title: Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters

city: Hong Kong SAR

first: Xiangzhi

last: Meng

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

summary: COVID-19 is the third outbreak of zoonotic coronavirus (CoV) of the century after the epidemic Severe acute respiratory syndrome CoV (SARS-CoV) in 2003 and Middle East respiratory syndrome CoV (MERS-CoV) in 2012. Treatment options for CoVs are largely lacking. Here, we show that clofazimine, an anti-leprosy drug with favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. The FDA-approved molecule was found to inhibit multiple steps of viral replication, suggesting polypharmacology is likely underlying its antiviral activity. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic and therapeutic administration of clofazimine significantly reduced lung viral load and fecal viral shedding, as well as reversal of cytokine storm. Additionally, clofazimine exhibited antiviral drug synergy when administered with remdesivir. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. Taken together, our data provide evidence that clofazimine may prove effective against current pandemic SARS-CoV-2, endemic MERS-CoV in the Middle East, and, possibly most importantly, emerging CoV of the future.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: For experiment on Caco-2 cells, cells were infected with or without SARS-CoV-2 (MOI=4) and treated with clofazimine (10 µM) or DMSO vehicle control for 3hours or 6 hours. For the experiment on golden hamsters, we delivered clofazimine through oral route utilizing corn oil as vehicle.  Prophylactic treatment through oral administration of clofazimine was given at -3, -2 and -1 dpi (days post infection) (25 mg/kg/day), followed by virus challenge at 0dpi through intranasal route; therapeutic post-exposure administration of clofazimine was performed at 1, 2, and 3 dpi applying the same drug dosage and virus inoculum. Lung tissues were collected at 4dpi for prophylactic and therapeutic groups. For uninfected group, clofazimine was given for 3 consecutive days and lung tissues were collected on day 4.

first: Shuofeng

last: Yuan

first: Ren

last: Sun

first: Sumit

last: Chanda

first: Kwok-Yung

last: Yuen


title: CD73+ CD127high long-term memory CD4 T cells are highly proliferative in response to recall antigens and are early targets in HIV-1 infection

status: Public on Feb 02 2021

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

summary: HIV-1 infection rapidly leads to a loss of the proliferative response of memory CD4+ T lymphocytes, when cultured with recall antigens. We report here that CD73 expression defines a subset of resting memory CD4 T cells which highly express the alpha-chain of the receptor for IL-7 (CD127), but not CD38 or Ki-67 in vivo, yet are highly proliferative in response to mitogen and recall antigens, and to IL-7, in vitro. These cells also preferentially express CCR5 and produce IL-2. We reasoned that CD73+ memory CD4+ T cells decrease early in HIV-1 infection. We compared gene expression profiles of healthy subjects recovered CD4+CD73+ to CD4+CD73- T cells, and also CD8+CD73+ to CD8+CD73- T cells

overall_design: Lymphocytes were recovered from healthy subjects. T lymphocytes CD4+CD73+ were compared to CD4+CD73- and CD8+CD73+ were compared to CD8+CD73-

first: C

last: Lefebvre

first: H

last: Hocini


title: Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

type: Expression profiling by high throughput sequencing

summary: The connection between different tissues is vital for the development and function of all organs and systems. In the musculoskeletal system, the attachment of elastic tendons to stiff bones poses a mechanical challenge that is solved by the formation of a transitional tissue, which allows the transfer of muscle forces to the skeleton without tearing. Here, we show that tendon-to-bone attachment cells are bi-fated, activating a mixture of  chondrocyte and tenocyte transcriptomes, which is regulated by sharing regulatory elements with these cells and by Krüppel-like factors transcription factors (KLF).  To uncover the molecular identity of attachment cells, we first applied high-throughput bulk and single-cell RNA sequencing to murine humeral attachment cells. The results, which were validated by in situ and single-molecule in situ hybridization, reveal that together with the expression of unique sets of genes, the attachment cells express hundreds of chondrogenic and tenogenic genes. In search for the underlying mechanism, we performed ATAC sequencing and found that attachment cells share a significant fraction of accessible intergenic chromatin areas with either tenocytes or chondrocytes. Epigenomic analysis further revealed transcriptional enhancer signatures for the majority of these regions. We then examined a subset of these regions using transgenic mouse enhancer reporter assay. Results verified the shared activity of some of these enhancers, supporting the possibility that the transcriptome of attachment cells is regulated by enhancers with shared activities in tenocytes or chondrocytes. Finally, integrative chromatin and motif analyses, as well as the transcriptome data, indicated that KLFs are regulators of attachment cells. Indeed, blocking the expression of Klf2 and Klf4 in the developing limb mesenchyme led to abnormal differentiation of attachment cells, establishing these factors as key regulators of the fate of these cells. In summary, our findings show how the molecular identity of bi-fated attachment cells enables the formation of the unique transitional tissue that connects tendon to bone. More broadly, we show how mixing the transcriptomes of two cell types through shared enhancers and a dedicated set of transcription factors can lead to the formation of a new cell fate that connects them.

overall_design: Sox9+/Scx+ FACS-sorted attachment progenitors from E13.5 dissected forelimbs (proximal side). The cells were genetically co-labeled by Sox9-CreERT2;Rosa26-tdTomato+;ScxGFP+ and were prepared for 10x Chromium single-cell RNA-Seq.

first: Shiri

last: Kult

first: Tsviya

last: Olender

first: Marco

last: Osterwalder

first: Svetalana

last: Markman

first: Sharon

last: Krief

first: Ronnie

last: Blecher-Gonen

first: Shani

last: Ben-Moshe

first: Lydia

last: Farack

first: Hadas

last: Keren-Shaul

first: Tomer

last: Meir Salame

first: Terence

middle: D

last: Capellini

first: Shalev

last: Itzkovitz

first: Ido

last: Amit

first: Axel

last: Visel

first: Elazar

last: Zelzer


title: Antigen Presentation-Independent Reciprocal Immune Modulation by HLA-DRB1 Allelic Epitopes that Associate with Autoimmune Disease Risk or Protection

city: Ann Arbor

first: Joseph

last: Holoshitz

state: MI

address: 1150 W Medical Center Dr

department: Internal Medicine - Rheumatology

country: USA

institute: University of Michigan

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-seq of iPSC-ECs treated with and without uremic toxin mixtures (UT-H).

city: Macau

first: Ning-Yi

last: Shao

address: E12-3009, University of Macau

country: China

institute: University of Macau

summary: Three healthy iPSC lines were differentiated into ECs. iPSC-ECs were then treated with and without UT-H for 24 hours.

overall_design: RNA-seq of iPSC-ECs with and without UT-H over a period of 24 hours.

first: Ning

last: Yi-Shao

first: Sang-Ging

last: Ong


title: Antigen Presentation-Independent Reciprocal Immune Modulation by HLA-DRB1 Allelic Epitopes that Associate with Autoimmune Disease Risk or Protection in Human Macrophages

summary: We report RNA sequencing data that shows the the differential effects of HLA-DRb1*0401 (SE) and HLA-DRb1*0402 (PE) on marcophage gene expression under M1 polarizing cell culture conditions

overall_design: mRNA profiles obtained from human macrophages cultured in presence of synthetic peptides coding the 65-79 region of HLA-DRb1*0401 (SE) or HLA-DRb*0402 (PE) and IFNy

first: V

last: van Drongelen

first: B

last: Miglioranza Scavuzzi

first: S

last: Veloso Nogueira

first: F

middle: W

last: Miller

first: A

middle: H

last: Sawalha

first: J


title: A single-dose intranasal vaccination elicits systemic and mucosal immunity against SARS-CoV-2

city: Houston

first: Navin

last: Varadarajan

state: Texas

address: 4722 Calhoun Rd

department: Chemical and Biomolecular Engineering

institute: University of Houston

summary: Comparison of the NALT from two groups of mice immunized with and without a liposomally formulated adjuvant

overall_design: Single-cell RNA-sequencing of harvested NALT tissues from 2 groups of immunized mice (control and treated with Trimer-STINGa) at the time of euthanasia

first: Xingyue

last: An

first: Melisa

last: Martinez-Paniagua

first: Ali

last: Rezvan

first: Mohsen

last: Fathi

first: Shailbala

last: Singh

first: Sujit

last: Biswas

first: Melissa

last: Pourpak

first: Cassian

last: Yee

first: Xinli

last: Liu


title: Antigen Presentation-Independent Reciprocal Immune Modulation by HLA-DRB1 Allelic Epitopes that Associate with Autoimmune Disease Risk or Protection in Murine Macrophages

first: Joseph

last: Holoshitz

summary: We report RNA sequencing data that shows the differential effects of HLA-DRb1*0401 (SE) and HLA-DRb1*0402 (PE) on macrophage gene expression under M1 and M2 polarizing cell culture conditions.

overall_design: mRNA profiles obtained from cells cultured in presence of synthetic peptides coding the 65-79 region of HLA-DRb1*0401 (SE) or HLA-DRb*0402 (PE), and IFNy (for M1) or IL-4 (for M2).


title: SMAD4 haploinsufficiency in small intestinal neuroendocrine tumors

city: Gothenburg

first: Yvonne

last: Arvidsson

address: Box 425

department: Biomedicin

country: Sweden

institute: University of Gothenburg

type: Genome variation profiling by genome tiling array

summary: Background: Patients with small intestinal neuroendocrine tumors (SINETs) frequently present with lymph node and liver metastases at the time of diagnosis, but the molecular changes that lead to the progression of these tumors are largely unknown. Sequencing studies have only identified recurrent point mutations in a single gene, CDKN1B, with heterozygous mutations in less than 10% of all tumors. Although SINETs are genetically stable tumors with a low frequency of point mutations and indels, they often harbor recurrent hemizygous copy number alterations (CNAs) yet the functional implications of these CNA are unclear. Methods: Utilizing comparative genomic hybridization (CGH) arrays we analyzed the CNA profile of 131 SINETs from 117 patients. Two tumor suppressor genes and corresponding proteins i.e. SMAD4, and CDKN1B, were further characterized using a tissue microarray (TMA) with 846 SINETs. Immunohistochemistry (IHC) was used to quantify protein expression in TMA samples and this was correlated with chromosome number evaluated with fluorescent in-situ hybridization (FISH). Intestinal tissue from a Smad4+/- mouse model was used to detect entero-endocrine cell hyperplasia with IHC. Results: Analyzing the CGH arrays we found loss of chromosome 18q and SMAD4 in 71% of SINETs and that focal loss of chromosome 12 affecting the CDKN1B was present in 9.4% of SINETs. No homozygous loss of chromosome 18 was detected. Hemizygous loss of SMAD4, but not CDKN1B, significantly correlated with reduced protein levels but hemizygous loss of SMAD4 did not induce entero-endocrine cell hyperplasia in the Smad4+/- mouse model. Conclusions: Hemizygous loss of chromosome 18q and the SMAD4 gene is the most common genetic event in SINETs and our results suggests that this could influence SMAD4 protein expression. Although SMAD4 haploinsufficiency alone did not induce tumor initiation, loss of chromosome 18 could represent an evolutionary advantage in SINETs explaining the high prevalence of this aberration. Functional consequences of reduced SMAD4 protein levels could hypothetically be a potential mechanism as to why loss of chromosome 18 appears to be clonally selected in SINETs.

