title: PLK1 and NOTCH Positively Correlate in Melanoma and their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways

city: Madison

first: Nihal

last: Ahmad

state: WI

address: 1300 University Avenue

institute: University of Wisconsin-Madison

summary: Melanoma is one of the most serious forms of skin cancer, and its increasing incidence coupled with non-lasting therapeutic options for metastatic disease highlight the need for additional novel approaches for its management. In this study, we determined the potential interactions between polo-like kinase 1 (PLK1, a serine/threonine kinase involved in mitotic regulation) and NOTCH1 (a type I transmembrane protein deciding cell fate during development) in melanoma. Employing an in-house human melanoma tissue microarray (TMA) containing multiple cases of melanomas and benign nevi, coupled with high-throughput, multispectral quantitative fluorescence imaging analysis, we found a positive correlation between PLK1 and NOTCH1 in melanoma. Further, TCGA database analysis of melanoma patients showed an association of higher mRNA levels of PLK1 and NOTCH1 with poor overall as well as disease-free survival. Next, utilizing small-molecule inhibitors of PLK1 and NOTCH (BI 6727 and MK-0752, respectively), we found a synergistic anti-proliferative response of combined treatment in multiple human melanoma cells. To determine the molecular targets of the overall and synergistic responses of combined PLK1-NOTCH inhibition, we conducted RNA-sequencing analysis employing a unique regression model with interaction terms. We identified the modulations of several key genes relevant to melanoma progression/metastasis, including MAPK, PI3K, and RAS, as well as some new genes such as Apobec3G, BTK and FCER1G which have not been well-studied in melanoma. In conclusion, our study demonstrated a synergistic anti-proliferative response of a concomitant targeting of PLK1 and NOTCH in melanoma, unravelling a potential novel therapeutic approach for detailed preclinical/clinical evaluation.

overall_design: For RNA-seq analysis, total RNA was isolated from cells in 4 replicates in each  group. There are total 4 treatment groups:  DMSO as control, BI6727 treatment, MK-0752 treatment, and BI6727+MK-0752 combined treatment. A total of 16 samples were submitted to the University of Wisconsin Biotechnology Center Gene Expression Center for quality control, library construction and further analysis.

first: Shengqin

last: Su

first: Gagan

last: Chhabra

first: Colin

last: Dewey


title: Wnt Signaling Mediates Oncogenic Synergy Between Akt and Dlx5 in T-Cell Lymphomagenesis by Enhancing Cholesterol Synthesis [WTvsDP mouse RNA-seq]

status: Public on Oct 07 2020

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

country: USA

institute: Fox Chase Cancer Center

type: Expression profiling by high throughput sequencing

summary: Akt2;Dlx5 double transgenic mice develops T-ALL, and these cells have up regulated Cholesterol synthesis via Wnt pathway for survival

overall_design: mRNAseq

first: Yinfei

last: Tan


title: Transcriptional response of Mycobacterium tuberculosis to inhibition of Cytochrome bd oxidase and Cytochrome bcc:aa3 oxidase

city: Bronx

first: Erik

middle: James

last: Hasenoehrl

state: New York

address: 1301 Morris Park Ave. Price 569

department: Microbiology & Immunology

institute: Albert Einstein College of Medicine

summary: Comparative analysis of the transcriptional response, as quantified by RNA-Seq, of Mycobacterium tuberculosis (Mtb) during inhibition of the terminal cytochrome oxidases, Cytochrome bd oxidase and Cytochrome bcc:aa3. This study was designed to evaluate the efficacy if a novel small molecule inhibitor of the Cytochrome bd oxidase. Specifically, we compared the transcriptional response of Mtb during inhibition by Q203 with a Cytochrome bd deletion mutant to the transcriptional response of Mtb treated with a combination of Q203 and the purported Cytorchomre bd small molecule inhibitor (ND-011992).

overall_design: Comparison of mRNA transcript levels before and after drug treatment of WT Mycobacterium tuberculosis and Cytochrome bd oxidase mutant (∆CydAB). Measured before and after 6 h after treatment with Q203, ND-011992, or combination. Biological replicates: 3.

middle: J

first: Michael

last: Berney


title: Wnt Signaling Mediates Oncogenic Synergy Between Akt and Dlx5 in T-Cell Lymphomagenesis by Enhancing Cholesterol Synthesis [TCF ChIP]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq

first: Joseph

middle: R

last: Testa


title: Wnt Signaling Mediates Oncogenic Synergy Between Akt and Dlx5 in T-Cell Lymphomagenesis by Enhancing Cholesterol Synthesis [human PKF RNA-seq]

overall_design: mRNAseq. 'L001' and 'L002' in the titles represent technical replicates -- same library sequenced in different lanes.


title: Wnt Signaling Mediates Oncogenic Synergy Between Akt and Dlx5 in T-Cell Lymphomagenesis by Enhancing Cholesterol Synthesis

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Wnt Signaling Mediates Oncogenic Synergy Between Akt and Dlx5 in T-Cell Lymphomagenesis by Enhancing Cholesterol Synthesis [primary tumor RNA-seq]

overall_design: RNAseq


title: RNA sequencing of transgenic TNNT2 variant models

city: Farmington

first: Travis

last: Hinson

state: Connecticut

address: 10 Discovery Dr

institute: JAX-GM

summary: We identify genetic alterations in TNNT2 HCM and DCM

overall_design: Lentivirus was used to delivery TNNT2 variants to TNNT2ko human iPSC-CMs

first: Anthony

middle: M

last: Pettinato

first: J

middle: T


title: Wnt Signaling Mediates Oncogenic Synergy Between Akt and Dlx5 in T-Cell Lymphomagenesis by Enhancing Cholesterol Synthesis [mouse PKF RNA-seq]

overall_design: mRNAseq.  'L001' and 'L002' in the titles represent technical replicates -- same library sequenced in different lanes.


title: Expression profiling of dog primary mammary triple-negative breast cancer cells infected or not with a vaccinia virus deleted for the thymidine kinase gene

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS


title: Single-cell RNAseq profiling of dog primary mammary triple-negative breast cancer cells infected or not with a vaccinia virus deleted for the thymidine kinase gene

summary: Dog breast cancer cells were infected at a multiplicity of infection of 5 for 6 houurs or mock-infected (Control) for 6 hours prior to analyses by single-cell RNA sequencing. The objective was to study the distribution of host cell and viral gene expression on the cancer cell population and to compare the effect of viral infection on these cells.

overall_design: Uninfected and infected cells were processed independently and single cell RNAseq profiling was performed using the 10x Genomics single-cell 3' V2 chemistry.

first: Virginie

last: Magnone

first: Pascal

last: Barbry

first: Bernard

last: Mari

first: Georges

last: Vassaux


title: Whole genome RNA-sequencing from root tips of Arabidopsis thaliana med16-2 mutant under High and Low phosphate conditions

city: Irapuato

first: Luis

middle: Rafael

last: Herrera-Estrella

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: Langebio

country: Mexico

institute: Cinvestav - Langebio

summary: Total mRNA was extracted from the root tips (2-3 mm from the root apex) of wild-type plants (Col-0 accession) and med16-2 mutants grown under low and high phosphate conditions 4 days after germination, using and sequenced by RNA-seq methodology.

overall_design: Analysis of 4 different treatments, 2 different genotypes (Col-0, med16-2), 2 different phosphate concentration treatments (High Pi, Low Pi), 1 biological replicate for treatment

first: Javier

last: Raya-Gonzalez

first: Jonathan

middle: O

last: Ojeda-Rivera


title: Single-cell DNA replication sequencing (scRepli-seq): a method for mapping replication timing domains genome wide in single mammalian cells

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

country: Japan

institute: Mie University

summary: Replication timing (RT) domains are stable units of chromosome structure that are regulated in the context of development and disease. Conventional genome-wide RT mapping methods require a large number of S-phase cells for either effective enrichment of replicating DNA through BrdU immunoprecipitation or the determination of copy number differences during S-phase, which restricts their application to non-abundant cell types. Here, we provide a simple, cost-effective, and robust protocol for single-cell DNA replication sequencing (scRepli-seq). The scRepli-seq methodology relies on the whole-genome amplification (WGA) of genomic DNA (gDNA) from single S-phase cells and next-generation sequencing (NGS)-based determination of copy number differences that arise between replicated and unreplicated DNA. We also provide computational pipelines that are key components of the methodology. NGS library preparation takes 3 d.

overall_design: Single-cell Repli-seq experiments in hTERT-RPE1. We deposited single-cell data sets passed (or not passed) by our MAD score-based quality control. Total 26 samples.

first: Hisashi

last: Miura

first: Saori

last: Takahashi

first: Ichiro

last: Hiratani


title: Characterization of young and aged lung tissue-resident influenza nucleoprotein-specific CD8 memory T cells

status: Public on Oct 06 2020

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 1st St SW

department: medicine, immunology

institute: mayo clinic

summary: To identify the disparaties of D^b-nucleoprotein specific resident memory CD8 T cells between young and aged mice, we pooled n=11 aged or n=18 young lungs together after intraveounously labeling T cells and sorted ivCD90- CD8a+ CD44hi CD69+ D^b-NP tetramer (PE+ & APC+) cells. By scRNA-seq, we found the aged population was missing a cluster in the young population that resembled typical functional resident memory CD8 T cells indicating that aged resident memory CD8 T cells of this specificity would have poor recall function.

overall_design: Examined with lung-resident memory CD8+ T cells sorted from influenza PR8-infected young (2months at infection) or aged (22 months at infection) C57BL/6 mice (60 days post infection) by scRNA-seq

first: Nick

middle: P

last: Goplen


title: Characterization of young and aged lung tissue RNA 60 days post-influenza infection

summary: To identify molecular characteristics of young and aged lungs post-influenza infection, we isolated RNA from lungs 60 days post-infection and examined by bulk RNAseq. We found a large number of genes remain upregulated in aged compared to young lungs. Comparison with expression of immune system-related genes from Nanostring expriments indicated this was largely infection-induced rather than baseline differences between age. This indicates that aged lungs fail to return to homeostasis following a viral respiratory infection

overall_design: Examined with bulk lung tissue from influenza PR8-infected young (2months at infection) or aged (22 months at infection) C57BL/6 mice (60 days post infection)


title: Hyperactive CDK2 Activity in Basal-like Breast Cancer Imposes a Genome Integrity Liability that can be Exploited by Targeting DNA Polymerase Epsilon

city: New York

first: Richard

last: Possemato

state: NY

address: 550 First Avenue

department: Pathology

institute: NYU School of Medicine

summary: RNAseq data for MDA-MB-231, CAMA-1, and MCF7 cells expressing shPOLE and either a vector control or cDNA POLE rescue

overall_design: Cell Lines express an shRNA targeting DNA Polymerase epsilon (POLE) and either a POLE cDNA or vector control.


title: 4EHP and GIGYF1/2 induce translation-coupled messenger RNA decay [Wildtype and ZNF598-null]

