title: Data-driven identification of inherent features of eukaryotic stress-responsive genes

city: Barcelona

first: Francesc

last: Posas

address: Baldiri Reixac 10

institute: IRB Barcelona

summary: Virtually all living organisms are challenged by changes in their environment, such as sudden increases in osmolarity. To survive, cells have developed stress-responsive mechanisms that tune functions such as metabolism and gene expression. The response of Saccharomyces cerevisiae to osmostress includes a massive reprogramming of gene expression. Identifying the inherent features of stress-responsive genes is of significant interest for understanding the basic principles underlying the rewiring of gene expression upon stress. Here we generated a comprehensive catalog of osmotress-responsive genes from 5 independent RNA-seq experiments. We explored 30 features of yeast genes and found that 25 (83.34%) were distinct in osmostress-responsive genes. We then identified a subset of 13 non-redundant minimal osmostress gene traits and used statistical modeling to generate a ranking of the most stress-predictive features. Our findings reveal that the most relevant features of osmostress-responsive genes are the number of transcription factors targeting a gene and gene conservation. The same features that define yeast osmostress-responsive genes can also be used to predict osmostress-responsive genes in humans, although the most predictive features in humans are GC content and mRNA half-life. Our study provides a holistic understanding of the basic principles of the regulation of stress-responsive gene expression across eukaryotes.

overall_design: RNA-seq gene counts from yeast cells (HOG1-WT or HOG1-KO) challenged with hypertonic stress (0.4 M NaCl, 15 min) or kept in regular medium. Each condition in triplicates. 18 samples.

first: Eulalia

last: de Nadal


title: RNA Expression QTL mapping in Striatum of an F2 cross of BALB/cJ and BALB/cByJ mice to identify candidate genes for behavioral/metabolic QTLs

status: Public on Feb 11 2022

city: Boston

first: Camron

middle: D

last: Bryant

state: Massachusetts

address: 72 E Concord St

department: Pharmacology

country: USA

institute: Boston University School of Medicine

type: Expression profiling by high throughput sequencing

summary: We found BALB/cByJ and BALB/cJ mice differ in their responses to oxycodone state dependent conditioned place preference, whole brain [oxycodone] and its metabolites [noroxycodone] and [oxymorphone] following oxycodone administration, the 53.5°C hot plate, mechanical stimulation in the von Frey test, and gross brain weight. We then identified a quantitative trait locus (QTL) on chromosome 15 for whole brain (LOD = 7.07; p < 0.001), 13 for hot plate sensitivity (LOD = 10.7; p < 0.001; peak = 56 Mb) and a QTL for brain weight on chromosome 5 (LOD = 8.7; p < 0.001). These tissues were used for expression QTL mapping to highlight the candidate genes Zhx2 (57 Mb) as the top transcript with the strongest association at the ch15 oxymorphone locus and identified H2afy (56 Mb) as the top transcript with the strongest association at the ch13 hot plate locus.

overall_design: 64 BALBcJ x BALBcByJ F2 mice (32M, 32F) were used for eQTL mapping and were 78–127 days old on day 1 of testing. Mice were trained using a CPP protocol with either saline (i.p.) or 1.25 mg/kg OXY (i.p.) (Kirkpatrick & Bryant, 2015) and were then sacrificed by rapid decapitation on the final day of experimental testing, 30 min after receiving either saline (i.p.) or OXY (1.25 mg/kg, i.p.). Using a brain matrix, striatal and hippocampal tissues were dissected. Striatal punches were harvested at bregma 1.5 - -0.5mm and sampled with a 2 mm punch. Hippocampal tissues were dissected from bregma --0.5 - -2.5 using a sterile metal spatula to peel away the cortical layer. Tissues were collected and preserved in RNAlater. RNA was extracted in RNAlater-preserved tissue using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), DNAse digestion (Qiagen), and elution with RNAse and nucleotide free water (Yazdani et al., 2015) and diluted to 100 ng/ul. RNA library preparation (poly-A selection) and RNA-seq were conducted at the University of Chicago Genomics Facility on an Illumina NovaSeq 6000 using a NovaSEQ SP-100 bp flowcell/reagent cassette. We used the R/Bioconductor package “scruff” to conduct demultiplexing, read alignment, read counting, quality checking and data visualization (Wang et al., 2019). Reads were trimmed for quality using Trimmomatic (Bolger et al., 2014). Trimmed reads were then aligned to the mm10 mouse reference genome (Ensembl) to generate BAM files for alignment using STAR (Dobin et al., 2013). For differential gene analysis in the spinal cord, the featureCounts read summarization program was used to count reads mapping to the “exon” feature in a GTF file obtained from Ensembl (GRCm38). Genes without 10 reads per million in at least 3 samples were excluded from analysis using EdgeR 51, and differential gene expression analysis of normalized counts was conducted using an appropriate design matrix, and reported using the topTable function.

first: Jacob

middle: A

last: Beierle


title: ATAC-Seq of single myofibers and muscle stem cells (MuSCs)

status: Public on Feb 13 2022

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of single myofiber ATAC-Seq (smfATAC-Seq) to investigate the  chromatin accessibility of a single myofiber without the presence of confounding muscle resident cell types. This method demonstrates that open chromatin regions of myonuclei can be tagmentated and high-quality sequencing ready libraries can be generated from these fragments. To perform comparative analysis as well as to demonstrate the applicability of the smfATAC-Sew to study changes in chromatin of myonuclei within different contexts, smfATAC-Seq was performed both on uninjured myofibers as well as injured myofibers seven days after induced injury. Furthermore, ATAC-Seq on 5000 muscle stem cells (MuSCs) was also performed according to the previously described OMNI ATAC-Seq protocol (Corces, M.R. et al. Nature Methods, 2017) in order to compare the sequencing quality of the smfATAC-Seq as well as to demonstrate the changes in open chromatin that occur from the stem cell state to the fully differentiated myofibers. smfATAC-seq resulted in comparable coverage and sequencing depth to the ATAC-seq performed on MuSCs and allowed for peak calling and differential peak analysis. These analysis revealed that the open chromatin state of uninjured and injured myofibers after seven days are mostly similar although some regions invovled in immune response remain in an open state in the injured myofibers compared to the uninjured myofibers and the regions involved in structural formation of the muscle are more accessible in the case of regeneration. Even though certain differences in the open chromatin are observed, smfATAC-Seq analysis suggest that overall, the open chromatin state of the myonuclei returns back to homeostasis after seven days of regeneration. Furthermore, smfATAC-Seq comparison with the ATAC-Seq from MuSCs show the differences in open chromatin regions between these conditions. Increased accessibility of genes involved in myogenesis and structural components can be observed in the myofibers compared to MuSCs while MuSCs show increased accessibility in regions involved in membrane permeability and signalling pathways. In addition, the regions that are accessible for both conditions include genes involved in mitochondrial transport, regulation of transcription and regulation of metabolites and energy. Overall, this study introduces smfATAC-Seq that succesfully assesses the genome-wide chromatin accessibility of a single myofiber with relatively high sequencing depth. The smfATAC-Seq can be used to perform comparative analysis between different conditions such as injury. However, this method can be readily applied to study differences between young and old myofibers or in the context of muscular dystrophy, cachexia, and exercise.

overall_design: smfATAC-Seq was performed on an uninjured single myofiber as well as injured myofiber isolated from Extensor Digitorum Longus (EDL). In addition, ATAC-seq on 5000 MuSCs is performed by following the OMNI ATAC-Seq protocol. The comparative analysis were performed between uninjured and injured myofibers and between uninjured myofibers and MuSCs.

first: Marie-Michelle

last: Simon


title: RNA Expression QTL mapping in an F2 cross of BALB/cJ and BALB/cByJ mice to identify candidate genes for behavioral/metabolic QTLs

overall_design: 64 BALBcJ x BALBcByJ F2 mice (32M, 32F) were used for eQTL mapping and were 78–127 days old on day 1 of testing. Mice were trained using a CPP protocol with either saline (i.p.) or 1.25 mg/kg OXY (i.p.) (Kirkpatrick & Bryant, 2015) and were then sacrificed by rapid decapitation on the final day of experimental testing, 30 min after receiving either saline (i.p.) or OXY (1.25 mg/kg, i.p.). Using a brain matrix, striatal and hippocampal tissues were dissected. Striatal punches were harvested at bregma 1.5 - -0.5mm and sampled with a 2 mm punch. Hippocampal tissues were dissected from bregma --0.5 - -2.5 using a sterile metal spatula to peel away the cortical layer. Tissues were collected and preserved in RNAlater. RNA was extracted in RNAlater-preserved tissue using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), DNAse digestion (Qiagen), and elution with RNAse and nucleotide free water (Yazdani et al., 2015) and diluted to 100 ng/ul. RNA library preparation (poly-A selection) and RNA-seq were conducted at the University of Chicago Genomics Facility on an Illumina NovaSEQ6000 using a NovaSEQ SP-100 bp flowcell/reagent cassette. We used the R/Bioconductor package “scruff” to conduct demultiplexing, read alignment, read counting, quality checking and data visualization (Wang et al., 2019). Reads were trimmed for quality using Trimmomatic (Bolger et al., 2014). Trimmed reads were then aligned to the mm10 mouse reference genome (Ensembl) to generate BAM files for alignment using STAR (Dobin et al., 2013). For differential gene analysis in the spinal cord, the featureCounts read summarization program was used to count reads mapping to the “exon” feature in a GTF file obtained from Ensembl (GRCm38). Genes without 10 reads per million in at least 3 samples were excluded from analysis using EdgeR 51, and differential gene expression analysis of normalized counts was conducted using an appropriate design matrix, and reported using the topTable function.


title: Obesity-induced senescent macrophages activate a fibrotic transcriptional program in adipocyte progenitors

first: Nabil

last: Rabhi

address: Silvio Conte Building, 72 E. Concord St

department: Biochemistry

institute: Boston University

summary: Adipose tissue fibrosis is regulated by the chronic and progressive metabolic imbalance caused by differences in caloric intake and energy expenditure. By exploring the cellular heterogeneity within fibrotic adipose tissue, we demonstrate that early adipocyte progenitor cells expressing both platelet derived growth factor receptor (PDGFR) α and β are the major contributors to extracellular matrix deposition. We show that the fibrotic program is promoted by senescent macrophages. These macrophages were enriched in the fibrotic stroma and exhibit a distinct expression profile. Furthermore, we demonstrate that these cells display a blunted phagocytotic capacity and acquire a senescence-associated secretory phenotype. Finally, we determined that osteopontin, which was expressed by senescent macrophages in the fibrotic environment promoted progenitor cell proliferation, fibrotic gene expression, and inhibited adipogenesis. Our work reveals that obesity promotes macrophage senescence and provides a conceptual framework for the discovery of rational therapeutic targets for metabolic and inflammatory disease associated with obesity.

