the appropriate volume was calculated for a target capture of 8000 cells. Samples below the required cell concentration as defined by the user guide were pelleted by beads containing cell Barcode, and then formed as Gel Bead-in-Emulsions. Therewith, reverse transcription and RT-PCR reaction performed in those beads, and cDNA library construction were made using the 10x Genomics Single Cell v2 kit following the 10x Genomics protocol. Libraries were sequenced on the Illumina NovaSeq 6000 system.

first: Zehe

last: Song

first: Xi

last: He


title: Chidamide suppresses adipogenic differentiation of bone marrow derived mesenchymal stem cells

city: Jining

first: Mingtai

last: Chen

state: China

institute: Affiliated Hospital of Jining Medical University

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

summary: To explore the potential mechanism of chidamide in BM-MSC-mediated adipogenesis, we have employed mRNA microarray expression profiling platform to identify significant differential genes associated with adipogenic differentiation and chidamide management.

overall_design: BM-MSCs were untreated (UN) or induced towards adipogenic differentiation (AD) simultaneously added with DMSO (DMSO) or chidamide (CHI) for 8 days. Then the four groups of cells were collected and mRNA microarray was performed.

first: Xianning


title: Single cell RNA sequencing analysis of mouse skin samples with multiple conditions (10x scRNA-seq)

city: New Haven

first: Rihao

state: CT

address: 300 George Street

institute: BBS Program, Yale University

summary: Single cell RNA sequencing of embryonic mouse dorsolateral skin were microdissected. All live cells were collected and submitted in bulk for droplet-based cDNA library preparation (9000 cells/sample)

overall_design: 3 embryos at indicated embryonic days per condition were pooled and FACS sorted for all live cells. Each sample represents one experiment with littermate control and indicated mutations.

first: Peggy

last: Myung


title: Inhibitory mechanism of combined hydroxychavicol with epigallocatechin-3-gallate against glioma cancer cell lines: A transcriptomic analysis

city: Sungai Buloh

first: Amirah

last: Abdul Rahman

state: SELANGOR

address: Sungai Buloh Campus, UiTM Cawangan Selangor

department: Dept. of Biochemistry & Molecular Medicine

country: Malaysia

institute: Universiti Teknologi MARA

summary: We reported the molecular mechanisms of low combination doses of epigallocatechin-3-gallate and hydroxychavicol (EGCG+HC) in glioma cell lines 1321N1 and LN18. Using high throughput RNA sequencing, combined EGCG+HC exerted its anticancer effect by downregulating the axon guidance process and metabolic pathways, while simultaneously interfering with endoplasmic reticulum unfolded protein response pathway. Furthermore, EGCG+HC exerted its apoptotic effect through the alteration of mitochondrial genes such as MT-CO3 and MT-RNR2 in 1321N1 and LN18 cells respectively. EGCG+HC dynamically altered DYNLL1 alternative splicing expression in 1321N1 and DLD splicing expression in LN18 cell lines.

overall_design: Transcriptomic profiles of glioma cell lines (1321N1, LN18) treated with EGCG+HC, EGCG, HC and vehicle control

first: Wan

middle: Z

last: Wan Ngah

first: Rahman

last: Jamal

first: Suzana

last: Makpol

first: Roslan

last: Harun

first: Norfilza

last: Mokhtar


title: Single-cell transcriptome comparison of bladder cancer revels its ecosystem

city: Shenzhen

first: Yongxiang

last: Luo

state: Guangdong

address: 47 Youyi Road, Luohu District, Shenzhen

institute: The Third Affiliated Hospital of Shenzhen  University

summary: To comprehensively understand the biological significance behind different grades of bladder cancer, we screened samples of different grades of bladder cancer and glandular cystitis from three patients for single-cell sequencing. In this study, We found that N-Glycan biosynthesis pathway was activated in high-grade bladder cancer while TNF-related pathway was activated in cystitis glandularis. More importantly, We discovered that N-Glycan biosynthesis is a potential target by cell assay and inhibition of this pathway may contribute to the treatment of bladder cancer.

overall_design: The three primary bladder cancer samples, one recurrent bladder cancer sample and one cystitis glandularis bladder sample from 3 patients were collected for single-cell RNA sequencing.

first: Y

first: T

last: Tao


title: Popliteal adipocytes from mice infected with Listeria monocytogenes

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

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

overall_design: Refer to individual Series


title: Interleukin enhancer-binding factor 2 promotes cell proliferation and DNA damage response in metastatic melanoma

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary:
This study aimed to understand the role of ILF2 upregulation in metastatic melanoma cutaneous progression and DNA damage response.
The goal of RPPA analysis was to determine the protein expression profiles in DP-0574 and IM-0223 melanoma cell lines with ILF2 overexpression (ILF2-OV) or control empty vector (EV). By analysis of RPPA in both metastatic melanoma cell lines, we found that ILF2-OV controls significantly increased RAD50 expression.

overall_design: RPPA profiles for DP-0574 and IM-0223 cell lines with ILF2 overexpression (ILF2-OV) or control empty vector (EV) were generated in triplicates.

first: Zhang

last: Xiaoqing

first: Matias

middle: A

last: Bustos


title: Popliteal adopose tissue tromal vascular fraction cells from mice infected with L. monocytogenes

summary: A wild type strain of Listeria monocytogenes (L. mono) was used for infections. Mice were infected subcutaneously on the footpad with a sublethal dose of 1 × 106 colony-forming units (CFU). Mice were left for 2 days before being sacrificed. Control cells were from either PBS injected mouse or from the uninjected leg of infected animal.

overall_design: Stromal vascular fraction cells from adipose tissue were isolated and single live cells were purified and sequenced using the 10X Genomics Chromium controller. One sample per condition was used.

first: George

last: Caputa

first: Mai

last: Matsushita

first: David

middle: E

last: Sanin

first: Edward

last: Pearce

first: Erika

middle: L


title: The transcriptome of Pa1-/-  and Pa1F/F Sertoli cells purified from 20d-old mice testes

city: Xi'an

first: Bo

last: Liu

address: No.169 Changle West Road

institute: the Fourth Military Medical University

summary: The blood-testis barrier (BTB) is essential to the microenvironment of spermatogenesis, and Sertoli cells provide the cellular basis for BTB construction. Numerous nuclear transcription factors have been identified to be vital for the proper functioning of Sertoli cells. PA1 has been reported to play important roles during diverse biological processes, yet its potential function in male reproduction is still unknown. Here, we show that PA1 was highly expressed in human and mouse testis and predominantly localized in the nuclei of Sertoli cells. Sertoli cell-specific Pa1 knockout resulted in an azoospermia-like phenotype in mice. The knockout of this gene led to multiple defects in spermatogenesis, such as the disorganization of the cytoskeleton during basal and apical ectoplasmic specialization and the disruption of the BTB. Further transcriptomic analysis, together with Cut-Tag results of PA1 in Sertoli cells, revealed that PA1 could affect the expression of a subset of genes that are essential for the normal function of Sertoli cells, including those genes associated with actin organization and cellular junctions such as Connexin43 (Cx43). We further demonstrated that the expression of Cx43 depended on the interaction between JUN, one of the AP-1 complex transcription factors, and PA1. Overall, our findings reveal that PA1 is essential for the maintenance of BTB integrity in Sertoli cells and regulates BTB construction-related gene expression via transcription factors. Thus, this newly discovered mechanism in Sertoli cells provides a potential diagnostic or even therapeutic target for some individuals with azoospermia.

first: Chao

first: Sai

last: Xiao

first: Wei

last: Li

first: Zhen


title: Genome-wide maps of PA1-bound sites in mice Sertoli cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Blood-testis barrier (BTB) is essential to the microenvironment of spermatogenesis, and Sertoli cells provide the cellular basis for BTB construction. Numerous nuclear transcription factors have been identified to be vital for the proper functions of Sertoli cells. PA1 has been reported to play important roles during diverse biological processes, while its potential function in male reproduction is still unknown. Here, we show that PA1 was highly expressed in human and mouse testis and predominantly localized in the nuclei of Sertoli cells. Sertoli cell-specific Pa1 knockout resulted in azoospermia-like phenotype in mice. The knockout of this gene lead to multiple defects in spermatogenesis, such as the disorganization of cytoskeleton at basal and apical ectoplasmic specialization and the disruption of the BTB. Further transcriptomic analysis together with Cut-Tag results of PA1 in Sertoli cells revealed that PA1 could affect the expression of a subset of genes which are essential for the normal functions of Sertoli cells including those genes associated with actin organization and cellular junction such as Connexin43 (Cx43). We further demonstrated that the expression of Cx43 depended on the interaction between JUN, one of the AP-1 complex transcription factors, and PA1. Overall, our findings firstly revealed that PA1 is essential to the maintaining of BTB integrity in Sertoli cells, it regulates BTB construction-related gene expression via interacting a transcription factor, thus providing a potential diagnostic or even therapeutic target for some azoospermia patients.

overall_design: Examination of PA1-bound sites in mouse Sertoli cells.


title: SETDB1 interactions with PELP1 contributes to breast cancer endocrine therapy resistance via Akt activation