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

country: Switzerland

institute: University of Zurich

summary: Although canonical mRNA degradation is generally recognized to be translation dependent, our understanding of the molecular events that coordinate ribosome movement with the decay machinery is still limited. Here, we show that the 4EHP–GIGYF1/2 complex triggers co-translational mRNA decay as a result of altered ribosome activity during elongation. Human cells lacking 4EHP and GIGYF1 and 2 proteins accumulate transcripts known to be degraded in a translation dependent manner or with prominent ribosome pausing. These include mRNAs encoding secretory and membrane-bound proteins or specific tubulin isotypes, among others. 4EHP–GIGYF1/2 fails to reduce target mRNA levels in the absence of ribosome stalling or upon disruption of its interaction with the cap structure, DDX6 and a GYF domain-associated protein. Our studies reveal how a repressor complex linked to neurological disorders minimizes the protein output of a subset of mRNAs.

overall_design: Two cell types with two biological replicates analysed using RNA-Seq and Ribo-Seq

first: Cátia

last: Igreja


title: Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution

city: Tokyo

first: Masayuki

last: Tsukasaki

address: 7-3-1 Hongo Bukyo-ku

department: Department of Immunology  Graduate School of Medicine and Faculty of Medicine

institute: The University of Tokyo

summary: To unveil cell fate decision pathways during osteoclast differentiation at single-cell resolution, we performed single-cell RNA sequencing (scRNA-seq) on the osteoclast culture system, in parallel with bulk RNA-seq and proteome analyses

overall_design: scRNA-seq, bulk RNA-seq and proteome analyses were performed on in vitro osteoclastogenesis at Day 0 (before RANKL stimulation), Day 1 (1 day after RANKL stimulation) and Day 3 (3 days after RANKL stimulation).


title: DNA demethylation in CD4-CD8-TCR-ab compared to CD8+ T cells in B6.MRL-FASlpr mice

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

type: Methylation profiling by high throughput sequencing

summary: To understand the DNA methylation differences associated with CD4-CD8-TCR-ab (DN) T cells that accumulate in the B6.MRL-FASlpr mouse model we performed reduced representation bisulfite sequencing on these cells compared to CD8+ T cells derived from the lymph nodes.  Overall we observed that 95% of the differential CpG were demethylated in DN T cells compared to CD8+ T cells.

overall_design: RRBS on CD4-CD8-TCR-ab compared to CD8+ T cells in B6.MRL-FASlpr mice

first: C

middle: D

first: R

last: Budd


title: RNAseq profiling of dog primary mammary triple-negative breast cancer cells infected or not with a vaccinia virus deleted for the thymidine kinase gene

first: Kevin

last: Lebrigand

summary: Dog breast cancer cells were infected at a multiplicity of infection of 5 for 6 hours or mock-infected (Control) for 6 hours prior to analyses by single-cell RNA sequencing. The objective was to study the distribution of host cell and viral gene expression.on the cancer cell population and to compare the effect of viral infection on these cells.

overall_design: RNA-seq profiling of uninfected and infected cells at different time points in 2 replicates

first: Virginie

last: Magnone

first: Pascal

last: Barbry

first: Bernard

last: Mari

first: Georges


title: Expression data of CD107aLow and CD107aHigh cells isolated  from human adipose tissue

city: Baltimore

first: Aaron

middle: W

last: James

state: MD

address: 600 North Wolfe Street

institute: Johns Hopkins University School of Medicine

summary: The tunica adventitia of vessels within adipose tissue (AT) represents a heterogenous microanatomical niche for multipotent mesenchymal precursor cells.  To investigate this heterogeneity, cell surface antibody array among CD34+ human adventicytes identified 13 novel antigens enriched within perivascular mesenchyme, including the endolysomal associated protein CD107a (LAMP1).  Membranous CD107a can be used to divide perivascular / adventitial precursor cells into functional relevant subsets.  CD107alow cells from human AT demonstrated high colony forming efficiency, osteoprogenitor cell frequency, and osteogenic potential.  Conversely, CD107ahigh cells demonstrated heightened adipoprogenitor cell frequency and adipogenic potential.  Knockdown experiments did not identity a functional role for CD107a in osteo/adipogenic differentiation.  Instead, CD107a protein trafficking to the cell surface was associated with exocytosis during early adipogenic differentiation.  Bulk and single cell RNA Sequencing suggested that CD107alow cells represent a precursor population for CD107ahigh cells.  Functional roles for CD107alow/high subsets were confirmed in transplantation experiments.  Intramuscular transplantation of CD107alow cells yielded increased bone formation in comparison to their CD107ahigh counterparts.  Further, CD107alow cells induced spine fusion whereas their CD107ahigh counterparts did not.  In sum, cell surface CD107a in mesenchymal progenitors correlates with exocytosis during early adipogenesis, and can be used to divide osteo- from adipogenic progenitor cells within human fat tissue.

overall_design: 6 Total samples were analyzed: 3 CD107aHigh biological replicates and three CD107aLow controls as determined by FACS.

first: Jiajia

last: Xu


title: RNA-sequencing of L. monocytogenes under PrfA-inducing conditions refines the PrfA regulon and reveals a putative novel PrfA-dependent gene and its associated PrfA box

city: Ithaca

first: Martin

last: Wiedmann

address: 341 Stocking Hall

department: Food Science

institute: Cornell University

summary:
Purpose: The objective of the present study was to refine the PrfA regulatory network using RNA-seq to characterize the L. monocytogenes transcriptome in a wt, ∆prfA, and prfA* under PrfA-inducing conditions.
Methods: Sequence reads were aligned to the L. monocytogenes 10403S genome using the BWA-MEM algorithm, version 0.7.3a. The data for coverage per base on the sense and antisense strands were analyzed separately using SAMtools. Differential expression of genes in each strain comparison (wt/∆prfA, wt/prfA*, and prfA*/∆prfA) were analyzed using the baySeq package for R version 2.2.0. Transcripts were considered differentially expressed if the FDR (False Discovery Rate) was ≤ 0.05, the FC (Fold Change) was ≥ 2.0 for up-regulated transcripts and ≤ 0.5 for down-regulated transcripts.
Results: Our data indicate that we (i) confirmed transcription of known PrfA-dependent genes and (ii) identified a novel PrfA box and its putative ������A-dependent promoter region.
Conclusions: Combined with many studies that have investigated the PrfA regulon and virulence in L. monocytogenes, we have shown tha PrfA directly regulates a small subset of genes; however, using RNA-seq and bioinformatics we were able to identify a novel PrfA-dependent gene and its putative PrfA box. This finding highlights the importance of using advanced approaches to analyze RNA-seq data, which can potentially reveal previously unidentified genes regulated under specific conditions.

overall_design: RNA-sequencing characterization of the PrfA regulon by comparing the transcript level between (i) wt (10403S) and prfA*, (ii) wt and ∆prfA, and (iii) prfA* and ∆prfA in triplicate, NextSeq 500

first: Lory

last: Henderson


title: Continued Bcl6 expression prevents the transdifferentiation of established Tfh cells into Th1 cells during acute viral infection

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

country: Germany

institute: University Hospital Bonn

summary: By using a temporally-controlled system for the ablation of Bcl6 and Cxcr5 speficially in CD4 T cells, the requirements of both factors for the maintenance of Tfh cells were investigated

overall_design: Cd4-CreERT2+ mice without floxed alleles were used as controls in all experiments.   Bcl6 ablation in SMARTA cells in LCMV infection: iBcl6KO (n=5), Ctrls (n=3)  Cxcr5 ablation in SMARTA cells in LCMV infection: iCxcr5KO (Tfh: n=4, Th1: n=4), Ctels (Tfh: n=3; Th1: n=5)  Cxcr5 ablation in NP-KLH immunization: iCxcr5KO (Tfh: n=6), Ctrls (Tfh: n=4; non-Tfh: n=4)

first: Dominik

last: Alterauge

first: Johannes

last: Bagnoli


title: Shiftwork induction of adipose tissue gene expression

status: Public on Oct 05 2020

city: Duarte

first: Ke

last: Ma

state: CA

address: 1500 E. Duarte Rd

department: Diabetes Complications & Metabolism

institute: City of Hope-BRI

summary: We applied an environmental lighting-induced weekly rotating shift schedule for 6 months to uncover its metabolic consequence specifically in visceral and subcutaneous adipose tissue. Through global gene expression profiling together with functional analysis, we show that chronic clock dysregulation results in striking adipose tissue hypertrophy with overt inflammatory response and fibrotic sequala that predispose to insulin resistance.

overall_design: RNA-seq analysis of the visceral fat epididymal white adipose tissue (eWAT) at ZT3 (8AM) and ZT12 (5PM) samples and the subcutaneous fat inguinal white adipose tissue (iWAT) at ZT3 (8AM) samples for normal control and the shiftwork groups.

first: Xuekai

last: Xiong

first: Xiwei

last: Wu

first: Charles

last: Warden


title: Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

institute: Yale University

overall_design: Refer to individual Series


title: Imbalance of regulatory and cytotoxic SARS-CoV-2-reactive CD4+ T cells in COVID-19

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

summary: The contribution of CD4+ T cells to protective or pathogenic immune responses to SARS-CoV-2 infection remains unknown. Here, we present a large-scale single-cell transcriptomic analysis of viral antigen-reactive CD4+ T cells from 40 COVID-19 patients. In hospitalized patients compared to non-hospitalized patients, we found increased proportions of cytotoxic follicular helper (TFH) cells and cytotoxic T helper cells (CD4-CTLs) responding to SARS-CoV-2, and reduced proportion of SARS-CoV-2-reactive regulatory T cells (TREG). Importantly, in hospitalized COVID-19 patients, a strong cytotoxic TFH response was observed early in the illness which correlated negatively with antibody levels to SARS-CoV-2 spike protein. Polyfunctional T helper (TH)1 and TH17 cell subsets were underrepresented in the repertoire of SARS-CoV-2-reactive CD4+ T cells compared to influenza-reactive CD4+ T cells. Together, our analyses provide so far unprecedented insights into the gene expression patterns of SARS-CoV-2-reactive CD4+ T cells in distinct disease severities.

overall_design: Single-cell RNA-seq were performed from pure populations of virus-reactive memory CD4+ T cells isolated ex vivo from SARS-CoV-2 infected individuals (n=40) and healthy controls (n=13).

first: Benjamin

last: Meckiff

first: Ciro

last: Suastegui

first: Vicente

middle: F

last: Rosas

first: Serena

last: Chee

first: Anthony

last: Kusnadi

first: Hayley

last: Simon

first: Alba

last: Grifoni

first: Emanuela

last: Pelosi

first: Alessandro

last: Sette

first: Ferhat

last: Ay

first: Grégory

last: Seumois

first: Christian

middle: H

last: Ottensmeier


title: Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection [ATAC-seq]

summary: Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here we performed a genome-wide CRISPR screen with SARS-CoV-2 in Vero-E6 cells, identifying known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex, the alarmin HMGB1, and the transcription factors Smad3 and Smad4. Small molecule inhibitors of these pathways inhibited SARS-CoV-2-infection in both monkey and human cells, demonstrating the conserved role of these genetic hits across species. We also revealed that HMGB1 is a novel regulator of ACE2 expression and critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.