overall_design: Single cell of the stromal vascular fraction from mice epididymal adipose tissue following 24 weeks of either high fat or low fat diet feeding

first: Kathleen

last: Desevin

first: Anna

middle: C

last: Belkina

first: Andrew

last: Tilston-Lunel

first: Xaralabos

last: Varelas

first: Matthew

last: Layne

first: Stephen

middle: R

last: Farmer


title: Global transcriptomic analyses of pluripotent stem cell-derived airway epithelial cells at 1 and 3 days after infection with SARS-CoV-2

status: Public on Feb 10 2022

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

summary: We performed transcriptomic profiling of human iPSC-derived airway epithelial cells after infection with SARS-Co-V2. Using a recently described protocol to first generate airway basal cells from iPSCs and sunsequently differentiate those basal cells (iBCs) into a mucociliary epithelium in air-liquid interface culture. In this experiment we generated airway epithelial cultures from two different iPSC lines ("BU3 NGPT"  and "1566"). In stage 6 of this protocol (>D45) iBCs are identified and purified by sorting on NGFR+ cells, and purified cells are expanded and differentiated on Transwells in dual-SMAD inhibition media then transitioned to ALI media when >80% confluent. Apical chamber media is removed to initiate ALI to recapitulate a physiologically-relevant environment and stimulate differentiation.  After 14 days, iBCs form a pseudostratified airway epithelium that displays morphologic, molecular, and functional similarities to primary human airway epithelial cells and is comprised of the major airway cell types of multi-ciliated, secretory, and basal cellscomposed of the major airway epithelial cell types, that is permissive to SARS-CoV-2 infection. We studied the response of these iPSC-derived airway epithelial cells to SARS-CoV-2 infection using RNA-Sequencing 1 and 3 days post infection (DPI).

overall_design: On day 24 of ALI culture, 6 replicate wells of iPSC-airways from BU3 NGPT were infected with SARS-CoV-2 from the apical surface and 6 replicate wells were mock-infected.  Three wells per condition were harvested at each 1 and 3 dpi. 3 replicate wells of 1566 were infected with SARS-CoV-2 in the identical manner and three wells were mock infected. All samples were harvested at 1 dpi.

first: Ruby

first: Jonathan

last: Lindstrom-Vautrin

first: Carlos

last: Villacorta-Martin

first: Finn

last: Hawkins


title: Discordant genome assemblies drastically alter the interpretation of single cell RNA sequencing data which can be mitigated by a novel integration method

city: Oxford

first: Mathilda

middle: TM

last: Mommersteeg

state: Oxfordshire

address: Sherrington Building

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

summary: Advances in sequencing and assembly technology has led to the creation of genome assemblies for a wide variety of non-model organisms. The rapid production and proliferation of updated, novel assembly versions can create create vexing problems for researchers when multiple genome as-sembly versions are available at once, requiring researchers to work with more than one reference genome. Multiple genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells as single cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. Using the Astyanax mexicanus this study highlights how the interpretation of a single cell dataset from the same sample changes when aligned to its two different available genome assemblies. We found that the number of cells and expressed genes detected were drastically different when aligning to the different assemblies. When the genome assemblies were used in isolation with their respective annotation, cell type identification was confounded as some classic cell type markers were assembly-specific, whilst other genes showed differential patterns of expression between the two assemblies.  To overcome the problems posed by multiple genome assemblies, we propose that researchers align to each available assembly and then integrate the resultant datasets to produce a final dataset in which all genome alignments can be used simultaneously. We found this approach increased the accuracy of cell type identification and maximised the amount of data that could be extracted from our single cell sample by capturing all possible cells and transcripts. As scRNAseq becomes more widely available, it is imperative that the single cell community is aware how genome assembly alignment can alter single cell data and its interpretation, especially when reviewing studies on non-model organisms.

overall_design: 10X Single Cell RNAseq data from 3 pooled surface fish ventricles (n=1) was aligned to the v1.0.2 and v2.0 A. mexicanus genome assemblies (Ensembl 103 release).

first: Helen

middle: G

last: Potts

first: Madeleine

middle: E

last: Lemieux

first: Edward

middle: S

last: Rice

first: Wesley

last: Warren

first: Robin

middle: P

last: Choudhury

middle: T


title: Therapeutic Targeting of EZH2 and BET BRD4 in Pediatric Rhabdoid Tumor

city: Chicago

first: Yukitomo

last: Ishi

state: IL

address: 303 East Superior Street, Simpson Querrey

institute: Northwestern University

summary: We proved that histone H3K27me3 and H3K27ac were elevated in AT/RT cells and distributed in distinct chromatin regions to regulate specific gene expression and to promote AT/RT growth. Targeting EZH2 and BRD4 activity is therefore a potential combination therapy for AT/RT.

overall_design: DNA methylation array was used to determine the molecular profile of AT/RT cell lines. Genome Studio v2011.1 was used for data processing.

first: Yongzhan

last: Zhang

first: Ali

first: Takahiro

last: Sasaki

first: Andrea

last: Piunti

first: Amreena

last: Suri

first: Jun

last: Watanabe

first: Kouki

last: Abe

first: Xingyao

last: He

first: Hiroaki

last: Katagi

first: Pankaj

last: Bhalla

first: Manabu

last: Natsumeda

first: Lihua

last: Zou

last: Shilatifard

first: Rintaro

last: Hashizume


title: Follistatin promotes LIN28B mediated supporting cell reprogramming and hair cell regeneration in the murine cochlea

city: Baltimore

first: Angelika

last: Doetzlhofer

state: MD

address: 855 North Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

summary:
Purpose: To identify how follistatin (FST) and LIN28B re-activation augments the regenerative competence of cochlear supporting cells (SCs), we used bulk-RNA sequencing to analyze the transcriptome of SC-containing control, FST, LIN28B and FST+LIN28B overexpressing organoids after 7 days of culture. The 7 day time point was chosen as it correlates with the peak of SC proliferation and presumed SC reprogramming.
Methods:  Samples were processed using Illumina's TruSeq stranded Total RNA kit, using the UDI indexes. The samples were sequenced on the NovaSeq 6000, paired end, 2x50 base pair reads.We used kallisto (v0.46.1) to pseudo-align reads to the reference mouse transcriptome Ensembl Mus musculus v96 and to quantify transcript abundance. The companion tool sleuth was used to determine differentially expressed genes (DEGs) comparing control to LIN28B and or FST overexpressing conditions.
Results:  Applying Wald test we identified 423DEGs for FST+LIN28B(q-value< 0.01), 764 DEGs for LIN28B (q-value< 0.01) and 37 DEGs for FST (q-value< 0.05). The list of downregulated genes included structural genes (Tecta, Col2a1, Col11a2, Col9a3) as well as transcription factor known to promote neuronal/glial cell differentiation (Zbtb20,Nfix, Nfib) and cochlear maturation (Thrb).The list of upregulated genes contained a large number of let-7 target genes known to promote in stemness (e.g., Hmga2, Arid3a, Trim71,Igf2bp1), and to regulate stem cell metabolism (e.g.,Hk2),as well as genes involved in cell cycle regulation (e.g.,Ccnd2,Ccnd3, Cdkn1a, Cdkn2a) and cell fate specification (e.g. Sox11).

overall_design: mRNA profiles of control, LIN28B, FST and FST+LIN28B overexpressing organoids established with cochlear epithelial cells from 5-day old mice

first: Xiaojun

last: Li

first: Charles

last: Morgan

first: Loyal

last: Goff


title: Genetic basis of thermal nociceptive sensitivity and brain weight in a BALB/c reduced complexity cross: BALB/cJ vs BALB/cByJ Spinal Cord RNAseq

first: Camron

last: Bryant

summary: We found BALB/cByJ mice showed enhanced sensitivity on the 53.5°C hot plate and mechanical stimulation in the von Frey test compared to BALB/cJ mice and replicated decreased gross brain weight in BALB/cByJ versus BALB/cJ. We then identified a quantitative trait locus (QTL) on chromosome 13 for hot plate sensitivity (LOD = 10.7; p < 0.001; peak = 56 Mb) and a QTL for brain weight on chromosome 5 (LOD = 8.7; p < 0.001). Expression QTL mapping of brain tissues identified H2afy (56.07 Mb) as the top transcript with the strongest association at the hot plate locus (FDR = 0.0002) and spliceome analysis identified differential exon usage within H2afy associated with the same locus. These data are spinal cord RNAseq to confirm differential expression of H2afy and other candidate genes.

overall_design: 16 Male and Female BALB/cJ vs BALB/cByJ (N=4/group) mice underwent pain testing at KUMC (PMID:35088629), were sacrificed, spinal cord tissues collected an preserved in RNAlater. RNA was extracted in RNAlater-preserved tissue using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), DNAse digestion (Qiagen), and elution with RNAse and nucleotide free water (Yazdani et al., 2015) and diluted to 100 ng/ul. RNA library preparation (poly-A selection) and RNA-seq were conducted at the University of Chicago Genomics Facility on an Illumina NovaSEQ6000 using a NovaSEQ SP-100 bp flowcell/reagent cassette. We used the R/Bioconductor package “scruff” to conduct demultiplexing, read alignment, read counting, quality checking and data visualization (Wang et al., 2019). Reads were trimmed for quality using Trimmomatic (Bolger et al., 2014). Trimmed reads were then aligned to the mm10 mouse reference genome (Ensembl) to generate BAM files for alignment using STAR (Dobin et al., 2013). For differential gene analysis in the spinal cord, the featureCounts read summarization program was used to count reads mapping to the “exon” feature in a GTF file obtained from Ensembl (GRCm38). Genes without 10 reads per million in at least 3 samples were excluded from analysis using EdgeR 51, and differential gene expression analysis of normalized counts was conducted using an appropriate design matrix, and reported using the topTable function.

first: Jacob

last: Beierle

first: Erin

last: Young


title: Global characterization of peripheral B cells in Parkinson’s disease by single-cell RNA and BCR sequencing

city: Harbin

first: Pingping

last: Wang

state: China

address: 92 West Dazhi Street,Nan Gang

country: China

institute: HIT

summary: Fresh blood samples were collected from 8 PD patients and 6 age-matched healthy controls. Then, peripheral blood mononuclear cells (PBMCs) were isolated by Percoll density gradient centrifugation. Next, CD19+ B cells were sorted using fluorescence-activated cell sorting (FACS). Single-cell 5’ gene expression libraries and V(D)J enriched libraries were prepared according to the standard protocols provided by the 10x Genomics Chromium Single Cell Immune Profiling Solution. Finally, single-cell 5’ gene expression and V(D)J libraries were sequenced on Illumina Noveseq 6000, providing 150 bp paired-end reads.

overall_design: Single cell RNA and BCR sequencing for B cells from 8 PD patients and 6 age-matched healthy controls.

