title: Global genomic profiling of HIF-1a-regulated genes in bone marrow B cells from OVX mice

first: Zhen

last: Lin

summary: HIF-1a works as a stress-induced transcription factor to induce target genes mediating cell proliferation, meabolism and inflammation. To gain new insights into HIF-1a biology, we used high-throughput sequencing to analyze global HIF-1a transcriptional networks in bone marrow B cells from OVX mice.

overall_design: ChIP-seq was performed to determine the genome-wide HIF-1a binding sites in bone marrow B cells from OVX mice. RNA-seq was used to define differentially expressed genes in bone marrow B cells from OVX mice and sham control mice.

first: Xianyi

last: Meng

first: Aline

last: Bozec


title: Effects of plasma-derived exosomes from the normal and thin camels on hepatocellular carcinoma and their differences at transcriptome and proteomics levels

status: Public on Feb 23 2022

city: shanghai

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

country: China

institute: LC sciences

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Hepatocellular carcinoma (HCC) is a common malignant primary tumor. Camels have high economic and social values, but their potential medical value has not been studied. This study aimed to investigate the effects of thin and normal camel plasma-derived exosomes on HCC.
Methods: Plasma was obtained from thin and normal camels, and used to isolate exosomes by ultracentrifugation. The exosomes were then characterized by transmission electron microscopy and Nano particle tracking analyzer. In vivo imaging of nude mice and hematoxylin eosin (HE) staining of liver tissues were used to explore the effects of the exosomes on tumor growth. Finally, the differences of the two exosomes were further analyzed using small RNA sequencing and proteomics.
Results: In vivo imaging and HE staining showed that no significant differences were found in fluorescence value and liver tissue morphology between the control mice and the mice treated with the exosomes from thin camels; while the fluorescence value and the live histology changes were alleviated in the mice with the exosomes from normal camels. After sequencing and proteomic analysis, 40 DE-miRNAs (15 down-regulated and 25 up-regulated) and 172 DEPs (77 up-regulated and 95 down-regulated) were identified in the plasma-derived exosomes from normal camels. These identified DE-miRNAs and DEPs were significantly enriched in many signaling pathways.
Conclusions: Normal camel plasma-derived exosomes may inhibit the growth of HCC cells through regulating pathways of Ras, Rap1, PI3K-Akt, MAPK, AMPK, and canonical Wnt signaling pathways.

overall_design: Two groups, five replicates per group

first: Guangjie

last: Zhang

first: Yawen

first: Zhaoxing

last: Bai

first: Hongqiang

last: Yao


title: Robust Expansion of Human Pancreatic Progenitors by Small Molecules [CUT&TAG]

status: Public on Feb 24 2022

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: An unlimited source of functional human pancreatic β cells are in highly demand. Even with recent advances in pancreatic β-like cell differentiation from human pluripotent stem cells (hPSCs), several hurdles obviously remain and the differentiation protocols need to be further improved. Chemical strategies are particularly useful to address these challenges. Here, through chemical screening, we unexpectedly identified that BET bromodomain inhibitor I-BET151 could robustly promote the expansion of PDX1 and NKX6.1 double-positive human pancreatic progenitors (PPs). These hPSC-derived expandable pancreatic progenitors (ePPs) can proliferate extensively in a chemically defined condition with I-BET151. Even after long-term expansion, these ePPs maintain pancreatic progenitor cell status. In addition, ePPs can efficiently differentiate into pancreatic β-like cells (ePP-β cells). These ePP-β cells are functional and demonstrate glucose-stimulation insulin-secretion (GSIS) capacity. Mechanistically, I-BET151 can activate Notch signaling and promote the expression of key pancreatic progenitor-associated genes and transcriptional network. Conclusively, our studies achieve the long-term goal of robust expansion of human pancreatic progenitors and represent a significant step towards unlimited supplies of functional human pancreatic β cells that are of great interest for biomedical research and regenerative medicine.

first: Xiaojie

last: Ma

first: Ziyu

last: Zhou

first: Saiyong

last: Zhu


title: The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis [RNA-seq]

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

type: Expression profiling by high throughput sequencing

summary: The contribution of epigenetic dysregulation to metastasis remains understudied. Through a meta-analysis of gene expression datasets followed by a mini-screen, we identified PHF8, a histone demethylase of the Jumonji C protein family, as a novel pro-metastatic gene in melanoma. Loss- and gain-of-function approaches demonstrate that PHF8 promotes cell invasion without affecting proliferation in vitro, and increases dissemination but not sub-cutaneous tumor growth in vivo, thus supporting its specific contribution to the acquisition of metastatic potential. PHF8 requires its histone demethylase activity to enhance melanoma cell invasion. Transcriptomic and epigenomic analyses revealed that PHF8 orchestrates a molecular program that directly controls the TGFβ signaling pathway and as a consequence, melanoma invasion and metastasis. Our findings bring a mechanistic understanding of epigenetic regulation of metastatic fitness in cancer, which may pave the way for improved therapeutic interventions.

overall_design: PHF8 loss-of-function (sgRNA) cellular model was generated in SKMEL-147 melanoma cell line.

first: Rana

last: Moubarak

first: Eva

last: Hernando


title: Robust Expansion of Human Pancreatic Progenitors by Small Molecules [ChIP-seq]


title: NGS analysis of small RNAs under nitrogen excess stress in shoot and root of 2 week old barley plants

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

summary: In order to identify microRNAs involved in response to nitrogen excess stress we performed deep sequencing of sRNA libraries constructed form RNA isolated from roots and shoots of two week old barley plants that have been grown under nitrogen excess stress and control conditions.

overall_design: barley plants grown under conditions and nitrogen excess stress small RNA sequencing

first: Dawid

last: Bielewicz

first: Artur

last: Jarmolowski

first: Aleksandra

last: Grabowska

last: Smoczyńska

first: Andrzej

last: Pacak


title: Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity (ATAC-Seq data).

city: ShangHai

first: Yunguang

last: Li

address: 320, Yueyang Road

institute: Center for Excellence in Molecular Cell Science, CAS

summary: Chromatin accessibility plays an essential role in controlling cellular identity and the therapeutic response of human cancers. However, the chromatin accessibility landscape and gene regulatory network of pancreatic cancer are largely uncharacterized. Here, we integrate the chromatin accessibility profiles of 84 pancreatic cancer organoid lines with whole-genome sequencing data, transcriptomic sequencing data and the results of drug sensitivity analysis of 283 epigenetic-related chemicals and 5 chemotherapeutic drugs. We identify distinct transcription factors that distinguish molecular subtypes of pancreatic cancer, predict numerous chromatin accessibility peaks associated with gene regulatory networks, discover novel regulatory noncoding mutations with potential as cancer drivers, and reveal the chromatin accessibility signatures associated with drug sensitivity. These results not only provide the chromatin accessibility atlas of pancreatic cancer but also suggest a systematic approach to comprehensively understand the gene regulatory network of pancreatic cancer in order to advance diagnosis and potential personalized medicine applications.

overall_design:
For each PDPCO line, we prepared two sequencing libraries (technical replicates). ATAC-seq libraries were generated using a TruePrep DNA Library Prep Kit V2 for Illumina according to the manufacturer’s instructions. For each technical replicate, we selected the one with the higher QC score to quantify the chromatin accessibility of this sample. We used ChIP-seq-defined chromHMM states from the Roadmap Epigenomics Project to investigate the distribution of exocrine reproducible PDPCO peaks in the chromatin states. To investigate the similarity between the reproducible peaks in the PDPCO and pan-cancer data, we performed principal coordinates analysis, which takes a set of dissimilarities or distances as input and returns a set of points. We used the SCENIC workflow to identify the gene regulatory network (TF regulon) and scored the activity of the TF regulon. To identify the key regulators for specific peaks, we performed motif enrichment with HOMER. We also identified subtype-specific regulons by integrating RNA-seq and ATAC-seq data, links between ATAC-seq peak openness and targeted gene expression, and links between ATAC-seq peak openness and drug sensitivity.

***Please note that
the raw data has been uploaded to a domestic repository National Omics Data Encyclopedia (NODE; https://www.biosino.org/node/index) with controlled access mechanisms under accession number OEP001744.
the PDPCO_drug_screening.txt contains drug sensitivity AUC for each sample
the transcriptomic sequencing data is repreasent in GEO under GSE194249.

first: Dong

last: Gao


title: Synergistic anti-tumor efficacy of mutant isocitrate dehydrogenase 1 inhibitor SYC-435 with standard therapy in patient-derived xenograft mouse models of glioma

city: Cincinnati

first: Frank

last: Huang

state: OHIO

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Isocitrate dehydrogenase 1 (IDH1) is mutated in >70% of these tumors, making it an attractive therapeutic target.  To determine the efficacy of our newly developed mutant IDH1 inhibitor, SYC-435 (1-hydroxypyridin-2-one), we treated orthotopic glioma xenograft model (IC-BT142AOA) carrying R132H mutation and our newly established orthotopic patient-derived xenograft (PDX) model of recurrent anaplastic oligoastrocytoma (IC-V0914AOA) bearing R132C mutation.  In addition to suppressing IDH1 mutant cell proliferation in vitro, SYC-435 (15 mg/kg, daily x 28 days) synergistically prolonged animal survival times with standard therapies (Temozolomide + fractionated radiation) mediated by reduction of H3K4/H3K9 methylation and expression of mitochondrial DNA (mtDNA)-encoded molecules. Furthermore, RNA-seq of the remnant tumors identified genes (MYO1F, CTC1 and BCL9) and pathways (base excision repair, TCA cycle II, sirtuin signaling, protein kinase A, eukaryotic initiation factor 2 and α-adrenergic signaling) as mediators of therapy resistance.

overall_design: To understand drug model of mechanism of SYC-435, we conducted bulk RNA sequencing analysis of patient-derived xenograft mice model of glioma with SYC-435 treatment, radiation treatement and combination treatment


title: Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity

overall_design:
Total RNA of PDPCOs (n=84) and NPOs (n=3) with enough amount (3 μg) and high quality were used to prepare the transcriptome library. RNA-seq libraries were generated following the manufacturer’s instructions (NEBNext Ultra RNA Library Prep Kit, New England Biolabs, E7530L). Library quality was measured on an Qxcel Bioanalyzer for product size. Paired-end libraries were sequenced by the Illumina HiSeq X Ten platform. TopHat were used to map the sequencing reads to the human reference genome hg19. The fragments per kilobase of exon per million mapped reads (FPKM) values were determined using Cufflinks. Genes with FPKM values <1 in all 87 samples were filtered out. Finally, 15,819 protein-coding genes remained for further analysis.