overall_design: RNAseq, ChIPseq (H3K4me3, H3K27ac) and ATACseq of Vero-E6 cell lines in control sgRNA and HMGB1 KO sgRNA conditions.

first: Wesley

middle: L

last: Cai

first: Will

last: Culligan

first: Shang-Min

last: Zhang

first: Jin

last: Wei

first: Craig

last: Wilen


title: Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection [RNA-seq]

first: Qin

last: Yan


title: Inhibition of CXCR1/2 in human colitis-derived pluripotent stem cell intestinal organoids attenuates the inflammatory phenotype

city: Cleveland

first: Emina

last: Huang

state: OH

address: 9500 Euclid Ave

department: Stem Cell

institute: Lerner Research Institute/Cleveland Clinic

summary: We report the results of RNA-Seq on iPSCs, Definitive Endoderm (DE), Spheroids (Sph), and induced human intestinal organoids (iHIOs) from colitic and normal primary patient colon tissues

overall_design: Transcriptome analysis of iPSCs, DE, Spheroids and iHIOs isolated from colitic and normal primary tissues.

first: E


city: Orange

first: Matthew

state: CT

address: 100 West Campus Drive, Ste MIC 231

department: Molecular Biophysics and Biochemistry

summary: Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. A genome-wide CRISPR screen with SARS-CoV-2 was performed in Vero-E6 cells (data not provided here), identifying known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex, the alarmin HMGB1, and the transcription factors Smad3 and Smad4. Small molecule inhibitors of these pathways inhibited SARS-CoV-2-infection in both monkey and human cells, demonstrating the conserved role of these genetic hits across species. We also revealed that HMGB1 is a novel regulator of ACE2 expression and critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.

overall_design: Examination of H3K27ac in wild-type and HMGB1 knockout Vero-E6 cells

middle: B

first: William

last: Lu-Culligan


title: Specific ectodermal enhancers control the expression of Hoxc genes in developing mammalian teguments [ATAC-seq]

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

summary: Vertebrate Hox genes are key players in the establishment of structures during the development of the main body axis. Subsequently, they play important roles either in organizing secondary axial structures such as the appendages, or during homeostasis in postnatal stages and adulthood. Here we set up to analyze their elusive function in the ectodermal compartment, using the mouse limb bud as a model. We report that the HoxC gene cluster was globally co-opted to be transcribed in the distal limb ectoderm, where it is activated following the rule of temporal colinearity. These ectodermal cells subsequently produce various keratinized organs such as nails or claws. Accordingly, deletion of the HoxC cluster led to mice lacking nails (anonychia) and also hairs (alopecia), a condition stronger than the previously reported loss of function of Hoxc13, which is causative of the ectodermal dysplasia 9 (ECTD9) syndrome in human patients. We further identified, in mammals only, two ectodermal-specific enhancers located upstream the gene cluster, which act synergistically to regulate Hoxc genes in these ectodermal organs. Deletion of these enhancers alone or in combination revealed a strong quantitative component in the regulation of these genes in the ectoderm, suggesting that these two enhancers may have evolved along with mammals to provide the level of HOXC proteins necessary for the full development of hairs and nails.

overall_design: ATAC-seq datasets of ectoderm of the distal part of forelimb and hindlimb at E14.5 as well as E13.5 forebrain

first: M

last: Fernandez-Guerrero

first: C

middle: C

last: Bolt

first: L

first: D

last: Duboule

last: Ros


title: Transcription-driven cohesin accumulation is associated with secretory phenotype of senescence [ChIP-Seq]

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: Senescence is a stable form of cell cycle arrest that is triggered in response to various pathophysiological stimuli. The three-dimensional structure of senescent cells has been previously characterised, mostly in terms of macro-domains or changes between large heterochromatic regions. In the present body of work, using a combination of HiC and targetted Capture Hi-C, we aimed to investigate the association between gene expression and local chromatin structure in senescence, particularly focusing on enhancer-promoter (EP) interactions. We show that many EP contacts are rewired in RAS-induced Senescence compared to ‘normal’, growing cells and that these are associated with cohesin binding changes and possible loop re-organisation. The genes affected by altered chromatin interactions correspond to the two main axes of senescence gene regulation: cell cycle and inflammation. Our findings are potentially relevant during ageing and in cancers with cohesin mutations, where cell cycle and inflammation are also deregulated.

overall_design: ChIP-seq of CTCF and cohesin components RAD21 and SMC3 in growing and (RAS-induced) senescent IMR90 fibroblasts

first: Aled

last: Parry


title: Transcription-driven cohesin accumulation is associated with secretory phenotype of senescence [HiC]

overall_design: HiC and Capture HiC of growing and (RAS-induced) senescent IMR90 fibroblasts


title: Ribosome profiling and RNA-seq of Tsc2+/- hippocampal slices

city: Worcester

first: Annie

last: Hien

state: MA

address: 373 Plantation Street

department: Molecular Medicine

institute: UMass Medical School Worcester

summary: Tuberous sclerosis (TSC) is caused by loss of function in Tsc2 and haploinsufficiency of the protein product tuberin.

overall_design: Ribosome profiling and RNA-seq of hippocampal slices from WT and littermate Tsc2+/- mice before and after DHPG-mGluR stimulation

first: Gemma

last: Molinaro

first: Botao

last: Liu

first: Kimberly

last: Huber

first: Joel

last: Richter


title: Bidirectional perisomatic inhibitory plasticity of a Fos neuronal network

status: Public on Oct 04 2020

city: Boston

first: Michael

middle: E.

last: Greenberg

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

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


title: Bidirectional perisomatic inhibitory plasticity of a Fos neuronal network [Ribotag]

summary: Behavioral experiences activate the Fos transcription factor (TF) in sparse populations of neurons that are critical for encoding and recalling specific events. However, there is limited understanding of the mechanisms by which experience drives circuit reorganization to establish a network of Fos-activated cells. Additionally, it is unknown if Fos is required in this process beyond serving as a marker of recent neural activity and, if so, which of its many gene targets underlie circuit reorganization. Here we demonstrate that when mice engage in spatial exploration of novel environments, perisomatic inhibition of Fos-expressing hippocampal CA1 pyramidal neurons by parvalbumin (PV)-interneurons (INs) is enhanced, while perisomatic inhibition by cholecystokinin (CCK)-INs is weakened. This bidirectional modulation of inhibition is specific to Fos-expressing neurons and is abolished when the function of the Fos TF complex is disrupted. Single-cell RNA-sequencing, ribosome-associated mRNA profiling, and chromatin analyses, combined with electrophysiology reveal that Fos activates the transcription of Scg2 (secretogranin II), a gene that encodes multiple distinct neuropeptides, to coordinate these changes in inhibition. As PV- and CCK-INs mediate distinct features of pyramidal cell activity, the Scg2-dependent reorganization of inhibitory synaptic input might be predicted to affect network function in vivo. Consistent with this prediction, hippocampal gamma rhythms and pyramidal cell coupling to CA1 theta are significantly altered with loss of Scg2. Together these findings reveal an instructive role for Fos and Scg2 in establishing a network of Fos-activated neurons via the rewiring of local inhibition from an initially broad to a selectively modulated state. The opposing plasticity mechanisms on distinct inhibitory pathways may support the consolidation of memories over time.

overall_design: CaMK2a-Cre; lox-STOP-lox-Rpl22-HA or PV-Cre; lox-STOP-lox-Rpl22-HA mice were intraperitoneally injected with kainic acid (KA) or phosphate buffered saline (PBS). After 6 hours, hippocampal CA1 tissue was rapidly dissected from mice and subsequently used for isolation of ribosome-bound mRNAs. Immunopurification of ribosome-bound mRNAs was performed as previously described (Sanz PNAS 2009) with 10mM Ribonucleoside Vanadyl Complex present in the lysis buffer and using the mouse monoclonal anti-HA antibody (Sigma HA-7, H3663, 12 ug/IP). A small fraction of lysate before the immunoprecipitation (IP) was used as input for each sample. For CaMK2a-Ribotag, 3 bioreplicates were used per condition, with CA1 tissue from 4 mice pooled per bioreplicate. For PV-Ribotag, 4 bioreplicates were used per condition, with CA1 tissue from 9-10 mice pooled per bioreplicate.

first: Ee-Lynn

last: Yap

first: David

middle: A

last: Harmin

middle: E


title: Bidirectional perisomatic inhibitory plasticity of a Fos neuronal network [snRNA-seq]

overall_design: We performed single-nucleus RNA-sequencing in Fos/Fosb/Junb conditional knockout mice injected with Cre- or deltaCre-GFP AAVs to study the role of AP-1 factors in activity-dependent gene expression. These mice received either AAV Cre-GFP (Cre+) or deltaCre-GFP (Cre-) injected into one hippocampal CA1 hemisphere, leaving cells in the contralateral hemisphere non-transduced as a control. Mice were subjected to 4h of KA, and CA1 nuclei were isolated and subsequently sorted using the micro-fluidic-based 10X Genomics platform.


title: Transcription-driven cohesin accumulation is associated with secretory phenotype of senescence


title: Effect of Cryopreservation on Autologous Chimeric Antigen Receptor T Cell Characteristics

status: Public on Oct 03 2020

city: BETHESDA

first: PING

last: JIN

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

summary: As clinical applications for chimeric antigen receptor T cell (CART) therapy extend beyond early phase trials, commercial manufacture incorporating preservation steps becomes a logistical necessity. The effect of cryopreservation on CART characteristics is unclear. We retrospectively evaluated the effect of cryopreservation on product release criteria and in vivo characteristics in 158 autologous CART products from 6 single-center clinical trials. Further, from 3 healthy donor manufacturing runs, we prospectively identified differentially expressed cell surface markers and gene signatures among fresh versus cryopreserved CARTs. Within 2 days of culture initiation, cell viability of the starting fraction (peripheral blood mononuclear cells [PBMNCs]) decreased significantly in the cryo-thawed arm compared to the fresh arm. Despite this, PBMNC cryopreservation did not affect final CART fold expansion, transduction efficiency, CD3%, or CD4:CD8 ratios. In vivo CART persistence and clinical responses did not differ among fresh and cryopreserved final products. In healthy donors, compared to fresh CARTs, early apoptotic cell-surface markers were significantly elevated in cryo-thawed CARTs. Cryo-thawed CARTs also demonstrated significantly elevated expression of mitochondrial dysfunction, apoptosis signaling, and cell cycle damage pathways. Cryopreservation during CART manufacture is a viable strategy, based on standard product release parameters. The clinical impact of cryopreservationrelated subtle micro-cellular damage needs further study

overall_design: To study T cell phenotypic changes and gene expression prospectively, 3 healthy donor PBMNCs were used to manufacture CARTs using 4 different manufacturing schemes: (1) starting manufacturing with fresh PBMNCs and analysis of fresh CARTs, (2) starting with fresh PBMNCs and analysis of cryopreserved CARTs, (3) starting with cryopreserved PBMNCs and analysis of fresh CARTs, and (4) starting with cryopreserved PBMNCs and analysis of cryopreserved CARTs.