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: In this study, we examined the mechanisms by which SETDB1 regulate the cell viability of estrogen receptor (ER) positive breast cancer cells. MCF7 cells were stably transfected with non-targeted shRNA or SETDB1 shRNA  via lentiviral transduction. Total  RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that SETDB1 regulates the expression of subsets of genes involved in ER-and Akt-signaling.

overall_design: Total RNA from MCF7 control-shRNA and SETDB1-shRNA cells were isolated using RNeasy mini kit (Qiagen). For whole-genome transcriptome profiling, 2 libraries (3 replicates each for knockdown and control) were generated from total RNA from non-targeted shRNA and SETDB1-shRNA transfected MCF7 cells, using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.). Samples were sequenced on the Illumina HiSeq 3000 platform (Illumina Inc.) using the 50 base-pair single-read (50SR) sequencing module.

first: Ratna

middle: K

last: Vadlamudi

first: Zhao

last: Lai


title: PA1 Participates in the Maintenance of Blood-Testis Barrier Integrity via Cooperation with JUN in the Sertoli Cells of Mice


title: Transcriptomic data on the response of macropohages to monosodium urate crystals (MSUc)

city: La Jolla

first: Isidoro

last: Cobo

address: Dept. of Cellular & Molecular Medicine, GPL210 9500 Gilman Drive, MC 0651

department: Cellular and Molecular Medicine

institute: University California San Diego

summary: We dissect the mechanism of how MSUc activate a distinct inflammatory and metabolic program in macrophages by regulating JUN-JNK.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Seq data on mouse BMDM and human mDM treated with control PBS, LPS or MSUc in the presence or absence of JNKi or SLC2A1 Bay-876

first: Monica

last: Guma

first: Christopher

last: Glass


title: Expression analysis of human pure squamous cell carcinoma of the bladder (Pure SCC) and muscle-invasive urothelial carcinoma without squamous differentiation (MIBC non-SD)

city: Leeds

first: Margaret

last: Knowles

address: Beckett Street

country: United Kingdom

institute: University of Leeds

summary:
Expression data derived from this analysis was used to compare expression features of pure bladder SCC and MIBC non-SD samples
In this dataset, we include the expression data obtained from 16 Pure SCC and 18 MIBC non-SD samples

overall_design: 34 bladder tumour samples were analysed on the Affymetrix HTA 2.0 platform

first: Carolyn

middle: D

last: Hurst


title: CRISPR screen identifies loss of IFNγR signaling and downstream adhesion as a resistance mechanism to CAR T-cell cytotoxicity in solid tumors

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

state: MA

address: 75 Ames St

institute: Broad Institute

summary: U87-CBG-GFP cells selected with blasticidin to stably express Cas9 were transduced with an MOI (< 1) of Brunello guide library (with puromycin resistance in the guide backbone). Cells were rested for 2 days then selected with puromycin antibiotic until the control, untransduced arm was killed (6-7 days). The guide-transduced cells were then pooled and replated in preparation for the screen. There were 12 arms to the screen, two control arms performed in technical duplicate and 8 sample arms from 6 normal donor CAR T-cells (2 were run in technical duplicate). At the time of CAR T-cell addition 2 arms were taken down as technical duplicates to measure guide frequency at the beginning of the screen. 2 additional arms received no CAR T-cells to serve as proliferation controls and were passaged the same as the sample CAR T conditions about to be described. CAR T-cells were added at a 1:10 effector:target cell ratio. After 18 hours of co-culture the CAR T-cells were removed by aspiration and the tumor cells were gently rinsed 4 times with PBS to remove any remaining CAR T-cells. The tumor cells were then passaged so that any remaining dying cells would not survive. After a 2-day recovery period, the tumor cells were rinsed once with PBS and harvested. Their DNA was isolated (NucleoSpin Blood XL, Macherey-Nagel) and prepared for PCR (Onestep PCR Inhibitor, Zymo Research) prior to processing for guide PCR amplification and sequencing by the Genetic Perturbation Platform (GPP) facility at the Broad Institute based on Broad recommended preparation protocols.

overall_design: Genome wide CRISPR knockout screen in glioblastoma was utilized to identify mechanisms of resistance to CAR T cell cytotoxicity via loss of a single gene.

first: Rebecca

last: Larson

first: Kai

last: Stewart


title: Stanniocalcin 1 promotes metastasis by enhancing lipid metabolism via FOXC2/ITGB6 signaling axis in ovarian cancer

city: Shanghai

first: Feikai

last: Lin

address: No. 1665, Kong Jiang Road

institute: Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: Stanniocalcin 1 (STC1) plays an integral role in the metastasis of ovarian cancer. However, the functional role of STC1 in lipid metabolism is not fully understood. Single-cell sequencing assays verified that STC1 expression was significantly enhanced in ovarian cancer tissues compared with para-carcinoma tissues, and it was further up-regulated in peritoneal metastasis tissues compared with tumor tissues. In vitro and in vivo experiments demonstrated that STC1 promoted cell proliferation and metastasis by enhancing lipid metabolism. Mechanistically, STC1 directly bound to integrin β6 (ITGB6) and activated the PI3K signaling pathway. Moreover, STC1 was directly regulated by FOXC2 and FOXC2 was up-regulated and positively correlated with STC1 in ovarian cancer. Notably, STC1 knockdown had a synergistic effect with cisplatin (DDP) chemotherapy.Overall, these findings reveal that STC1 increases metastasis by promoting lipid metabolism via the FOXC2/ITGB6 signaling axis and may be a potential target for chemotherapy-resistant ovarian cancer.

overall_design: Single-cell sequencing was performed to reveal STC1 expression profiles in patients’ tissues. Lipid metabolism and metastasis were tested subsequently. Cell-based in-vitro and in-vivo assays were subsequently conducted to gain insight into the underlying mechanism of STC1 in ovarian cancer.

first: Xiaoduan

first: Xinjing

last: Wang

first: Huizhen

last: Sun

first: Ziliang

first: Xipeng


title: Female and Male C57Bl/6J Offspring Exposed to Maternal Obesogenic Diet Develop Altered Hypothalamic Energy Metabolism in Adulthood

city: Minneapolis

first: Megan

last: Paulsen

address: 2450 Riverside Avenue, S AO-401

department: Pediatrics

institute: University of Minnesota

summary:
Purpose: Study a cohort of C57Bl/6J dams, treated with a control or high-fat-high-sugar diet, and their adult offspring to explore potential hypothalamic mechanisms to explain the link between maternal and offspring obesity.  Hypothalamic differential gene expression analysis was conducted following next-generation sequencing (NGS) and analyzed in Ingenuity Pathway Analysis.  This methodology was supplementary to in vivo studies which characterized offspring metabolic phenotype.
Methods: Total RNA was extracted from a subset of offspring hypothalamus tissue using a RNeasy Mini Kit (Qiagen, Germantown, MD). Tissues were homogenized in RLT buffer using mechanized syringe homogenization. RNA was assessed for purity and concentration using the NanoDrop (NanoDrop Technologies). Approximately 4ug of total RNA was used to generate cDNA by reverse transcription using a cDNA synthesis kit (Applied Biosystems, Carlsbad, CA).
Results: There were 31,637 differentially expressed genes in adult OB offspring hypothalamus compared with control diet.  Of the identified differentially expressed genes, there were 2510 differentially expressed genes that were significantly different between CON and OB offspring (Supplemental Table 3).  In OB offspring, 65% of the identified differentially expressed genes were downregulated whereas 35% were upregulated.
Conclusions: Collectively, data demonstrate that maternal obesity without diabetes is associated with adiposity and decreased hypothalamic energy production.

overall_design: Hypothalamus mRNA profiles of 4-month old C57Bl/6J mice exposed to maternal control and obesogenic diets

first: Juan

last: Abrahante


title: A comparative kidney transcriptome analysis of bicarbonate-loaded insrr-null mice

city: Moscow

first: Daniil

middle: M.

last: Bobrovskiy

address: Leninskiye Gory, MSU, 1-73, Faculty of Bioengineering and Bioinformatics, office 433

country: Russia

institute: Lomonosov Moscow State University

summary: The maintenance of physiological pH level is critical for the life of all organisms. Well known, that kidney is key organ for acid-base regulation in vertebrates. Metabolic alkalosis is the most common acid-base disorder in hospitalized patients, particularly in the surgical critical care unit. The receptor tyrosine kinase IRR (insulin receptor-related receptor), a receptor like the insulin receptor, is involved in acid-base regulation by kidney due to its ability to autophosphorylate under alkalization of extracellular medium (pH > 7.9). IRR expressed in only β-intercalated cells. In mice with a knockout of the insrr gene, which encoding IRR, bicarbonate secretion to the urine is impaired. Here for the first time, we present analysis of kidney transcriptomes from wild type and insrr gene knockout mice under basal or bicarbonate-loaded conditions by 250 mM NaHCO3 in drinking water. Analysis of NGS sequencing data revealed changes in the expression of a number of genes in the kidney. Using real-time PCR we confirmed change of expression of the slc51b, slc26a4, rps7, slc5a2, aqp6, plcd1, gapdh, rny3, lypd2, kcnk5, slc6a6  , atp6v1g3 genes in IRR knockout mice. Also, we found that expression of kcnk5 gene is increased in wild type mice after bicarbonate loading but didn’t change in knockout mice. Gene set enrichment between the IRR knockout and wildtype samples identified that knockout causes alterations in expression of genes related mostly to the ATP metabolic and electron transport chain processes. Thus, for the first time, we described some details of the functioning of the IRR in the kidneys.

