title: Native G-quadruplexes Stabilization Impairs Transcription Initiation

status: Public on Jul 19 2021

city: Wuhan

first: Yin

last: Zhinang

state: Hubei

address: Donghu road 185

institute: Wuhan University

summary: G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines. They are distributed genome-widely and participate in multiple biological processes including gene transcription, and quadruplex-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, the roles of G-quadruplexes in transcriptional regulation remains elusive. Here, we establish a sensitive G4-CUT&Tag method for genome-wide profiling of native G-quadruplexes with high resolution and specificity. We find that native G-quadruplex signals are cell-type specific and are associated with transcriptional regulatory elements with active epigenetic modifications. Promoter-proximal RNA polymerase II pausing promotes native G-quadruplex formation, oppositely, G-quadruplex stabilization by quadruplex-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis. Moreover, G-quadruplex stabilization modulates chromatin states and impedes transcription initiation via inhibiting the loading of general transcription factors to promoters.Together, these studies reveal a reciprocal regulation between native G-quadruplex dynamics and gene transcription in the genome, which will deepen our knowledge of G-quadruplex biology towards considering therapeutically targeting G-quadruplexes in human diseases.

overall_design: In this study, we firstly reported a native G-quadruplex profiling method, G4-CUT&Tag, by combining the G-quadruplex specific BG4 antibody with the sensitive CUT&Tag technique (Kaya-Okur et al. 2019; Wang et al. 2019).our studies provided a more effective strategy for comprehensively profiling native G-quadruplexes in the human genome and demonstrated that disruption of G-quadruplex dynamics could cause a rapid and genome-wide alteration in chromatin states and impairment of transcription initiation.These studies revealed the underlying mechanisms for the intertwinement of RNA polymeraseII, chromatin states, and native G-quadruplexes, providing a paradigm for functional studies of the noncanonical DNA secondary structures and advancing our understanding of quadruplex-targeting therapies.

first: Kaiwei

last: Liang


title: Single-cell transcriptomic profiling of non-hematopoietic circulating cells in mid-gestational embryos

status: Public on Jul 31 2021

city: Guangzhou

first: Yanjuan

last: Chen

state: Guangdong

address: Guangzhou

department: Department of Geriatrics and Division of Rheumatology and Research

country: China

institute: The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital)

type: Expression profiling by high throughput sequencing

summary: Combined with FACS and single-cell RNA sequencing technology, this study systematically illuminated remarkable cell types and gene expression characteristics of non-hematopoietic cells in the circulation of mid-gestational embryos at the level of single-cell transcriptome for the first time, providing a reference for comprehensively analyzing the coordinated regulation of cells in different tissues and organs during embryonic development.

overall_design: We performed Smart-Seq scRNA-seq of 300 cells to firstly construct a molecular landscape of non-hematopoietic circulating cells in mid-gestational mouse embryos

first: Yanyan

last: Li

first: Xiaona

last: Zheng

first: Yun

last: Gao

first: Yuxuan

first: Zongcheng

first: Han

last: He

first: Fuchou

last: Tang

first: Bing

last: Liu

first: Yu

last: Lan


title: Genomic context sensitivity of insulator function

city: New York

first: Matthew

middle: T

last: Maurano

state: New York

address: 435 East 30th Street

department: Institute for Systems Genetics

country: USA

institute: NYU Grossman School of Medicine

summary: Analysis of randomly integrated barcoded enhancer blocker reporter activity in K562 cells

overall_design: 5 replicate experiments, each consisting of a set of transfections of multiple distinct reporter constructs distinguished by 16 nt barcodes. Each transfection was profiled with DNA, RNA, and iPCR libraries; Experiments 4 and 5 also include 10x scRNA-seq.

first: André

middle: M

last: Ribeiro-dos-Santos

first: Megan

middle: S

last: Hogan

first: Raven

middle: D

last: Luther


title: RNA profiling of human lymphatic endothelial cells exposed to melanoma exosomes

status: Public on Jul 16 2021

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: In order to study the influence of melanoma-derived exosomes in the lymphatic vasculature within the lymph nodes, we have profile the transcriptional changes occurring in human lymphatic endothelial cells treated with melanoma-secreted exosomes or with the conditioned medium from melanoma cells depleted of exosomes.

overall_design: Human lymphatic endothelial cells (HMVECs) were treated for 24h and 48h with exosomes from SK-MEL-147 melanoma cell line and conditioned medium from the same line depleted of exosomes. RNA was extracted with trizol and subsequent Qiagen columns. RNA sequencing was performed afterwards.

first: Susana

middle: G

last: Silva

first: Hector

last: Peinado


title: Transcriptome-wide identification of transcripts regulated by PHF5A in colorectal cancer cells

city: Shanghai

first: Alvin

last: Casper

address: RongJin

institute: Alvin

summary: Dysregulated alternative splicing (AS) plays critical roles in driving cancer progression, and the underlying mechanisms remain largely unknown. Here we demonstrated that PHF5A, a component of U2 snRNPs, was frequently upregulated in colorectal cancer (CRC) samples and associated with poor prognosis. PHF5A promoted proliferation and metastasis of CRC cells in vitro and in vivo. Transcriptomic analysis identified PHF5A-regulated AS targets and pathways. Particularly, PHF5A induced TEAD2 exon 2 inclusion to activate YAP signaling, and interference of TEAD2-L partially reversed the PHF5A-mediated tumor progression. Pharmacological inhibition of PHF5A using pladienolide B had potent antitumor activity. Collectively, these data revealed the oncogenic role of PHF5A in CRC through regulating AS, and established PHF5A as potential therapeutic target.

overall_design: RNA sequencing using RNA retrieved from PHF5A knockdown and control HCT116 cells.

first: Cheng

first: Xiaoyuan

last: Chu


title: miRNA regulation of T cell exhaustion in cutaneous T cell lymphoma

status: Public on Aug 04 2021

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A monocyte/dendritic cell molecular signature of SARS-CoV2-related multisystem  inflammatory syndrome in children (MIS-C) with severe myocarditis

status: Public on Jul 13 2021

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine


title: A monocyte/dendritic cell molecular signature of SARS-CoV2-related multisystem  inflammatory syndrome in children (MIS-C) with severe myocarditis [Bulk RNAseq]

summary: SARS-CoV-2 infection in children is generally milder than in adults, yet a proportion of cases result in hyperinflammatory conditions often including myocarditis. To better understand these cases, we applied a multi-parametric approach to the study of blood cells of 56 children hospitalized with suspicion of SARS-CoV-2 infection. The most severe forms of MIS-C (multisystem inflammatory syndrome in children related to SARS-CoV-2), that resulted in myocarditis, were characterized by elevated levels of pro-angiogenesis cytokines and several chemokines. Single-cell transcriptomic analyses identified a unique monocyte/dendritic cell gene signature that correlated with the occurrence of myocarditis, characterized by sustained NF-kB activity, associated with decreased gene expression of NF-kB inhibitors and TNF-a signaling . We also found a weak response to type-I and type-II interferons, hyperinflammation and response to oxidative stress related to increased HIF-1a and VEGF signaling. These results provide potential for a better understanding of disease pathophysiology.

overall_design: bulk-RNAseq on PBMC from 7 CTL, 7 MIS-C (CoV2+), 9 MIS-C_MYO (CoV2+) and 9 KD (CoV2-)

first: Camille

last: de Cevins

first: Marine

last: Luka

first: Nikaïa

last: Smith

first: Sonia

last: Meynier

first: Aude

last: Magérus

first: Francesco

last: Carbone

first: Víctor

last: Garcia Paredes

first: Laura

last: Barnabei

first: Maxime

last: Batignes

first: Alexandre

last: Boullé

first: Marie-Claude

last: Stolzenberg

first: Brieuc

middle: P

last: Pérot

first: Bruno

last: Charbit

first: Tinhinane

last: Fali

first: Vithura

last: Pirabarakan

first: Boris

last: Sorin

first: Quentin

last: Riller

first: Ghaith

last: Abdessalem

last: Beretta

first: Ludivine

last: Grzelak

first: Pedro

last: Goncalves

first: James

last: Di Santo

first: Hugo

last: Mouquet

first: Olivier

last: Schwartz

first: Mohammed

last: Zarhrate

first: Mélanie

last: Parisot

first: Christine

last: Bole-Feysot

first: Cécile

last: Masson

first: Nicolas

last: Cagnard

first: Aurélien

last: Corneau

last: Bruneau

first: Shen-Ying

last: Zhang

first: Jean-Laurent

last: Casanova

first: Brigitte

last: Bader Meunier

first: Julien

last: Harroche

first: Isabelle

last: Melki

first: Mathie

last: Lorrot

first: Mehdi

last: Oualha

first: Florence

last: Moulin

first: Damien

last: Bonnet

first: Zahra

last: Belhadjer

first: Marianne

last: Leruez

first: Slimane

last: Allali

first: Christèle

last: Gras Leguen

first: Loïc

last: de Pontual


title: Cyclophilin acts as a ribosome biogenesis factor by chaperoning the ribosomal protein in filamentous fungi

status: Public on Jul 10 2021

first: Chenmi

last: Mo

address: Shizishan street 1st

institute: HuaZhong Argriculture university

summary: The rapid transport of ribosomal proteins (RPs) into the nucleus and their efficient assembly into rRNA are prerequisites for ribosome biogenesis. Proteins that act as dedicated chaperones for RPs to maintain their stability and facilitate their assembly have not been identified in filamentous fungi. PlCYP5 is a nuclear cyclophilin in the nematophagous fungus Purpureocillium lilacinum, and up-regulated expression in response to abiotic stress and nematode egg-parasitism. Here, we found that PlCYP5 interacted with the unassembled small ribosomal subunit protein, PlRPS15, of the uS19 family. PlRPS15 contained a eukaryote-specific N-terminal extension that mediated the interaction. The phenotypes of the PlCYP5 loss-of-function mutant were similar to those of the PlRPS15 knockdown mutant (e.g., growth and ribosome biogenesis defects). PlCYP5 maintained the solubility of PlRPS15 independent of its catalytic peptide-prolyl isomerase function and supported the integration of PlRPS15 into pre-ribosomes. PlCYP5 homologs in Arabidopsis thaliana, Homo sapiens, Schizosaccharomyces pombe, Sclerotinia sclerotiorum, Botytis cinerea, and Metarhizium anisopliae were identified. Notably, the interaction of their homologs corresponding to the PlCYP5-PlRPS15 pattern existed in three filamentous fungi, while lacked in other species. In summary, our data disclosed a special RP dedicated chaperone system in filamentous fungi, in which cyclophilin was enlisted to perform the chaperone funtion.

overall_design: mRNA profiles of cultured mycelia samples of Purpureocillium linacinum wildtype and PlCYP5 gene mutant

first: Chong

last: Xie

first: Xueqiong

last: Xiao

first: Yannong


title: Ground tissue circuitry regulates organ complexity in monocot roots [root meristem scRNA-seq]

status: Public on Jul 01 2021

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

summary: Most plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology like flood tolerance and symbiosis. However, little is known about how cortical layers form outside the highly reduced anatomy of the model Arabidopsis. Here we use single-cell RNAseq to rapidly generate a cell-resolution map of the maize root, revealing an alternative configuration of the tissue-formative SHORT-ROOT (SHR) signaling pathway adjacent to the expanded cortex. We show that maize SHR protein is hypermobile, moving at least eight cell layers into the cortex. Higher order SHR mutants in both maize and Setaria have reduced numbers of cortical layers, showing that the SHR pathway controls expansion of cortical tissue in monocots that sets up anatomical complexity and a host of key traits.

