title: Absence of KpsM (Slr0977) impairs the secretion of extracellular polymeric substances (EPS) and impacts carbon fluxes in Synechocystis sp. PCC 6803

status: Public on Jan 20 2021

city: Porto

first: Marina

middle: Patrícia

last: Santos

state: Porto

address: R. Alfredo Allen 208

department: Host Pathogen Interaction

country: Portugal

institute: i3S - Instituto de Investigação e Inovação em Saúde

summary:
Purpose: To obtain an overview of the metabolic changes associated to the absence of KpsM in  Synechocystis, in particular on carbon-related metabolic pathways
Methods: The trancriptomes of Synechocystis wild type and kpsM mutant were analyzed by RNA sequencing, using three biological replicates. Cultures were grown until reaching an OD730nm of 1.5. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina®. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina). Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. Paired-end clean reads were mapped to the reference genome using HISAT2 software.HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Results: Approximately 700 genes (out of the 3636 identified and  215 quantified, representing a coverage of 85,12%) were significantly differentially expressed (P  216 value < 0.05) in the kpsM mutant compared to the wild type. Of those, 406 were down217  regulated, while 297 were up-regulated.
Conclusions: Overall, our transcriptomic  data indicates alterations in the mechanisms of  energy production and conversion in the kpsM mutant compared to the wild type. The approach resulted in the identification of altered levels of transcripts belonging  to a variety of functional categories and highlighting a number of key metabolic processes affected  by the disruption of kpsM, namely photosynthesis, oxidative phosphorylation and carbon  metabolism.

overall_design: mRNA profiles of Synehcocystis wild type (wt) and kpsM mutant

first: Paula

last: Tamagnini


title: Comparison of gene expression with immunofluorescent chromosome banding and ChIP-seq of histone modifications  in cell-cycle sorted lymphoblastoid and HeLa cells [array]

status: Public on Jan 22 2021

city: Birmingham

first: John

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary:
Metaphase chromosome staining was used to provide a high level overview of the pattern of histone modifications (H3K27ac, H3K27me3 and H3K4me3) at a single cell level in human lymphoblastoidand HeLa cells. A higher resolution view was achieved using ChIP-seq in cell-cycle sorted cells.
These epigenomic haplotypes were related to various genomic features including gene and CpG island density as well as gene expression.

overall_design: A 6 array study using RNA extracted from 3 separate cultures each of human lymphoblastoid cells and HeLa cells

middle: A

first: Bryan

middle: M

last: Turner


title: DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS [4C-Seq]

status: Public on Jan 23 2021

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

summary: During tetrapod limb development, the HOXA13 and HOXD13 transcription factors are critical for the emergence and organization of the autopods, the most distal aspect where digits will develop. Since previous work had suggested that the Dbx2 gene is a target of these factors, we set up to analyze in detail this potential regulatory interaction. We used a chromatin conformation capture approach (4Cseq) to characterize the regulatory domain and interactions of the transcription factor Dbx2 and of its neighboring genes Nell2 and Ano6 in distal and/ or proximal forelimbs of E12 mouse embryos. In particular, we analyzed their interaction with distal limb specific regulatory elements (DLE1 and DLE2) by the analysis of H2K27ac coverages (Beccari et al 2016) and Hoxa13/Hoxd13 binding (Sheth R et al 2016). We report that Dbx2, Nell2 and Ano6 are expressed in distal limb buds and are controlled by the same enhancers located close to Dbx2. As the Nell2 and Ano6 genes are localized into two different topologically associating domains (TADs) flanking the Dbx2 locus, we conclude that these enhancers can overcome TAD boundaries in either direction, to co-regulate a set of genes located in distinct chromatin domains.

overall_design: 4C seq analysis of the interaction profiles of the Dbx2, Nell2 and Ano6 promoters in E12 embryonic limbs and of the distal limb specific regulatory elements DLE1 and DLE2

first: Leonardo

last: Beccari

first: Eddie

last: Rodriguez-Carballo

first: Gabriel

last: Jaquier

first: Denis

last: Duboule


title: Global Absence and Targeting of Protective Immune States in Severe COVID-19

city: San Francisco

first: Arjun

middle: Arkal

last: Rao

state: CA

address: 505 Parnassus Ave, S-447

department: CoLabs

country: USA

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

summary: While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum.  Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease. Examination of the serum from severe patients demonstrates that they uniquely produce antibodies that functionally block the production of the mild disease-associated ISG-expressing cells, by engaging conserved signaling circuits that dampen cellular responses to interferons. Overzealous and auto-directed antibody responses pit the immune system against itself in many COVID-19 patients and this defines targets for immunotherapies to allow immune systems to provide viral defense.

overall_design: Examination of immune states in patients with and without SARS-Cov2, having mild and severe phenotypes versus healthy controls. (COVID- mild: 6 ; COVID- severe: 5 ;  COVID+ mild: 11 ; COVID+ severe: 10 ; healthy controls: 14). M/M = Mild/Moderate

first: Alexis

middle: J

last: Combes

first: Tristan

last: Courau

first: Nicholas

middle: F

last: Kuhn

first: Kenneth

middle: H

last: Hu

first: Arja

last: Ray

first: Matthew

last: Krummel


title: Genome-wide mapping of transcription initiation in the asexual stages of Toxoplasma gondii

city: Cambridge

first: Benedikt

last: Markus

state: MA

address: 455 Main Street

institute: Whitehead Institute

summary: The lack of a comprehensive map of transcription start sites in Toxoplasma gondii has impeded advances in decrypting the molecular mechanisms underlying the regulation of gene expression. Genome-wide approaches for mapping transcription initiation have been instrumental in defining the determinants of transcription initiation in a range of model eukaryotes. We used a protocol for 5′-end RNA sequencing, called RAMPAGE, to sequence the 5′-ends of capped mRNA from ME49 and RH tachyzoites, as well as from ME49 bradyzoites. This allowed us to generate maps of transcription initiation events at single-nucleotide resolution across the asexual stages of the parasite.

overall_design: Examination of the 5′-ends of capped mRNA in ME49 tachyzoites and alkaline-stress–induced bradyzoites, as well as in RH tachyzoites; each evaluated in two biological replicates.

first: Benjamin

middle: S

last: Waldman

first: Hernan

last: Lorenzi

first: Sebastian

last: Lourido


title: A cutting-edge approach unravels a novel role for CDK6 in leukemic progenitor cells

city: Vienna

first: Markus

last: Zojer

address: Josef-Baumanngasse

department: Institute for Pharmakology and Toxokology

country: Austria

institute: University of Veterinary Medicine

summary: CDK6 induces a complex transcriptional program to block p53 in hematopoietic cells.  CDK6 binds to the promoters of genes including p53-antagonists. Cells lacking CDK6 kinase function are required to mutate p53 to achieve a fully transformed immortalized state.

overall_design: Studies of molecular mechanisms of hematopoiesis and leukemogenesis are hampered by the unavailability of progenitor cell lines that accurately mimic the situation in vivo. We now report a robust method to generate and maintain LSK (lin-, Sca-1+, c-Kit+) cells which closely resemble MPP1 cells. HPCLSK reconstitute hematopoiesis in lethally irradiated recipient mice over more than eight months. Upon transformation with different oncogenes including BCR/ABL, FLT3-ITD or MLL-AF9 their leukemic counterparts maintain stem cell properties in vitro and recapitulate leukemia formation in vivo. The method to generate HPCLSK can be applied to transgenic mice and we illustrate it for CDK6-deficient animals. Upon BCR/ABLp210 transformation, Cdk6-/- HPCLSKs induce disease with a significantly enhanced latency and reduced incidence, showing the importance of CDK6 in leukemia formation. Studies of the CDK6 transcriptome in murine HPCLSK and human BCR/ABL+ cells have verified that certain pathways depend on CDK6 and have uncovered a novel CDK6-dependent signature, suggesting a role for CDK6 in leukemic progenitor cell homing. Loss of CDK6 may thus lead to a defect in homing. The HPCLSK system represents a unique tool for combined in vitro and in vivo studies and enables the production of large quantities of genetically modifiable hematopoietic or leukemic stem/progenitor cells.

first: Eszter

last: Doma

first: Isabella

last: Mayer

first: Karoline

last: Kollmann

first: Gerwin

last: Heller

first: Veronika

last: Sexl


title: Whole-genome DNA methylation analysis in hydrogen peroxide overproducing transgenic tobacco

status: Public on Jan 19 2021

city: Irapuato

first: Luis

middle: F.

last: Garcia-Ortega

state: Guanajuato

address: Km 9.6 Libramiento Norte

department: Department of Genetic Engineering

country: Mexico

institute: Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav)

type: Methylation profiling by high throughput sequencing

summary: We compared the level of methylated cytosines between hydrogen peroxide overproducing  (L8) and azygotes (L1) tobacco plants. We generated single base resolution maps of DNA methylation by whole genome bisulfite sequencing for 6-week-old plants from both transgenic tobacco lines. In total, we found 4,765 and 4,667 hyper and hypomethylated cytosines, respectively. These DmCs were associated with different regions of the genome, resulting in 1034 genes with at less one DMCs. 83 of these 1034 genes also showed differential expression. In this set of genes we found some correspond to proton transport, such as the V-type proton ATPase, and the ABC transporter. Our results corroborate that H2O2, as part of the balance of reactive oxygen species, plays a key role in the physiological adaptation of plants mediated by the methylation regulation.

overall_design: Examination of 2 different hydrogen peroxide overproducing transgenic tobacco lines, with  3 biological replicates by sample.

first: Ana

middle: L

last: Villagómez-Aranda

last: García-Ortega

first: Irineo

last: Torres-Pacheco

first: Ramón

middle: G

last: Guevara-González


title: The WDR5 WIN site interactome

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: The WIN site of WDR5 is a druggable pocket that is crucial for WDR5 protein function and carries therapeutic potential for treating cancer. This study evaluates the protein interactions affected by small molecule blockade of the WIN site of WDR5. We find that PDPK1 directly binds the WIN site of WDR5, and we investigate this newfound interaction through proteomic, biochemical, and genomic methods.

overall_design: RNA-seq was used to monitor transcriptional changes resulting from targeting PDPK1 and WDR5. Degradation systems for PDPK1 and WDR5 were generated in U2OS cells. RNA-seq was performed in these cell lines after treatments for 24 hours with DMSO vehicle control or 500 nM dTAG47 to induce degradation. In HEK293 cells the PDPK1 R3A point mutation was introduced using CRISPR genome editing and retroviral transductions. RNA-seq was performed in these engineered cells.

first: William

last: Tansey

first: Alissa

last: Guarnaccia

first: Qi

last: Liu


title: Gene expression under high salt stress for coconut

city: Wenchang City

first: Yaodong

last: Yang

state: Hainan

address: No. 496 Wenqing Av.