overall_design: Mouse kidney RNA-seq Wild Type and IRR(-/-) mouse with bicarbonate loading and no treatment

first: Igor

last: Deyev

first: Elena

last: Gantsova


title: Gene expression profile at single cell level of FACS sorted CD8+ T cells from subcutaneous MB49 tumors from male and female mice

city: Columbus

first: HYUNWOO

last: KWON

state: OH

address: 460 W 12th Ave

institute: The Ohio State University

summary: Tumor-infiltrating CD8+ T cells are phenotypically heterogeneous with varying degrees of functional defects. We used single cell RNA sequencing (scRNA-seq) to analyze their sex differences.

overall_design: Tumor-infiltrating CD8+ T cells in male and female mice were isolated by Fluorescence-Activated Cell Sorting (FACS) from MB49 s.q. tumors on Day 10 post inoculation according to their CD3 and CD8 expression and analyzed using scRNA-seq

first: Hyunwoo

last: Kwon

first: Zihai

last: Li


title: Transcriptome data on gene expression in Drosophila strains with deletions of sulfur metabolism genes: CBS and CSE

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

institute: Engelhardt Molecular Biology Institute

summary: To reveal the role of sulfur metabolism genes in memory formation processes, transcriptome libraries were obtained from the heads of 5-day-old naive males. The libraries were generated from Drosophila strains created in our laboratory with deleted cbs genes ( CBS-/-(5) and CBS-/-(8), cse (CSE-/-) and strains with double deletion of cbs and cse genes (CBS-/-,CSE-/-(1) and (CBS-/-,CSE-/-(2). Strain 58492, in which deletions were  introduced by the CRISP/CAS9 method, was used as a control strain.

overall_design: Deep sequencing of polyA-RNA extracted from naive male heads of Drosophola melanogaster

first: Olga

last: Zatsepina


title: Selective mTORC1 inhibition prevents and treats NAFLD and NASH

city: Philadelphia

first: Bridget

last: Gosis

state: PA

address: 1819 Montrose St.

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: We find that selective inhibition of one arm of mTORC1 signaling, via deletion of FLCN, promotes activation of the transcription factor TFE3 and profoundly protects against NAFLD and NASH in mice. (1) We performed genome-wide RNA-seq on livers from Control, liver-specific Flcn-null mice (LiFKO), and Flcn/Tfe3 double knock-out (DKO) mice fed either normal chow (NC) or a NAFLD-inducing diet (AMLN). We find TFE3-mediated induction of lysosomal and mitochondrial gene programs, and also suppression of de novo lipogenesis genes. (2) To understand whether TFE3 directly affects gene expression, we performed TFE3 ChIP-seq on livers from Control and LiFKO mice on normal chow. We find TFE3 occupancy on the chromatin at lysosomal genes, Ppargc1a (a driver of mitochondrial genes), and at de novo lipogenesis genes. (3) Finally, we wanted to test whether TFE3 antagonistically competes with the pro-lipogenic transcription factor SREBP-1c on chromatin. We therefore injected HA-tagged constitutively nuclear (active) SREBP-1c (nSREBP-1c), or a control virus, into control and LiFKO mice, treated them with a NAFLD-inducing diet (FPC diet), and collected liver tissue. We consequently performed HA-nSREBP-1c and TFE3 ChIP-seq experiments and observed no evidence of antagonistic competition.

overall_design: Flcn floxed mice were injected with AAV8-TBG-GFP or -Cre to yield Control and hepatocyte-specific Flcn-null (LiFKO) mice. Flcn floxed; Tfe3 -/Y (a whole body deletion of Tfe3) mice were also injected with either AAV8-TBG-GFP or -Cre to yield Tfe3 KO or Flcn/Tfe3 double knock-out (DKO) mice. (1) RNA-seq: Control, LiFKO, and DKO mice were placed on 17-18.5 weeks of normal chow or AMLN diet, and RNA-seq was performed on livers. (2) Normal chow TFE3 ChIP-seq: Control, LiFKO, and Tfe3 KO mice were fed normal chow, and livers were used for TFE3 ChIP-seq. (3) FPC diet TFE3 and HA-nSREBP-1c ChIP-seq: Control, LiFKO, and Tfe3 KO mice were additionally injected with either an AAV8 expressing HA-nSREBP-1c (“1c”) driven by a liver-specific ApoE/AAT promoter or a control virus (AAV8-TBG-GFP or -Cre) and treated with 9 days of FPC diet. Livers were then subjected to both TFE3 ChIP-seq and HA ChIP-seq.

first: Shogo

last: Wada

first: Joshua

last: Rhoades

first: Yifan

last: Yang

first: Z

last: Arany


title: Macrophage elastase (MMP12) critically contributes to the development of subretinal fibrosis

city: Changsha

first: Caijiao

last: Yi

address: Tianxin District

department: Aier School of Ophthalmology

institute: Central South University

summary: Macular subretinal fibrosis is the end-stage complication of neovascular age-related macular degeneration (nAMD).  RPE/Choroid from control and subretinal fibrosis mice were collected and processed for RNA sequencing (RNA-seq) analysis to investigate the molecular mechanism of subretinal fibrosis.

overall_design: Subretinal fibrosis was induced in C57BL/6J mice using the two-stage laser-induced protocol. Twenty days later, RPE-Choroids from 3 subretinal fibrosis mice and 3 healthy control mice  were collected and processed for RNA sequencing (RNA-seq) analysis. DESeq2 was used to determine the differentially expressed genes (DEGs). Gene Ontology (GO) and KEGG were used to analyze the enriched pathways. The expression of the notable DEGs was verified by qPCR.

first: Jian

last: Liu


title: Raw potato starch alters the cecal microbiome and gene expression in mice fed a Western diet (Proximal Colon)

city: Beltsville

first: Celine

last: Chen

address: 10300 Baltimore Ave, B307C, RM211E

institute: USDA

summary: We investigated the effect of feeding mice a Total Western Diet formulated using the 50th percentile daily intake levels for macro and micronutrients from the National Health and Nutrition Examination Survey (NHANES) with 0, 2, 5, or 10% added raw potato starch on the cecal microbiome (16S) and cecum, proximal and distal colon gene expression by RNASeq analysis.

overall_design: Three-week old mice were fed the Total Western Diet (TWD) for 6 weeks and then subgroups of mice were fed either the TWD or TWD plus 2. 5. or10% raw potato starch for an additional  3 weeks.  Mice were then euthanized and cecal contents and various tissues collected for analysis.

first: Allen

last: Smith

first: Harry

last: Dawson

first: Lumei

last: Cheung


title: Genome-wide differential binding pattern of  NFKB2/p52 under prolonged culture conditions

city: Chicago

first: Bakhtiar

last: Yamini

address: 900 E 57th St

department: Department of Surgery

institute: University of Chicago

summary: We report the application of ChIP-Seq analysis for high-throughput profiling of NFKB2/p52 binding pattern under prolonged culture conditions. Briefly, we investigate the genome wide binding behavior of endogenous p52 in WI-38 cells. The cells was cultured with regular DMEM medium for prolonged time (7 days). Chromatin immunoprecipitated DNA was converted to libraries for sequencing with HiSeq 4000. We find that there is a distinct binding pattern of p52 under prolonged culture condtion. This study provides a preliminary but solid basis to our understanding of NFKB2/p52 binding dynamics during aging process.

overall_design: ChIP-Seq experiments were performed with ChIP-grade p52 antibody under designed condtions, and library from WI-38 cells input was used for background correction.

first: Longtao

last: Wu

first: Giovanna

last: Bernal


title: RNA-seq of Srsf10-KD or control liver samples after feeding with HFD.