first: Qinghua

last: Jiang


title: Single-cell RNA-seq in a comparative primate skeletal cell culture model [1]

first: Genevieve

last: Housman

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

summary: We evaluated the degree to which gene expression patterns in primate skeletal cells differ across cell types and species. First, we optimized differentiation protocols of human and chimpanzee iPSCs through an intermediate MSC state and into chondrogenic or osteogenic cells. Single-cell RNA sequencing was collected from each stage of differentiation (iPSCs, MSCs, chondrogenic cells, and osteogenic cells) using the 10X Genomics platform to characterize gene expression variation.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: One human iPSC line (H23555) and one chimpanzee iPSC line (C8861) were differentiated into MSCs, chondrogenic cells, and osteogenic cells.


title: Single-cell RNA-seq in a comparative primate skeletal cell culture model [2]

summary: We evaluated the degree to which gene expression patterns in primate skeletal cells differ across cell types and species. First, we optimized differentiation protocols of human and chimpanzee iPSCs through an intermediate MSC state and into osteogenic cells. Single-cell RNA sequencing was collected from each stage of differentiation (iPSCs, MSCs, and osteogenic cells) using the 10X Genomics platform to characterize gene expression variation.

overall_design: Six human iPSC lines and six chimpanzee iPSC lines were differentiated into MSCs and osteogenic cells.


title: Depletion of AUF1 from myeloid cells protects from allergic airway and tumor infiltration and alters pro-angiogenic macrophage polarization by adenosines

status: Public on Feb 09 2022

city: Vari

first: Dimitris

middle: L.

last: Kontoyiannis

state: Attiki

address: 34 Fleming

department: Institute for Fundamental Biomedical Research

country: Greece

institute: BSRC "Alexander Fleming"

summary: Our data demonstrate that in innate immune cells, AUF1 does not act as a generic anti-inflammatory factor but has a rather distinct role in selective macrophage phenotypes.

overall_design: We use a conditional allele for the myeloid deletion of the hnRNPD gene and employ a disease-oriented phenotypic screen to assess the requirement of AUF1 in contexts of innate immune reactivity.

first: Sofia

last: Gargani

first: Niki

last: Lourou

first: Christina

last: Arapatzi

last: Tzanos

first: Marania

last: Saridakι

first: Esmeralda

last: Dushku

first: Margarita

last: Chatzimike

first: Nikolaos

last: Sidiropoulos

last: Andreadou

first: Vassilios

last: Ntafis

first: Pantelis

last: Hatzis

first: Vassiliki

last: Kostourou

middle: L


title: Next Generation Sequencing Facilitates Quantitative Analysis of control and MvuB-deficient Embryonic Stem Cells Transcriptomes

city: Nanjing

first: wang

middle: cong

last: cong

state: Jiangsu

address: 12 Xuefu Road

institute: Nanjing University

summary: Purpose: The goals of this study are to compare control and MuvB-dificient embryonic stem cells transcriptome profiling (RNA-seq) to evaluate the target genes regulated by MuvB

overall_design: mRNA profiles of  control and MuvB-dificient embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina Novaseq6000.

first: Congcong

first: JinZhong

last: Qin


title: Single-cell RNA-seq in a comparative primate skeletal cell culture model

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

overall_design: Refer to individual Series


title: Hippocampus-based mitochondrial respiratory function decline is responsible for perioperative neurocognitive disorders

city: Hefei

first: Keqiang

last: He

address: 17 Lujiang Road, P.R.China

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

summary: Background: Perioperative neurocognitive disorders (PND), a postoperative cognitive dysfunction occurs more often in the elderly. The etiology of PND remains largely elusive. This study aims to understand the etiology in a mouse model with tibial fracture (a surgical trauma), by examining the transcriptome-wide response of hippocampus, a brain region that is tightly associated with memory formation.    Methods: Mice at age of 7~8 months were randomly divided into two groups, surgery (tibial fracture) group and control (sham) group. At day (d) 1 after the surgical operation, hippocampal tissues were isolated and then subjected to RNA extraction and RNA sequencing (RNA-seq).     Findings: Levels of respiratory complex related genes are significantly decreased in the brain of mice subjected to surgery. Consequently, the activities of multiple respiratory complexes and respiratory chain function is decreased in the hippocampus of mice with surgical operation.    Interpretation: We here propose a novel mechanism of mitochondrial dysfunction in PND etiology, and also provide a potential therapeutic target for PND.

overall_design: Mice were randomly allocated to two groups, sham and tibial fracture group.  Control group of mice were subjected to anesthesia only, and surgery group of mice were subjected to anesthesia followed with tibial fracture operation. At day 1 of post operation, RNA was isolated from the hippocampus and then subjected to RNA-seq analysis.

first: Juan

last: Zhang

first: Dingfeng

last: Li

first: Qiang

last: Liu


title: Voluntary running and IV nicotinamide riboside synergise to boost mouse skeletal muscle NAD+ without impacting OXPHOS capacity or insulin sensitivity

status: Public on Feb 08 2022

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: In clinical trials, oral supplementation with nicotinamide riboside (NR) fails to increase muscle mitochondrial respiratory capacity and insulin sensitivity, but also does not increase muscle NAD+ levels. This study tests the feasibility of chronically elevating skeletal muscle NAD+ in mice and investigates the putative effects on mitochondrial respiratory capacity, insulin sensitivity, and gene expression. Accordingly, to improve bioavailability to skeletal muscle, we developed an experimental model for administering NR repeatedly through a jugular vein catheter. Mice on a Western diet were treated with various combinations of NR, pterostilbene (PT), and voluntary wheel running, but metabolic effects of NR and PT treatment were modest. We conclude that chronic elevation of skeletal muscle NAD+ by intravenous injection of NR is possible but does not affect muscle respiratory capacity or insulin sensitivity in either sedentary or physically active mice. Our data have implications for NAD+ precursor supplementation regimes.

overall_design: 2^3 full-factorial setup with the three factors nicotinamide riboside (NR), pterostilbene (PT) and voluntary wheel running

first: Mads

middle: V

last: Damgaard

first: Thomas

last: Nielsen

first: Astrid

last: Basse

first: Sabina

last: Chubanava

first: Kajetan

last: Trost

last: Moritz

first: Ryan

middle: W

last: Dellinger

first: Steen

last: Larsen

first: Jonas

last: Treebak


title: Effect of nitrogen addition timing of an enological yeast strain gene expression

city: Montpellier

first: Virginie

last: Galeote

address: 2, place Pierre Viala

country: France

institute: UMR SPO, INRAE

summary: The aim of this study was to evaluate the effect of timing of nitrogen added on a Saccharomyces cerevisiae yeast wine strain. We studied several addition timings and evaluated gene expression at different times after nitrogen addition (30min and 2h). We found that there were no major differences between the two samples after addition. 305 induced genes were common to both addition timings and represented amino acid biosynthetic functions. 147 induced genes were only induced after an addition made at the beginning of the stationary phase and 142 exclusively after an addition made at the end of the stationary phase. These genes represented translation and ribosomal RNA synthesis functions respectively.   150 genes were only repressed after an addition made at the beginning of the stationary phase and represented functions of responses to stress and nutritional deficiencies but also oxidoreductase activity. The repressed genes common to both timings (284) represented the same functions. Finally, the 127 genes only repressed after an addition made close to the end of the fermentation represented functions coding for lipid metabolism and cell wall organization.

overall_design: The yeast Saccharomyces cerevisiae EC1118 is a commercial wine yeast from Lallemand SA. Fermentation experiments were carried out in triplicates. The fermentation medium mimicks a standard natural must and has the same composition as the SM140 with  previously described (Bely et al 1990). Fermentations were conducted under constant stirring at 24°C in 1.2 L flasks equipped with locks to maintain anaerobiosis. Production of CO2 was monitored by weighing the flasks every 20 min, to determine weight loss. The rate of CO2 production was estimated using a polynomial smoothing as previously described in Sablayrolles et al (1987). The number of cells was determined with a particle counter (Coulter counter, Beckman Coulter). Two timings of addition were carried out on the fermentations. One addition was made at the beginning of the stationary phase of fermentation (20g/L of CO2 released). The second addition timing corresponds to the three quarters of the stationary phase of fermentation (50g/L of CO2 released). Two samples were taken after each addition: 30min and 2h after nitrogen addition. A control without addition was carried out and the samples were taken at the CO2 released corresponding to the fermentations with nitrogen additions.

first: Joséphine

last: Godillot

first: Martine

last: Pradal

first: Isabelle

last: Sanchez

first: Jean-Roch

last: Mouret


title: Single-cell Transcriptome Analysis Revealed that EGFR Mutation Leads to a Suppressive Tumor Immune Microenvironment in Lung Adenocarcinoma

city: Guangzhou

first: Qing

last: Zhou

state: Guangdong

address: 106#，ZHONG SHAN ER ROAD

institute: Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China

summary: We analyzed 40,799 single cells from nine samples and found that in EGFR-mutant LUAD, tumor cells generated an immunosuppressive microenvironment by releasing cytokines to attract suppressive immune cells such as myeloid-derived suppressor cells (MDSCs) directly or indirectly by interacting with macrophages, dendritic cells, or other cell types. By contrast, EGFR wild-type LUAD had a greater ability to recruit immunocompetent T cells such as TRMs and Th1 cells, thus driving a proinflammatory microenvironment.

overall_design: To evaluate the cellular landscape of the TME of lung adenocarcinoma based on EGFR mutation status, we collected nine tumor samples from eight patients with treatment-naïve LUAD for scRNA-seq and bioinformatic analyses.

first: Lei

last: Yang


title: Myocardial cellular gene expression during pressure overload: evidence for transient partial endothelial to mesenchymal transition [scDROP-seq]

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

country: Germany

institute: Medizinische Fakultät Mannheim

summary: Pathological processes underlying pressure overload triggered heart failure were mainly analyzed from a cardiomyocyte centric view. To identify new cellular mechanisms, we isolated cardiomyocytes, endothelial cells and fibroblasts as most abundant cardiac cell types from mice in the subacute and chronic stages of pressure overload (by transverse aortic constriction, TAC) and performed RNA-sequencing. We detected highly cell-type specific transcriptional responses with characteristic time courses and active intercellular communication, especially early after TAC. We focused on endothelial cells, and single-cell sequencing in this population showed enhanced expression of collagens and inflammatory mediators at this stage. Importantly, these endothelial transcriptional changes were transduced to the translational level as shown by Ribo-Tag sequencing and verification of collagen protein production by cardiac endothelial cells. In conclusion, we provide a resource of cardiac cellular gene expression in pressure overload and reveal the induction of collagens by endothelial cells as potential therapeutic target.