country: China

institute: Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences

summary: Coconut has a redundant gene pool to flourish under salt stress conditions; in particular the retention of genes resulting from the WGD p and the high genome size with a high TE content is a favourable context for gene innovation (e.g. sub or even neo-functionalization events) regarding abiotic stress tolerance. Four known pathways (ABA, ABA independent, ROS, Calcium/PLC and SOS) are present and expressed. Several strategies are in place: (moderate) high constitutive expression with a few number of gene candidates, moderate expression with a higher number of gene candidates, expression regulation of gene candidates.

overall_design: A Salt stress experiment was conducted on coconut palms seedlings, weekly irrigated on Murashige and Skoog (MS) culture medium and then enriched with 200 mM NaCl  (time 0). After four hours the osmotic stress reached the leaves but not yet the cation stress; after six days the osmotic stress was still present in the leaves and the ionic stress could be felt; at seven days, a second irrigation of MS with 200 mM was performed; after ten days the osmotic and cation stresses should be present in the leaves (after two irrigation there was a NaCl accumulation).Varieties used are Hainan Tall (DB) and Aromatic Coconut (XS).  Sampling at 0 time point were used as a control, samples were taken at 4hr, 6day and 10 days after 200 mM NaCl treatment. The experiments were done in three replications but one to two samples were missing for 10 days sampling.  A Salt stress experiment was conducted on coconut palms seedlings, weekly irrigated on Murashige and Skoog (MS) culture medium and then enriched with 200 mM NaCl  (time 0). After four hours the osmotic stress reached the leaves but not yet the cation stress; after six days the osmotic stress was still present in the leaves and the ionic stress could be felt; at seven days, a second irrigation of MS with 200 mM was performed; after ten days the osmotic and cation stresses should be present in the leaves (after two irrigation there was a NaCl accumulation).Varieties used are Hainan Tall (DB) and Aromatic Coconut (XS).Sampling at 0 time point were used as a control, samples were taken at 4hr, 6day and 10 days after 200 mM NaCl treatment. The experiments were done in three replications but one to two samples were missing for 10 days sampling.

first: Luc

last: Baudouin

first: Stéphanie

last: Bocs


title: DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS [ChIP-Seq reanalysis]

first: Lucille

last: Lopez-Delisle

type: Genome binding/occupancy profiling by high throughput sequencing

relation:
Reanalysis of: GSM2061120
Reanalysis of: GSM2061121
Reanalysis of: GSM2061122
Reanalysis of: GSM2061123
Reanalysis of: GSM2061125
Reanalysis of: GSM2061132
Reanalysis of: GSM2061133
Reanalysis of: GSM2151013
Reanalysis of: GSM2151014
SubSeries of: GSE161386

overall_design:
ChIP reanalysis of GSM2151013,GSM2151014 from Sheth et al. 2016 and GSE77900 from Becarri et al. 2016
Data processing
Adapter sequence and bad quality bases were removed with cutadapt (http://dx.doi.org/10.14806/ej.17.1.200) version 1.16 with options -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 30 -m 15 (-A beeing used only in PE datasets).
Reads were mapped with bowtie 2.3.5 (https://doi.org/10.1038/nmeth.1923) with default parameters on mm10. Alignment with a mapping quality below 30 was discarded with samtools view version 1.9 (https://doi.org/10.1093/bioinformatics/btp352, https://doi.org/10.1093/bioinformatics/btr509).
For Hoxa13 and Hoxd13, coverage and peak calling were computed by macs2 version 2.1.1.20160309 with options --call-summits -f BAMPE -B. Coverage was then normalized by the number of million fragments used in macs2 coverage. For histone marks, coverage and peak calling were computed by macs2 with options -f BAM --nomodel --extsize 200 --broad using the BAM of input in -c. The coverage was then normalized by the number of million tags used in macs2 coverage.
For DFL_E12_H3K27ac, the two replicates were averaged.
all scripts are available at  at https://github.com/lldelisle/scriptsForBeccariEtAl2021
Genome build: mm10
Files: bigwig: coverage normalized to the million tags/fragments used, narrowPeak/broadPeak: the peaks as called by macs2

first: Leonardo

last: Beccari

first: Denis

last: Duboule


title: DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS [HiC reanalysis]

type:
Other
Third-party reanalysis

relation:
Reanalysis of: GSM2533818
Reanalysis of: GSM2533819
Reanalysis of: GSM2533820
Reanalysis of: GSM2533821
Reanalysis of: GSM2533839
Reanalysis of: GSM2533840
Reanalysis of: GSM2533841
Reanalysis of: GSM2533842
Reanalysis of: GSM2713716
Reanalysis of: GSM3182470
Reanalysis of: GSM3182471
SubSeries of: GSE161386

sample_organism:
Gallus gallus
Mus musculus

overall_design:
HiC reanalysis of GSM2713716 from Rodriguez-Carballo et al. 2017, GSM2533818 to GSM2533821 and GSM2533839 to GSM2533842 from Bonev et al. 2017 and GSE115562 from Yakushiji-Kaminatsui et al.
Data Processing:
For capture Hi-C on chicken, data were processed independently using HiCUP v0.8.0 (https://doi.org/10.1126/science.1181369) on galGal6. Valid pairs were obtained using a custom python script.
For downstream analysis FL and HL valid pair files were concatenated.
For data from Bonev et al. 2017, valid pairs were downloaded from GSEXXXXX.
For all, the valid pairs of all studies were loaded in cool file using cooler version 0.8.10 (https://doi.org/10.1093/bioinformatics/btz540) using resolution of 5Kb, 20Kb or 40Kb. Matrices were balanced using cooler balance –cis-only. The TAD-separation score and the domains were obtained using hicFindTADs version 3.5.2 ( https://doi.org/10.1093/nar/gkaa220, https://doi.org/10.1093/nar/gky504, https://doi.org/10.1038/s41467-017-02525-w) with --minBoundaryDistance 100000 and either default parameters for the choice of window size or a fixed window size of 120Kb.
all scripts are available at  at https://github.com/lldelisle/scriptsForBeccariEtAl2021
Genome build: mm10, galGal6
Files: *validPairs*: valid pairs in juicebox format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2><frag2> <mapq1> <mapq2> with str = strand (0 for forward, anything else for reverse), pos = middle of the fragment.)  *.cool: matrices in cool format balanced using cooler  *domains.bed.gz: TAD coordinates (default were obtained with default parameters, 120kb were obtained with fixed window size of 120kb)


title: CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system

status: Public on Jan 18 2021

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

institute: University of Lausanne

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

overall_design: Refer to individual Series


title: Whole genome gene expression differences between a coumaphos resistant and susceptible population of Varroa destructor

status: Public on Jan 21 2021

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

summary: Coumaphos is an acaricide that is widely used to control Varroa mites in bee colonies. However, the extensive use of coumaphos against Varroa has resulted in the development of coumaphos resistant Varroa populations. In this study, the whole genome gene expression profile of 1) a coumaphos resistant V. destructor population (AN-CR) or 2) a coumaphos resistant V. destructor population pretreated with coumaphos (tAN-CR), was compared to the gene expression profile of a susceptible V. destructor population (ATH-S) using Illumina RNAseq.

overall_design: In total 12 RNA-seq samples (2 populations, ATH-S and AN-CR, with two different treatments for AN-CR; 4 biological replicates per population/treatment) from Varroa destructor, were generated. RNA was collected from adult V. destructor females. For each sample, Illumina mRNA-seq libraries were constructed and stranded, paired-end 125 bp RNA-seq Illumina reads were generated. The obtained reads were used to quantify gene expression in each sample.

first: Spyros

last: Vlogiannitis

first: Kostas

last: Mavridis

first: Simon

last: Snoeck

first: Thomas

last: Van Leeuwen

first: John

last: Vontas


title: CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [RNA-seq]

summary: CCCTC-binding factor (CTCF) is a conserved protein able to block communication between regulatory elements and gene promoters in flies and mammals. Here, we studied CTCF function in the Drosophila central nervous system (CNS) in which we find CTCF plays a vital role. RNA-sequencing of CNSs of CTCF[0] mutants that completely lack CTCF identified putative targets that are expressed in altered patterns. We find that CTCF recruits Centrosomal protein 190 kDa (Cp190) to CTCF's binding sites to co-regulate a substantial fraction of common genes that we find are also altered in CNSs of Cp190[KO] mutants carrying a CRISPR/Cas9-mediated deletion of the Cp190 open reading frame.

overall_design: Wildtype (WT, corresponding to the Drosophila w[1118] reference strain), CTCF[0] and Cp190[KO] mutant third instar larval central nervous systems were dissected and stranded mRNA-sequencing libraries were prepared in biological triplicate.

first: Anjali

last: Kaushal

first: Giriram

last: Mohana

first: Julien

last: Dorier

first: Isa

last: Özdemir

first: Arina

last: Omer

first: Michael

last: Taschner

first: Pascal

last: Cousin

first: Oleksandr

last: Dergai

first: Anastasiia

last: Semenova

first: Flavia

last: Marzetta

first: Christian

last: Iseli

first: Yossi

last: Eliaz

first: Nicolas

last: Guex

first: Erez

last: Aiden

first: Maria

middle: C


title: CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [Hi-C]

first: Maria Cristina

last: Gambetta

summary: CCCTC-binding factor (CTCF) is a conserved protein able to block communication between regulatory elements and gene promoters in flies and mammals. Here, we studied CTCF function in the Drosophila central nervous system (CNS) in which we find CTCF plays a vital role. Hi-C experiments on dissected larval CNSs of wildtype controls and CTCF[0] mutants that completely lack CTCF revealed that CTCF forms hundreds of physical boundaries in fly chromosomes.

overall_design: 60 wildtype (WT, corresponding to the Drosophila w[1118] reference strain) and CTCF[0] mutant third instar larval CNSs were dissected in biological triplicate and Hi-C libraries were prepared. Hi-C libraries were also prepared from single whole-bodied female flies that were WT or CTCF[0] mutant.


