title: NGS Analysis of human mRNAs in mouse cells following a 12-hr 2D-coculture

status: Public on Nov 28 2021

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary:
Background: We have previously known that mRNAs can transfer in mammalian cells via membrane nanotubes. However, genome-wide study of mRNA was lacking
Objective: In this study, we wanted to characterize the range of human mRNAs that undergo transfer to neighbouring mouse cells when co-cultured together for 12 hours
Results: We found that a large part of human mRNAs can traffic to adjoining mouse cells, the number of mRNAs transferred is dependent on gene expression. We also also detected significant differential gene regulation in mouse cells in response to co-culture with human cells
Conclusion: In addition to sequencing analysis, we have used molecular biological and imaging techniques to demonstate expression-dependent mRNA transfer from mouse to human cells.

overall_design: human mRNAs from purified mouse cells are detected after 12-hour of in-vitro co-culture. For control, human and mouse cells were mixed and immediately sorted using antigen-based magnetic sorting (Human cells: MCF7; Mouse cells: MEF). In addition, differential gene expression of mouse RNAs in MEF is also analyzed.

first: Sandipan

last: Dasgupta

first: Daniella

last: Dayagi

first: Gal

last: Haimovich

first: Emanuel

last: Wyler

first: Robert

last: Singer

first: Markus

last: Landthaler

first: Jeffrey

last: Gerst


title: DNA methylation data for older persons with vs. without mild cognitive impairment

status: Public on Dec 10 2021

city: Boston

first: Olivia

last: Okereke

state: MASSACHUSETTS

address: One bowdoin square, room no. 745

country: USA

institute: Massachusetts General Hospital

summary: Genome wide DNA methylation assays was conducted using the Illumina Infinium MethylationEPIC BeadArray technology (Methyl850K chip) that allows genome-wide DNA methylation analysis of 866,836 CpG sites. We included baseline and 2-year follow-up samples from 25 persons with mild cognitive impairment (cases) and 20 persons with cognitively normal (controls). Sample was balanced by age and sex.

overall_design: Bisulfite conversion, or bisulfite treatment, whole genome amplification (WGA), hybridization and single base extension were carried out to get labeled nucleotide using standard protocol. Dual color (Cy3 and Cy5) staining was used for allowing the nucleotide to be detected by the iSCAN reader and is converted to genotype during the analysis.

middle: I

first: Chirag

middle: M

last: Vyas


title: aCGH and high-throughput transcriptome profiling of non-small cell lung cancer cell lines sensitive or resistant to CPL304110 FGFR inhibitor

status: Public on Nov 23 2021

city: Gliwice

first: Alexander

middle: Jorge

last: Cortez

state: Silesia

address: Wybrzeze Armii Krajowej 15

department: Department of Biostatistics and Bioinformatics

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch

type: Genome variation profiling by genome tiling array

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: aCGH profiling for non-small cell lung cancer cell lines sensitive or resistant to CPL304110 FGFR inhibitor

summary: FGFR signalling is one of the most prominent pathways involved in cell growth and development, as well as cancer progression. FGFR1 amplification occurs in approximately 20% of all squamous cell lung carcinomas (SCC) - one of the most common subtypes of non-small cell lung carcinoma (NSCLC), indicating FGFR as a potential target for the new anti-cancer therapies. However, acquired resistance to this type of therapies remains a clinical issue. Here, we investigated the NSCLC cell lines response and potential mechanism of acquired resistance to novel selective FGFR inhibitor CPL304110. We found that despite significant genomic differences between CPL304110-sensitive cell lines, their resistant variants were characterized by upregulated p38 expression/phosphorylation, as well as enhanced expression of genes involved in MAPK signalling. We revealed that p38 inhibition restored sensitivity to CPL304110 in these cells. Moreover, overexpression of this kinase in parental cells led to impaired response to FGFR inhibition, thus confirming that p38 MAPK is a driver of resistance to a novel FGFR inhibitor. Taken together, our results provide an insight into the potential direction for NSCLC targeted therapy.

overall_design: The array-based comparative genomic hybridization (aCGH) was used to reveal copy number changes (amplifications and deletions) in the genome of sensitive versus resistant variant of two non-small cell lung cancer cell lines (NCI-H1581 vs. NCI-H1581R and NCI-H1703 vs. NCI-H1703R) to FGFR inhibitor CPL304110.

first: Izabela

last: Zarczynska

first: Monika

last: Gorska-Arcisz

middle: J

first: Katarzyna

middle: A

last: Kujawa

first: Agata

last: Wilk

first: Andrzej

middle: C

last: Skladanowski

first: Aleksandra

last: Stanczak

last: Skupinska

first: Maciej

last: Wieczorek

last: Lisowska

first: Rafal

last: Sadej

first: Kamila

last: Kitowska


title: ADAR1-isoforms specific editome: RNA sequencing of A-to-I editing deficient mouse embryonic fibroblast transfected with ADAR1p150 or ADAR1p110 or RFP.

status: Public on Nov 17 2021

city: Vienna

first: Renata

last: Kleinova

address: Schwarzspanierstrasse 17

department: CACB

country: Austria

institute: Medical University of Vienna

summary: Adenosine deaminase acting on RNA (ADAR) (also known as ADAR1) promotes A-to-I conversion in double-stranded and highly structured RNAs. ADAR1 has two isoforms transcribed from different promoters: ADAR1p150, which is mainly cytoplasmic and interferon-inducible, and constitutively expressed ADAR1p110 that is primarily localized in the nucleus. Mutations in ADAR1 cause Aicardi – Goutières syndrome (AGS), a severe autoinflammatory disease in humans associated with aberrant IFN production. In mice, deletion of ADAR1 or selective knockout of the p150 isoform alone leads to embryonic lethality driven by overexpression of interferon-stimulated genes. This phenotype can be rescued by concurrent deletion of cytoplasmic dsRNA-sensor MDA5. These findings indicate that the interferon-inducible p150 isoform is indispensable and cannot be rescued by the ADAR1p110 isoform. Nevertheless, editing sites uniquely targeted by ADAR1p150 but also mechanisms of isoform- specificity remain elusive. To identify ADAR1 isoform-specific ‘editome’, we transfected A-to-I editing deficient mouse embryonic fibroblasts (MEFs) with ADAR1p150- or ADAR1p110- or RFP-editing negative control. We subjected the samples to RNA sequencing and detected editing at known-editing sites.

overall_design: To identify editing sites preferentially edited by ADAR1p150 or p110, we transfected (electroporated) A-to-I editing deficient MEFs (of the genotype: Adar-/-; Adarb1-/-; Gria2R/R) with p150 or p110 ADAR1-isoform. The experiment was conducted in biological triplicates. Transfection with an RFP-expressing vector was included as editase-negative control (1 sample - processed with the first replica).

first: Ernesto

last: Picardi

first: Michael

middle: F

last: Jantsch


title: Epigenome of ASXL1-mutant and ASXL1-wildtype chronic myelomonocytic leukemia

status: Public on Feb 21 2022

city: Rochester

first: Mrinal

middle: M.

last: Patnaik

state: MN

address: 200 First Street SW

department: Division of Hematology

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: We report the chromatin characteristics of human chronic myelomonocytic leukemia by performing chromatin immunoprecipitation sequencing of histone modifications (ChIP-seq), immunoprecipitation sequencing of (hydroxy-)methylated residues (DIP-seq), and transposase accessibility sequencing (ATAC-seq) of bone marrow mononuclear cells of patients with chronic myelomonocytic leukemia.

overall_design: Comparison of chromatin characteristics between ASXL1-mutant and ASXL1-wildtype chronic myelomonocytic leukemia.


title: ANKLE1 digests mitochondrial DNA and contributes to cancer risk by driving the Warburg effect and apoptosis resistance

status: Public on Oct 29 2021

city: Farmington

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

summary: Alleles within the chr19p13.1 locus are associated with increased risk of both ovarian and breast cancer and increased expression of the ANKLE1 gene. ANKLE1 is molecularly characterized as an endonuclease that shuttles between the nucleus and cytoplasm and efficiently cuts branched DNA. However, the role of ANKLE1 in mammalian development and homeostasis remains unknown. In normal development ANKLE1 expression is limited to the erythroblast lineage and we found that ANKLE1's role is to cleave the mitochondrial genome during erythropoiesis. We show that ectopic expression of ANKLE1 in breast epithelial-derived cells leads to genome instability and mitochondrial DNA (mtDNA) digestion. mtDNA cleavage then leads to mitophagy and causes a shift from oxidative phosphorylation to glycolysis (Warburg effect). Moreover, mtDNA degradation activates STAT1 and expression of epithelial-mesenchymal transition (EMT) genes. Reduction in mitochondrial content contributes to apoptosis resistance, which may allow precancerous cells to avoid apoptotic checkpoints and proliferate. These findings provide evidence that ANKLE1 is the causative gene in the chr19p13.1 locus and provides mechanisms by which higher ANKLE1 expression promotes cancer risk.

overall_design: RNA-seq on 22 samples; control pEGFP-C1 or pEGFP-C1-ANKLE1 overexpressing HEK293T cells; 1, 3 and 7 days after transfection; 4 biological replicates each for Day 1; 4 biological replicates each for Day 3; 3 biological replicates each for Day 7

first: Piotr

last: Przanowski

first: Roza

middle: K

last: Przanowska


title: A virus-specific monocyte inflammatory phenotype is induced by SARS-CoV2 at the immune-epithelial interface

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: RNAseq analysis of human immune cells (monocytes CD14+ and B cells CD19+) cocultured with SARS-CoV2, influenza A or Ebola viruses-infected epithelial cells as well as directly  infected or SARS-CoV2 single protein transfected epithelial cells

overall_design:
To assess whether and how immunocytes are triggered by SARS-CoV2-infected cells, we established a co-culture model in which ex vivo blood immunocytes were placed in direct contact with virus-infected epithelial cells or SARS-CoV2 single protein transfected epithelial cells. We used as a virus SARS-CoV2 and two other relevant viruses for comparison : influenza A virus and Ebola virus. Thirty-five hours after viral infection of the Caco-2 monolayer, unbound virus was removed and peripheral blood mononuclear cells (PBMC) from healthy donors (HD) were added to the cultures. These were harvested 14 h later, and subpopulations (epithelial cells, CD45+CD19+ and CD45+CD14+) were magnetically purified for transcriptome profiling by RNAseq. We used the same coculture model to assess the role of individual SARS-CoV2 proteins : Caco-2 cells were transfected, in biological duplicates, with a panel of 27 plasmids encoding single viral proteins or GFP as a control; Forty-eight hour later, these transfectants were co-cultured with HD PBMCs, and the monocytes as well as the transfected epithelial cells were profiled by RNAseq after 14 h.