Raw data are not available for this Series due to human genetic resources policy in China.


title: Transcriptomic profiling of interferon signature in Systemic Lupus Erythematosus

city: Stanford

first: Gloria

last: Yiu

state: CA

address: CCSR Building Room 2215

institute: Stanford University

summary: The establishment of an interferon (IFN) signature to subset SLE patients on disease severity has led to therapeutics targeting IFNa. Here, we investigate IFN signaling in SLE by first determining the IFN signature for SLE patients (n=81) from the Stanford Lupus Registry using fluidigm qPCR. We measured 44 previously determined IFN-inducible transcripts to subset patients as IFN-high (IFN-H) or IFN-low (IFN-L).

overall_design: 81 SLE samples and 26 healthy controls, in duplicate

first: P

middle: J

last: Utz


title: Aerosol delivery, but not intramuscular injection, of adenovirus-vectored tuberculosis vaccine induces respiratory-mucosal immunity in humans

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St West

department: Department of Medicine

country: Canada

institute: McMaster University

summary: Since besides mucosal adaptive immunity, respiratory delivery of AdHu5Ag85A vaccine in experimental animals induced a trained phenotype in airway macrophages, we examined whether aerosol vaccination with AdHu5Ag85A could also alter the immune property of human alveolar macrophages (AM). To this end, we elected to examine the transcriptomics of BALF cells obtained from 5 participants before (wk0) and after (wk8) 1x106PFU AdHu5Ag85A aerosol vaccination. Before RNA isolation, the cells, upon revival from frozen stock, were enriched for AM and cultured with or without stimulation with M.tb lysates and transcriptionally profiled by RNAseq analysis. Principal component analysis (PCA) revealed that unstimulated (US) and stimulated (S) AM populations were separated away from each other. We then identified the differentially expressed genes (DEGs) by comparing wk0- and wk8-stimulated AM with respective unstimulated AM. By this pairwise analysis, we identified 194 and 426 genes uniquely upregulated and downregulated, respectively, in stimulated AM from aerosol vaccinated participants. The uniquely up-regulated genes in stimulated wk8 aerosol AM showed enrichment in a number of biological processes including response to anoxia (OXTR, CTGF), inflammatory response to antigenic stimuli (IL2RA, IL1B, IL20RB), tyrosine phosphorylation of STAT protein (IFNG, F2R, OSM), regulation of IL-10 production (CD83, IRF4, IL20RB, IDO1), response to IL-1 (RIPK2, SRC, IRAK2, IL1R1, XYLT1, RELA) and histone demethylation (KDM6B, KDM5B, KDM1A, KDM7A, JMJD6). In comparison, the uniquely down-regulated genes in wk8 aerosol AM did not appear significantly enriched for any biological processes. These data suggest that aerosol vaccination leads to persisting transcriptional changes in airway-resident alveolar macrophages poised for defense responses.

overall_design: Airway macrophage mRNA profile at baseline and at 8wks after AdHu5Ag85A aerosol vaccination with and without ex vivo stimulation with M. tuberculosis cell lysate

first: Mangalakumari

last: Jeyanathan

first: Zhou

last: Xing

first: Fiona

last: Smaill


title: Transcriptomes of SARS-CoV-2 naïve and recovered individuals vaccinated with inactivated vaccine

city: Jinan

first: yuwei

last: Zhang

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

institute: SDCDC

summary: The urgent approval of the use of the inactivated COVID-19 vaccine is essential to reduce the threat and burden of the epidemic on global public health, however, our current understanding of the host immune response to inactivated vaccine remains limited. We performed transcriptomics analysis on 20 SARS-CoV-2 naïve individuals who received multiple doses of inactivated vaccine and five SARS-CoV-2 recovered individuals who received single dose of inactivated vaccine. These data help us understand the reaction mechanism of the host's molecular immune system to the inactivated vaccine, and provide a basis for the choice of vaccination strategy.

overall_design: Retinal mRNA profiles of 20 SARS-CoV-2 naïve individuals who received multiple doses of inactivated vaccine and five SARS-CoV-2 recovered individuals who received single dose of inactivated vaccine after 14 days.

first: Xiaolin

last: Jiang

first: Yuwei


title: Expression data from durvalumab, oleclumab and combo-treated xenograft NSCLC tumors

city: Gaithersburg

first: Eric

last: Tu

state: MD

address: 1 Medimmune way

institute: AstraZeneca

summary:
Non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations do not respond to anti-PD-1 (L1) as well as tumors without an EGFR mutation. We showed in a xenograft mouse model of EGFR-mutated NSCLC that, neither durvalumab nor oleclumab alone inhibited tumor growth compared to the isotype control. In contrast, the combination of both antibodies significantly inhibited tumor growth and increased gene expressions that corresponded to inflammation and T cell function in tumors treated.
We used microarrays to study gene expressions that corresponded to enhanced immune response in antibody-treated mice.

overall_design: Tumor-bearing mice were treated with durvalumab, oleclumab or combination of both antibodies, together with tumor antigen-specific T cells. Total RNA was extracted from tumors and converted to biotin-labeled cRNA, which was then fragmented and hybridized on Affymetrix GeneChip.

first: Kelly

last: McGlinchey

first: Jixin

last: Wang

first: Steven

last: Ching

first: Katie

last: Streicher


title: Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

country: Germany

institute: Twincore

summary:
Purpose : The goal of this study was to use RNA Seq to explore the success of lasR mutants in the opportunistic pathogen Pseudomonas aeruginosa in a clinical context by profiling the functional consequences of patho-adaptive mutations in clinical isolates.
Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples by deep sequencing.Ribosomal RNA was removed by using the RiboZero Bacteria kit (Illumina). cDNA libraries were synthesized using the SMARTScribe Reverse Transcriptase (Takara) followed by a PCR enrichment using the AccuPrime HiFi Taq polymerase (Invitrogen). Enzymatic reactions were carried out in the presence of SUPERase·In™ RNase Inhibitor (Invitrogen); RNACleanXP beads (Agencourt) were used for all RNA purification steps. Quality checks were performed before, during and after cDNA library preparation with the RNA Nano Kit and an Agilent Bioanalyzer 2100 (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end mode; 2 x 50 bp) and mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with customized settings and mapped to the NC_008463.1 (PA14) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with the settings “--very-sensitive-local; --no-mixed; --fr; --no-unal”.

overall_design: mRNA profiles from Pseudomonas aeruginosa derived from cells that were either grown in LB to an OD600 =2 (planktonic) or inoculated at a starting OD600 of 0.002 in LB and grown statically in half-area 96-well µClear microtiter plates at 37 °C in humid atmosphere for 48 h and deep sequenced using Illumina NovaSeq6000.

first: Alexander

last: Jeske

first: Alejandro

last: Arce-Rodriguez

first: Janne

middle: G

last: Thöming

first: Jürgen

last: Tomasch


title: Urinary sediment mRNA level of CREBBP and CYBA in children with steroid-resistant nephrotic syndrome

city: HangZhou

first: Danni

address: 3333 Binsheng Rd, Hangzhou,Zhejiang

institute: Children's Hospital Affiliated to Zhejiang University

summary: This study aimed to evaluate gene expression patterns in urinary sediment samples of children with steroid-resistant nephrotic syndrome (SRNS).

overall_design: The messenger RNA (mRNA) levels of 770 autoimmune-related genes were detected using a NanoString nCounter platform. To verify the NanoString results, quantitative analysis of nine gene mRNAs was performed using real-time RT-PCR in more samples.

first: Wei

last: Li

first: Wenqing

last: Xiang

first: Lin

last: He

first: Haidong

last: Fu

first: Jianhua

last: Mao


title: Influence of Age and Sex on microRNA Response and Recovery in the Hippocampus Following Sepsis

city: Gainesville

first: Thomas

middle: C

last: Foster

state: FL

address: 1149 S Newell Dr.

department: Neuroscience

institute: University of Florida

summary: Sepsis, defined as a life-threatening organ dysfunction caused by a dysregulated host immune response to infection, is a common and dangerous clinical syndrome.  Sepsis results in an excessive host inflammatory response that can induce immediate and persistent cognitive decline, and this is known to be worse in older individuals.  Sex-specific differences in the outcome of infectious diseases and sepsis appear to favor females.  These differences likely involve sex steroids, sex chromosomes, and possibly epigenetic mechanisms.  We employed a murine model to examine the influence of age and sex on the brain's microRNA (miR) response following sepsis.  Young (~ 4 months) and old (~ 20 months) adult mice (C57BL/6) of both sexes underwent cecal ligation and puncture (CLP) with daily restraint stress.  Differential expression of hippocampal miR was examined in age- and sex-matched controls at 1 and 4 days post-CLP.  A sexually dimorphic miR response was observed.  Similar to previous work examining the transcription profile, young females exhibited a better recovery of the miR profile from day1 to day4, relative to young males and old females.  For young males and all female groups, the initial response mainly involved a decrease in miR expression.  In contrast, old males exhibited only upregulated miR on day1 and day4, with 22 miR upregulated across days.  Examination of the relationship of these 22 upregulated miR with mRNA expression indicated downregulation of mRNA with time from induction of sepsis and was more pronounced for mRNA that were associated with multiple upregulated miR.  The results emphasize age and sex differences in epigenetic mechanisms that likely contribute sexually dimorphic responses to sepsis.

overall_design: This study was conducted on 48 mice either 24 hours or 4 days after sepsis [young male control (n = 4), young male 24 hours post-sepsis (n = 4), young male 4 days post-sepsis (n = 4), old male control (n = 4), old male 24 hours post-sepsis (n = 4), old male 4 days post-sepsis (n = 4), young female control (n = 4), young female 24 hours post-sepsis (n = 4), young female 4 days post-sepsis (n = 4), old female control (n = 4), old female 24 hours post-sepsis (n = 4), and old female 4 days post-sepsis (n = 4)]. Hippocampal microRNA was used to investigate how sepsis altered the response in the brain within different age and sex groups.

first: Asha

last: Rani

first: Jolie

last: Barter

first: Ashok

last: Kumar

first: Julie

middle: A

last: Stortz

first: McKenzie

last: Hollen

first: Dina

last: Nacionales

first: Lyle

middle: L

last: Moldawer

first: Philip

last: Efron


title: Synergistic regulation of transcription and translation in Escherichia coli revealed by co-directional increases in mRNA concentration and translation efficiency

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

summary: Translational regulation was investigated at the genome scale in Escherichia coli cells. Using the polysome profiling method, the ribosome occupancy (RO) and ribosome density (RD) of different mRNA copies were determined for several hundred mRNAs during the exponential and stationary phases, providing the most complete characterisation of such regulation in E. coli. Although for most genes, nearly all mRNAs (>90%) were undergoing translation, they were loaded with far fewer than the theoretical maximum number of ribosomes, suggesting translation limitation at the initiation step. Multiple linear regression was used to identify key intrinsic factors involved in the genome-wide regulation of RO and RD (i.e., open reading frame GC%, protein function and localisation). Unexpectedly, mRNA concentration, a factor that depends on cell physiology, was predicted to positively regulate RO and RD during the exponential and stationary phases. Using a set of selected genes controlled by an inducible promoter, we confirmed that increasing the mRNA concentration upon transcription induction led to increases in both RO and ribosome load. The fact that this relationship between mRNA concentration and translation parameters was also effective when E. coli cells naturally adapted to carbon source changes demonstrates its physiological relevance. This work demonstrates that translation regulation is positively controlled by transcript availability. This new mechanism contributes to the co-directional regulation of transcription and translation with synergistic effects on gene expression, and provides a systemic understanding of E. coli cell function.