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type, Mga-/-, L3mbtl2-/- and Pcgf6-/- Embryonic Stem Cells Transcriptomes

city: Nanjing

first: Su

last: Ting

address: No. 12, Xuefu Road, Pukou District

department: Model Animal Research Center

institute: Nanjing University

summary: Purpose: The goals of this study are to compare Mga-/-, L3mbtl2-/-, Pcgf6-/- and Wild type embryonic stem cells transcriptome profiling (RNA-seq) and compare the target genes of Mga, L3mbtl2 and Pcgf6.

overall_design: mRNA profiles of Mga-/- and wild type embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina HiSeq4000. mRNA profiles of L3mbtl2-/- and Pcgf6-/- embryonic stem cells were generated by deep sequencing, in double, using Illumina HiSeq4000.

first: Ting

last: Su

first: Jinzhong

last: Qin


title: The clinical significance and potential molecular mechanism of PTTG1 in esophageal squamous cell carcinoma

status: Public on Jan 17 2021

city: Nanning

first: Fu

middle: hua

last: Zhou

state: Guangxi

address: No. 6 Shuangyong Road, Qingxiu District

department: Department of Cardio-Thoracic Surgery,

institute: The First Affiliated Hospital of Guangxi Medical University

summary: Esophageal squamous cell carcinoma (ESCC) is the major histological type of esophageal cancers worldwide. Transcription factor PTTG1 was seen highly expressed in a variety of tumors and was related to the degree of tumor differentiation, invasion, and metastasis. However, the clinical significance of PTTG1 had yet to be verified, and the mechanism of abnormal PTTG1 expression in ESCC was not clear. In this study, we collected eight pairs of ESCC samples and corresponding adjacent normal esophageal tissues for RNA-seq from eight ESCC patients underwent radical resection of EC. None of these ESCC patients received preoperative chemotherapy or radiotherapy.The tissue samples were stored at -80°C immediately after resection. These 8 patients included 6 males and 2 females with a median age of 60 years. RNA-seq was executed by Wuhan Seqhealth Technology Co.LTD. TRIzol reagent (Invitrogen, Carlsbad, CA, USA) was applied to extract and prepare total RNA from tumors and paired adjacent non-ESCC tissues. A total amount of 3 μg RNA per sample was used as initial material for the RNA sample preparations. Nanodrop™ 1000 spectrophotometer was applied to examined RNA purity. RNA concentration was determined using a Qubit® 3.0 Fluorometer. RNA integrity was determined using an RNA Nano 6000 Assay Kit and a Bioanalyzer 2100 system. Afterward, the sequencing libraries were established using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina base on manufacturer’s protocols. The 200 Illumina HiSeq X Ten platform was used to sequence the libraries. RNA sequencing reads were aligned to the reference of homo_sapiens.GRCh38. In the current study, we obtained the data on log2 (x + 0.001) conversion level 3 and reported RNA-seq data in transcripts per kilobase million (TPM).

overall_design: mRNA profiles of ESCC samples and corresponding adjacent normal esophageal tissues.

first: Hua

first: Shang

middle: W

last: Chen

first: Han

last: Zhang

first: Rong

middle: Q

last: He

first: Zhi

last: Huang

first: Yi

last: Dang

first: Gang


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Max-/- Embryonic Stem Cells Transcriptomes

summary: Purpose: The goals of this study are to compare Max-/- with wild type embryonic stem cells transcriptome profiling (RNA-seq) to evaluate the target genes regulated by Max.

overall_design: mRNA profiles of wild type (WT) and Max-/- embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina Novaseq6000.

first: JinZhong


title: The effect on the transcriptome by inhibition of mitochondrial function by metformin in intestinal cells

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

institute: University of Cambridge

summary: We purified mouse duodenal cells from organoids derived from two different transgenic mouse lines (GIP-Cre tdRFP, SST-Cre tdRFP), and identified transcripts enriched in metformin-treated cells.

overall_design: Comparative transcriptomic study of 4x cell populations by bulk RNAseq, with 3x biological replicates after vehicle control, and 3x biological replicates after 1mM metformin treatment.

first: Ming

last: Yang


title: Gene expression of mouse gonadotropin-releasing hormone neurons from male and female mice

city: Budapest

first: Norbert

last: Solymosi

state: Budapest

address: István u. 2.

country: Hungary

institute: ATE

summary:
Background: Gonadotropin-releasing hormone (GnRH) neurons play a pivotal role in regulation of the hypothalamic-pituitary gonadal axis in a sex-specific manner. We hypothesized that the differences seen in reproductive functions of males and females are associated with a sexually dimorphic gene expression profile of GnRH neurons.  Methods and Results: We compared the transcriptome of GnRH neurons obtained from intact, metestrous female and male GnRH-GFP transgenic mice. About 1500 individual GnRH neurons from each sex were sampled with laser capture microdissection followed by whole transcriptome amplification for gene expression profiling. Under stringent selection criteria (fold change > 1.6, adjusted p-value 0.01), Affymetrix Mouse Genome 430 PM array analysis identified 543 differentially expressed genes. Sexual dimorphism was most apparent in gene clusters associated with synaptic communication, signal transduction, cell adhesion, vesicular transport and cell metabolism. To validate microarray results, 57 genes were selected and 91% of their differential expression was confirmed by real-time PCR. Similarly, 88% of microarray results were confirmed with PCR from independent samples obtained by patch pipette harvesting and pooling of 30 GnRH neurons from each sex. We found significant differences in expression of genes involved in vesicle priming and docking (Syt1, Cplx1), GABAergic (Gabra3, Gabrb3, Gabrg2) and glutamatergic (Gria1, Grin1, Slc17a6) neurotransmission, peptide signaling (Sstr3, Npr2, Cxcr4) and the regulation of intracellular ion homeostasis (Cacna1, Cacnb1, Cacng5, Kcnq2, Kcnc1).
Conclusion: The striking sexual dimorphism of the GnRH neuron transcriptome we report here contributes to the better understanding the differences in cellular mechanisms of GnRH neurons in the two sexes.

overall_design: The transcriptome of GnRH neurons obtained from six intact, metestrous female and six male GnRH-GFP transgenic mice was compared. About 1500 individual GnRH neurons (250 GnRH neurons on average from each brain) from male and female mice were sampled with laser capture microdissection for total RNA isolation and whole transcriptome amplification (WTA) followed by hybridization on Affymetrix microarrays.

first: Csaba

last: Vastagh

first: Annie

last: Rodolosse

first: Imre

last: Farkas

first: Herbert

last: Auer

first: Miklós

last: Sárvári

first: Zsolt

last: Liposits


title: CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [ChIP-seq]

first: Maria Cristina

last: Gambetta

summary: CCCTC-binding factor (CTCF) is a conserved protein able to block communication between regulatory elements and gene promoters in flies and mammals. Here, we studied CTCF function in the Drosophila central nervous system (CNS) in which we find CTCF plays a vital role. Chromatin immunoprecipitation (ChIP)-sequencing of CTCF and its partner protein Centrosomal protein 190 kDa (Cp190) in CNSs of wildtype (WT), CTCF[0] mutants completely lacking CTCF and Cp190[KO] mutants with a CRISPR/Cas9-mediated deletion of the Cp190 open reading frame identified CTCF and Cp190 peaks defined as enriched in WT relative to each respective mutant control. These experiments also revealed that CTCF recruits Cp190 to CTCF's binding sites, but Cp190 is  dispensable for CTCF binding to most of CTCF's sites.

overall_design: Chromatin was prepared from wildtype (WT, corresponding to the Drosophila w[1118] reference strain), CTCF[0] and Cp190[KO] mutant thid instar larval CNSs in biological duplicate. Two separate ChIP experiments were performed with CTCF or Cp190 antibodies.

first: Anjali

last: Kaushal

first: Giriram

last: Mohana

first: Julien

last: Dorier

first: Isa

last: Özdemir

first: Arina

last: Omer

first: Michael

last: Taschner

first: Pascal

last: Cousin

first: Oleksandr

last: Dergai

first: Anastasiia

last: Semenova

first: Flavia

last: Marzetta

first: Christian

last: Iseli

first: Yossi

last: Eliaz

first: Nicolas

last: Guex

first: Erez

last: Aiden

first: Maria


title: Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci.

status: Public on Jan 15 2021

city: Philadelphia

first: Matthew

last: Pahl

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia


title: BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2

city: Shenzhen

first: Ruilin

last: Tian

address: 1088 Xueyuan Avenue

institute: SUSTech

summary: We performed RNA sequencing of Calu-3 cells after treatment with the BET-domain inhibitors JQ-1 and ABBV-744 as well as BRD2 CRISPRi knockdown. We also included CRISPRi knockdown of two other validated hit genes from our screen, COMP and ACE2.

overall_design: The Quant-seq experiments were performed using Calu-3 cells in the following 6 conditions: 1) untreated, 2)10uM JQ1 treament for 72hrs, 3) 10uM ABBV-744 treatment for 72hrs, 4) ACE2 knnockdown, 5) BRD2 knockdown, 6) COMP knockdown and 7) ProteinE overexpression. Each sample was sequenced twice and two sequecing runs were combined for further analysis.

first: Avi

last: Samelson

first: Merissa

last: Chen

first: Martin

last: Kampmann


title: Mapping genomic loci bound to BRD2 in Calu-3 cells

summary: we performed CUT&RUN to comprehensively map genomic loci bound to BRD2 in Calu-3 cells. We also included H3K4me3 and IgG antibodies as postive and negative controls, repectively

overall_design: The CUT&RUN experiment was performed with BRD2 antibody as well as the IgG and H3K4Me control antibodies with 1 million Calu-3 cells.


title: Pulmonary immune cell transcriptome changes in double-hit model of BPD induced by chorioamnionitis and postnatal hyperoxia

first: Sankar

last: Addya

address: 233 South 10th Street

department: Kimmel Cancer Center

institute: Thomas Jefferson University Hospital

summary: Preterm infants with bronchopulmonary dysplasia (BPD) have lifelong increased risk of respiratory morbidities associated with environmental pathogen exposure and underlying mechanisms are poorly understood. The resident immune cells of the lung play vital roles in host defense. However, the effect of perinatal events associated with BPD on pulmonary-specific immune cells is not well understood. We used a double-hit model of BPD induced by prenatal chorioamnionitis followed by postnatal hyperoxia, and performed global transcriptome analysis of all resident pulmonary immune cells. This is the first comprehensive report delineating transcriptomic changes in resident immune cells of the lung in a translationally relevant double-hit model of BPD.

overall_design: Control group consisted of pups injected prenatally with intra-amniotic normal saline and exposed to normoxia after birth. Experimental group was injected prenatally with intra-amniotic lipopolysaccharide and exposed to hyperoxia after birth. A total of six samples were used with three biological replicates per control and experimental group.

first: Deepthi

last: Alapati


title: HOXD13 Suppresses Prostate Cancer Metastasis and BMP4-induced EMT by Inhibiting SMAD1

city: shanghai

first: Wei

last: Xue

state: State...

address: pujian road no.160

institute: renji hospital, school of medicine, shanghai jiao tong university

summary: HOX genes regulate organ development and their abrrative expressions are also implicated in cancer progressions. It is a universal strategy for tumors to regain cell plasticity through disruption of Hox boundaries. Along with this clue, we identified HOXD13 as a pivotal component since HOXD13 deprivation alone is enough to induce more aggressive phenotypes in prostate cancer cells.  Here we subjected HOXD13 manipulated prostate cancer cells (LNCaP) to HiSeq RNA-Seq to identify its target genes involved in the antitumor activity.

overall_design: mRNA profiles of HOXD13 overexpression LNCaP cells and control cells.