overall_design: Expression profiling of the maize root meristem at single-cell resolution was performed usingh high-throughput droplet-based technology.

first: Carlos

last: Ortiz-Ramirez

first: Poliana

last: Coqueiro

first: Sanqiang

last: Zhang

first: Edgar

last: Demesa-Arevalo

first: Xiosa

last: Xu

first: Ramin

last: Rahni

first: Thomas

middle: R

last: Gingeras

first: David

last: Jackson

first: Kimberly

middle: L

last: Gallagher


title: Ground tissue circuitry regulates organ complexity in monocot roots [roottissues]

overall_design: mRNA profiles of Maize root tissues collected using FACS


title: A monocyte/dendritic cell molecular signature of SARS-CoV2-related multisystem  inflammatory syndrome in children (MIS-C) with severe myocarditis [Single cell RNAseq]

first: Mickael

last: Menager

overall_design: scRNAseq on PBMC from 9 CTL (two of which had replicates), 1 Acute-Inf (CoV2-), 4 Acute-Inf (CoV2+), 2 MIS-C (CoV2+), 6 MIS-C_MYO (CoV2+) and 2 KD (CoV2-)

first: Camille

last: de Cevins

first: Marine

last: Luka

first: Nikaïa

last: Smith

first: Sonia

last: Meynier

first: Aude

last: Magérus

first: Francesco

last: Carbone

first: Victor

last: Garcia Paredes

first: Laura

last: Barnabei

first: Maxime

last: Batignes

first: Alexandre

last: Boullé

first: Marie-Claude

last: Stolzenberg

first: Brieuc

last: Pérot

first: Bruno

last: Charbit

first: Tinhinane

last: Fali

first: Vithura

last: Pirabarakan

first: Boris

last: Sorin

first: Quentin

last: Riller

first: Ghaith

last: Abdessalem

last: Beretta

first: Ludivine

last: Grzelak

first: Pedro

last: Goncalves

first: James

last: Di Santo

first: Hugo

last: Mouquet

first: Olivier

last: Schwartz

first: Mohammed

last: Zarhrate

first: Mélanie

last: Parisot

first: Christine

last: Bole-Feysot

first: Cécile

last: Masson

first: Nicolas

last: Cagnard

first: Aurélien

last: Corneau

last: Bruneau

first: Shen-Ying

first: Jean-Laurent

last: Casanova

first: Brigitte

last: Bader Meunier

first: Julien

last: Harroche

first: Isabelle

last: Melki

first: Mathie

last: Lorrot

first: Mehdi

last: Oualha

first: Florence

last: Moulin

first: Damien

last: Bonnet

first: Zahra

last: Belhadjer

first: Marianne

last: Leruez

first: Slimane


title: Transcriptional Reprogramming and Epigenomic Landscape Dynamics During Grapevine Somatic Embryogenesis Process

status: Public on Jul 07 2021

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

summary: Somatic embryogenesis (SE), a morphogenic process that takes advantage of the regenerative potential of plants to replicate whole plants starting from somatic explants, can be a source of variation with potential applications in plant breeding. It is one of the most suitable tools to apply functional genomics studies and genetic improvement in plants. However, beyond a few pioneering works mainly focused on model plants, the molecular characterization of SE mechanisms is still elusive, especially for woody species. In grapevine, this process is affected by many factors such as explant type, culture conditions and, most importantly, genotype. Many cultivars, in fact, have shown recalcitrance to tissue culture and transformation, and very low SE competence. Thus, the understanding of SE competence behind the regenerative aptitude is fundamental to the widespread application of the so-called “next-generation breeding techniques”, such as cisgenesis and genome editing, in grapevine.   Here, we explored genetic and epigenetic features of the SE process in grapevine by investigating the behavior of two genotypes showing opposite SE competence. Embryogenic tissues were induced from immature stamens excised from field-collected flower clusters of Sangiovese (highly competent for embryogenesis) and Cabernet Sauvignon (poorly competent for embryogenesis). A multilayered approach was used to profile mRNA, smallRNAs and methylated DNA with high-throughput sequencing technologies in the initial explants, on undifferentiated calli induced after 40 days of culture, and in embryogenic and non-embryogenic calli after 3 months of culture.  A comprehensive comparison of transcriptomes of the different types of calli with the grapevine gene expression atlas revealed that, in grapevine, the dedifferentiation to the callus formation during the embryogenesis process occurs via a ‘berry’ developmental pathway. This is dissimilar from that shown in Arabidopsis, in which dedifferentiated calli are more similar to the tip of a root meristem. Interestingly, a Gene Ontology (GO) analysis revealed that secondary metabolism and gene expression regulation/epigenetics are the enriched functional categories of genes differentially down- and up-regulated in embryogenic vs non-embryogenic calli, respectively. These results prompted us to define the epigenetic landscape dynamics during SE in grapevine, revealing a significant increase in DNA methylation, especially in intergenic regions, in the embryogenic calli tissues. Finally, we proposed potential key regulators of SE in different genotypes that could represent putative targets of next-generation breeding techniques in grapevine.

overall_design: We report a whole characterization of molecular mechanisms associated to somatic embryogenesis in different genotypes of Vitis vinifera through RNA-seq, small RNA-seq and Reduced Representation Bisulﬁte Sequencing (RRBS) experiments. Embryogenic (EC), not embryogenic (NEC) and undifferentiated callus (40d) tissues of two grapevine cultivars (Sangiovese - SG - and Cabernet Sauvignon - CS -) that have different aptitudes for embryogenesis were compared.

first: Emanuele

last: De Paoli

first: Chiara

last: Pagliarani

first: Alessandra

last: Amato

first: Cristian

last: Del Fabbro

first: Giorgio

last: Gambino

first: Mario

last: Pezzotti

first: Irene

last: Perrone


title: Ground tissue circuitry regulates organ complexity in monocot roots

first: Kenneth

last: Birnbaum

relation:
SuperSeries of: GSE172277
SuperSeries of: GSE172280
SuperSeries of: GSE173087


title: The regulation and role of SCO2027, iron importer protein in Streptomyces coelicolor

city: Seoul

first: Jung-Hye

last: Roe

address: 1 Gwanak-ro, Gwanak-gu

department: Biological sciences

country: South Korea

institute: Seoul National University

summary: We determined genes that directly or indirectly regulated by CatR (or PerR), and hydrogen peroxide regulon in Streptomyces coelicolor.

overall_design: Transcriptome profiles of either hydrogen peroxide-treated or untreated wild type and catR mutant strains were obtained using Illumina HiSeq. RNA samples were prepared in biologically independent duplicates.

first: Yeonbum

last: Kim

first: Yong-Joon

last: Cho

first: Joo-Hong

last: Park

first: Kang-Lok

last: Lee


title: Muscleblind Splicing Factor Regulates Longevity Through p38 MAPK Signaling

status: Public on Jul 20 2021

city: Helsinki

first: Olli

last: Matilainen

address: Viikinkaari 9C

country: Finland

institute: University of Helsinki

summary: Muscleblind-like splicing regulators (MBNLs) are RNA-binding factors that have an important role in developmental processes. Dysfunction of these factors is a key contributor of different neuromuscular degenerative disorders, including Myotonic Dystrophy type 1 (DM1). Since DM1 is a multisystemic disease characterized by symptoms resembling accelerated aging, we asked which cellular processes do MBNLs regulate that make them necessary for normal lifespan. By utilizing the model organism Caenorhabditis elegans, we found that loss of MBL-1 (the sole ortholog of mammalian MBNLs), which is known to be required for normal lifespan, shortens lifespan by decreasing the activity of p38 MAPK/PMK-1 as well as the function of transcription factors ATF-7 and SKN-1. Furthermore, we show that mitochondrial stress caused by knockdown of mitochondrial electron transport chain components promotes the longevity of mbl-1 mutants in a partially PMK-1-dependent manner. Together, the data establish a mechanism of how DM1-associated loss of muscleblind affects lifespan. Furthermore, this study suggests that mitochondrial stress could alleviate symptoms caused by the dysfunction of muscleblind splicing factor, creating a potential approach to investigate for therapy.

overall_design: Comparison of gene expression profiles between wild-type C. elegans (N2) and muscleblind splicing factor mutant mbl-1(tm1563)

first: Ana

last: Ribeiro

first: Jens

last: Verbeeren

first: Murat

last: Cetinbas

first: Heini

last: Sood

first: Ruslan

middle: I

last: Sadreyev

first: Susana

last: Garcia


title: Small molecule activation of a pseudoexon triggers huntingtin-lowering

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics


title: Small molecule activation of a pseudoexon triggers huntingtin-lowering (RNA-Seq)

summary: Huntington’s disease (HD) is a hereditary neurodegenerative disorder caused by abnormal expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats in the huntingtin gene (HTT). The resultant mutant protein is ubiquitously expressed and drives pathogenesis of HD through a toxic gain-of-function mechanism. Animal models of HD have demonstrated that reducing huntingtin protein (HTT) levels alleviates HD-associated motor and neuropathological abnormalities, confirming the importance of huntingtin-lowering as a therapeutic approach. Several therapies in development repress HTT transcription or translation, including antisense oligonucleotides, virally-delivered microRNAs, and zinc finger protein transcription factors. However, they all require invasive procedures to reach the central nervous system (CNS) and do not distribute evenly to target areas in the brain. Systemically distributed therapeutics are needed to address the CNS and peripheral dysfunctions associated with HD. Here we report the discovery of small molecule splicing modifiers that lower HTT expression by selective modulation of pre-mRNA splicing. These compounds promote the inclusion of a pseudoexon containing a premature termination codon triggering HTT mRNA degradation and a reduction of HTT protein levels in vitro and in vivo. These orally bioavailable small molecules represent a non-invasive treatment option for HD and our findings support their continued development for the treatment of HD.

overall_design: RNAseq of HTT-C2 treatment of SHSY5Y cells; RNAseq of U1 GA-variant treatment of HEK293 cells.