overall_design: Comparative genomic hybridization was conducted on tumor biopsies from 131 small intestinal neuroendocrine tumors (SINETs), Primary tumor, lymph node metastasis, liver metastasis

first: T

last: Hofving

first: Erik

last: Elias

first: Ola

last: Nilsson


title: Transcriptome analysis of lncRNA–mRNA interactions in chronic atrophic gastritis

city: Changchun

first: Yang

last: Chao

address: Xiantai Street

institute: China-Japan Union Hospital of Jilin University

summary: The aims of this study are to identify prognosis-related differentially expressed lncRNAs and mRNAs in chronic atrophic gastritis (CAG). By analysis of high-throughput whole-transcriptome sequencing data, levels of lncRNAs and mRNAs between CAG and chronic nonatrophic gastritis (CNAG) were compared pairwisely. Finally, 97,282 lncRNA transcripts and 20,307 mRNA transcripts were acquired, including 50 upregulated and 66 downregulated lncRNAs and 377 upregulated and 763 downregulated mRNAs in CAG were identified (P< 0.05, fold change ≥2). Moreover, the interactions of the differentially expressed genes in CAG were investigated by gene ontology (GO) enrichment analysis, showing that the enriched genes are involved in many biological processes, such as MAP kinase activity, heat generation, and protein modification processes. Through the construction of co-expression networks of the differentially expressed genes in CAG, three critical lncRNAs nodes were identified as potential key factors in CAG. Eight mRNAs common in both the co-expression network and the protein-protein interaction (PPI) network were selected via Venn analysis, including DGKA, EIF6, HKDC1, DHRS11, CPS1, KRT15, TESPA1, and CDHR2.Finally, the expression levels of five differentially expressed lncRNAs in CAG were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). In conclusion, this study presents novel promising biomarkers for the diagnosis of CAG.

overall_design: To seek new biomarker for chronic atrophic gastritis

first: Jingpeng

last: Jin

first: Liqiang

last: Wang

first: Xiya

first: Lei

last: Yang

first: Bin

last: Zhang


title: EZH2 RIP-seq identifies pNEAT1 as regulator of myogenesis in pigs

city: Wuhan

first: shanshan

state: Hubei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province · 430070 · P.R.China

department: Animal Sciences & Technology

institute: Huazhong Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: We introduced RIP-seq and lincRNA-seq methods to identify EZH2-binding lincRNAs.

overall_design: EZH2 pull downed lincRNA and total lincRNA profiles one-month-old pig longissimus dorsi muscle

first: Bo

last: Zuo

first: Shanshan

first: Feng

last: Zhu


title: Perivascular adipose tissue inflammation in ischemic heart disease

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
We performed microarray analyses comparing perivascular adipose tissue gene expression of thoracic aortic vs. left internal mammary artery in human subjects with coronary artery disease.
300 genes were significantly upregulated in aortic fat, with at least 63 genes involved in inflammation and atherosclerosis. qPCR validation demonstrated increased expression of WNT-5A related genes, and CCL-2, CCL-8, JNK, and IL-6 gene expression.

overall_design: Gene profiling was performed using Human Gene 2.0 ST microarrays with RNA from perivascular adipose tissue samples collected from the proximal aorta and left internal mammary artery of 5 patients during coronary artery bypass surgery.

first: Celestina

last: Mazzotta

first: Noyan

last: Gokce


title: Inferring time-course chromatin states for promoter-enhancer pairs based on Hi-C data

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Co-localized combinations of histone modifications ("chromatin states") have been shown to correlate with promoter and enhancer activity. Changes in chromatin states over multiple time points ("chromatin state trajectories") have previously been analyzed at promoter and enhancers separately. With the advent of time-course Hi-C data it is now possible to connect promoters and enhancers and to analyze chromatin state trajectories at promoter-enhancer pairs. We present TimelessFlex, a framework for investigating chromatin state trajectories at promoter-enhancer pairs based on Hi-C information.

overall_design: Investigation of chromatin state trajectories at promoter-enhancer pairs based on Hi-C information

first: H

last: Miko

first: U

last: Ohler


title: Plasmid-encoded Small Regulatory RNAs Regulate Chromosome Gene Expression in Bacillus anthracis

first: Theresa

middle: Marie

last: Koehler

address: 6431 Fannin Street, MSB 1.508

department: Microbiology and Molecular Genetics

institute: McGovern Medical School

summary:
Purpose: Small regulatory RNAs (sRNAs) are short transcripts that base-pair to mRNA targets or interact with regulatory proteins. sRNA function has been extensively studied in Gram-negative bacteria; comparatively less is known about sRNAs in Firmicutes. Here we investigate two sRNAs encoded by the virulence plasmid pXO1 of Bacillus anthracis, the causative agent of anthrax. We designated the sRNAs as as “XrrA” and “XrrB” (for pXO1-encoded regulatory RNA). We constructed deletion mutants ∆xrrA, ∆xrrB, and ∆xrrA∆xrrB in an Ames strain background and compared gene expression of these mutants to that of the Ames-derived parent strain using RNA-seq.
Methods: Total RNA from Ames strains UTA37 (Parent), UTA38 (∆xrrB), UTA39 (∆xrrA), UTA41 (∆xrrA∆xrrB) was isolated from cultures grown in CA-CO2 in triplicate, using saturated phenol: chloroform extraction. One microgram of pure and quality-checked RNA from each sample was subjected to Illumina sequencing by synthesis using a NextSeq550 sequencer. Sequencing by synthesis was performed to generate 75bp paired-end reads. Two 130M-read sequencing runs (Run1 and Run2) were performed and an average of 31M reads per sample were obtained.
Results: All bioinformatic analysis was performed using the publicly available Galaxy web resource (https://usegalaxy.org/). Comparison of the transcriptomes of a virulent Ames-derived strain to isogenic sRNA-null mutants revealed multiple 4.0- to >100-fold differences in gene expression. Deletion of xrrA resulted in 50 transcripts showing a ≥ 4.0-fold change in expression compared to the parent strain. In contrast, deletion of xrrB led to one transcript having a ≥ 4.0-fold change in expression compared to the parent strain. In the ∆xrrA∆xrrB mutant, levels of 116 transcripts were affected with a fold-change of ≥ 4.0. Many sRNA-regulated targets were chromosome genes associated with branched-chain amino acid metabolism, proteolysis, and transmembrane transport.
Conclusions: In this work, we provide experimental evidence for sRNA-mediated regulation in the mammalian pathogen B. anthracis. XrrA and XrrB are the first regulatory RNAs examined in B. anthracis and are shown here to have multiple effects on gene expression in this pathogen. The data suggest distinct regulatory roles for XrrA, as well as some functional overlap between XrrA and XrrB.

overall_design: Transcriptomes of sRNA-null mutants and an Ames parent strain were obtained by RNA-seq. mRNA profiles of the parent strain and deletion mutants (∆xrrA, ∆xrrB, and ∆xrrA∆xrrB) were compared to discern regulatory function of XrrA and XrrB in B. anthracis.

first: Ileana

last: Corsi

middle: M


title: Deep minimal residual disease assessment redefines outcome and unveils different modes of treatment resistance in standard and high-risk multiple myeloma

city: Pamplona

first: Ibai

last: Goicoechea

state: Navarra

address: Centro de Investigación Médica Aplicada (CIMA) Avenida Pío XII, 55

country: Spain

institute: Universidad de Navarra

summary: mRNA profiles of tumor plasma cells derived from 40 multiple myeloma patients at diagnosis and at MRD

first: I


title: Monocyte and Macrophage Transcriptional Phenotypes in Systemic Juvenile Idiopathic Arthritis Reveal TRIM8 as a Mediator of IFN-γ Hyper-responsiveness and Risk for Macrophage Activation Syndrome

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Systemic juvenile idiopathic arthritis (SJIA) confers high risk for macrophage activation syndrome (MAS), a life-threatening episode of hyperinflammation driven by IFN-γ. Monocytes in SJIA display IFN-γhyperresponsiveness, but the molecular basis of this remains unclear. The objective of this study is to identify monocyte and macrophage polarization phenotypes including features of interferon response. Bulk RNA-seq of purified SJIA monocytes revealed marked transcriptional changes in patients with elevated ferritin levels. We identified substantial overlap with multiple polarization states but little evidence of IFN-induced signature. Interestingly, among the most highly upregulated genes was tripartite motif containing 8 (TRIM8), a positive regulator of IFN-γ signaling. Single cell RNA-seq of bone marrow macrophages (BMM) from a patient with SJIA and early MAS identified a distinct subpopulation of BMM with altered transcriptomes consistent with hemophagocytes, including upregulated IFN-γ response pathways. These BMM also showed significantly increased expression of TRIM8. In vitro knock-down of TRIM8 in macrophages caused significant reductions in IFN-γ responsiveness. In conclusions, we identify a clear IFN-γ response phenotype in BMM during MAS. TRIM8 is upregulated in both monocytes and macrophages in SJIA, and required for macrophage IFN-γ response in vitro, providing a molecular mechanism and novel therapeutic for monocyte hyperresponsiveness to IFN-.

overall_design: Leftover BM aspirates were obtained from patients where no hematologic or oncologic abnormalities were found (control BM) or from patient with suspected SJIA. After red cell lysis, BM cells were stored at -80C in freezing media until sequencing. After thawing, macrophage single cell suspensions were obtained using cell sorting for live (7AAD-) populations expressing the monocyte and macrophage surface markers CD14 and CD163 while excluding cells expressing the granulocyte/monocyte marker CD15. This suspension was then loaded onto the Fluidigm C1 Single-Cell Auto Prep System, which captures up to 96 single cells per chip.  These cells were subsequently lysed, and extracted RNA converted into cDNA and sequenced as a pooled library using the Illumina platform, providing approximately 3.5-4 million reads per single cell.

first: Grant S

last: Schulert

first: Alex

middle: V

last: Pickering

first: Thuy

last: Do

first: Sanjeev

last: Dhakal

first: Ndate

last: Fall

first: Mario

last: Medvedovic

first: Sherry

last: Thornton

first: Alexei

middle: A

last: Grom


title: OBF1 and Oct factors control the germinal center transcriptional program [Mouse]

city: Basel

first: Shuang

last: Song

state: Basel

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: OBF1 is a specific coactivator of the POU family transcription factors OCT1 and OCT2. OBF1 and OCT2 are B cell-specific and indispensable for germinal center (GC) formation, but their mechanism of action is unclear. Here, we show by ChIP-seq that OBF1 extensively colocalizes with OCT1 and OCT2 and stabilizes their binding. We found that these factors also often colocalize with transcription factors of the ETS family, such as PU.1 and ETS1. Furthermore, we showed that OBF1, OCT2 and OCT1 bind widely to the promoters or enhancers of genes involved in GC formation, such as the master regulators Bcl6 and Foxo1. shRNA knockdown experiments demonstrated that OCT1, OCT2 and OBF1 are essential for proliferation of GC-derived lymphoma cell lines. OBF1 downregulation disrupts the GC transcriptional program: genes involved in GC maintenance -such as BCL6- are downregulated, while genes related to exit from the GC program are upregulated. Ectopic expression of BCL6 does not restore the proliferation of GC-derived Raji cells depleted of OBF1 unless IRF4 is also depleted, indicating that OBF1 controls a critical regulatory node in GC differentiation.