first: Fan

last: Xu

first: Xun

last: Shangguan

first: Ni

last: Li

first: Min

last: Jiang


title: Global repression driven by RNA polymerase II stalling in yeast

city: Ithaca

first: B. Franklin

last: Pugh

state: New York

address: 465 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

summary: In multicellular eukaryotes, RNA polymerase (pol) II pauses transcription ~30-50 bp after initiation, and involves DSIF and other factors. While the budding yeast Saccharomyces has its transcription mechanisms mostly conserved with other eukaryotes, it appears to lack this fundamental promoter-proximal pausing.  However, we now discover that acute stress (e.g., peroxide) causes most yeast genes, including constitutive and stress-induced genes, to manifest two distinct pausing or stall sites during the early elongation phase of Pol II transcription. The first stall occurs at the promoter, where Pol II melts the DNA and acquires all tested interactions normally. The second stall occurs 100-200 bp downstream. It too has most, but not all, of the tested interactions. This stall is phenocopied by depletion of DSIF. Our results suggest that similar to other eukaryotes, in yeast stalling globally down regulates nearly all Pol II transcription, but primarily in response to acute stimuli, whereas in other eukaryotes it represents the default state in all cells.

overall_design: ChIP-exo was used to study the stalling of RNA polymerase II following acute stress by hydrogen peroxide.

first: Nitika

last: Badjatia

last: Rossi

first: Alain

middle: R

last: Bataille

first: William

middle: K

last: Lai

first: B


title: Single-cell RNA Sequencing reveals the expansion of Cytotoxic CD4+ T lymphocytes and the heterogeneity of pathogenesis in primary Sjögren’s syndrome patients

city: 深圳

first: Shuhui

last: Meng

state: 广东

address: 翠竹街道

institute: SHENZHEN PEOPLE' HOSPITAL

summary: By single cell RNA sequencing,our data revealed disease-specific immune cell subsets and provide some potential new targets of pSS, specific expansion of CD4+ CTLs may be involved in the pathogenesis of pSS, which might give a valuable insights for therapeutic interventions of pSS.

overall_design: We applied single cell RNA sequencing (scRNA-seq) to 57, 288 peripheral blood mononuclear cells (PBMCs) from 5 patients with pSS and 5 healthy controls. The immune cell subsets and susceptibility genes involved in the pathogenesis of pSS were analyzed.

last: Yang

first: Yong

last: Dai

first: Xiaoping

last: Hong


title: Subcellular Single Cell Sequencing: mRNA Diversity of Individual Glutamatergic and GABAergic Hippocampal Neurons and their Dendrites.

city: Frankfurt

first: Julio

middle: David

last: Perez

state: Hessen

department: Synaptic plasticity

country: Germany

institute: Max Planck Institute for Brain Research

summary: Neurons transport a variety of mRNAs to their dendritic and axonal compartments where they are locally translated. These processes are essential for the functional specialization of these cellular structures. To explore both the intercellular variability and intracellular dynamics of neuronal compartments we characterized the somatic and dendritic transcriptome of single neurons. We used Laser Capture Microdissection to isolate the dendrites and soma of individual neurons from primary hippocampal cultures, followed by scRNA-seq to profile the mRNA content of these compartments. In total, we sequence 276 dendrites and their respective somata, 227 somata without the dendrites, and 16 negative controls (LCM cuts of areas without cellular content). We observed less cell-type specific differences in the dendritic transcriptome than in the somatic transcriptome. However, the dendritic localization of a subset of mRNAs does vary in a cell-type specific manner. Furthermore, we observed that the relation between somatic and dendritic abundance varies according to gene and is strongly influenced by cellular function. This study provides a framework for the regulation of the dendritic transcriptome within and across individual neurons.

overall_design: Examination of somatic and dendritic transcriptome of single neurons

middle: D

first: Erin

last: Schuman


title: A unique subset of glycolytic tumor propagating cells drives squamous cell carcinoma

status: Public on Jan 14 2021

city: Boston

first: Raul

last: Mostoslavsky

address: 185 Cambridge street, CPZN 4100

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Head and Neck Squamous Cell Carcinoma (HNSCC) remains among the most aggressive human cancers. Tumor progression and aggressiveness in SCC are largely driven by Tumor Propagating Cells (TPCs). Aerobic glycolysis, also known as the Warburg Effect, represents a characteristic of many cancers, yet whether this adaptation is functionally important in SCC, and at which stage, remains poorly understood. Here, we show that the NAD+-dependent histone deacetylase Sirtuin 6 (SIRT6) is a robust tumor suppressor in SCC, acting as a modulator of glycolysis in these tumors. Remarkably, rather than a late adaptation, we find enhanced glycolysis specifically in TPCs. More importantly, using single cell RNA sequencing of TPCs, we identify a subset of TPCs with higher glycolysis and enhanced pentose phosphate pathway and glutathione metabolism, characteristics that are strongly associated with a better antioxidant response. Altogether, our studies uncover enhanced glycolysis as a main driver in SCC, and, more importantly, identify a subset of TPCs as the cell-of-origin for the Warburg effect, defining metabolism as a key feature of intra-tumor heterogeneity.

overall_design: RNA-seq of SIRT6 cKO and WT tumor subpopulations with following markers: low a6 and negative for CD34, or high a6 and +/- for CD34

first: Jee-Eun

last: Choi

first: Murat

last: Cetinbas

first: Ruslan

last: Sadreyev


title: Transcriptome of Moesziomyces albugensis in response to different biotic factors (A. laibachii & SynCom) on A. thaliana leaves

city: Cologne

first: Gunther

last: Doehlemann

address: Zülpicher Straße 47a

department: CEPLAS / Institute of Botany

institute: University of Cologne

summary: As the phyllosphere is a resource-limited niche, microbes have evolved different survival strategies by collaborating or competing with other organisms. This leads to the establishment of network structures which are stabilised by so-called microbial hub organisms. An already identified hub in the Arabidopsis thaliana phyllosphere is the oomycete pathogen Albugo laibachii. From wild Arabidopsis plants with white rust symptoms we isolated the basidiomycete yeast Moesziomyces albugensis, which is closely related to plant pathogenic smut fungi. It suppresses the infection of A. laibachii in lab experiments and inhibits growth of several bacterial phyllosphere members. The transcriptomic response of M. albugensis to presence of A. laibachii and bacterial SynCom members was investigated by using RNA sequencing. Interestingly, several genes encoding secretory proteins, mostly glycoside hydrolases and peptidases, are particularly induced upon interaction with A. laibachii.

sample_organism:
Arabidopsis thaliana
Albugo laibachii
Moesziomyces sp. GD-2020a

overall_design: To analyze the response of M. albugensis to specific biotic interactions in the A. thaliana phyllosphere transcriptomic profiling of M. albugensis was done. Samples were treated as in A. laibachii infections. Members of the phyllosphere network were sprayed first onto the leaf surface and a stable community was established after 2 days. The samples were then challenged with A. laibachii and incubated at 0°C over night. 1 day after cold treatment (4 days after spraying of Moesziomyces) cells were peeled from the leaf surface by using liquid latex. To determine plant specific responses, we used an M. albugensis axenic culture and compared its transcriptome to M. albugensis being alone on the plant surface. For on plant controls we used M. albugensis in one to one interactions with A. laibachii and the bacterial SynCom and compared them to the test condition of all being together on the plant surface.

first: Katharina

last: Eitzen

first: Eric

last: Kemen


title: Optogenetic Stimulation of Prelimbic Pyramidal Neurons Maintains Fear Memories and Modulates Amygdala Pyramidal Neuron Transcriptome

city: Rome

first: Daniela

last: Laricchiuta

state: Rome

address: Via del fosso di fiorano, 64

department: Preclinical neuroscience

country: Italy

institute: IRCCS Fondazione Santa Lucia

summary: The suppression of fear memory in the absence of danger (fear extinction) requires coordinated neural activity within the amygdala and medial prefrontal (prelimbic and infralimbic) cortex. Any behavior has a transcriptomic signature that is modified by environmental experiences, and specific genes are involved in functional plasticity and synaptic wiring during fear memory and extinction. In the present study, we investigated the effects of optogenetic manipulations of prelimbic pyramidal neurons on amygdala gene expression to analyze the specific transcriptional pathways involved in fear extinction. To this aim, transgenic mice (Thy1-COP4) having cortical and amygdala pyramidal neurons optogenetically excitable were (or not) fear-conditioned. During the extinction phase, the mice received optogenetic (or sham) stimulations to maintain the activation of the prelimbic pyramidal neurons and impair fear extinction. At the end of behavioral testing, electrophysiological (Excitatory Post-Synaptic Currents) and morphological (spinogenesis) correlates were evaluated in the pyramidal neurons of prelimbic cortex. Furthermore, transcriptomic cell-specific RNA-analyses (differential gene expression profiling and functional enrichment analyses) were performed in amygdala pyramidal neurons. Results demonstrate that pyramidal neurons of prelimbic cortex are involved in modulation of the fear responses during extinction phase and their optogenetic stimulation in fear-conditioned mice results in strong modifications of the amygdala transcriptome. Understanding the transcriptomic architecture of fear extinction may facilitate the comprehension of fear-related disorders.

overall_design: RNA extracted by amygdala pyramidal neurons of 14 B6.Cg-Tg(Thy1-COP4/EYFP)18Gfng/J (Thy1-COP4) (Jackson Laboratories, Maine, USA) mice

first: Giuseppe

last: Sciamanna

first: Juliette

last: Gimenez

first: Andrea

last: Termine

first: Carlo

last: Fabrizio

first: Silvia

last: Caioli

first: Francesca

last: Balsamo

first: Anna

last: Panuccio

first: Marco

last: De Bardi

first: Luana

last: Saba

first: Noemi

last: Passarello

first: Debora

last: Cutuli

last: Mattioni

first: Cristina

last: Zona

first: Valerio

last: Orlando

first: Laura

last: Petrosini


title: A genome-wide CRISPR/Cas9 screen in acute myeloid leukemia cells identifies regulators of TAK-243 sensitivity

status: Public on Jan 13 2021

city: Toronto

first: Aaron

last: Schimmer

state: ON

address: 101 College Street

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary: TAK-243 is a first-in-class inhibitor of ubiquitin-like modifier activating enzyme 1 (UBA1) that catalyzes ubiquitin activation, the first step in the ubiquitylation cascade. Based on its preclinical efficacy and tolerability, TAK-243 has been advanced to phase 1 clinical trials in advanced malignancies. Nonetheless, the determinants of TAK-243 sensitivity remain largely unknown. Here, we conducted a genome-wide CRISPR/Cas9 knockout screen in acute myeloid leukemia (AML) cells in the presence of TAK-243 to identify genes essential for TAK-243 action. We identified BEN domain-containing protein 3 (BEND3), a transcriptional repressor and a regulator of chromatin organization, as the top gene whose knockout confers resistance to TAK-243

overall_design: A positive-selection genome-wide CRISPR/Cas9 knockout screen in OCI-AML2 cells to identify gRNAs significantly enriched in the presence of TAK-243. Specifically, cells were  treated with DMSO or TAK-243 at 25 nM or 30 nM for 32 days or 36 days, followed by extraction of genomic DNA and sequencing

first: Samir

last: Barghout


city: Cambridge

first: Thomas

middle: James

last: LaSalle

address: 415 Main Street

institute: Broad Institute

overall_design: We examined 284 tumor propagating cells (TPCs) from two wild type (WT) and two Sirt6-/- mice using the Smart-seq2 protocol for single-cell transcriptomics.