Please note that the records have been updated with two additional samples, along with the updated Genes_count_table.tsv file on Dec 12, 2022.

first: Juliette

last: Leon

first: Daniel

last: Michelson

first: Judith

last: Olejnik

first: Kaitavjeet

last: Chowdhary

first: Hyung

middle: S

last: Oh

first: Adam

last: Hume

first: Silvia

last: Galván-Peña

first: Yangyang

last: Zhu

first: David

last: Knipe

first: Elke

last: Mühlberger

first: Christophe

last: Benoist


title: High-throughput transcriptome profiling of non-small cell lung cancer cell lines sensitive or resistant to CPL304110 FGFR inhibitor

first: Alexander

last: Cortez

overall_design: For RNA-seq experiment, NCI-H1581 and NCI-H1703 cell lines (each in sensitive and resistant variants to CPL304110 FGFR inhibitior) were used. Two biological replicates was made for each variant.

first: Izabela

last: Zarczynska

first: Monika

last: Gorska-Arcisz

first: Katarzyna

last: Kujawa

first: Agata

last: Wilk

first: Andrzej

last: Skladanowski

first: Aleksandra

last: Stanczak

last: Skupinska

first: Maciej

last: Wieczorek

last: Lisowska

first: Rafal

last: Sadej

first: Kamila

last: Kitowska


title: Immune gene expression analysis for oral leukplakia samples

status: Public on Oct 15 2021

first: Glenn

last: Hanna

address: 450 Brookline Avenue, Dana 2-140

department: Medical Oncology

institute: Dana-Farber Cancer Institute, Harvard Medical School

summary: Oral leukoplakia is common and may in some cases progress to carcinoma. Proliferative leukoplakia (PL) is a progressive, often multifocal subtype with a high rate of malignant transformation (MT) compared to the more common localized leukoplakia (LL). We hypothesized that the immune microenvironment and gene expression patterns would be distinct for PL compared to LL. We summarize key clinicopathologic features among PL and LL and compare cancer-free survival (CFS) between subgroups. We analyze immunologic gene expression profiling (GEP) in PL and LL tissue samples (NanoString PanCancer Immune Oncology Profiling). We integrate immune cell activation and spatial distribution patterns in tissue samples using multiplexed immunofluorescence and digital image capture to further define PL and LL. Among N=58 patients (PL: 29, LL: 29), only the clinical diagnosis of PL was associated with significantly decreased CFS (HR 11.25, p<0.01); 5-year CFS 46.8% and 83.6% among PL and LL patients, respectively. CD8+ T cells and Tregs were more abundant among PL samples (p<0.01) regardless of degree of epithelial dysplasia, and often colocalized to the dysplasia-stromal interface. Gene set analysis identified granzyme-M (GZMM) as the most differentially expressed gene favoring the PL subgroup (log2 fold change 1.93, adjusted p<0.001). PD-L1 was comparatively over-expressed among PL samples, with higher (>5) PD-L1 scores predicting worse CFS (p<0.01). PL predicts a high rate of MT within 5-years of diagnosis. Robust CD8+ T cell and Treg signature along with relative PD-L1 over-expression compared with LL provides strong rationale for PD-1/L1 axis blockade using preventative immunotherapy.

overall_design: RNA from each oral leukoplakia (OL) specimen was isolated from cores punched from areas of epithelial dysplasia (High Pure FFPET RNA Isolation Kit, Roche Diagnostics, Indianapolis, Indiana) marked on FFPE tissue slides and quantified. From our initial retrospective single institution cohort of 149 patients first diagnosed with an OL between 2000 and 2018, 78 had LL and 71 had PL. Among 58 randomly selected patients with available (non-exhausted) tissue samples the two prespecified groups of LL (N=29) and PL (N=29) were balanced in terms of baseline characteristics such as age, gender, smoking history, oral cavity subsite, and pathologic diagnosis. We first compared immune cell type RNA expression profiles for all LL and PL samples, and by degree of histologic atypia. We also sought to interrogate which cytotoxicity genes accounted for immune cell type profiling differences among the LL and PL subgroups. Global significance scores (GSS) were determined to measure the overall differential expression of selected genes relative to LL or PL phenotype ignoring whether genes were up- or down-regulated. Of the 58 samples, 49 passed Nanostring quality metrics for analysis.


title: Gene network landscape of murine splenocytes reveals integrin as the A151 ODN-responsive hub in immune transcriptome

status: Public on Oct 01 2021

city: Ankara

first: Ihsan

last: Gursel

state: Cankaya

address: Faculty of Science, Ihsan Dogramaci Bilkent University

department: Molecular Biology and Genetics

country: Turkey

institute: Bilkent University

summary: PURPOSE: Homeostatic restoration of an inflammatory response requires quenching of the immune system after pathogen threats vanish. A continued assault orchestrated by host defense results in tissue destruction or autoimmunity. A151 is the epitome of synthetic oligodeoxynucleotides (ODNs) that curb immune response by a subset of white corpuscles through repetitive telomere derived TTAGGG sequences. Nevertheless, the genuine effect A151 has on immune cell transcriptome still remains unknown. METHODS: We leveraged an integrative approach in which weighted gene co-expression network analysis (WGCNA) and differential gene expression analysis of our in-house microarray data sets aided our understanding of how A151 ODN suppresses immune response in mouse splenocytes. We fed raw gene expression data from two different (scrambled ODN and A151 ODN) treatment groups with a varying number of replicate arrays (29 and 16, respectively) into WGCNA, limma, and GSEA separetely to understand different dimensions of the A151 ODN-driven immune modulation at the transcriptome level. RESULTS: Together with experimental and in silico validations, we demonstrated that A151 ODN acts on components of integrin complexes, namely Itgam and Itga6, to interfere with immune cell adhesion, and thereby, suppress the immune response in mouse. Furthermore, we revealed that cell adhesion by integrin complexes serves as a focal point for cellular response to A151 ODN treatment in immune cells. CONCLUSION: A refined set of co-hub genes led by Itgam and Itga6 plays a pivotal role in A151 ODN-driven suppression of immune response. Also, A151 ODN treatment appears to interfere with immune cell adhesion to quench immune response in mouse splenocytes. The outcome of this study sheds light on the molecular basis of immune suppression by a clinically useful DNA-based therapeutic agent and may open new revenues for A151 ODN research.

overall_design: Two-condition experiment, control (scrambled ODN)- vs. case (A151 ODN)-treated mouse splenocytes. Biological replicates: 29 control and 16 A151 ODN. One replicate per array. Dual channel, non-commercial arrays with a common reference design covering murine splenocyte genome using a set of 16897 unique probes.

first: Sven

last: Klaschik


title: Loci-specific differences in blood DNA methylation in HBV-negative populations at risk for hepatocellular carcinoma development - post-diagnostic HCC blood samples

status: Public on Jan 31 2022

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

country: Canada

institute: The University of British Columbia

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of blood samples collected from patients after diagnosis with hepatocellular carcinoma (HCC) (cases) vs. blood samples collected from healthy individuals without family history of cancer (controls). The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human samples corresponding to cases (post-diagnostic HCC) and controls. Samples included 24 cases and 24 controls. Cases were matched with controls on gender, age, ethnicity, hepatitis C infection, and diabetes. The presence or absence of HCC in our study was determined based on the AASLD criteria.

overall_design: Bisulphite converted DNA from the 42 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

last: Lubecka

first: Kirsty

last: Flower

first: Megan

last: Beetch

first: Jay

last: Qiu

first: Lucinda

last: Kurzava

first: Hannah

last: Buvala

first: Adam

last: Ruhayel

first: Samer

last: Gawrieh

first: Suthat

last: Liangpunsakul

first: Tracy

last: Gonzalez

first: George

last: McCabe

first: Naga

last: Chalasani

first: James

last: Flanagan


title: Analyses of Methamphetamine-Exposed and HIV- infected Human Monocyte-Derived Macrophages (hMDM)

status: Public on Sep 28 2021

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

summary: Human monocyte-derived macrophages (hMDM) were differentiated in the presence and absence of methamphetamine. Post differentiation, hMDMs were infected with human immunodeficiency virus (HIVADA). To investigate the effects of Meth exposure on infected macrophages day 5 post HIVADA infection, RNA was isolated from HIVADA hMDMs and sequenced using Next Generation Sequencing performed on the Illumina NextSeq550.

overall_design: Macrophages differentiation in the presence or absence of Methamphetmine, infected with HIV, treated or not with Methamphetamine. RNA was isolated from HIV-infected macrophages and subjected to RNAseq

first: Katarzyna

last: Macur

first: Sarah

last: Zieschang

first: Shulei

last: Lei

first: Brenda

last: Morsey

first: Spencer

last: Jaquet

first: Michael

last: Belshan

first: Howard

last: Fox

first: Pawel

last: Ciborowski


title: Functional state of lung cancer-reactive cytotoxic T cells is shaped during 2 T cell priming and determines sensitivity to immunotherapy

status: Public on Sep 20 2021

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

address: 500 Main St

department: Koch Institute

institute: MIT

summary: In non-small cell lung cancer (NSCLC), response to checkpoint blockade therapy (CBT) is associated with PD-L1 expression, induced by IFN-g-producing, tumor-infiltrating CD8+ T cells. However, not all tumors with a CD8+ T cell infiltrate respond to CBT, and little is known about the mechanisms governing CBT resistance in T cell-infiltrated NSCLC. We used a pre-clinical orthotopic NSCLC mouse model to study CBT-refractory CD8+ T cell responses. Single-cell RNA sequencing revealed that lung cancer-specific tumor-infiltrating CD8+ T cells exhibited clonal expansion but lacked expression of genes associated with effector and exhausted T cell responses, indicating that they underwent a differentiation program distinct from conventional T cell exhaustion. Mechanistic studies revealed that this lung cancer-specific T cell dysfunction program was established early during priming in the mediastinal lymph node. This program was characterized by robust T cell proliferation and acquisition of lung-homing factors but a failed upregulation of markers of effector and exhausted T cells. Intriguingly, CD8+ T cells from NSCLC patients expressed an analogous gene expression program which was associated with lung cancer specific T cell dysfunction and distinct from conventional T cell exhaustion. As a proof-of-concept that this lung cancer-specific T cell differentiation program could be therapeutically manipulated, we administrated recombinant IL-2 and IL-12, which was sufficient to restore effector T cell differentiation and induce control of lung tumors. These findings imply that a lung cancer-specific CD8+ T cell differentiation trajectory, activated during T cell priming in the mediastinal lymph node, limits the response of CD8+ T cells to CBT and thereby contributes to failed responses following CBT in T cell-infiltrated NSCLC.