first: Anu

last: Bhattacharyya

first: Chris

last: Trotta

first: Kerstin

last: Effenberger

first: Minakshi

last: Jani


title: Small molecule activation of a pseudoexon triggers huntingtin-lowering (AmpliSeq)

overall_design: HTT gene Ampliseq of HTT-C1 treatment of HD patient-derived B-lymphocytes;


title: Correlation guided Network Integration (CoNI) reveals novel genes affecting hepatic metabolism

status: Public on Jul 09 2021

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

summary:
Obesity-induced ectopic fat disposition in the liver is a major risk factor in the pathogenesis of type 2 diabetes as it impairs hepatic insulin sensitivity, a crucial component of whole body glucose homeostasis; however molecular mechanisms remain largely elusive. Understanding the pathogenesis of fatty liver, including the identification of novel genetic regulators that are involved in the regulation of liver metabolism under excess energy supply, is crucial for the development and implementation of efficient prevention and treatment strategies.
We here developed a new method to integrate metabolomics and transcriptomics data based on pairwise correlation analysis of metabolites coupled to partial correlation combining the metabolite correlations with the transcript expression profiles followed by the construction of undirected, weighted graphs.This Correlation based Network Integration (CoNI) approach was applied to liver metabolome and transcriptome datasets of lean and HFD-fed obese mice to unravel previously hidden local regulator genes (LRG). The selected candidate genes were validated by transcriptome-proteome correlation analysis, by association studies with liver lipid metabolism in humans and by analysis of cellular metabolite levels after siRNA knockdown. Overall, the new bioinformatic CoNI approach for Omics datasets allowed us to identify genes regulating metabolic networks in livers of obese mice that if solely analyzing the transcriptome dataset would have remained hidden.

overall_design: We performed gene expression microarray analysis of liver from mice treated with high fat diet and control mice

first: Valentina

last: Klaus

first: Sonja

middle: C

last: Schriever

first: José Manuel

last: Monroy Kuhn

first: Andreas

last: Peter

first: Martin

last: Irmler

first: Janina

last: Tokarz

first: Cornelia

last: Prehn

first: Gabi

last: Kastenmüller

first: Jerzy

last: Adamski

first: Alfred

last: Königsrainer

first: Timo

last: Müller

last: Heni

first: Matthias

middle: H

last: Tschöp

first: Paul

last: Pfluger

first: Dominik

last: Lutter


title: Mesenchymal stromal cells ameliorate epithelial damage after extended partial hepatectomy in the pig by modulation of thrombospondin-1/TGF-β [liver]

city: Leipzig

first: Bruno

last: Christ

state: Saxony

address: Liebigstraße 21

department: Department of Surgery

institute: University of Leipzig

summary:
By using high-density DNA microarrays, we analyzed the gene-expression profile of liver biopsies from pigs
Brückner et al. 2021 published

overall_design: RNA was extracted from liver biopsies and analyzed with Affymetrix Porcine Gene 1.0 ST microarrays.

first: Sandra

last: Brückner

first: Hans-Michael

last: Tautenhahn

first: Sebastian

last: Vlaic


title: Mesenchymal stromal cells ameliorate epithelial damage after extended partial hepatectomy in the pig by modulation of thrombospondin-1/TGF-β [lung]

summary: By using high-density DNA microarrays, we analyzed the gene-expression profile of lung biopsies from pigs.


title: Ground tissue circuitry regulates organ complexity in monocot roots [slices]

first: Kenneth

last: Birnbaum

overall_design: mRNA profiles of Maize root developmental zones

first: Carlos

last: Ortiz-Ramirez

first: Poliana

last: Coqueiro

first: Sanqiang

last: Zhang

first: Edgar

last: Demesa-Arevalo

first: Xiosa

last: Xu

first: Ramin

last: Rahni

first: Thomas

last: Gingeras

first: David

last: Jackson

first: Kimberly

last: Gallagher


title: Human papillary thyroid carcinoma landscape and its immunological link with Hashimoto's thyroiditis at single cell resolution

city: Hangzhou

first: Fang

last: Ye

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Tumor microenvironment heterogeneity sheltered our understanding of papillary thyroid cancer. However, molecular characteristics of papillary thyroid cancer has not been reported at single cell resolution. The immunological link between papillary thyroid cancer and Hashimoto's thyroiditis is also in doubt.We identified 24 cell clusters in human papillary thyroid cancer based on their heterogeneous gene expression pattern. Follicular epithelial cell subsets in papillary thyroid cancer with Hashimoto's thyroiditis and papillary thyroid cancer without Hashimoto's thyroiditis showed different malignant level. Machine learning model identified potential biomarker to evaluate tumor epithelial cell development. Together with immunostaining, lymphocytes heterogeneity indicated an obvious B cell infiltration pattern in papillary thyroid cancer with Hashimoto's thyroiditis. Additionally, trajectory analysis of B cell and plasma cell suggest the migration potential from normal adjacent tissue of Hashimoto's thyroiditis to papillary thyroid cancer tissue. Our results provide the first single cell landscape of Papillary thyroid cancer. Single cell data resource of Papillary thyroid cancer with Hashimoto's thyroiditis promote our understanding of molecular heterogeneity and immunological link between papillary thyroid cancer and Hashimoto's thyroiditis.

overall_design: Microwell datasets of 8 papillary thyroid carcinoma samples and 2 adjacent tissue(5 samples without Hashimoto's thyroiditis, 3  samples with Hashimoto's thyroiditis and 2paired samples from normal adjacent tissue)

first: Yijun

last: Wu

first: Guoji

last: Guo

first: Jun

last: Pan

first: Chengxuan

last: Yu


title: AP-2alpha-mediated activation of E2F and EZH2 drives melanoma metastasis [ChIP-seq]

status: Public on Jun 29 2021

city: Iowa City

first: Jeffrey

last: White

state: Iowa

address: 285 Newton Road 5269 CBRB

institute: University of Iowa

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In melanoma metastasis, the role of the AP-2alpha transcription factor, which is encoded by TFAP2A, is controversial as some findings have suggested tumor suppressor activity while other studies have shown high TFAP2A expression in node-positive melanoma associated with poor prognosis. Here we demonstrate that AP-2alpha facilitates melanoma metastasis through transcriptional activation of genes within the E2F pathway including EZH2. A BioID screen found that AP-2alpha interacts with members of the nucleosome remodeling and deacetylase (NuRD) complex. Loss of AP-2alpha removed activating chromatin marks in the promoters of EZH2 and other E2F target genes through activation of the NuRD repression complex. In melanoma cells, treatment witj tazemetostat, an FDA-approved and highly specific EZH2 inhibitor, substantially reduced anchorage-independent colony formation and demonstrated heritable anti-metastatic effects, which were dependent on AP-2alpha. Single cell RNA-seq analysis of a metastatic melanoma mouse model revealed hyperexpansion of Tfap2aHigh/E2F activated cell populations in transformed melanoma relative to progenitor melanocyte stem cells. These findings demonstrate that melanoma metastasis is driven by the AP-2alpha/EZH2 pathway and suggest that AP-2alpha expression can be used as a biomarker to predict responsiveness to EZH2 inhibitors for the treatment of advanced melanomas.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq of melanoma cell lines using TFAP2A monoclonal antibody.


title: Expression profiling and methylation analysis of DNMT1 inhibitor treated AML cell lines

status: Public on Jun 30 2021

city: Collegeville

first: Shawn

middle: W

last: Foley

state: PA

address: 1250 S. Collegeville Rd

department: Oncology

institute: GlaxoSmithKline


title: Mesenchymal stromal cells ameliorate epithelial damage after extended partial hepatectomy in the pig by modulation of thrombospondin-1/TGF-β

first: Bruno

last: Christ


title: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits [snRNA-seq]

status: Public on Jun 23 2021

city: Ann Arbor

first: Stephen

last: Parker

state: MI

address: 100 Washtenaw Avenue

institute: University of Michigan

summary: Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33,862 nuclei and identify seven cell types ranging in abundance from 59.6% to 1.0% of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (~3.5% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, transcription factor motifs, and target genes for type 2 diabetes signals. These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for nominating causal GWAS SNPs and cell types.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design:
Open chromatin profiling (snATAC-seq), transcriptomic profiling (snRNA-seq), and multiome profiling (joint open chromatin profiling and gene expression profiling) of single nuclei from rat and human skeletal muscle using the 10x Genomics Chromium platform.
***Raw data are unavailable due to patient privacy concerns***

first: Peter

last: Orchard

first: Nandini

last: Manickam

first: Christa

last: Ventresca

first: Swarooparani

last: Vadlamudi

first: Arushi

last: Varshney

first: Vivek

last: Rai

first: Jeremy

last: Kaplan

first: Claudia

last: Lalancette

first: Karen

last: Mohlke

first: Katherine

first: Charles

middle: F

last: Burant


title: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

overall_design: Refer to individual Series


title: Transcriptome and translatome of human regulatory T cells differentiated with TGFbeta and mTOR inhibitor everolimus

status: Public on Jun 22 2021

city: Laurel

first: Amanda

last: Ernlund

address: 11100 Johns Hopkins Rd

department: REDD

institute: Johns Hopkins APL

summary:
Regulatory T cells (Tregs) inhibit effector T cells and maintain immune system homeostasis. Treg maturation in peripheral sites (pTregs) is poorly understood but is known to require inhibition of protein kinase mTORC1 (e.g.RAD001) and exposure to TGFb. Paradoxically, Treg maturation requires protein synthesis yet mTORC1 inhibition downregulates it, leaving unanswered how Tregs carry-out essential mRNA translation for development and immune suppression activity.
Using human CD4+ T cells differentiated in culture (iTregs) and genome-wide transcription and translation profiling, we show that TGFb transcriptionally reprograms naïve T cells to express iTreg differentiation and immune suppression mRNAs, while mTORC1 inhibition impairs translation of  T cell mRNAs but not those induced by TGFb. TGFb-induced Treg mRNAs were found to utilize an alternate mechanism for cap-dependent mRNA translation directed by the DAP5/eIF3d complex rather than canonical mTORC1/eIF4E during Treg development, which is directed by their 5’-untranslated regions. iTreg differentiation is therefore mediated by combined TGFb transcriptional and translational reprogramming and a privileged mechanism of mRNA translation

overall_design: Naïve human T cells were isolated from healthy donor PBMCs. Cells were activated with anti-CD3/anti-CD28 and IL-2, treated with TGFbeta + RAD001 (mTOR inhibitor), TGFbeta alone, RAD001 alone, or left untreated. Cells were maintained in culture fo 13 days with treatments, then harvested. Double and single treated cells were enriched for Tregs by magnetic-beads sorting, and processed for RNA extraction. RNA was sedimented on a sucrose gradient to separate actively translating ribosomes (polysomes).  Polysomal RNA (HD - high density) and total RNA (TOT) was loaded on Affymetrix chip for microarray analysis

first: Viviana

last: Volta

first: Robert

middle: J

last: Schneider


title: AP-2alpha-mediated activation of E2F and EZH2 drives melanoma metastasis [RNA-seq]

first: Jeffrey

last: White

overall_design: Examining changes to the transcriptome with loss of AP-2Alpha.


title: Transcriptome of Wdr5 and (or) p53 double knockout ESCs and embryoid bodies

first: Rajesh

last: Rao

state: Michigan

address: 1000 Wall Street

summary: This study describes the transcriptome profiling of day 6 SFEBq embryonic bodies (EBs): 1) WT; 2) Wdr5 KO ; 3) Wdr5 KO with T12h hWDR5 rescue; 4) Wdr5 KO with T48h hWDR5 rescue

overall_design: RNA-Seq profiling on mouse Rx:GFP KI embryonic stem cell during differeniatiation via SFEBq method. Biological duplicates of each sample are labled as rep1/2.