first: Jee-Eun

last: Choi

last: Gonye

first: Moshe

last: Sade-Feldman

first: Nir

last: Hacohen

first: Raul

last: Mostoslavsky


title: Adenosine triphosphate Binding Cassette subfamily C member 1 (ABCC1) overexpression reduces APP processing and increases alpha- versus beta-secretase activity, in vitro.

city: Phoenix

first: Matthew

last: Huentelman

state: AZ

address: 445 N Fifth Street

department: Neurogenomics

institute: Translational Genomics Research Institute

summary: The organic anion transporter Adenosine triphosphate Binding Cassette subfamily C member 1 (ABCC1), also known as MRP1, has been demonstrated in murine models of Alzheimer's disease (AD) to export amyloid beta (Abeta) from the endothelial cells of the blood-brain barrier to the periphery, and that pharmaceutical activation of ABCC1 can reduce amyloid plaque deposition in the brain. Here, we show that ABCC1 is not only capable of exporting Abeta from the cytoplasm of human cells, but also that it's overexpression significantly reduces Abeta production and increases the ratio of alpha- versus beta-secretase mediated cleavage of the Amyloid Precursor Protein (APP), likely via indirect modulation of alpha-, beta-, and gamma-secretase activity.

overall_design: Transcriptomic analysis of BE(2)-m17 human neuroblastoma cells transfected with overexpression vectors encoding human reference APP and either empty vector control (pSBbi-Pur) or "codon-optimized) human reference ABCC1 (pSBbi-Pur-ABCC1).

first: Wayne

middle: M

last: Jepsen

last: De Both

first: Ashley

last: Siniard

first: Keri

last: Ramsey

first: Ignazio

last: Piras

first: Marcus

last: Naymik

first: Adrienne

last: Henderson


title: Plexin-B2 reduces glioma cell cohesion and regulates glioma-vascular interactions

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: The diffuse invasion of glioblastoma (GBM) cells into healthy brain tissue is a main contributor for the high lethality of this most frequent form of malignant brain tumor. Plexins are cell surface receptors for semaphorins and control cell adhesion and cytoskeletal dynamics in development and in adult physiology. Gene expression of Plexin-B2 is upregulated in GBM and correlates with its lethality. We show here that Plexin-B2 activity can reduce the cohesiveness of GBM cells, which facilitates their invasive capacity. Targeted deletion of Plexin-B2 in GBM cells increased their cohesion to each other, revealing that a major function of Plexin-B2 activity is to downregulate cell-cell adhesion, possibly by downregulating other cell adhesion systems. In an in vivo intracranial transplant model, invasion of Plexin-B2 mutant GBM cells was impaired, with cells invading shorter distances. Interestingly, the loss of Plexin-B2 also changed the migration mode of cells, with the balance of cells in brain stroma vs. capillary space shifted: Plexin-B2 mutant cells were more likely to adhere to the vasculature. Our structure-function analyses revealed that the Ras-GAP domain of Plexin-B2 that is the main functional output responsible for the cohesion regulating function of Plexin-B2. Transcriptomic analyses of Plexin-B2 KO cells suggests that Plexin-B2 loss in different GBM cell lines has no direct transcriptional target genes, however, consistently, cell adhesion molecules were changed in expression, suggesting that cells compensate for loss of Plexin-B2. Thus, Plexin-B2 acts as a key regulator of the cohesiveness of GBM cells, thereby facilitating their invasiveness.

overall_design: GBM cell lines with knockout mutations of Plexin-B2

first: Yong

last: Huang

first: Rut

last: Tejero

first: Igor

last: Katsyv

first: Michael

last: Kluge

first: Caroline

last: Friedel

first: Ramsey

last: Foty

first: Hongyan

last: Zou

first: Roland


title: LINE-1 promoter methylation analysis in brain development

city: Milan

first: Beatrice

last: Bodega

address: Via Francesco Sforza 35

institute: INGM Istituto Nazionale Genetica Molecolare

summary: We performed methylation analisys of L1MdTf sequence and IAPLTR1a during mouse brain development, in cortex, hippocampus and cerebellum at different developmental stages (E15.5, E18.5, P0, P3, P14). We defined specific waves of methylation for L1MdTf promoter.

overall_design: Bisulfite conversion based methylation analysis of L1MdTf and IAPLTR1a elements during mouse brain development. We analyzed cerebellum, cortex and hippocampus at 5 different developmental stages E15.5, E18.5, P0, P3 and P14. 4 mice at each developmental stage were analyzed.

first: Monica

last: Fumagalli


title: Transcriptionally active enhancers in human cancer cells

status: Public on Jan 12 2021

city: Goettingen

last: Lidschreiber

address: Am Fassberg 11

institute: Max-Planck-Institute for Multidisciplinary Scienes

summary: The growth of human cancer cells is driven by aberrant enhancer and gene transcription activity. Here we use Transient Transcriptome sequencing (TT-seq) to map thousands of transcriptionally active putative enhancers in fourteen human cancer cell lines covering seven cancer types. We conducted an in-depth analysis of the data, derived thousands of putative enhancer-promoter pairs, and extracted general features of active enhancer and transcription landscapes in cancer cells. We provide a comprehensive catalog of transcribed candidate enhancers with cancer-associated somatic mutations and putative enhancer-promoter pairs involving cancer-associated genes. Overall our results serve as a resource to study enhancer activity and gene regulation, and to select candidate enhancers for functional studies.

overall_design: Twelve human cancer cell lines (M059J, U-118 MG, BT-20, MDA-MB-231, GP5d, HCT 116, LoVo, 769-P, 786-O, DU 145, PC-3, SK-UT-1) were labeled with 500 µM 4-thiouridine for 5 min in biological duplicates. For each duplicate libraries of total fragmented RNA (RNA-seq) and 4sU-labelled RNA (TT-seq) were sequenced. Total number of samples sequenced: 48. Published TT-seq data sets of two additional cancer cell lines, K562 (Schwalb et al. 2016) and Jurkat (Michel et al. 2017) were incorporated in the eRNA and enhancer annotation data.

first: Katja

first: Lisa

middle: A

last: Jung

first: Henrik

last: von der Emde

first: Kashyap

last: Dave

first: Jussi

last: Taipale

first: Patrick

last: Cramer


title: Transcriptome Analysis of Tra Catfish (Pangasianodon hypophthalmus) Early Development Provides Novel Insights for the Terrestrial Adaptation

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: Channel catfish (Ictalurus punctatus) and tra catfish (Pangasianodon hypophthalmus) both belong to the order Siluriformes. Channel catfish does not possess an air-breathing organ (ABO), and thus cannot breathe in the air, while tra catfish is a facultative air-breather and use the swim bladder as its air-breathing organ, which provides for aerial breathing in low oxygen conditions. Tra and channel catfish serve as a great comparative model for studying the transition of life from water to terrestrial living, as well as for understanding genes that are crucial for development of the swim bladder and the function of air-breathing in tra catfish. We selected seven developmental stages in tra catfish for RNA-Seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated in tra catfish, and a total of 21, 448 unique genes were detected. A comparative genomic analysis was conducted between channel catfish and tra catfish. Gene expression analysis was performed for these tra catfish specific genes. Hypoxia challenge and microtomy experiments collectively suggested that there are critical timepoints for the development of the air-breathing function and swim bladder development stages in tra catfish. Key genes were identified to be the best candidates of genes related to the air-breathing ability in tra catfish. This study provides a large data resource for functional genomic studies in air-breathing function in tra catfish, and sheds light on the adaption of aquatic organisms to the terrestrial environment.

overall_design: Profile of transcriptome-wide gene expression levels in seven early development stages of Pangasianodon hypophthalmus

first: Xiaoli

last: Ma

first: Rex

last: Dunham


title: Critical Role of Synovial Tissue-resident Macrophage Niche in Joint Homeostasis and Suppression of Chronic Inflammation

city: Wilmette

first: Richard

last: Pope

state: IL

address: 1932 Central Ave

department: Medicine

institute: Northwestern University

summary: During synovial tissue homeostasis, both monocyte-derived F4/80int, and self-renewing F4/80hi tissue-resident, macrophage populations were identified. In contrast, in HUPO mice, decreased synovial tissue-resident macrophages preceded chronic arthritis, opened a niche permitting the influx of activated monocytes, which differentiated into F4/80hi macrophages.

overall_design: HUPO mice with established arthritis and littermate or age/gender matched control mice were sacrificed to harvest blood and ankle cells for RNA-seq. CM and NCM and 5 subsets of synovial tissue macrophages from ankles were stained as described, then sorted by flow cytometryacross 6 control and 7 HUPO populations of cells.   Quality control for the 49 samples was performed excluding5 low quality samples (alignment < 82%, duplicates > 66%, and mapped reads< 2.3x106) from groups with >3 replicates. To maintain consistent numbers of replicates (n=3) in each experimental group, we removed the least correlated sample from an additional 3 control mice under the assumption that the most similar samples better reflect steady-state conditions. We also removed 2 HUPO samples from F4/80hisubsets which appeared to have been contaminated based on the high expression of neutrophil-specific genes. Thus, 39 samples reflecting 3 replicates for each of the 13 groups remained. We defined 7,778 “expressed genes” with log2(FPKM+1)≥ 4 in at least 2 out of the39 individual samples.  K-means clustering for control mice and comparing HUPO and control mice.  The GENE-E software (http://softerware.broadinstitute.ord/GENE-E/) was employed for the pairwise Pearson’s correlation and K-means clustering analyses, performed using the default settings. Principle component analysis (PCA) was performed using the prcomp functionin R with the FPKM matrix of the expressed genes. Gene ontology (GO)associations were determined by Gorilla(http://cbl-gorilla.cs.technion.ac.il).

first: Qi-Quan

last: Huang

first: Renee

last: Doyle

first: Shang-Yang

last: Chen

first: Qicong

last: Sheng

first: Alexander

middle: V

last: Misharin

first: Qinwen

last: Mao

first: Deborah

last: Winter


title: Transcriptome analysis and comparison of three Aspergillus aculeatus strains