overall_design:
Analysis of tumor-infiltrating cells from mice bearing either flank or lung KP tumors.
Single-cell of SIY-specific cells: FlankSIY (treatment: Flank) LungSIY (treatment: Lung)
BulkRNA of 2C cells: 2C_Flank* (treatment: Flank), 2C_Lung* (treatment: Lung)

first: B

middle: L

last: Horton

first: D

first: N

last: Momin

first: M

last: Zagorulya

first: E

last: Torres-Mejia

first: V

last: Bhandarkar

first: K

middle: D

last: Wittrup

first: J

last: Love

first: S

last: Spranger


title: Next Generation Sequencing Facilitates Quantitative Analysis of PIGS-KO, PIGS-HRD1-DKO, PIGS-HRD1-CD55-TKO, and PIGS-HRD1-CD55-TKO+HA-CD55 Transcriptomes

status: Public on Sep 29 2021

city: Wuxi

first: Yi-Shi

last: Liu

state: Jiangsu

address: No.1800, Lihu road

department: School of Biotechnology

country: China

institute: Jiangnan University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the genes expression difference at transcriptome level;
Methods: Total RNA was extracted from whole cells with the mirVana miRNA Isolation Kit according to the manufacturer’s protocol. RNA quality and integrity were evaluated with an Agilent 2100 Bioanalyzer. Samples with an RNA integrity number (RIN) ≥ 7 were considered to be of high quality and were processed further and subjected to subsequent analysis. Total RNA-seq libraries were generated using 4 μg of total RNA, which was analyzed using the TruSeq Stranded mRNA LTSample Prep Kit. These libraries were then sequenced using the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten), and 125-bp/150-bp paired-end reads were generated.
Results: The raw reads containing adaptors and the low-quality reads from the raw data were removed using Trimmomatic to obtain clean reads. Transcriptome sequencing was conducted by OE Biotech Co., Ltd. (Shanghai, China), and clean reads were provided. The clean reads were mapped to the hg38 reference genome using hisat2 (version 2.1.0). The output BAM files were converted to SAM files using SAMtools 1.9. The final TPM values were obtained using Stringtie 1.3.5.
Conclusions: To understand the mechanistic basis of GPI biosynthesis upregulation by the CD55 precursor, we performed RNA- sequencing (RNA-seq) of samples of parental PIGS-HRD1-DKO, PIGS-HRD1-CD55-TKO, and PIGS-HRD1-CD55-TKO stably overexpressed HA-CD55 stably overexpressing cells. Total RNA was extracted and analyzed. The expression profile of GPI biosynthesis -related genes was not significantly affected by CD55.

overall_design: HEK293 cells PIGS-HRD1-DKO, PIGS-HRD1-CD55-TKO, and PIGS-HRD1-CD55-TKO stably overexpressed HA-CD55

first: Taroh

last: Kinoshita


title: Transcriptional profiling of cochlear spiral ganglion neurons and lateral wall cells

status: Public on Sep 08 2021

first: Gabriela

last: Pregernig

state: Massachusetts

address: 1325 Boylston Street, Suite 500

institute: Decibel Therapeutics

summary: In order to characterize the response to noise of various cell types in the inner ear, the cochleae from wild-type mice, naive or subjected to a 2h, 105 dB SPL noise insult, were dissected out. To further examine spiral ganglion neurons in more detail, non-neuronal populations were removed in one set of samples. In another set of samples, the lateral wall tissue was isolated to better understand how cells from the stria respond to noise insults. The resulting tissue was then dissociated to obtain a single cell suspension, and profiled by single cell RNA-seq.

overall_design: 4 naïve and 4 noise-exposed samples (biological replicates) were profiled for each of the neuronal- and lateral wall-focused dissections, for a total of 16 samples.

first: Joseph

last: Burns

first: Kathy

last: So

first: Jonathan

last: Sellon

first: Adam

last: Palermo


title: Expression data from NRF3 knockdown or overexpression cells

status: Public on Oct 20 2021

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

country: Japan

institute: Doshisha University

summary:
The genetic association of a transcription factor NRF3 with obesity has been reported, although the molecular mechanisms remain unknown
We used microarrays to identify NRF3-regulated gene expression network related to lipid metabolism.

overall_design: For RNA extraction and hybridization on Affymetrix microarrays, we prepated HCT116 cells transciently transfected NRF3 or control siRNA, p53-deficient HCT116 (HCT116-p53KO) cells transciently transfected NRF3 or control siRNA, and H1299 cells stably expressing NRF3 or GFP.

first: Akira

last: Kobayashi


title: Clonal and molecular changes in hematopoietic system upon acute platelet depletion revealed using RNA barcoding studies

status: Public on Nov 07 2021

city: Norwich

first: Edyta

last: Wojtowicz

state: Norfolk

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

summary:
Purpose: RNA cellular barcoding has enabled the analysis of anucleate platelets and their upstream progenitors and stem cells using single cell RNA seq, using Smart Seq2
Methods: Single stem cell, megakaryocytic progenitor or erythroid progenitors from transplanted animals with barcoded stem cells were used for Smart Seq2 protocol and sequenced on NovaSeq. Obtained from the sequencer Fastq files were used for alignment to Mus musculus transcriptome version M38 using STAR aligner and count reads (Dobin et al., 2013).
Results: Subsequent analysis was performed in R using Seurat version 4.0.0(Papalexi et al., 2021). Cells showing gene counts lower than 50000 reads and a mitochondrial gene expression percentage higher than 10% were excluded from further analysis. Within Seurat, data were normalised using the NormalizeData function  (using  the LogNormalize method and scale.factor = 10000). We recovered 2569 single cells meeting above criteria from 8 analysed animals in total (4 control and 4 platelet depleted).
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Bone marrow stem and progenitor single cell RNA profiles of transplanted C57BL6 mice with barcoded stem cells analysed 28-32 weeks post transplantation.

first: Iain

last: Macaulay


title: Complete tumor regression by hetIL-15 locoregional administration is associated with a novel intratumoral CD103intCD11b+ dendritic cell population

status: Public on Jul 30 2021

city: Bethesda

first: Katherine

last: Goldfarbmuren

state: MD

address: 41 Center Dr

department: Advanced Biomedical Computational Science

institute: NCI, Frederick National Laboratory for Cancer Research

summary: Locoregional administration of heterodimeric IL-15 (hetIL-15) in a triple-negative breast cancer (TNBC) mouse model resulted in tumor eradication in 40% of treated mice, reduction of metastasis and induction of immunological memory against breast cancer cells. hetIL-15 re-shaped the tumor microenvironment by promoting the intratumoral accumulation of cytotoxic lymphocytes, conventional type 1 dendritic cells (cDC1) and a distinct DC population expressing both CD11b and CD103. These CD103intCD11b+DC share phenotypic and gene expression characteristics of both cDC1 and cDC2, have transcriptomic profile similar to monocyte-derived DC (moDC) and they correlate with tumor regression. Therefore, hetIL-15, a factor directly affecting lymphocytes and inducing cytotoxic cells, has also rapid and significant effects on the recruitment of myeloid cells, initiating a cascade for tumor elimination though innate and adoptive immune mechanisms. Our findings suggest a role for hetIL-15 in the treatment of breast cancer.

overall_design: Cd11c sorted dendritic cell populations from IL15 treated and untreated EO771 tumors in mouse

first: Dimitrios

last: Stellas

first: Sevasti

last: Karaliota

first: Matthew

last: Angel

first: Vasiliki

last: Stravokefalou

first: Cristina

last: Bergamaschi

first: George

last: Pavlakis

first: Barbara

last: Felber

first: Bethany

last: Nagy


title: Identification of target genes differentially expressed after pulse expression of Neisseria gonorrhoeae sRNAs

status: Public on Jul 28 2021

city: Würzburg

first: Dagmar

middle: Hannelore Irmgard

last: Beier

address: Am Hubland

department: Chair of Microbiology

country: Germany

institute: Biocenter, University of Würzburg

summary:
Purpose: The goal of this study was the identification of target genes of the Neisseria gonorrhoeae sRNAs NgncR_237, NgncR_162 and NgncR_163.
Methods: RNA was isolated from N. gonorrhoeae using the miRNeasy Micro Kit (Qiagen). Enrichment of mRNA was done using the Universal Ribodepletion Kit followed by Next Ultra Directional Library Preparation Kit for Illumina (NEB). The cDNA was sequenced on Illumina HiSeq 3000 platform with 100 bp paired end reads. Adapters from Fastq sequences were removed using cutadapt version 1.2.1. Only reads exceeding a mean base quality 5 within all sliding windows of 5 bp were mapped to the genome of strain N. gonorrhoeae MS11 (reference genome ASM15685v2). Annotation of non-coding RNAs was according to Remmele et al.(2014). Read mapping was conducted using Bowtie2  v2.1.0.  DeSEQ2 version 1.6.2 was used to identify differentially regulated transcripts.
Results: N. gonorrhoeae genes were identified which were upregulated or downregulated upon induced expression of sRNAs NgncR_237, NgncR_162 and NgncR_163.
Conclusions: sRNA NgncR_237, NgncR_162 and NgncR_163 are involved in the regulation of genes involved in type IV pilus biogenesis, energy metabolism and transport processes.

overall_design: RNAseq was performed on N. gonorrhoeae wild-type, sRNA knockout mutant Ng MS11 Δ237, a derivative of this strain expressing sRNA NgncR_237 under control of the Ptet promoter, sRNA double knockout mutant Ng MS11 ΔΔ162/163 and derivatives of this strain expressing sRNA NgncR_162 or NgncR_163 under control of the Ptet promoter. Strains were cultivated in the presence of anhydrous tetracycline for 30 min.  Experiments were performed in triplicates.

first: Maximilian

last: Klepsch


title: Transcriptome analysis induced by CTN, CV-A16, CVS and EV-A71 infection

status: Public on Aug 24 2021

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

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

overall_design: Refer to individual Series


title: Transcriptome of red oak leaf lettuce grown under OSC filters

status: Public on Jul 17 2021

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

summary: To characterize plant growth in net zero energy greenhouse models with semi-transparent organic solar cell (OSC) filter roofs, RNA was extracted from red oak leaf lettuce leaves grown under 3 OPV filters (FTAZ:IT-M, PTB7-Th:IEICO-4F, FTAZ:PCBM) an clear and shaded glass controls. 2 light intensity experiments were used. PPPFD Controlled (PC) treatments had a constant light intensity and different light spectra created by the filters. Height Controlled (HC) treatments varied in both light intensity and spectra, according to the light transmission of each filter. When light intensity was controlled, plants grown under FTAZ:IT-M had a DEG profile distinct from plants grown under the other 2 filters. Key genes were up or down-regulated that indicate changes in anthocyanin accumulation, nitrogen metabolism and pest defense.

overall_design:
Leaf tissue mRNA sampled from 4 individual plants grown under 1 of 8 light spectra and intensity conditions

The Sample title and characteristics were updated on June 14, 2022.

first: Melodi

last: Charles

first: Brianne

last: Edwards

first: John

last: Calero


title: Nanoparticle stereochemistry-dependent endocytosis improves in vivo mRNA delivery

status: Public on Aug 04 2021

city: Atlanta

first: James

middle: E

last: Dahlman

state: GA

address: 313 Ferst Dr NW

department: BME

institute: Georgia Institute of Technology

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of lipid nanoparticles (LNPs) carrying mRNA in murine liver non parenchymal cells. We report that LNPs containing stereopure 20α-hydroxycholesterol (20α) deliver mRNA to these cells up to three-fold more efficiently than LNPs containing both 20α- and 20ß- hydroxycholesterols (20mix). We show from the sequencing data that 20mix LNPs were sorted into phagocytic pathways, resulting in different functional delivery between stereopure and non-stereopure LNPs. We performed scRNA-seq using the 10X Chromium System, loading ~2,000 cells per condition, and processed the resulting data using Cell Ranger, resulting in an average read depth of ~100,000 reads per cell. These data suggest that stereochemistry-dependent interactions between LNPs and target cells can be exploited to improve mRNA delivery.