overall_design: Cardiac EC lysates were sequenced as single cells either from Sham or TAC after 1week by the help of Dro-seq

first: Julio

last: Cordero

first: Gergana

last: Dobreva


title: Myocardial cellular gene expression during pressure overload: evidence for transient partial endothelial to mesenchymal transition [Ribo-seq]

overall_design: Ribo-tag mice were crossed with Cdh5-CreERT2 mice expressing the Cre recombinase under the control of the Cadherin 5 (Cdh5) promoter (Cdh5-CreERT2:Ribo-tag). At 9 weeks of age, male mice underwent transverse aortic constriction or sham operation

first: Christoph

last: Dieterich

first: Etienne

last: Boileau


title: BEND3 safeguards pluripotency by repressing differentiation-associated genes

city: Urbana

first: Supriya

last: Prasanth

state: Illinois

address: 601S Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois Urbana-Champaign

summary: We have uncovered that BEND3 is a heterochromatin-associated protein that functions as a transcription repressor.  Expression of BEND3 correlates with the state of pluripotency, with a significant decline in BEND3 levels in differentiated cells. Cells lacking BEND3 show defects in cell cycle progression with failure to enter S-phase. BEND3 affects the transcription of cellular genes that modulate chromatin organization and cellular differentiation and that downregulation of BEND3 is critical for cellular differentiation.

overall_design: BEND3 LacZ and sh60 mRNA profile in Ntera-2 cell line


title: Transcriptional analysis of 12 breast cancer patients

city: Brussels

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

summary: Targeted gene expression on 12 breast cancer patients using the human panCancer Immune panel (NanoString Technologies)

overall_design: Total RNA was extracted from a pre-treatment taken core needle biopsy from 12 BC patients, subsequently 50ng of total RNA was used as input material and human PanCancer Immune panel used for gene expression profiling. Assay was performed at the nCounter® MAX instrument.

first: Hanne

last: Locy


title: Analysis of myocardial cellular gene expression during pressure overload reveals matrix based functional intercellular communication


title: 5-methylcytosine modification-mediated mRNA stabilization is associated with sexual development of malaria parasites [Half-life]

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

institute: TongJi University

summary: 5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. falciparum) malaria parasites transcriptome and depicted a comprehensive characterization landscape of m5C mRNA modification at single-nucleotide resolution (RNA-BisSeq) from asexual replicating stage to gametocyte development. Through transcriptome-wide profiling of mRNA m5C modification, we found that m5C modified mRNA displayed higher stability than non-m5C modified mRNA during the development of Plasmodium. We identified Plasmodium ortholog of NSUN2 as an mRNA m5C methyltransferase in malaria parasites. LC–MS/MS and RNA-BisSeq analysis revealed a large decrease in mRNA m5C modification at transcriptome-wide level upon Nsun2 knockout. Absence of Nsun2 severely reduced gametocyte production in either rodent (P. yoelii) or human (P. falciparum) malaria parasites. Meanwhile, some genes related to gametocytogenesis displayed a great reduction of m5C modification. Together, our data provides comprehensive mRNA m5C profiles in Plasmodium genus and reveals m5C modification-mediated mRNA stability as a novel mechanism regulating sexual differentiation of a unicellular eukaryote.

overall_design: mRNAs were extracted from parasites harvested at sexual gametocyte (G) stage in P. yoelii.

first: Meng

last: Liu


title: Comparative expression study regarding leukemia samples with DDX41 mutation

status: Public on Feb 07 2022

city: Seoul

first: Jieun

last: Kim

state: Yongsan-gu

department: Department of Laboratory Medicine

country: South Korea

institute: Soonchunhyang University Seoul Hospital

summary:
Genetic expression profiling (GEP) has previously proven useful in B-ALL for identifying signatures of oncogenes, with the recognition of novel subgroups, as well as with outcome. Therefore, we adopted GEP of bonemarrow samples of B-ALL with t(9;22) to uncover the contribution of DDX41 to leukemogenesis.
The germline mutations of DDX41, also known as DEAD box RNA helicase 41, have been found in about 1.5% of myeloid neoplasms (MNs). Development of MDS/AML is relatively common in germline DDX41 mutations. However, a variety of hematological malignancies (HMs) have been reported.   We report a novel case of bi-alleleic DDX41 mutations in B-cell lymphoblastic leukemia (B-ALL), with unusual location of DDX41 mutations. The gene expression profile (GEP) of Ph+ B-ALL with bi-alleleic DDX41 mutations showed heterogeneously transitional GEP and altered gene expression levels of genes involved in the process essential for red blood cells and myeloid cell differentiation were noted.  We report that DDX41 mutations are unusual but can be an underlying event in Ph+B-ALL and screening DDX41 mutations can be also informative for patients awaiting for haploidentical stem cell transplantation and choosing the therapy.

overall_design: RNA was extracted from proband’s BM samples at initial diagnosis and compared the differentially expressed genes of Ph+B-ALLIKZF1+/DDX41dm with two cases of Ph+B-ALLIKZF1+/DDX41- in order to elucidate the role of DDX41 in leukemogenesis.

first: Woo

middle: Y

last: Shin


title: 5-methylcytosine modification-mediated mRNA stabilization is associated with sexual development of malaria parasites [RNA-seq]

sample_organism:
Plasmodium falciparum
Plasmodium yoelii

platform_organism:
Plasmodium falciparum
Plasmodium yoelii

overall_design: mRNAs were extracted from highly synchronized parasites harvested over the development at asexual schizont (S) stage and sexual gametocyte (G) stages in P. falciparum and P. yoelii.


title: PLCG2 is Associated with the Inflammatory Response and is Induced by Amyloid Plaques in Alzheimer's Disease

city: Stanford

first: Andy

last: Tsai

state: California

address: 290 Jane Stanford Way E365

institute: Stanford University

summary: Differential expression analysis in Plcg2-inactivated mouse model identified inflammation-related genes and pathways.

overall_design: To investigate the role of PLCG2, differential expression analysis by comparing Plcg2-inactivated mice with WT mice at one month of age was performed using gene expression data from the NanoString Neuroinflammation panel

first: Chuanpeng

last: Dong

first: Peter

middle: B

last: Lin

first: Evan

middle: J

last: Messenger

first: Brad

last: Casali

first: Miguel

last: Moutinho

first: Yunlong

first: Adrian

last: Oblak

first: Bruce

last: Lamb

first: Gary

last: Landreth

first: Stephanie

last: Bissel

first: Kwangsik

last: Nho


title: Characterization of Mfsd2a-deficient lung AT2 cells.

city: Singapore

first: Bernice

last: Wong

address: 8 College Road

department: Cardiovascular and Metabolic Disorders

country: Singapore

institute: Duke-NUS Medical School

summary: RNA-seq was performed to understand transcriptome changes with Mfsd2a deficiency in lung AT2 cells. Gene expression analysis was performed using DESeq2.

overall_design: Mfsd2a floxed mice (2afl/fl) were generated as described previously (Wong et. al., JBC, 2016). Tamoxifen-inducible AT2-specific knockout mice (AT2aKO) were generated by crossing 2afl/fl with Sftpc-Cre/ERT2 driver [B6.129S-Sftpctm1(cre/ERT2)Blh/J. Total RNA was extracted from AT2 cells isolated from 2 weeks post-tamoxifen induced 2afl/fl or AT2aKO mice for RNA-sequencing. 4 mice per genotype was used.

middle: H

first: David

last: Silver


title: Myocardial cellular gene expression during pressure overload: evidence for transient partial endothelial to mesenchymal transition [Bulk RNA-seq]

first: Joerg

last: Heineke

overall_design: Three type of cardiac cells, Endothelial, myocytes, and Fibroblast were isolated from 8-10weeks old mice. They were either sham or 1 or 8 weeks after transversal aorta constriction (TAC)

first: Julio

last: Cordero

first: Gergana

last: Dobreva


title: 5-methylcytosine modification-mediated mRNA stabilization is associated with sexual development of malaria parasites [BisRNA-seq]

first: meng

last: liu

type: Methylation profiling by high throughput sequencing

first: Meng

last: Liu


title: Targeting DNA topoisomerases or checkpoint kinases forces a shift in global protein homeostasis, triggering widespread protein aggregation

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

summary: A loss of the checkpoint kinase ATM leads to impairments in the DNA damage response, and in humans causes cerebellar neurodegeneration, and a high risk to cancer. A loss of ATM is also associated with increased protein aggregation. The relevance and characteristics of this aggregation are still incompletely understood. Moreover, it is unclear to what extent other genotoxic conditions can trigger protein aggregation as well. Here, we show that targeting ATM, but also ATR or DNA topoisomerases result in a similar, widespread aggregation of a metastable, disease-associated subfraction of the proteome. Aggregation-prone model substrates, including expanded polyglutamine repeats, aggregate faster under these conditions. This increased aggregation results from an overload of chaperone systems, which lowers the cell-intrinsic threshold for proteins to aggregate. In line with this, we find that inhibition of the HSP70 chaperone system further exacerbates the increased protein aggregation. Moreover, we identify the molecular chaperone HSPB5 as a potent suppressor of it. Our findings reveal that various genotoxic conditions trigger protein aggregation, in a manner that is highly reminiscent of the widespread aggregation occurring in situations of proteotoxic stress and in proteinopathies.

overall_design: Bulk RNA-seq of RNA extracted from HEK293T and U2OS cells. HEK293T cells were treated with either DMSO of Camptothecin. U2OS cells were either wild type or knockout for ATM. 4 replicates per group.

first: Wouter

last: Huiting

first: Suzanne

last: Dekker

first: Joris

middle: C

last: van der Lienden

first: Rafaella

last: Mergener

first: Gabriel

last: Furtado

first: Maiara

middle: K

last: Musskopf

first: Mehrnoosh

last: Oghbaie

first: Luciano

last: Di Stefano

first: Maria

middle: A

last: van Waarde-Verhagen

first: Lara

last: Barazzuol

first: John

last: LaCava

first: Harm

last: Kampinga

first: Steven

last: Bergink


title: Circular RNA expression profile in human bladder cancer cell line and human urothelial immortalized cell line

city: Nanning

first: Aruo

state: Guangxi

address: Guangxi Medical University, Nanning 530021, Guangxi, China

institute: Guangxi Medical University

summary: To further explore the differential expression profile of circRNA in human bladder cancer, we have employed circRNA microarray expression profiling as a discovery platform to identify potential differential expression profile of circRNA between human bladder cancer cell (UM-UC-3 cell) and urothelial immortalized cell (SV-HUC-1 cell). Results showed a large number of differentially expressed circRNAs. In this study, we screened the eight circRNAs that were most significantly downregulated in the circRNA differential expression profile of bladder cancer cells, designed primers across the splice site, and detected them using qPCR. We found that hsa_circ_0047253 (circLAMA3) was most significantly decreased in the bladder cancer cells, then its biological function and action mechanism have been further explored in this study.

overall_design: To explore the role of circRNA in bladder cancer, we conducted circRNA microarray analysis using human urothelial immortalized SV-HUC-1 cells as a control group and human bladder cancer UM-UC-3 cells as an experimental group.