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

summary: The aim of this study was to find candidate genes in A. aculeatus involved in the cellulase production

overall_design: Transcriptome data on plant biomasses were used to find candidate gene for cellulose production

first: Duriya

last: Chantasingh

first: Varodom

last: Chareonsawan

first: Salisa

last: Charoensri


title: Combined analysis of transcriptome and metabolome in tilapia (GIFT, Oreochromis niloticus) exposed to acute hypoxia stress

city: Wuxi

first: Jun

last: Qiang

state: Jiangsu

address: 9 Shanshi East road

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

summary: Dissolved oxygen (DO) in cultured water is one of the important environment factor in fish farming. Hypoxic environment affects fish growth, metabolism and immune system. Multi-omics integrative analysis helps to uncover the underlying molecular mechanisms. In this study, the 96h median lethal hypoxia (96h-LH50) for Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) was first analyzed by linear interpolation. We built control (5mg/l) and hypoxic stress (96h-LH50) groups, and extracted the liver tissues for high-throughput transcriptome and metabolome sequencing. The identification and quantification results of metabolites showed that a total of 19656 metabolites had been obtained, of which 10390 were annotated. There were 3028 differentially expressed (DE) metabolites, of which 1596 metabolites were up-regulated and 1432 metabolites were down-regulated. We obtained 2375 DE genes, of which 1201 genes were up-regulated and 1174 genes were down-regulated. We verified 8 DE genes by quantitative real-time PCR. Our finding reveals the changes in metabolites and genes expression of GIFT and facilitate the understanding of regulatory pathways under hypoxic stress, which will help reduce the damage caused by hypoxic stress during culture.

overall_design: A total of 90 experimental fish were used for the acute hypoxic stress experiment. Eighteen experimental fish were randomly placed in six tanks (3 fish per tank), three treatment tanks and three 5mg/L control tanks. The DO of the three treatment tanks was rapidly reduced to 0.7-0.8mg/L by pumping nitrogen into water from a nitrogen gas cylinder. Real-time reading with a DO meter were used to control the DO in water by adjusting oxygen intake. The sampling time was 96h. Three fish were taken from each tank and anesthetized with 200mg/L MS-222. The liver tissues were removed, divided into two parts, frozen in liquid nitrogen, and stored in -80℃. One part of liver was used to do high-throughput transcriptome and metabolome sequencing. The other part of the sample was used to analyze the expression levels of the genes at different DO by qRT-PCR

first: Jun-Lei

first: Jie

last: He

first: Yi-Fan

last: Tao

first: Pao

last: Xu

first: Jin-Wen

last: Bao


title: Biallelic loss of BCMA as a resistance mechanism to CAR T cell therapy in a patient with Multiple Myeloma

status: Public on Jan 11 2021

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: BCMA targeting chimeric antigen receptor (CAR) T cell therapy have shown deep and durable responses in multiple myeloma. However, relapse following therapy is frequently observed, and mechanisms of resistance remain ill-defined. We performed single cell genomic characterization of longitudinal samples from a patient who relapsed after initial CAR T cell treatment with lack of response to retreatment.

overall_design:
A single cell cell RNA sequencing has been done for 8 longititunal samples collected from the same patient.

*** Submitter states that raw data will be submitted to dbGaP due to patient privacy concerns ***

first: Nikhil

last: Munshi


title: High-Content Imaging-Based Pooled CRISPR Screens in Mammalian Cells

city: San Francisco

first: Xiaowei

last: Yan

institute: UCSF

summary: We developed a microscopy-based approach, which we name optical enrichment, to select cells displaying a particular CRISPR-induced phenotype by automated imaging-based computation, mark them by photo-activation of an expressed photo-activatable fluorescent protein, and then isolate the fluorescent cells using fluorescence-activated cell sorting (FACS). One proof-of-principle screen, a nuclear size screen, a FSC screen and a H2B-mGFP screen were performed to validate the method.

overall_design: For mIFP proof-of-principle screen, sorted mIFP positive sample, sorted mIFP negative sample and unanalyzed sample identified from microscopy were separately collected by FACS and sequenced with 2 replicates.  For nuclear size screen, cells with nuclear size larger than 1,000 μm² were identified from microscopy and collected together with unanalyzed sample by FACS and prepared for sequencing with 2 replicates (4 runs per replicate).  For H2B-mGFP screen and FSC screen, the top 10 percentile of cells based on either GFP fluorescence or FSC signal were separately sorted and prepared for high throughput sequencing with 2 replicates.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptome profile in IEC 4.1 cells in response to Cryptosporidium parvum

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

summary: The lincRNA-NR_033736 is an early-primary gene controlled by the type I IFN signaling in murine intestinal epithelial cells. This study aims to measure the impact of lincRNA-NR_033736 knockdown on the transcriptome profile in cultured IEC 4.1 in response to C. parvum infection. Cells were treated with a specific siRNA to knockdown lincRNA-NR_033736  and then exposed to C. parvum infection. Cells treated with a scrambled non-specific siRNA were used as the control. Total RNA was collected for the genome-wide analysis using RNA-seq

overall_design: The IEC 4.1 murine intestinal epithelial cells were grown to 80% confluence for four groups: the siRNA control (Group A, cells treated with a non-specific scrambled siRNA control), the  C. parvum infected (Group B, cells treated with the siRNA control plus C. parvum stimulation), lincRNA-NR_033736 (Group C, cells treated with an siRNA to lincRNA-NR_033736), and lincRNA-NR_033736 siRNA/C. parvum infected (Group D, cells treated with the lincRNA-NR_033736 plus C. parvum infection). Cells were treated with the siRNAs for 16h, then exposed to C. parvum infection for 24h. Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.


title: Crosstalk between Three Fungus-specific Transcription Factors, WetA, VosA, and VelB, in Asexual Spores of Aspergillus nidulans

city: Nashville

first: Antonis

last: Rokas

address: VU Station B 35-1364

department: Biological Sciences

institute: Vanderbilt University

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

overall_design: Refer to individual Series


title: A genetic screen identifies Etl4-deficiency capable of stabilizing the haploidy in embryonic stem cells

city: Beijing

first: Xiao

middle: wen

last: Li

state: Beijing

address: Dong Dan San Tiao 5

department: Medical genetics

institute: Chinese Academy of Medical Sciences Institute of Basic Medical Sciences

summary: We performed a genome-wild loss-of-function screening and revealed several gene mutations could significantly reduce the rate of self-diploidization in haESCs. We further demonstrated that CRISPR/Cas9 mediated Etl4 knockout stabilizes the haploid state in different haploid cell lines. More interestingly, Etl4 deficiency could increase the mitochondrial oxidative phosphorylation (OXPHOS) capacity and decrease glycolysis in haESCs. Collectively, our study identifies Etl4 as a novel haploidy-related factor and suggests that the changes of energy metabolism is associated with self-diploidization.

overall_design: mRNA profiles of  Etl4 knockout haploid ESCs and wild type haploid ESCs

first: Guozhong

last: Zhang

first: Xiaowen

first: Yi

last: Sun

first: Xue

last: Wang


title: Crosstalk between Three Fungus-specific Transcription Factors, WetA, VosA, and VelB, in Asexual Spores of Aspergillus nidulans [RNA-seq]

summary: In filamentous fungi, asexual sporulation involves morphological differentiation and metabolic changes. The process of asexual spore formation is tightly regulated by a variety of transcription factors including VosA, VelB, and WetA. A number of studies have demonstrated that these three transcription factors are key regulators of asexual spore formation and maturation in the model filamentous fungus Aspergillus nidulans. To gain a more mechanistic view of the roles these transcription factors play in asexual spores, genome-wide and metabolomic analyses were conducted in A. nidulans conidia. RNA sequencing and chromatin immunoprecipitation-based sequencing data suggested that the three transcription factors directly or indirectly regulate the expression of genes associated with spore-wall integrity, asexual development, and secondary metabolism. In addition, metabolomics analysis of conidia extracts showed strikingly different primary and secondary metabolite profiles for wild-type and mutant conidia. These results suggest that WetA, VosA, and VelB play key roles in the morphological development of and metabolic changes in conidia. This entry is for the RNA-seq data.

overall_design: Three technical replicates of each genotype (wild type, deltavelB, and deltavosA) were sequenced.

first: Ming-Yueh

last: Wu

first: Matthew

middle: E

last: Mead

first: Mi-Kyung

last: Lee

first: George

middle: F

last: Neuhaus

first: Donovon

last: Adpressa

first: Julia

middle: I

last: Martien

first: Ye-Eun

last: Son

first: Heungyun

last: Moon

first: Daniel

last: Amador-Noguez

first: Kap-Hoon

last: Han

first: Sandra

last: Loesgen

first: Jae-Hyuk

last: Yu

first: Hee-Soo

last: Park


title: miRNA sequencing signature in acquired radioresistant and normal colorectal cancer cells.

status: Public on Jan 10 2021

city: Shanghai

first: shang

last: yuanyuan

address: 150 Jimo Road, Pudong New Area

institute: Shanghai East Hospital, Tongji University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore the mechanisms underlying the radioresistance of colorectal cancer, we established specifically radioresistant HCT116 cell line (HCT116-R cells) and RKO cell line (RKO-R cells) derived from HCT116 and RKO cell lines by repeatedly exposing to multi-fractionated irradiation. Then, the aberrantly expressed miRNA were detected by miRNA sequencing and their bioinformatics were analyzed.

overall_design: MiRNA expressions of acquired radioresistant colorectal cancer cells, HCT116-R and RKO-R, and normal colorectal cancer cells, HCT116 and RKO, were measured.

first: Chuan-gang

last: Fu

first: Yuanyuan

last: Shang

first: Lin

last: Chen


title: Mitochondrial TSPO Deficiency Triggers Retrograde Signaling in MA-10 Mouse Tumor Leydig Cells

status: Public on Jan 09 2021

city: Los Angeles

first: Vassilios

last: Papadopoulos

state: CA

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences, School of

institute: University of Southern California

summary: The mitochondrial translocator protein (TSPO) has been shown to bind cholesterol with high affinity and is involved in mediating its availability for steroidogenesis. We recently reported that targeted Tspo gene deletion in MA-10 mouse tumor Leydig cells resulted in reduced cAMP-stimulated steroid formation and significant reduction in the mitochondrial membrane potential (ΔΨm) compared to control cells. We hypothesized that ΔΨm reduction in the absence of TSPO probably reflects the dysregulation and/or maintenance failure of some basic mitochondrial function(s). To explore the consequences of TSPO depletion via CRISPR-Cas9-mediated deletion (indel) mutation in MA-10 cells, we assessed the transcriptome changes in TSPO-mutant versus wild-type (Wt) cells using RNA-seq. Gene expression profiles were validated using real-time PCR. We report herein that there are significant changes in nuclear gene expression in Tspo mutant versus Wt cells. The identified transcriptome changes were mapped to several signaling pathways including the regulation of membrane potential, calcium signaling, extracellular matrix, and phagocytosis. This is a retrograde signaling pathway from the mitochondria to the nucleus and is probably the result of changes in expression of several transcription factors, including key members of the NF-κB pathway. In conclusion, TSPO regulates nuclear gene expression through intracellular signaling. This is the first evidence of a compensatory response to the loss of TSPO with transcriptome changes at the cellular level.