overall_design: We reported RNA-seq data for translatome experiments performed in E. coli MG1655 in two growth phases (exponential phase and stationary phase). In each phase, translatome experiments consisting of 7 RNA-seq for each polysomal fraction from A to G were carried out in triplicates.

first: Huong

last: Nguyen

first: Marie-Pierre

last: Duviau

first: Sandrine

last: Laguerre

first: Sébastien

last: Nouaille

first: Muriel

last: Cocaign-Bousquet


title: Loss of TET reprograms Wnt signaling through impaired demethylation to promote lung cancer development

city: Shanghai

first: Chao

last: Wang

address: 320 Yue Yang Road

institute: Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Oncogenic imbalance of DNA methylation is well-recognized in cancer development. Ten-eleven translocation (TET) family of dioxygenases, which facilitate DNA demethylation, are frequently dysregulated in cancers. How such dysregulation contributes to tumorigenesis remains poorly understood, especially in solid tumors which present infrequent mutational incidence of TET genes. Here we identify TET mutations in 7.4% of human lung adenocarcinoma (LUAD), which frequently co-occur with oncogenic KRAS mutations, and this co-occurrence is predictive of poor survival in LUAD patients. Using autochthonous mouse model of KrasG12D-driven LUAD, we show that individual or combinational loss of Tet genes markedly promotes tumor development. In this Kras-mutant and Tet-deficient model, pre-malignant lung epithelium undergoes neoplastic reprogramming of DNA methylation and transcription, with a particular impact on Wnt signaling. Among the Wnt-associated components that undergo reprogramming, multiple canonical Wnt antagonizing genes present impaired expression arising from elevated DNA methylation, triggering aberrant activation of Wnt signaling. These impairments can be largely reversed upon the restoration of TET activity. Correspondingly, genetic depletion of β-catenin, the transcriptional effector of Wnt signaling, substantially reverts the malignant progression of Tet-deficient LUAD. These findings reveal TET enzymes as critical epigenetic barriers against lung tumorigenesis and highlight the therapeutic vulnerability of TET-mutant lung cancer through targeting Wnt signaling.

overall_design: Low-input RNA-seq and low-input WGBS were performed on mouse pre-malignant lung epithelial cells in the setting of mutant Kras to compare gene expression and DNA methylation differences between Tet-deficient and wild type samples. Bulk RNA-seq and Bulk TAPS were performed on KrasG12D/+; Tet-deficient (KT) LUAD cell lines derived from tumor-bearing mouse lung tissues following constitutive expression of Tet2CD or Tet2HD to examine alterations in gene expression and DNA methylation upon re-introduction of TET catalytic activity.

first: Qin

last: Xu


title: Human-induced CD49a+ NK cells promote fetal growth

city: Hefei

first: Xianghui

last: Du

state: Anhui

address: 443 Huangshan Road

department: Institute of Immunology

institute: Division of Life Sciences and Medicine

summary: CD49a+ natural killer (NK) cells are critical in promoting fetal development and maintaining immune tolerance at the maternal-fetal interface in early pregnancy. However, their tissue residency in human tissue hinder thorough studies and clinical application. How to induce functional human CD49a+ NK cells that could benefit pregnancy outcomes is still unknown. Here, we have established three no feeder cell induction systems to induce human CD49a+ NK cells from umbilical cord blood hematopoietic stem cells (HSCs), bone marrow HSCs or peripheral blood NK cells, respectively. These induced NK cells (iNKs) from three cell induction systems show high expression of CD49a, CD9, CD39, CD151, low expression of CD16, and no obvious cytotoxic capability, phenotypically and functionally similar with decidual NK cells. Furthermore, these iNKs also have high expression of growth-promoting factors and proangiogenic factors. Importantly, these iNKs have shown their capabilities to promote fetal growth and improve uterine artery blood flow in a murine pregnancy model in vivo. This research reveals properties of human-induced CD49a+ NK cells in promoting fetal growth from three cell induction systems, which may improve the feasibility of applying these iNKs to the patients having adverse pregnancy outcomes.

overall_design: The mRNA profiles of decidual NK cells, peripheral blood NK cells, induced CD49a+ NK cells from umbilical cord blood hematopoietic stem cells (HSCs), bone marrow HSCs or peripheral blood NK cells. Samples were all from healthy people.


title: Expression data of primary osteoarthritic chondrocytes treated with Galectin-4

city: Wien

first: Katharina

middle: M.

last: Pichler

state: Wien

address: Odoakergasse

department: Department of Orthopedics and Trauma Surgery

country: Austria

institute: Medical University of Vienna

summary: The severity of osteoarthritis is linked to elevated levels of galectins. Here, the aim of the study was to evaluate the role of Galectin-4 in osteoarthritic cartilage.

overall_design: From five osteoarthritis (OA) patients chondrocytes were isolated and treated with Galectin-4. Thereafter total RNA was isolated and an Affymetrix microarray was performed.

middle: M

first: Stefan

last: Toegel


title: RpoN/Sfa2-dependent activation of the Pseudomonas aeruginosa H2-T6SS and its cognate arsenal of antibacterial toxins

city: London

first: Luke

last: Allsopp

address: Emmanuel Kaye Building, 1B Manresa Roa

country: United Kingdom

institute: Imperial College

summary: Pseudomonas aeruginosa uses three type six secretion systems (H1-, H2- and H3-T6SS) to manipulate its environment, subvert host cells and compete with microbial competitors. These T6SS machines can be loaded with a variety of effectors/toxins, many being associated with a specific VgrG. How P. aeruginosa transcriptionally coordinates the three main T6SS clusters and the multiple vgrG islands spread through the genome is unknown. Here we show an unprecedented level of control of the regulator RsmA in repressing most known T6SS-related genes. Moreover, it is noticeable that a sigma factor activator (SFA) protein is encoded in each of H2- and H3-T6SS clusters, Sfa2 and Sfa3, respectively. SFA proteins are enhancer binding proteins that usually work in concert with the sigma factor RpoN. Using a combination of RNA-seq, ChIP-seq and molecular biology approaches, we demonstrate that RpoN coordinates the T6SSs of P. aeruginosa by activating the H2-T6SS but repressing the H1- and H3-T6SS. Furthermore, RpoN and Sfa2 control the expression of all H2-T6SS-linked VgrG and effector arsenal to enable very effective interbacterial killing. Such RpoN-dependent control is exerted both directly and indirectly. The function of the SFA protein is specific since the H3-T6SS associated Sfa3 cannot complement loss of Sfa2. Our study further delineates the multiple regulatory mechanisms that modulate the deployment of an arsenal of T6SS effectors likely to respond and adapt to a range of environmental conditions that a versatile organism like P. aeruginosa would encounter.

overall_design: Five different samples (PA14, PA14rsmA, PA14rsmAsfa2, PA14rsmArpoN, PA14rsmAsfa2, PA14rsmAsfa3) with three replicate for each. Anaylsis perfromed against all samples but foucs of the study is the comparision against PA14rsmA.

middle: P

first: Alain

last: Filloux


title: Sucrose and temperature stress to Liberibacter crescens

first: Kaylie

last: Padgett-Pagliai

state: Florida

address: 2033 Mowry Road, Lab 325 CGRC

summary: RNA sequencing of L. crescens grown in different stress conditions.

overall_design: L. crescens BT-1 cultures were cultured at 25°C in the presence and absence of 100 mM sucrose, or 0.05% DMSO. For the heat stress, L. crescens cells were grown at 32°C.

first: Fernando

last: Pagliai

first: Danilo

last: da Silva

first: Christopher

last: Gardner

first: Graciela

last: Lorca

first: Claudio

last: Gonzalez


title: Hydrogen gas inhibits the formation of neutrophil extracellular traps

city: Tokyo

first: Kohsuke

last: Shirakawa

address: 35 Shinanomachi, Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medicine

summary: Neutrophil extracellular traps (NETs) contribute to inflammatory pathogenesis, especially in infectious and cardiovascular diseases. H2 gas acts as an antioxidant and has been clinically and experimentally proven to ameliorate inflammation. Therefore, we investigated whether H2 gas could inhibit NET formation associated with excessive neutrophil activation. Phorbol-12-myristate-13-acetate (PMA)-stimulated human neutrophils exposed to H2 exhibited reduced citrullination of histones, membrane disruption by chromatin complexes, and release of NET components over controls. Mechanistically, H2 suppressed the phosphorylation of Ser-139 residue in H2AX, a marker of DNA damage, thereby reducing the expression of CXC-chemokine receptor 4 (CXCR4) in PMA-stimulated neutrophils. Along with the upregulation of CXCR4, the intracellular content of myeloperoxidase (MPO) and the production of MPO-derived hypochlorous acid (HOCl) was increased; however, these effects were markedly suppressed in H2-exposed cultures. Thus, H2 neutralized HOCl produced by the oxidative burst, inhibited DNA damage, and subsequently inhibited NET formation. We further confirmed that inhalation of H2 inhibited the formation and release of NET components in the blood and bronchoalveolar lavage of a lipopolysaccharide-induced sepsis model in mice and aged minipigs. Therefore, H2 therapy has the potential to be a new therapeutic agent for inflammatory diseases involving NETs associated with excessive neutrophil activation.

overall_design: 9 samples; Cell cultures of neutrophils in RPMI 1640 medium containing 15 mM HEPES were exposed to hydrogen gas using a hydrogen-filling device with a built-in hydrogen-absorbing alloy. The control medium was left untreated. Aliquots containing 1×10^7 isolated human neutrophils were stimulated with 100 nM phorbol 12-myristate 13-acetate (PMA) in the control or hydrogen gas-exposed medium at 37 °C for 1 h.

first: Motoaki

last: Sano


title: ACSL4 effect on renal ischemia-reperfusion (I/R) injury

city: Nanjing

first: Xinghua

last: Gao

address: jiangning longmian avenue 639,nanjing

institute: china pharmaceutical university

summary: Analysis of acute kidney injury (AKI) with  knockdown of ACSL4. Results provide insight into the role of ACSL4 in the regulation of ferroptosis.

overall_design: Kidney Tissues mRNA profiles of control and ACSL4 knockdown mice were generated by deep sequencing, in duplicate.