overall_design: RNA-seq of mouse CD19+ B cells between LPS and anti-CD40/IL4 stimulation


title: Drosera rotundifolia induces gene expression changes in human bronchial epithelial cells 16HBE

city: Verona

first: Fabio

last: Arruda-Silva

state: VR

address: strada Le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

summary:
16HBE cells were incubated for 3 or 6h with a homeopathic preparation of Drosera r. or the solvent control and the transcriptome was analyzed by RNA sequencing. The expression changes of the main statistically significant genes were validated through follow-up experiments using RT-qPCR.
Compared with the control solution, Drosera r. changed the expression of dozens of genes already after 3h and this effect was amplified after 6 hours of treatment. The main target genes were some ligands of epithelial growth factor receptor (EREG, AREG, EPGN), genes involved in xenobiotic detoxification (CYP1B1, TIPARP) and chemokines. The network of the main biological functions included epithelial cell proliferation, regulation of angiogenesis, cell chemotaxis, and wound healing.
Drosera r. acts on a complex and faceted set of genes, potentially involved in different layers of the bronchial mucosa. The global effect of the plant in 16HBE epithelial cells is a mild stress response that primes the epithelial reparative process and recruits the innate cell defense.

overall_design: Evaluation of differential expressed genes by 16HBE cells upon Drosera 3x treatment

first: Paolo

last: Bellavite

first: Marta

last: Marzotto


title: Aanalysis transcriptomes of Schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing

city: shanghai

first: Qingshan

last: Chen

address: Changhai road 255

institute: Third Affiliated Hospital of Second Military Medical University

summary: Transcriptome analysis is an effective method to study a comprehensive understanding of molecular mechanisms involved in biological processes and diseases by RNA-Sequencing (RNA-Seq). This study aimed to elucidate the possible mechanisms of Schisandrin B on CCl4-induced liver fibrosis through detecteing hepatic gene expression profiles by RNA-Seq.

overall_design: Liver mRNA profiles of normal, liver fibrosis, Schisandrin B treated rtas were generated by deep sequencing, in triplicate.

first: Hai

last: Zhang

first: Guoqing


title: OBF1 and Oct factors control the germinal center transcriptional program [Human]

overall_design: RNA-seq between wild type and OBF1 knockdown Raji cells (Obf1sh1) and Control Raji cells (SHC002)


title: Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response in Arabidopsis

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

institute: Swedish University of Agricultural Sciences

type: Methylation profiling by high throughput sequencing

summary: Environmentally induced changes in the epigenome help individuals to quickly adapt to fluctuations in the conditions of their habitats. Here we explored those changes in Arabidopsis thaliana plants subjected to multiple biotic and abiotic stresses, and identified transposable element (TE) activation in plants infested with the green peach aphid, Myzus persicae. We performed a genome-wide analysis of DNA methylation, mRNA expression, mRNA degradation and small RNAs accumulation. Our results demonstrate that aphid feeding induces loss of methylation of hundreds of loci, mainly TEs with labile chromatin characteristics. This loss of methylation has the potential to regulate gene expression and we found evidence that it is involved in the control of key plant immunity genes. Accordingly, we find that mutant plants deficient in epigenetic silencing show increased resistance to M.persicae infestation. Collectively, our results show that changes in DNA methylation play a significant role in the regulation of the plant transcriptional response and induction of defence response against aphid feeding.

overall_design: Analysis of RNA, sRNA and bisulfite sequencing during aphid infestation at 72hrs in Arabidopsis thaliana rosette leaves


title: OBF1 and Oct factors control the germinal center transcriptional program [ChIP-seq]

overall_design: mapping OCT1, OCT2, OBF1 and histone modifications in mouse CD19+ splenic B cells treated with LPS or anti-CD40/IL4


title: Kruppel-like factor 2 is important for endoderm-related gene regulation with Ring1b-mediated mechanism in mESCs

status: Public on Feb 01 2021

city: Daejeon

first: Lin

last: Seo

address: Basic Science Bld Rm414, 291 Daehak-ro, Yuseong-gu, KAIST

department: Department of Biological Sciences

country: South Korea

institute: KAIST

summary: We report the RNA-seq data of Klf2 KO and Ring1b KD from mouse embryonic stem cells. Wild type and Klf2 knockout cells were knockdowned with Ring1b shRNA. Samples were lysed with total RNA prep kit.

overall_design:
Two biological replicates were analyzed. RNA-seq samples in wild-type (WT) and Klf2 knockout were treated with Ring1b knockdown in mouse embryonic stem cells (E14TG2a).
Please note that each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.

first: Jaehoon

last: Kim


title: Modified Vaccinia Ankara Vector-Based Vaccine Protects Macaques from SARS-CoV-2 Infection, Immune Pathology and Dysfunction in the Lung

city: Atlanta

first: Arun

last: Boddapati

state: GA

address: 954 Gatewood Road, NE

department: Genomics Core

institute: Yerkes National Primate research center

summary: Study show that modified vaccinia Ankara (MVA)-based COVID-19 vaccine expressing membrane anchored pre-fusion stabilized spike (MVA/S) induces both neutralizing antibodies and CD8+ T cells in the blood and lung and protects from SARS-CoV-2 challenge. Single-cell RNA sequencing analysis of lung cells at day 4 post-infection revealed that MVA/S vaccination also protected macaques from infection-induced inflammation and B cell abnormalities, and lowered induction of interferon stimulated genes.

overall_design: To test the immunogenicity and protective ability of the MVA/S vaccine we immunized rhesus macaques (n=5/group) either with MVA/S vaccine or MVA/Wt vaccine delivered intramuscularly on weeks 0 and 4. At week 8 (4 weeks after the boost) animals were challenged intranasally and intratracheally with live SARS-CoV-2 virus. To understand MVA/S vaccine offered inflammatory sequelae in the airway, we performed single-cell RNA-Seq on the cellular fraction recovered from BAL at Day 4 after infection. This analysis shows MVA/S vaccination reduces transcripts associated with inflammation and hyperimmune activation in lung macrophages.

first: Rama

last: Amara


title: seekCRIT: detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

summary: Recently, it has been demonstrated that genomes of many species express single stranded RNAs with covalently closed ends, named circular RNAs. Their regulatory potential and functional relevance are just starting to be revealed. Here we present a novel computational tool, seekCRIT (seek for differentially expressed Circular RNAs In Transcriptome), that identifies circular RNAs and detects their differential expression between two conditions. Using seekCRIT we identified the circular RNAs that are expressed in the neural retina and determined that the majority of them (74%) are expressed in both, ischemic and normal conditions. We identified over 40 circular RNAs that were differentially expressed between both conditions and validated these experimentally using qRT-PCR. The high validation rate of 90% with a false discovery rate (FDR) of < 5% demonstrates the accuracy and reliability of seekCRIT.

overall_design: RNA from rat’s retina was extracted using the RNeasy Lipid Tissue Mini Kit. Two retinal samples were sequenced: a sample subjected to ischemia-reperfusion (IR) injury and collected 12 hours after the reperfusion (IR12) and a control sample (CTRL) subjected to a sham-procedure. 350ng of total RNA samples was used for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina). Single-end 150 bp reads were generated on a NextSeq 550 sequencer.

first: Juw

last: Park

first: Nigel

last: Cooper


title: Expression data from FACS sorted cell populations of immortalized stromovascular fraction mouse cells derived from inguinal white adipose tissue, showing either high or low binding to FcsFNDC4

city: Munich

first: Anastasia

last: Georgiadi

state: Germany

address: Ingolstädter Landstraße 1

department: Departement of Diabetic Complications

country: Germany

institute: Helmholtz Centre Munich

summary:
Soluble FNDC4 (sFNDC4) is a novel hepatokine which promotes glucose tolerance in mice and positively associates with increased glucose tolerance in humans. To identify potential receptors for sFNDC4 we screened a population of immortalized stromovascular mouse cells derived from inguinal white fat for cells, which showed high (high binding cells-HBC) or low binding (low binding cells-LBC) to recombinant FcsFNDC4.
We utilised microarray to identify differentially expressed genes between HBC and LBC. After comparing the global gene expression between HBC and LBC we were able to identify several differentially expressed genes encoding for cellular receptors. Experimental validations of these results and further experimental sutdies supported that GPR116 is the receptor for sFNDC4.

overall_design: Adherent immortalised SVF cells referenced in Duteil D. et al, PNAS 2017 were scraped and incubated for 40min at 4oC with FcsFNDC4 100nM, then wahsed twiced with 3%FBS (in PBS) at 4oC and incubated with secondary human IgG conjugated to PE (Phycoerythrin) for 40 min at 4oC. After two final washes, cells were checked for the levels of FcsFNDC4 bound protein by reading the levels of PE fluorescence with FACS.The fluorescence intesity was proportional to the amount of FcsFNDC4 bound to the cells.  Cells which showed high amounts of FcsFNDC4 bound to them  (HBC) or low amount of bound FcsFNDC4 (LBC) were sorted and plated in cell culure media. When cells reached 80% conlfuency, they were passaged to allow proliferation. The assay to test for FcsFNDC4 binding, as well as sorting on HBC and LBC via FACS was repeated for 20 times,  when we finally had obtained HBC and LBC with consistently high and low levels of FcsFNDC4 binding.

first: Stephan

last: Herzig


title: OBF1 and Oct factors control the germinal center transcriptional program

first: Shuang

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

overall_design: Refer to individual Series


title: The thymoproteasome hardwires the TCR repertoire of CD8+ T cells in the cortex independent of negative selection

city: Bethesda

first: Michael

middle: C

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

summary: The thymoproteasome expressed specifically in thymic cortical epithelium optimizes the generation of CD8+ T cells. However, how the thymoproteasome contributes to CD8+ T cell development is unclear. Here we show that the thymoproteasome shapes the TCR repertoire directly in cortical thymocytes before migration to the thymic medulla. We further show that the thymoproteasome optimizes CD8+ T cell production independent of the thymic medulla, independent of additional antigen-presenting cells including medullary thymic epithelial cells and dendritic cells, and independent of apoptosis-mediated negative selection. These results indicate that the thymoproteasome hardwires the TCR repertoire of CD8+ T cells with cortical positive selection independent of negative selection in the thymus.

overall_design: Single cell 5' RNA-Seq on thymocyte subpopulations from Beta5t-deficient I-A-deficient and control I-A-deficient mice.