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: RNA processing is dysregulated in the liver during the early stages of diet induced liver disease and obesity. Furthermore SR proteins are dysregulated as well. In order to look at the contribution of reduced SRSF10 levels in obesity and liver disease, RNA-seq was performed on liver samples from mice which had been injected with an AAV expressing an shRNA against Srsf10 or luciferase and subsequently fed a HFD for 12 weeks.

overall_design: RNA-seq of liver tissue samples from Srsf10-KD or control mice after 12 weeks of HFD (60% calories from fat).

first: Andrew

last: Jobbins

first: Marian

last: Dore

first: Yi-Fang

last: Wang

first: Santiago

last: Vernia


title: Gene expression and alternative splicing profiles of N2a siEwsr1 cells

city: Barcelona

first: Riccardo

last: Aiese Cigliano

address: Calle Comte D'Urgell 240

country: Spain

institute: Sequentia Biotech SL

summary: N2a cells treated with either control or siEwsr1 oligonucleotides

overall_design: Examination of 2 different RNA from N2a cells transfected with  sicontrol oligonucleotide and examination of 3 different RNA from N2a cells transfected with siEwsr1 oligonucleotide

first: M

middle: P

last: Paronetto

first: V

last: Verdile


title: Single-cell RNA-seq analysis of syngeneic tumors treated with intratumoral NHS-rmIL12 immunotherapy

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

summary: Established MOC22 tumors in WT B6 mice were treated with three intratumoral injections of 0.4 ug NHS-rmIL12; control and treated tumors were analyzed for immune correlative changes with single-cell RNA-seq.

overall_design: Two control tumors treated with PBS and two tumors treated with NHS-rmIL12 were digested into single cell suspensions, and whole tumors were subjected to single cell capture on the 10X Chromium Controller (3' chemistry, v3 kit).

first: Clint

last: Allen


title: Effects on gene expression of doxorubicin treatment in genome-edited human induced pluripotent stem cell-derived cardiomyocytes

city: Vancouver

first: Liam

last: Brunham

state: British Columbia

address: 1081 Burrard Street

department: Department of Medicine

country: Canada

institute: University of British Columbia

summary: To gain further insight into the mechanisms of doxorubicin-induced cardiotoxicty in genome-edited isogenic induced pluripotent stem cell-derived cardiomyocytes with or without the RARG variant S427L, we performed RNA-seq in doxorubicin- or vehicle-treated cardiomyocytes in both genotypes and investigate the differential expression genes as well as enriched molecular pathways.

overall_design: hiPSC-derived cardiomyocytes of original (RARG-WT/S427L) and repaired (RARG-WT/WT) cell lines were treated with 1uM doxorubicin in experiment group and vehicle (DMSO) in control group in 12-well plates for 24 hours with 3 replicates in each condition.

first: Haojun

last: Huang

first: Effimia

last: Christidi


title: ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC

first: Hailong

last: Ma

address: Zhizaoju Rd

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

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effects of ethyl carbamate exposure on C. elegans transcriptome

city: Saskatoon

first: Cheng-Wei

state: SK

address: 52 Campus Drive

institute: University of Saskatchewan

summary: Ethyl carbamate is a common food contaminant prevalent in fermented food with probable carcinogenic effects in animals. To date, other toxicological properties of ethyl carbamate are not well characterized. Using the genetic model Caenorhabditis elegans, we found that chronic exposure to ethyl carbamate during larval development inhibits growth while exposure at adulthood inhibits reproduction, shortens lifespan, and promotes degeneration of dopaminergic neurons. Through whole-transcriptome RNA-sequencing, we found that ethyl carbamate invokes a widespread transcriptomic response inducing the differential expression of > 4,000 genes by at least 2-fold. Functional analysis of RNA-sequencing data revealed that genes up-regulated enrich to various neuron regulatory processes and xenobiotic defense. Gene expression analysis confirms that various genes functioning within phase 1 and 2 detoxification responses along with ABC transporters are highly up-regulated in response to ethyl carbamate exposure, suggesting the induction of oxidative stress. Overall, these findings demonstrates new toxicological properties of chronic ethyl carbamate exposure and provide new insights into the effects in has on transcriptome regulation in the C. elegans model.

overall_design: Total RNA was prepared from gravid young adult Caenorhabditis elegans with three biological replicates per group and sent to NovoGene for PE150 sequencing. Sequencing library were constructured with oligo-dT enrichment. Gene expression data were analyzed by DEGSeq.


title: LATS1 is a Central Signal Transmitter for Achieving Full Type-I Interferon Activity [2fTGH cells]

city: Suzhou

first: Yibo

last: Zuo

address: Renai road 199

institute: Soochow university

summary: Interferons (IFNs) possess broad-spectrum antiviral activity to resist virus epidemic. However, IFNs antiviral efficacy needs to be greatly improved. Here, we reveal that LATS1 is a vital signal transmitter governing full type-I-interferon (IFN-I) signaling activity. Importantly, LATS1 deficiency restricts IFN-I signaling and attenuates host antiviral immune response.

overall_design: twelve samples


title: SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [AML01 scTEM-seq]

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

summary: Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. By targeting high-copy LINE-1 and SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of annotated loci covered in each scTEM-seq library. Parallel transcriptome analysis of the same single cell is also performed to link global DNA methylation heterogeneity with transcriptional consequences. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary cells from an AML patient. Treatment of KG1a cells with the hypomethylating agent, decitabine, induces global DNA methylation heterogeneity associated with altered expression of viral response pathways. We also compare global levels of DNA methylation to expression of transposable elements and find a predominance of negative correlations in both the KG1a and patient cells. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated KG1a cells. These observations suggest that viral mimicry processes important for epigenetic therapy and tumour immunogenicity are variably active in AML cells. By linking global DNA methylation heterogeneity with transcriptional consequences, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: scTEM-seq (single-cell transposable element methylation sequencing)

first: Kooper

middle: V

last: Hunt

first: Sean

middle: M

last: Burnard

first: Ellise

last: Roper

first: Danielle

last: Bond

first: Matthew

last: Dun

first: Nicole

last: Verrills

first: Anoop

last: Enjeti


title: SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [KG1a DAC scTEM-seq]


title: SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [RNA-seq]

overall_design: scRNA-seq


title: Human bladder cancer cell line high throughput sequencing

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Circular RNAs (circRNAs) have been increasingly indicated to be important participants in the development and progression of various malignant tumors. In this study, we analyzed circRNA high-throughout sequencing from human bladder cancer tissues and paired adjacent normal tissues. Then we focused on the upregulated circRNAs and identified a novel circular RNA, hsa_circ_0008399 , as a new candidate circRNA derived from RBM2 gene. FISH assay has been proved that hsa_circ_0008399 mainly located in nucleus. Transcriptome analysis was performed to find the potential genes that could be regulated by hsa_circ_0008399.

overall_design: In order to screen downstream genes regulated by hsa_circ_0008399, transcriptome analysis was performed in EJ and T24T cells transfected with has_circ_0008399 and compaired vector.

first: Wenjie

last: Wei

first: Hui

last: Zhang


title: MicroRNA sequencing of plasma-derived exosomes from LLC tumor-bearing mice

city: Miyagi

first: Me-Tzu

last: Su

address: 4-1 Seiryo-machi, Aoba-ku, Sendai

department: Department of Experimental Immunology

country: Japan

institute: Institute of Development, Aging and Cancer

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the role of leukocyte immunoglobulin-like receptor subfamily B member 4 (LILRB4)/gp49B in the regulation of  exosomal miRNA composition in tumor-bearing mice by next-generation sequencing

overall_design: WT and gp49B deficiency mice were inoculated with Lewis Lung Cancer (LLC) cells by intravenous injection. After inoculation, LLC--bearing mice were sacrificed on day 21, and plasma samples were harvested for exosome isolation. miRNA contents in plasma-derived exosome were anlyzed using an Illumina NextSeq-500 Sequencing System (Illumina, San Diego, CA, USA).

first: Mei-Tzu

first: Sakiko

last: Kumata

first: Toshiyuki

last: Takai

first: Yoshinori

last: Okada


title: Genome-wide chromatin accessibility changes in cultured primary human monocytes cultured at low density and high density.

city: Southampton

first: Rosanna

middle: C G

last: Smith

state: Hampshire

address: Centre for Cancer Immunology, University Hospital Southampton (MP 127), Tremona Road

department: Cancer Sciences Unit, Faculty of Medicine

institute: University of Southampton

summary: ATAC sequencing of primary human monocytes cultured at low and high density. Monocytes isolated from PBMCs of 3 healthy donors were cultured at low density (1 x 10^6 cells/mL) or at high density (1 x10^7 cells/mL) for 24hrs and harvested for ATAC sequencing. Protein expression of FcgR2b is higher on monocytes in high density conditions compared to low density conditions, where expression is negligble. This study provides information on genome-wide chromatin accessibility changes that occur in high density culture in order to study associations with FcgR2b expression.

overall_design: ATAC-seq study of primary human monocytes cultured at high and low densities.

middle: G

first: Mohammadmersad

last: Ghorbani

first: Khyiam

last: Hussain

first: Mark

last: Cragg


title: Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fiber length, lint percentage, and Fusarium wilt resistance

city: Beijing

last: Zhao

address: China Agricultural University Yuanmingyuan West Road 2#,Haidian District Beijing

institute: China Agricultural University

summary: Sea Island cotton (Gossypium barbadense) is the source of the world’s finest fiber-quality cotton, yet relatively little is understood about the genetic variation among diverse germplasm, the genes underlying important traits, and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fiber quality, yield, disease resistance, maturity, and plant architecture. The highest number of associated loci was for fiber quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments we confirmed the role of five candidate genes regulating four key traits, i.e., disease resistance, fiber length, fiber strength, and lint percentage. Geographical and temporal considerations demonstrate selection for the superior fiber quality (fiber length and fiber strength), and high lint-percentage in improving G. barbadense in China. Pedigree selection breeding wholly increased Fusarium wilt disease resistance, and separately improved fiber-quality and yield. Our work provides a foundation for understanding genomic variation in and selective breeding of Sea Island cotton.

overall_design: RNA-seq profiles of six different periods in five sea island cotton varieties.