first: Sandhya

last: Panch

first: Sandeep

middle: K

last: Srivastava

first: Ping

last: Jin


title: The NS1 Protein of the Parvovirus MVM Aids in the Localization of the Viral Genome to Cellular Sites of DNA Damage

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

summary: The autonomous parvovirus Minute Virus of Mice (MVM) localizes to cellular sites of DNA damage to establish viral replication centers, visualized by focal depositions of the essential MVM phosphoprotein NS1. However, how such foci are established remains unknown. Here, we show that MVM NS1 localized to cellular sites of DNA damage independently of its known ability to covalently bind the viral genome at its known consensus DNA binding site. NS1 that retained its capacity to bind its cognate DNA binding sequence could relocate either the viral genome, or heterologous DNA, containing those sites, to cellular sites of DNA damage. These findings suggest that another way that NS1 can facilitate virus infection is by localizing the genome to cellular sites which contain replication and expression proteins.

overall_design: Examination of MVM non-structural protein NS1 binding to cellular sites relative to sites of DNA damage during ectopic expression in mouse cells.

middle: J

last: Pintel


title: Gene expression data from BEAS-2B cells upon exposure to particulate matter (PM2.5) from biomass combustion

city: Freiburg

first: Stefan

last: Günther

department: Institute of Pharmaceutical Sciences

institute: Albert-Ludwigs University Freiburg

summary:
Exposure to PM2.5 affects gene expression of BEAS-2B cells
Gene expression microarrays were used to detail changes in the transcriptome upon exposure to PM2.5

overall_design: BEAS-2B cells were exposed to PM2.5 for 5 weeks before extraction of total RNA and microarray analysis

first: Regina

last: Merck

first: Katherina

last: Heßelbach

first: Anastasiya

last: Osipova

first: Désirée

last: Popadić

first: Gwang-Jin

last: Kim

first: Thomas

last: Häupl

first: Marc

last: Bonin

first: Irmgard

last: Merfort

first: Matjaz

last: Humar


title: Basal gene expression of Xiphophorus skin over a 24 hour period

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

summary: Gene expression profiles of Xiphophorus skin over a 24 hour period were established to identify cyclic transcriptional patterns

overall_design: Fish were euthanized every 3 hours throughtout a day for transcriptome profiling using RNA-Seq. Basal level gene expression is quantified and can be further utilized to identify genes exhibting cyclic expression pattern.

first: Ronald

last: Walter


title: Microglia-derived Il6 deficient Vs floxed mice with/without cryolesion

city: Bellaterra

first: Paula

last: Sanchis

state: Barcelona

address: calle de la vall moronta s/n

department: Department of Cellular Biology, Physiology and Immunology, and Institute of Neurosciences

country: Spain

institute: Universitat Autònoma de Barcelona

summary: We have examined the role of microglia-derived IL-6 by analyzing the transcriptome of the brain cortex following a cryolesion. We performed oligonucleotide array analysis using the right fronto-parietal cortex of microglia-derived Il6 deficient (Il6ΔMic) and floxed (Il6lox/lox) mice , under control and cryolesion conditions.

overall_design: Four-condition experiment: control floxed mice; cryolesioned floxed mice; control microglia-derived Il6 deficient mice; cryolesioned microglia-derived Il6 deficient mice   Biological replicates: 4 per condition.

first: Juan

last: Hidalgo


title: Bidirectional perisomatic inhibitory plasticity of a Fos neuronal network [CUT&RUN]

first: Michael

last: Greenberg

overall_design: CaMK2a-Cre; lox-STOP-lox-Sun1-GFP mice were intraperitoneally injected with kainic acid (KA) or phosphate buffered saline (PBS). After 2 hours, hippocampal CA1 tissue was dissected from these mice and dounce homogenized. Nuclei were isolated from tissue homogenates and used as input for flow cytometry to isolate CaMK2a+ nuclei, marked by Sun1-GFP. CaMK2a+ nuclei were used as input for CUT&RUN to profile c-Fos binding, with CUT&RUN for IgG used as a negative control. Three biological replicates for c-Fos and IgG CUT&RUN were performed.

first: Ee-Lynn

last: Yap

first: Christopher

last: Davis


title: YAP/TAZ deficiency reprograms macrophage phenotype and improves infarct healing and cardiac function after myocardial infarction

status: Public on Oct 02 2020

city: Singapore

first: Manvendra

middle: Kumar

last: Singh

state: Singapore

address: 8 College Road

department: Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS Medical School

summary: Adverse cardiac remodeling after myocardial infarction (MI) causes structural and functional changes in the heart leading to heart failure. The initial pro-inflammatory response followed by an anti-inflammatory or reparative response post-MI is essential for minimizing the myocardial damage, healing, and scar formation. Bone marrow-derived macrophages (BMDMs) are recruited to the injured myocardium and essential for cardiac repair as they can adopt both pro-inflammatory (M1) or anti-inflammatory/reparative (M2) phenotypes to modulate inflammatory and reparative response, respectively. YAP and TAZ are the key mediators of the Hippo signaling pathway and essential for cardiac regeneration and repair. However, their role in macrophage polarization and post-MI inflammation, remodeling, and healing are not well established. Here, we demonstrate that expression of YAP and TAZ is increased in macrophages undergoing M1 or M2 polarization. Genetic deletion of YAP/TAZ leads to impaired M1 polarization and enhanced M2 polarization. Consistently, YAP activation/overexpression enhanced M1 and impaired M2 polarization. We show that YAP/TAZ promote M1 polarization by increasing IL6 expression, and impede M2 polarization by decreasing Arg1 expression through interaction with the HDAC3-NCoR1 repressor complex. These changes in macrophages polarization due to YAP/TAZ deletion results in reduced fibrosis, and hypertrophy and increased angiogenesis, leading to improved cardiac function after MI. Also, YAP activation augmented MI-induced cardiac fibrosis and remodeling. In summary, we identify YAP/TAZ as important regulators of macrophage-mediated pro- and anti-inflammatory responses post-MI.

overall_design: 12 BMDM samples are analyzed comprises of untreated control (n = 3), untreated Yap/Taz knockout (n = 3), LPS/IFNg treated control (n = 3), LPS/IFNg treated Yap/Taz knockout (n = 3)

first: Masum

middle: M

last: Mia

first: Dasan

last: Cibi

first: Siti

last: Ghani

first: Weihua

last: Song

first: Nicole

last: Tee

first: Sujoy

last: Ghosh

first: Junhao

last: Mao

first: Eric

middle: N

last: Olson

first: Monalisa

last: Hota


title: Ribosome profiling and RNA-seq of wild-type hippocampal slices

first: Annie

last: Hien

summary: Metabotropic glutamate receptor-mediated long-term depression (mGluR-LTD) is a form of synaptic plasticity that is dysregulated in multiple mouse models of autism, including fragile X syndrome and tuberous sclerosis.

overall_design: Ribosome profiling and RNA-seq of hippocampal slices from wild-type mice before and after DHPG-mGluR stimulation

first: Gemma

last: Molinaro

first: Botao

last: Liu

first: Kimberly

last: Huber

first: Joel

last: Richter


title: The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression

city: Milan

first: Fabio

last: Marchiano

address: Via Alessandro Manzoni 56

country: Italy

institute: Humanitas

summary:
Skeletal muscles are comprised of gigantic multinucleated cells called muscle fibers, which often span several centimetres in length. Each muscle fiber is densely packed with contractile force-producing  myofibrils and ATP-producing mitochondria. During animal development the  size of the individual muscle fibers must dramatically increase to match the growth of the animal and to connect growing skeletal elements. How such dramatic tissue growth is coordinated with growth of the  contractile apparatus in the muscle fibers is not well understood. Here, we use the large Drosophila flight muscles to mechanistically decipher how muscle fiber growth is controlled during development.
We isolated flight muscles from Drosophila melanogaster pupae at 24 h and 32 h APF of the genotypes wt, Dlg5-IR, Slmap-IR, Yorkie-CA, Hippo-IR and isolated total RNA for subsequent BRB-seq sequencing.
Our study reveals that regulated activity of core members of the Hippo pathway, Hippo, Warts  and Yorkie is required to support post-mitotic flight muscle growth.  Interestingly, we identify Dlg5 and Slmap as important members of the  STRIPAK phosphatase complex, which negatively regulates Hippo activity  and therefore enables post-mitotic muscle growth. Mechanistically, we  find that the Hippo pathway controls the timing and the levels of  sarcomeric gene expression during muscle development and thus regulates  the key components that mediate muscle fiber growth. Since Dlg5, STRIPAK  and the Hippo pathway are conserved in mammals a similar mechanism may  contribute to skeletal muscle or cardiac growth in humans.

overall_design: Indirect flight muscle mRNA profiles in Drosophila Melanogaster at two different time points (24h APF and 32h APF) for different conditions (wt, Dlg5-IR, Slmap-IR, Yorkie-CA, Hippo-IR). At least 3 biological replicates per condition are provided.

first: Aynur

last: Kaya-Çopur

first: Marco

middle: Y

last: Hein

first: Daniel

last: Alpern

first: Julie

last: Russeil

first: Nuno

last: Luis

first: Matthias

last: Mann

first: Bart

last: Deplancke

first: Bianca

last: Habermann

first: Frank

last: Schnorrer


title: TPR Knockdown Frac-Seq

city: Ipswich

first: Eric

last: Wolf

email: ewolf@neb.com, ericjwolf1@gmail.com

address: 240 County Road

department: RNA Division

institute: New England Biolabs

summary: How splicing regulates the nuclear export of mRNAs has been a source of much debate. While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export. We provide evidence that TPR is required for the nuclear export of mRNAs and lncRNAs that are generated from intronless or intron-poor genes. In contrast, TPR is not required for the nuclear retention of mRNAs that have retained introns, or unused 5’ splice site motifs. In summary, our study provides one of the first examples of a factor that is specifically required for the nuclear export of intronless mRNAs.

overall_design: Examination of nucleocytoplasmic transcript distribution upon TPR knockdown in U2OS cells

first: Eliza

middle: S

last: Lee

first: Alexander

last: Palazzo


title: Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine encephalon. [miRNA-Seq]

city: Leioa

first: Begoña

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

institute: University of the Basque Country (UPV/EHU)