first: Shuilian

last: Wu

first: Xin

last: Wang

first: Ruirui

last: Zhang

first: Jialei

last: Yang

first: Wenmin

last: Lu

first: Jie

first: Xiaofei

last: Li

first: Sixian

last: Chen

first: Haotian

last: Xu


title: Dosage compensation in Bombyx mori is achieved by partial repression of both Z chromosomes in males

status: Public on Feb 05 2022

city: Buffalo

first: Dahong

state: Other

address: 955 Main Street

institute: SUNY Buffalo

summary: We report the ATAC-seq data that reveal chromatin accessibility during Bombyx mori development

overall_design: Examine chromatin accessibility with ATAC-seq

first: Leah

middle: F

last: Rosin

first: Yang

first: Elissa

last: Lei


title: RpoN is required for a functional type III secretion system in Yersinia pseudotuberculosis

status: Public on Feb 04 2022

city: Umea

first: Maria

last: Fallman

address: Petrus Laestadius väg

department: Molecular Biology

country: Sweden

institute: Umea university

summary:
One milliliter of triplicate bacterial cultures in both Wild type (WT) and rpoN mutant were immediately pelleted by centrifugation at 9000 rpm at room temperature for 2 minutes after adding phenol:ethanol. The supernatant were removed and the pellets resuspended in 0.5 ml Trizol solution.
For Gram-negative bacteria, the cells were homogenized in Trizol solution by pipetting up and down 15 times. For Gram-positive bacteria, culture suspensions in Trizol were transferred to previously cooled bead beater tubes containing 0.1-mm glass beads and treated with Mini-Beadbeater (Biospec Products Inc, USA) twice at a fixed speed for 45 seconds, and then cooled on ice for 1 minute between the treatments.
Culture homogenates were incubated at room temperature for 5 minutes and then supplemented with 0.2 ml chloroform, thoroughly mixed by shaking 10 times, and incubated for 3 minutes. After centrifugation at 12 000 g at 4°C for 15 minutes, the aqueous upper phase was carefully transferred to new RNase free tubes. An equal volume of 99% ethanol was added to the transferred aqueous phase and isolation continued using the Direct-Zol RNA Miniprep Plus (Zymo Research, USA) RNA purification kit protocol.
Total RNAs were eluted in RNase free water in RNase free tubes. The total RNA concentrations were measured using the Qubit BR RNA Assay Kit (ThermoFisher Scientific, USA) and RNA integrity confirmed on a 0.8% agarose gel in TBE buffer. All rRNA-depleted RNA-seq library preparations were performed according to Shishkin et al.,2015 with minor modifications. RNAtag-Seq allows multiple library preparations in one tube, with initial tagging of total RNA samples with modified (5'P and 3'ddC) DNA barcoded adaptors, each harboring a unique 8 nt sequence used to demultiplex individual libraries after sequencing
We combined the library preparation of three biological replicates from WT and ∆rpon preparations in one tube for each bacterial strain. Therefore, 24 unique barcoded adaptors were used to tag the 24 replicates. A total of 100 ng total RNA was used for each biological replicate. The total RNA was fragmented in 2X FastAP Thermosensitive Alkaline Phosphatase buffer for 3 minutes at 94°C, DNase treated, and dephosphorylated with a combination of TURBO DNase and Thermosensitive Alkaline Phosphatase in 1X FastAP buffer for 30 minutes at 37°C. Fragmented, DNase-treated, and dephosphorylated total RNAs were cleaned with a 2X reaction volume of Agencourt RNAClean XP beads. Cleaned total RNAs were incubated with 100 pmol of a unique DNA barcode adaptor at 70°C for 3 minutes, and then ligated with T4 RNA ligase 1 for 90 minutes at 22°C.
The ligation was stopped and the enzyme denatured by the addition of RLT buffer. The 36 denatured ligation mixes were then pooled and cleaned in a Zymo Clean & ConcentratorTM-5 column according to the manufacturer's 200 nt cut-off protocol. The RNAs were eluted in 32 ml of RNase free water. The ribosomal RNA was depleted using the Ribo-ZeroTM Magnetic Gold Kit (Bacteria) according to the manufacturer's instructions. The first strand cDNA of each pool was generated using an AffinityScript Multiple Temperature cDNA synthesis kit with 50 pmol of AR2 primer at 55°C for 55 minutes. The RNA was degraded by adding a 10% reaction volume of 1 N NaOH at 70°C for 12 minutes and the reaction neutralized with an 18% reaction volume of 0.5 M acetic acid. After cleaning the reverse transcription primers with a 2X reaction volume of RNAClean XP beads, the 3Tr3 adapter was ligated with T4 RNA ligase 1 at 22°C with overnight incubation. The second ligation was cleaned first with a 2X, and secondly 1.5X, reaction volume of RNAClean XP beads. The cDNA was then used as the template for PCR reaction with FailSafeTM PCR enzyme mix using 12.5 pmol 2P_univP5 as forward primers and 12.5 pmol ScriptSeqTM Index (barcode) PCR primers as reverse primers. The PCR cycles were as follows: 95°C for 3 minutes, followed by 12 cycles at 95°C for 30 seconds, 55°C for 30 seconds, and 68°C for 3 minutes, and then finishing at 68°C for 7 minutes. The PCR product was cleaned first with a 1.5X, and secondly 0.8X, reaction volume of AMPure beads and eluted in RNAse free water. The library concentrations were measured using the QubitTM dsDNA HS Assay Kit and the library insert size determined by the Agilent DNA 1000 Kit in a 2100 Electrophoresis Bioanalyser Instrument (Agilent, USA). The libraries were sequenced by Illumina NovaSeq 6000

overall_design: Transcriptomics

last: Fållman

first: A

last: Firoj Mahmud


title: Regulation of alternative splicing by a novel BRR2 interactor C9ORF78

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

institute: Max-Planck-Institut für molekulare Genetik

summary: The RNA helicase BRR2 (SNRNP200) is one of the key remodeling factors of the spliceosome. Here we show its direct interaction with C9ORF78, a poorly characterized protein predicted to be largely intrinsically disordered. We present cryo-EM structures showing how C9ORF78 and the spliceosomal B-complex protein FBP21 wrap around the C-terminal helicase cassette of BRR2 and that binding of the two proteins is mutually exclusive. C9ORF78 associates with the spliceosome, as we confirm via proteomics and RNA UV-crosslinking. An siRNA mediated C9ORF78 knockdown reveals changes in alternative splicing of specific target pre-mRNAs, which in part depend on its interaction with BRR2. In particular, C9ORF78 regulates a substantial number of alternative 3’ splice sites, which might be facilitated through an additional interaction with human PRP22 (DHX8).

overall_design: Identification of C9orf78 RNA targets with FLASH, using GFP as a negative control

first: Ibrahim

last: Ilik

first: Alexandra

last: Bergfort

first: Marco

last: Preußner


title: Effects of androgen excess-related metabolic disturbances on granulosa cell function and follicular development

city: Beijing

first: Yanli

last: Pang

state: Beijing

address: No.49 Huayuan-Bei Road , Haidian District

institute: Reproductive Medicial Center , Peking University Third Hospital

summary: The purpose of this study was to explore the difference in transcript profiles between the ovarian granulosa cells from healthy women and women with polycystic ovary syndrome (PCOS). Quantitative reverse transcription polymerase chain reaction (qRT–PCR) was applied to validate results of RNA sequencing in the present study.

overall_design: Granulosa cells collected from two individuals were pooled as one sample for RNA-sequencing, and there was three samples in control and PCOS group.

first: Baoying

last: Liao

first: Xinyu

last: Qi

first: Chuyu

last: Yun

last: Qiao


title: 5-methylcytosine modification-mediated mRNA stabilization is associated with sexual development of malaria parasites

first: meng

last: liu

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

overall_design: Refer to individual Series


title: Contribution of host miRNA-223-3p to SARS-CoV-induced lung inflammatory pathology

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Severe acute respiratory syndrome coronavirus (SARS-CoV) and the closely related SARS-CoV-2 are emergent highly pathogenic human respiratory viruses causing acute lethal disease associated with lung damage and dysregulated inflammatory responses. SARS-CoV envelope protein (E) is a virulence factor involved in the activation of various inflammatory pathways. Here, we study the contribution of host miRNAs to the virulence mediated by E protein. Small RNAseq analysis of infected mouse lungs identified miRNA-223 as a potential regulator of pulmonary inflammation, since it was significantly increased in SARS-CoV-WT virulent infection as compared to the attenuated SARS-CoV-∆E infection. In vivo inhibition of miRNA-223-3p increased mRNA levels of pro-inflammatory cytokines and NLRP3 inflammasome, suggesting that during lung infection, miRNA-223 might contribute to restrict an excessive inflammatory response. Interestingly, miRNA-223-3p inhibition also increased the levels of the CFTR transporter, which is involved in edema resolution and was significantly downregulated in the lungs of mice infected with the virulent SARS-CoV-WT virus. At the histopathological level, a decrease in the pulmonary edema was observed when miR-223-3p was inhibited, suggesting that miRNA-223-3p was involved in the regulation of the SARS-CoV-induced inflammatory pathology. These results indicate that miRNA-223 participates in the regulation of E protein mediated- inflammatory response during SARS-CoV infection by targeting different host mRNAs involved in the pulmonary inflammation and identify miRNA-223 as a potential therapeutic target in SARS-CoV infection.

overall_design: Standard RNA-seq (Illumina 100nt single-ends, strand-specific, total RNA) of two or three biological replicates per sample. Two time points (2dpi and 4dpi). Three infection types (infected with rSARS-CoV-deltaE, infected with rSARS-CoV wild type and Mock).

first: Lucía

last: Morales

first: Raúl

last: Fernández-Delgado

first: Gonzalo

last: Vigara

first: Luis

last: Enjuanes

first: Isabel

last: Sola


title: Brain transcriptome analysis of Slc6a20a heterozygous and homozygous mutant mice

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

summary: SLC6A20A is a proline and glycine transporter known to regulate glycine homeostasis and NMDA receptor (NMDAR) function in the brain. A previous study on Slc6a20a-haploinsufficient mice reported increases in ambient glycine levels and NMDA receptor-mediated synaptic transmission in the brain, but whether Slc6a20a deficiency leads to disease-related behavioral deficits in mice remains unknown. Here, we report that Slc6a20a heterozygous and homozygous mutant mice display gene dosage-dependent behavioral phenotypes in locomotor, repetitive behavioral, and fear memory domains. In addition, Slc6a20a heterozygous and homozygous mutant brains showed transcriptomic changes in synapse, ribosome, and mitochondria-related genes as well as autism, epilepsy, and neuron-related genes. These results suggest that Slc6a20a deletion leads to gene dosage-dependent behavioral deficits in mice and transcriptomic changes in genes associated with synapse, ribosome, mitochondria, ASD, epilepsy, and neurons

overall_design: Whole-brain transcriptome analysis of Slc6a20a heterozygous and homozygous mutant mice age of P120

first: Junhyung

first: Hyojin

last: Kang


title: Single-cell RNA sequencing of the CFS414 zebra finch cell line

city: New York

first: Matthew

middle: T

last: Biegler

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line from zebra finch embryonic fibroblasts using the SV40 large and small T antigens, designated CFS414. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. This single-cell RNA sequencing experiment provided information on the gene expression landscape of the cell line, informing on its cell type, transcriptomic stability, and value to researchers utilizing the zebra finch as a model organism.