overall_design: Examination of FACS isolated liver non parenchymal cells three hours after systemically injecting mice with PBS, 20α LNPs carrying 0.3 mg/kg Cre mRNA, or 20mix LNPs carrying 0.3 mg/kg Cre mRNA

first: Marine

middle: Z

last: Hatit

first: Curtis

middle: N

last: Dobrowolski

first: Melissa

middle: P

last: Lokugamage

first: David

last: Loughrey

first: Huanzhen

last: Ni

first: Chiara

last: Zurla

first: Alejandro

last: Da Silva Sanchez

first: Afsane

last: Radmand

first: Sebastian

middle: G

last: Huayamares

first: Kalina

last: Paunovska

first: Hannah

last: Peck

first: Jinwhan

last: Kim

first: Manaka

last: Sato

first: Jacob

last: Feldman

first: Michael-Alexander

last: Rivera

first: Ana

last: Cristian

first: Yongtae

first: Philip

last: Santangelo


title: Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression

status: Public on Jun 29 2021

city: Aurora

first: Amy

middle: E.

last: Campbell

state: CO

institute: University of Colorado Anschutz Medical Campus


summary: Nonsense-mediated RNA decay (NMD) degrades transcripts carrying premature termination codons. NMD is thought to prevent the synthesis of toxic truncated proteins. However, whether loss of NMD results in widespread production of truncated proteins is unclear. A human genetic disease, facioscapulohumeral muscular dystrophy (FSHD), features acute inhibition of NMD upon expression of the disease-causing transcription factor, DUX4. Using a cell-based model of FSHD, we show production of truncated proteins from physiological NMD targets and find that RNA-binding proteins are enriched for aberrant truncations. The NMD isoform of one RNA-binding protein, SRSF3, is translated to produce a stable truncated protein, which is detected in FSHD patient-derived myotubes. Ectopic expression of truncated SRSF3 confers toxicity, and its downregulation is cytoprotective. Our results delineate the genome-scale impact of NMD loss. This widespread production of potentially deleterious truncated proteins has implications for FSHD biology as well as other genetic diseases where NMD is therapeutically modulated.

overall_design: Ribosome profiling (Ribo-seq) of human myoblasts harboring an inducible DUX4 transgene was performed on ribosome-protected RNA samples collected from 3 separate biological replicates treated for 0, 4, 8, or 14 h with doxycycline to induce DUX4 expression.

first: Michael

last: Dyle

first: Roberto

last: Albanese

first: Tyler

last: Matheny

first: Kavitha

last: Sudheendran

middle: A

last: Cortazar

first: Thomas

last: Forman

first: Rui

last: Fu

first: Austin

last: Gillen

first: Marvin

middle: H

last: Caruthers

first: Stephen

last: Floor

first: Lorenzo

last: Calviello

first: Sujatha

last: Jagannathan


overall_design: RNA-seq of human myoblasts harboring an inducible DUX4 transgene was performed on RNA samples collected from 3 separate biological replicates treated for 0, 4, 8, or 14 h with doxycycline to induce DUX4 expression.

middle: C


title: Auxin-degron system identifies immediate mechanisms of Oct4 [RNA-seq]

status: Public on Jun 17 2021

city: Edinburgh

first: Lawrence

last: Bates

address: Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh

summary: The pluripotency factor Oct4 is essential for the maintenance of naïve pluripotent stem cells in vitro and in vivo. However, the specific role of Oct4 in this process remains unknown. Here, we developed a rapid protein-level Oct4 depletion system that demonstrates that the immediate downstream response to loss of Oct4 is reduced expression of key pluripotency factors. Our data show a requirement for Oct4 for the efficient transcription of several key pluripotency factors, and suggest that expression of trophectoderm markers is a subsequent event. Additionally, we find that Nanog is competent to bind to the genome in the absence of Oct4, and this binding is in fact enhanced. Globally, however, active enhancer associated histone mark H3K27ac is depleted. Our work establishes that while Oct4 is required for the maintenance of the naïve transcription factor network, at a normal ESC level it antagonises this network through inhibition of Nanog binding

overall_design: Mouse ESCs and iPSCs in which Oct4 could be depleted were analysed at different times following removal of Oct4 for changes in gene expression by RNA sequencing, in their epigenetic landscape by H3K27ac ChIP sequencing, and in Nanog binding by Nanog ChIP sequencing

first: Jose

last: Silva


title: Auxin-degron system identifies immediate mechanisms of Oct4 [Nanog ChIP-seq]


title: Auxin-degron system identifies immediate mechanisms of Oct4 [H3K27ac ChIP-seq]


title: PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos

status: Public on Jun 03 2021

city: Staten Island

first: Cesar

last: Arenas-Mena

state: New York

address: 2800 Victory Boulevard

department: Biology

institute: CSI CUNY


title: Auxin-degron system identifies immediate mechanisms of Oct4


title: PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ATAC-Seq)

summary: PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.

overall_design: Machine learning models are trained and tested wit the different epigenetic marks for the precdiction of genomic with active reporter gene activity.

first: Sevinc

last: Ercan


title: PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (PRO-Seq)

overall_design: Machine learning models are trained and tested wit the different epigenetic marks for the prediction of genomic with active reporter gene activity.

first: Charles

last: Danko


title: The role of RUNX1 chromatin interaction in follicle functions during pre- and peri-ovulation (ChIP-seq)

status: Public on Jun 22 2021

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

summary: RUNX1 is induced by the LH surge in the ovary and plays an important role in granulosa cells in the peri-ovulatory window through the induction of key gene expression. The ablation of the canonical heterodimer partner of RUNX1 (CBFβ) leads to ovulatory failure and subfertility in female mice. A possible interaction between RUNX1 and PGR on the chromatin level has also been indicated. However, the properties of RUNX1 chromatin binding in granulosa cells in response to the LH surge remains unknown. This study aims to characterise the RUNX1 cistrome in pre- and peri-ovulatory granulosa cells and explore the potential interaction between RUNX1 and the key ovulatory factor PGR.

overall_design: 2 replicates of RUNX1 ChIP-seq were performed from granulosa cells pre- and post-hCG stimulation, with pooled input control for each time point

first: Barbara

last: Nicol

first: Karina

last: Rodriguez

first: James

last: Breen

first: Rebecca

last: Robker

first: Humphrey

last: Yao

first: Darryl

last: Russell


title: Identification of 5'isomiR in HCC patients.

status: Public on May 19 2021

city: Seoul

first: Hee Doo

last: Hee Doo

address: Banpo-Dong Seocho-Gu

country: South Korea

institute: The Catholic Univ. of Korea

type: Non-coding RNA profiling by high throughput sequencing

summary: The microRNA (miRNA) processing is a critical step for production of mature miRNAs. Its dysregulation leads to the increase of miRNA isoforms with heterogenous 5’ ends (isomiRs), recognizing distinct target sites with a shifted seed sequence. Although some miRNA genes display productive expression of their 5’-isomiRs in cancers, how the production is controlled and how they impact on tumor progression are unexplored yet. In this study, we identified tumor-specific production of isomiRs and investigated biological function of isomiRs in liver cancer.

overall_design: 15 Normal liver (NL), 60 HCC (TG1=10, TG2=25, TG3=19, HPC=6) samples who underwent small RNA-Seq

first: Hee

last: Yang

first: Jungwoo

last: Eun

first: Suk

middle: W

last: Nam


title: Transcription factor EGR2 controls homing and pathogenicity of TH17 cells in the central nervous system.

city: Arlington

first: Vanja

last: Lazarevic

state: VA

address: 1820 N Tuckahoe Street,

department: National Cancer Institute

institute: National Institutes of Health

summary: CD4+ T helper 17 (TH17) cells protect barrier tissues but also trigger autoimmunity. The mechanisms behind these opposing processes remain unclear. Here, we found that the transcription factor EGR2 controlled the transcriptional program of pathogenic TH17 cells in the central nervous system (CNS) but not that of protective TH17 cells at barrier sites. EGR2 was significantly elevated in myelin-reactive CD4+ T cells from patients with multiple sclerosis and mice with autoimmune neuroinflammation. The EGR2 transcriptional program was intricately woven within the TH17 cell transcriptional regulatory network and showed high interconnectivity with core TH17 cell-specific transcription factors. Mechanistically, EGR2 enhanced TH17 cell differentiation and myeloid cell recruitment to the CNS by upregulating pathogenesis-associated genes and myelomonocytic chemokines. T cell-specific deletion of Egr2 attenuated neuroinflammation without compromising the host’s ability to control infections. Our study shows that EGR2 regulates tissue-specific and disease-specific functions in pathogenic TH17 cells in the CNS.

overall_design: A: mRNA profiles of Th17 cells transduced with empty control retrovirus under non-pathogenic Th17 cell-polarizing conditions (Th17(b): IL-6+TGFb1+aIFN-g+aIL-4), 3 biological replicates; B: mRNA profiles of Th17 cells transduced with Egr2-expressing retrovirus under non-pathogenic Th17 cell-polarizing conditions (Th17(b): IL-6+TGFb1+aIFN-g+aIL-4), 3 biological replicates; C: mRNA profiles of Th17 cells transduced with empty control retrovirus under pathogenic Th17 cell-polarizing conditions in the presence of IL-23 (Th17(23): IL-6+TGFb1+aIFN-g+aIL-4 --> IL-23), 3 biological replicates; D: mRNA profiles of Th17 cells transduced with empty control retrovirus under pathogenic Th17 alternative (alt.) differentiation pathway in the presence of IL-1b+IL-6+IL-23; 3 biological replicates E: 2D2 Egr2-/- CD4+ T cells were differentiated under pathogenic Th17(23) conditions for 5 days. After reactivation on anti-CD3/CD28 coated plates for 48 hrs in the presence of IL-23, 2D2 Egr2-/- Th17(23) cells were transferred into TCRb-/- mice. During peak of EAE disease (day 20 after transfer), 2D2 Egr2-/- Th17 cells were purified from the spleens of Tcrb-/- mice for RNA-Seq, 3 biological replicates; F: 2D2 WT CD4+ T cells were differentiated under pathogenic Th17(23) conditions for 5 days. After reactivation on anti-CD3/CD28 coated plates for 48 hrs in the presence of IL-23, 2D2 WT Th17(23) cells were transferred into TCRb-/- mice. During peak of EAE disease (day 20 after transfer), 2D2 WT Th17(23) cells were purified from the spleens of Tcrb-/- mice for RNA-Seq,  4 biological replicates; G: 2D2 Egr2-/- CD4+ T cells were differentiated under pathogenic Th17(23) conditions prior 5 days. After reactivation on anti-CD3/CD28 coated plates for 48 hrs in the presence of IL-23, 2D2 Egr2-/- Th17(23) cells were transferred into TCRb-/- mice. During peak of EAE disease (day 20 after transfer), 2D2 Egr2-/- Th17 cells were purified from the CNS of Tcrb-/- mice for RNA-Seq,  3 biological replicates; H: 2D2 WT CD4+ T cells were differentiated under pathogenic Th17(23) conditions for 5 days. After reactivation on anti-CD3/CD28 coated plates for 48 hrs in the presence of IL-23, 2D2 WT Th17(23) cells were transferred into TCRb-/- mice. During peak of EAE disease (day 20 after transfer), 2D2 WT Th17(23) cells were purified from the CNS of Tcrb-/- mice for RNA-Seq,  4 biological replicates;