title: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits [snATAC-seq]

first: Stephen

last: Gallagher


title: Genome profiling of WDR5 and H3K4me3 binding in mouse embryonic stem cells

summary: This study describes the binding profile of  WDR5 and H3K4me3 in Wdr5 and p53 double knockout ESC rescued with WDR5WT or WDR5S91KY191F

overall_design: ChIP-Seq profile of WDR5 and H3K4me3 Wdr5 and p53 double knockout ESC rescued with WDR5WT or WDR5S91KY191F.  Corresponding sequence profiles of genomic DNA (Input) for each data set are also included.


title: Genome profiling of MAX binding in mouse embryonic bodies using SFEBq differentiation methods

summary: This study describes the binding profile of  MAX in mouse embryonic bodies at day 2 (WT, Wdr5 KO, Wdr5 and p53 double knockout)

overall_design: Cut & Run profile of MAX binding in day2 embryonic embryoid bodies  (WT, Wdr5 KO, Wdr5 and p53 double knockout)


title: Wdr5

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


title: Gene expression in total sexual mycelium and perithecia of Sordaria macrospora

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

summary: The aim of this analysis was to analyze gene expression in developing fruiting bodies (perithecia) of the filamentous ascomycete Sordaria macrospora, and to identify genes that are differentially regulated in the three developmental mutants delta-spt3, delta-asm2, and delta-asm3.

overall_design: Two independent biological replicates were performed and sequenced for each sample.

first: Ramona

last: Lütkenhaus


title: ATAC-seq analysis of C1qbp sufficient and deficient CD8+ T cells sorted from mice post infection with LCMV Armstrong

status: Public on Jun 09 2021

city: Xiamen

first: liu

last: kai

state: Fujian

address: Xiang'an Campus, Xiamen University, Xiang'an District

institute: Xiamen University

summary: This study is aimed to explore whether C1qbp deficiency affects the epigenetic modification during the differentiation stage of CD8+ T cells. Transferred WT and C1qbp KO P14 cells sorted from the spleen of donor mice on day 5 post-infection with LCMV Armstrong were collected and treated for ATAC-seq. ATAC-Seq analysis provided sufficient but not necessary evidence of epigenetic changes between WT and C1qbp KO CD8+ T cells. Our study have shown that, on day 5 post-infection with LCMV Armstrong, even WT and C1qbp KO CD8+ T cells have different mRNA expressing profiling, the ATAC-seq shows slight changes in chromatin accessibility of indicated genes.

overall_design: ATAC-Seq analysis of transferred WT and C1qbp KO P14 cells sorted from the spleen of donor mice on day 5 post-infection with LCMV Armstrong

first: Kai

last: Liu

first: Xingyuan

last: Zhai

first: Hongkun

last: Fang


title: CUT-tag analysis of C1qbp sufficient and deficient CD8+ T cells

summary: This study is aimed to Investigate whether C1qbp deficiency affects the histone modification during the differentiation stage of CD8+ T cells. Transferred WT and C1qbp KO P14 cells sorted from the spleen of donor mice on day 5 post-infection with LCMV Armstrong were collected and treated for CUT-tag. CUT-tag-Seq analysis provided evidence of histone modification changes between WT and C1qbp KO CD8+ T cells. Our study shows that on day 5 post-infection with LCMV Armstrong, along with mRNA expressing profiling, the CUT-tag-seq exhibits obvious changes in H3K27me3 and H3K27Ac modification of indicated genes of WT and C1qbp KO CD8+ T cells.

overall_design: C1qbp sufficient and deficient P14 cells were transferred into donor mice and sorted from the spleen of donor mice on day 5 post-infection with LCMV Armstrong. Peaks bound by H3K27ac and H3K27me3 were obtained using CUT-tag.

first: Quan

last: Zhang


title: Cell-intrinsic Innate Immune Responses against Chikungunya Virus in a Human Ex Vivo Synovial Fibroblast Model [scRNA-seq]

city: Berlin

first: Fabian

last: Pott

state: Berlin

address: Charitéplatz 1

department: Institute for Virology

institute: Charité - Universitaetsmedizin Berlin

summary: Single-cell RNAseq dataset on CHIKV-infected fibroblasts. Overall conclusions: Strong induction of innate immune responses, depending on the amount of viral RNA in the cells we found an antagonism against transcription factors such as STAT1 and JAK1.

overall_design: Human primary synovial fibroblasts were infected with CHIKV at different MOIs and at 6 and 24 hours post infected subjected to single-cell RNAseq. In total, 12 samples were analyzed. From two different donors, for each timepoint two infected samples and one mock-infected sample were analyzed.

first: Dylan

last: Postmus

first: Richard

last: Brown

first: Emanuel

last: Wyler

first: Elena

last: Neumann

first: Markus

last: Landthaler

first: Christine

last: Goffinet


title: RNA sequencing analysis of transferred C1qbp sufficient and deficient CD8+ T cells sorted from donor mice post infection with LCMV Armstrong

status: Public on Jun 08 2021

summary: Tthis study is aimed to explore how C1qbp deficiency affects the mRNA expressing profiling during the differentiation stage of CD8+ T cells.Naïve WT and C1qbp KO P14 cells and transferred WT and C1qbp KO P14 cells sorted from the spleen of donor mice on day 3, 5, 7 post-infection with LCMV Armstrong were collected and treated for RNA-seq. RNA-Seq analysis revealed transcriptomic changes between WT and C1qbp KO CD8+ T cells. Naïve WT and C1qbp KO CD8+ T cells showed similar gene expressing profiling. On day 3, 5, 7 post-infection with LCMV Armstrong, WT and C1qbp KO CD8+ T cells showed 341, 1,164 and 437 differentially expressed genes respectively.

overall_design: RNA-Seq analysis of naïve WT and C1qbp KO P14 cells, and transferred WT and C1qbp KO P14 cells sorted from the spleen of donor mice on day 3, 5, 7 post-infection with LCMV Armstrong


title: Gene expression altered by Sox2 T258A mutation in mouse embryonic stem cells

status: Public on Jun 06 2021

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

institute: National Cancer Center

summary: mRNA expression profiles of mouse embryonic stem cells harboring Sox2 WT and a Sox2 T258A mutation

overall_design: The T258A mutation in which threonine, the 258th residue of Sox2 was mutated to alanine, was introduced into one allele of E14 cells using the CRISPR-Cas9 editing system. Whole transcripts of E14 wild-type cells and Sox2 T258A mutant cells were analyzed by RNA-seq.

first: Jang

last: Lee


title: Translatomics probes into the role of lycopene on improving hepatic steatosis induced by high-fat diet

status: Public on Jun 17 2021

city: chengdu

first: Tengda

last: Huang

state: Sichuan

address: gaopeng road

department: West China Hospital

institute: Sichuan University

summary: Liver is an important organ for fat metabolism. Excessive intake of a high-fat/energy diet is a major cause of hepatic steatosis and its complications such as nonalcoholic fatty liver disease and nonalcoholic steatohepatitis. Supplementation with lycopene, a natural compound, is effective in lowering triglyceride levels in the liver, although the underlying mechanism at the translational level is unclear. In this study, mice were fed a high-fat diet (HFD) to induce hepatic steatosis and treated with or without lycopene. Translation omics and transcriptome sequencing were performed on the liver to explore the regulatory mechanism of lycopene in liver steatosis induced by HFD, and identify differentially expressed genes (DEGs).

overall_design: Total RNA and ribosome-bound RNA were extracted from the livers of high-fat diet- (HFD) and High-fat diet plus lycopene (LYC)-fed mice, and the polyA+ mRNA was sequenced using Illumina HiSeq X Ten sequencer. The reads were mapped to RefSeq RNA reference sequences and the expression level were quantified by rpkM calculation.

first: Jingsu

last: Yu

first: Zeqiang

last: Ma

first: Qinghua

last: Fu

first: Siqi

first: Zupeng

last: Luo

first: Kang

first: Lin

first: Weiwei

last: Miao

first: Dongling

first: Ziyi

last: Song

first: Yixing

last: Li

first: Lei

last: Zhou

first: Gaoxiao

last: Xu


title: RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing (eCLIP)

status: Public on Jun 03 2021

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Homozygous R636S mutation was created by genome editing in an iPS cell line generated from a healthy female patient. Mutant and wild-type cells were differentiated into cardiomyocytes by modulating the WNT signaling pathway, and then are subjected to the lactate purification method. eCLIP was performed to identify targets of RBM20 in mutant and wild-type iPSC-CMs.

overall_design: RNAseq of iPS cell-derived cardiomyocytes with 4 different genotypes as replicates

first: Yuichiro

last: Miyaoka

first: Steven

last: Mayerl

first: Amanda

last: Chan

first: Bruce

last: Conklin

last: Blue

first: Shashank

last: Sathe

first: Gene

last: Yeo


title: Chromatin accessibility profiling of mouse embryonic stem cells and embryonic bodies using SFEBq differentiation methods upon Wdr5 and P53 deletion with or without WT or mutant hWDR5 rescue

first: Rajesh

last: Rao

summary: This study describes time-course chromatin accessibility profiling of mouse ESC and embryonic bodies n Wdr5 and p53 knockout (with or without WT or mutant hWDR5 rescue)

overall_design: ATAC-seq profile of undifferentiated ESCs, day 2, day 4  embryoid bodies in WT, Wdr5 and p53 doubleknockout (with or without WT and mutant WDR5 resuce) groups, in 2 replicates (rep-1 ad rep-2).


title: Cyclic dinucleotide stimulation of Nematostella vectensis

city: Berkeley

first: Shally

middle: Rebecca

last: Margolis

address: 415 Life Sciences

department: Molecular and Cell Biology

institute: UC Berkeley

summary: In mammals, the cGAS-cGAMP-STING pathway is crucial for sensing viral infection and initiating an anti-viral type I interferon response. cGAS and STING are highly conserved genes that originated in bacteria and are present in most animals. By contrast, interferons only emerged in vertebrates; thus, the function of STING in invertebrates is unclear. Here, we use the STING ligand 2'3'-cGAMP to activate immune responses in a model cnidarian invertebrate, the starlet sea anemone Nematostella vectensis. Using RNA-Seq, we found that 2'3'-cGAMP induces robust transcription of both anti-viral and anti-bacterial genes, including the conserved transcription factor NF-κB. Knockdown experiments identified a role for NF-κB in specifically inducing anti-bacterial genes downstream of 2'3'-cGAMP, and some of these genes were also found to be induced during Pseudomonas aeruginosa infection. Furthermore, we characterized the protein product of one of the putative anti-bacterial genes, the N. vectensis homolog of Dae4, and found that it has conserved anti-bacterial activity. This work describes an unexpected role of a cGAMP sensing pathway in anti-bacterial immunity and suggests that a broad transcriptional response is an evolutionarily ancestral output of 2'3'-cGAMP signaling in animals.

overall_design: Examine the response of N. vectensis polyps with cyclic dinucleotides (untreated, c-di-AMP, c-di-GMP, 2'3'-cGAMP, 3'3'-cGAMP). To determine factors required for the response to 2'3'-cGAMP, microinjected N. vectensis embryos with shRNAs targeting GFP (control), nvSTING, nvSTAT, and nvNF-kB and treated with 2'3'-cGAMP.