overall_design: The cells used for total RNA extraction were cultured in 6-well plates to 80% confluence. Total RNA samples from Wt and Tspo mutant cells were extracted using TRIzol  reagent (Invitrogen; Thermo Fisher Scientific, Waltham, MA, USA) and then quantified with  an Agilent 2100 bioanalyzer. The quantified RNA samples were used for NEBNext® (New  England Biolabs, Ipswich, MA, USA) rRNA-depleted (Human/Mouse/Rat) stranded  library preparation. Total transcripts of the cells were sequenced at McGill University  and the Genome Quebec Innovation Center

first: Jinjiang

last: Fan


title: Expression profile of peripheral immune cells-derived coding and long non-coding RNAs in patients with proliferative vitreoretinopathy

city: Guangzhou

first: Yao

last: Ni

address: 54 South Xianlie Road

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

summary:
Peripheral immune response has been revealed to play a critical role in proliferative vitreoretinopathy (PVR). However, the reliable immune-related factors that are acting as prognostic indicators or therapeutic targets for PVR remain to explore further.
Methods: In the current study, we applied whole-transcriptome sequencing to profile peripheral blood mononuclear cells (PBMCs) from PVR patients and also analyzed lncRNA-mRNA interactions in peripheral immune cells to explore the pathways that might mediate immunopathology and resultant retinal damage in PVR. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and Ingenuity Pathway Analysis (IPA) were employed to classify the function of these differentially expressed genes (DEGs).
Results: Compared to the controls, there were 319 genes upregulated, and 191 genes downregulated in PVR patients. GO, and KEGG enrichment analyses as well as IPA showed that these upregulated genes were significantly enriched in immune-related and infection-relate terms. Immune-related gene NFKBIA, CXCL2, and CXCL8 were detected as hub-genes in the co-expression network, while lncRNAs such as AC007032.1, AC037198.2, AL929472.2, and SLED1 were highly co-expressed with them. lncRNA-mRNA interactions analysis also showed that putative targeted genes of these differentially expressed lncRNAs were also significantly enriched in immune-related or infection-relate pathways.
Conclusion: Our study highlights the transformation of immune-related genes/pathways in PVR by comparing controls, and validates several critical genes and lncRNAs, which are serving as potential diagnostic markers for PVR patients.

overall_design: peripheral blood mononuclear cells mRNA profiles of proliferative vitreoretinopathy patients and idiopathic epiretinal membrane patients.

first: Zhaotian

last: Zhang

first: Xiao

last: Hu

first: Fangyuan

last: Liu


title: RNA-seq transcriptome profiling and whole exome sequencing data on Hypertrophic cardiomyopathy (HCM) patients

city: Boston

first: Bradley

last: Maron

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital

summary: This study is to examine gene expression profiles in 18 HCM patients and compare them with those in 5 healthy controls. The hypothesis tested here is whether patient individual-level transcriptome data integrated with the human interactom can implicate the heterogenity of HCM phenotypes.In this study, we also analyze DNA whole-exome sequencing (WES) data from 18 patients.

overall_design: Transcriptome analysis was performed on anterior septal tissues from frozen hearts of HCM patients and left ventriular wall tissue from healthy controls  by deep sequencing. Whole exome sequencing were performed on the same tissues for 18 HCM patients.

first: Andriy

last: Samokhin

first: Martin

first: Gordon

last: Huggins

first: Stavros

last: Drakos


title: Crosstalk between Three Fungus-specific Transcription Factors, WetA, VosA, and VelB, in Asexual Spores of Aspergillus nidulans [ChIP-seq]

first: Antonis

last: Rokas

summary: In filamentous fungi, asexual sporulation involves morphological differentiation and metabolic changes. The process of asexual spore formation is tightly regulated by a variety of transcription factors including VosA, VelB, and WetA. A number of studies have demonstrated that these three transcription factors are key regulators of asexual spore formation and maturation in the model filamentous fungus Aspergillus nidulans. To gain a more mechanistic view of the roles these transcription factors play in asexual spores, genome-wide and metabolomic analyses were conducted in A. nidulans conidia. RNA sequencing and chromatin immunoprecipitation-based sequencing data suggested that the three transcription factors directly or indirectly regulate the expression of genes associated with spore-wall integrity, asexual development, and secondary metabolism. In addition, metabolomics analysis of conidia extracts showed strikingly different primary and secondary metabolite profiles for wild-type and mutant conidia. These results suggest that WetA, VosA, and VelB play key roles in the morphological development of and metabolic changes in conidia. This entry is for the ChIP-seq data.

overall_design: To identify the VelB direct target genes and compare the putative direct target genes of VosA and VelB, ChIP experiments, followed by high-throughput sequencing of the enriched DNA fragments in the conidia from the WT strain and strains containing VosA-FLAG or VelB-FLAG conidia, were carried out. A commercially available anti-FLAG antibody-Dynabead complex was used. WT samples (that did not contain the FLAG epitope) were compared to samples from strains that contained the FLAG epitope on the proteins of interest. Separate WT samples, prepared using the same methods, were analyzed for VosA-FLAG and VelB-FLAG experiments. Six replicates were analyzed the VosA-FLAG samples. Three replicates were analyzed for all other samples.

first: Ming-Yueh

last: Wu

first: Matthew

last: Mead

first: Mi-Kyung

last: Lee

first: George

last: Neuhaus

first: Donovon

last: Adpressa

first: Julia

last: Martien

first: Ye-Eun

last: Son

first: Heungyun

last: Moon

first: Daniel

last: Amador-Noguez

first: Kap-Hoon

last: Han

first: Sandra

last: Loesgen

first: Jae-Hyuk


title: CD8+ T-cell exhaustion induced by leukemic cells drives progression in Chronic Lymphocytic Leukemia

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

country: Spain

institute: CNAG-CRG

summary: Mechanisms mediating to disease progression from diagnosis in chronic lymphocytic leukemia (CLL) are not fully elucidated. The acquisition of molecular changes at the time of progression has been observed in a small fraction of patients, suggesting that CLL progression is not mainly driven by dynamic clonal evolution. In order to shed light on mechanisms that lead to CLL progression, we investigated longitudinal changes in both the genetic and immunological landscapes. For that, we analyzed paired samples obtained from CLL patients at diagnosis and progression before front-line treatment or at diagnosis and long-term asymptomatic follow-up. By whole-exome sequencing, we found that CLL cells displayed limited genetic evolution at progression. Conversely, T cells from progressing patients showed significant immunophenotypical and transcriptional changes over time not observed in patients that did not progress. Specifically, we found that CD8+ T cells at progression were characterized by an increasing terminally exhausted effector phenotype (T-betdim/-EomeshiPD1hi) with high co-expression of inhibitory receptors (PD1, CD244 and CD160). This exhausted status in CD8+ T cells was induced by progressing leukemic cells mainly through a mechanism dependent on soluble factors, including IL-10. Thus, we demonstrate that immunological changes are of paramount importance for CLL clinical progression, thereby providing a rationale for the use of early immunotherapeutic intervention in this disease.

overall_design: We performed paired RNA-Seq analysis on isolated T cells (>85% CD3+ of purity): 13 patients were analyzed at time of diagnosis and progression before treatment and 6 patients were analyzed at time of diagnosis and long-term asymptomatic follow-up (non-progression)

first: Isabel

last: Jiménez

first: Marta

last: Crespo

first: Francesc

last: Bosch


title: Outcome of SARS-CoV-2 infection is linked to MAIT cell activation and cytotoxicity

status: Public on Jan 08 2021

city: Paris

first: Agnes

last: Lehuen

address: 123, bd de Port-Royal

country: France

institute: Institut Cochin

summary: Immune system dysfunction is paramount in Coronavirus disease 2019 (COVID-19) severity and fatality rate. MAIT cells are innate-like T cells involved in mucosal immunity and protection against viral infections. Here, we studied the immune cell landscape, with emphasis on MAIT cells, in cohorts of 208 patients at various stages of disease activity. MAIT cell frequency is strongly reduced in blood. They display a strong activated and cytotoxic phenotype that is more pronounced in lungs. Blood MAIT cell alterations positively correlate with other innate cell activation; pro-inflammatory cytokines, notably IL-18; and with the severity and mortality of SARS-CoV-2 infection. We also identified a monocyte/macrophage Interferon-a-IL-18 cytokine shift and the ability of infected macrophages to induce cytotoxicity of MAIT cells in an MR1-dependent manner. Together our results suggest that altered MAIT cell functions due to IFN-a-IL-18 imbalance contribute to disease severity and their therapeutic manipulation might prevent deleterious inflammation in COVID-19 aggravation.

overall_design: MAIT cells single cell analysis from uninfected SARS-CoV-2 patients (n=4)  and infected severe cases infected SARS-CoV-patients  (n=4) . No replicates.

first: Héloïse

last: Flament

first: Matthieu

last: Rouland

first: Lucie

last: Beaudoin

first: Amine

last: Toubal

first: Léo

last: Bertrand

first: Samuel

last: Lebourgeois

first: Camille

last: Rousseau

first: Pauline

last: Soulard

first: Zouriatou

last: Gouda

last: Cagninacci

first: Antoine

middle: C

last: Monteiro

first: Margarita

last: Hurtado-Nedelec

first: Sandrine

last: Luce

first: Karine

last: Bailly

first: Muriel

last: Andrieu

first: Benjamin

last: Saintpierre

first: Franck

last: Letourneur

first: Youenn

last: Jouan

first: Mustapha

last: Si-Tahar

first: Thomas

last: Baranek

first: Christophe

last: Paget

first: Christian

last: Boitard

first: Anaïs

last: Vallet-Pichard

first: Jean-François

last: Gautier

first: Nadine

last: Ajzenberg

last: Terrier

first: Frédéric

last: Pène

first: Jade

last: Ghosn

first: Xavier

last: Lescure

first: Yazdan

last: Yazdanpanah

first: Benoit

last: Visseaux

first: Diane

last: Descamps

last: Timsit

first: Renato

first: Agnès


title: An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis

status: Public on Jan 07 2021

city: Pozuelo de Alarcon

first: Miguel

middle: Angel

last: Moreno-Risueno

state: Madrid

department: Biotechnology

institute: Center for Plant Biotechnology and Genomics

type: Genome variation profiling by high throughput sequencing


title: Acetyltransferase Enok regulates transposon silencing by promoting transcription at piRNA clusters and genes involved in piRNA biosynthesis [H3 and H3K23 ChIP-seq]

city: Taipei

first: Fu

last: Huang

address: 128, Academia Road Sec. 2, Nankang

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: The PIWI-interacting RNA (piRNA) pathway is an important mechanism to suppress transposon activation in the germline that is highly conserved between Drosophila and mammals. This pathway starts from transcribing piRNA clusters to generate long piRNA precursors. The majority of piRNA clusters lacks a conventional promoter, and therefore their transcription is considered to utilize a noncanonical mechanism. However, information regarding transcriptional regulation of piRNA clusters is limited. Here, we report that the fly KAT6 acetyltransferase, Enok, is important for transposon silencing in the germline. Further small RNA-seq analysis revealed that Enok is critical for piRNA production from a specific subset of piRNA clusters including 42AB, one of the two major sources of piRNAs. Enok is the major enzyme for establishing the H3K23ac mark, and was shown to promote gene expression by acetylating H3K23. Surprisingly, our RNA-seq and ChIP-seq/ChIP-qPCR results suggest that Enok regulates expression of genes involved in the piRNA production by H3K23ac-dependent mechanisms, and also promotes transcription at piRNA clusters through H3K23ac-independent pathways. Our co-immunoprecipitation assay further suggests that Enok interacts with RNA polymerase II to facilitate transcription of piRNA clusters. Taken together, our study provides novel insights into the regulation of noncanonical transcription at piRNA clusters and transposon silencing.