first: Y

last: Gao

last: Wang

first: D

last: Chauss

first: A

middle: V

last: Villarino

first: V

middle: M

last: Link

first: H

last: Nagashima

first: C

last: Spinner

last: Koparde

first: N

last: Bouladoux

first: M

last: Abers

first: T

middle: J

last: Break

first: L

middle: B

last: Chopp

first: J

last: Park

last: Zhu

last: Wiest

first: W

last: Leonard

last: Lionakis

last: O'Shea

first: B

last: Afzali

last: Belkaid


title: Aneuploid cells activate NF-κB to promote their immune clearance by NK cells

status: Public on May 18 2021

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: The immune system plays a major role in the protection against cancer. Identifying and characterizing the pathways mediating this immune surveillance is thus critical for understanding how cancer cells are recognized and eliminated. Aneuploidy is a hallmark of cancer and we previously found that untransformed cells that had undergone senescence due to highly abnormal karyotypes are eliminated by Natural Killer (NK) cells in vitro. However, the mechanisms underlying this process remained elusive. Here we show that NK-mediated immune clearance of aneuploid cells is predominantly mediated by non-cell autonomous mechanisms. Our data indicate that NF-κB signaling in aneuploid cells is central to elicit this immune response. Inactivating NF-κB abolishes NK-cell mediated clearance of untransformed aneuploid cells in vitro. In cancer cell lines, NF-κB activation correlates with degree of aneuploidy, raising the possibility that aneuploidy-induced immune recognition is partially retained in cancer.

overall_design: In one experiment, six replicates of untreated RPE-1 hTERT cells were compared to three replicates of doxorubicin treated,  palbociclib treated, nutlin3 treated, aneuploid cycling, or ArCK cells generated in the same cell line background. In the second experiment, two replicates of euploid cycling cells were compared to two replicates of ArCK cells generated in the control background. Three replicates of euploid cycling cells were compared to three replicates of ArCK cells generated in the STAT1 KO background.

first: Ruoxi

last: Wang

first: Sonia

last: Viganò

first: Uri

last: Ben-David

first: Angelika

last: Amon

first: Stefano

last: Santaguida


title: Single-cell RNA sequencing of emigrating cells from human psoriasis skin and control normal skin

status: Public on May 03 2021

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

summary: Single-cell RNA sequencing is transforming how we understand skin immunology, but previous human skin single-cell RNA sequencing data included only a small fraction of inflammatory cells among the overall cell population, such that functional subsets may be difficult to ascertain. We have overcome these obstacles by harvesting inflammatory cells emigrating from a half of 6 mm punch biopsy skin after 48-hour incubation in culture medium without any enzyme, and then analyzing the harvested cells with single-cell RNA sequencing. By this strategy, we obtained single-cell RNA sequencing data of 24,354 cells (leukocytes 46.0%, keratinocytes 49.6%, and melanocytes 2.4%) from 13 human psoriasis skin and 5 healthy volunteer skin. Unsupervised clustering identified NK cells, CD161+ T-cells, CD8+ T-cells, CD4+ T-cells, regulatory T-cells, mature & semimature dendritic cells, melanocytes, and keratinocytes in different layers - S. (Stratum) corneum, S. granulosum, S. spinosum, and S. basale. To understand psoriasis immunopathogenesis at single-cell levels, we compared gene expression between psoriasis cells vs. control cells within each inflammatory cell subtype clusters.

overall_design: Transcriptome profiles of 13 human psoriasis lesional skin and 5 healthy volunteers' normal control skin were generated by droplet-based single cell RNA-sequencing.

first: Jaehwan

last: Kim

first: James

last: Krueger


title: PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ChIP-seq)

first: Cesar

last: Arenas-Mena

first: Sevinc

last: Ercan


title: Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production

status: Public on May 01 2021

city: Wuerzburg

first: Franziska

last: Faber

state: Bavaria

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: University of Wuerzburg

summary: Much of our current knowledge about cellular RNA–protein complexes in bacteria is derived from analyses in gram-negative model organisms, with the discovery of RNA-binding proteins (RBPs) generally lagging behind in Gram-positive species. Here, we have applied Grad-seq analysis of native RNA–protein complexes to a major Gram-positive human pathogen, Clostridioides difficile, whose RNA biology remains largely unexplored. Our analysis resolves in-gradient distributions for ∼88% of all annotated transcripts and ∼50% of all proteins, thereby providing a comprehensive resource for the discovery of RNA–protein and protein–protein complexes in C. difficile and related microbes. The sedimentation profiles together with pulldown approaches identify KhpB, previously identified in Streptococcus pneumoniae, as an uncharacterized, pervasive RBP in C. difficile. Global RIP-seq analysis establishes a large suite of mRNA and small RNA targets of KhpB, similar to the scope of the Hfq targetome in C. difficile. The KhpB-bound transcripts include several functionally related mRNAs encoding virulence-associated metabolic pathways and toxin A whose transcript levels are observed to be increased in a khpB deletion strain. Moreover, the production of toxin protein is also increased upon khpB deletion. In summary, this study expands our knowledge of cellular RNA protein interactions in C. difficile and supports the emerging view that KhpB homologues constitute a new class of globally acting RBPs in Gram-positive bacteria.

overall_design: Grad-seq was performed in C. difficile strain 630 to identify RNA-regulatory networks and potential RNA-binding proteins. RIP-seq was carried out to identify RNAs bound by KhpB in C. difficile. dRNA-seq was carried out to investigate differential expressed transcripts in a KhpB knockout mutant.

first: Vanessa

last: Lamm-Schmidt

first: Manuela

last: Fuchs

first: Joannes

last: Sulzer

first: Milan

last: Gerovac

first: Jens

last: Hör

first: Petra

last: Dersch

first: Jörg

last: Vogel


title: Xyloglucan processing by Xanthomonas plant pathogens and its role in the activation of virulence factors.

status: Public on May 17 2021

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: Xyloglucans are highly substituted polysaccharides found in the primary cell walls of all vascular plants, acting as a first barrier against pathogens. Herein, we revealed that the diverse and economically relevant Xanthomonas phytopathogens are endowed with an enzymatic system targeting xyloglucans. Furthermore, we demonstrate that the products generated by this system elicit the expression of multiple virulence factors including the type III secretion system, a membrane-embedded machinery to deliver effector proteins into the host cells. Together, these findings illuminate the intricate enzymatic apparatus employed by Xanthomonas to break down xyloglucans and connect this system to the pathogenesis through activating the expression of key virulence factors.

overall_design: mRNA profiles of  X. citri grown on minimal media XVM2m containing xyloglucan-oligosaccharides relative to the media XVM2m containing glucose as a reference.

first: Isabela

last: Bonfim

first: Douglas

last: Paixão

first: Priscila

middle: O

last: Giuseppe

first: Mario

middle: T

last: Murakami


title: Patient derived colonoids as drug testing platforms - critical importance of oxygen concentration

status: Public on Apr 21 2021

city: Trondheim

first: Atle

middle: van  Beelen

last: Granlund

address: Postboks 8905 MTFS

country: Norway

institute: Norwegian University of Science and Technology

summary: Treatment of inflammatory bowel disease (IBD) is challenging, with a series of available drugs each helping only a fraction of patients. Patients may face time-consuming drug trials while the disease is active, thus there is an unmet need for biomarkers and assays to predict drug effect. It is well known that the intestinal epithelium is an important factor in disease pathogenesis, exhibiting physical, biochemical and immunologic driven barrier dysfunctions. One promising test system to study effects of existing or emerging IBD treatments targeting intestinal epithelial cells (IECs) is intestinal organoids (“mini-guts”). However, the fact that healthy intestinal epithelium is in a physiologically hypoxic state has largely been neglected, and studies with intestinal organoids are mainly performed at oxygen concentration of 20%. We hypothesized that lowering the incubator oxygen level from 20% to 2% would recapitulate better the in vivo physiological environment of colonic epithelial cells and enhance the translational value of intestinal organoids as a drug testing platform. In the present study we examine the effects of the key IBD cytokines and drug targets TNF/IL17 on human colonic organoids (colonoids) under atmospheric (20%) or reduced (2%) O2. We show that colonoids derived from both healthy controls and IBD-patients are viable and responsive to IBD-relevant cytokines at 2% oxygen. Because chemokine release is one of the important immunoregulatory traits of the epithelium that may be fine-tuned by IBD-drugs, we also examined chemokine expression and release at different oxygen concentrations. We show that chemokine responses to TNF/IL17 in organoids display similarities to inflamed epithelium in IBD-patients. However, inflammation-associated genes induced by TNF/IL17 were attenuated at low oxygen concentration. We detected substantial oxygen-dependent differences in gene expression in untreated as well as TNF/IL17 treated colonoids in all donors. Further, for some of the IBD-relevant cytokines differences between colonoids from healthy controls and IBD patients were more pronounced in 2% O2 than 20% O2. Our results strongly indicate that an oxygen concentration similar to the in vivo epithelial cell environment is of essence in experimental pharmacology.

overall_design:
Gene expression data of differentiated colon organoids from 6 donors (3 Ulcerative colitis and 3 healthy controls) investigating effects of short-term hypoxia on drug-treatment targets such as TNF alone or in combination with IL17.