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the application of miRNA sequencing technology for high-throughput profiling of the aluminium hydroxide adjuvant mechanism of action in an in vivo experiment on sheep.  We mapped about 13.1 million sequence reads per sample to the sheep genome (build Oar3.1) and identified 299 miRNAs in the encephalon of sheep treated with commercial vaccines, with the adjuvant alone or with PBS (control group). A total of 2, 38 and 7 differentialy expressed miRNAs were identified in the Vaccine vs. Control, Adjuvant vs. Control and Adjuvant vs. Vaccine comparisons, respectively. Furthermore, miRNA target prediction was performed and it was integrated with previous RNA-seq data in the same animals to predict reliable miRNA-mRNA interactions. Previously reported miRNAs related to brain injury and neurodegenerative diseases were found differentially expressed. Within the negatively correlated targets of the differentially expressed miRNAs there are factors that are clearly related with mitochondria, to maintenance of neuronal polarity and axon growth and to apoptosis. Taken together, our analysis provides characterization of alterations in the miRNAome caused by the aluminium adjuvant alone, while the commercial vaccine not cause great changes, and identifies some targets of the differentially expressed miRNAs which have been previously linked to mitochondrial dysfunction. Aluminum might be causing an imbalance in metal ion levels, among them Mg, in the parietal lobe cortex of animals vaccinated with the adjuvant alone.

overall_design: Encephalon miRNA profiles of thirteen age-matched Rasa sheep after inoculation of nine different commercial vaccines based of aluminium hydroxide (the vaccine group composed of 4 animals), with the aluminium adjuvant alone in an equivalent dose (the adjuvant group composed of 4 animals) or PBS (the control group composed of 5 animals) were generated by deep sequencing on an Illumina HiSeq2500 sequencer.

first: Endika

last: Varela-Martínez

first: Martín

last: Bilbao-Arribas

first: Naiara

last: Abendaño

first: Javier

last: Asín

first: Maialen

last: Sistiaga-Poveda

first: Marta

last: Pérez

first: Ramsés

last: Reina

first: Damián

last: de Andrés

first: Lluís

last: Luján


title: Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine encephalon. [RNA-Seq]

summary: We report the application of RNA sequencing technology for high-throughput profiling of the aluminium hydroxide adjuvant mechanism of action in an in vivo experiment on sheep treated with commercial vaccines, with the adjuvant alone or with PBS (control group). We mapped about 74.1 million sequence reads per sample to the sheep genome (build Oar3.1) and after filtering 16,369 genes were expressed, of which 14,387 were annotated genes in Ensembl and 1,982 were candidate lncRNAs. A total of 13, 63 and 76 differentialy expressed genes were identified in the Vaccine vs. Control, Adjuvant vs. Control and Adjuvant vs. Vaccine comparisons, respectively. Previously reported genes related to neuronal development, brain transport and neurotransmission, brain injury and neurodegenerative diseases associated with aluminum were found differentially expressed, namely VCAM1, TRPM4, GDF10 and NTN1.

overall_design: Encephalon Total RNA profiles of twelve age-matched Rasa sheep after inoculation of nine different commercial vaccines based of aluminium hydroxide (the vaccine group composed of 4 animals), with the aluminium adjuvant alone in an equivalent dose (the adjuvant group composed of 4 animals) or with PBS (the control group composed of 4 animals) were generated by deep sequencing on an Illumina HiSeq2000 sequencer.


title: Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine encephalon.

overall_design: Refer to individual Series


title: RNA-seq profiles of WT and QK-KO microglia

city: Houston

first: Jian

last: Hu

state: Texas

address: 1881 East Rd

department: Department of Cancer Biology, Division of Basic Sciences

institute: The University of Texas MD Anderson Cancer Center

summary: This study is to analyze the transcriptomic profiles of 6 weeks 0.2% cuprizone treated Cx3cr1-CreER;QKLoxP/LoxP (Qk-KO) and Cx3cr1-CreER;QK LoxP/+ (WT) mice

overall_design: 8 weeks old of Cx3cr1-CreER;QKLoxP/LoxP (Qk-KO) and Cx3cr1-CreER;QKLoxP/+ (WT) mice were injected with tamoxifen, and fed with 0.2% Cupurizone for 6 weeks to indue demyelination. Then the corpus callosum were dissected and microglia were isolated. The total RNAs were extracted by Rnasey kit and sent for sequencing with llumina HiSeq2000 Sequencer.

first: Hu

last: Jian

first: Ren

last: Jiangong


title: Human effector/memory CD4 T cell subsets: deep TCR profiling.

status: Public on Oct 01 2020

city: Moscow

first: Sofya

middle: A.

last: Kasatskaya

address: Bolshoy Boulevard 30, bld. 1

department: Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: Clonal fate of helper T cells is governed by early costimulatory signals but may also depend on the mode of TCR interaction with peptide-MHC on APCs. We investigate TCR repertoires of eight effector/memory CD4+ T-cell subsets (Th1, Th2, nonclassical Th2 (Th2a), Th17, Th1-17, Tfh, Treg, Th22), revealing subset-specific physicochemical and recombinational features reproducible across donors. At a threshold of 3 reads per UMI, the number of obtained UMI-labeled cDNA molecules per repertoire per sample ranged from 5,300 to 303,500, and the number of CDR3 clonotype variants at the nucleotide level per repertoire per sample ranged from 1,200 to 83,200. Deep unbiased TCR profiling allowed us to assess the natural level of in vivo CD4+ subsets plasticity. We observed a major clonal exchange between  Th17/Th22/Th2/Th2a and the high stability of Treg and Tfh subsets. The latter two subsets also show higher repertoire publicity across donors. Tfh repertoire features reflect those of mature antibodies and indicate stringent selection of highly antigen-specific, low cross-reactive TCRs.  We conclude that functional subsets are marked with non-random universal for donors and specific features of passed selection. In future TCR sequencing applications, subset-specific profiling could provide better insights of normal and pathological states of adaptive immunity compared to the classical approach when TCR profiling is performed on bulk T cells or after rough division into CD4 and CD8-enriched populations.

overall_design: Dataset consists of 86 samples: T cell receptor clonesets from 5 healthy donors. For each of the donors, 8 functional CD4 T cell subsets were sorted and for each subset alpha and beta TCR libraries were prepared for NGS. Deep TCR profiling was achieved with UMI libraries barcoding according to Milaboratory protocol. Additionally, for 3 samples from donor 4 there are biological replicates: 3 replicate TCR alpha and 3 TCR beta libraries.

first: Kristin

last: Ladell

first: David

last: Price

first: Alexey

last: Davydov

first: Dmitriy

last: Chudakov

first: Olga

middle: V

last: Britanova


title: Transcriptional profiling of human MCF7 cell lines by RNASeq

city: Dublin

first: Jochen

last: Prehn

address: 123 St. Stephen's Green

department: Physiology and Medical Physics

country: Ireland

institute: Royal College of Surgeons in Ireland (RCSI)

summary: The BCL2 family of proteins regulate apoptosis by controlling mitochondrial outer membrane permeability. However, effects on mitochondrial structure and bioenergetics have also been reported. Here we comprehensively characterized the effects of BCL2 and BCL(X)L on cellular energetics in MCF7 breast cancer cells using time-lapse confocal single cell imaging and mitochondrial and cytosolic FRET reporters. We found that BCL2 and BCL(X)L increase the metabolic robustness of MCF7 cells and that this was associated with increased mitochondrial NAD(P)H and ATP levels. Experiments with the F1F0 synthase inhibitor oligomycin demonstrated that BCL2 and in particular BCL(X)L, while not affecting ATP synthase activity, more efficiently coupled the mitochondrial proton motive force with ATP production. This metabolic advantage was associated with an increased resistance to nutrient deprivation and enhanced clonogenic survival in response to metabolic stress, in the absence of profound effects on cell death. Our data suggest that a primary function of BCL(X)L and BCL2 overexpression in tumor cells is to increase their resistance to metabolic stress in the tumor microenvironment, independent of cell death signaling.

overall_design: mRNA profiles of untreated MCF7 cell lines (parental PSFFV, and BCL2- and BCL-xL-overexpressing clones in duplicates)

first: Federico

last: Lucantoni

first: Manuela

last: Salvucci


title: Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer

city: New York

first: Alec

last: Kimmelman

address: 550 1st Avenue

department: Department of Radiation Oncology, Perlmutter Cancer Center

institute: NYU School of Medicine


title: High throughput small molecule screening reveals NRF2-dependent and -independent pathways of cellular stress resistance

city: Ann Arbor

last: Lombard

state: Michigan

address: 3015 BSRB, 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan Ann Arbor

summary: Biological aging is the dominant risk factor for most chronic diseases. Development of anti-aging interventions offers the promise of simultaneously preventing or even treating many chronic illnesses. Cellular stress resistance is an evolutionarily conserved feature of longevity. Here, we identify compounds that confer resistance to the superoxide generator paraquat (PQ), the heavy metal cadmium (Cd), and the DNA alkylator methyl methanesulfonate (MMS). Some rescue compounds conferred resistance to a single stressor, while others conferred multiplex stress resistance. Induction of stress resistance in mouse fibroblasts was highly predictive of longevity extension in a published large-scale longevity screen in C. elegans. Transcriptomic analysis implicated NRF2 signaling in stress resistance provided by two protective compounds, cardamonin and AEG 3482.  Molecules that conferred resistance to PQ also induced cellular inflammatory pathways, and core pathways such as AMPK signaling. Following further optimization, small molecules identified in this work, particularly those that promote resistance to multiple distinct stressors, may represent attractive candidates to evaluate for potential pro-health and pro-longevity effects in mammals.

overall_design: RNA-seq was performed on mouse tail fibroblasts treated with a drug (three replicates) or DMSO control (5 replicates), with a total of 30 samples on an Illumina HiSeq4000. The transcriptome was analyzed using Kallisto, counted using Tximport, and differential expression was determined using DESeq2.

first: William

last: Kohler

first: Angela

last: Guo

first: Christi

last: Gendron

first: Melissa

last: Han

first: Weiqiao

last: Ding

first: Yang

last: Lyu

first: Xinna

last: Li

first: Xiaofang

last: Shi

first: Zaneta

last: Nikolovska-Coleska

first: Thomas

last: Girke

first: Ao-Lin

last: Hsu

first: Scott

middle: D

last: Pletcher

first: Richard

last: Miller


title: Human pluripotent stem cell fate regulation by SMARCB1

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

summary: Epigenetic regulation by the SWI/SNF complex is essential for normal self-renewal capacity and pluripotency of human pluripotent stem cells (hPSCs). It has been shown that different subunits of the complex have a distinct role in this regulation. Specifically, the SMARCB1 core subunit has been shown to regulate the activity of enhancers in diverse types of cells, including hPSCs. Here we report the establishment of conditional hPSC lines, which enable the control of SMARCB1 expression from complete loss of function (LOF) to significant overexpression. Using this system, we show that any deviation from normal SMARCB1 expression leads to rapid differentiation of the cells. We further found that SMARCB1 expression is not required for the differentiation of hPSCs into progenitor cells of the three germ layers, but rather for later stages of differentiation. Moreover, we identify SMARCB1 as a critical player in the regulation of cell-cell and cell-extracellular matrix (ECM) interactions in hPSCs. Finally, our results show that complete SMARCB1 LOF affects hPSC fate in a different way than the effect of partial downregulation of the gene and thus emphasizes the complex regulation of hPSCs by SMARCB1.