title: Gene expression altered by Sox2 T258A mutation in teratomas

first: Hyonchol

last: Jang

summary: mRNA expression profiles of teratomas derived from mouse embryonic stem cells containing Sox2 WT and Sox2 T258A mutations

overall_design: The T258A mutation in which threonine, the 258th residue of Sox2 was mutated to alanine, was introduced into one allele of E14 cells using the CRISPR-Cas9 editing system. E14 wild-type and Sox2 T258A mutant cells were transplanted into nude mice. Whole transcripts of resulting teratomas were analyzed by RNA-seq.

first: Jang

last: Lee


title: RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing (RiboMinus RNA-Seq)

status: Public on Jun 01 2021

summary: RBM20 heterozygous (Het) and homozygous (Homo) R636S and homozygous 8-bp deletion (which causes nonsense-mediated decay) mutations were created by genome editing in an iPS cell line generated from a healthy male patient. Those cells were differentiated into cardiomyocytes by modulating the WNT signaling pathway, and then are subjected to the lactate purification method.


title: Negative Feedback Regulation of Cholesterol Biosynthesis by MMAB

city: New Haven

first: Alberto

last: Canfrán-Duque

state: CT

address: 10 Amistad

department: Comparative Medicine

institute: Yale University

summary: Intricate regulatory networks govern the net balance of cholesterol biosynthesis, uptake and efflux; however, the mechanisms surrounding cholesterol homeostasis remain incompletely understood. Here, we develop an integrative genomic strategy to detect regulators of LDLR activity and identify 250 genes whose knockdown affects LDL-cholesterol uptake and whose expression is modulated by intracellular cholesterol levels in human hepatic cells. From these hits, we focus on MMAB, an enzyme which catalyzes the conversion of vitamin B12 to adenosylcobalamin, and whose expression has previously been linked to altered levels of circulating cholesterol in humans. We demonstrate that hepatic levels of MMAB are modulated by dietary and cellular cholesterol levels through SREBP2, the master transcriptional regulator of cholesterol homeostasis.  Knockdown of MMAB decreases intracellular cholesterol levels and augments SREBP2-mediated gene expression and LDL-cholesterol uptake in human and mouse hepatic cell lines. Reductions in total sterol content were attributed to increased intracellular levels of propionic and methylmalonic acid and subsequent inhibition of HMGCR activity and cholesterol biosynthesis. Moreover, mice treated with antisense inhibitors of MMAB display a significant reduction in hepatic HMGCR activity and hepatic sterol content and increased expression of SREBP2-mediated genes. Collectively, these findings reveal an unexpected role for the adenosylcobalamin pathway in regulating LDLR expression and identify MMAB as an additional control point by which cholesterol biosynthesis is regulated by its end product.

overall_design: mRNA profiles from liver tissue isolated from WT mice treated with antisense inhibitors of MMAB (MMAB ASO) or antisense inhibitor control (Control ASO). Mice received one i.p. injection per week of 50 mg/kg Control ASO or MMAB ASO for 6 weeks. 48 hours after the last injection animals were sacrificed and liver sample were collected. Total RNA from liver samples of mice treated with 50 mg/kg Control ASO or MMAB ASO  was extracted and purified using the RNeasy isolation Kit (Qiagen) according to the manufacturer’s instructions and treated with DNAse to remove genomic contamination (RNA MinElute Cleanup, Qiagen). rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries were performed using TrueSeq Small RNA Library preparation (Illumina). Libraries were sequenced for 45 cycles on Illumina HiSeq 2000 platform (1 x 100bp read length).

first: Leigh

last: Goedeke

first: Carlos

last: Fernandez-Hernando


title: Transcriptome profile of Haemaphysalis longicornis (Acari: Ixodidae) exposed to C. citratus essential oil and citronellal

city: Shijiazhuang

first: Desmond

middle: Onyeka

last: Agwunobi

address: No. 20 Road East 2nd Ring South Yuhua District

institute: Hebei Normal University

summary: Many genes responsive to C. citratus oil and citronellal were stress-related and they include genes associated with adrenergic signalling/calcium channels, cGMP-PKG signaling, apoptosis, focal adhesion, ECM-receptor interaction, ubiquitin mediated proteolysis, mTOR signalling pathway, and longevity regulating pathway.

overall_design: Transcriptome profile of adult unfed ticks treated with three concentrations of C. citratus essential oil and citronellal

middle: O

first: Zhijun

last: Yu

first: Jingze

last: Liu


title: RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing (WTB RNA-Seq)

first: Nathan

last: Salomonis

summary: RBM20 heterozygous (Het) mutation was created by genome editing in an iPS cell line generated from a healthy female patient. Those cells were differentiated into cardiomyocytes by modulating the WNT signaling pathway, and then are subjected to the lactate purification method.

overall_design: RNAseq of iPS cell-derived cardiomyocytes with 2 different genotypes as replicates

last: Miyaoka


title: Apoptolidin family glycomacrolides target leukemia through inhibition of ATP synthase

status: Public on May 31 2021

city: Nashville

first: Benjamin

last: Reisman

state: TN

address: 1234 Stevenson Center Dr. Rm 7330

department: Chemistry

institute: Vanderbilt University

summary: Cancer cells have long been recognized to exhibit unique bioenergetic requirements. The apoptolidin family of glycomacrolides are distinguished by their selective cytotoxicity towards oncogene transformed cells, yet their molecular mechanism remains uncertain. We used photoaffinity analogs of the apoptolidins to identify the F1 subcomplex of mitochondrial ATP synthase as the target of apoptolidin A. CryoEM of apoptolidin and ammocidin-ATP synthase complexes revealed a novel shared mode of inhibition that was confirmed by deep mutational scanning of the binding interface to reveal resistance mutations which were confirmed using CRISPR-Cas9. Ammocidin A was found to suppress leukemia progression in vivo at doses that were tolerated with minimal toxicity. These studies reveal that OXPHOS dependent cancers are vulnerable to ATP synthase inhibition by apoptolidin family glycomacrolides compounds.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design:
The goal of this experiment was to identify mutations within the glycomacrolide binding site on the human ATP synthase that conferred resistance to apoptolidin and ammocidin. A library of ATP synthase mutants (420 total genes: ATP5F1A, ATP5F1B, ATP5F1C) was generated in vitro using nicking mutagenesis on a attB containing plasmid and transferred into HEK293 cells expressing a Bxb1 attP ‘landing pad,’ such that each cell can express one protein variant. After selection for cells which had undergone successful recombination, each pool of mutants was split into 6 wells and treated with different doses of ammocidin A, apoptolidin A, or vehicle for 4 days on, 3 days off, for two weeks. Resistant mutants were expanded, genomic DNA extracted, and the transgene was amplified by PCR and subjected to next generation sequencing.
The mutant library was initially validated by amplifying the transgene from the plasmid to verify the presence of the targeted mutations. A wildtype library (WT) was included as a negative control at both the library validation stage and in cells. A single pooled library was transfected into three separate dishes containing HEK293T-LP-neg (empty landing pad) cells to create three separate biological replicates. After selection for successful recombination each pool was treated with each of the drug conditions, for a total of three biological replicates for each condition. Each sample was compared to its own ‘parent’ representing the library after selection for recombined cells prior to drug selection. A vehicle control was passaged for 1 week after selection for recombined cells as a negative control. Cells were also transfected with WT library and treated with compounds, though no cells were recovered from the drug treated conditions except for apoptolidin A, 100 nM.

first: Brian

last: Bachmann


title: RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing

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

overall_design: Refer to individual Series


title: Reversion analysis reveals the immunogenicity in vivo of a poorly MHC I-binding cancer neoepitope

city: Farmington

first: Marmar

last: Moussa

address: Farmington

department: School of Medicine

institute: University of Connecticut

summary: A mutation that results in tumor rejection activity in a neoepitope (which is a poor binder of Kd) influences the immunogenicity of the tumor as a whole. Our results demonstrate the activity in vivo of a poorly-MHC I-binding cancer neoepitope.

overall_design: Examination of tumor microenvironment (TME) of different CRISPR edited mouse Meth A fibrosarcoma (REV, MUT1 and MUT2) as well as TME of mice immunized with mutant Ccdc85c and Alms1.

first: Hakimeh

last: Ebrahimi-Nik


title: AP-2alpha-mediated activation of E2F and EZH2 drives melanoma metastasis

first: Jeffrey

last: White


title: Transcriptome in replicatively senescent HUVEC

city: Fujisawa

first: Momoko

last: Ohori

state: Kanagawa

address: 26-1, Muraokashicashi2

country: Japan

institute: Takeda pharmaceutical company

summary: To clarify the transcriptome landscape of HUVECs during replicative senescence, we analyzed changes in gene expression and genome-encoded splicing using comprehensive multi-technical RNA-seq analysis.

overall_design: Examination of mRNA expression and splicing profile in two independent HUVEC clone with four different culture periods.

first: M

first: Y

last: Nakayama

last: Shimizu

first: H

last: Toyoshiba

first: A

last: Nakanishi

first: S

last: Araki

last: Aparicio


title: Gene expression in tissues of root tips from Pinus pinaster seedlings under ammonium nutrition

status: Public on May 28 2021

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

summary: In the present study, the gene expression changes in four different tissues of root tips from maritime pine were analyzed. The roots were under two nutritional conditions (only watered or fertilised with 3 mM of ammonium) and harvested after 24 hours of the treatment.

overall_design: Pine seedlings were subdivided into two groups. The control group was irrigated with 80 mL of water (C), the second group was supplied with 80 mL of 3 mM NH4Cl. Root samples were collected 24 houres after the irrigation. Seedling’s root tips were cut and tissues of 5 - 6 mm were imbibed in a specimen holder with Tissue‐Tek optimal cutting temperature embedding medium (Sakura Finetek, Alphen aan den Rijn, The Netherlands) and immediately frozen in liquid nitrogen for cryostat sectioning. The 24 samples were sequenced on an Illumina NovaSeq 6000 as paired-end reads of 150 bp length.

first: Francisco

last: Ortigosa

first: César

last: Lobato-Fernández


title: Lung and primary pulmonary endothelial single cell RNA seq data

status: Public on May 26 2021

first: Jonas

last: Schupp

address: 300 Cedar Street

department: PCCSM

institute: YALE UNIVERSITY

summary: Single Cell RNAseq of Whole Lung Dissociates from control lungs and primary pulmonary endothelial cells

overall_design:
Exploratory analysis of healthy lung cell populations and of primary pulmonary endothelial cells
Raw data for samples GSM5020379-GSM5020382 not provided due to patient privacy concerns.

first: Naftali

last: Kaminski

first: Ivan

last: Rosa

first: Taylor

middle: S

last: Adams

first: Laura

middle: E

last: Niklason

first: Richard

last: Pierce

first: Yifan

last: Yuan


title: Genomic modules and intramodular networks of susceptibility and resilience in multimodeled stress in male mice

status: Public on May 19 2021

city: New York

first: Jordan

last: Marrocco

address: 1230 York Ave

institute: The Rockefeller University

summary: It was our goal to discern the genomic signatures of the ventral hippocampus, in male mice after exposure to exogenous corticosterone, an animal model that induces a blunted response to stress. In addition to wildtype mice, we used mice heterozygous for the single nucleotide polymorphism of the gene encoding for brain-derived neurotrophic factor, BDNF Val66Met, a mouse model that shows susceptibility to stress.