first: Yong

last: Yang

first: Yue


title: Upregulation of cytokine signalling in platelet increases risk of thrombophilia in severe COVID-19 patients

city: Faridabad

first: Prasenjit

last: Guchhait

state: Haryana

address: Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad-Gurgaon Expressway, 3rd Milestone,

country: India

institute: Prasenjit Guchhait

summary: Our study reports that the over-expression of cytokine receptors as well as prothombotic genes of the platelets and high plasma level of proinflammatory cytokines aggravates thrombophilia in severly ill patients with COVID-19.

overall_design: Platelet mRNA profiles of asymptomatic and severe symptomatic COVID-19 patients

first: Kaur

last: Simrandeep

first: Singh

last: Anamika

last: Jaskaran

first: Verma

last: Nikhil

first: Pandey

middle: K

last: Anil

first: Das

last: Suman

first: Bhattacharyya

last: Sankar

first: Guchhait

last: Prasenjit


title: Whole-transcriptome analysis and construction of ceRNA-miRNA-target gene regulatory networks in anther development of Chinese cabbage (Brassica campestris L. ssp. pekinensis) [Anther & mixed parts mRNA]

city: Shenyang

first: Zhiyong

last: Liu

state: Liaoning Province

address: Dongling Road 120

institute: Shenyang Agriculral University

summary: Anther development is a complex process, and the study of its molecular mechanism has an important impact on plant breeding. This study aims to identify microRNA (miRNA), mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) related to anther development of Chinese cabbage, so as to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge for the exploration of pollen development mechanism of Chinese cabbage. A total of 9055 mRNA, 585 miRNA, 1344 lncRNA, and 165 circRNA were identified as differentially expressed in the anther of Chinese cabbage compared with Mix (roots, stems and leaves) by whole-transcriptome sequencing. The anther-related ceRNA-miRNA-target gene regulatory network through miRNA targeting relationships was constructed and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions were obtained in Chinese cabbage. The genes in the ceRNA network were enriched in the pathways including starch and sucrose metabolism, carbon metabolism, pyruvate metabolism and carbon fixation in photosynthetic organisms, plant hormone signal transduction, and RNA degradation. This study identified some important genes and their interaction lncRNAs, circRNAs, and miRNAs involved in microsporogenesis (BraA06g035480.3C), tapetum and callose layer development (BraA09g009280.3C, BraA04g028920.3C, and BraA10g022680.3C etc), pollen wall formation (BraA06g000980.3C, BraA02g023130.3C, and BraA10g029650.3C etc), and anther dehiscence (BraA10g027200.3C, BraA04g023740.3C, and BraA04g030860.3C etc). Additionally, we analyzed the promoter activity of six anther predominant expression genes, and the results showed that they were all expressed specifically in the anther of Chinese cabbage. This study lay the foundation for further research on the molecular mechanism of anther growth and development.

overall_design: we performed the whole-transcriptome sequencing of anther and Mix (roots, stems and leaves), and identified expression changes of miRNAs, lncRNAs, circRNAs, and mRNAs, and analyzed their potential regulatory roles with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG)

first: Fengyan

last: Shi

first: Zhijin

last: Pang


title: A microarray of circular RNAs in human keloid dermal fibroblasts

city: Hangzhou

first: qianqian

last: pang

address: Qingchun road

department: Plastic Surgery

institute: The First Affiliated Hospital, School of Medicine, Zhejiang University,

summary: To further explore the  expression of circular RNAs in keloid，we have completed the Arraystar Human circRNA Array V2 analysis of the 8 samples，including 4 patients-derived keloid dermal fibroblasts and 4 normal dermal fibroblasts.

overall_design: Eight samples were analyzed,including 4 patients-derived keloid dermal fibroblasts and 4 normal dermal fibroblasts.

first: jiaqi

last: sun

first: xiaohu

last: lin


title: Whole-transcriptome analysis and construction of ceRNA-miRNA-target gene regulatory networks in anther development of Chinese cabbage (Brassica campestris L. ssp. pekinensis) [Anther & mixed parts miRNA-seq]


title: Genome-wide Analyses Revealed the Global Impacts of SARS-CoV-2 Viral Gene Orf9c on Human Cardiomyocytes

city: Indianapolis

first: Lei

state: Indiana

address: 1044 W Walnut Street, R4 272

department: Department of Pediatrics

institute: Indiana University School of Medicine

summary: Coronavirus disease 2019 (COVID-19) is a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 patients accompany with high frequencies of cardiac complications, which prominently contributed to the overall SARS-CoV-2-caused mortality. SARS-CoV-2 genome was reported to encode up to 14 genes. Currently, molecular mechanisms underlying SARS-CoV-2 viral gene-induced cardiac manifestations still remain elusive. Here, we overexpressed Orf9c, a SARS-CoV-2 encoded gene, in human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs). Multiple genome-wide analyses were performed to investigate the global impacts of Orf9c on hPSC-CMs. The mRNA-seq indicated stress-related signaling pathways, including cell death, immune and inflammation responses, activated by Orf9c. High-throughput proteomics and Co-immunoprecipitation mass spectrometry studies revealed the global influence of Orf9c on the proteome of hPSC-CMs and Orf9c-interactive protein network in hPSC-CMs. Orf9c overexpression elevated protein expressions of key factors essential for apoptosis while suppressing protein factors crucial for ATP synthesis. Further experimental validations confirmed that Orf9c overexpression induced prominent cell death, abnormal calcium handling and electrical properties, and significantly reduced cellular ATP level in hPSC-CMs. Finally, administration of two FDA-approved drugs, Ivermectin and Meclizine, were proven by our study to restore ATP level to prominently ameliorate Orf9c-induced cell death and electrical abnormalities of hPSC-CMs. Overall, we comprehensively manifest global responses of host human heart muscle cells to SARS-CoV-2 gene Orf9c, characterized molecular mechanisms underlying Orf9c-induced cardiac abnormalities, and explored potentially therapeutic approaches to ameliorate cardiac dysfunctions in COVID-19 patients.

overall_design: RNA-seq of 6 hPSC-CM samples (3 control + 3 Orf9c OE)

first: Juli


title: From cohorts to molecules: adverse impacts of endocrine disrupting mixtures. Transcriptomics Analysis

city: Milano

first: Nicolò

last: Caporale

state: MI

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncolology

summary: Convergent evidence associates exposure to endocrine disrupting chemicals (EDCs) with major human diseases, even at regulation-compliant concentrations. This might be because humans are exposed to EDC mixtures, whereas chemical regulation is based on a risk assessment of individual compounds. Here, we developed a mixture-centered risk assessment strategy that integrates epidemiological and experimental evidence. We identified that exposure to an EDC mixture in early pregnancy is associated with language delay in offspring. At human-relevant concentrations, this mixture disrupted hormone-regulated and disease-relevant regulatory networks in human brain organoids and in the model organisms Xenopus leavis and Danio rerio, as well as behavioral responses. Reinterrogating epidemiological data, we found that up to 54% of the children had prenatal exposures above experimentally derived levels of concern, reaching, for the upper decile compared with the lowest decile of exposure, a 3.3 times higher risk of language delay.

overall_design: Examination of multiple doses of EDC mixture effects on the transcriptome of human cortical brain organoids and fetal neural progenitors.

first: Cristina

last: Cheroni

first: Pierre

last: Germain

first: Giuseppe

last: Testa


title: Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 Infection

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

summary: The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing worldwide has led to major issues in scaling the efforts of diagnostic labs and even in securing basic supplies for collection and processing of samples. This has in turn led to worldwide efforts by the scientific community to establish improved protocols that are cheaper, more scalable, and not as resource intensive. One such effort resulted in an assay called “Swab-Seq”, which was so named because it was originally developed to work with dry nasal swab samples, but is actually flexible in terms of the sample type it can accommodate for testing. The assay adapts the existing gold standard (RNA extracted from a nasopharyngeal (NP) swab that is subjected to quantitative reverse transcription polymerase chain reaction, “qRT-PCR”) to a next-generation sequencing readout. By pairing this modification with extraction-free sampling techniques it is possible to achieve high scalability at low cost per sample, and a reasonable turnaround time for reporting results. We evaluated the effectiveness of this assay both on samples collected from asymptomatic individuals using the traditional NP swab and using alternative extraction-free sampling techniques, including saliva and a saline mouth gargle protocol, and found the assay to be highly sensitive (comparable to the standard qRT-PCR assay), flexible (adaptable to saliva and gargle samples stored at room temperature up to a week), and scalable (easily accommodating hundreds of samples at a time). Continued development in the future will lead to more effective testing regimes that reduce the burden of transmissible respiratory infections on the global community.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: Through a series of experiments, we evaluated the performance of Swab-Seq in detecting SARS-CoV-2 in various sample types, including: extracted RNA samples from asymptomatic individuals, extration-free saliva samples, and extraction-free saline gargle samples. This project involves a total of 9 different experiments.

first: HyunJin

last: Kang

first: Sheilah

last: Allison

first: Amber

last: Spangenberg

first: Tara

last: Carr

first: Ryan

last: Sprissler

first: Marilyn

last: Halonen


title: A Selective PPARγ modulator, Pemafibrate Suppressed NLRP3 Inflammasome Activation Both in Liver and Heart in a Model of “Steatohepatitis-Related Cardiomyopathy”

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: It has been recently reported that the patients with non-alcoholic fatty liver diseases (NAFLD) had accompanied with cardiac dysfunction.  However, an animal model of steatohepatitis related cardiomyopathy has not been reported.  In the current study, we have developed a mouse model of steatohepatitis-related cardiomyopathy and examined whether a selective PPARα modulator, pemafibrate would improve both steatohepatitis and cardiomyopathy. C57Bl/6 male mice were fed 1. normal chow diet (C group), 2. high fat/high cholesterol/high sucrose/bile acid diet (N group), or 3. N with pemafibrate 0.1 mg/kg (NP group) for three or eight weeks, respectively.  Cardiac function was evaluated by ultra-high magnetic field 7-Tesla magnetic resonance imaging (7T-MRI).  Even at the eight weeks, we have detected cholesterol crystals, free cholesterol accumulation in liver, followed by macrophage infiltration and fibrosis as wells as activation of NLRP3, caspase-1 and IL-1βmRNA.  At the same time in heart, the ratio of heart to body was increased in N group compared to C group.  Left ventricular (LV) ejection fraction (LVEF) was moderately decreased in N group compared to C group (50.2±2.8 vs 59.8±2.1, p<0.05).  LV circumferential strain and radial strain are focally attenuated in N group, suggesting the early lesion of myocardial damages.  mRNA expression of Nlrp3, Caspase1 and Il1b were enhanced in N group, followed by increased protein levels of Caspase-1 and Asc.  Rna-sequence analysis revealed that NOD-like receptor and PI3 kinase-AKT pathways were up-regulated, suggesting hypertrophic phenotypes. in N group.  Importantly, NLRP3 inflammasome activation were suppressed both in liver and heart in NP group, suggesting pemafibrate had the beneficial effect on steatohepatitis and cardiomyopathy.  In addition, four week treatment by pemafibrate improved steatohepatitis and cardiomyopathy after development for eight week. We have first developed the animal model of steatohepatitis-related cardiomyopathy, characterized by the activation of NLRP3 inflammasome pathway both in liver and heart.  Steatohepatitis-related cardiomyopathy displayed moderate reduction of LVEF and focal impairment of LV strain by 7T-MRI.  Pemafibrate suppressed steatohepatitis, hepatic fibrosis and cardiomyopathy.