first: Weiran

last: Wang

first: Corrinne

last: Grover

first: Kaiyun

first: Zhuanxia

last: Pan

first: Baosheng

last: Guo

first: Jiahui

last: Zhu

first: Ying

first: Meng

first: Hushuai

last: Nie

first: Li

last: Xiao

first: Anhui

first: Jing

last: Yang

first: Cheng

last: Cheng

first: Xinmi

last: Ning

first: Bin

last: Li

first: Haijiang

last: Xu

first: Daniel

last: Iyaah

first: Aierxi

last: Alifu

first: Pengbo

first: Junyi

last: Geng

first: Jonathan

middle: F

last: Wendel

first: Jie

last: Kong

first: Jinping

last: Hua


title: Raw potato starch alters the cecal microbiome and gene expression in mice fed a Western diet (Cecum)

first: Celine

last: Chen

first: Allen

last: Smith

first: Harry

last: Dawson

first: Lumei

last: Cheung


title: Raw potato starch alters the cecal microbiome and gene expression in mice fed a Western diet (Distal Colon)


title: ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [RNA-seq]

city: Shanghai

first: Hailong

last: Ma

summary: To determine the targets underlying ALKBH5 during head and neck squamouse cell carcinoma progression, Methylated RNA immunoprecipitation (MeRIP) with an m6A specific antibody followed by RNA sequencing (MeRIP-seq) and next generation  sequencing were combined to screen the potential targets haboring m6A  modificatios and mRNA level alteration after ALKBH5 knockdown in a HNSCC cell line.

overall_design: RNA-seq was conducted in Cal27 cells after ALKBH5 silencing for 24 h.

first: Shufang

last: Jin


title: Dynamic circRNAs expression profiles and circRNA-associated-ceRNA networks during B-cell development and differentiation in mouse bone marrow

city: Shenzhen

first: Saineng

last: Hu

address: Lianhua Road Futian District

department: Biomedical Research Institute

institute: Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center

summary: Our findings further expand the current knowledge regarding the biology of ceRNAs and their regulatory roles in B-cell development and differentiation process. These newly discovered networks provide more ideas for further research about B-cell development in the future.

overall_design: we used miRNA sequencing and LncRNA sequencing to detect several develoment stages of B-cell  sorted from mouse bone marrow by using FACS (Pro-B cells, Pre-B cells, Immature B cells and mature Bcells) to study the underlying biological mechanisms in the rapid development of B-cell.

first: Wei

last: Zhang

last: Pan


title: ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [MeRIP-seq]

overall_design: MeRIP-seq was conducted in Cal27 cells after ALKBH5 silencing for 24 h.


title: Microarray timecourse profiling of gene expression changes in primary human monocytes and B-cells cultured at high density to investigate FcgR2b associated gene expression changes

first: Rosanna

summary: Whole-genome microarray gene expression profiling of primary human monocytes and B-cells cultured at high density. Monocytes and B-cells were isolated from PMBCs of 2 healthy donors and cultured at 1x10^7 cells/mL (high density). Samples were harvested for microarray gene expresssion profiling at 0, 2, 10 or 24hrs (monocytes) or 0 or 24hrs (B-cells). Protein expression of FcgR2b is higher on monocytes in high density conditions compared to low density (1x10^6 cells/mL) conditions where expression is negligble. This study provides information on genome-wide gene expression changes that occur in high density culture in order to study associations with FcgR2b expression.  B-cells cultured at high density and low density show similar levels of moderate FcgR2b expression. B cells at 0hr and after 24hr of high density culture are included in this dataset as a comparators.

overall_design: Microarray timecourse profiling of primary human monocytes and B-cells cultured at high density for 24hr.

middle: C

first: Stephen

last: Thirdborough

first: Khyiam

last: Hussain

first: Mark

last: Cragg


title: Transcriptome-wide expression changes over time in cultured primary human monocytes due to DMOG treatment

summary: RNA sequencing of primary human monocytes cultured with and without hypoxia-mimetic agent DMOG (Dimethyloxalylglycine). Monocytes isolated from PBMCs of 7 healthy donors were cultured with and without DMOG for 24hrs and harvested at 0, 2, 10 or 24hrs for RNA sequencing. DMOG suppresses HIF Prolyl hydroxylase (HIF-PH) activity by acting as a small molecule competitive inhibitor. HIF-PH inhibition leads to increase in endogenous HIF protein levels and mimics aspects of hypoxia. This RNA-seq study allows analysis of transciptome-wide expression pattern changes over time due to DMOG treatment.

overall_design: Timecourse RNA-seq study of primary human monocytes cultured with and without the hypoxia-mimetic agent DMOG.

middle: S


title: Genome-wide chromatin accessibility changes over time in cultured primary human monocytes due to DMOG treatment

summary: ATAC sequencing of primary human monocytes cultured with and without hypoxia-mimetic agent DMOG (Dimethyloxalylglycine). Monocytes isolated from PBMCs of 7 healthy donors were cultured with and without DMOG for 24hrs and harvested at 0, 2, 10 or 24hrs for RNA sequencing. DMOG suppresses HIF Prolyl hydroxylase (HIF-PH) activity by acting as a small molecule competitive inhibitor. HIF-PH inhibition leads to increase in endogenous HIF protein levels and mimics aspects of hypoxia. This ATAC-seq study allows analysis of genome-wide changes to chromatin accessibility due to DMOG treatment.

overall_design: Timecourse ATAC-seq study of primary human monocytes cultured with and without the hypoxia-mimetic agent DMOG.

first: Mohammadmersad

last: Ghorbani


title: Ribo-Seq experiments in HCT116 WT and TP53-/- cells upon neocarzinostatin treatment

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

country: Germany

institute: Heidelberg University

summary: The transcription factor p53 exerts its tumor suppressive effects through transcriptional activation of numerous target genes controlling cell cycle arrest, apoptosis, cellular senescence and DNA repair. In addition, there is evidence that p53 influences the translation of specific mRNAs, including translational attenuation of ribosomal protein synthesis and translational activation of MDM2. A challenge in the analysis of translational control is that changes in mRNA abundance exert a kinetic (passive) effect on ribosome densities. In order to separate these passive effects from active regulation of translation efficiency in response to p53 activation, we conducted a comprehensive analysis of translational regulation by comparative analysis of mRNA levels and ribosome densities upon DNA damage induced by neocarzinostatin in wild-type and TP53-/- HCT116 colorectal carcinoma cells. Thereby, we identified a specific group of mRNAs whose translation is actively up-regulated in response to p53 activation, the majority of which are transcribed from p53 target genes including MDM2, SESN1 and CDKN1A. By subsequent polysome profile analysis, we could demonstrate that a p53-dependent switch in transcript isoform expression is responsible for translational activation of SESN1, whereas translational activation of CDKN1A occurs through a trans-acting mechanism that affects multiple transcript isoforms.

overall_design: RNaseI digested ribosome footprint of cytoplasmic mRNAs or monosome fraction after sucrose gradient ultracentrifugation, or alkaline fragmentated total mRNA in HCT116 WT and TP53-/- cells upon neocarzinostatin treatment

first: Miharu

last: Hisaoka

first: Doris

last: Lindner

first: Georg

last: Stoecklin


title: MiR-181b Targets Semaphorin 3a to Mediate TGF-β-induced Endothelial to Mesenchymal Transition: Implication in Atrial Fibrillation

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
Background:This study investigated if and how atrial endothelial cells may transform to mesenchymal cells and contribute to atrial fibrosis via endothelial-to-mesenchymal transition (EndMT).
Results:We show a novel mechanistic link between TGF-β1/SMAD signaling and decreased Sema3a expression through the induction of miR-181b; this pathway plays an important role in EndMT associated with the pathogenesis of AF. Both miR-181b and Sema3a are potential therapeutic targets in AF.

overall_design: The AAECs were isolated from 3 patients and were treated TGFbeta(5ng/mL) for 24hr to mimic the pathogenesis and performed miRNA arrays

first: Ying-Ju

last: Lai

first: Feng-Chun

last: Tsai

first: Gwo-Jyh

last: Chang

first: Shang-Hung

first: Chung-Chi

last: Huang

first: Wei-Jan

last: Chen

first: Yung-Hsin

last: Yeh


title: SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells

first: Heather

overall_design: Refer to individual Series


title: Abundant small RNAs in the reproductive tissues of the honey bee, Apis mellifera, are a plausible mechanism for epigenetic inheritance and parental manipulation of gene expression

city: Darlington

first: Owen

last: Watson

address: 2 Butlin Ave, G08 - Molecular Bioscience Building The University of Sydney

department: School of Life and Environmental Sciences

institute: Sydney University

summary: Here we present the first characterisation of small RNAs in honey bee reproductive tissues. We conclude that small RNAs are likely to play an integral role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of origin-effects on gene expression and reproductive physiology. present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes.