overall_design: Comparison between global gene expression of normal ( WT, WT_dox, kiko ,ki) SMARCB1 LOF  (kiko WO dox) and SMARCB1 GOF (ki dox) hPSCs

first: Ilana

last: Carmel-Gross

first: Leah

last: Armon

first: Etgar

last: Levy

first: Orly

last: Yaron

first: Achia

last: Urbach


title: Thymidylate synthase drives the phenotypes of epithelial-to-mesenchymal transition in non-small cell lung cancer

city: PHILADELPHIA

first: Irfan

last: Asangani

state: PA

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

summary: Epithelial to mesenchymal transition (EMT) is a developmental process driving metastasis and chemoresistance. Thymidylate synthase (TS) is a proliferation enzyme and a chemotherapeutic drug target we previously correlated with EMT. Here we report a rather direct role of TS in determining EMT phenotypes in non-small cell lung cancer (NSCLC). TS knockdown and a promoter reporter system revealed the control of TS on EMT, and upstream regulators (HMGA2, HOXC6) and downstream effectors (AXL, SPARC, FOSL1) were identified. In vivo, TS knockdown suppressed lung colonization and metastasis formation in a proliferation-independent manner. Transcriptomic analyses showed a significant enrichment of EMT signature genes in NSCLC patients with high TS levels. These results establish the role of TS as a theranostic NSCLC marker mediating survival, chemo-resistance and EMT, and identifies a regulatory network that could be exploited to target EMT-driven NSCLC.

overall_design: Gene epxression analysis by RNAseq in Lung Adenocarcinma Cell Lines A549 and Calu1 with knock down of Thymidylate Synthase and scrambled pLKO control.

first: Paolo

last: Ceppi

first: Ram

last: Natesan


title: T cell receptor is required for differentiation but not maintenance of intestinal CD4+ intraepithelial lymphocytes

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: The gut epithelium is populated by intraepithelial lymphocytes (IELs), a heterogeneous T cell population with cytotoxic and regulatory properties, which can be imprinted on CD4+ T cells at the epithelium. However, the role of the T cell receptor (TCR) in this process remains unclear. Single-cell transcriptomic analyses revealed distinct clonal expansions between cell states, with CD4-IELs being one of the least diverse populations. Conditional deletion of TCR on differentiating CD4+ T cells or of MHCII on intestinal epithelial cells prevented CD4-IEL differentiation. However, TCR ablation on differentiated CD4-IELs, or long-term cognate antigen withdraw, did not affect their maintenance. TCR re-engaging of antigen-specific CD4-IELs during Listeria monocytogenes infection did not alter their state but correlated with reduced bacteria invasion. Thus, local antigen recognition is an essential signal for differentiation of T cells at the epithelium but differentiated CD4-IELs are able to preserve an effector program in the absence of TCR signaling.

overall_design: Full transcriptome profiles  of bulk populations  and single cells  of intraepithelial lymphocytes (IELs) with TCR repertoire of single cells.

first: Angelina

last: Bilate

first: Mariya

last: London

first: Tiago Bruno

middle: R

first: Luka

last: Mesin

first: Juliana

last: Bortolatto

first: Suppawat

last: Kongthong

first: Audrey

last: Harnagel

first: Gabriel

last: Victora

first: Daniel

last: Mucida


title: Next Generation Sequencing of BAL cells from cadmium exposed mice

city: Birmingham

first: Jennifer

middle: L

last: Larson-Casey

state: AL

address: 1918 University Blvd 710 MCLM

institute: University of Alabama at Birmingham

summary: To understand the bioenergetics in cadmium-exposed macrophages, RNA sequencing (RNA-seq) was performed in lung macrophages isolated from vehicle- and cadmium-exposed mice.

overall_design: 8- to 12-week-old male and female C57/BL6 mice were intratracheally administered 100 ng/kg of CdCl2 or saline, as a vehicle control, after being anesthetized with 3% isoflurane using a precision Fortec vaporizer. Mice were euthanized 7 days after exposure and BAL was performed.

first: David

last: Crossman


title: Dual-Sequencing of dendritic cells infected with cytomegalovirus

city: Jena

first: Bastian

last: Seelbinder

address: Adolf-Reichwein-Straße 23

department: Systems Biology and Bioinformatics

institute: Hans-Knoell-Institute Jena

summary: Dendritic cells were infected with human cytomegalovirus (CMV) for 4, 8 or 12 hours. Single-cultures of dendritic cells serve as controls. RNA was isolated and processed for next generation sequencing.

sample_organism:
Homo sapiens
Human betaherpesvirus 5

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: 7 samples, no replicates, DC cells grown for 4h, 8h and 12h with and without CMV

first: Julia

last: Wallstabe

first: Jürgen

last: Löffler

first: Sascha

last: Schäuble


title: Autophagy mitigates ethanol-induced mitochondrial dysfunction and oxidative stress in esophageal keratinocytes

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

summary: The current study is focused on elucidating the effect of acute alcohol challenge on esophageal epithelial cells. We employed in vivo mouse models, ex-vivo 3D-organoids and 2D cell culture to answer this question. RNA-Seq was employed to identify acute alcohol-induced transcriptional changes in human esophageal epithelial cells in-vitro.  Acute-alcohol promoted strong mitochondrial damage resulting in bioenergenitic imbalance in esophageal epithelial cells. Autophagy was activated potentially via the AMPK-mTORC1 pathway to promtoe the clearance of damaged mitochondria.

overall_design: Transcriptional analysis of 3 independent human esophageal epithelial cells lines exposed to 0% and 2% alcohol (ethanol)

first: Hiroshi

last: Nakagawa

first: Prasanna

last: Chandramouleeswaran


title: Single cell RNA sequencing analysis of alveolar epithelial type II cells (AE2) isolated from young and old mice with and without lung injury

city: Hannover

first: Christina

last: Brandenberger

address: Carl-Neuberg-Str. 1

department: Institute of Functional and Applied Anatomy

institute: Hannover Medical School

summary: The objective of the analysis was to investiage how AE2 cell function is effected by age and lung injury at single cell transcriptomic level

overall_design: For single cell RNA sequencing analysis, young and old mice treated with saline or LPS were sacrificed 24 h later. The lungs were digested and a cell suspension was generated. For the current experiment, a cell hashing based experimental approach was used to demultiplex pooled cell samples. This approach uses oligo-tagged antibodies to label cells prior to mixing. Accordingly, the harvested lung cell suspension was incubated with biotinylated EpCAM antibody (BioLegend #118203) for 30 min on ice, followed by washing steps and 30 min incubation with oligo barcoded PE streptavidin TotalSeq™-A antibodies (BioLegend #405251, 405253, 405255, 405257) as described in the supplier’s manual. For each experimental group (young control, young 24 h LPS, old control, old 24 h LPS) a different oligo barcoded antibody was used. The cells were then sorted for EpCAM positive cells. DAPI was used to detect and exclude dead cells. The harvested cells were counted and the four experimental groups were pooled in equal number for scRNA-seq analysis. The pooled samples were loaded on one 10x Genomics lane. The whole experiment was performed twice in the form of an independent biological replica experiment.

first: Oliver

last: Dittrich-Breiholz

first: Torsten

last: Glomb


title: A proprietary GMP human platelet lysate for the expansion of dermal fibroblasts for clinical applications

city: Sevilla

first: Luis

last: Lopez Navas

state: Sevilla

address: c/ Americo Vespucio, 15, Ed. S-2

department: Preclinical Research

institute: Red Andaluza de diseño y traslación de Terapias Avanzadas

summary: Recent years have witnessed the introduction of ex vivo expanded dermal fibroblasts for several cell therapy and tissue-engineering applications, including the treatment of facial scars and burns, representing a promising cell type for regenerative medicine. We tested different in-house produced human platelet lysate (HPL) solutions against fetal bovine serum as supplements for in vitro fibroblast expansion by comparing cell yield, molecular marker expression, extracellular matrix (ECM) generation, genomic stability and global gene expression. Our in-house produced HPL supported fibroblast growth at levels similar to those for FBS and commercial HPL products and was superior to AB human serum. Cells grown in HPL maintained a fibroblast phenotype (VIM+, CD44+, CD13+, CD90+), ECM generation capacity (FN+, COL1+) and a normal karyotype, although gene expression profiling revealed changes related to cell metabolism, adhesion and cellular senescence. The HPL manufacturing process was validated within a GMP compliant system and the solution was stable at -80ºC and -20ºC for 2 years. Dermal fibroblasts expanded in vitro with HPL maintain a normal karyotype and expression of fibroblast markers, with only minor changes in their global gene expression profile. Our in-house produced GMP-HPL is an efficient, safe and economical cell culture supplement that can help increase the healthcare activity of blood transfusion centers through the re-use of transfusional plasma and platelets approaching their expiration date. Currently, our HPL solution is approved by the Spanish Agency of Medicines and Medical Devices and is being used in the manufacture of cell therapy products.

overall_design: 9 total samples were analyzed. Fibroblasts were cultured for 8 passages either with 10% Fetal Bovine Serum (FBS), 5% or 15% in-house HPL2 solution (n=3, respectively) as culture supplement. Biological replicates are included. Differentially expressed genes (DEGs) were obtained applying a threshold of ± 2 fold change as well as a false discovery rate p-value less than or equal to 0.05 (FDR-P val ≤ 0.05).

first: Mónica

last: Santos-González

last: Lopez-Navas


title: Human iPSC-derived neuronal cells from CTBP1-mutated patients reveal altered expression of neurodevelopmental gene networks

status: Public on Sep 30 2020

city: Saint Louis

first: Govindaswamy

last: Chinnadurai

state: MO

address: 1100 S. Grand Blvd.

department: Molecular Microbiology and Immunology

institute: Saint Louis University

summary: A recurrent de novo mutation in the transcriptional corepressor CTBP1 is associated with neurodevelopmental disabilities in children (Beck et al., 2016; Beck et al., 2019; Sommerville et al., 2017).  All reported patients harbor a single recurrent de novo heterozygous missense mutation (p.R342W) within the cofactor recruitment domain of CtBP1.  To investigate the transcriptional activity of the pathogenic CTBP1 mutant allele in physiologically relevant human cell models, we generated induced pluripotent stem cells (iPSC) from the dermal fibroblasts derived from patients and normal donors.  The transcriptional profiles of the iPSC-derived ‘early’ neurons were determined by RNA-sequencing.  Comparison of the RNA-seq data of the neurons from patients and normal donors revealed down regulation of gene networks involved in neurodevelopment, synaptic adhesion and anti-viral (interferon) response.  Consistent with the altered gene expression patterns, the patient-derived neurons exhibited morphological and electrophysiological abnormalities, and susceptibility to viral infection.  Taken together, our studies using iPSC-derived neuron models provide novel insights into the pathological activities of the CTBP1 p.R342W allele.

overall_design: Total RNA samples were isolated from iPSC-derived neurons of two healthy donors and two CTBP1-mutated patients and analyzed by high- throughput RNA sequencing.