overall_design: We compared the three (C, N and NP)goups in duplicates.

first: Kotaro

last: Kanno

first: Masahiro

last: Koseki


title: Identifying novel surface markers for megakaryocyte progenitor cells [10x D27]

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: We carried out 10X sequencing of D27 induced pluripotent stem cell-derived megakaryocyte population which had been sorted for surface markers of megakaryocyte progenitors.

overall_design: cDNA was sequenced from each cell.

first: Moyra

last: Lawrence

first: Arash

last: Shahsavari

first: Cedric

last: Ghevaert


title: Loss of REST in breast cancer promotes tumor progression through estrogen sensitization, MMP24 and CEMIP overexpression

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Loss of REST function is seen in ~20% of breast cancers and is associated with a more aggressive phenotype and poor prognosis. Despite the frequent loss of REST, little is known about the role of REST in the molecular pathogenesis of breast cancer. We then utilized gene knockdown in MCF-7 cells in the presence or absence of steroid hormones estrogen and/ progesterone followed by RNA sequencing in an attempt to understand the tumor suppressor role of REST in breast cancer. We show that REST directly regulates CEMIP (cell migration-inducing and hyaluronan-binding protein, KIAA1199) and MMP24 (matrix metallopeptidase 24), genes known to have roles in invasion and metastasis. REST knockdown in breast cancer cells leads to significant upregulation of CEMIP and MMP24. In addition, we found REST binds to RE-1 sites (repressor element-1) within the genes and influences their transcription. Furthermore, we found that the estrogen receptor (ESR1) signaling pathway is activated in the absence of REST, regardless of hormone treatment. We demonstrate a critical role for the loss of REST in aggressive breast cancer pathogenesis and provide evidence for REST as an important diagnostic marker for personalized treatment plans.

overall_design: mRNA profiles of MCF-7 cells treated with vehicle, estrogen, progesterone, or both in the presence of siControl or siREST transfections. Duplicates of each sample were included.

first: Ashley

last: Cloud

first: Aditya

last: Vargheese

first: Raeann

last: Shimak

first: Sornakala

last: Ganeshkumar

first: Easwari

last: Kumaraswamy

first: Roy

last: Jensen

first: Vargheese

last: Chennathukuzhi


title: Identifying novel surface markers for megakaryocyte progenitor cells [timecourse transgene]

summary: We carried out 10X sequencing of a timecourse of human induced pluripotent stem cells over a course of 20 days as they differentiated towards megakaryocytes.

overall_design: Two single-cell transgene libraries were generated from a pool of cells, using primers specific for the ends of inserted lentiviral transgenes used to initiate differentiation.


title: Identifying novel surface markers for megakaryocyte progenitor cells [D27 transgene]

overall_design: Two sets of transgene libraries, one overexpressing TAL1 and the other overexpressing GATA1 and FLI1, were generated from each cell, using primers specific for the ends of inserted lentiviral transgenes used to initiate differentiation.


title: Adipose-derived stem cells contribute to vascular remodeling via Clec11a+ subpopulation

first: Yao

last: Xie

state: Zhejiang

address: 88 Jiefang Road

department: Department of Cardiology

institute: Zhejiang University School of Medicine Second Affiliated Hospital

summary: Recent researches identified the existence of adipose derived stem cells (ADSCs) in adipose tissue. Perivascular ADSCs (PV-ADSCs) locate around vasculatures and can differentiate into vascular lineages. However, the detailed cellular heterogeneity within PV-ADSCs has not been investigated. Therefore, we performed single-cell profiling of subcutaneous (S-) and perivascular (PV-) ADSCs from wild-type and obese mice. After referring to the clustering strategies from other ADSCs’ single-cell data, we provided a more comprehensive picture and trajectory, especially for PV-ADSCs. Both single-cell analysis and in vitro experiments revealed that S-ADSCs from obese mice had impaired abilities of cell migration and proliferation compared to wild-type S-ADSCs. PV-ADSCs have distinctively intrinsic properties. We uncovered 4 subpopulations of PV-ADSCs including Dpp4+, Col4a2+, Clec11a+ and Sult1e1+ cells. Notably, the differentiative function of PV-ADSCs towards vascular lineages was mainly attributed to the existence of Clec11a+ subpopulation, which highly expressed Mgp. The present study provided an integrative view of the ADSCs’ variance from the perspective of origins and obesity.

overall_design: We performed single-cell sequencing by applying droplet-based 10X genomics platform for different ADSCs. Perivascular or subcutaneous AT was harvested from either DB/DB or wildtype mice. After the digestion, stromal vascular fraction (SVF) was passed through a 100 μm and then a 70 μm filter to remove any adipocytes and debris. CD45, live/dead staining, DAPI were applied to exclude CD45+ cells, dead cells and erythrocytes.

first: Meixiang

last: Xiang

first: Yongli

last: Ji

first: Yunrui

last: Lu


title: Dysregulated lipid metabolism blunts the sensitivity of B16F10 melanoma cells to EZH2 inhibitor

city: BEIJING

first: Qianqian

last: Yin

address: 49 North Garden Road, Haidian District

department: Center of Basic Medical Research

institute: Peking University Third Hospital

summary: The sensitivity has been the key issue for EZH2 inhibitor in cancer therapy. Although it has been approved by Food and Drug Administration (FDA) in 2020, the relative narrow scope still limits its clinical application. In this study, we utilized B16F10 melanoma cell line which is resistant to EZH2 inhibitor GSK126 to an extent to investigate the underlying mechanism. We found that although the proliferative phenotype didn't show any difference upon treatment with GSK126 at 10 μM, the transcriptome and metabolome changed profoundly. Gene set enrichment analysis and metabolites pathway enrichment analysis revealed that GSK126 induced broad shifts in glucose, amino acids and lipid metabolism. Lipid synthesis were strengthened with elevated abundance of unsaturated fatty acids. We also found attenuated tricarboxylic acid cycle metabolism, and decreased amino acids levels. The liver lipid accumulation and the increased blood triglycerides level after GSK126 treatment were further confirmed in a mouse model. Indeed, the combination of GSK126 and lipolysis agent fenofibrate significantly attenuated the proliferation of B16F10 and increased the sensitivity to GSK126. Therefore, the dysregulated lipid metabolism blunts the sensitivity of B16F10 to GSK126. This study uncovered the iceberg under the sea and identified the Achilles heel of EZH2 inhibitor, so that it provides the novel strategy for further combination therapy.

overall_design: mRNA profiles of GSK126-treated  and DMSO-treated B16F10 melanoma cells

first: Tengrui

last: Zhang

first: Zhengyang

last: Guo

first: Yueqing

last: Gong

first: Yan

last: Wang

first: Lixiang

last: Xue


title: Identifying novel surface markers for megakaryocyte progenitor cells

first: Irina

last: Mohorianu

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

overall_design: Refer to individual Series


title: Identifying novel surface markers for megakaryocyte progenitor cells [10x timecourse]

first: Moyra

last: Lawrence

first: Arash

last: Shahsavari

first: Cedric

last: Ghevaert


title: Gene expression signatures for breast cancer cell lines

city: Guangzhou

first: Yingying

last: Ye

state: Guangdong

address: Guangdong Provincial Key Lab，Chinaoratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Guangzhou

institute: Sun Yat-sen University

summary: To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish breast cancer cells sensitive and resistant to anti -CD47.

overall_design: Breast cancer cell lines were devided into groups sensitive and resistant to anti-CD47. Biological replicates: 2 replicates.

first: Jiang

last: Li


title: Identifying novel surface markers for megakaryocyte progenitor cells [SMART-seq]

summary: We carried out Smart-Seq of a D40 induced pluripotent stem cell-derived megakaryocyte culture

overall_design: Whole genome single cell transcriptome analysis of long-term MK culture (one hiPSC line), balanced for the eight transgenic patterns (upstream FACS using transgene expression reporters)

first: Amanda

last: Dalby

first: Winnie

last: Lau

first: James

last: Baye

first: Lila

last: Diamanti

first: Berthold

last: Gottgens

first: Thomas

last: Moreau


title: Transcriptome Profiling Provides Insights into Mongolian Gerbil as an Ideal NAFLD Model : Earlier Onset of Inflammation and Fibrosis as Well as High Expression of HCC-Associated Genes

first: Chen

last: Zhiyun

address: No. 9, Street 9, Xiasha economic development zone, Jianggan district

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

summary: Mongolian gerbil (Meriones unguiculatus) is an ideal animal model for non-alcoholic fatty liver disease/nonalcoholic steatohepatitis (NAFLD/NASH) which is under development. Currently, the research and application of Mongolian gerbils have been largely limited due to the lack of genomic and transcriptome information. In the present study, we sought to better understand the underlying mechanism of the rapid development of NASH in high-fat diet (HFD)-fed Mongolian gerbils by analyzing the transcriptome profilings of different modeling times. Eight hub genes CD44, APP, CDC42, CD68, CXCR4, CSF1R, ADGRE1 and FERMT3 were obtained, which are all involved in inflammation response and CDC42 and FERMT3 are associated with hepatocellular carcinoma (HCC). Most of the hub genes showed high expression levels in the first stage of modeling-building (HFD for 4 weeks). We observed that feeding HFD for 4 weeks is sufficient to induce high expression of pro-fibrotic factors such as PDGFB and CTGF and to form collagen deposits. Intriguingly, we found four significant independent prognostic factors for HCC: GPC1, ARPC1B, DAB2 and CFL  exhibiting high expression levels during the modeling time. Our findings indicated that, Mongolian gerbil is an ideal NAFLD model with rapid progression in inflammation and fibrosis. Prolonging the modeling time may lead to the formation of NAFLD-related HCC and further research is needed to investigate this possibility.

overall_design: 18 male gerbils were randomly divided into two groups, namely normal feeding diet (ND) group and high-fat diet (HFD) group. Each group was divided into three time points of 4-week (4W), 8-week (8W) and 16-week (16W), with 3 gerbils in each group. The gerbils in ND group were fed with normal feed and had water freely. The gerbils in HFD group were fed with high-fat diet and had water freely.

first: Wei

last: Hong

first: Tingting

last: Zhang

first: Junbin

last: Yan

first: Jianshun

last: Yu

first: Beihui

last: He

first: Liyan

last: Wu

first: Zhiyun

last: Chen


title: Two DNA binding domains of MGA act I combination to suppress abnormal activation of meiosis-related genes in mouse ESCs.