overall_design:
Wild-type mice or BDNF Val66Met male mice were maintained on chronic oral corticosterone  or vehicle for six weeks prior dissection of the ventral hippocampus and extraction of RNA for sequencing.
VV/WT = Wildtyple, VM/BDNF = Heterozygous BDNF Val66Met, VEH = vehicle, CORT = corticosterone

first: Salvatore

middle: G

last: Caradonna

first: Nathen

last: Einhorn


title: RNAseq analysis of PS+ vs PS- non-naive CD8 T cells sorted from peripheral blood of COVID-19 patients

status: Public on May 21 2021

city: Planegg-Martinsried

first: Jan

last: Kranich

address: Grosshadernerstr. 9

department: Institute for Immunology

institute: Ludwig-Maximilians-Universität München

summary: We report the transcriptional profile of phosphatidylserine (PS) positive and PS negative non-naive peripheral blood CD8 T cells from patients infected with SARS-CoV-2. PS+ CD8 T cells showed increased expression of cell cyclce and cell division associated genes and reduced expression of genes regulating translational initiation, when compared to PS- CD 8 T cells. Furthermore, PS+ CD8 T cells show increased expression of effector T cell genes.

overall_design:
non-naive (CCR7+CD45RA-, CCR7-CD45RA-, CCR7-CD45RA+) PS+ and PS- peripheral blood CD8 T cells were sorted from 4 COVID-19 patients and analysed by RNAseq

WHOmax: the maximal COVID-19 disease severity score of the patient, classified using the World Health Organization's (WHO) eight-point ordinal scale for COVID-19 trial endpoints.

first: Lisa

last: Rausch

first: Thomas

last: Brocker


title: Single cell RNA sequencing of post-traumatic brain injury day 4 ipsilateral brain leukocytes in C57BL/6 adult male mice

status: Public on May 25 2021

city: San Francisco

first: Walter

last: Eckalbar

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

summary: The goals of this project include 1) determining the cellular immune response induced by acute traumatic brain injury in vivo with a focus on microglia and monocyte/macrophages, and 2) correlate immune responses with improved function post-TBI in Ccr2-/- TBI mice, which lack monocyte infiltration into the injured brain and are resistant to brain damage, compared to WT TBI mice.

overall_design: Leukocytes were isolated from ipsilateral brain tissues from four groups of mice:  wildtype (WT) TBI mice (n=3), Ccr2-/- TBI mice (n=3), WT normal (n=3), Ccr2-/- normal (n=2).  CD45+ Ly6G- LIVE cells were sorted by flow cytometry, and cells were processed for single-cell RNA sequencing using the 10X Genomics platform v3 chemistry.

first: Christine

last: Hsieh

first: Joshua

last: Rudolph

first: Kerri

last: Somebang


title: A Single Cell Atlas of Alveolar Development

status: Public on May 05 2021

first: Jennifer

last: Sucre

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

summary: The later stages of lung development are defined by the structural processes of sacculation and alveolarization, with dramatic shifts in the spatial organization and function of epithelial, endothelial, and mesenchymal cells. To investigate the coordination of the cellular changes in the lung parenchyma during development we performed a single cell RNA sequencing time-series yielding 92,238 epithelial, endothelial, and mesenchymal cells across 8 time points from embryonic day 12 (E12) to postnatal day 14 (P14). We combined new computational analysis with RNA in situ hybridization to explore transcriptional velocity, fate likelihood prediction, and temporally and spatial localization of cell populations during the transition between the saccular and alveolar stages. We interrogated this atlas to illustrate the complexity of elastin assembly and demonstrate an integrated view of the cellular dynamics during later lung development.

overall_design: Single Cell RNAseq of dissociated mouse lungs at ages: E12, E15, P3, P5, and P7. Suspensions were enriched for cells that were CD45 negative, Ter119 negative, and viable. P7 lungs were enriched for epithelial cells by collecting EPCAM positive cells.

first: Nicholas

middle: M

last: Negretti

first: Erin

last: Plosa

first: John

middle: T

last: Benjamin

first: Bryce

last: Schuler

first: A

last: Habermann

first: Christopher

last: Jetter

first: Peter

last: Gulleman

first: Chase

last: Taylor

first: David

last: Nichols

first: Brittany

middle: K

last: Matlock

first: Susan

last: Guttentag

first: Timothy

last: Blackwell

last: Banovich

first: Jonathan

last: Kropski


title: Transcriptome of the audiogenic rat strain and identification of possible audiogenic epilepsy-associated genes

city: Moscow

first: Sergei

last: Funikov

state: Moscow

address: Vavilov str. 32

country: Russia

institute: Engelhardt Insitute of Molecular Biology

summary: Audiogenic epilepsy (AE), developing in rodent strains in response to loud sound, is widely used as the model of generalized convulsive epilepsy. The molecular and genetic mechanisms that determine the expression of AE are currently non well understood. In the present work we compared transcriptomes from the inferior and superior colliculi (corpora quadrigemina), the crucial epileptogenic midbrain zone for AE in order to identify genes associated to the AE phenotype. Transcriptomes of rats from three strains were compared: Krushinsky-Molodkina (KM) strain (100% AE-prone); Wistar outbred rats (with no AE proneness) and "0" strain, selected from F2 KMxWistar hybrids for the lack of AE. It is shown that KM strain gene expression profile have a number of characteristic differences from those of Wistar and "0" strains. In particular, KM has increased expression of a number of genes involved in positive regulation of the MAPK signaling cascade, as well as genes, responsible for positive regulation of apoptotic processes. The next characteristic difference between the KM strain from Wistar and "0" is a multiple increase in the expression level of the Ttr gene, which is known to be associated with family amyloid polyneuropathy in humans. Further, the KM strain showed a significant decrease in the expression of the Msh3 gene involved in the DNA mismatch repair system, Acsm5, coding a mitochondrial acyl-CoA synthetase specific for medium chain family member 5, and in a number of genes of the oxidative phosphorylation system, and a number of some other genes. Our data confirm the complex multigenic nature of AE inheritance in rodents. A comparison with the data obtained from other AE rodent strains suggests that the convulsive phenotype could develop differently in audiogenic rat strains selected independently. Although, the finding of parallel differences in certain genes expression in AE-prone hamsters (another rodent species) indicate the common (and crucial) neurogenetic defects, leading to AE phenotype in rodents in general.

overall_design: KM - audiogenic epilepsy rat strain; W - wistar control rat strain; 0 - outbred strain from KM rats


title: CRISPR-Cas9 Screens Reveal Genes Regulating a G0-like State in Human Neural Progenitors [CRISPR]

status: Public on May 13 2021

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: The coordination of developmental potential and proliferation in stem and progenitor cells is essential for mammalian development and tissue homeostasis. To better understand this coordination in human neural progenitor cells (hNPCs), we performed CRISPR-Cas9 screens and identified genes that limit their expansion. These screens revealed that knockout of growth-limiting genes, including CREBBP, NF2, PTPN14, TAOK1, or TP53, caused increased hNPC expansion via skipping of a transient G0-like state, accompanied by transcriptional reprogramming of G1 subpopulations. Hallmarks of the G0-like state included expression of genes associated with quiescent neural stem cells and neural development and molecular features found in quiescent cells (e.g., hypo-phosphorylated Rb, CDK2low activity, and p27high). Further, G0-skip genes act through both distinct and convergent downstream effectors, including cell cycle, Hippo-YAP, and novel targets. The results suggest that hNPC expansion is constrained by a transient G0-like state, regulated by multiple pathways, that facilitates retention of neurodevelopmental identity.

overall_design: 3 independent libraries were assayed in hNPCs at different timepoints (either ~3 weeks or 10 days). CRISPR-Cas9 screens include 3-4 replicates and Day 0 (post-selection) control samples.

first: Heather

last: Feldman

first: Chad

last: Toledo

first: Pia

last: Hoellerbauer

first: Philip

last: Corrin

first: Lucas

last: Carter

first: Megan

last: Kufeld

first: Hamid

last: Bolouri

first: Ryan

last: Basom

first: Jeffrey

last: Delrow

first: Joshua

last: Meier

first: Feng

last: Zhang

first: Jose

middle: L

last: McFaline-Figueroa

first: Cole

last: Trapnell

first: Steven

last: Pollard

last: Plaisier

first: Patrick

last: Paddison


title: CRISPR-Cas9 Screens Reveal Genes Regulating a G0-like State in Human Neural Progenitors [Bulk RNA-seq]

last: Arora

overall_design: 33 samples in total were analyzed for gene expression using RNA-sequencing including either the entire population, sorted for G0/G1 (mCherry-CDT1(aa30/120)-positive), or partial differentiation following removal of growth factors for 7 days. Bulk RNA-seq include 2-3 replicates and controls include wild-type NPCs, non-targeting CRISPR-Cas9 NPCs, and unsorted/undifferentiated NPCs.

first: Christopher


title: Predicting Master Transcription Factors from Pan-Cancer Expression Data

status: Public on Apr 19 2021

city: Los Angeles

first: Robbin

last: Nameki

state: CA

address: 8700 Beverly Blvd

department: Obstetrics and Gynecology

institute: Cedars-Sinai Medical Center

summary: Critical developmental “master transcription factors” (MTFs) can be subverted during tumorigenesis to control expression of oncogenic transcriptional programs. Current approaches to identify MTFs rely on chromatin immunoprecipitation-sequencing data, which is currently unavailable for many cancer types. We developed the CaCTS (Cancer Core Transcription factor Specificity) algorithm to prioritize candidate MTFs using pan-cancer RNA-sequencing data. CaCTS identified candidate MTFs across 34 tumor types and 140 subtypes, including known MTFs. We also made novel predictions, including for cancer types/subtypes for which MTFs are unknown. This included PAX8, SOX17, and MECOM as candidate MTFs in ovarian cancer (OV). In OV cells, these factors are required for viability, lie proximal to super-enhancers, co-occupy regulatory elements globally and co-bind at critical gene loci encoding OV biomarkers. Identification of tumor MTFs, especially for tumor types with limited understanding of transcriptional drivers, paves the way to therapeutic targeting of MTFs in a broad spectrum of cancers.

overall_design: RNA-seq results of OVCAR4 cells treated with si controls, siPAX8, siSOX17,siDual(siPAX8/siSOX17), siMECOM, or siWT1

first: Jessica

last: Reddy

first: Marcos

last: Fonsseca

first: Rosario

middle: I

last: Corona

first: Felipe

last: Dezem

first: Heidi

last: Chang

first: Xianzhi

last: Lin

first: Forough

last: Abbasi

first: Brian

last: Abraham

first: Kate

last: Lawrenson


title: Baiting out a full length sequence from unmapped RNA-seq data

status: Public on Apr 22 2021

city: Shenzhen

first: JING

last: LUO

email: luoj17@lzu.edu.cn, luojing9520@163.com

address: No 7,Pengfei Road,Dapeng District

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

summary: Usually, unmapped reads have been considered as useless and been trashed or ignored. Here, we develop a strategy to mining the full length sequence by unmapped reads combining with specific reverse transcription primers design and high throughput sequencing. In this study, we salvage 36 unmapped reads from standard RNA-Seq data(GSM3188619) and randomly select one 149 bp read as a model(CTGGTGCCATAATTCAGGGAACTGTGTTCTTGATGTACTATCTGAGACATTTGTGCTTCCCCCCATCCAGCTATCAGGCTGTTAGGCAATGCACTTCTAGGAATTAGAATTCTATAAGGAATCTCATGCTGGAAGAACAAAAAGACCCA  ). Specific reverse transcription primers(5' end:CTGGTGCCATAATTCAGGGA, 3' end:GGATCTTCACGTAACGGATTGT) are designed to amplify its both ends, followed by next generation sequencing. Then we use a statistical model base on power law distribution to estimate its integrality and significance. Further, we validate it by Sanger sequencing. The result shows that the full length is 1,556 bp, with InDel mutation in microsatellite structure. This would be a useful strategy to extract the sequences information from the unmapped RNA-seq data.