***Please note that raw data is not provided as Norwegian law does not allow public access to human sequences raw data***

first: Helene

middle: K

last: Skovdahl

first: Shreya

last: Gopalakrishnan

first: Tarjei

middle: D

last: Svendsen

last: van Beelen Granlund

first: Ingunn

last: Bakke

first: Arnar

last: Flatberg

first: Zekarias

last: Ginbot

first: Silje

last: Thorsvik

first: Jenny

last: Ostrop

first: Bjørnar

last: Sporsheim

first: Tom

middle: E

last: Mollnes

first: Arne

last: Sandvik

first: Torunn

last: Bruland


title: Hypomethylation mediates genetic association with the major histocompatibility complex genes in Sjögren's syndrome

status: Public on Mar 25 2021

city: Berkeley

first: Xiaorong

last: Shao

address: 431 Stanley Hall

institute: University of California, Berkeley

summary: A causal mediation analysis of DNA methylation as a mediator of nearby genetic association with Sjögren's syndrome using data collected from 131 female members of the Sjögren's International Collaborative Clinical Alliance registry, comprising of 64 Sjögren's syndrome cases and 67 non-cases.

overall_design: DNA methylation was measured for each subject using the Illumina 450K Infinium Methylation BeadChip (450K) platform for 28 subjects and the Infinium MethylationEPIC (EPIC) platform for 103 subjects.

first: Calvin

last: Chi


title: RNA-seq of Arabidopsis thaliana seedlings exposed to the MAMP flg22 in the presence of individual commensal bacteria [MAE]

status: Public on Mar 27 2021

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

institute: University of São Paulo (ESALQ/USP)

summary: This study evaluates the transcriptome of Arabidopsis thaliana seedlings exposed to the MAMP flg22 in the presence of 35 different bacteria

overall_design: Arabidopsis seeds (wild-type Col-0) were germinated on Johnson medium and grown for 7 days in the vertical position. Plants were then transferred to media containing 1 uM flg22 or not in the presence of a commensal bacteria strain (10E5 c.f.u / mL). Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night). Whole seedlings were harvested twelve days after treatment. The experiment includes nine biological replicates from three independent experiments.

first: Jeff

last: Dangl


title: LSD1 functions through CoREST to maternally reprogram histone methylation

status: Public on Mar 03 2021

first: Brandon

middle: S.

last: Carpenter

state: Georgia

address: 615 Michael St., SOM: Cell Biology Dept.

department: Cell Biology

institute: Emory University

summary: Since the germline mortality phenotype of met-2; spr-1 mutants lie between spr-5; met-2 mutants and single mutants, it raises the possibility that maternal SPR-5 reprogramming may be partially dependent upon the SPR-5 interacting partner SPR-1. If mutating spr-1 partially compromises SPR-5 maternal reprogramming, we would expect that the gene expression changes in met-2; spr-1 mutants would be similar to spr-5; met-2 mutants, but that the changes would be less severe in met-2; spr-1 mutants. To test this possibility, we performed RNA-seq on spr-1, met-2, and met-2; spr-1 mutant L1 progeny compared to N2 L1 progeny.

overall_design: RNA-seq analysis on spr-1, met-2, and met-2; spr-1  L1 progeny to determine differentially expressed genes compared to wild-type ( N2)

middle: S

first: Alyssa

last: Scott

first: Robert

last: Golden

first: Sindy

middle: R

last: Chavez

first: Dexter

last: Myrick

first: Marcus

last: Curlee

first: Schmeichel

last: Karen

first: David

last: Katz


title: Phenotypic diversity and sensitivity to injury of the pulmonary endothelium during a period of rapid postnatal growth

status: Public on May 05 2021

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

institute: University of New South Wales

summary:
Background: Endothelial cells (EC) sit at the forefront of dramatic physiologic changes occurring in the pulmonary circulation during late embryonic and early postnatal life. First, as the lung moves from the hypoxic fetal environment to oxygen-rich postnatal environment, marked changes in pulmonary EC structure and function facilitate a marked increase in blood flow from the placenta to the lungs. Subsequently, pulmonary angiogenesis expands the microvasculature to drive exponential distal lung growth during early postnatal life. Yet, how these marked physiologic changes alter distinct EC subtypes to facilitate the transition of the pulmonary circulation and regulate vascular growth and remodeling remains incompletely understood.

Methods: In this report, we employed single cell RNA-transcriptomics and in situ RNA imaging to profile pulmonary EC in the developing mouse lung from just before birth through this period of rapid postnatal growth.

Results: Multiple, transcriptionally distinct macro- and microvascular EC were identified in the late embryonic and early postnatal lung, with gene expression profiles distinct from their adult EC counterparts. A novel arterial subtype, unique to the developing lung localized to the distal parenchyma and expressed genes that regulate vascular growth and patterning. Birth particularly heightened microvascular diversity, inducing dramatic shifts in the transcriptome of distinct microvascular subtypes in pathways related to proliferation, migration and antigen presentation. Two distinct waves of EC proliferation were identified, including one just prior to birth, and a second during early alveolarization, a time of exponential pulmonary angiogenesis. Chronic hyperoxia, an injury that impairs parenchymal and vascular growth, induced a common gene signature among all pulmonary EC, unique alterations to distinct microvascular EC subtypes, and disrupted EC-EC and EC-immune cell cross talk.

Conclusions: Taken together, these data reveal tremendous diversity of pulmonary EC during a critical window of postnatal vascular growth, and provide a detailed molecular map that can be used to inform both normal vascular development and alterations in EC diversity upon injury. These data have important implications for lung diseases marked by dysregulated angiogenesis and pathologic pulmonary vascular remodeling.

overall_design: scRNA-Seq on FACS sorted cells

first: Xibing

last: Che

first: Min

last: Liu

first: Racquel

last: Domingo-Gonzales

first: Stephen

middle: H

last: Duo

middle: C

last: Jones

last: Quake

middle: N

last: Cornfield

first: Cristina

last: Alvira


title: Cytotoxic CNS-associated T cells drive axon degeneration in aging and myelin disease

status: Public on Feb 08 2021

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: 1. Aging is a major risk factor for the development of nervous system functional decline, even in the absence of diseases or trauma. The axon–myelin units and synaptic terminals are some of the neural structures most vulnerable to aging-related deterioration, but the underlying mechanisms are poorly understood. In the peripheral nervous system, macrophages—important representatives of the innate immune system—are prominent drivers of structural and functional decline of myelinated fibers and motor endplates during aging. Similarly, in the aging central nervous system (CNS), microglial cells promote damage of myelinated axons and synapses. Here we examine the role of cytotoxic CD8+ T lymphocytes, a type of adaptive immune cells previously identified as amplifiers of axonal perturbation in various models of genetically mediated CNS diseases but understudied in the aging CNS. We show that accumulation of CD8+ T cells drives axon degeneration in the normal aging mouse CNS and contributes to age-related cognitive and motor decline. We characterize CD8+ T-cell population heterogeneity in the adult and aged mouse brain by single-cell transcriptomics and identify aging-related changes. Mechanistically, we provide evidence that CD8+ T cells drive axon degeneration in a T-cell receptor- and granzyme B-dependent manner. Cytotoxic neural damage is further aggravated by systemic inflammation in aged but not adult mice. We also find increased densities of T cells in white matter autopsy material from older humans. Our results suggest that targeting CD8+ CNS-associated T cells in older adults might mitigate aging-related decline of brain structure and function.   2. Myelin defects lead to neurological dysfunction in various diseases and in normal aging. Chronic neuroinflammation often contributes to axon-myelin damage in these  conditions and can be initiated and/or sustained by perturbed myelinating glia. We have previously shown that distinct mutations in the PLP1 gene result in neurodegeneration that is largely driven by adaptive immune cells. Here we characterize CD8+ CNS-associated T cells in these myelin mutants using single-cell transcriptomics and identify population heterogeneity and disease-associated changes. We demonstrate that early sphingosine-1-phosphate receptor modulation attenuates the recruitment of T cells and neural damage, while later targeting of CNS-associated T cell populations is inefficient and has no effect on neurodegeneration. Applying bone marrow chimerism and utilizing random X chromosome inactivation, we provide evidence that axonal damage is driven by cytotoxic, antigen specific CD8+ T cells that target mutant oligodendrocyte myelin. These findings offer insights into neural-immune interactions and are of translational relevance for neurological conditions associated with myelin defects and neuroinflammation.

overall_design: To characterize CD8+ CNS-associated T cells we comprehensively analyzed their transcriptomic profiles using single-cell RNA sequencing of CD45highCD8+ T lymphocytes freshly sorted from 12- and 24-month-old brains, as well as from 12-month-old brains from mice with PLP mutations. A total of 5,017, 5,504, and 6,467 cells were captured and a median gene number per cell of 1,325, 1,279, and 1,283 could be retrieved for adult and aged cells and cells from myelin mutants, respectively.

first: Janos

last: Groh

first: Konrad

last: Knöpper

first: Panagiota

last: Arampatzi

first: Xidi

last: Yuan

first: Lena

last: Lößlein

first: Wolfgang

last: Kastenmüller

first: Rudolf

last: Martini

first: Tassnim

last: Abdelwahab

last: Stadler


title: Ectodermal-neural cortex 1 affects the biological function of lung cancer through the MAPK pathway

status: Public on Feb 03 2021

city: Wuhu

first: wei

middle: cheng

last: wu

address: 2 Zheshan West Road, Jinghu District

institute: Yijishan Hospital of Wannan Medical College

summary: The objective of this study is to investigate the effects of ENC1 on the biological functions of lung cancer cells.

overall_design: Overall gene expression was evaluated in siRNA transfected A549 cells. The transcriptome of A549 cells transfected with si-NC and si-ENC1 were compared.

first: Chengwei

last: Wu

first: Xingwu

last: Chen


title: The gut microbiome regulates memory function.

status: Public on Feb 25 2021

city: Los Angeles

first: Yen-Wei

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

institute: University of California, Los Angeles

summary: The mammalian gastrointestinal tract contains a diverse ecosystem of microbial species collectively making up the gut microbiome. Emerging evidence highlights a critical relationship between gut microbiota and neurocognitive development. Consumption of unhealthy yet palatable dietary factors associated with obesity and metabolic dysfunction (e.g., saturated fat, added sugar) produces microbiota dysbiosis and negatively impacts neurocognitive function, particularly when consumed during early life developmental periods. Here we explore whether excessive early life consumption of added sugars negatively impacts neurocognitive development via the gut microbiome. Using a rodent model of habitual sugar-sweetened beverage (SSB) consumption during the adolescent stage of development, we first show that excessive early life sugar intake impairs hippocampal-dependent memory function when tested during adulthood while preserving other neurocognitive domains. Gut microbiome genomic sequencing analyses reveal that early life SSB consumption alters the abundance of various bacterial populations, including elevations in operational taxonomic units within the genus Parabacteroides (P. distasonis and P. johnsonii) whose abundance negatively correlated with memory task performance. Additional results reveal that in vivo Parabacteroides enrichment of cultured P. distasonis and P. johnsonii bacterial species in adolescent rats severely impairs memory function during adulthood. Hippocampus transcriptome analyses identify gene expression alterations in neurotransmitter synaptic signaling, intracellular kinase signaling, metabolic function, neurodegenerative disease, and dopaminergic synaptic signaling-associated pathways as potential mechanisms linking microbiome outcomes with memory impairment. Collectively these results identify microbiota dysbiosis as a mechanism through which early life unhealthy dietary patterns negatively impact neurocognitive outcomes.