overall_design: Bioinformatic analysis of sRNA-Seq data from honeybee reproductive tissue

first: O

middle: T

first: A

last: Ashe

first: B

last: Oldroyd

first: G

last: Buchmann

first: P

last: Young

first: K

last: Lo

first: E

last: Remnant

last: Yagound

first: M

last: Sambrook

last: Hill


title: Genome-wide chromatin accessibility and transcriptome-wide expression changes over time in cultured primary human monocytes due to DMOG treatment

first: Rosanna

last: Smith


title: Raw potato starch alters the cecal microbiome and gene expression in mice fed a Western diet

city: Beltsville

first: Celine

address: 10300 Baltimore Ave, B307C, RM211E

institute: USDA

relation:
SuperSeries of: GSE182454
SuperSeries of: GSE182456
SuperSeries of: GSE182457


title: SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [PBAT]

last: Lee

overall_design: scTEM-seq (single-cell transposable element methylation sequencing); post-bisulphite adaptor tagging (PBAT)

first: Kooper

last: Hunt

first: Sean

last: Burnard

first: Ellise

middle: A

last: Roper

first: Danielle

middle: R

last: Bond

first: Matthew

last: Dun

first: Nicole

last: Verrills

first: Anoop

last: Enjeti

middle: J


title: Downregulation of KRAB zinc finger proteins in 5-fluorouracil resistant colorectal cancer cells

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Département de microbiologie et infectiologie

institute: Université de Sherbrooke

summary: The radio-chemotherapy with 5-fluorouracil (5-FU) is the standard of care treatment for patients with locally advanced rectal cancer (LARC) but it is only effective for a third of them. The proteomic and transcriptomic response of three colorectal cancer (CRC) cell lines to 5-FU and radiation was assessed and correlated with their genetic background. The induction of a 5-FU-resistance in those cell lines negatively affects the levels of transcripts corresponding to Krüppel-associated box (KRAB)-containing zinc finger proteins (ZFPs), the largest family of transcriptional repressors. Among nearly 350 KRAB-ZFPs, almost a quarter are down-regulated after the induction of a 5-FU-resistance including a common one between the three CRC cell lines, ZNF649, whose role is still unknown. This proteomic, transcriptomic and genomic analysis of intrinsic and acquired resistance highlights possible new mechanisms involved in resistance to treatment and therefore potential new therapeutic targets to overcome this resistance.

overall_design: RNAseq analysis of radio-chemoresistance in colorectal cancer cell lines

first: Anais

last: Chauvin

first: Danny

last: Bergeron

first: Dominiue

last: Lévesque

first: Benoît

last: Paquette

first: Michelle

last: Scott

first: François-Michel

last: Boisvert


title: Single-cell transcriptomics reveals diverse and complex gene expression alterations in human trisomy 18

city: Xiamen

first: Jing

last: Wang

state: Fujian

address: 668 Jimei Road

department: School of Medicine and School of Biomedical Sciences

institute: Huaqiao University

summary: we analyzed the transcriptomics of single cell of amniotic fluid both from normal and trisomy 18 individuals by using 10x Genomics.

overall_design: The RNAs for the transcriptomics of single cell of amniotic fluid both from three normal and three trisomy 18 individuals by using 10x Genomics.

first: Tao

last: Sun


title: Whole blood RNA-seq from healthy adults after vaccination with a replication-competent tetravalent dengue vaccine

city: Chicago

first: Yan

last: Che

state: Illinois

address: 303 E Superior St

institute: Northwestern University

summary: The primary aim of this study was to characterize the transcriptomic differences between individuals with different follow-up geometric mean neutralizing antibody titers at one month

overall_design: 20 healthy adults were sampled for whole blood at five timepoints (d0, d2, d4, d7, d92).

first: Eun-Young

last: Kim

first: Ramon

last: Lorenzo-Redondo

first: Caroline

middle: K

last: Keller

first: Daniel

last: Whorf

first: Dawson

last: Mill

first: Ana

last: Fernandez-Sesma

first: Hansi

last: Dean

first: Heejin

first: Steven

last: Wolinsky


title: Enhancer RNA transcription defines novel CSF1 enhancer in triple-negative breast cancer

status: Public on Apr 12 2022

city: Chapel Hill

first: Hector

middle: L

last: Franco

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: UNC Lineberger Cancer Center

summary: We report the results of employing CRISPR interference (CRISPRi) to epigenetically perturb the CSF1 transcription start site or novel CSF1 enhancer, followed by high-throughput RNA-sequencing to identify downstream gene expression changes in human triple negative breast cancer cells.

overall_design: Study of genome-wide gene expression changes in response to epigenetic perturbation of the CSF1 enhancer or CSF1 transcription start site in triple-negative breast cancer.

first: Michael

last: Lewis


title: tRFs and tiRNA expression profile in human OA ACL cells and NA ACL cells.

city: guangzhou

first: dianbo

last: long

state: guangdong

address: Zhongshan second road

institute: First Affiliated Hospital of Sun Yat-sen University

summary:
tRNA-derived fragments (tRFs) are new noncoding RNAs, and recent studies have shown that tRNAs and tRFs have important functions in cell metabolism via posttranscriptional regulation of gene expression. However, whether tRFs regulate cellular metabolism of the anterior cruciate ligament (ACL) remains elusive. The aim of this study was to investigate the role and action mechanism of tRFs in ACL cell metabolism.
Arraystar_tRF&tiRNA was used to determine tRFs and tiRNA expression profiles in  human OA ACL cells and NA ACL cells。

overall_design: Eexamnation of two group, OA ACL and NA ACL，each group contain 3 independent sample.

first: Dianbo

last: Long

first: Yiyang

last: Xu

first: Guping

last: Mao

first: Aishan

last: He

first: Ziji

last: Zhang

last: Kang


title: Aspirin-triggered Resolvin D1 Reduces Chronic Dust-induced Lung Pathology Without Altering Susceptibility to Dust-enhanced Carcinogenesis.

city: Fort Collins

first: Tara

last: Nordgren

state: CO

address: Colorado State University, Physiology 133

department: Environmental and Radiological Health Sciences

institute: Colorado State University

summary: Farm workers are at an increased risk for the development of acute and chronic lung inflammatory diseases from their everyday exposures to organic dust. Previous investigations have examined the inflammatory effects in mice from single and repetitive exposures to dust from swine confinement facilities, however, no study has explored these effects in a chronic model. To address this research gap, we established a chronic dust exposure mouse model of lung tumor-igenesis that was also used to measure the efficacy of omega-3 fatty acid-derived lipid mediators as therapeutics for mitigating these induced responses. Our results from these investigations are the first to evaluate the chronic inflammatory, and carcinogenic effects of these dusts, as well as identify a potential therapeutic strategy for mitigating the inflammatory effects by using an omega-3 fatty acid-derived bioactive lipid mediator.

overall_design: Of the 65 total mice used in these studies, 24 left lung tissues were randomly selected among the saline-only, HDE-only, saline+NNK, and HDE+NNK-exposed groups, for transcript and pathway gene expression analyses using the NanoString platform. Left lung tissues were homogenized and RNA was extracted using the PureLink RNA Mini Kit (Invitrogen, Carlsbad, California, USA) and sample quality was quantified using the NanoDrop ND-100 (NanoDrop Technologies, Inc, Wilmington, DE, USA) and an Agilent 2100 Bioanalyzer (UC Riverside Core Facilities, Agilent Technologies, Santa Clara, CA, USA). We utilized the mouse PanCancer Immune Profiling Panel (NanoS-tring Technologies, Seattle, WA, USA) codeset which is a pre-designed panel containing 770 target genes related to immune response and carcinogenesis.

first: Edward

last: Dominguez

first: Rattapol

last: Phandthong

first: Matthew

last: Nguyen

first: Arzu

last: Ulu

first: Stephanie

last: Guardado

first: Stefanie

last: Sveiven

first: Prue

last: Talbot


title: Gastric cancer samples of Mexican patients

city: Ciudad de México

first: Martha

middle: Eugenia

last: Ruiz-Tachiquín

state: CIudad de México

address: Av. Cuauhtémoc No.330, Col. Doctores, Deleg. Cuauhtémoc.

department: Tercer piso. UMAE-Hospital de Oncología

country: Mexico

institute: Centro Médico Nacional Siglo XXI-IMSS

summary: Cancer Gastric (CG) is a multifactorial disease with an important genetics background, per example copy number variants (CNV). Microarray data analysis were performed to identify CNV that could be contributing to those Mexican patient's clinical phenotypes

overall_design: Affymetrix CytoScan HD arrays were performed according to the manufacturer's  instructions. Copy number analysis of Cytoscan Affymetrix arrays was performed with ChAS software for 20 adult samples, 6 benign gastritis, 7 intestinal gastric cancer  and 7 cancer gastric diffuse with their respective adjacent tissue.

middle: E

last: Ruiz-Tachiquin

first: Javier

last: Torres


title: Postprandial effects of protein from salmon by-products and whey on gene expression in liver cells.

city: Oslo

first: Thomas

last: Sæther

state: Oslo

address: Sognsvannsveien 9

department: Dept. of Molecular Medicine

institute: University of Oslo

summary: Exploring the metabolic effects of fish protein is important, as by-products from fish contain large amounts of proteins that could be used for human consumption. The aim of this study was to investigate the postprandial effects of intake of protein from salmon by-products, compared to whey. As part of this effort, the effects on gene expression in liver cells were studied in vitro. This was done by incubating HepG2 cells with human serum taken before (fasting) or 30 and 60 min after intake of salmon protein or whey and comparing that with HepG2 cells incubated in serum-free  medium. Transcriptomic profiling of the cells was done with RNA sequencing.