first: Ohigashi

last: Izumi

first: Frantzeskakis

last: Melina

first: Jacques

last: Alison

first: Fujimori

last: Sayumi

first: Ushio

last: Aya

first: Yamashita

last: Fusano

first: Ishimaru

last: Naozumi

first: Yin

last: Da

first: Cam

last: Margaret

first: Kelly

last: Michael

first: Awasthi

last: Parirokh

first: Takada

last: Kensuke

first: Takahama

last: Yousuke


title: Genome-wide transcriptome analysis of liver sinusoidal endothelial cells in the pathogenesis of NASH

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

summary: We isolated liver sinusoidal endothelial cells (LSEC) from mice fed control chow (Chow) or the nonalcoholic steatohepatitis (NASH)-inducing high fat, fructose and cholesterol (FFC) diet, and subjected the cells to bulk RNA-seq. Out of 13993 transcripts detected, the adhesion molecule Vcam1 was significantly upregulated in LSEC from FFC-fed mice compared to Chow-fed mice (Log2FC: 0.925, p: 3.6x10E-18), whereas the upregulation of another adhesion molecule Icam1 (Log2FC: 0.416, p: 0.014) was not as striking as Vcam1.

overall_design: Liver sinusoidial endothelial cells from NASH and control mice were subjected to bulk RNA-seq analysis.

first: Petra

last: Hirsova

first: Samar

last: Ibrahim


title: Genome-wide open chromatin analysis of liver sinusoidal endothelial cells in the pathogenesis of NASH

summary: We isolated liver sinusoidal endothelial cells (LSEC) from mice fed control chow (Chow) or the nonalcoholic steatohepatitis (NASH)-inducing high fat, fructose and cholesterol (FFC) diet, and subjected the cells to Omni-ATAC-seq. Out of the top 500 differentially abundant open chromatin regions between the two groups, 498 were more robust in FFC-fed mice compared with Chow-fed mice, suggesting a genome-wide active epigenetic regulation in LSEC during NASH development. Furthermore, in combination with RNA-seq, we demonstrated a robust transcriptional upregulation of the adhesion molecule VCAM-1 in LSEC in NASH pathogenesis.

overall_design: Liver sinusodial endothelial cells from NASH and control mice were subjected to Omni-ATAC-seq analysis.

first: Kunimaro

last: Furuta

first: Qianqian

last: Guo


title: RNAseq in immortalized human podocyte cell line following PRDM15 CRISPR knock-out

first: Nina

last: Mann

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: We recently identified variants in PRDM15 in affected individuals with proteinuric kidney disease. To determine the downstream pathways mediated by PRDM15 knock-down, PRDM15 knock-out immortalized podocyte cell lines were generated using CRISPR/Cas genome editing. Two different guide RNAs were utilized to generate two different cell lines, while a scramble guide RNA was utilized as control. We performed RNAseq and identified 151 differentially regulated genes, which coalesced upon pathways involved in renal development.

overall_design: RNAseq in control and PRDM15 knock-out immortalized human podocyte cell lines

first: Friedhelm

last: Hildebrandt


title: Plasmodium falciparum PfAP2-G2 KO asexual microarray timecourse

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: Differentiation  from asexual blood stages  to sexual gametocytes is required for  transmission  of  malaria  parasites  from  the  human  to  the  mosquito  host. Preventing  gametocyte  commitment  and  development  would  block  parasite transmission,  but  the  underlying  molecular  mechanisms  behind  these  processes remain  poorly  understood.  Here,  we  report  that  the  ApiAP2  transcription  factor, PfAP2-G2  (PF3D7_1408200)  plays  a  critical  role  in  the  maturation  of  Plasmodium falciparum gametocytes. PfAP2-G2 binds to the promoters of a wide array of genes that are expressed at many stages of the parasite life cycle. Interestingly, we also find binding  of  PfAP2-G2  within  the  gene  body  of  almost  3000  genes,  which  strongly correlates with the location of H3K36me3 and several other histone modifications as well as Heterochromatin Protein 1 (HP1), suggesting that occupancy of PfAP2-G2 in gene bodies may serve as an alternative regulatory mechanism. Disruption of pfap2-g2 does not impact asexual development, parasite multiplication rate, or commitment to  sexual  development  but  the  majority  of  sexual  parasites  are  unable  to  mature beyond  stage  III gametocytes. The absence of  pfap2-g2 leads  to  overexpression  of 28%  of  the  genes  bound  by  PfAP2-G2  and none  of  the  PfAP2-g2  bound  are downregulated, suggesting that it is a repressor. We also find that PfAP2-G2 interacts with  chromatin  remodeling  proteins,  a  microrchidia  (MORC)  protein,  and  another ApiAP2 protein (PF3D7_1139300). Overall our data demonstrate that PfAP2-G2 is an important  transcription  factor  that establishes an essential gametocyte maturation program in association with other chromatin-related proteins.

overall_design: RNA was extracted from tightly synchronized PfAP2-G2::KO and WT parasites every 6 hours, starting at 3 hpi, for 48 hours life cycle in asexual stages using TRIzol (ThermoFisher Scientific), following the manufacturer’s protocol. This resulted in collection of 8 KO and 8 WT RNA samples. The asexual reference pool, which has cDNA from 3D7 WT parasites, was dye coupled using Cy3 and the sample was coupled to Cy5.

first: Suprita

last: Singh

first: Joana

last: Santos

first: Lindsey

last: Orchard

first: Naomi

last: Yamada

first: Riette

last: van Biljon

first: Heather

middle: J

last: Painter

first: Shaun

last: Mahony


title: NASH pathogenesis


title: Plasmodium falciparum PfAP2-G2 KO gametocyte microarray timecourse

overall_design: RNA was extracted from induced PfAP2-G2::KO and WT parasites every 12 hours, starting at day 1 of gametocytes for 7.5 days using TRIzol (ThermoFisher Scientific) following the manufacturer's protocol, resulting in collection of 14 KO and 14 WT samples (time point 6 was not recovered). These timepoints incorporated stage I to stage IV of gametocytes. Reference pool for gametocytes samples contained asexual and sexual stages. The reference pool was dye coupled using Cy3 and the sample was coupled to Cy5.


title: Dynamic transcription of all genes in Triticum urartu endosperms throughout grain-filling stages

city: København

first: Guangbin

last: Luo

state: Denmark

address: Strynøgade 5，Østerbro Kollegiet, 2, 208

department: Institute of Genetics and Developmental Biology

institute: Chinese Academy of Sciences

summary: Endosperms (with the embryo, aleurone, seed coat, and pericarp removed) at 5, 10, 15, 20, and 25 DPAs of the T. urartu accession PI 428198 were used for RNA-Seq analysis. Each sample had three independent biological replicates. The total RNA of endosperms was isolated and a library with an insert length of ~350 bp was sequenced using the Illumina HiSeq 2000 (San Diego, CA, USA). An integrated reference sequence of T. urartu PI 428198 was prepared by combining the annotated gene set (ftp://ftp.ensemblgenomes.org/pub/plants/release3 9/fasta/triticum_urartu) with cloned low-molecule-weight glutenin subunit genes and gliadin genes after gene redundancy removal. The relative transcript abundance of seed storage protein genes and the 41,507 predicted genes from genome sequences were calculated using the unique aligned reads as the expected number of fragments per kilobase of the transcript sequence per million base pairs sequenced (FPKM).

overall_design: Elucidate the transcription dynamics of each gene in Triticum urartu endosperms throughout grain-filling stages using RNA-Seq analysis

first: Aimin

last: Zhang


title: Transcriptomic analysis of naïve human embryonic stem cells cultured in three-dimensional PEG scaffolds

first: G Rasul

last: Chaudhry

state: MI

address: 118 Library Dr

department: Biological Sciences

institute: Oakland University

summary: Naïve human embryonic stem cells (ESCs) are characterized by improved viability, proliferation, and differentiation capacity in comparison to traditionally derived primed human ESCs. However, currently used two-dimensional (2-D) cell culture techniques fail to mimic the three-dimensional (3-D) in vivo microenvironment, altering morphological and molecular characteristics of ESCs. Here, we describe the use of 3-D self-assembling scaffolds that support growth and maintenance of the naïve state characteristics of ESC line, Elf1. Scaffolds were formed via a Michael addition reaction upon combination of two 8-arm polyethylene glycol (PEG) polymers functionalized with thiol (PEG-8-SH) and acrylate (PEG-8-Acr) end groups. 3-D scaffold environment maintained the naïve state and supported long-term growth of ESCs. RNA-sequencing demonstrated significant changes in gene expression profiles between 2-D and 3-D grown cells. Gene Ontology analysis revealed upregulation of biological processes involved in the regulation of transcription and translation, extracellular matrix organization, and chromatin remodeling in 3-D grown cells. 3-D culture conditions also induced upregulation of genes associated with Wnt and focal adhesion signaling, while p53 signaling pathway associated genes were downregulated. Our findings for the first time provide insight into the possible mechanisms of self-renewal of naïve ESCs stimulated by the transduction of mechanical signals from the 3-D microenvironment.

overall_design: RNA-seq comparison of two biological replicates of naïve human embryonic stem cell line (Elf1) grown in two culture conditions: grown in 2-D culture (adherent culture), and 3-D culture in PEG self-assembling scaffolds.

first: G

middle: R


title: Whole-genome transcritome analysis of diet-induced murine NASH

first: Mrunal

last: Dehankar

summary: Whole liver from mice with diet-induced nonalcoholic fatty liver disease (NASH) was subjected to bulk RNA-seq. Ingenuity pathway analysis implicated pathways related to the leukocyte adhesion and differentiation in the pathogenesis of NASH. Among the adhesion molecules expressed in endothelial cells, only Icam1 (Log2FC: 1.99; FDR: 1.55E-37) and Vcam1 (Log2FC: 1.93; FDR: 9.32E-35) were differentially upregulated in NASH liver.

overall_design: Whole liver RNA-seq to investigate the mechanism of NASH using a mouse model of diet-induced NASH.

first: Samar


title: Single cell RNA seq of the developing murine adrenal gland reveals correlation of Schwann cell precursor signature to neuroblastoma phenotype.

city: Utrecht

first: Tito

last: Candelli

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: Neuroblastoma is the most common extracranial solid tumor and accounts for ~10% of pediatric cancer-related deaths. The exact cell-of-origin has yet to be elucidated, but it is generally accepted that neuroblastoma derives from the neural crest and should thus be considered an embryonal malignancy. About 50% of primary neuroblastoma tumors arise in the adrenal gland. Here we present an atlas of the developing mouse adrenal gland at a single cell level. Five main cell cluster groups (medulla, cortex, endothelial, stroma and immune) make up the mouse adrenal gland during fetal development. The medulla group, which is of neural crest origin, is further divided into seven clusters. Of interest is the Schwann cell precursor (SCP) and the neuroblast cluster, a highly cycling cluster that shares markers with sympathoblasts. The signature of the medullary SCP cluster differentiates neuroblastoma patients based on disease phenotype: the SCP signature score anti- correlates with ALK and MYCN expression, two indicators of poor prognosis. Furthermore, a high SCP signature score is associated with better overall survival rates. This study provides an insight in the developing adrenal gland and introduces the SCP gene signature as being of interest for further research in understanding neuroblastoma phenotype.