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

summary: MGA plays important roles in DNA binding as well as constructing the complex as a scaffolding component. MGA bears two distinct DNA-binding domains termed bHLHZ and T-box. Both DNA binding domain of MGA are involved in repression of rather distinct sets of genes in ESCs. But, substantial numbers of meiosis-related genes are included in both gene sets. Notably, Meiosin gene that plays essential roles in meiotic entry in collaboration with Stra8 is included among genes regulated exclusively by the bHLHZ domain, suggesting that the negative regulation by MGA resides upstream of positive regulation by STRA8/MEIOSIN complex within the transcriptional network of meiotic onset.

overall_design: Dox-treated Max-KO ESCs bearing exogenous Max cDNA whose expression is under the control of tet-off system or two different Mga mutant ESCs producing MGA protein lacking either bHLHZ or T-box domain that were cultured under conventional culture condition for mouse ESCs were used for RNA sources. These RNAs were used to compare their global expression profiles by DNA microarray analyses. Samples, from Dox-untreated Max cKO ESCs or empty virus-infected ESCs under conventional culture condition were used as reference samples.

first: Kousuke

last: Uranishi

first: Yosuke

last: Mizuno

first: Masataka

last: Hirasaki

first: Ayumu

last: Suzuki


title: RNA Sequencing Facilitates Quantitative Analysis of Wild Type(MRL-mpj) and MRL-lpr (PBS or MSC treated) Hippocampoal Transcriptomes

first: Han

last: Xiaojuan

state: Jiangsu

address: Zhongshan Road 321

institute: Nanjing Drum Tower Hospital,  The Affiliated Hospital of Nanjing University Medical School

summary: Up to 75% of systematic lupus erythematosus (SLE) patients experience neuropsychiatric (NP) symptoms, called neuropsychiatric SLE (NPSLE), yet the underlying mechanisms remain elusive. Complement cascades mediate synaptic pruning by microglia during early postnatal brain development. The process in NPSLE remains unclear. Here, we show that complement-coordinated elimination of synaptic terminals participated in NPSLE in MRL/lpr mice, a lupus-prone murine model. We elucidated that lupus mice developed increased anxiety-like behaviors and persistent phagocytic microglia reactivation before overt peripheral lupus pathology. Microglial engulfment of synapses explained behavioral disorders. We further determined that neuronal Nr4a1 signaling was essential for attracting C1q synaptic deposition then apposition of phagocytic microglia, ensuing synaptic loss and neurological disease. Minocycline-deactivated microglia, antibody-blocked C1q, or neuronal Nr4a1 restore protected lupus mice from synapse loss and NP manifestations. Our findings revealed an active role of neurons in coordinating microglia-mediated synaptic loss and highlight neuronal Nr4a1 and C1q as critical components amenable to pharmacological intervention.

overall_design: RNA sequencing in hippocampus tissues from WT(MRL-mpj) mice and MRL-lpr mice with or without MSC(mesenchymal stem cell) administration, in triplicate.

first: X

last: Han

first: L

last: Sun


title: RNA-sequencing analysis of Takifugu rubripes spleen and gill in response to Vibrio harveyi infection

city: Dalian

first: dongxu

last: gao

address: Heishijiao

institute: Dalian Ocean University

summary: In this research, we used RNA-sequencing technology to detect genome-wide differentially expressed genes in  spleen and gill of Vibrio harveyi -infected Takifugu rubripes.This high-throughput sequencing could help us to understand new mechanisms of action of V. harveyi induced aquaculture fish disease.

overall_design: Takifugu rubripes spleen and gill mRNA profiles of control and  Vibrio harveyi treatment groups

first: Dongxu

last: Gao

first: Shigen

last: Ye


title: Vitamin D receptor and STAT3 cooperate to TET2-mediated acquisition of tolerogenesis [DNA methylation profile]

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary: The active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), induces stable tolerogenesis in dendritic cells (DC). This process involves the Vitamin D receptor (VDR) which translocates to the nucleus, binds its cognate genomic sites and promotes epigenetic and transcriptional remodeling. In this study, we investigated the interplay between the vitamin D receptor (VDR) and transcription factors to induce DNA methylation changes, which might provide phenotypic stability to the tolerogenic phenotype of DCs.

overall_design: DNA methylation profile with EPIC arrays (Illumina) on human monocytes (MO) and monocyte-derived dendritic cells in the absence (DC) or presence (tolDC) of the active form of vitamin D (calcitriol)

first: Francesc

last: Català-Moll


title: Robust Expansion of Human Pancreatic Progenitors by Small Molecules

first: Yunkun

last: Lu

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University


title: Vitamin D Receptor (VDR) ChIP-seq reported in "Vitamin D receptor and STAT3 cooperate to TET2-mediated acquisition of tolerogenesis"

overall_design: Vitamin D Receptor (VDR) ChIP-seq on human monocytes (MO) and monocyte-derived dendritic cells in the abscence (DC) or presence (tolDC) of the acitve form of vitamin D (calcitriol)


title: Single-Cell RNA-sequencing of human embryonic stem cell-derived macrophages

city: Cheongju-si

first: Sang Cheol

last: Kim

address: Osong Health Technology Administration Complex, 187, Osongsaengmyeong 2-ro, Osong-eup

country: South Korea

institute: Korea National Institute of Health

summary: Macrophages are major innate immune cells located in various human organs, and related in disease progression and regression. Therefore, genetic data of human macrophages are considered as a potential resource to understand of human diseases. Here, we performed large-scale transcriptome analysis of 2,931(raw data: 3,323) human embryonic stem cells-derived macrophages (iMACs) using single-cell RNA-sequencing technology, and provided public data resource for better understanding of the human macrophages’ characteristics and their heterogeneity.

overall_design: transcription profiling by high throughput sequencing design

first: Hyang-Hee

last: Seo

first: Hyo-Won

first: Soo

last: Koo

first: Seong

middle: H

last: Cho

first: Sang

first: Jung-Hyun


title: Development of gene expression signatures for human liver fibrosis

status: Public on Feb 22 2022

city: Shanghai

first: Tao

last: Le

address: LANXI ROAD 164

institute: Shanghai University of traditional Chinese Medicine

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

summary: To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to to study the genes that change in the progress of human liver fibrosis, so as to provide a basis for the clinical treatment of liver fibrosis.

overall_design: Gene expression was detected in 4 patients with liver fibrosis and 4 normal people

first: Cheng

last: Liu


title: The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine


title: Transcriptome analysis of Scramble control and CDK14-sh MDA-MB-231 cells

city: wuhan

first: Mengna

last: Zhang

state: State...

address: Donghu Road, No. 115, Wuchang District

institute: wuhan university

summary: Wnt/β-catenin signaling pathway has become a key signaling pathway regulating mammary organogenesis and oncogenesis. However, the therapeutic methods by targeting Wnt pathway against breast cancer has been limited. To address this challenge, we investigated the function of cyclin-dependent kinase 14 (CDK14), a member of Wnt signaling pathway, in mammary development and breast cancer progression. We showed that CDK14 was expressed in the mammary basal layer and elevated in triple negative breast cancer (TNBC). CDK14 knockdown reduces colony formation ability and regeneration capacity of mammary basal cells, and significantly inhibits murine MMTV-Wnt-1 basal-like mammary tumor progression. Excitingly, knockdown of CDK14 or pharmacological inhibition of CDK14 by FMF-04-159-2 significantly inhibited the progression and metastasis of human TNBC. Mechanistically, CDK14 inhibition inhibits mammary regeneration and TNBC progression by attenuating Wnt/β-catenin signaling. Together, we demonstrated that CDK14 regulates mammary regeneration and breast tumorigenesis, and is a promising therapeutic target for TNBC.

overall_design: Examination the different mRNA level in Scramble control and CDK14-sh MDA-MB-231 cells

first: Cheguo

last: Cai

first: Lingxian


title: Negative autoregulation of BMP dependent transcription by SIN3B splicing reveals a role for RBM39

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

institute: Wellcome Trust Centre for Human Genetics

summary: We conducted RNASeq using mRNA extracted from C2C12 mouse myoblast cells transfected with non-targeting control (NTC) or RBM39 siRNA, to elucidate the effect of RBM39 on regulation of BMP4 pathway

overall_design: 6 RNASeq samples across 2 conditions:  Non targeting control transfected (n=3) and RBM39 siRNA transfected (n=3)

first: Noel

last: Faherty

first: Shoumo

last: Bhattacharya

first: John

last: Broxholme


title: Transcriptomic data of cord blood CD34+ cells as controls of transcriptome cohort of pediatric acute myeloid leukemia

city: Memphis

first: Jeffery

last: Klco

state: Tennessee

address: 262 Danny Thomas Place, D4047B

department: Pathology

institute: St Jude Children's Research Hospital

summary: We established a transcriptome cohort of pediatric acute myeloid leukemia (n=553) with RNA sequencing. This dataset of cord blood CD34+ cells (n=5, indivisual lots) is normal controls to characterize leukemia-specific expression patterns.

overall_design: Human RNASeq samples for cord blood CD34+ cells (n=5, indivisual lots) are normal controls to characterize leukemia-specific expression patterns.

first: Tamara

last: Westover

first: Masayuki

last: Umeda

first: Jing

last: Ma


title: Expression data from cord blood CD34+ cells transduced with UBTF wildtype expression vectors, UBTF-TD expression vectors, or empty control vector.

summary: UBTF tandem duplications (UBTF-TD) were identified frequently in relapsed pediatric acute myeloid leukemia. The purpose of this study is to investigate the functional consequence of the overexpression of UBTF-TD in normal cord blood CD34+ cells.

overall_design: RNA sequencing of CD34+ cells transduced with UBTF wildtype expression vectors (n=6), UBTF-TD expression vectors (n=6), or empty control vector (n=3).


title: Temporal and Spatial Transcriptomic Dynamics across Brain Development in Xenopus laevis tadpoles

city: La Jolla

first: Caroline

middle: R

last: McKeown

state: CA

address: 10550 N. Torrey Pines Rd., DNC-216

department: Dorris Neuroscience Center

institute: The Scripps Research Institute

summary: We conducted differential gene expression analyses of the developing X. laevis tadpole midbrain between stages 44 and 61, and across brain regions at stage 46. We found that genes pertaining to positive regulation of neural progenitor cell proliferation as well as known progenitor cell markers were upregulated in the midbrain prior to metamorphic climax; concurrently, expression of cell cycle timing regulators decreased across this period. We also found that at the start of metamorphosis, neural progenitor populations appeared to be similar across the fore-, mid-, and hindbrain regions. Genes pertaining to negative regulation of differentiation were upregulated in the spinal cord compared to the rest of the brain. Finally, we found that regulation of biological processes like cell fate commitment and synaptic signaling follow similar trajectories in the brain across early tadpole metamorphosis and mid- to late-embryonic mouse development.