overall_design: In a randomised controlled, cross-over trial, five healthy male participants consumed 5.2 grams of protein from either salmon fishmeal or whey. Blood samples were taken before (fasting), and 30 and 60 min after intake. To investigate the postprandial effects of fishmeal or whey on hepatic gene expression, cultured HepG2 cells were incubated for 6 hours with or without serum from the cross-over trial, and transcriptomic profiling performed by RNA sequencing. Total RNA from HepG2 cells incubated with serum from all five participant [before (n=5; fasting), and 30 min (n=5) and 60 min after (n=5) intake of both fishmeal and whey], as well as RNA from six serum-free HepG2 cultures - 36 samples in total - was sequenced.

first: Marit

last: Hjorth

first: Natalia

last: Galigniana

first: Ola

last: Ween

first: Stine

last: Ulven

first: Kirsten

middle: B

last: Holven

first: Knut

last: Dalen


title: 16S sequencing of mouse gut microbial DNA after 10 days of intermittent fasting or ad libitum with and without vancomycin treatment

city: London

first: Elisabeth

last: Serger

state: London

address: Du Cane Road

department: Brain Sciences

institute: Imperial College London

summary: To compare the changes in the gut microbial composition in the cecum of mice following the 4 treatments (IFvsAL with(out) vancomycin co-treatment)

overall_design: Mice (6-8 weeks) underwent following procedures: a) 10 days of ad libitum food supply b) 10 days of intermittent fasting c) 10 days of ad libitum food co-treated with vancomycin in the drinking water (50mg/kg/day; 214.27 mg/l) d) 10 days of intermittent fasting food cotreated with vancomycin in the drinking water. The cecum content was removed and microbial genomic DNA extracted.

first: Adesola

last: Bello

first: Simone

last: Di Giovanni


title: scRNA-seq analysis of hydrosalphinx disease state Vs healthy state of human fallopian tubes

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

summary: Hydrosalpinx is common cause of tubal factor infertility in women in which the fallopian tube becomes blocked, fills with fluid, and consequently is nonfunctional. Single cell RNA-seq analysis has provided an unparalleled approach to characterize tissue types and explore pathologies in unbiased manner. Here we use scRNA-seq to define and compare major and rare cell types of the human fallopian tube in the healthy and hydrosalpinx disease state.

overall_design: Characterizing cellular composition and heterogeneity of healthy state and hydrosalpinx disease state of the human fallopian tubes using 10x scRNA-seq analysis

first: Saher

last: Hammoud


title: Long-term longitudinal analysis of peripheral blood transcriptome in COVID-19 patients

city: Beijing

first: Yan

last: Zhang

state: Not Applicable

address: Dongdajie street

institute: Beijing institute of Biotechnology

summary: We performed the longitudinal peripheral blood transcriptome profiling after diagnosis in five patients, and found that patients' blood transcriptomes undergo dramatic and consistent changes in early recovery stage (ERS). Meanwhile, the blood transcriptome did not fully return to the healthy state even after more than one month of recovery. We also realized that differential expressed genes (DEGs) are enriched in biological processes of antigen processing and related processes, and promoter regions of these genes enrich key transcription factors (TFs) involved in T cell differentiation and activation. We further provided potential mechanisms underlying these orchestrated processes, by revealing these specific TFs mediated gene co-expression network.

overall_design: Examination between recovery stage and healthy control. Differential gene expression analysis was performed using DESeq2 (Love et al., 2014). Genes that displayed ±1 log2FC (FDR <0.01) between ERS or LRS and healthy control samples were considered as significantly differentially expressed.

first: Zhihu

last: Zhao

first: Jing

last: Tian

first: Ruiwen

last: Ren


title: Transcript profiling in WT, CRTC3 KO and CRTC3-rescued B16F1 cells.

city: La Jolla

first: Jelena

last: Ostojic

state: CA

address: 10010 N Torrey Pines Road

department: PBL-M

institute: Salk Institute for Biological Studies

summary: Triggering of cAMP and mitogen-activated (MAPK) pathways in response to hormonal and growth factor cues promotes melanocyte pigmentation and survival in part through induction of the master regulator MITF by cAMP-responsive factor CREB. We examined the role of CREB coactivators (CRTC1-3) in transduction of cAMP and MAPK signals in melanocytes. We found that CRTC3 knock-out in mice and B16F1 melanoma cells decreases pigmentation by directly regulating the expression of the melanosomal transporter OCA2. In addition to effects of cAMP, CRTC3 activation was also promoted by ERK1/2-mediated phosphorylation at Ser391; amounts of phosphorylated CRTC3-S391 were constitutively elevated in human melanoma cells expressing mutated BRAF or NF1. Knock-out of CRTC3 in A375 melanoma cells impaired their anchorage-independent growth, migration and invasiveness, whereas CRTC3 over-expression increased survival in response to BRAF inhibition by vemurafenib. Analysis of spontaneous CRTC3 mutations in melanomas reveals that increased activity of this co-activator associates with reduced patient survival. Our results highlight the importance of CRTC3 in pigmentation and melanoma progression.

overall_design: RNA profiles of WT, CRTC3 KO and CRTC3-rescued B16F1 cells (N=2 per group for WT and CRTC3 KO, 1 for rescued cells). Cells were treated with vehicle (DMSO) or cAMP agonist forskolin (FSK, 1µM) for 1h.

first: Marc

last: Montminy


title: Analysis of CRTC3 genomic occupancy upon forskolin stimulus in B16F1 cells.

overall_design: Profiles of genomic occupancy of CRTC3 in B16F1 cells treated with vehicle or cAMP agonist forskolin. Controls include CREB, MITF, phospho-PolII and acetylated Histone3 (H3acK27).


title: CRTC3 is a coincidence detector for cAMP and growth factor signals in melanocytes and melanoma.

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


title: Transcript profiling in WT and CRTC3 KO A375 cells.

overall_design: RNA profiles of WT and CRTC3 KO A375 cells (N=2 per group), treated with vehicle (DMSO) or cAMP agonist forskolin (FSK, 1µM) for 1h.


title: Effect of MOG-7 disruption on the C. elegans transcriptome

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

institute: Monash University

summary: In higher eukaryotes, splicing of introns from pre-mRNAs is required for gene expression. Here, we report that Caenorhabditis elegans MOG-7 is a hybrid RNA splicing factor that contains conserved splicing domains from both yeast and mammals. Acute removal of MOG-7 from the C. elegans germline causes intron retention in the majority of genes, resulting in sterility, germline masculinization and germ cell morphology defects. Despite the deleterious consequences caused by MOG-7 loss, the germline can functionally recover to produce viable and fertile progeny once MOG-7 expression is restored through apoptotic clearance of defective germ cells.

overall_design: 6 replicates in each condition; 3 conditions (No auxin treatment, 1 hour auxin; 2 hour auxin)

first: Roger

last: Pocock

first: Wei

last: Cao


title: Fn1079 (Fn-Nap): a novel virulence factor of Fusobacterium nucleatum, reduces erythrocytes and promotes metastasis via CCL2/CCL7-induced EMT in colorectal cancer

status: Public on Apr 11 2022

city: Guangzhou

first: Songhe

last: Guo

state: Guangdong

address: No.132 Waihuandong Road, University Town

institute: Sun Yat-sen University

summary: We then performed gene expression profiling analysis using data obtained from RNA-seq of RAW 264.7 treated with or without Fn1079

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RAW 264.7 treated with or without Fn1079

first: Yixian

last: Wu


title: Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

city: Egham

first: Alessandra

last: Devoto

address: Egham Hill

department: Biological Sciences

institute: Royal Holloway, University of London

summary: We report the application of ChIP-Seq of H4ac and H3K27me3 histone modifications to jasmonate-treated wild type (DR5) and HDA6 mutant (axe1-5) whole A. thaliana seedlings

overall_design: Examination of two different histone modifications in whole A. thaliana seedlings

first: Stacey

last: Vincent

first: Imma

last: Perez-Salamo


title: Transcriptomic analysis of SiHa cells stably expressing shCtrl or shSYT7

city: Nanning

first: Junying

last: Chen

address: 6 Shuangyong Road,

institute: First Affiliated Hospital of Guangxi Medical University

summary:
GeneChip PrimeView Human PathArrayTM was performed using the SiHa cells-stably expressing shCtrl or shSYT7.
To investigate the underlying mechanism of tumor-suppressive phenotypes of CESC with SYT7 knockdown, we used GeneChip PrimeView Gene Expression Array that could detect expression profiling of over 36,000 transcripts and variants using the SiHa-shCtrl and shSYT7-cDNAs

overall_design: Transcriptomic analysis of SiHa-shCtrl and shSYT7-cDNAs

first: Jinbing

last: Huang

first: Qiaoqiao

first: Erling

first: Ji

last: Li

first: Wensheng

last: Xu


title: Transcript profiling in whole skins of WT and CRTC3 KO mice.