overall_design: 2 Samples at separate passage timepoints

first: Paul

last: Collier

first: Hagen

middle: U

last: Tilgner

first: Erich

middle: D

last: Jarvis


title: Uhrf1 control the proliferation and the differentiation of satellite cells

city: Toon

first: Hiroshi

last: Sakai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

summary: DNA methylation is an essential form of epigenetic regulation responsible for cellular identity. In muscle stem cells, termed satellite cells, DNA methylation patterns are tightly regulated during differentiation. However, it is unclear how these DNA methylation patterns affect the function of satellite cells. We demonstrate that a key epigenetic regulator, ubiquitin like with PHD and RING finger domains 1 (Uhrf1), is activated in proliferating myogenic cells but not expressed in quiescent satellite cells or differentiated myogenic cells in mice. Ablation of Uhrf1 in mouse satellite cells impairs their proliferation and differentiation, leading to failed muscle regeneration. Uhrf1-deficient myogenic cells exhibited aberrant up-regulation of transcripts, including Sox9, with the reduction of DNA methylation level of their promoter and enhancer region. These findings show that Uhrf1 is a critical epigenetic regulator of proliferation and differentiation in satellite cells, by controlling cell type-specific gene expression via maintenance of DNA methylation.


title: Uhrf1 control the proliferation and the differentiation of satellite cells [RNA-Seq]

summary: DNA methylation is an essential epigenetic regulation for cellular identity. In muscle stem cells, termed satellite cells, DNA methylation patterns are dynamically changed during muscle regeneration. However, how these DNA methylation patterns are maintained remain unclear. Here, we demonstrate that a key epigenetic regulator Uhrf1 (ubiquitin-like with PHD and RING finger domains 1) is activated in proliferating but not expressed in quiescent or differentiated satellite cells. Ablation of Uhrf1 in satellite cell impairs the proliferation and differentiation of satellite cells, leading to failure of muscle regeneration. Loss of Uhrf1 in satellite cells alters transcriptional programs and leads to DNA hypomethylation with the activation of Cdkn1a and Notch signalling. Down-regulation of Cdkn1a and Notch signalling rescued the proliferation and differentiation defect in Uhrf1-deficient satellite cells. Therefore, this study suggest that Uhrf1 can regulate the self-renewal and differentiation of satellite cells through DNA methylation patterning.

overall_design: RNA-Seq of activated satellite cells in vitro from Control, Cre Control, and Uhrf1-deficient mice in satellite cells.

first: Yuuki

last: Imai

first: Yuichiro

last: Sawada


title: Microbiome mediated plasticity promotes thermal adaptation in Nematostella vectensis

city: Düsseldorf

first: Sebastian

last: Fraune

state: North Rhine-Westphalia

address: Universitätsstr. 1, Building: 26.24, Floor/Room: 02.114

department: Institute for Zoology and Organismic Interactions

institute: Heinrich-Heine-University

summary: We wanted to infer the contribution of host vs symbiotic microbiota plasticities on thermal acclimation of the holobiont. We long-term acclimated anymals of the same clonal line to 3 different temperatures (15, 20 and 25°C) and monitored along time the changes in fitness, microbiota composition, and host transcriptome.

overall_design: we submitted 15 samples of acclimated female polyps representing 5 replicates from each treatment temperature (15, 20, 25°C).

first: Laura

last: Baldassarre

first: Hua

last: Ying

first: Adam

last: Reitzel


title: Contribution of host an viral small non-coding RNAs to SARS-CoV lung pathology

first: Juan

last: Oliveros

type: Non-coding RNA profiling by high throughput sequencing

summary: Severe acute respiratory syndrome coronavirus (SARS-CoV) causes lethal disease in humans, with viral E protein promoting the exacerbated inflammatory response. By deep sequencing RNAs from the lungs of infected mice, we have addressed the relevance of small, non-coding RNAs in SARS-CoV pathology. Host microRNAs (miRNAs) expressed during infection by a virulent virus encoding the E protein were significantly enriched for cytokine-mediated inflammatory pathways when compared with attenuated SARS-CoV-∆E, suggesting contribution of miRNAs to E protein-induced inflammation. The discovery of three 18-22 nt small viral RNAs (svRNAs) derived from the nsp3 and N genomic regions of SARS-CoV in mouse lung and cell cultures is also described. Depletion of these svRNAs significantly reduced viral titers and genomic RNA levels, indicating their positive contribution to virus growth. Remarkably, svRNA-N antagomirs significantly reduced in vivo lung pathology and pro-inflammatory cytokine expression, indicating that svRNAs contribute to SARS-CoV pathogenesis and highlighting the potential of these antagomirs as antivirals.

overall_design: Strand-specific, single-end, reads were generated for detecting smallRNAs (18 nts or more) in lungs (mouse). Three or four replicates were prepared per sample type.

first: Lucía

last: Morales

first: Raúl

last: Fernández-Delgado

first: Benjamin

middle: R

last: tenOever


title: Conventional RNA-seq and 3'end-seq data from HEK293T

status: Public on Feb 03 2022

city: Shenzhen

first: Yan

last: Zhao

address: No. 1088,Xueyuandadao

department: BIology

institute: Southern University of Science and Technology

summary: To inverstigate off-target effects of CRISPR-iPAS, we transfected HEK293TAPA reporter cells with dPguCas13b and gUSE (showed most effective APA-interference) or non-targeting gRNA (gNT) respectively. 3'end-seq and RNA-seq were performed to investigate if the global change on the endogenous PAS usage and gene expression caused by CRISPR-iPAS. Comparing with gNT, dPguCas13b with gUSE showed high specificity.

overall_design: 3'end-seq and RNA-seq were performed on HEK293TAPA cells co-transfected with dPguCas13b and gUSE or gNT respecitively.

first: Wei

last: Chen

first: Shuye

last: Tian


title: External stresses affect gonococcal type 4 pilus dynamics

status: Public on Feb 02 2022

city: Cologne

first: Isabel

last: Rathmann

address: Zülpicher Str. 47 a

department: Institute for Biological Physics

institute: University of Cologne

summary: Bacterial type 4 pili (T4P) are extracellular polymers that serve both as adhesins and molecular motors. Functionally, they are involved in adhesion, colony formation, twitching motility, and horizontal gene transfer. T4P of the human pathogen Neisseria gonorrhoeae have been shown to enhance survivability under treatment with antibiotics or hydrogen peroxide. However, little is known about the effect of external stresses on T4P production and motor properties. Here, we address this question by directly visualizing gonococcal T4P dynamics. We show that in the absence of stress gonococci produce T4P at a remarkably high rate of ~ 200 T4P min-1. T4P retraction succeeds elongation without detectable time delay. Treatment with azithromycin or ceftriaxone reduces the T4P production rate. RNA sequencing results suggest that reduced piliation is caused by combined downregulation of the complexes required for T4P extrusion from the cell envelope and cellular energy depletion. Various other stresses including inhibitors of cell wall synthesis and DNA replication, as well as hydrogen peroxide and lactic acid, inhibit T4P production. Moreover, hydrogen peroxide and acidic pH strongly affect pilus length and motor function. In summary, we show that gonococcal T4P are highly dynamic and diverse external stresses reduce piliation despite the protective effect of T4P against some of these stresses.

overall_design: We perform transcriptome analysis of Neisseria gonorrhoeae (MS11 strain, ΔG4) after treatment with two antibiotics (azithromycin or ceftriaxone) for 15 and 60 minutes. The response is compared to the control, grown in DMSO.

last: Kraus-Römer

first: Isabelle

last: Wielert

first: Jan

last: Grossbach

first: Berenike

last: Maier


title: Single-cell Sequencing Reveals Brain/Spinal Cord Oligodendrocyte Precursor Heterogeneity and Requirement for mTOR in Cholesterol Biosynthesis and Myelin Maintenance

city: Newark

first: Yun-juan

last: Chang

state: NJ

address: 185 South Orange Ave.

department: OARC

institute: Rutgers University

summary: The goal of this study was to compare oligodendroglial heterogeneity specifically between brain and spinal cord and to determine the function of the mTOR in this heterogeneity.

overall_design: Oligodendroglia were isolated from developmentally stage matched brain (postnatal day 14) and spinal cord (postnatal day 10) based on expression of the O4 cell surface antigen (Miltenyl) and used for single cell RNA sequencing. Samples included control and mTOR conditional knockout (CNP-Cre; mTOR fl/fl) cells.

first: Luipa

last: Khandker

first: Yun-Juan

first: Teresa

middle: L

last: Wood


title: Uhrf1 control the proliferation and the differentiation of satellite cells [MBD-seq]

first: Hiroshi

last: Sakai

overall_design: MBD2-Seq of activated satellite cells in vitro from Control and Uhrf1-deficient mice in satellite cells.

first: Yuuki

last: Imai

first: Yuichiro

last: Sawada


title: RNA Sequence Analysis of Postnatal Day 7 dental pulp from Osterix-Cre control and Osterix-Cre:Tgfbr2f/f mice mandibular first molars

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: Dental pulp was extracted from mandibular first molars of Osterix-Cre:Tgfbr2wt/wt and Osterix-Cre:Tgfbr2f/f pups on postnatal day 7. 1ng-limiting cell RNA Sequence analysis was performed on 4 samples from each genotype.

overall_design: Dental pulp tissue were harvested and RNA was isolated separately and analyzed for genetic alterations.

first: Sarah

last: Peters

last: Webb


title: RNA squencing of human NK cells activated with IL-15, a combination of IL-12, IL-15, and IL-18, or with a trimeric fusion protein 18/12/TxM

city: St. Louis

first: Todd

last: Fehniger

state: MO

address: 660 S Euclid Ave, Campus Box 8007

department: Oncology

institute: Washington University School of Medicine

summary: Gene expression analysis of human NK cells at baseline, Day 1, and Day 6 after activation with IL-15, IL-12/15/18, or the 18/12/TxM molecule

overall_design: NK cells were isolated from 3 distinct human donors (CD56+ CD3-), incubated with low-dose IL-15 (1 ng/mL), IL-12, IL-15, and IL-18 (IL-12 - 10ng/mL, IL-15 - 50 ng/mL, IL-18 50ng/mL), or 18/12/TxM (38.8nM) for 16 hours, washed, and cultured in 1ng/mL  IL-15  for 6 days before isolation for sequencing analysis


title: Comparison of lncRNAs expression in uterus between periods of embryo implantation and labor in mouse

status: Public on Feb 01 2022

city: Changchun

first: Zijiao

last: Zhao

state: Jilin Provience

address: No. 5333 Xi'an Road

institute: Jilin University

summary: We report the expression of mRNA and lncRNA in mouse uterus between periods of embryo implantation and labor by high-throughput seq. By the seq analysis of mRNA and lncRNA expression, 1971 differentially expressed (DE) mRNAs and 1543 DE lncRNAs were found between E0.5 and E4.5 at the embryo implantation stage, while 1149 DE mRNAs and 410 DE lncRNAs were found between E15.5 and E18.5 at the labor stage. While 117 DE mRNAs and 19 DE lncRNAs were commonly expressed between the two stages. This study provides a basic gene expression of altered pregnancy status.