overall_design: Two experimental desiign were involved. First one is compare hiippocampus responses beetween rats given sugar water (65% fructose and 35% sucrose, SUG group). Second one is to compare hippocampus response in the following treatments. Rats treated with saline for 21 days (Sal_Sal), Rats treated with antibiotics cocktail (Vancomycin (50 mg/kg), Neomycin (100 mg/kg), and Metronidazole (100 mg/kg)  ) along with 1 mg/mL of ampicillin in their drinking water) for 7 days followed by saline till PN 83 (Abx_Sal), Rats treated by antibiotcs cocktail for 7 days and 1:1 ratio of Parabacteroides distasonis and Parabacteroides johnsonii gavage till PN 83(Abx_Pb)

first: Scott

last: Kanoski

first: Emily

last: Noble


title: Cancer of Unknown Primary stem-like cells model multi-organ metastasis and unveil liability to MEK inhibition

city: Naples

first: Gennaro

last: Gambardella

address: Via Campi Flegrei 34,

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

summary: Cancers of Unknown Primary (CUPs), featuring metastatic dissemination in the absence of a primary tumor, are a biological enigma and a fatal disease. We propose that CUPs are a distinct, yet unrecognized, pathological entity originating from stem-like cells endowed with distinguished properties. These cells can be isolated in vitro (agnospheres) and propagated in vivo by serial transplantation, displaying  a high tumor-initiating cell frequency. After subcutaneous engraftment, agnospheres recapitulated the CUP phenotype, by spontaneously and quickly disseminating, and forming widespread established metastases. Regardless of different genetic backgrounds, agnospheres invariably displayed cell-autonomous proliferation and self-renewal, mostly relying on unrestrained activation of the MAP kinase/MYC axis, which confers sensitivity to MEK inhibitors in vitro and in vivo. Such sensitivity is associated with a transcriptomic signature predicting that more than 70% of CUP patients could be eligible to MEK inhibition. These data shed light on CUP biology and unveil an opportunity for therapeutic intervention.

overall_design: Transcriptional characterization of CUP stem-like cells and CUP tissues

first: Carla

last: Boccaccio

first: Federica

last: Verginelli


title: Genetic toolkit for sociality predicts castes across the spectrum of social complexity in wasps

status: Public on Jan 31 2021

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

institute: UCL

summary: Here we reveal evidence of a shared genetic toolkit across the full spectrum of social complexity found in Vespid wasps, from simple group living where castes remain plastic throughout life, to complex superorganismal societies comprised of mutually dependent insects with irreversible castes determined during development. We generated brain transcriptomic data for castes in nine representative species; using a machine learning approach we identified thousands of shared orthologs which consistently describe castes (queens and workers), from species with the simplest (Mischocyttarus paper wasps) to the most complex (e.g. Vespine wasps) levels of social organisation. The top 400 genes were enriched in synaptic transport genes, suggesting that these changes could affect brain neural function and connectivity. Fine-scale dissection of these patterns revealed that the molecular processes underpinning the simpler societies (which likely represent the origins of social living) are conserved throughout the major transition, but that additional processes may come into play in the more complex societies, especially at the point of no return where societies transition to be committed superorganisms. These analyses provide the first evidence of a conserved toolkit regulating social behaviour across the full spectrum of social complexity in any social insect. Importantly, they also provide evidence that there may be fundamental differences discriminating superorganismal societies from non-superorganismal societies. We suggest that the evolution of irreversible caste commitment (in superorganisms) is accompanied by a fundamental shift in the underlying regulatory molecular machinery; such shifts may also typify other major evolutionary transitions that are characterised by the emergence of a committed division of labour, such as the evolution of multicellularity.

sample_organism:
Vespa crabro
Vespula vulgaris
Angiopolybia pallens
Brachygastra mellifica
Metapolybia cingulata
Polistes canadensis
Agelaia cajennensis
Mischocyttarus basimacula
Polybia quadricincta

overall_design: Whole brain RNA-Seq (pool of individuals)

first: Seirian

last: Sumner

last: Bell

first: Elli

last: Leadbeater


title: Gene expression profiles associated with ITGBL1 overexpression

city: Gliwice

first: Alexander

middle: Jorge

last: Cortez

state: Silesia

address: Wybrzeze Armii Krajowej 15

department: Department of Biostatistics and Bioinformatics

institute: Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch

summary:
In our previous microarray study we identified two subgroups of high-grade serous ovarian cancers with distinct gene expression and different survival. Among differentially expressed genes was an Integrin beta-like 1 (ITGBL1), coding for a poorly characterized protein comprised of ten EGF-like repeats.
In this study we investigated ITGBL1 influence on ovarian cancer cells phenotype. Using various functional assays we found that ITGBL1 overexpression affected cellular adhesion, migration and invasiveness, while it had no effect on proliferation rate and the cell cycle. ITGBL1-overexpressing cells were significantly more resistant to cisplatin and paclitaxel, major drugs used in ovarian cancer treatment.  Global gene expression analysis revealed that signaling pathways affected by ITGBL1 overexpression were mostly those related to extracellular matrix organization and function, integrin signaling, focal adhesion, cellular communication and motility; these results were consistent with the findings of our functional studies.  Overall, our results indicate that higher expression of ITGBL1 in ovarian cancer is associated with features that may worsen clinical course of the disease.

overall_design: We investigated transcriptional activity of ovarian cancer cell lines OAW42 and SKOV3 modified to overexpress ITGBL1 by transduction with PLNCX2-ITGBL1 construct, in contrast with two types of control (wild-type and transduced with empty PLNCX2 vector). Gene expression profiles were determined by RNA extraction and hybrydization on Affymetrix Human Transcriptome Arrays in three replicates for each variant.

middle: J

first: Katarzyna

middle: M

last: Lisowska


title: Persistent Variations of Blood DNA Methylation Associated with Treatment Exposures and Risk for Cardiometabolic Outcomes in Childhood Cancer Survivors

status: Public on Mar 19 2021

city: Memphis

first: Zhaoming

last: Wang

state: TN

address: 262 Danny Thomas Place

department: Epidemiology & Cancer Control

institute: St. Jude Children's Research Hospital

summary:
Background: It is well-established that cancer treatment substantially increases risk of long-term adverse health outcomes among childhood cancer survivors. However, there is limited research on the underlying mechanisms. To elucidate the pathophysiology and a possible causal pathway from treatment exposures to cardiometabolic conditions, we conducted epigenome-wide association studies (EWAS) to identify DNA methylation (DNAm) sites associated with cancer treatment exposures and examined whether treatment-associated DNAm sites mediate associations between specific treatments and cardiometabolic conditions.
Methods: We included 2,052 survivors (median age 33.7 years) of European ancestry from the St. Jude Lifetime Cohort Study, a retrospective hospital-based study with prospective clinical follow-up. Cumulative doses of chemotherapy and region-specific radiation were abstracted from medical records. Seven cardiometabolic conditions were clinically assessed. DNAm profile was measured using MethylationEPIC BeadChip with blood-derived DNA.
Results: By performing multiple treatment-specific EWAS, we identified 935 5’-cytosine-phosphate-guanine-3′ (CpG) sites mapped to 538 genes/regions associated with one or more cancer treatments at epigenome-wide significance level (P<9×10-8). Among the treatment-associated CpGs, 8 were associated with obesity, 63 with hypercholesterolemia, and 17 with hypertriglyceridemia (False-Discovery-Rate-Adjusted P<0.05). We observed substantial mediation by methylation at four independent CpGs (cg06963130, cg21922478, cg22976567, cg07403981) for association between abdominal field radiotherapy (abdominal-RT) and risk of hypercholesterolemia (70.3%) and by methylation at three CpGs (cg19634849, cg13552692, cg09853238) for association between abdominal-RT and hypertriglyceridemia (54.6%). In addition, three CpGs (cg26572901, cg12715065, cg21163477) partially mediated the association between brain-RT and obesity with 32.9% mediation effect and two CpGs mediated the association between corticosteroids and obesity (cg22351187, 14.2%) and between brain-RT and hypertriglyceridemia (cg13360224, 10.5%). Notably, several mediator CpGs reside in the proximity of well-established dyslipidemia genes: cg21922478 (ITGA1) and cg22976567 (LMNA).
Conclusions: In childhood cancer survivors, cancer treatment exposures are associated with DNAm patterns present decades following the exposure. Treatment-associated DNAm sites may mediate the causal pathway from specific treatment exposures to certain cardiometabolic conditions, suggesting the utility of DNAm sites as risk predictors and potential mechanistic targets for future intervention studies.

last: Song

first: Chia-Wei

last: Hsu

first: Haitao

last: Pan

first: Yinan

last: Zheng

first: Lifang

last: Hou

first: Jin-ah

last: Sim

first: Zhenghong

last: Li

first: Heather

last: Mulder

first: John

last: Easton

last: Walker

first: Geoffrey

last: Neale

first: Carmen

middle: L

last: Wilson

first: Kirsten

last: Ness

first: Kevin

last: Krull

first: Deo

last: Srivastava

first: Yutaka

last: Yasui

first: Jinghui

last: Zhang

first: Melissa

last: Hudson

first: Leslie

last: Robison

first: I-Chan

last: Huang


title: Transcriptome profiles of alternative MED19 LNCaP and control LNCaP cells cultured under androgen deprivation with vehicle or R1881

status: Public on Jan 20 2021

city: New York

first: Michael

last: Garabedian

state: NY

address: 550 First Avenue

department: Microbiology

institute: NYU School of Medicine

summary: We report the application of ChIP and RNA sequencing to identify the mechanism whereby stable overexpression of MED19 in androgen-dependent LNCaP cells promotes growth under conditions of androgen deprivation. We determined the MED19 and AR transcriptomes and cistromes in control and MED19 LNCaP cells. We also examined genome-wide H3K27 acetylation in both the absence and presence of androgens. We found that MED19 overexpression selectively alters AR occupancy, H3K27 acetylation, and gene expression. Under conditions of androgen deprivation, genes regulated by MED19 correspond to genes regulated by ELK1, a transcription factor that binds the AR N-terminus to induce select AR target gene expression and proliferation. This study provides important insight into the mechanisms of prostate cancer cell growth under low androgen, and underscores the importance of the MED19 in this process.

overall_design: Examination by RNA seq in contorl LNCaP and MED19 LNCaP cells with and without androgen treatment

first: Hannah

last: Weber

first: Rachel

last: Ruoff


title: Stable overexpression of MED19 in androgen-dependent LNCaP cells promotes growth under conditions of androgen deprivation

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

overall_design: Refer to individual Series


title: H3K9me2 and H3K9me3 in mice apidose under high-fat diet

status: Public on Jan 10 2021

city: Shanghai

first: Zhe

last: Wang

state: Shanghai

address: Siping Road, Shanghai

institute: Tongji university

summary: The BAT and WAT of mice were removed and cut into small pieces. H3K9me2 and H3K9me3 were used for immunoprecipitation.

overall_design: High-fat feeding began at 6 weeks, and the body weight was measured once a week. After 12 weeks, the BAT and WAT of the mice were obtained for H3K9me2 and H3K9me3 ChIP sequencing (ChIP-seq) experiments.