overall_design: Comparison of mRNA profiles in the X. laevis midbrain at stages 44, 46, 55, 61; and across the spinal cord, hindbrain, midbrain, and forebrain at stage 46

first: Aaron

last: Ta

first: Lin-Chien

last: Huang

first: Jennifer

last: Bestman

first: Kendall

last: Van Keuren-Jensen

first: Hollis

middle: T

last: Cline


title: TERT activates endogenous retroviruses contributing to immunosuppressive tumour microenvironment III

city: Hangzhou

first: Jian

last: Mao

address: 2318 Yuhangtang Rd

institute: Hangzhou Normal University

summary: Telomerase plays a pivotal role in tumorigenesis by both telomere-dependent and telomere-independent activities, although the underlying mechanisms are not completely understood. Using single-sample gene set enrichment analysis (ssGSEA) across 9,264 tumour samples, we observed that expression of telomerase reverse transcriptase (TERT) is closely associated with immune-suppressive signatures. We demonstrated that TERT can activate a subclass of endogenous retroviruses (ERVs) to form double-stranded RNAs (dsRNAs), which were sensed by the RIG-1/MDA5-MAVS signalling pathway and triggered interferon signalling in cancer cells. Furthermore, we showed that TERT-induced ERVs/interferon signalling stimulated the expression of chemokines, including CXCL10, which induced suppressed T cell infiltration with increased percentage of CD4+ and FOXP3+ cells. These data reveal an unanticipated role for telomerase as a transcriptional activator of ERVs and provide strong evidence that TERT-mediated ERVs/interferon signalling contributes to immune suppression in tumours.

overall_design: dsRNA profiles of U2OS cells transfected with pcDNA3.1-TERT-WT or pcDNA3.1-TERT-K626A using Lipofectamine 3000 according to the manufacturer’s instructions for 48 h.

first: Qian

first: Yu-sheng

last: Cong


title: TERT activates endogenous retroviruses to promote an immunosuppressive tumour microenvironment

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptional integration of separated and simultaneous microbial and nutritional signals by the intestinal epithelium

city: Durham

last: Rawls

state: North Carolina

address: Duke University 213 Research Drive, Box 3580 DUMC CARL Building 327

institute: Duke University

summary: We performed RNA-seq, H3K27ac ChIP-seq, and HNF4a ChIP-seq on jejunal intestinal epithelial cells, which are primarily responsible for the absorption of fatty acids, in four conditions: Germ-free (GF), Germ-free plus high fat meal (GF+HFM), ex-GF colonized with a conventional microbiota for 2 weeks (Colonized, CV), and Colonized plus high fat meal (CV+HFM). We, for the first time, map genomewide HFM responsive regulatory regions in the intestine. We identify that in the absence of microbes the HNF4a transcriptional program supports a FAO program in enterocytes while suppressing a proliferation program.

overall_design: Generation and analysis of RNA-seq, H3K27ac ChIP-seq, and Hnf4a ChIP-seq from primary IECs isolated from the jejunum of Germ-Free (GF), Colonized (CV), Germ-Free+High Fat Meal (GF+HFM), and CV+HFM (Colonized+High Fat Meal) mice.

first: Colin

last: Lickwar

first: James

last: Davison

middle: F


title: TERT activates endogenous retroviruses contributing to immunosuppressive tumour microenvironment II

overall_design: Liver mRNA profiles of wild type (WT) and G1 Tert-/- mice treated by saline or ENU.

last: Zhang


title: Epigenome analysis of normal and PLK1 knockdown samples

first: Peng

last: Yuchong

address: The First Affiliated Hospital, Guangdong Pharmaceutical University, 19 Nonglinxia Road, Yuexiu District, Guangzhou, Guangdong, China

department: Clinical Pharmacy of the First Affiliated Hospital

institute: Guangdong Pharmaceutical University

type: Methylation profiling by genome tiling array

summary: The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles  in normal and PLK1 knockdown DU145 cell samples. Samples included normal and PLK1 knockdown DU145 cell samples, Each sample is repeated three times.

overall_design:
Bisulphite converted DNA from the normal (E1) and PLK1 knockdown (P1) DU145 cell samples were hybridized to the Illumina Infinium 850k Human Methylation Beadchip.
Oebiotech (contributor)

first: Yuchong

last: Peng


title: TERT activates endogenous retroviruses contributing to immunosuppressive tumour microenvironment I

overall_design: mRNA profiles of U2OS cells transfected with pcDNA3.1-TERT-WT, pcDNA3.1-TERT-K626A or empty vector using Lipofectamine 3000 according to the manufacturer’s instructions for 48 h.


title: Temperature-induced transcriptome profiles of endosprem and embryo during seed development and germination in Brassica oleracea

city: Norwich

first: Xiaochao

last: Chen

address: Norwich Research Park, Colney Ln

department: Crop Genetics

institute: John Innes Centre

summary: To understand how endosperm and embryo perceive temperature signals to control seed vigour in Brassica oleracea, we grow plants in 16°C till bent-cotyledon stage, which is a key stage sensing temperature. Then plants were either transferred to 26°C or kept in 16°C. Endosperm/seed coat and embryo RNA samples were collected for RNA-seq at day0, day1, day3, day7, day18 and day22. Further, RNA-seq was also performed in imbibed seeds matured in 16°C and 26°C, at 1 hour, 24 hours and 72 hour after imbibition.

overall_design: We investigated transcriptome profiles at 10 time points in Brassica endosperm/seed coat and embryo in response to different temperatures

first: Steven

last: Penfield


title: Epigenome analysis of DU145 samples

summary: Bisulphite converted DNA from DU145 cell samples were hybridized to the Illumina Infinium 850k Human Methylation Beadchip.

overall_design:
The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles in DU145 cell samples.Genomic DNA was isolated from DU145 cells and bisulfite conversion was performed. Add 0.1 N NaOH to the sample to denature the DNA to single-stranded DNA. After neutralization, add the whole genome amplification reagent, and incubate overnight at 37 °C. The DNA fragments were precipitated by adding isopropanol, and the fragmented DNA was enriched by centrifugation at 4 °C and purified. After the precipitated DNA is dried in the air, a hybridization buffer reagent is added to re-dissolve the DNA precipitate. Hybridize the resuspended DNA sample with the prepared chip and place it in a hybridization oven overnight. Wash away unhybridized and non-specifically hybridized DNA for subsequent staining and extension. Using the captured DNA as a template, a single-base extension reaction is performed on the chip, and a detectable label group is added to the chip to distinguish the methylation of the sample. Put the reaction-completed chip into XC4 reagent and then put it in a vacuum environment to dry for 1 hour. Put the processed chip into a scanner, use laser to excite the fluorescent group of the single-base extension product on the chip, and the scanner obtains the fluorescence emitted by the fluorescent group and generates a high-resolution picture. The data thus obtained is directly imported into GenomeStudio software for analysis, so as to obtain the methylation data of each sample. Samples included normal , PLK1 knockdown and PLK1 knockdown with over-expression UHRF1 DU145 cell samples, Each sample is repeated three times.
[contributor] Oebiotech


title: Gene expression data from endometrial cancer patient-derived cells (PDCs)

first: Kazuhiro

last: Ikeda

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


title: Gene expression data from endometrial cancer patient-derived cells (PDCs) treated with aldehyde dehydrogenase inhibitor

summary: Three lines of PDCs (EnC-A, EnC-B, and EnC-C) were established from endometrial cancer specimens. Aldehyde dehydrogenase (ALDH) inhibition repressed the cell growth with altered gene expression.

overall_design: Three lines of PDCs (EnC-A, EnC-B, and EnC-C) were established from 3 distinct patients with endometrial cancer. To examine the effect of aldehyde dehydrogenase (ALDH) on gene expression, the PDCs were treated with ALDH inhibitor, N,N-diethylaminobenzaldehyde (DEAB) or vehicle (DMSO) for 8 h. Total RNAs were extracted from these cells and then used for Affymetrix microarrays analysis.

first: Sachiko

last: Shiba

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Gene expression data from metastatic endometrial cancer patient-derived cells (PDCs)

summary: Immune-related genes were upregulated in the metastatic PDC line (EnC-C) established from endometrial cancer specimen.

overall_design: Endometrial cancer PDCs (EnC-C) were established by spheroid culture. The EnC-C PDCs generated metastatic liver and lung tumors in immunodeficient mice. To examine the metastasis-associated gene expression, secondary PDCs were prepared from the liver and lung metastases. Total RNAs were extracted from these cells and then used for Affymetrix microarrays analysis.


title: Gene expression data from endometrial cancer patient-derived cells (PDCs) treated with estrogen/progesterone

summary: Estrogen and progesterone regulate expression of immune-related genes in the PDC line (EnC-A) established from endometrial cancer specimen.

overall_design: Endometrial cancer PDCs (EnC-A) were established by spheroid culture. To examine the effects of estrogen and progesterone on gene expression, the PDCs were treated with estrogen, progesterone, mixed estrogen and progesterone, or vehicle (ethanol) for 24 h. Total RNAs were extracted from these cells and then used for Affymetrix microarrays analysis.


title: Cold atmospheric plasma affects stem cell renewal and differentiation and is associated with a regeneration process in an intestinal organoid culture model

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: Cold atmospheric plasma (CAP) has recently been proposed as an anti-cancer therapy, mainly driven by the concentration of reactive oxygen and nitrogen species (RONS), whereas several studies suggest its selectivity on cancer cells. However, the underlying mechanisms of this “selectivity” are largely poorly understood and rely exclusively on 2D (dimensional) unicellular monolayers, which do not recapitulate the in vivo epithelial context. In this study, we aimed to evaluate phenotypically and transcriptomically the effect of different modalities of CAP’s application (direct, indirect and plasma activated medium) on intestinal organoids derived from wild type (WT), VillinCreERT2/Apc floxflox and VillinCreERT2/Apc WT adult mice.  The phenotype analysis of different modalities (direct, indirect, plasma activated medium) of CAP’s application revealed that direct and indirect CAP treatment decrease WT intestinal organoid survival associated to a predominance of spheroids organoids, this reduction in survival was not observed for organoids derived from Villin CreERT2/Apc flox flox mice. Moreover, transcriptome analyses of control’s organoids showed that indirect and plasma activated applications induced a transcriptomic reprogramming, highlighted by a decrease of intestinal stem cell pool, cell cycle arrest, cell death, altogether associated to a regeneration repair process. These results have been validated at the protein level. In conclusion, in a 3D organoid model, the selectivity of CAP on cancer cells does not seem to be confirmed.

overall_design: mRNA profiles of duodenum derived organoids from wild type mice at adult stage exposed to different modalities of CAP.

first: Alia

last: Hadefi

first: Morgane

last: Leprovots

first: Kawthar

last: Mohamed

first: Maryam

last: Marefati

first: Max

last: Thulliez

first: Oriane

last: Bastin

first: Antoine

last: Nonclercq

first: Alain

last: Delchambre

first: François

last: Reniers

first: Anne

last: Lefort

first: Frédérick

first: Jacques

last: Devière

first: Marie-Isabelle

last: Garcia


title: Pathogenesis of alcoholic hepatitis

city: Lille

first: Laurent

last: Dubuquoy

address: Faculté de Médecine - Pôle Recherche, place Verdun.