first: G

first: S

last: Vijayalingam

first: Uthayashanker

last: Ezekiel


title: Development of a DNA methylation-based diagnostic signature to distinguish benign oncocytoma from renal cell carcinoma

city: Manchester

first: Caroline

last: Dive

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road

institute: Cancer Research UK Manchester Institute

type: Methylation profiling by genome tiling array

summary: We profiled DNA methylation in fresh-frozen oncocytoma and chRCC tumors and tumor-adjacent adjacent normal tissue to identify a signature of differentially methylated CpG sites that robustly distinguish oncocytoma from chRCC. DNA methylation profiles were generated for renal oncocytomas (n=12), primary kidney chromophobes (chRCC) (n=8) and primary kidney clear cell carcinomas (ccRCC) (n=2). Also profiled were three oncocytic neoplasms of unclear pathological diagnosis, including two masses described as hybrid oncocytic/chromophobe type (n=2), and one mass described as hybrid oncocytic renal neoplasm. Also profiled were histologically normal adjacent kidney parenchyma tissue (NKP) from a subset of these patients, including NKP from oncocytoma (n=7), chRCC (n=5), ccRCC (n=1), hybrid oncocytic/chromophobe type (n=1), and hybrid oncocytic renal neoplasm (n=1) bearing kidneys (combined n=15 NKP).

overall_design: DNA methylation arrays were used to profile genome-wide DNA methylation of renal neoplasms and normal tumor-adjacent tissues.

first: Olivier

last: Gevaert

first: John

middle: T

last: Leppert


title: Transcriptional profiling by RNA-seq of A. baumannii AB5075 wild-type, abaI::Tn26 and ∆abaM::Tn26 QS mutants.

city: Nottingham

first: Mario

last: López-Martín

address: Centre for Biomolecular Sciences, Biodiscovery, Institute

department: School of Life Sciences

institute: University of Nottingham

summary: Acinetobacter baumannii possesses a single divergent luxR/luxI-type quorum sensing (QS) locus named abaR/abaI. This locus also contains a third gene located between abaR and abaI which we term abaM that codes for an uncharacterized member of the RsaM protein family known to regulate N-acylhomoserine lactone (AHL) dependent QS and the expression of diverse genes in other β- and γ-proteobacteria. However, abaM has never been charatcerized in Acinetobacter baumannii, and the studies about the regulon of abaI are limited. In this study we revealed that AbaM differentially regulates at least 76 genes including the csu pilus operon and the acinetin 505 lipopeptide biosynthetic operon, that are involved in surface adherence, biofilm formation and virulence. A comparison of the wild type, abaM::Tn26 and abaI::Tn26 transcriptomes,  indicates that AbaM regulates ~21% of the QS regulon including the csu operon. Moreover, the QS genes (abaI/abaR) were among the most upregulated in the abaM::Tn26 mutant. Overall, our data suggests that abaM is a key regulator of Acinetobacter baumannii QS and gene expression.

overall_design: RNA-seq of total RNA extractions from A. baumannii AB5075 wild-type, ∆abaI and ∆abaM grown statically for 18h in low-salt LB at 37 ºC.

first: Paul

last: Williams

first: Morgan

last: Alexander


title: RNA-seq analysis of liver cancer patients' plasma

city: Beijing

first: Yumin

last: Zhu

address: Tsinghua University

department: Life Science

country: China

institute: Tsinghua University

summary: Liver cancer is one of the most lethal cancers worldwide. Liquid biopsy provides a noninvasive approach in detecting and monitoring cancer biomarkers to overcome current limitations associated with tissue biopsies, comprising the analysis of circulating tumor-derived material. In this study, we profiled plasma cell-free RNA-seq to identify recurrently dysregulated RNA biomarkers for the liquid biopsy of cancer.

overall_design: RNA-seq of plasma collected from liver cancer patients and healthy donors


title: lncRNA lncMGPF contributes to the genome-wide expression during myogenic differentiation

city: Wuhan

first: lvwei

middle: jian

last: jun

state: Hubei

address: shizishan street, NO.1

department: College of Animal science and technology

institute: huazhong agriculture university

summary: In order to screen the target genes regulated by lncMGPF,we transfected the siRNA to knock down lncMGPF gene (si-lncMGPF) and negative control siRNA (si-NC), induced cells to differentiate for 2 days.

overall_design: We further transfected the siRNA to knock down lncMGPF gene (si-lncMGPF) and induced cells to differentiate for 2 days. Then, we used microarray to analyze genome-wide gene changes after lncMGPF knockdown in C2C12 cells differentiated for 2 days.

first: B

last: Zuo

first: J

last: Jun


title: Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer [RNA-Seq]

first: Alec

last: Kimmelman

summary:
Purpose: Modeling microenvironmental influences in cell culture has been challenging, and technical limitations have hampered the comprehensive study of tumor-specific metabolism in vivo. To systematically interrogate metabolic vulnerabilities in PDA, we employed parallel CRISPR-Cas9 genetic screens using both in vivo and in vitro model systems.
Methods: 2D culture collected 3 days after plating grown in DMEM, 10%fbs, 1%p/s.  3D culture collected 3 days after plating grown in DMEM, 10%fbs, 1% p/s, 5% matrigel.  Tumors were collected from orthotopic injections collected at endpoint of experiment.
Results: This work revealed striking overlap of in vivo metabolic dependencies with those in vitro, validating that standard 2D culture conditions are a reliable system for studying cancer metabolism. Moreover, we identified that intercellular nutrient sharing can mask cancer dependencies in pooled screening experiments, highlighting an important limitation of this approach to study tumor metabolism
Conclusions: Our work demonstrates the power of genetic screening approaches to define the compendium of in vivo metabolic dependencies in PDA and highlights critical metabolic pathways that may have therapeutic utility.

first: Douglas

last: Biancur

first: Kevin

last: Kapner


title: Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer [CRISPR Screen]

summary:
Purpose: Modeling microenvironmental influences in cell culture has been challenging, and technical limitations have hampered the comprehensive study of tumor-specific metabolism in vivo. To systematically interrogate metabolic vulnerabilities in PDA, we employed parallel CRISPR-Cas9 genetic screens using both in vivo and in vitro model systems.
Methods: A custom library of lentiviral vectors encoding ~18,000 sgRNAs targeting ~3,000 mouse metabolic genes and performed CRISPR-Cas9 screens using a C/57BL6 (B6) mouse pancreatic cancer cell line derived from a KrasG12D-driven autochthonous PDA model. After transduction and selection, parallel screens were performed by in vitro passage or tumor implantation subcutaneously into the flanks of syngeneic hosts. Genomic DNA was then harvaested in vitro after 7 passages (21 days in culture) and in vivo 21 days after implantation.
Results: This work revealed striking overlap of in vivo metabolic dependencies with those in vitro, validating that standard 2D culture conditions are a reliable system for studying cancer metabolism. Moreover, we identified that intercellular nutrient sharing can mask cancer dependencies in pooled screening experiments, highlighting an important limitation of this approach to study tumor metabolism
Conclusions:Our work demonstrates the power of genetic screening approaches to define the compendium of in vivo metabolic dependencies in PDA and highlights critical metabolic pathways that may have therapeutic utility.

overall_design: 42 Total samples. 3 Total conditions. 3 sets of replicates for corresponding screen.


title: RNA sequencing of tomato seed tissues matured in different environments

status: Public on Sep 29 2020

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

institute: INRAE

summary: During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. The maternal environment during maturation can influence seed quality. RNA-seq analyses of the embryo and the endosperm of seed matured ex planta under standard or stressful condition (high temperature and/or dim light) will underly how light and temperature and a combination of both have an impact on the molecular mechanisms governing seed quality at harvest.

overall_design: Fruits at breaker stage (i.e 63 DAF) were collected from mother plants grown in greenhouse and transfered to growth chambers under 4 different environments: standard temperature + high light; standard temperature + dim light; high temperature + high light or high temperature + dim light. Three or four replicates of 10 fresh tomato seeds were harvested at mature stage for each maturation environment. RNA-seq data of isolated seed tissues was obtained for each maturation condition

first: Elise

last: Bizouerne

last: Leprince


title: The effect of DZNeP-exposure on activation of hepatic stellate cells analyzed by RNA-sequencing.

city: Shanghai

first: Yan

last: Jiang

address: Yixueyuan Rd. 138

department: Institutes of biomedical sciences

institute: Fudan Universtiy

summary: DZNeP is the inhibitor of Ezh2 and paly negative roles on activation of hepatic stellate cells. We used RNA sequencing to identify the effective genes of DZNeP in rat HSCs. The primary rat HSCs was isolated and purified from SD rats, and cultured in DMEM culture medium with 20% FBS for 24 hours. Then the rat HSCs was administrated with DZNeP at 1μM concentration, or with similar volume of DMSO as negative control. 48 hour later, the cells were harvested and cell lysis was subjected to RNA-sequencing. This study identified that DZNeP regulated HSC activation through upregulating the expression of many key anti-fibrotic factors including Tgfβ signaling inhibitor: Bambi; cell cycle inhibitors: p21, Gadd45s; and immunomodulatory cytokine IL10.

overall_design: Analysis of gene expression profiles using RNA-seq in rat primary HSCs.

first: Y

last: Zhang

first: Haijian

last: Wang


title: Targeting OCA-B/Pou2af1 blocks type-1 diabetes and reduces infiltration of activated, islet-reactive T cells

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

summary: The transcriptional coregulator OCA-B is induced in stimulated naïve CD4+ T cells, where docks with transcription factor Oct1 to regulate genes such as Il2 and Ifng. OCA-B regulates its targets in cases of repeated antigen exposure, a necessary feature of autoimmunity. Polymorphisms in binding sites for Oct1, and by extension OCA-B, as associated with multiple forms of autoimmunity including autoimmune (type-1) diabetes. We hypothesized that T cell-specific OCA-B deletion would protect mice from type-1 diabetes, and that pharmacologic OCA-B inhibition would provide similar protection. We developed an Ocab (Pou2af1) conditional allele and backcrossed it onto a diabetes-prone NOD/ShiLtJ strain background. T cell-specific OCA-B loss protected mice from spontaneous T1D. To clarify the mechanism, we profiled leukocytes from prediabetic islets by single-cell RNA sequencing and T cell receptor clonotype analysis.

overall_design: Leukocytes were isolated from pancreata or pancreatic lymph nodes pre-diabetic week-old females of Ocabfl/fl (control) and Ocabfl/fl.CD4Cre.

first: Heejoo

last: Kim

first: Jelena

last: Perovanovic


title: Distinct metabolic programs control the effector fate of γδ T cell subsets and their activities in the tumour microenvironment

status: Public on Sep 28 2020

city: London

first: Daniel

last: Pennington

address: 4 Newark Street

institute: Blizard Institute

summary: Metabolic programming controls immune cell lineages and functions, but little is known about γδ T cell metabolism. Here we found that γδ T cell subsets making either IFN-γ or IL-17 have intrinsically distinct metabolic requirements. Whereas IFN-γ+ γδ T cells were almost exclusively dependent on glycolysis, IL-17+ γδ T cells strongly engaged oxidative metabolism, with increased mitochondrial mass and activity. These distinct metabolic signatures were surprisingly imprinted early during γδ thymic development, and were stably maintained in the periphery and within tumours.