overall_design: The library of full length sequence of unmapped reads captured by specific reverse transcription primers

first: Dongwei

last: Li

first: Qitong

last: Huang


title: microRNAs Restrain Proliferation in BRAFV600E Melanocytic Nevi

city: Salt Lake City

first: Robert

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah


title: Transcriptomic analysis of mouse nervous endothelial cells treated by Porfimer sodium-mediated photodynamic therapy

status: Public on Apr 17 2021

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

institute: Henan University

summary: We report the application of Porfimer sodium-mediated photodynamic therapy on mouse brain endothelial cells, and further identified the impact of PDT on the normal vessel cells.

overall_design: Examination of transcriptome level in mouse brain endothelial cell treated with PDT.

first: Yanyan

last: He

first: Yingkun


title: CRISPR-Cas9 Screens Reveal Genes Regulating a G0-like State in Human Neural Progenitors

first: Sonali

last: Arora


title: CRISPR-Cas9 Screens Reveal Genes Regulating a G0-like State in Human Neural Progenitors [scRNA-seq]

overall_design: 4 samples of hNPCs were analyzed through single-cell RNA-sequencing using the GemCode platform (10x Genomics). The samples were either the entire population of cells or sorted for G0/G1 through the presence of a G1 reporter, mCherry-CDT1 (aa30/120). Single cell RNA-seq includes >2000 cells and wild-type NPC control samples.

first: Heather

last: Feldman

first: Chad

last: Toledo

first: Pia

last: Hoellerbauer

first: Philip

last: Corrin

first: Lucas

last: Carter

first: Megan

last: Kufeld

first: Hamid

last: Bolouri

first: Ryan

last: Basom

first: Jeffrey

last: Delrow

first: Joshua

last: Meier

first: Feng

last: Zhang

first: Jose

last: McFaline-Figueroa

first: Cole

last: Trapnell

first: Steven

last: Pollard

first: Christopher

last: Plaisier

first: Patrick

last: Paddison


title: scRNA-seq experiments on primed mouse epiblast stem cells, blastocyst-like cell reprogramming and mouse embryonic stem cells.

status: Public on Apr 13 2021

city: Kobe

first: Cody

last: Kime

state: Hyogo

address: Minatojima Minamimachi, 2-2-3

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: Recently, a new wave of synthetic embryo systems (SESs) have been established from cultured cells toward efficient and ethical embryonic development research. We recently reported our epiblast stem cell (EPISC) reprogramming SES that generates numerous blastocyst (BC)-like hemispheres (BCLH) with pluripotent and extraembryonic cell features detected microscopically. Here, we further explored the system over key time points with unprecedented single-cell RNA sequencing (scRNA-seq) analysis and revealed broad induction of the 2C-like reporter MERVL and RNA velocity diverging three major population regions with genetic expression resembling pluripotent epiblast (EPI), primitive endoderm (PE), and trophectoderm (TE). Enrichment of those three BC-like cell fates involved key regulons, zygotic genome activation (ZGA) related genes, specific RNA splicing, and select cells meaningfully distinguished critical regulons of model cells. This analysis confirms the induction of the extraembryonic cell populations during the reprogramming and we anticipate that our unique BCLH SES and rich data may uncover new facets of cell potency, improve developmental biology, and help biomedicine advance.

overall_design:
Cell culture samples were prepared as approximately 3,000 single cells and then sampled for scRNA-seq 10x Genomics 3' (v3 Chemistry) library construction with standard protocol. Libraries were sequenced with paired-end reads on Illumina HiSeq X at one library per lane and then mapped to a custom reference mouse genome (mm10) using Cell Ranger (Version 3.1), including two transgenes for EGFP and mCherry involved in the related study.
The related study at https://doi.org/10.1101/2020.09.29.318279

first: Haiming

last: Hu

first: Hashimita

last: Sanyal

first: Yoshiki

last: Sahara


title: Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways

status: Public on Apr 11 2021

city: London

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

country: United Kingdom

institute: The Francis Crick Institute

summary: The goal of this scRNA-seq study was to characterize the pseudo-spatial distribution of Nodal and BMP effectors (SMADs) expression prior to the onset of gastrulation

overall_design: scRNA-seq was performed on Zebrafish embryos at sphere stage

first: Luca

last: Guglielmi

first: Caroline

last: Hill


title: Transcriptomic analysis of differential epression of genes of HSC4 cells on treatment with SSTP1 in comparison to its inactive mutant SSTP2

status: Public on Apr 23 2021

city: Trivandrum

first: Tessy

middle: Thomas

last: Maliekal

state: Kerala

address: Poojappura

country: India

institute: Rajiv Gandhi Centre for Biotechnology

summary: RNA was isolated from HSC 4 cells after treatment with peptides SSTP1 and SSTP 2 using RNeasy mini kit (Qiagen) as per the manufacturer’s instruction and reverse transcribed to double-stranded cDNA. RNA-Seq analysis was done on Illumina platform to identify the target genes on treatment with SSTP1 in comparison with SSTP2, in HSC4 cells. Out of the 34 to 37 million reads obtained, 31 to 34 million reads per samples were mapped on the indexed Human reference genome GRCh38.p7. 208 up-regulated genes and 118 down-regulated genes were identified through differential gene expression analysis.The RNA-Seq results were validated by 12 up-regulated and four down-regulated genes by RT-PCR and q-PCR.

overall_design:
RNA seq. analysis for comparing differential gene expression on treatment with SSTP1 in comaprison with SSTP2.

Contributor: Shyla, G.

last: Thomas Maliekal


title: Transcriptome comparison of the irt1-2 mutant (pam42) and the corresponding wild type (Col-0)

status: Public on Mar 31 2021

city: Bochum

first: Ute

last: Kraemer

address: Universitaetstrasse 150

institute: RUB University Bochum

summary:
IRT1 is the root high-affinity Fe uptake system. Despite severe Fe deficiency symptoms and reduced Fe levels in the shoots of irt1 mutants, we find that root Fe concentrations are higher in the irt1-2 mutant than in the wild type, unexpectedly. The goal of this experiment was to identify candidate transcripts contributing to the observed alteration in root-to-shoot Fe partitioning of irt1.
We analysed gene expression in shoots and roots of the wild type grown under control conditions, the wild type exposed to severe Fe deficiency for 5 d, as well as of the irt1-2 (pam42) mutant grown under control conditions.

overall_design: Seedlings were grown on plates  in - Fe or + Fe media for 5 days, subsequent to an initial pre-cultivation period in control media for 10 d.

first: Julia

last: Quintana

first: María

last: Bernal

first: Marleen

last: Scholle

first: Heike

last: Holländer-Czytko

first: Nga

last: Nguyen

first: Markus

last: Piotrowski

first: David

last: Mendoza-Cózatl

first: Mike

last: Haydon


title: The BAF complex blocks Myogenesis in rhabdomyosarcoma

status: Public on Apr 01 2021

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Rhabdomyosarcoma (RMS) is a highly malignant pediatric cancer of skeletal muscle lineage. The aggressive alveolar subtype is commonly characterized by t(2;13) or t(1;13) translocations with the expression of PAX3- or PAX7-FOXO1 fusion transcription factors respectively and is known as fusion positive RMS (FP-RMS). FP-RMS tumors rely on the fusion gene to maintain their proliferative state while avoiding terminal differentiation program. Since disruptions of normal development are likely governed by epigenetic changes in these low-mutational-burden tumors, we investigated the contributions of chromatin regulatory complexes to RMS tumor maintenance. We demonstrate the essentiality of the mSWI/SNF ATPase BRG1 for FP-RMS proliferation and discover that RMS significantly overexpress SMARCA4 (encoding BRG1) compared to skeletal muscle. We define the mSWI/SNF subunit repertoire in FP-RMS and provide evidence for the assembly of multiple mSWI/SNF complexes including canonical BAF, PBAF and non-canonical (nc)BAF in FP-RMS. Proteomic studies suggest proximity between PAX3-FOXO1 and BAF complexes, which was further supported by genome-wide binding profiles revealing enhancer colocalization of BAF with FP-RMS core regulatory transcription factors. We report that mSWI/SNF complexes act as sensors of chromatin state, which are recruited to sites of de novo histone acetylation. Phenotypically, interference with mSWI/SNF complex function induces transcriptional activation of the skeletal muscle differentiation program associated with MYCN enhancer invasion at myogenic target genes. Finally, BRG1 targeting compounds reproduce the effects of genetic ablation. We conclude that inhibition of BRG1 overcomes the differentiation blockade of FP-RMS cells and may provide a therapeutic strategy for treating this lethal childhood tumor.

overall_design: Biological triplicate samples of Cas9 expressing RH4 transduced with indicated sgRNAs were collected 7 days after transduction for RNA isolation. Total RNAs were extracted by RNeasy Plus Mini Kit (Qiagen). Paired-end mRNA libraries were prepared using Truseq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on a Novaseq system as 2x150 base reads by Atlas Biolab GmbH (Berlin, Germany).

first: Berkley

last: Gryder

first: Xinyu

last: Wen

first: Jun

last: Wei


title: A partial picture of the single-cell transcriptomics of human IgA nephropathy

status: Public on Apr 02 2021

city: CHANG SHA

first: YONG

last: ZHONG

address: XIANGYA ROAD

institute: XIANGYA HOSPITAL

summary: The comprehensive analysis of kidney biopsy specimen demonstrated different gene expression profile, potential pathologic ligand-receptor crosstalk, signaling pathways in human IgAN. These results offer new insight into pathogenesis and identify new therapeutic targets for patients with IgA nephropathy.

overall_design: Single-cell RNA sequencing (scRNA-seq) was applied to kidney biopsies from 4 IgAN and 1 control subjects to define the transcriptomic landscape at the single-cell resolution.