overall_design: Pregnant 8 weeks old ICR mice at E0.5, E4.5, E15.5, and E18.5 (n=3/E) were used for a RNA-seq-based analysis of mRNA and lncRNA expression

first: Xu

last: Zhou

first: Chunjin

last: Li

first: Lu

last: Chen


title: Digital spatial profiling revealed the mechanism involved in the progression of affected glomeruli in ANCA associated glomerulonephritis [RNA-Seq]

city: Changsha

first: Lin

last: Ye

address: 139 Renmin Middle Road, Furong district, Changsha

institute: Central South University

summary: We previously showed that the rupture of Bowman’s capsule (BC) promotes the progression of crescent glomerulonephritis by enhancing CD8+ T cell entry into the glomeruli. In the present study, we utilized digital spatial profiling to simultaneously profile the altered mRNA transcript and protein abundances in the glomerular and periglomerular areas of biopsy samples of ANCA-associated glomerulonephritis. The paraffin-embedded biopsy samples were stained with Collagen IV, CD45, and Syto13 to distinguish the glomeruli with crescent formation but intact BC, with focal BC rupture, and with extensive rupture of BC and glomeruli without crescent formation and leukocytes infiltration in ANCA-GN. By assessing multiple discrete glomerular areas, we found that the transcript expression level of secreted phosphoprotein 1and its receptor CD44 were upregulated significantly in the glomeruli with more severe ruptures of BC, and their expression levels correlated positively with the fibrotic markers. We also found that 1) both alternative and classic complement pathways were activated in the glomeruli from patients with ANCA-GN; 2) M1 macrophages involved mostly in the early stage of BC rupture while M2 macrophages were involved in the late stage and may contribute to the fibrosis process of the crescents, and 3) apoptosis is likely the mechanism mediating the loss of glomerular cells in ANCA-GN. Our results demonstrate that digital spatial profiling allows the comparative analysis of mRNA and protein profiles in the individual glomeruli affected differently by the disease processes and to identify potential novel mechanisms in patients with ANCA-GN.

overall_design: Digital spatial profiling of 4 ANCA patients and 2 MCD patients for RNA, and 3 ANCA patients (seletcted from the 4 ANCA patients) for protein

first: Yu

last: Liu

first: Anqun


title: RNA-seq of polarized macrophages from wild-type and Dicer1-deleted mice

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: We compare transcriptomes between macrophages polarized with LPS + IFNg or with IL-4 + IL-13 in the presence or absence of Dicer1.

overall_design: Examination of polarization state on macrophage transcriptome in the setting or absence of Dicer1-dependent microRNAs.

first: Alan

last: Morrison

first: Nicolle

last: Ceneri


title: Bulk RNAseq of Mouse Splenic Dendritic Cell Subsets

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

summary: Dendritic cells (DCs) are comprised of a heterogenous population. Here we characterize the transcriptomic profiles of mouse splenic DC subsets at steady state to highlight key differences between subsets.

overall_design: Mouse splenic DCs at steady state were enriched and sorted into 3 subsets: CD8+ Conventional DC 1 (cDC1), CD8- cDC2 and plasmacytoid DC (pDC). 3 biological replicates per subset from a pool of 15-17 C57BL/6J mice per replicate.

first: EeShan

last: Pang

first: Meredith

last: O'Keeffe


title: Spleen RNA expression in control mice versus mice bred on gluten-free diet

city: Frederiksberg C

first: Camilla

middle: Hartmann Friis

last: Hansen

address: Ridebanevej 9, 2nd floor

department: Faculty of Health Sciences

institute: University of Copenhagen

summary: A Gluten-free diet can modulate the immune defence to protect against immuno-mediated diseases such as type I diabetes. In this sequencing study there is a difference in the expression level of immune genes between gluten-freem,GF, and control, C, mice.

overall_design: 2 groups of mice, control,C, and gluten-free, GF, age= 4 weeks

last: Hartmann Friis Hansen

first: Caroline

middle: M

last: Junker Mentzel


title: Digital spatial profiling revealed the mechanism involved in the progression of affected glomeruli in ANCA associated glomerulonephritis [GEOmx]


title: Trained ILC3 Responses Promote Intestinal Defense

status: Public on Jan 31 2022

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Group 3 innate lymphoid cells (ILC3) are innate immune effectors that contribute to host defense. Whether ILC3 functions are stably modified following pathogen encounter is unknown. Here we assess the impact of a time-restricted enterobacterial challenge to long-term ILC3 activation. We found that intestinal ILC3 persist for months in an activated state following exposure to Citrobacter rodentium. Upon rechallenge, these “trained” ILC3 proliferate, display enhanced interleukin (IL)-22 responses, and have a superior cell-intrinsic capacity to control infection compared to naïve ILC3. Metabolic changes occur in C. rodentium-exposed ILC3 but only trained ILC3 have enhanced proliferative capacity that contributes to elevated IL-22 production. Accordingly, a limited encounter with a pathogen can promote durable phenotypic and functional changes in intestinal ILC3 that contribute to long-term mucosal defense.

overall_design: 24 samples from murine small intestine

first: Nicolas

last: Serafini

first: Angélique

last: Jarade

first: Laura

last: Surace

first: Pedro

last: Goncalves

first: Odile

last: Sismeiro

first: Hugo

last: Varet

first: Jean-Yves

last: Coppée

first: Olivier

last: Disson

first: Scott

last: Durum

first: Gad

last: Frankel

first: James

last: Di Santo


title: RNA-Seq on whole mouse kidney upon regeneration in telomerase modulation conditions

city: Nice

first: Melanie

last: Pousse

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

institute: IRCAN

summary: Homeostatic renal filtration relies on the integrity of podocytes, which function in glomerular filtration. These highly specialized cells are damaged in 90% of chronic kidney disease, representing the leading cause of end-stage renal failure. Although modest podocyte renewal has been documented in adult mice, the mechanisms regulating this process remain largely unknown and controversial. Using a mouse model of ADR-induced nephropathy, we find that the recovery of filtration requires up-regulation of the endogenous telomerase component TERT. Previous work has shown that transient overexpression of catalytically inactive TERT (i-TERTci mouse model) has an unexpected role in triggering dramatic podocyte proliferation and renewal. We therefore used this model to conduct specific and stochastic lineage-tracing strategies in combination with high throughput sequencing methods. These experiments provide evidence that TERT drives the activation and clonal expansion of podocyte progenitor cells. Our findings demonstrate that the adult kidney bears intrinsic regenerative capabilities involving the protein component of telomerase, paving the way for innovative research toward the development of chronic kidney diseases therapeutics.

overall_design: Paired-end RNA-Seq performed on kidneys collected 8 days after switching-off expression of transgenic TERTci in i-TERTci mice.  Paired-end RNA-Seq performed on kidneys collected from either wild-type or TERT knock-out mice 18 days after adriamycin-induced injury or saline injection.

first: Tynhinane

last: Hamidouche

first: Marina

last: Shkreli


title: Digital spatial profiling revealed the mechanism involved in the progression of affected glomeruli in ANCA associated glomerulonephritis

first: Lin

last: Ye

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

overall_design: Refer to individual Series


title: Multi-omics association reveals the effects of intestinal microbiome-host interactions on fat deposition in broiler lines divergently selected for abdominal fat content

city: Harbin

first: Hui

last: Yuan

state: Heilongjiang

address: XiangFang

department: College of Animal Science and Technology

institute: Northeast Agricultural University

summary: The lean and fat broilers were derived from the 21st generation of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). In brief, broilers in the two lines (lean line and fat line) of the NEAUHLF have the same Arbor Acres ancestry, but were divergently selected by the concentration of very low-density lipoprotein and abdominal fat percentage (AFP) at 7 weeks old. After 21 generations of selection, there is over a 10-fold difference in abdominal fat percentage between the two lines, representing a classical obese-lean-study model. At age of 7 weeks, ten male individuals of each line were selected randomly to investigate the interactions between gut microbiome, host gene expression and obesity.

overall_design: All broilers were raised in similar feeding surroundings and had free access to feed and water. At age of 7 weeks, ten male individuals of each line were selected randomly to investigate the interactions between gut microbiome, host gene expression and obesity.


title: A novel regulatory mechanism of U2 spliceosome proteostasis that controls the transcriptome and therapy response in cancer [TTseq_CUTLL1_E7107_15min]

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Aberrant splicing is an important cause of cancer, and the production of noncanonical, cancer-specific, mRNA transcripts associate with transformation. Studies have focused on characterizing the effect of spliceosome mutations on disease progression. Here, we have uncovered a novel mode of regulation of the U2 complex component SF3B1 in leukemia via lysosomal degradation. Elevated levels of SF3B1 protein control splicing and active transcription via direct interaction with the general transcriptional machinery and are critical for leukemia growth due to the control of cell cycle and DNA damage response-related transcripts, such as the serine/threonine kinase CHEK2. We further exploited these findings to show that clinically-used SF3B1 inhibitors synergize with transcriptional inhibitors, CHEK2 inhibitors and chemotherapy drugs to block leukemia growth. Our study provides the proof-of-principle for post-translational regulation of the splicing machinery via the lysosome and associated splicing-dependent and -independent roles of the U2 complex in cancer, that can be exploited for therapeutic purposes.

overall_design: 10 million/per group CUTLL1 cells were treat with DMSO or 3nm E7107 for 15min. 500 μM fresh 4-thiouridine (4sU) labeled cells for 10min and harvest cells to extract the RNA by TRIzol. Total RNA was fragmented and then were biotinylated using MTSEA-biotin and enriched on streptavidin magnetic beads prior to rRNA depletion (NEBNext rRNA depletion kit, NEB#E6310L). Sequencing library were prepared with NEBNext Ultra II directional RNA Library Prep Kit chapter start from chapter 5 of the instruction manual, NEB# E7645S.