overall_design: Tetramethylrhodamine, ethyl ester (TMRE)-labelled γδ T cells, from fetal C57BL/6 thymic lobes cultured for 2 days, were sorted into TMREhi and TMRElo CD24+ γδ T cells.

first: Nital

last: Sumaria


title: Biological significance of CDYL in  endometrial receptivity

first: Xiaowei

last: Zhou

email: 453311049@qq.com, zpxiaxy@shsmu.edu.cn

address: 197 Ruijin 2nd Road

institute: School of Medicine, Shanghai Jiao Tong University

summary: Impaired endometrial receptivity is one of the major causes of recurrent implantation failure (RIF), and the underlying molecular mechanism has not been fully elucidated. We demonstrated that Chromodomain Y like (CDYL) was highly expressed in the endometrium at mid-secretory phase during the normal menstrual cycles. However, the expression of CDYL was down-regulated in the endometrial tissues obtained from women with RIF, consistently with the protein level of LIF, which is the marker of endometrial receptivity. Knockdown of CDYL significantly decreased the cell migration of human endometrial Ishikawa cells and primary endometrial cells. Genomic analyses revealed that CDYL gene silencing resulted in decreased expression of many genes associated with cytoskeleton and migration regulation.

overall_design: Gene expression profile of CDYL silencing by CDYL shRNA compared with control shRNA in Ishikawa cells


title: NSP4 in myeloid progenitors

status: Public on Sep 26 2020

city: South San Francisco

first: Luz

last: Orozco

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech Inc.

summary: Determine if there is NSP4-dependent expression of solute carriers responsible for loading histamine into secretory granules.

overall_design: Analyze sorted myeloid progenitors from WT and NSP4 KO mice.

first: Jason

last: Hackney

first: Yanli

last: Hou


title: Dual-RNA sequencing of dendritic cells challenged with Aspergillus fumigatus

first: Bastian

last: Seelbinder

summary: Dendritic cells and A. fumigatus were co-cultured with two different MOIs (1 or 0,5) for 2, 4 or 6 hours. Single-cultures of dendritic cells and A. fumigatus serve as controls. RNA was isolated and processed for next generation sequencing.

sample_organism:
Homo sapiens
Aspergillus fumigatus

platform_organism:
Homo sapiens
Aspergillus fumigatus

overall_design: 12 samples, varying degrees MOI and treatment duration, no replicates

last: Wallstabe

first: Jürgen

last: Löffler

first: Jörg

last: Linde

first: Thomas

last: Wolf

first: Pauline

last: Putzmann


title: Single-cell mapping of progressive fetal-to-adult transition in human hematopoiesis. [CD4 & CD8 single-cell RNAseq]

status: Public on Sep 25 2020

city: San Francisco

last: Bunis

state: California

address: 35 Medical Center Way, Regeneration Medicine Building 903B

institute: University of California, San Francisco

summary: Whereas the human fetal immune system is poised to generate immune tolerance and suppress inflammation in utero, an adult-like immune system emerges to orchestrate anti-pathogen immune responses in post-natal life. It has been posited that cells of the adult immune system arise as a discrete ontological “layer” of hematopoietic stem-progenitor cells (HSPCs) and their progeny; evidence supporting this model in humans has, however, been inconclusive.  Here, we combine bulk and single-cell transcriptional profiling of lymphoid, myeloid, and HSPCs from fetal, perinatal, and adult developmental stages to demonstrate that the fetal-to-adult transition occurs progressively along a continuum of maturity—with a substantial degree of interindividual variation at the time of birth—rather than via a transition between discrete waves. These findings have important implications in the design of strategies for prophylaxis against infection in the newborn, and for the use of umbilical cord blood (UCB) in the setting of transplantation. Naïve CD4 and CD8 T cells, and CD34+ hematopoietic stem and progenitor cells (HSPCs) were isolated from human samples of three different groups: Fetal (18-23 gestational weeks), full-term newborn (37+ gestational weeks at birth), and adults age 23 to 53. For each group, five independent donors were analyzed, but not all cell types could be sequenced for every patient.

overall_design:
Single-cell RNAseq of FACSorted naïve CD4 (CD4+CD45RA+CD27+CD25-) and CD8 (+CD45RA+CD27+CCR7+CD95-) T cells from human samples: Fetal (18-23 gestational weeks) spleen, full-term newborn (37+ gestational weeks at birth) umbilical cord blood, and adult (ages 23 to 53) peripheral blood. CD34+ HSPCs were also sorted from these same donors for single-cell RNAseq, and a separate set of naive CD4 T cells were also sorted from these same donors for bulk RNAseq.

Analysis code:
https://github.com/dtm2451/ProgressiveHematopoiesis
Figures:
https://figshare.com/projects/Single-cell_mapping_of_progressive_fetal-to-adult_transition_in_human_naive_T_cells/76143

>>>Raw data are not available due to patient privacy concerns<<<

first: Yelena

last: Bronevetsky

first: Elisabeth

last: Krow-Lucal

first: Nirav

last: Bhakta

first: Charles

middle: C

first: Srilaxmi

last: Nerella

first: Norman

last: Jones

first: Ventura

middle: F

last: Mendoza

first: Yvonne

last: Bryson

first: James

last: Gern

first: Rachel

last: Rutishauser

first: Chun

last: Ye

first: Marina

last: Sirota

first: Joseph

last: McCune

first: Trevor

last: Burt


title: Single-cell mapping of progressive fetal-to-adult transition in human hematopoiesis. [CD4 - bulk RNAseq]

first: Daniel

overall_design:
Bulk RNAseq of 50,000 FACSorted naïve CD4 (CD4+CD45RA+CD27+CD25-) T cells from human samples: Fetal (18-23 gestational weeks) spleen, full-term newborn (37+ gestational weeks at birth) umbilical cord blood, and adult (ages 23 to 53) peripheral blood. A separate set of naive CD4 T cells, as well as naive CD8 T cells and CD34+ HSPCs were also sorted from the same set of donors for single-cell RNAseq.

Analysis code:
https://github.com/dtm2451/ProgressiveHematopoiesis
Figures:
https://figshare.com/projects/Single-cell_mapping_of_progressive_fetal-to-adult_transition_in_human_naive_T_cells/76143

>>>Raw data are not available due to patient privacy concerns<<<

last: Kim

middle: E


title: Single-cell mapping of progressive fetal-to-adult transition in human hematopoiesis [HSPCs single-cell RNAseq]

overall_design:
Single-cell RNAseq of FACSorted hematopoietic stem and progenitor cells (HSPCs; CD34+CD45mid) from human samples: Fetal (18-23 gestational weeks) bone marrow, full-term newborn (37+ gestational weeks at birth) umbilical cord blood, and adult (ages 23 to 53) bone marrow. CD4 and CD8 naive T cells were also sorted from these same donors for RNAseq.

Analysis code:
https://github.com/dtm2451/ProgressiveHematopoiesis
Figures:
https://figshare.com/projects/Single-cell_mapping_of_progressive_fetal-to-adult_transition_in_human_naive_T_cells/76143

>>>Raw data are not available due to patient privacy concerns<<<


title: Microarray comparison of human fetal and adult peripheral blood naïve T cells

summary: Whereas the human fetal immune system is poised to generate immune tolerance and suppress inflammation in utero, an adult-like immune system emerges to orchestrate anti-pathogen immune responses in post-natal life. It has been posited that cells of the adult immune system arise as a discrete ontological “layer” of hematopoietic stem-progenitor cells (HSPCs) and their progeny; evidence supporting this model in humans has, however, been inconclusive.  Here, we combine bulk and single-cell transcriptional profiling of lymphoid, myeloid, and HSPCs from fetal, perinatal, and adult developmental stages to demonstrate that the fetal-to-adult transition occurs progressively along a continuum of maturity—with a substantial degree of interindividual variation at the time of birth—rather than via a transition between discrete waves. These findings have important implications in the design of strategies for prophylaxis against infection in the newborn, and for the use of umbilical cord blood (UCB) in the setting of transplantation.

overall_design: gene expression profiling of fetal and adult CD4 T cells and monocytes.


title: Global Genome Conformational Programming during Neuronal Development by CTCF and nFGFR1 - The Genome Archipelago Model

city: Buffalo

first: Brandon

last: Decker

state: NY

address: 955 Main St

department: Pathology and Anatomical Sciences

institute: University at Buffalo

summary: This study advances a topologically integrated genome archipelago model that undergoes extensive structural transformations through the formation of nFGFR1-associated Topologically Associated Domains (TADs), replacing CTCF TADs, during the development of the stem cells to neurons. The makeover of the TAD islands serves to recruit distinct ontogenic programs.

overall_design: Examination of chromatin structure alongside previous nFGFR1 binding, and gene expression changes (GSE65698) in mouse stem cells and in neurons. Two biological replicates of HiC, FGFR1 HiChIP, and CTCF HiChIP were completed in both ESC and NCC.

first: Michal

last: Liput

first: Hussam

last: Abdellatif

first: Donald

last: Yergeau

first: Yongho

last: Bae

first: Josep

last: Jornet

first: Ewa

middle: K

last: Stachowiak


title: In silico APC/C substrate discovery reveals cell-cycle-dependent degradation of UHRF1 and other chromatin regulators

status: Public on Sep 23 2020

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

summary: E3 ubiquitin ligases are the final regulatory enzymes in the ubiquitin cascade, responsible for choosing substrates for ubiquitylation. Despite their central role in governing ubiquitin pathways, technical challenges have precluded development of simple and robust methods to systematically map their substrates. The Anaphase Promoting Complex/Cyclosome (APC/C) is an E3 ligase and master regulator of cell cycle progression and genome maintenance. Here, we develop a sensitive and specific computational strategy to predict APC/C substrates, leveraging orthogonal features among known targets. Interestingly, chromatin regulatory proteins are enriched among putative substrates and we validate several here. We reveal detailed ubiquitylation mechanisms of a key reader and writer of histone modifications, UHRF1, and show that its degradation regulates cell cycle and D methylation maintenance. Our results uncover mechanisms underlying the coordination between cell cycle and the chromatin landscape, and suggest an extensive, post-translational crosstalk with far-reaching consequences in normal cell physiology and disease.

overall_design: Genomic D was isolated from Parental U2OS cells and U2OS cells overexpressing either GFP-UHRF1WT or GFP-UHRF1KEN/AAA. All samples groups (total of 9 samples all together) were processed in biological triplicate, and the Parental U2OS cells served as the control.

first: Jennifer

last: Franks

first: Raquel

last: Martinez-Chacin

first: Xianxi

last: Wang

first: Rochelle

last: Tiedemann

first: Thomas

last: Bonacci

first: Rajarshi

last: Choudhury

first: Derek

last: Bolhuis

first: Jeffrey

last: Damrauer

first: Feng

last: Yan

last: Harrison

first: Michael

middle: B

last: Major

first: Katherine

last: Hoadley

first: Aussie

last: Suzuki

first: Nicholas

middle: G

last: Brown

middle: J

last: Emanuele