institute: Inserm

summary: NOT PROVIDED; REQUESTED

overall_design: To compare RNA profiles in microdissected hepatocytes from human liver in 3 groups of patients.


title: maxATAC: genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks

status: Public on Feb 21 2022

city: Cincinnati

first: Tareian

last: Cazares

state: OH

address: 3333 Burnet Avenue, MLC 7038

department: Immunobiology and Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular behavior. The 2017 ENCODE-DREAM in vivo Transcription-Factor Binding Site (TFBS) Prediction Challenge highlighted the value of chromatin accessibility data to TFBS prediction, establishing state-of-the-art methods. Yet, while Assay-for-Transposase-Accessible-Chromatin (ATAC)-seq datasets grow exponentially, suboptimal motif scanning is commonly used for TFBS prediction from ATAC-seq. Here, we present “maxATAC”, a suite of user-friendly, deep neural network models for genome-wide TFBS prediction from ATAC-seq in any cell type. With models available for 127 human TFs, maxATAC is the largest collection of state-of-the-art TFBS models to date. maxATAC performance extends to primary cells and single-cell ATAC-seq, enabling state-of-the-art TFBS prediction in vivo. We demonstrate maxATAC’s capabilities by identifying TFBS associated with allele-dependent chromatin accessibility at atopic dermatitis genetic risk loci.

overall_design: Bulk OMNI ATAC-seq on 50k cells

first: Emily

last: Miraldi

first: Leah

last: Kottyan

first: Artem

last: Barski

first: Faiz

middle: W

last: Rizvi

first: Xiaoting

last: Chen

first: Anthony

last: Bejjani

first: V

middle: B

last: Prasath

first: Balaji

last: Iyer

first: Benjamin

last: Wronowski

first: Omer

last: Donmez

first: Michael

last: Kotliar

first: Sreeja

last: Parameswaran

first: Joseph

last: Wayman

first: Matthew

last: Weirauch


title: Monocytes transition to monocyte-macrophages within the inflamed vasculature via CCR2 on monocytes and endothelial TNFR2

city: Boston

first: Tanya

last: Mayadas

state: MA

address: 77 Avenue Louis Pasteur, NRB  Rm. 752K

department: Department of Pathology

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Our study reports that CCR2 dependent functional specialization of monocytes into immature macrophages occurs within the TNF-TNFR2 activated vasculature and establishes a chemokine-based autocrine, feed-forward loop that may aplify the inflammation and renal injury.

overall_design: Nephrotoxic Nephritis induced in 10, eight week old WT mice. Different populations of monocytes were FACS sorted and cells were processed for bulk RNAseq

first: Suhail

last: Tahir


title: Full-length transcriptome of Glycyrrhiza uralensis Fisch. in under eight treatment

city: Yinchuan

first: Xiang

last: Xiao

state: Ningxia

address: Shengli Street

institute: Ningxia Medical University

summary:
Purpose: The goal of this study are to reveal the internal mechanism of silicon increased Glycyrrhiza uralensis Fisch. seedlings drought-tolerance,salt-tolerance and  salt-drought tolerance by RNA-Seq.
Methods: mRNA profiles of Glycyrrhiza uralensis Fisch. Seedling in eight treatment: control treatment with or without silicon,salt treatment with or without silicon,drought treatment with or without silicon,salt-drought treatment with or without silicon. Each treatment group sequenced the aerial (stems, leaves, buds and all the above ground parts) and underground parts (roots and all the underground parts) respectively
Results:A total of 48 samples were sequenced and 372.37GB of clean data was acquired. The clean data of every sample reached 5.96GB, and the percentage of Q30 base was 94.63% or above. Clean reads of each sample were sequentially aligned with the specified reference genome, and alignment efficiency ranged from 85.27% to 92.66%. Therefore, the transcriptome data of samples were obtained with a high correct rate and good genomic coverage.Results of sequencing analysis showed that compared with CK group, there were 1426 DEGs (771 up-regulated and 655 down-regulated), 1386 DEGs (571 up-regulated and 815 down-regulated) and 4192 DEGs (1668 up-regulated and 2524 down-regulated) in aerial part, and 1462 DEGs (730 up-regulated and 732 down-regulated), 2212 DEGs (939 up-regulated and 1273 down-regulated) and 3735 DEGs (1768 up-regulated and 1986 down-regulated) in underground part of D, S and SD group respectively.
Conclusions: Our study help to better understand the underlying molecular mechanisms of silicon improve the drought-tolerance,salt-tolerance and salt-drought tolerance of G. uralensis.

overall_design: Full-length transcriptome analysis of Glycyrrhiza uralensis Fisch. seedling under control treatment with or without silicon, salt treatment with or without silicon, drought treatment with or without silicon and salt-drought treatment with or without silicon.

first: Xinhui

last: Zhang

first: Xin

last: Ma


title: A machine learning breast cancer prediction model based on a panel from circulating exosomal miRNAs

city: Zhanjiang

first: Yan

last: Zeng

address: No. 236 Yuanzhu Road, Chikan District, Zhanjiang , Guangdong

institute: Precision clinical laboratory Central People's Hospital of Zhanjiang

summary: In this study, we aim to reveal the value of plasma exo-miRNA in early diagnosis of breast cancer.In this study, after determining the success of plasma exocrine separation, we analyzed the expression of miRNA in plasma exocrine and selected 16 strong correlation features miRNA by Lasso logistic regression. Different machine learning algorithm models were constructed to evaluate the performance of 16 miRNA for early detection and diagnosis of breast cancer. The biological significance of 16 characteristic miRNAs was evaluated by bioinformatics analysis. Overall, these data highlight the value of exo-miRNA as a biomarker for breast cancer. They may be used for early detection and diagnosis of breast cancer in future clinical practice.

overall_design: Exosomes isolated from plasma were identified by Nanoparticle Tracking Analysis (NTA), Transmission Electron Microscope (TEM) and Western Blot. MiRNA expression in plasma samples from 56 BC patients and 40 normal controls (NCS) was analyzed by high-throughput sequencing. MiRNAs with strong correlation characteristics were selected by Lasso logistic regression. Then, we build the training set and test set, evaluated the Lasso regression accuracy, and evaluated the performance of different models in the training set and test set. Finally, GO analysis, KEGG and Reactome pathway enrichment analysis were used to understand the biological significance of 16 characteristic miRNAs.

first: Mingfeng

last: Liu

first: Xiaoli

last: Xu

first: Ting

last: Luo

first: Ying

last: Zhao

first: Zicheng

first: Jiangqin


title: RNA-seq of NPL knock-down in THP1 cells

city: Winston-Salem

first: Swapan

last: Das

state: NC

address: Bowman Gray Center for Medical Education, 475 Vine St

department: Department of Internal Medicine, Section of Endocrinology and Metabolism

institute: Wake Forest School of Medicine

summary: The NPL encodes an enzyme that regulates cellular concentrations of sialic acid (N-acetyl-neuraminic acid) by mediating the reversible conversion of sialic acid into N-acetylmannosamine and pyruvate. As functions of NPL gene in obesity and gluco-metabolic phenotypes is not studied, we knocked down NPL in THP1 cells to understand its roles in modulating the human monocyte-macrophage expression network. Transduction of THP1 cells by NPL-specific lentiviral shRNA stably knocked down its expression at baseline monocytes and in the PMA-induced macrophage state. Global transcriptomic analysis by RNA-seq validated the downregulation of NPL, and comparison of NPL knockdown cells with control-shRNA treated cells further identified 1,183 differentially expressed genes (DEGs). Genes downregulated by the NPL knockdown were significantly enriched for cytokine production, while upregulated genes were enriched for extracellular structure organization. We further compared the effect of macrophage conditioned media (MCM) derived from NPL-shRNA and control-shRNA-expressing THP1 macrophages on SGBS adipocytes. Compared to unconditioned media, MCM derived from either of the THP1 cells differentially regulated key genes involved in adipocyte function and IR. The expression of ADIPOQ, peroxisome proliferator activated receptor gamma (PPARG), and glucose transporter-4 (SLC2A4/GLUT4) was downregulated, while expression of LEP was upregulated in SGBS cells treated with MCM starting from day 4 of the in vitro differentiation. However, PPARG was less repressed and LEP was less activated when SGBS adipocytes were treated on day 4 differentiation with MCM from NPL-shRNA-THP1 cells, suggesting knockdown of NPL partially ameliorated macrophage-induced inflammation of adipocytes.

overall_design: RNA-seq was performed in the NPL-shRNA and control-shRNA expressing THP1 cells at 48hr PMA treated condition

first: Peng

first: Neeraj

last: Sharma

first: Bin


title: Regulator of G protein signaling contributes to the development and aflatoxin biosynthesis in Aspergillus flavus through the regulation of Gα activity.

city: Fuzhou

first: rui

last: xie

address: shangxiadian street

institute: Fujian Agriculture and Forestry University

summary:
purpose: to further gain insight into the effect of RGS proteins on aflatoxin biosynthesis in A. flavus NRRL3357.
methods: two mutants ΔrgsA and ΔrgsE separately compared to WT were chose to conduct the analysis of transcriptomics.
results: 1750 DEGs are found, including 720 upregulated genes and 1030 downregulated genes in (ΔrgsA vs WT);  aflB, aflD, aflF, aflG, aflN, aflP, aflS from ΔrgsE were transcriptionally reduced relative to ΔrgsA in their expressions.

overall_design: mRNA profiles of  wild type (WT), ΔrgsA and ΔrgsE.

first: Rui

last: Xie

first: Shihua

last: Wang

first: Kunlong

last: Yang


title: Role of Set2 in regulating transcription coupled-nucleotide excision repair

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: Repair of UV damage from the transcribed strand (TS) of yeast genes is rapid due to the transcription coupled nucleotide excision repair (TC-NER) pathway. TC-NER is triggered when RNA polymerase stalls at UV damage, such as a UV-induced cyclobutane pyrimidine dimer (CPD). During transcription, the histone methyltransferase Set2 methylates histone H3K36, but it is not known if Set2 regulates TC-NER. Here, we report genome-wide repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast cells lacking Set2.

overall_design: UV-induced CPD lesions were mapped in yeast cells both immediately after UV damage formation (0hr time point) and following two or three hours of repair (2hr or 3hr time point) using the CPD-seq method. Repair of CPD lesions was measured in yeast cells mutated in the gene encoding the Set2 histone methyltransferase or a WT control. Repair was also analyzed in a rad16∆set2∆ double mutant, which is deficient in the global genomic NER (GG-NER) pathway.

first: Kathiresan

last: Selvam