overall_design: Sequencing of adrenal gland single cells in duplicate for embrionic days 13.5, 14.5, 17.5, 18.5 and postnatal days 1 and 2

first: Evelyn

last: Hanemaaijer

first: Thanasis

last: Margaritis

first: Karin

last: Sanders

first: Frank

last: Bos

first: Hanin

last: Al-Saati

first: Marc

last: van de Wetering

last: Holstege

first: Hans

last: Clevers


title: SARS-CoV-2 infection of human pancreatic islets

city: Ulm

first: Alexander

last: Kleger

address: Albert Einstein Allee 23

institute: Ulm University

summary: We performed RNA-sequencing in uninfected, SARS-CoV-2-infected, and additionally remdesivir treated ex vivo cultured human islets from two donors to shed light on the transcriptional changes occurring upon viral infection.

overall_design: Islet preparations of two different donors were infected with SARS-CoV-2 and treated with Remdesivir for 5 days. Uninfected pancreatic islets served as control.

first: Sandra

last: Heller

first: Rüdiger

last: Groß

first: Carina

last: Conzelmann

first: Janis

last: Müller

first: Jana

last: Krüger

first: Michael

last: Schuster

first: Markus

last: Breunig

first: Jan

last: Münch


title: H3K27me3 chip-seq in cadmium resistant 231 breast cancer cells

city: Aurora

first: Joshua

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

summary: In this study we investigate genome wide changes in H3K27me3 with respect to cadmium resistance in MDA-MB-231 cells.

overall_design: Examination of H3K27me3 in cadmium resistant breast cancer cells

first: Philip

last: Tatman

first: Gregory

last: Wright


title: Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis

city: Providence

first: Alper

last: Uzun

state: RI

address: 200 Chestnut St.

department: Pediatrics

institute: Women and Infants Hospital of Rhode Island

summary: Candida parapsilosis has emerged as a frequent cause of invasive candidiasis with increasing evidence of unique biological features relative to C. albicans.  As it adapts to conditions within a mammalian host, rapid changes in gene expression are necessary to facilitate colonization and persistence in this environment.  Adhesion of the organism to biological surfaces is a key first step in this process and is the focus of this study.  Building on previous observations showing the importance of a member of the ALS gene family in C. parapsilosis adhesion, three clinical isolates were cultured under two conditions that mimic the mammalian host and promote adhesion, incubation at 37°C in tissue culture medium 199 or in human plasma.  Transcriptional profiles using RNA-seq were obtained in these adhesion-inducing conditions and compared to profiles following growth in yeast media that suppress adhesion to identify gene expression profiles associated with adhesion. Overall gene expression profiles among the three strains were similar in both adhesion inducing conditions and distinct from adhesion suppressing conditions.  Pairwise analysis among the three growth conditions identified 133 genes that were differentially expressed at a cutoff of +/- 4-fold, with the most upregulated genes significantly enriched in iron acquisition and transmembrane transport, while the most downregulated genes were enriched in oxidation-reduction processes. Gene family enrichment analysis identified gene families with diverse function that may have an important role in this important step for colonization and disease.

overall_design: Total RNA was prepared from three clinical Candida parapsilosis isolates exhibiting adhesive phenotypes which were incubated at 37°C  in YPD, M199, or pooled human plasma. All samples were prepared in triplicate. rRNA depleted RNA was sequenced with 150bp paired-end reads using the Illumina HiSeq2000 platform. Reads were aligned and gene-level expression count estimates were calculated using Salmon in mapping-based mode.

first: George

last: Tollefson

first: Joe

last: Bliss

first: Sunil

last: Shaw


title: Single nucleus RNA sequencing of kidney from five-month-old Pdss2 kd/kd mice compared to age-matched controls

city: Boston

first: Eriene-Heidi

last: Sidhom

state: MA

address: 4 Blackfan Circle HIM 536

institute: Harvard Medical School

summary: We report trancriptional changes between wildtype C57BL/6J and in mice harboring a spontaneous missense mutation in Pdss2 (V117M, Pdss2 kd/kd).

overall_design: Single nucleus RNA sequencing of 3 control and 3 disease mice at 5-months-old.

first: Anna

last: Greka


title: A novel lesional transciptional signature separates atherosclerosis with and without diabetes in Yorkshire swine and humans

first: Stefan

last: Haemmig

address: 77 Avenue Louis Pasteur, NRB-742

department: Medicine

institute: Brigham and Women Hospital / Harvard Medical School

summary: This study identifies evolutionarily conserved gene signatures and signaling pathways in a stage-specific manner that successfully distinguishes diabetes and non-diabetes-associated atherosclerosis. These findings establish new molecular insights and therapeutic opportunities to potentially control accelerated atherosclerotic lesion formation in diabetes.

overall_design: Serial 3-mm coronary artery segments of hypercholesterolemic Yorkshire swine and diabetic-hypercholesterolemic swine were characterized as mild, moderate, or severe phenotypic manifestations of coronary atherosclerosis based on histopathology. Lesional RNA-Sequencing was performed (n=3-8 lesions per group) corresponding to increasing phenotypic severity. Differentially expressed genes, transcription factors, upstream regulators, and hubs were validated using NanoString technology and a human atherosclerotic specimen cohort.

first: Mark

last: Feinberg

first: Ali

last: Gheinani

first: Peter

last: Stone


title: Hedgehog signaling alters the balance of fibroblast subtypes in pancreatic cancer [bulk RNA-seq]

city: Ann Arbor

first: Marina

last: Pasca di Magliano

address: 1500 E medical drive

institute: University of Michigan

summary: A better understanding of the roles of signaling pathways differentially activated in distinct fibroblast populations will shed light on the complexity of fibroblast heterogeneity in pancreatic cancer. Here, we show that Hedgehog pathway inhibition alters the fibroblast composition towards a more inflammatory microenvironment, opening the possibility for future combination therapies.

overall_design: Total RNA samples were isolated Trizol, according to manufacturer’s instructions. RNA concentration and quality were determined and ribosomal depleted mRNA libraries were prepared by the University of Michigan Advanced Genomics Core. Libraries were sequenced using 150 paired end NovaSeq 6000 (Illumina). Mouse tumors were treated with Vehicle or HH inhibitor for 14 days after formation of tumors. For sorting of fibroblasts from KPC tumors, cells were stained for 30 minutes with CD45-Alexa Fluor 488 (103122; BioLegend), CD326 (EpCAM)-Alexa Fluor 647 (118212; BioLegend), CD324 (E-cadherin)-Alexa Fluor 647 (147307; BioLegend), PDPN-APC/Cy7 (127418; BioLegend), and for 15 minutes with DAPI. DAPI- CD45- EpCAM- ECAD- PDPN+ cells were sorted on the FACSAria cell sorter (BD) and processed for RNA-sequencing. N=2 replicates for LDE225 group, N=3 for Vehicle group

first: Giulia

last: Biffi

first: Nina

last: Steele


title: Hedgehog signaling alters the balance of fibroblast subtypes in pancreatic cancer

overall_design: Refer to individual Series


title: Mechanisms of Triggering Malaria Gametocytogenesis by AP2-G [DIP-seq]

city: Tsu

first: Tsubasa

last: Nishi

state: Mie

address: Edobashi

country: Japan

institute: Mie university

summary: AP2-G is a transcription factor (TF) that is essential for gametocytogenesis of malaria parasites; however, the mechanisms for its inducing the cell linage for sexual reproduction remain unclear. In this paper, this problem is addressed by investigating its expression profile and by determining target genes genome-wide in Plasmodium berghei.

overall_design: Mice were infected with P. berghei expressing GFP-fused AP2-G. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Chromatins associated with GFP-tagged AP2-G was IPed with anti-GFP antibody, and.target genes of this transcription factor were predicted.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Yuho

last: Murata


title: Hedgehog signaling alters the balance of fibroblast subtypes in pancreatic cancer [scRNA-seq]

overall_design: 10 Genomix single cell RNA sequencing of one mouse pancreatic tumor from a KrasLSL-G12D/+; Trp53LSL-R172H/+; Ptf1a-Cre mouse at 19 weeks of age(n=1)


title: Gene expression plofile in human articular cartilage-derived cells cultured by different culture methods

city: Suita Osaka

first: Takashi

last: Kanamoto

address: 2-2 Yamadaoka

institute: Osaka University

summary: Atelocollagen gel is often used for three-dimensional culture of articular cartilage-derived cells, but further knowledge is needed about the effect of atelocollagen gel on cells. We performed a microarray analysis using human articular cartilage-derived cells cultured in three different methods (2D culture, 3D culture with atelocollagen gel, and 3D culture without atelocollagen gel).

overall_design: We performed a microarray analysis using cells in the growth phase of flat culture or cells on day 4 of 3D culture and compared the expression profiles.


title: Transcriptome analysis of conidium germination of Aspergillus fumigatus in different growth conditions

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Gene expression level of Aspergillus fumigatus CEA17_ΔakuBKU80 during germination in two different medium

overall_design: Two media (GPA and MM) with three different replicates  per medium This comparison was based on germinated conidial  samples with similar germ tube length which are reached at different times of germination for these two media. At these two  time points, the germ tube stopped to grow  in GPA (but the fungus is still alive) while the germ tubes  continue to grow in MM.

first: François

last: Danion

first: Odile

last: Sismeiro

first: Hugo

last: Varet

first: Isabelle

last: Mouyna


title: Genome-wide map of RECQ1 binding in breast cancer cells.

first: Lorinc

last: Pongor

address: 37 Convent Dr,

department: DTB

institute: NIH

summary: RECQ1 is a DNA helicase that is important for DNA replication and repair. Recent evidences indicate a role for RECQ1 in regulation of gene expression. However, the mechanisms by which RECQ1 regulates gene expression are unknown.  We find that RECQ1 plays an direct role in gene regulation in breast cancer cells in collaboration with master transcription factors ER alpha and FOXA1.

overall_design: Genome-wide profiles for RECQ1 and ER alpha in breast cancer cells.

first: Sudha

last: Sharma

first: Xinyu

last: Wen

first: Christophe

last: Redon

first: Ashish

last: Lal


title: Expression data from C2C12 cells

city: Shenzhen

first: Yong Sheng

last: Zhang

address: pengfei road 7

institute: CAAS AGIS

summary:
MicroRNAs (miRNAs) play a critical role in cells differentiation by targeting protein coding genes. The expression level of miRNA and mRNA between D0 and D4 differentiated C2C12 showed a great significance. It is closely related to myogenesis, and is helpful to understand function of miRNAs and disease related to muscle.
We  performed microarray and transcriptome profiling in differentiating C2C12 cells cells (at 0 and 4 days named D0 and D4, respectively) to detail the expression of mRNA and miRNAs during differentiation.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Differentiated  C2C12 for D0 and D4 was induced by 2% pregnant mare serum. MRNA was extracted for microarray each for 3 replicates.