first: Ming

last: Zhu

first: Meng

first: Cong


title: Genome-wide maps of the androgen receptor and H3K27 upon MED19 overexpression in LNCaP cells

summary: We report the application of ChIP and RNA sequencing to identify the mechanism whereby  stable overexpression of MED19 in androgen-dependent LNCaP cells promotes growth under conditions of androgen deprivation.  We determined the MED19 and AR transcriptomes and cistromes in control and MED19 LNCaP cells.  We also examined genome-wide H3K27 acetylation in both the absence and presence of androgens. We found that MED19 overexpression selectively alters AR occupancy, H3K27 acetylation, and gene expression. Under conditions of androgen deprivation, genes regulated by MED19 correspond to genes regulated by ELK1, a transcription factor that binds the AR N-terminus to induce select AR target gene expression and proliferation.  This study provides important insight into the mechanisms of prostate cancer cell growth under low androgen, and underscores the importance of the MED19 in this process.

overall_design: Examination by CHIP seq of AR, MED19 and H3K27ac in contorl LNCaP and MED19 LNCaP cells with and without androgen treatment.  Also performed RNA seq in contorl LNCaP and MED19 LNCaP cells with and without androgen treatment.


title: Transcriptional profiling in adult onset ADPKD mouse model based on Pkd2 inactivation

status: Public on Dec 31 2020

city: New Haven

first: Stefan

last: Somlo

state: Connecticut

address: 333 Cedar Street

department: Internal Medicine/Nephrology

institute: Yale University

summary: We performed unbiased transcriptional profiling in an adult-onset Pkd2 mouse model at an early stage before cysts formed using as controls wild type and PC2+cilia double knockout mice which are protected from ADPKD. By a tripartite comparison, we identified differetially expressed genes which have significant different expression in Pkd2-only knockout with same direction of change from both wild type and Pkd2+Cilia double knockout.

overall_design: RNA-Seq profiling using kidneys from Pkd2 knockout and controls wild type and Pkd2+cilia double knockout mice at 10 weeks old with three biological replicates for each genotype were performed.


title: Identification of novel serum biomarkers in early-stage HCC patients.

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

institute: Ajou University of Korea

summary: Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and is the one of the few cancers in which a continued increase in incidence has been observed over several years. HCC associated with chronic liver disease evolves from precancerous lesion and early HCC to overt cancer, and identifying key molecules contributing to early stage HCC is an urgent need. α-Fetoprotein (AFP) is the best serum biomarker for diagnosis of HCC, but sensitivity is low, particularly in detection of early-stage HCC. Therefore, novel and reliable diagnostic biomarkers to complement AFP are needed to improve HCC diagnosis. We aim to determine transcriptome-based molecular signature of multistep hepatocarcinogenesis, and to identify novel serum biomarkers to diagnose early stage HCC patient.

overall_design: 15 Normal liver (NL), 20 Chronic hepatitis (CH), 10 Liver Cirrhosis (LC), 10 Dysplastic nodule (DN), 18 Early HCC (eHCC), and 45 Advanced HCC (avHCC) samples of 86 patients who underwent NGS RNA-Seq.

first: JungWoo

first: SukWoo

last: Nam

first: Keunhong

last: Son

first: Hyungseok

last: Kim


title: Single-cell  analysis  of  adipose tissue  T cells in diabetic persons with HIV  reveals high proportions of clonally expanded CMV-like CD4+ T cells with cytotoxic RNA transcriptomes

status: Public on Oct 22 2020

city: Nashville

first: John

last: Koethe

address: 1211 Medical Center Drive

department: Internal Medicine

institute: VUMC

summary: Persons with HIV have a disproportionate burden of metabolic disease, including type 2 diabetes. We hypothesized that the accumulation of chronically activated T cells in the adipose tissue of HIV+ persons is a central mechanism promoting local macrophage activation, impaired adipocyte function, and the development of HIV-associated glucose intolerance. Prior studies of immune activation and HIV-associated metabolic disease have only measured circulating T cell subsets. In contrast, in our study we recruited a longitudinal cohort of HIV+ patients on antiretroviral therapy ranging from insulin sensitive to overtly diabetic, in addition to HIV-negative diabetic controls, to identify potential mechanistic linkages between adipose-resident T cell cytokine signaling, adipose tissue inflammation, and glucose intolerance in HIV+ persons. This study may also provide further insight into the role of T cells in the development of glucose intolerance in HIV-negative patients.

overall_design: Subcutaneous adipose tissue and matched peripheral blood CD3+ memory T cells were analyzed from diabetic, non-diabetic persons with HIV and diabetic HIV-negative persons for a total of 16 subjects - 32 samples

first: Celestine

last: Wanjalla


title: Type I interferome in human gut CD4 T cells

status: Public on Oct 02 2020

city: Aurora

first: Kejun

last: Guo

state: Colorado

department: Division of Infectious Diseases

institute: University of Colorado Anschutz Medical Campus

summary:
Rationale: Humans encode 12 different IFNa proteins. All of them, except IFNa1 (only binds with IFNAR1), bind with IFNAR1 and IFNAR2 to activate their downstream functions. Currently in the field, it is still a debate whether there are qualitative difference between different IFNa subtypes or the differences are merely quantitative. The current study was set out to elucidate the question.
Methods: CD4 T cells purified from LPMCs from gut biopsies from 3 donors, subsequently were mock treated or with ISRE activity normalized IFNa1, IFNa2, IFNa5, IFNa8, IFNa14, or IFNb. RNAs were extracted from cells after 18 hrs of incubation. RNASeq libraries were generated using Lexogen Quant Seq 3’ mRNA-Seq library Prep Kit. RNASeq were performed on Illumina HiSeq 2500.
Results: An average of 11.4 million gene counts were identified for each donor/treatment. A total of 31,465 genes were mapped, and among them 1,981 genes were differentially expressed due to type I interferon treatments. Each of IFNa subtypes or IFNb has their specifically regulated genes.
Conclusion: There are qualitative differences between type I interferons.

overall_design: Transcriptomic profiles of CD4 T cells treated with different Type I interferons.

first: Jon

last: Kibbie

first: Tania

last: Gonzalez

first: Mario

last: Santiago


title: Single-cell Transcriptomics Reveals the Divergent Developmental Lineage Trajectories during Human Pituitary Development

status: Public on Sep 19 2020

city: Beijing

first: Shu

last: Zhang

state: Beijing

address: Peking University, No.5 Yiheyuan Road Haidian District

institute: BIOPIC

summary: The anterior pituitary gland plays central roles in body growth, reproduction, metabolism and the stress response. In this study, we performed single-cell RNA-sequencing (scRNA-seq) of 4,113 individual cells from human fetal pituitaries. We characterized divergent developmental trajectories with distinct transitional intermediate states in five hormone-producing cell lineages. Furthermore, we characterized the cellular heterogeneity of pituitary stem cells, identifying a hybrid epithelial/mesenchymal state and an early-to-late state transition. These analyses define a single-cell resolution roadmap for human pituitary development.

overall_design:
In this study, we performed single-cell RNA-sequencing (scRNA-seq) of 4,113 individual cells from human fetal pituitaries.
Raw data of human fetal pituitary have been deposited in the GSA (Genome Sequence Archive) databases of the National Genomics Data Center (NGDC, https://bigd.big.ac.cn/) under the BioProject accession number PRJCA003249.

first: Yueli

last: Cui

first: Lu

last: Wen

first: Jie

last: Qiao

first: Fuchou

last: Tang


title: The EBV microRNA targetome

status: Public on Aug 01 2020

city: New Orleans

first: Erik

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: In EBV-associated tumors, such as gastric cancer (GC) and Burkitt’s lymphoma (BL), a high proportion of microRNAs are virally encoded. To explore the targets of both viral and host microRNAs, we performed Crosslinking, Ligation, and Sequencing of Hybrids (CLASH). With this approach, we were able to quantify each Argonaute-bound microRNA-mRNA interaction in a GC (SNU719), and BL (Akata) cell line.

overall_design: CLASH analysis of Akata and SNU719 cells, 3 biological replicates of each. miRNA-seq of Akata and SNU719 cells, 3 biological replicates of each.


title: Gene expression profile in human LPMCs during chronic HIV-1 infection [untreated LPMC]

summary: Human gut is the primary site for HIV-1 infection. However, most of transcriptomic studies so far were based on peripheral blood (PBMC). The current study compared the transcriptomes of human LPMC between healthy controls and chronically HIV-1 infected patients.

overall_design: Transcriptomic profiles of human lamina propria mononuclear cells (LPMC) isolated from gut biopsy during chronic HIV-1 infection.

first: Steph

last: Dillon


title: Prognostic Molecular Biomarkers for Metastatic Progression in Stage I and II Clear Cell Renal Cell Carcinomas

status: Public on Jul 28 2020

city: Mahasset

first: Andrew

last: Shih

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

summary: Presented is the differential expression of mRNA and miRNA in 44 Stage I and Stage II patients who developed metastasis within 5 years of nephrectomy, compared to 21 patients who remained disease free. Extracted RNA from nephrectomy specimens preserved in FFPE blocks was sequenced using RNAseq. MiRNA expression was done using the TaqMan OpenArray qPCR protocol.

overall_design: Examination of molecular differences between metatstatic versus non-metatstatic in stage I and stage II

first: Xin-hua

last: Zhu


title: Genetic profiling of fetal human hepatocytes immortalized with hTERT

status: Public on Jul 11 2020

city: Bronx

first: Sanjeev

last: Gupta

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

summary:
The successfully immortalized fetal human hepatocytes expressed large numbers of hepatic and other genes. The expression of gene groups and networks
was maintained over extended culture.

overall_design: Cells were examined with Affimetrix microarrays for gene expression over prolonged passaging after immortalization. The major goal was to demonstrate genetic stability.


title: Prognostic Molecular Signatures and Biomarkers for Metastatic Progression in Stage I and II Clear Cell Renal Cell Carcinomas


title: Hammer-seq to measure kinetics of DNA methylation maintenance in HeLa cells

status: Public on Jun 26 2020

first: Zhuqiang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

summary: Simultaneous measurement of the methylation status of parent and daughter strands of newly replicated DNA at the single molecule level has not been experimentally achieved, which is essential for measurements the kinetics of DNA methylation maintenance at base level genome wide. To achieve this, we developed a new method termed Hammer-seq (Hairpin assisted mapping of methylation of replicated DNA), which combines EdU labeling, biotin conjugation, immunopurification and hairpin bisulfite sequencing technologies. We were able to pulse label HeLa cells with EdU for as short as 4 min to capture newly synthesized DNA, and the paired-end hairpin bisulfite sequencing allowed us to simultaneously measure the methylation status of parent and daughter strands at the single molecular level with base resolution. Hammer-seq displayed strong enrichment of newly replicated regions and successfully captured maintenance intermediates, and also had robustness of measurements.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this study, we arrested HeLa cells at the G1/S boundary with thymidine-aphidicolin double block, pulse labeled with EdU for 4 min immediately after cell cycle release, chased for various time points up to 24 h and performed Hammer-seq to measure the maintenance kinetics during and after S phase.

first: Xuan

last: Ming

first: Zhuoning

last: Zou

first: Cong

last: Lv

first: Qixiang

last: He

first: Yingfeng

last: Li

first: Hailin

last: Wang

first: Bing