overall_design: Whole skin RNA profiles of WT and CRTC3 KO neaonates (P2, N=4 per group)


title: Combined metabolomic and transcriptomic profiling approaches reveal   the cardiac response to high-fat diet

city: New York

first: John

last: Morrow

state: NY

address: 650 W 168th Street

department: Medicine

institute: College of Physicians and Surgeons of Columbia University

summary:
Purpose: Observing the response of the heart to dietary interventation at the metabolomic and transcriptomic level may have relevance for cardiovascular diseases
Methods: RNA Seq of 12 week old WT male mice on chow or HFD and WT female mice on Chow or HFD; RNA was extracted and reverse-transcribed after polyA selection to complementary DNA for sequencing on an Illumina NovaSeq platform
Results: RNAseq from heart tissue revealed significant differences in expression of 292 mRNA, with an FDR <0.05. PCA showed that there were significant sex differences in chow-fed mice. It also separated HFD-fed vs. Chow-fed samples for both male and female mice.
Conclusions: This work reveals the response of a vital organ to dietary intervention at both metabolomic and transcriptomic levels, which is a fundamental question in physiology that may have relevance for cardiovascular diseases. This work also reveals significant sex differences in cardiac metabolites and gene expression.

overall_design: RNA Seq of 12 week old WT male mice on Chow or HFD and WT female mice on Chow or HFD


title: Single cell analysis of zebrafish marrow in WT and gata2a mutant animals

city: Birmingham

first: Rui

last: Monteiro

state: Select One

address: Medical School, Vincent Drive, IBR West

department: Institute of Cancer and Genomic Sciences

institute: University of Birminhgam

overall_design: Analysing transcriptomics and chromatin acessability

first: Chris

last: Mahony


title: TGF-β and CIS inhibition overcomes NK cell suppression to restore anti-tumor immunity

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

institute: Walter and Eliza Hall Institute of Medical Research

summary: Antibodies targeting “immune checkpoints” have revolutionized cancer therapy by reactivating tumor-resident cytotoxic lymphocytes, primarily CD8 T cells. Interest in targeting analogous pathways in other cytotoxic lymphocytes is growing. Natural killer (NK) cells are key to cancer immunosurveillance by eradicating metastases and driving solid tumor inflammation. NK cell anti-tumor function is dependent on the cytokine interleukin (IL)-15. Ablation of the IL-15 signaling inhibitor CIS (Cish) enhances NK cell anti-tumor immunity by increasing NK cell metabolism and persistence within the tumor microenvironment (TME). The TME has also been shown to impair NK cell fitness via the production of immunosuppressive TGF-b, a suppression which occurs even in the presence of high IL-15 signaling. Here, we identified an unexpected interaction between CIS and the TGF-b signaling pathway in NK cells. Independently, Cish- and Tgfbr2- deficient NK cells are both hyper-responsive to IL-15 and hypo-responsive to TGF-b, with dramatically enhanced anti-tumor immunity. Remarkably, when both these immunosuppressive genes are simultaneously deleted in NK cells, mice are largely resistant to tumor development, suggesting that combining suppression of these two pathways might represent a novel therapeutic strategy to enhance innate anti-cancer immunity.

overall_design: RNA-seq of NK cells in three groups (WT, TGFBRII KO, and CIS KO) and three timepoints unstimulated, 4h TGFB stimulation, 24h TGFB stimulation)

first: Fernando

last: Souza-Fonseca-Guimaraes

first: Soroor

last: Hediyeh-zadeh

first: Momeneh

last: Foroutan

first: Nicholas

middle: D

last: Huntington


title: Gene expression changes after chemical knockout of ENL in Molm13 cells

city: Houston

first: Xin

state: TX

address: One Baylor Plz

department: Pharmacology & Chemical Biology

institute: Baylor College of Medicine

summary: ENL is required for expression of MLL1-target genes as well as the aberrant gene expression in MLL1-r leukemia. We investigated the gene expression changes after selective chemical knockout of ENL in leukemia cells.

overall_design: Molm-13 cells containing MLL-AF9 gene were treated with Cpd-1 for 4 days, and gene expression changes were evaluated.

first: Yuan

last: Yao

first: Fangrui

first: Yongcheng

last: Song


title: Role of SNHG1 on the polarization  of macrophages and inflammation in RAW264.7 cells

city: Zhengzhou

first: Chunling

last: Hu

address: No. 1 Jianshe East Road

institute: The First Affiliated Hospital of Zhengzhou University

summary: The aim of this experiment is to compare gene expression proflies of RAW264.7 cells transfected with no-targeting siRNA or shRNA against SNHG1.To study the effect of lncRNA-SNHG1 on the polarization  of macrophages and inflammation.

overall_design: RAW264.7 cells mRNA profiles of Control and sh-lncRNA-SNHG1 group were determined by High-throughput sequence.

first: Junlu

first: Yingshuai

last: Tan

first: Lihua

last: Xing


title: Linker histone H1FOO is required for bovine preimplantation development by regulating lineage specification and nucleosome assembly

city: Hangzhou

first: Kun

last: Zhang

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Linker histone H1 binds to the nucleosome and is implicated in the regulation of the chromatin structure and function. The H1 variant H1FOO is heavily expressed in oocytes and early embryos. However, given the poor homology of H1FOO among mammals, the functional role of H1FOO during early embryonic development remains largely unknown, especially in domestic animals. Here, we find that H1FOO is not only expressed in oocytes and early embryos but granulosa cells and spermatids in cattle. We then demonstrate that the interference of H1FOO results in early embryonic developmental arrest in cattle using either RNA editing or Trim-Away approach. H1FOO depletion leads to compromised expression of critical lineage-specific genes at the morula stage and affects the establishment of cell polarity. Interestingly, H1FOO depletion causes a significant increase in expression genes encoding other linker H1 and core histones. Concurrently, there is an increase of H3K9me3 and H3K27me3, two markers of repressive chromatin and a decrease of H4K16ac, a marker of open chromatin. Importantly, overexpression of bovine H1FOO results in severe embryonic developmental defects. In sum, we propose that H1FOO controls the proper chromatin structure that is crucial for the fidelity of cell polarization and lineage specification during bovine early development.

overall_design: PolyA RNA profiles of bovine embryos

first: Shuang


title: Effect of SARS-CoV-2 on the human placenta

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: SARS-CoV-2 infection during pregnancy leads to an increased risk of adverse pregnancy outcomes. To determine the host response of the human placenta to SARS-CoV-2 infection, we performed RNA-Seq on placentas from COVID-19+ and COVID-19- mothers, as well as placentas that presented with non-COVID related inflammatory pathologies. We found that placentas infected by SARS-CoV-2 at term show an induction of inflammatory genes, including a robust increase in chemokine and cytokine signaling. Furthermore, when SARS-CoV-2 is detected in the placenta, placenta cell marker identity genes are lost with a concomitant increase in macrophage gene expression. Furthermore, when infected ex vivo, a strong inflammatory response and cellular de-identification is similarly observed, along with an acute increase in cell death in response to viral infection. Our data describes the inflammatory responses that occur in the placenta after SARS-CoV-2 infection both acutely and long-term, and provides a comparison with other placental inflammatory pathologies.

overall_design: Examination of the transcriptomes of placenta samples at time of delivery (n=5 health control, n=17 maternal COVID+, n=4 other inflammatory pathologies) and when infected with SARS-CoV-2 ex vivo (n=3 biological replicates)

first: Tuo

first: Lauretta

last: Lacko


title: Endothelial-immune crosstalk contributes to vasculopathy in nonalcoholic fatty liver disease

city: Singapore

first: Christine

last: Cheung

state: Singapore

address: 59 Nanyang Drive

country: Singapore

institute: Lee Kong Chian School of Medicine

summary: Cardiovascular complications are major causes of death in non-alcoholic fatty liver disease (NAFLD) but the underlying endothelial pathophysiology remains understudied. Here, we cultivated blood outgrowth endothelial cells (BOECs) from NAFLD patients and healthy controls. Our transcriptomic analysis revealed that NAFLD BOECs were activated with chemokine hallmarks, in particular, enhanced CXCL12 was confirmed in arterial tissues of mouse NAFLD models. Immunoprofiling by single-cell analysis further uncovered T cell intensification and potentially T-helper type 1 inflammatory reactions in NAFLD. In evaluating CXCL12-CXCR4 axis in chemotaxis, CXCR4 antagonist (AMD3100) substantially modulated the migration of CD4+ Tcells, natural killer cells and monocytes towards NAFLD BOECs, which was not observed in healthy control coculture. We found that NAFLD and healthy BOECs might preferentially recruit distinct subsets of immune cells, as a result of unique chemokine ligand-receptor interactions. Finally, we enumerated two folds more circulating endothelial cells, a biomarker of vascular injury, in NAFLD patients than healthy subjects. Our work provides insights for modulation of endothelial-immune crosstalk as an avenue for mitigating endothelial dysfunction in NAFLD.

overall_design: scRNA-seq of patient/donor-derived PBMCs

first: Kan

middle: X

last: Wu