first: Cuijuan

last: Han

last: Jamayran

first: Yalu

last: Zhou

first: Adam

last: Lorch

first: Panagiotis

last: Ntziachristos


title: Loss of m6A methyltransferase METTL5 promotes cardiac hypertrophy through translational control of SUZ12

city: Guangzhou

first: Tailai

last: Du

state: Guangdong

address: No.58, Zhongshan 2nd road

department: The First Affiliated Hospital

institute: Sun Yat-sen University

summary: The methyltransferase-like5 (METTL5), which catalyzes m6A in 18S rRNA at position A1832, has been shown to regulate the efficient of mRNA translation in the differentiation of ES cell and the growth of cancer cells. It remains unknown that whether and how METTL5 regulates cardiac hypertrophy. In this study, we generated a mouse model (METTL5-cKO) with cardiac-specific abolishment of METTL5 in vivo. Loss function of METTL5 promotes pressure overload-induced cardiomyocyte hypertrophy and adverse remodeling. The regulatory function of METTL5 in hypertrophic growth of cardiomyocyte were further confirmed with both gain- and loss-of-function approaches in primary isolated cardiomyocytes. Mechanically, METTL5 was identified to modulate the mRNA translation of SUZ12, a core component of PRC2 complex, and further regulate the transcriptome shift during cardiac hypertrophy. Therefore, our study uncover an important translational regulator of cardiac hypertrophy.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: heart mRNA profiles of 1-month old Ctrl and Mettl5-KO mice; heart mRNA profiles of 3-month old Ctrl and Mettl5-cKO mice; heart mRNA profiles of Ctrl and Mettl5-cKO mice 4 weeks post-TAC; mRNA profiles of AdGFP and AdMettl5 NRVMs under PE stimulation.

first: Yanchuang

first: Siyao

last: Guo

first: Zhan-Peng

last: Huang


title: Gene expression analysis in complex canine chronic cutaneous lupus erythematosus (CCLE)

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a comparative immunology case study of client-owned dogs to determine if immune and skin gene expression profiles in spontaneous canine chronic cutaneous lupus erythematosus (CCLE) with concomitant systemic autoimmunity mirror those observed in human CCLE.

overall_design: Gene expression was analyzed using 160 custom Nanostring probes to analyze 4 canines with Chronic Cutaneous Lupus Erythematosus with concomitant systemic autoimmunity compared to 5 healthy controls (leg margin excisions).

first: Nicholas

last: Robinson


title: Changes in skeletal muscle PAK1 levels regulate tissue crosstalk to impact whole body glucose homeostasis

city: Duarte

first: Debbie

last: Thurmond

state: CA

address: City of Hope Beckman Research Institue

department: Molecular and Cellular Endocrinology

institute: City of Hope

summary: We have used RNA-seq to identify transcripts expressed in mouse skeletal muscle inducible PAK1 overexpression/knock-out.

overall_design: 15 mice preparation examed under 5 condition, WT with doxycyclin, skeletal muscle specific over expressed PAK1  with Doxycyclin or without doxycyclon, and skeletal muscle specific knock out PAK1 with or without doxycyclin.

first: Miwon

last: Ahn


title: A novel regulatory mechanism of U2 spliceosome proteostasis that controls the transcriptome and therapy response in cancer


title: A novel regulatory mechanism of U2 spliceosome proteostasis that controls the transcriptome and therapy response in cancer [RNAseq_CUTLL1_shSF3B1.2]

overall_design: Whole RNA was extracted from 1-5 million T-ALL (lines) cells using the Total RNA Mini Kit (Bio-Rad) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Illumina)) or Ribominus RNA was used for library preparation. cDNA preparation and unstranded library construction was performed using the TruSeq RNA Sample Preparation Kit. Libraries were sequenced on the NextSeq 500/550 using 76bp paired-end read method. Differential gene expression analysis was performed for each matched treatment vs control pairs, separately in each biological or technical replicate in CUTLL1 cell line. Five types of comparisons were tested: (a) Control vs SF3B1 knockdown CUTLL1 cells with shSF3B1.1, (b) Control vs SF3B1 knockdown CUTLL1 cells with shSF3B1.2, (c) Control vs E7107 treated CUTLL1 cells (24hr), (d)  Control vs E7107 treated CUTLL1 cells (15 and 30 min), (e) Control vs E7107 and/or NMDi treated CUTLL1 cells. Analysis was performed using edgeR package.


title: Human iPSC-derived renal organoids engineered to report oxidative stress can predict drug-induced nephrotoxicity

city: Edinburgh

first: Mona

last: Elhendawi

state: Midlothian

address: 7 George Square

institute: The University of Edinburgh

summary: The purpose of this study was primarily to find a reporter of nephrotoxicity that could be engineered into human pluripotent stem cells, and then to assess the performance of that reporter using a panel of test compounds. We treated renal organoids with two different concentrations of Gentamicin, 1mg/ml (low concentration) and 4 mg/ml (high concentration), and used RNA-seq to compare the expression profile of these groups to the expression profile of untreated control group. In our RNA-seq analyses, the profile of the 4 mg/ml gentamicin-treated samples was strikingly different from that of the control group.There were no genes expressed significantly differently between the control and the 1 mg/ml gentamicin-treated samples. classical markers of nephrotoxicity were either not up-regulated in response to injury (CLU) or were down-regulated (NGAL) in response to the known nephrotoxicant gentamicin. Among the transcripts showing increased expression was KIM-1 (log fold-change: 1.67; FDR-corrected p = 0.03), a biomarker commonly associated with renal tubular necrosis. Expression of the oxidative stress marker HMOX1 was also highly increased (log fold-change: 6.55; FDR-corrected p = 0.00015).  Based on the intersection of HMOX1 in several different toxicity pathways as well as its greater level of up-regulation, we identified HMOX1 as a potentially promising reporter for one large class of nephrotoxicants; those in which the OS pathway is activated.

overall_design: Nine samples were included and are divided into three groups;control (untreated) group, low-dose-gentamicin-treated group, and high-dose-gentamicin-treated group. Each group includes three different repeats

first: M

last: Lawrence

last: Morlock

first: W

last: Liu

first: S

first: A

last: Palakkan

first: L

last: Seidl

first: P

last: Hohenstein

last: Sjögren

first: J

last: Davies


title: Transcriptome effects of media and methotrexate on B-ALL cell lines

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: Human B-ALL cells become chemoresistant to multiple chemotherapies if exposed to adipocyte-secreted factors.   To identifiy gene alterations underlying adipocyte-mediated chemoresistance, we performed RNA-sequencing analysis on untreated human B-ALL cells and those treated with the chemotherapy metotrexate.

overall_design: Human B-ALL cell lines (n=2; REH and RCH-AcV) were cultured in unconditoned, bone marrow stromal cell, or adipocyte-conditioned medium (CM) for 48 hours or pretreated with CM for 24 hours followed by 24 hours of methotrexate treatment.  All samples were collected after 48 hours of the initial plating and process for RNA-sequencing.

first: C

last: Henry

last: Lee


title: A novel regulatory mechanism of U2 spliceosome proteostasis that controls the transcriptome and therapy response in cancer [RNAseq_CUTLL1_shSF3B1_MapR]

first: Alireza

last: Khodadadi-Jamayran

overall_design: 3 million/per group CUTLL1 cells were treat with DMSO or 3nm E7107 for 24h and harvest cells straightly follow the protocol from  Kavitha Sarma’s lab[67]. The protein GST-RNaseH-MNase and GST-RNaseH mut-MNase were provided by Kavitha Sarma.

first: Cuijuan

last: Han

last: Jamayran

first: Yalu

last: Zhou

first: Adam

last: Lorch

first: Panagiotis

last: Ntziachristos


title: Methylation of osteosarcoma patients

city: Oslo

first: Heidi

middle: Maria

last: Namløs

address: PO Box 4953 Nydalen

department: Institute for cancer research, The Norwegian Radium Hospital

country: Norway

institute: Oslo University Hospital

type: Methylation profiling by genome tiling array

summary: Osteosarcoma is the most common primary malignant tumour of bone occurring in children and young adolescents. Osteosarcoma is characterized by considerable phenotypic and genomic heterogeneity, and few recurrent targetable genetic changes have been reported. Osteosarcoma exhibits a complex karyotype with high genomic and chromosomal instability; and harbours multiple rearrangements across the genome, kataegis and chromothripsis as well as epigenetic changes. Here we have performed DNA methylation profiling on 10 osteosarcoma patient samples and four bones using the Infinium HumanMethylation450 BeadChip from Illumina, covering 485,000 CpG sites across the genome.

overall_design: Comparison of DNA methylation patterns in 10 osteosarcoma patient samples and 4 normal bone samples

first: Magne

last: Skårn

first: Deeqa

last: Ahmed

first: Iwona

last: Grad

first: Kim

last: Andresen

first: Stine

last: Kresse

first: Massimo

last: Serra

first: Katia

last: Scotlandi

first: Antonio

last: Llombart-Bosch

first: Ola

last: Myklebost

first: Guro

middle: E

last: Lind

first: Leonardo

last: Meza-Zepeda


title: SIAH ubiquitin E3 ligases as modulators of inflammatory gene expression

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: The functionally redundant ubiquitin E3 ligases SIAH1 and SIAH2 have been implicated in the regulation of several processes, but their role in inflammatory signaling and gene expression remains unclear. Here we have downregulated the expression of both SIAH proteins with specific siRNAs and investigated the functional consequences for IL-1α-induced gene expression and the signaling pathways activating NF-κB and AP1. The knockdown of SIAH1/2 had no significant impact on IL-1α-induced activation of NF-κB and MAPK signaling pathways, but modulated the expression of approximately one third of IL-1α-regulated genes. Most of the proteins encoded by SIAH1/2-regulated genes form a regulatory network of proinflammatory factors. Thus SIAH1/2 proteins function as variable rheostats that control the amplitude of inflammatory gene expression.

overall_design: Examining the role of SIAH1 and SIAH2 in inflammatory signaling and gene expression using RNA-seq.

first: Lienhard

last: Schmitz

first: Shashipavan

last: Chillappagari


title: A novel regulatory mechanism of U2 spliceosome proteostasis that controls the transcriptome and therapy response in cancer [RNAseq_CUTLL1_E7107_15min_30m]

first: Alireza

last: Khodadadi-Jamayran

country: USA

first: Cuijuan

last: Han

first: Yalu

last: Zhou

first: Adam

last: Lorch


title: RNA-Seq of post mortem human central Amygdala samples in patients affected by opioid use disorder (OUD) vs. unaffected control samples

status: Public on Jan 28 2022

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

summary: Differential expression analysis of human central Amygdala samples with a story of opioid use disorder (OUD) vs. unaffected control central Amygdala samples

overall_design: RNA-seq collected from 21 patients with a story of OUD vs. 21 healthy donors

first: Vez

last: Repunte-Canonigo

first: Federico

last: Giorgi

first: Yu

last: Fu

first: Pietro

middle: P

last: Sanna


title: A novel regulatory mechanism of U2 spliceosome proteostasis that controls the transcriptome and therapy response in cancer [TTseq_CUTLL1_E7107_24hr]

overall_design: 10 million/per group CUTLL1 cells were treat with DMSO or 3nm E7107 for 24h. 500 μM fresh 4-thiouridine (4sU) labeled cells for 10min and harvest cells to extract the RNA by TRIzol. Total RNA was fragmented and then were biotinylated using MTSEA-biotin and enriched on streptavidin magnetic beads prior to rRNA depletion (NEBNext rRNA depletion kit, NEB#E6310L). Sequencing library were prepared with NEBNext Ultra II directional RNA Library Prep Kit chapter start from chapter 5 of the instruction manual, NEB# E7645S.

last: Jamayran

first: Panagiotis

last: Ntziachristos