first: Zhang

middle: Y

last: Sheng

first: Yao

last: Long

first: Wang

middle: Z

last: Shuai

first: Tang

last: Lin


title: Transcriptional programme in Glmp KO mouse liver fibrosis model

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
Transcriptome of 8 and 18 weeks old mice where fibrosis developed upon the full-body knocking-out gene Glmp (glycosylated lysosomal membrane protein) (Glmpgt/gt; Glmp KO)
Glmp KO mice were compared to their wild-type (WT) littermates

overall_design: DNA-microarrays were hybridized with individual samples from livers of 16 male mice at age 8 and 18 weeks. 8 samples were from WT mice and 8 samples from Glmp KO mice.

first: Kaja

last: Blagotinšek Cokan

first: Žiga

last: Urlep

first: Xiang

last: Kong

first: Tadeja

last: Režen

first: Damjana

last: Rozman

first: Winnie

last: Eskild


title: H3K122succ expands the role of histone acylation in transcriptional regulation

city: Neuherberg

first: Lara

last: Zorro Shahidian

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute of Functional Epigenetics

institute: Helmholtz Zentrum Muenchen

summary: Histone post-translational modifications (PTMs) are key players in chromatin regulation. The recent identification of novel histone acylations raised important questions regarding their role in transcriptional regulation. In this study, we characterized the role of succinylation of H3K122 (H3K122succ), located on the lateral surface of the histone octamer, in transcription and in chromatin function. Using chromatin, site-specifically succinylated at H3K122, we found that the presence of H3K122succ is sufficient to stimulate transcription in vitro. In line with this H3K122succ was enriched on promoters of active genes in mammalian cells and enrichment levels scale with gene expression. Furthermore, we show that the p300 and CBP co-activators are H3K122 succinyltransferases and identify sirtuin 5 (SIRT5) as a new desuccinylase. By applying single molecule FRET assays we demonstrate a direct effect of H3K122succ on nucleosome stability indicating an important role for histone succinylation in modulating chromatin dynamics. Together, these data provide the first insights into the molecular mechanisms of H3K122succ in transcriptional regulation and they highlight a structural function for H3K122succ through direct perturbation of nucleosomes.

overall_design: Genome-wide profile of succinylated H3K122 in the human breast cancer MCF7 cell line.

first: Robert

last: Schneider

first: Sylvain

last: Daujat

last: Shahidian

first: Stephanie

last: Le Gras


title: RNA-seq of liver tissue from mice treated with PBS or extracellular vesicles (EV) from MCF10A or MDA-MB-231 cells

city: Duarte

first: wei

last: chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

summary: To identify gene expression changes in liver associated with circulating EV that carry high levels of miR-122 (from MDA-MB-231 and MCF10A/miR-122 cells), we analyzed RNA isolated from the liver of PBS- or EV-treated female NOD scid gamma (NSG) mice.  Mice had received tail-vein injected EV (or PBS) twice a week for 5 weeks (~10 ug EV per injection).  Gene expression in liver from mice treated with EV from MDA-MB-231 or MCF10A/miR-122 cells was compared to cells treated with PBS or EV from MCF10A cells, both of which served as controls in this experiment.

overall_design: RNA was extracted from liver tissue of mice that had received PBS or EV treatment, and subjected to library construction and RNA sequencing.

first: Xiwei

last: Wu

first: Shizhen

middle: E

last: Wang


title: Gene expression analysis of RECQ1-regulated transcriptome in breast cancer cells.

city: bethesda

first: Stefan

last: Ambs

state: md

address: 37 convent cir

summary: The goal of this study was to identify the RECQ1-regulated transcriptome and comparing it to the ER alpha-regulated transcriptome using RNA-seq in breast cancer cells.

overall_design: MCF7 cells were transfected with control siRNA or siRNAs (smartpool) against RECQ1 or ESR1. Total RNA was isolated and subjected to mRNA seq.

first: Sudha

last: Sharma

first: Wei

last: Tang


title: Suppression of MBD2 alternative splicing promotes breast cancer metastasis by activating FZD1 under hypoxia

city: Hefei

first: liu

last: zhaoji

state: Anhui

address: huangshan road

department: life science

institute: USTC

summary: Metastasis is responsible for the majority of breast cancer (BrCa) deaths; however, the underlying mechanisms remain largely elusive. Here, we report that suppression of MBD2 alternative splicing under hypoxia, which favors the production of MBD2a, facilitates BrCa metastasis. Specifically, we found that MBD2a promotes, whereas its less-known short form MBD2c suppresses metastasis. We elucidate that HIF-1 activation under hypoxia facilitates MBD2a production via repression of SRSF2-mediated alternative splicing and, as a result, the elevated MBD2a outcompetes MBD2c for binding to the promoter CpG islands to activate the expression of FZD1, thereby promoting EMT and metastasis. Strikingly, clinical data reveals significantly correlated expression pattern of MBD2a and MBD2c with the invasiveness of malignancy, indicating the opposing roles for MBD2 splicing variants in regulating human BrCa metastasis. Thus, our findings establish a novel link between MBD2 switching and tumor metastasis, and provide promising therapeutic strategy and predictive biomarkers for hypoxia-driven BrCa metastasis.

overall_design: MBD2a and MBD2c competitively bind to the CpG islands of FZD1 and inversely regulate the expression of downstream EMT markers

first: Zhaoji

last: Liu

first: Linchong

last: Sun

first: Yongping

last: Cai

first: Shenqi

last: Shen

first: Ping

last: Gao

first: Huafeng

last: Zhang


title: Identification of RCC subtype-specific microRNAs – meta-analysis of high-throughput RCC tumor microRNA expression data [miRNA-Seq]

city: Poznań

first: Arkadiusz

last: Kajdasz

state: wielkopolskie

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

summary: Renal cell carcinoma (RCC) is one of the most common cancers worldwide with nearly non-symptomatic course till advanced stage of disease. RCC can be distinguished into three subtypes: papillary (pRCC), chromophobe (chRCC) and clear cell renal cell carcinoma (ccRCC) representing up to 75% of all RCC cases. Detection and RCC monitoring tools are limited to standard imaging techniques, in combination with non-RCC specific morphological and biochemical read-outs. RCC subtype identification relays mainly on results of pathological examination of tumor slides. Molecular, clinically applicable and ideally non-invasive tools aiding RCC management are still non-existent, although molecular characterization of RCC is relatively advanced. Hence many research efforts concentrate on identification of molecular markers that will assist with RCC sub-classification and monitoring. Due to stability and tissue-specificity miRNAs are promising candidates for such biomarkers. Here we performed a meta-analysis study, utilized seven available NGS and seven microarray RCC studies in order to identify subtype-specific expression of miRNAs. We concentrated on four potentially oncocytoma-specific miRNAs (miRNA-424-5p, miRNA-146b-5p, miRNA-183-5p, miRNA-218-5p), two pRCC (miRNA-127-3p, miRNA-139-5p) and eight ccRCC specific miRNAs (miRNA-200c-3p, miRNA-362-5p, miRNA-363-3p and miRNA-204-5p, 21-5p, miRNA-224-5p, miRNA-155-5p, miRNA-210-3p) and validated their expression in an independent sample set. Additionally, we found ccRCC-specific miRNAs to be differentially expressed in ccRCC Fuhrman grades and identified alterations in their isoform composition in tumor tissue. Our results revealed that changes in expression of selected miRNA might be potentially utilized as a tool aiding ccRCC subclass discrimination and propose a miRNA panel aiding RCC subtype distinction.

overall_design: 26 ccRCC tumor samples and 6 normal adjacent kidney tissue samples

middle: P

first: Weronika

last: Majer

first: Katarzyna

last: Kluzek

first: Jacek

last: Sobkowiak

first: Tomasz

last: Milecki

first: Natalia

last: Derebecka

first: Zbigniew

last: Kwias

first: Hans

last: Bluyssen

first: Joanna

last: Wesoly


title: Whole genome bisulfite sequencing from primate brains (orthologous region to human BA46)

city: Atlanta

first: Soojin

last: Yi

state: GA

address: 950 Atlantic Dr

institute: Georgia Institute of Technology

summary: We carried out cell-type specific whole genome bisulfite sequencing from primate brains (orthologous region to human BA46) that underwent fluorescence-activated nuclei sorting (FANS).

sample_organism:
Macaca mulatta
Pan troglodytes

platform_organism:
Macaca mulatta
Pan troglodytes

overall_design: We compared the cell-type specific methylome profiling of sorted nuclei from humans to non-human primates. We analyzed genome-wide DNA methylation levels in adult human Brodmann area 46 (BA46, 27 individuals, GSE108066), and the homologous regions of chimpanzee (11 individuals), and rhesus macaque (15 individuals). Cell-type specific methylome data was obtained using fluorescence-activated nuclei sorting (FANS) with antibodies to either NeuN or OLIG2 to isolate neurons (NeuN) or oligodendrocytes (OLIG2) and their precursors, respectively.


title: Identification of RCC subtype-specific microRNAs – meta-analysis of high-throughput RCC tumor microRNA expression data

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


title: Identification of RCC subtype-specific microRNAs – meta-analysis of high-throughput RCC tumor microRNA expression data [RNA-Seq]

overall_design: 58 ccRCC tumor samples and 17 normal adjacent kidney tissue samples


title: THP-1 cells PMA-treated RNA-seq

city: Santa Cruz

first: Susan

last: Carpenter

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: Examination of differentially expressed genes during monocyte to macrophage differentiation in THP-1 cells

overall_design: Transcriptome analysis of THP-1 cells -/+ PMA treatment

first: Apple

last: Vollmers

first: Sergio

last: Covarrubias


title: Monocyte-derived macrophages (MDMs) treated with siRNA non-targeting control and pooled GAPLINC siRNAs

summary: Examination of differentially expressed genes in GAPLINC-knockdown MDMs

overall_design: Transcriptome analysis of GAPLINC-knockdown MDMs


title: Bone marrow and BMDMs (unstimulated) RNA-seq

summary: Examination of differentially expressed genes during macrophage differentiations (bone marrow vs. BMDMs)

overall_design: Transcriptome analysis of undifferentiated bone-marrow cells and differentiated macrophages


title: A conserved long noncoding RNA, GAPLINC, modulates the immune response during endotoxic shock

summary: GAPLINC is a conserved long noncoding RNA that we find to be highly expressed in macrophages. Inflammatory activation of macrophages results in a decrease in GAPLINC expression, and GAPLINC knockout results in an enhanced expression of inflammatory genes at baseline. To gain insights into the molecular mechanism of GAPLINC, we generated RNA-seq libraries from wild type and GAPLINC-deficient BMDMs untreated and treated with LPS.