overall_design: Investigation of the genome-wide distribution of Histone H3 and Histone H3K23 in Enok knock-down ovaries by ChIP-seq.

first: Shih

middle: Y

last: Tsai


title: Acetyltransferase Enok regulates transposon silencing by promoting transcription at piRNA clusters and genes involved in piRNA biosynthesis (Rhino ChIP-seq)

overall_design: Investigation of the genome-wide distribution of RNA polymerase II in control-knockdown and enok-knockdown ovaries.

first: Shih-Ying


title: SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites [sequencing]

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Glucocorticoid receptor (GR) is an essential transcription factor (TF), controlling metabolism, development and immune responses. SUMOylation regulates chromatin occupancy and target gene expression of GR in a locus-selective manner, but the mechanism of regulation has remained elusive. Here, we identify the protein network around chromatin-bound GR by using selective isolation of chromatin-associated proteins and show that the network is affected by receptor SUMOylation, with several nuclear receptor coregulators and chromatin modifiers preferring interaction with SUMOylation-deficient GR and proteins implicated in transcriptional repression preferring interaction with SUMOylation-competent GR. This difference is reflected in our chromatin binding, chromatin accessibility and gene expression data, showing that the SUMOylation-deficient GR is more potent in binding and opening chromatin at glucocorticoid-regulated enhancers and inducing expression of target loci. Blockage of SUMOylation by a SUMO-activating enzyme inhibitor (ML-792) phenocopied to a large extent the consequences of GR SUMOylation deficiency on chromatin binding and target gene expression. Our results thus show that SUMOylation modulates the specificity of GR by regulating its chromatin protein network and accessibility at GR-bound enhancers. We speculate that many other SUMOylated TFs utilize a similar regulatory mechanism.

overall_design: Examination of NCOA1, NCOR1, and H3K4me2 binding by ChIP-seq from isogenic HEK293 cells stably expressing GRwt (HEK293flpGR) or SUMOylation deficient GR (GR3KR; HEK293flpGR3KR). Examination of GR binding after SAE inhibitor ML-792 treatment by ChIP-seq from HEK293flpGR and HEK293flpGR3KR cells. In addition, examination of SUMO2/3, PIAS1+2, H3K4me2, and Pol2 binding by ChIP-seq from HEK293flpGR and isogenic HEK293 cells expressing in a tetracycline (tet)-inducible manner PIAS1 (HEK239flpPIAS1). Sequencing with Illumina HiSeq 2000, or Illumina NextSeq 500. IgG immunoprecipitated sample from HEK293flpFRT cells was used as control. Chromatin accessibility examined by ATAC-seq from HEK293flpGR and HEK293flpGR3KR cells, in biological duplicates, using Illumina NextSeq 500. Gene expression examined by RNA-seq after SAE inhibitor ML-792 treatment from HEK293flpGR or HEK293flpGR3KR cells, in biological duplicates, using Illumina NextSeq 500.

first: Marjo

last: Malinen

first: Joanna

last: Lempiäinen

first: Einari

last: Niskanen

first: Jorma

middle: J

last: Palvimo


title: Genome-wide profiles of gene expression levels in mouse nephron progenitor cells

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

summary: During embryonic kidney development, nephron progenitor cells (NPCs) self-renew and differentiate into all cells in mature nephrons. The Wnt signaling components Wnt9b and β-catenin are required for both NPC self-renewal and differentiation. A low level of Wnt/β-catenin are associated with NPC self-renewal while a high level with differentiation. To investigate the transcriptional mechanisms behind Wnt/β-catenin-driven regulation of NPCs states, we modeled NPC self-renewal and differentiation in vitro with NPEM (Brown et al., 2015) supplemented with low (1.25 μM) or high (5 μM) concentration of CHIR22091 (CHIR), a small molecule GSK3β inhibitor that stabilizes β-catenin. To investigate change of NPC chromatin landscape under influence of CHIR treatment, here we generated ATAC-Seq data from primary NPC, as well as NPC cultured in low and high CHIR concentration.

overall_design: RNA-Seq was performed in primary NPCs, as well as NPCs cultured in low (1.25 μM) CHIR and high (5 μM) CHIR conditions.

first: Qiuyu

last: Guo

first: Albert

last: Kim


title: Acetyltransferase Enok regulates transposon silencing by promoting transcription at piRNA clusters and genes involved in piRNA biosynthesis [ncRNA-seq]

overall_design: Comparison of piRNA levels between wild-type and mutant ovaries by small RNA-seq.


title: 3' mRNA-seq analysis from murine satellite cells upon lnc-Rewind knockdown

city: Rome

first: Andrea

last: Cipriano

state: Italy

address: Piazzale Aldo Moro 5

department: Biologia e Biotecnologue C. Darwin

institute: La Sapienza

summary: To dissect the transcriptional dynamics regulated by lnc-Rewind who is actively express in active proliferating murine myoblast, we applied 3' RNA-sequencing on proliferating murine skeletal muscle satellite cells uopon the GAPmer based knockdown of the lncRNA

overall_design: Skeletal Muscle satellite cells were transfected with GAP-scr and GAP-REW, and the polyA+ RNA was collected and analysed using 3 'RNA sequencing

first: Martina

last: Macino

first: Giulia

last: Buonaiuto

first: Tiziana

last: Santini

first: Beatrice

last: Biferali

first: Alessio

last: Colantoni

first: Giovanna

last: Peruzzi

first: Chiara

last: Mozzetta

first: Monica

last: Ballarino


title: Genome-wide map of open chromatin, trancription factor occupancy, chromatin marks and gene expression profiles in mouse nephron progenitor cells


title: Genome-wide map of Tcf/Lef transcription factors, β-catenin, Six2 and chromatin marks in mouse nephron progenitor cells

summary: During embryonic kidney development, nephron progenitor cells (NPCs) self-renew and differentiate into all cells in mature nephrons. The Wnt signaling components Wnt9b and β-catenin are required for both NPC self-renewal and differentiation. A low level of Wnt/β-catenin are associated with NPC self-renewal while a high level with differentiation. To investigate the transcriptional mechanisms behind Wnt/β-catenin-driven regulation of NPCs states, we modeled NPC self-renewal and differentiation in vitro with NPEM (Brown et al., 2015) supplemented with low (1.25 μM) or high (5 μM) concentration of CHIR22091 (CHIR), a small molecule GSK3β inhibitor that stabilizes β-catenin. We have found the Tcf/Lef family repressors Tcf7l1 and Tcf7l2 are enriched in low CHIR condition, while the activators Tcf7 and Lef1 in high CHIR condition, correlating with the NPC differentiation program transiting from being repressed to activated. To identify direct transcriptional targets of Tcf/Lef factors and β-catenin, here we generated ChIP-Seq data from primary NPC, as well as NPC cultured in low and high CHIR concentration.

overall_design: ChIP-Seq was performed in primary NPCs, as well as NPCs cultured in low (1.25 μM) CHIR and high (5 μM) CHIR conditions.


title: Genome-wide profiles of chromatin interaction in mouse nephron progenitor cells [HiC]

summary: During embryonic kidney development, nephron progenitor cells (NPCs) self-renew and differentiate into all cells in mature nephrons. The Wnt signaling components Wnt9b and β-catenin are required for both NPC self-renewal and differentiation. A low level of Wnt/β-catenin are associated with NPC self-renewal while a high level with differentiation. To investigate the transcriptional mechanisms behind Wnt/β-catenin-driven regulation of NPCs states, we modeled NPC self-renewal and differentiation in vitro with NPEM (Brown et al., 2015) supplemented with low (1.25 μM) or high (5 μM) concentration of CHIR22091 (CHIR), a small molecule GSK3β inhibitor that stabilizes β-catenin. To investigate change of higher-order chromatin structure of NPC under influence of CHIR treatment, here we generated HiC data from primary NPC, as well as NPC cultured in low and high CHIR concentration.

overall_design: HiC was performed in primary NPCs, as well as NPCs cultured in low (1.25 μM) CHIR and high (5 μM) CHIR conditions.

first: Bin

last: Li

first: Bing

last: Ren


title: Genome-wide map of open chromatin in mouse nephron progenitor cells

overall_design: ATAC-Seq was performed in primary NPCs, as well as NPCs cultured in low (1.25 μM) CHIR and high (5 μM) CHIR conditions.


title: Acetyltransferase Enok regulates transposon silencing by promoting transcription at piRNA clusters and genes involved in piRNA biosynthesis [Pol II ChIP-seq]

first: Fu

last: Huang

first: Shih-Ying

last: Tsai


title: Parental (F0) compared to MSC educated (F2) prostate cancer cell lines

status: Public on Jan 06 2021

city: Tampa

first: Conor

last: Lynch

state: FL

address: 12902 Magnolia Dr

institute: H. Lee Moffitt Cancer Center

summary: Our studies demonstrated that bone marrow derived mesenchymal stromal cells (MSCs) drive the emergence of an apoptosis resistant population of prostate cancer cells that are also cross resistant to chemotherapy such as docetaxel.  The goals of this RNAQuant study was to determine differential gene expression between the naïve and MSC educated prostate cancer cells in order to better understand the mechanisms underlying apoptosis resistance.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: In triplicate prostate cacner cells PAIII and DU145 were exposed to conditioned media from mesenchymal stem cells (MSCs), primary murine MSCs for PAIII and human MSCs purchased from Lonza for DU145.  After 72 hours of culture in the MSC conditioned media the cells were allowed to recover in complete media for 48 hours before a second round of 72 hours of culture in MSC conditioned media and the process repeated for a third time.  At this point the cell lines were recovered and called F2 PAIII or F2 DU145.  Total RNA was extracted using biological replicates collected in triplicate from each, F0 and F2 PaIII and F0 and F2 DU145 cell lines using the RNeasy kit (Qiagen Cat# 74104) followed by DNase treatment using the Max Kit (Qiagen Cat # 15200). RNA concentrations were measured using the Qubit RNA BR assay and RNA integrity was assessed using the Agilent 4200 Tapestation.  500ng of RNA per sample was processed by the Moffitt Molecular Genomics Core to generate libraries for gene expression analysis using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen Cat #015) following the manufacturer’s protocol.   At least 20 million 101-base single-end sequencing reads per sample were generated on the Illumina NextSeq 500 sequencer.  The Bluebee Genomics Platform provided with the QuantSeq kit from Lexogen was used for read for alignment, counting, and differential expression analysis.

first: Jeremy

last: McGuire

first: Sean

last: Yoder

first: Ling

last: Cen