first: Rong

last: Tang

first: Ting

last: Meng

first: Wei

last: Lin

first: Yong

last: Zhong

first: Xiangcheng

last: Xiao


title: NF1 mutation drives neuronal activity-dependent optic glioma initiation

status: Public on Mar 30 2021

city: St Louis

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: The study investigates the role of NF1 mutation and neuronal activity on the initiation of optic pathway glioma, a type of low-grade glioma.  the RNAseq dataset investigates mRNA expression profile of human pilocytic astrocytomas (WHO grade I)

overall_design: mRNA profiling of human non-neoplastic brains, NF1-associated pilocytic astrocytomas, and sporatic pilocytic astrocytomas

first: Yuan

last: Pan

first: Jared

middle: D

last: Hysinger

first: Nicki

last: Schindler

first: Olivia

last: Cobb

first: Xiaofan

last: Guo

first: Belgin

last: Yalcin

first: Corina

last: Anastasaki

first: Sara

middle: B

last: Mulinyawe

first: Anitha

last: Ponnuswami

first: Suzanne

last: Scheaffer

first: Yu

last: Ma

first: Kun-Che

last: Chang

first: Xin

last: Xia

first: Joseph

last: Toonen

first: James

last: Lennon

first: Linda

last: Liau

first: Jeffrey

last: Goldberg

first: Michelle

last: Monje

middle: H


title: Single cell RNA-seq characterizes neural cell population in mouse dorsal root ganglion tissue

city: Tarrytown

first: Tao

last: Yang

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary: We characterized the cell population in mouse dorsal root ganglion using single cell RNA-seq experiment. The data was generated to test the ability of deconvolution method AdRoit. Neural tissues typically have many closely related neuronal cell types and subtypes. The complex population composition forms a challenging testing ground for evaluating and benchmarking the accuracy and robustness of deconvolution methods.

overall_design: Perform single cell RNA-seq experiment on lumbar dorsal root ganglion tissue from 5 mice to characterize the neural cell population.

first: Nicole

last: Alessandri-Haber

first: Wen

last: Fury

first: Michael

last: Schaner

first: Robert

last: Breese

last: LaCroix-Fralish

first: Jinrang

last: Kim

first: Christina

last: Adler

first: Lynn

last: Macdonald

first: Gurinder

last: Atwal

last: Bai


title: Decoding the protein composition of whole nucleosomes with Nuc-MS

status: Public on Apr 20 2021

city: Chicago

first: Marta

last: Iwanaszko

state: IL

address: 303 E. Superior Street, Simpson Querrey 7th Floor,

department: Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Current proteomic approaches disassemble and digest nucleosome particles, blurring readouts of the ‘histone code’. To preserve nucleosome-level information, we developed Nuc-MS, which displays the landscape of histone variants and their post-translational modifications (PTMs) in a single mass spectrum. Combined with immunoprecipitation, Nuc-MS quantified nucleosome co-occupancy of histone H3.3 with variant H2A.Z (sixfold over bulk) and the co-occurrence of oncogenic H3.3K27M with euchromatic marks (for example, a >15-fold enrichment of dimethylated H3K79me2). Nuc-MS is highly concordant with chromatin immunoprecipitation-sequencing (ChIP-seq) and offers a new readout of nucleosome-level biology.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3.3, H2AZ as well as the histone modifications H3K79me2 and H4K16ac in HEK293T cells.

first: Luis

middle: F

last: Schachner

first: Marc

last: Morgan

first: Ali

last: Shilatifard

first: Neil

last: Kelleher


title: Single cell RNASeq of whole mouse kidneys from Uromodulin/Tamm horsfall protein knock-out mice

status: Public on Apr 08 2021

city: Indianapolis

first: Seth

last: Winfree

email: winfrees@iu.edu, swinfree@unmc.edu

state: Indiana

address: 950 W Walnut St

institute: Indiana University

summary: To elucidate changes in cellular populations in the ischemic acute kidney injury, we performed single cell RNAseq on mouse kidneys following ischemic reperfusion injury and a sham surgery.  Mice were subjected to bilateral clamping of the renal pedicule for 30 minutes.  After 6-7 hours of reperfusion the kidneys were removed and processed by a MACs cell isolation protocol and dead cell removal (PMID:33448928) , sorted on a 10X Chromium platform version 3 and libraries generated.  Sequencing was performed on an Illumina NovaSeq 6000.

overall_design: Uromodulin/Tamm horsfall protein knock-out 129ev mice were subjected to a Sham surgery or bilateral renal clamping for 30 minutes.

first: Tarek

last: El-Achkar


title: Transcriptome analysis of control and RBM6 KO cells before and after DNA damage

status: Public on Mar 23 2021

city: Haifa

first: Feras

last: Machour

address: Technion City

country: Israel

institute: Technion

summary: Control and RBM6-KO MCF10A-Hras cells were subjected to RNA-sequencing before and after 12hrs exposure to 5Gy ionizing radiation (IR). Transcriptome analysis revealed a subset of genes that are differentially regulated in RBM6-KO cells compared to control cells. In addition, transcriptome of RBM6-KO cells after IR showed upregulation of DNA damage genes, suggesting impaired DNA repair compared to control cells.

overall_design: RNA was purified from two biological replicates of control and RBM6 KO MCF10A-Hras cell line before and after 12hrs recovery from 5Gy IR. (4 conditions with two replicates each)


title: Leptospira rLRR20 stimulates gene expressions in HK2 cell

status: Public on Mar 24 2021

city: Taoyuan

first: Shen-Hsing

last: Hsu

address: 5 Fu-Shing St.

department: Kidney Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital

summary:
Leptospires are highly motile bacteria that migrate from the breached skin to blood circulation of in human, allowing for their rapid dissemination and subsequent colonization of the liver, lungs, and kidneys. Pathogenic Leptospira contained numerous leucine-rich repeat (LRR) genes compared to non-pathogenic species that acted as virulence factors. The functions of the LRR proteins are still unknown and the relative responses of the host cell provided clear evidence that the regulation of host cell during Leptospirosis.
We used microarrays to observation the global  gene expression of human kidney epithelial cell (HK2 cell) under the treatment of rLRR20 protein.

overall_design: HK2 cell were cultured to 70% confluence and serum-starved overnight before stimulating with 10 μM purified rLRR20 for 4 h. The control groups were treated with PBS buffer. The total RNA were extracted  and hybridization on Affymetrix microarrays.

first: Shen-hsing

first: Chih-wei

last: Yang


title: A single-cell atlas of the peripheral immune  response in patients with HFRS.

status: Public on Apr 28 2021

city: Xi'an

first: Yusi

last: Zhang

address: No.169 Changle West Road

department: Immunology

institute: Fourth Military Medical University

summary: Hemorrhagic Fever with Renal Syndrome (HFRS) is a regional infectious disease of epidemic potential caused by the Hantaan Virus (HTNV).The studies  on immunological responses during HTNV infection have continuously been performed. During HTNV infection, lymphocytes are following a tightly controlled genetic programme.The pathological changes of PBMCs also occured during HTNV infection. We used single cell RNA sequencing to detail the cellular components and gene expression profiles of PBMCs underlying HTNV infection.

overall_design: The PBMCs were isolated from the whole blood of HFRS patients. We selected PBMCs from acute phase of HFRS patients and performed scRNA seq.

first: Kang

last: Tang


title: Loss of Profilin3 impairs spermiogenesis by affecting acrosome biogenesis, autophagy, manchette development and mitochondrial organization

status: Public on Jun 01 2021

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

institute: INIA-CSIC

summary: Profilins (PFNs) are key regulatory proteins for the actin polymerization in cells and are encoded in mouse and humans by four Pfn genes. PFNs are involved in cell mobility, cell growth, neurogenesis and metastasis of tumor cells. The testis specific PFN3 is localized in the acroplaxome-manchette complex of developing sperm. We demonstrate, that PFN3 further localizes during spermiogenesis in the Golgi complex and proacrosomal vesicles, suggesting a role in acrosome formation. Autophagy is involved in proacrosomal vesicle fusion and transport to form the acrosome. Using CRISPR/Cas9 genome editing we generated mice deficient for Pfn3. Pfn3-/- males are sub-fertile displaying a type II-globozoospermia. We revealed, that Pfn3-/- sperm display abnormal manchette development leading to an amorphous sperm head shape. Additionally, Pfn3-/- sperm showed reduced sperm motility resulting from flagellum deformities. We show, that acrosome biogenesis is impaired starting from the Golgi phase.  RNA-seq analysis revealed an upregulation of Trim27 and downregulation of Atg2a. As a consequence mTOR was activated and AMPK was suppressed resulting in the inhibition of autophagy. This dysregulation of AMPK/ mTOR affected the autophagic flux which is hallmarked by LC3B accumulation and increased SQSTM1 protein levels. We conclude that this disruption leads to the observed malformation of the acrosome. Further, actin related protein ARPM1 was absent in the nuclear fraction of Pfn3-/- testis and sperm. This suggests, that lack of PFN3 leads to destabilization of the stable PFN3-ARPM1 complex resulting in the degradation of ARPM1. Interestingly, in the Pfn3-/- testis, we detected increased protein levels of essential actin regulatory proteins, cofilin-1 (CFL1), cofilin-2 (CFL2) and actin depolymerizing factor (ADF). Taken together, our results reveal the importance for PFN3 in male fertility and implicates this protein as a candidate for male factor infertility in humans.

overall_design: Testicular mRNA of wildtype, Pfn3-deficient and Pfn3-heterozygous mice

first: Naila

last: Umer

first: Irina

last: Kosterin

first: Sharang

last: Phadke

first: Keerthika

last: Lohanadan

first: Gregor

last: Kirfel

first: Jörg

last: Höhfeld

first: Dominik

last: Sons

first: Walter

last: Witke

first: Hubert

last: Schorle


title: Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns

status: Public on Mar 29 2021

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: Bioscience Bldg. 2-1, Hirosawa

summary: Chemical splicing modulators that bind to the spliceosome have provided an attractive venue for cancer treatment. Splicing modulators induce accumulation and subsequent translation of a subset of intron-retained mRNAs. Yet, the biological effect of proteins containing translated intron sequences remains unclear. Here we identified a number of truncated proteins generated upon treatment with the splicing modulator spliceostatin A (SSA) using genome-wide ribosome profiling and bio-orthogonal non-canonical amino-acid tagging (BONCAT) mass spectrometry. A subset of these truncated proteins has intrinsically disordered regions, forms insoluble cellular condensates, and triggers the proteotoxic stress response through JNK phosphorylation, thereby inhibiting the mTORC1 pathway. In turn, this reduces global translation. These findings indicate that creating an overburden of condensate-prone proteins derived from introns represses translation and prevents further production of harmful truncated proteins. This mechanism appears to contribute to the antiproliferative and proapoptotic activity of splicing modulators.

overall_design: Broadly, the objective of the study is to understand how cells cope with the aberrant splicing. We sought for the fates of each transcripts upon splicing modulation by a small molecule compound, spliceostatin A (SSA). Also, SSA is antitumor compound but the reason for the selective killing of cancer cells in vitro and in vivo has been unrevealed. Our study provides insight over it as well. we treated the HeLa S3 cells with either 100ng/mL SSA or two replicates with methanol (MeOH) (solvent for SSA as negative control) for 6 hours. Same cell lysate was simultaneously used to prepare RNA-seq and Ribosome profiling libraries.

first: Jagat

last: Chhipi-Shrestha

first: Tilman

last: Schneider-Poetsch

first: Takehiro

last: Suzuki

first: Mari

last: Mito

first: Khalid

last: Khan

first: Naoshi

last: Dohmae

first: Minoru

last: Yoshida