overall_design: Transcriptome analysis of undifferentiated bone-marrow-derived macrophages (BMDMs) of wild-type and GAPLINC-deficient mice


title: Exhausted T cells recovered from chronic antigen stimulation

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

overall_design: Refer to individual Series


title: Transcriptional landscape of three exhausted CD8 T cell subsets

summary: Transcriptional analysis of exhausted CD8 Tcell subsets after eliminating chronic antigen stimulation at the single cell level

overall_design: LCMV-specific P14 cells were sorted from mice infected with LCMV-Arm or LCMV-Cl13, as well as mice that received donor P14 TEX or TMEM were transcriptionally profiled

first: Mohamed

middle: S

last: Abdel-Hakeem

last: Wherry


title: Fetal lung maturation induced by chorioamnionitis and its interaction with antenatal corticosteroids in rhesus macaque fetuses

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

summary: Purpose: Our goal was to evaluate the pathways through which chorioamnionitis induces fetal lung maturation and how it interacts with a low-dose treatment with antenatal corticosteroids to further enhance fetal lung maturation. Methods: We treated pregnant rhesus macaque at 132 days (80% gestation) with intre-amniotic bacterla lipopolissacharide to model chorioamnionitis or a low-dose antenatal corticosteroids treatment with betamethasone-acetate (Beta-Ac 0.125mg/kg) or both treatments. Fetuses were delivered by c-section after 5 days and RNA-sequencing of whole lung tissue was performed. Another group of fetuses exposed to LPS was delivered 16h after treatment. Preterm controls were delivered at 132 days and term controls were delivered at 155 days and received no intervention. Results: Treatment with Beta-Ac in the setting of chorioamnionitis improves lung compliance and increases surfactant production relative to either treatment alone. RNA sequencing shows that these changes are mediated by suppression of proliferation and induction of mesenchymal cellular death.  The combined exposure results in a mature-like transcriptomic profile with inhibition of extracellular matrix development by suppression of collagen genes and regulators of lung development. ACS and inflammation also suppressed signature genes associated with proliferative mesenchymal progenitors similar to the term lung. Conclusion: Treatment with ACS in the setting of inflammation may result in early respiratory advantage to preterm infants, but this advantage may come at a cost of abnormal extracellular matrix development which may be associated with increased risk of chronic lung disease.

overall_design: Time-pregnant rhesus macaques received intra-amniotic injection of LPS or the combination of intra-amniotic LPS plus intrumuscular corticosteroids and were  delivered after 5 days. Another group of animals exposed to intra-amniotic LPS was delivered 16h after treatments

first: Paranthaman

last: Kannan

first: Presicce

last: Pietro

first: Jackson

last: Courtney

first: Lisa

last: Miller

first: Kallapur

middle: G

last: Suhas

first: Chougnet

last: Claire

first: Alan

last: Jobe


title: Transcriptomic characterization of the delayed wound healing response in a diabetic skin humanized mice model

city: Leganes

first: carlos

last: leon

state: Madrid

address: Avenida Universidad 30

department: Bioengineering

summary: Previously, we developed a new model of diabetes-induced wound healing impairment in skin-humanized mice models that faithfully recapitulates the major histo-physiological features of such skin repair-deficient condition. Aiming to dissect the molecular mechanisms responsible for the delayed wound closure, global gene expression studies were performed.

overall_design: 2mm biopsies of 7 control mice and 6 diabetes-induced humanized skin mice (samples at 0h) and 6mm biopsies of the same samples taken by repunching around the wound edge at 24h

first: Lucia

last: Martínez

first: Carlos

last: León


title: Epigenetic landscape of exhausted T cells upon eliminating chronic antigenic stimulation

summary: Open chromatin accessibility analysis of exhausted CD8 Tcell subsets after eliminating chronic antigen stimulation

overall_design: 2-3 Biological replicates were analyzed for each of the CD8 Tcell subsets


title: Mechanisms of Triggering Malaria Gametocytogenesis by AP2-G [ChIP-seq]

first: Tsubasa

last: Nishi

summary: AP2-G is a transcription factor (TF) that is essential for gametocytogenesis of malaria parasites; however, the mechanisms for its inducing the cell linage for sexual reproduction remain unclear. In this paper, this problem is addressed by investigating its expression profile and by determining target genes genome-wide in Plasmodium berghei.

overall_design: Mice were infected with P. berghei expressing GFP-fused AP2-G. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Chromatins associated with GFP-tagged AP2-G was IPed with anti-GFP antibody, and target genes of this transcription factor were predicted.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Yuho

last: Murata


title: Anterograde Regulation of Nuclear-encoded Mitochondrial Genes and FGF21 Signaling by Hepatic Histone Demethylase LSD1

city: Irvine

first: QIN

last: YANG

address: 825 Health Science Rd.

department: Physiology and Biophysics

institute: University of California, Irvine

summary: Mitochondrial biogenesis and function are controlled by anterograde regulatory pathways involving more than one thousand proteins encoded by nuclear genome. Transcriptional networks controlling the nuclear-encoded mitochondrial genes remain elucidated.  Here we show that histone demethylase LSD1 knockout from adult mouse liver (LSD1-LKO) reduces one-third of all nuclear-encoded mitochondrial genes and decreases mitochondrial biogenesis and function. LSD1-modulated histone methylation epigenetically regulates nuclear-encoded mitochondrial genes. Furthermore, LSD1 targets methylation of nicotinamide mononucleotide adenylyltransferase 1 (NMNAT1), the rate-limiting enzyme for nuclear NAD+ synthesis. Hepatic LSD1 knockout reduces NAD+-dependent Sirt1 and Sirt7 deacetylase activity, leading to hyperacetylation and hypofunctioning of GABP and PGC-1, the major transcriptional factor/cofactor for nuclear-encoded mitochondrial genes. Despite the reduced mitochondrial function, LSD1-LKO mice are protected from diet-induced hepatic steatosis and glucose intolerance, partially due to induction of hepatokine FGF21. Thus, LSD1 orchestrates a core regulatory network involving epigenetic modifications and NAD+ synthesis to control mitochondrial function and hepatokine production.

overall_design: ChIP-seq analysis of LSD1 and LSD1-targeted H3K4me2 in liver

first: Yang

last: Cao

first: Qiushi

last: Sun

first: Qin

last: Yang


title: Mechanisms of Triggering Malaria Gametocytogenesis by AP2-G

address: Edobashi


title: Novel Isoforms of the Epigenetic Regulator TET1 Differentially Control CNS Synaptic Function, Plasticity, and Cognition

city: Lewiston

first: Andrew

middle: John

last: Kennedy

state: ME

address: 5 Andrews Rd, Dana 322

department: Chemistry

institute: Bates College

summary: Two distinct Tet1 isoforms are expressed, one encoding full-length TET1 (Tet1L) and the other a truncated transcript (Tet1S), lacking a large portion of the N-terminus. Each isoform displays unique transcriptional regulation, subcellular protein localization and enzymatic activity. In neurons, Tet1L and Tet1S govern the expression and methylation levels of distinct gene ensembles that when disrupted.

overall_design: In mouse hippocampal cultured neurons, Tet1L and Tet1S were selectively overexpressed and downregulated to identify loci of differential DNA methylation and gene expression.

first: Celeste

middle: B

last: Greer

first: Garrett

last: Kaas


title: Mechanisms of Triggering Malaria Gametocytogenesis by AP2-G [RNA-seq]

city: Tsu

overall_design: Plasmodium berghei transcriptomes were analyzed in gametocytes.


title: Two distinct trophectoderm lineage stem cells from human pluripotent stem cells

city: Raleigh

first: Balaji

last: Rao

state: NC

institute: North Carolina State University

summary: We report the derivation of two distinct stem cells of the trophectoderm lineage from human pluripotent stem cells. The first is a CDX2- stem cell equivalent to primary hTSCs – they both exhibit identical expression of key markers, are maintained in culture and differentiate under similar conditions, and share high transcriptome similarity. The second is a CDX2+ putative human trophectoderm stem cell (hTESC) with distinct cell culture requirements and differences in gene expression and differentiation relative to hTSCs.

overall_design: RNA sequencing was conducted on the following cells/conditions: two primary hTSC lines (CT29, CT30), undifferentiated hESCs (two cell lines - H1, H9), hESCs after 3 days of differentiation to trophoblast (H1-day3, H9-day3),  hTSCs derived from hESCs (H1-hTSC, H9-hTSC), hTESCs derived from hESCs (H1-hTESC, H9-hTESC). Four biological replicates were used for each cell type/condition (10x4=40 samples total)


city: Hannover

first: Doris

last: Steinemann

address: Carl-Neuberg-Straße 1

department: Human Genetics

institute: Medizinische Hochschule Hannover

summary:
CN profiles of invasive lobular breast cancer with variant growth pattern display common CN loss of chromosome 16q.
Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues.

overall_design: Copy number analysis using Oncoscan (Thermoscientific) arrays was performed for 16 breast cancers

first: Jana

last: van Luttikhuizen

first: Matthias

last: Christgen

first: Hans

last: Kreipe


title: RNA-seq and ChIP-seq analysis of HA-JICD1 and NICD1 overexpressed Ink4a-/- murine astrocytes

city: Seoul

first: Eun-Jung

last: Kim

address: Anamro 5ga

institute: Korea University


title: Changes in mRNA in the dorsal root ganglion after stroke and subcutaneous neurotrophin-3 infusion in elderly rats

city: London

first: Lawrence

middle: DF

last: Moon

address: 16 - 18 Newcomen Street

department: Wolfson Centre for Age-Related Diseases

country: United Kingdom

institute: King's College London

summary: Brain and spinal injury often impair sensorimotor processing in the spinal cord and reduce mobility. Cortical stroke in rats leads to long-term deficits in dexterity and walking. Subcutaneous neurotrophin-3 infusion initiated at a clinically-feasible time-point after injury improved walking and dexterity. We discovered that Neurotrophin-3 is transported in sensory afferents from muscles to the dorsal root ganglia. Using genome-wide RNA sequencing of the whole cervical level 6-8 dorsal root ganglia, we sought gene changes in afferent neurons that were present at two timepoints after stroke.

overall_design: RNA-Seq was performed on whole C6-8 dorsal root ganglia of rats from three different groups: naïve rats, rats after unilateral cortical stroke+vehicle infusion and rats after unilateral cortical stroke and NT3 infusion. Differential expression was analyzed between each of the groups.

middle: D


title: Inhibition of longevity regulator PAPP-A modulates tissue homeostasis via restraint of mesenchymal stromal cells

city: South San Francisco

first: Adam

last: Freund

address: 1170 Veterans Blvd

institute: Calico Life Sciences LLC


title: Efficient differentiation of human Fanconi anemia hematopoietic progenitor cells by inducible complementation reveals a role for p53 in regulation of self-renewal and differentiation

city: Boston

first: Edroaldo

last: Lummertz da Rocha

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Fanconi anemia (FA) is a genetic disorder of DNA repair that manifests as bone marrow dysfunction typically occurring in childhood.  The lack of human model systems has impeded progress in identifying effective therapies.  To address this, efforts have focused on using directed differentiation of patient-derived human induced pluripotent stem cells (IPSCs) to hematopoietic stem and progenitor cells (HSPCs).  However, the requirement for an intact FA DNA repair pathway for efficient reprogramming of patient cells to pluripotency requires genetic complementation of FA pathway defects to efficiently generate IPSCs, precluding derivation of FA pathway-deficient human HSPCs for study.  To overcome this barrier, we employed a system of doxycycline-inducible complementation of FANCA deficient patient-derived IPS cells.  Doxycycline exposure allowed for the robust maintenance of undifferentiated IPS cells in culture.  Removal or retention of doxycycline exposure during directed differentiation of HSPCs allowed for the production of isogenic FANCA-deficient and FANCA-complemented human HSPCs.  IPS-derived, FANCA-deficient HSPCs showed impaired response to genotoxic stress, proliferation, and survival compared to complemented HSPCs.  Using these cells, we found that FANCA-deficient HSPCs showed expected impaired clonogenicity in methylcellulose culture and unexpected accelerated erythroid differentiation relative to complemented cells.  Activation of p53-mediated p21 transactivation in FANCA-deficient HSPCs serves to drive accelerated erythropoiesis as the expense of clonogenicity.  This study demonstrates the feasibility of inducible complementation in IPSCs as a method to generate isogenic FA-deficient and FA-complemented human HPSCs for disease modeling and uncovers a novel mechanism by which the FA pathway regulates the balance between stem cell maintenance and terminal differentiation.

overall_design: Hematopoietic stem and progenitor cells differentiated from induced pluripotent stem cells were used for whole RNA sequencing.  These were from three independent cell lines where the hematopoietic cells were generated either in the presence or absence of doxycycline to modulate expression/complementation of FANCA

first: Grant

last: Rowe


title: RNA-Seq of breast muscle

city: Zhengzhou

first: Donghua

last: Li

state: China

address: Wenhua Road 95, Zhengzhou City

institute: Henan Agricultural University

summary: High throughput sequencing technology was used to sequence the transcriptome of breast muscle tissue of Test II group and test group IV

overall_design: control group Test II group and test group IV

first: Yawei

last: Fu


title: RNA sequencing analysis of HA-JICD1 and NICD1 overexpressed Ink4a-/- murine astrocytes [RNA-seq]

summary: This study demonstrate the biological function of JAG1 intracellular domain (JICD1). In order to elucidate the characteristics of JICD1, HA-JICD1 and NICD1 overexpressed in murine Ink4a-/- astrocytes.

overall_design: Ink4a-/- murine astrocytes were transfected with pcDNA puro (control) or pcDNA HA-JICD1 puro (HA-JICD) or pcDNA NICD puro (NICD)


title: Reactivity of the corticotrope axis in rainbow trout (Oncorhynchus mykiss) exposed to chronic environmental stress

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

summary: Aquaculture conditions favourite exposure of farmed fish to stressful factors leading to negative impacts on welfare and performance. Among many factors, water quality is considered as one of the primary stressors in fish which affect growth and reduce feed intake. The present study aims to assess in rainbow trout the effect of a chronic exposure during 21 days to deteriorated water quality obtained by reduction of the water flow in the tank. Such protocol mainly led to a reduction in O2 levels (30-40% oxygen saturation) and a two fold increase in NH4-N and CO2 levels to non-stressful values. Thus, we questioned whether such chronic conditions which modified growth performances also affected basal and acute stress plasma cortisol levels and induced a deregulation of HPI (Hypothalamo-Pituitary-Interrenal) axis responsiveness. After 2 and 10 days exposure, no significant effect on basal and acute stress plasma cortisol levels was observed. Moreover, these treatments had very minor effects on expression of the HPI axis genes involved in regulation of cortisol secretion. However, after 21 days exposure, a significant increase in cortisol levels after an acute stress was observed. The most significant differences in gene expressions were also observed at the level of the head-kidney with genes involved in cortisol production and its regulation. These HPI axis responses are clearly different from those previously reported for other allostatic load experiences. Overall, the present study illustrates the pleiotropy of the HPI-axis response during allostatic load conditions, and the importance to consider not only the nature of the stressor but also its duration and intensity.

overall_design:
During the 3-week experiment (deteriorated water quality stress), the photoperiod was maintained at 12:12 (Light: Dark) and the mean water temperature increased from 10.5 to 12.25°C. The fish were fed ad libitum 3 times per day.
Total RNA from pituitary gland and head kidney was profilied.

first: P

last: Prunet

first: S

last: Peron

first: A

last: Le Cam

first: J-M

last: Le Calvez

first: L

last: Goardon

last: Labbé

first: I

last: Leguen


title: ChIP sequencing analysis of HA-JICD overexpressed Ink4a-/- murine astrocytes

summary: This study demonstrate the biological function of JAG1 intracellular domain (JICD1). In order to elucidate the transcriptional regulation of JICD1, ChIP sequencing were performed using HA and H3K9Ac antibody.

overall_design: Ink4a-/- murine astrocytes were transfected with pcDNA puro (control) or pcDNA HA-JICD puro (HA-JICD).


city: Kocaeli

first: Fatma

last: Aydinoglu

state: Turkey

address: GTU Mol. Bio. Gen.

department: Molecular Biology and Genetics

country: Turkey

institute: GTU

summary:
The exxpression profilling of chilling responsive and growth regulated microRNAs of maize hybrid ADA313 was conducted. Maize seedling were subjected to chilling temperature then meristem, elongation and mature growth zones were sampled. 321 known maize microRNA expression level were determined and compared between meristem, elongation and mature zones.
Determining and validating of chilling responsive microRNAs associated with leaf growth of hybrid maize (Zea mays L.) ADA313

overall_design: Leaf 4 of maize seedlings were used as a model to understand chilling stress affect on leaf growth processes

last: AYDINOGLU


title: Integrative transcriptomic and proteomic analyses reveal that NLRX1 and FASTDK5 orchestrate immunometabolic fitness to fuel HIV-1 replication

status: Public on Jan 31 2021

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

summary: We analyzed the transcriptome of CD4 T cells from HIV-1 patients and revealed that elevated oxidative phosphorylation (OXPHOS) pathway is associated with poor outcomes. Inhibition of OXPHOS by the FDA-approved drug metformin, which targets mitochondrial respiratory chain complex I, suppresses HIV-1 replication in human CD4 T cells and humanized mice. In patients, HIV-1 peak viremia positively correlates with the expression of NLRX1, a mitochondrial innate immune receptor.

overall_design: Quantitative proteomics and metabolic analyses reveal that NLRX1 enhances OXPHOS and glycolysis during HIV-1-infection of CD4 T cells to promote viral replication. At the mechanistic levels, HIV infection induces the association of NLRX1 with the mitochondrial protein, FASTKD5, to promote the expression of mitochondrial respiratory complexes components. This study uncovers the OXPHOS pathway in CD4 T cells as an un-appreciated target for HIV-1 therapy. Cells were collected and lysed for RNA extraction. Reverse transcription reactions were performed to obtain cDNAs which were hybridized to the Illumina Human HT-12 version 4 Expression BeadChip according to the manufacturer’s instruction, and quantified using an Illumina iScan System. The data were collected with Illumina GenomeStudio software.

first: Khader

last: Ghneim

first: Jeffrey

last: Tomalka

first: Rafick-Pierre

last: Sekaly

first: Haitao

last: Guo

first: Qi

last: Wang

first: Li

first: P-Y

last: Ting

first: Leigh

last: Eller

first: Merlin

last: Robb


title: ST18 represents a novel transcriptional repressor ensuring proper expression kinetics during early cortical development

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: Cortical development is a tightly spatiotemporally regulated process in which cell-fate specification is accompanied by stable resetting of transcriptional programs. However, the full repertoire of transcriptional regulators orchestrating such transcriptome changes remains largely incomprehensive. Applying a bioinformatics predictive approach we aimed to identify novel transcription factors contriuting to transcriptional reprogramming during embryonic neurogenesis and identified the neuronal tissue specific transcription factor St18 to be essential for neurogenesis in vitro and in vivo.  We find that embryonic stem cells deficient for St18 are not able to efficiently differentiate along neuronal lineage and St18 depleted cells in the developing cortex do not elongate in shape and reside in the VZ/SVZ region but display premature expression of the upper layer neuronal marker Satb2. Relation of St18 binding to genes deregulated upon St18 depletion in vivo revealed St18 to function as transcriptional repressor at the time when neurogenesis is initiated. St18 ensures efficient onset of cortical neurogenesis by inhibiting expression of the self-renewal maintaining factor Hes1 that represses differentiation genes in neuronal progenitors as well as downregulation of genes that are essential for differentiation into mesodermal and endodermal lineage such as Lama5, Traf4 and Tab1. Furthermore we find this transcriptional repressor to be bound to genes that are important for later stages of neurogenesis when the neuronal circuitry is established likely to keep them in repressed state in the time window of neurogenesis when they are not yet required. These genes important for axon guidance and neurite outgrowth are subsequently prematurely upregulated in St18 depleted cortical cells. We further observe St18 to be bound to a significant fraction of intergenic enhancers where it regulates expression of nearest genes that  Our data establish St18 as a novel transcriptional regulator during early onset of cortical neurogenesis that is essential to ensure timely expression kinetics of phase and lineage specific genes.

overall_design: 4 replicates of NTC electroporated brains and 4 replicates of shSt18 electroporated brains have been analyzed

first: Angela

last: Garding

first: Johannes

last: Jung

first: Sudhir

last: Thakurela

first: Vijay

last: Tiwari


title: Effect of restricted glycolysis on gene expression in MDA-MB-231 cells

city: Southampton

first: Jeremy

middle: Paul

last: Blaydes

state: Hampshire

address: Southampton General Hospital, Tremona Road

department: Faculty of Medicine

institute: University of Southampton

summary:
Cultured breast cancer cells in standard media are highly glycolytic
To determine the effect of glycolysis on gene expression in MDA-MB-231 we adapted cells to cuture in mediae containing 10 mM fructose, and compared the gene expression to cells cutured in standard high glucse (25 mM) DMEM

overall_design: Cells were adapted to growth in the different sugars for 25 days prior to analysis. Biological replicates represent separately adpated batches of cells.


title: Integrated microRNA and mRNA Signatures Associated with Survival in Triple Negative Breast Cancer II

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

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

summary: Triple negative breast cancer (TNBC) includes basal and non-basal subclasses. To further stratify TNBC we determined microRNA (miRNA) and mRNA expression profiles, linked specific miRNA signatures to patient survival and used miRNA/mRNA anti-correlations to identify TNBC subclasses associated with expression of canonical signal pathways

overall_design: RNA was isolated from formalin-fixed paraffin-embedded tissue cores of 165 primary tumors, 59 adjacent normal and 54 lymph node metastatic samples and expression of 664 miRNAs and 230 cancer-associated mRNAs was assessed for each sample using the nanoString nCounter platform. Kaplan-Meier distant-disease free and overall survival curves were compared using the log-rank test. Cox proportional hazard regression and risk score analysis were used to identify miRNAs for classification of patients with significantly different prognoses.

first: Pierluigi

last: Gasparini