title: NAA15 haploinsufficiency can cause congenital heart disease and perturbs protein levels in induced pluripotent stem cells

city: Boston

first: Jon

last: Seidman

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Rationale- NAA15 is a component of the N-terminal (Nt) acetyltransferase complex, NatA. The mechanism by which NAA15 haploinsufficiency causes congenital heart disease (CHD) remains unknown.  To better understand molecular processes by which NAA15 haploinsufficiency perturbs cardiac development, we introduced NAA15 variants into human induced pluripotent stem cells (iPSCs) and assessed the consequences of these mutations on RNA and protein expression. Objective- We aim to understand the role of NAA15 haploinsufficiency in cardiac development by investigating proteomic effects on NatA complex activity, and identifying proteins dependent upon a full amount of NAA15.Methods and Results - We introduced heterozygous LoF, compound heterozygous and missense residues (R276W) in iPS cells using CRISPR/Cas9. Haploinsufficient NAA15 iPS cells differentiate into cardiomyocytes, unlike NAA15-null iPS cells, presumably due to altered composition of NatA. Mass spectrometry (MS) analyses reveal ~80% of identified iPS cell NatA targeted proteins displayed partial or complete Nt-acetylation. Between null and haploinsufficient NAA15 cells Nt-acetylation levels of 32 and 9 NatA-specific targeted proteins were reduced, respectively. Similar acetylation loss in few proteins occurred in NAA15 R276W iPSCs. In addition, steady-state protein levels of 562 proteins were altered in both null and haploinsufficient NAA15 cells; eighteen were ribosomal-associated proteins. At least four proteins were encoded by genes known to cause autosomal dominant CHD. Conclusions - These studies define a set of human proteins that requires a full NAA15 complement for normal synthesis and development. A 50% reduction in the amount of NAA15 alters levels of at least 562 proteins and Nt-acetylation of only 9 proteins.  One or more modulated proteins are likely responsible for NAA15-haploinsufficiency mediated CHD. Additionally, genetically engineered iPS cells provide a platform for evaluating the consequences of amino acid sequence variants of unknown significance on NAA15 function.

overall_design: Examination of 6 cell lines (two biological replicates for independent iPS cell lines in NAA15+/+ and NAA15-mutant iPSCs and three replicates for each)

first: Tarsha

last: Ward

first: Warren

last: Tai

first: Min

middle: Y

last: Jang

first: Joshua

last: Gorham

first: Christine

first: J

middle: G


title: Circulating LncRNA expression profiling of  Hashimoto's Thyroiditis

status: Public on Nov 05 2020

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

country: China

institute: The Affiliated People’s Hospital of Jiangsu University

type: Non-coding RNA profiling by high throughput sequencing

summary: NGS was performed to detect human lncRNAs.  We found many upregulated and downregulated lncRNAs in HT patients. Through high-throughput sequencing technology, 69,544 upregulated and 27,742 down-regulated LncRNAs were detected between HT patient group and the healthy control group. Of the 218 LncRNAs with significant difference, 94 were up-regulated and 124 were down-regulated.

overall_design: Circulating lncRNA profiles of five Hashimoto's Thyroiditis patients and five healthy volunteers were generated by deep sequencing,using Illumina HiSeq 4000

first: Yingzhao

last: Liu

first: Huiyong

last: Peng

first: Si

last: Xiong

first: Xiangmei

last: Ding

first: Xuehua

last: Wang


title: Single nucleus RNA-seq analysis of the TA muscles from WT and Dmd Exon 51 Knockout mice

city: New York

first: Zhaoning

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

country: USA

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: Duchenne muscular dystrophy (DMD) is a fatal muscle disorder characterized by cycles of degeneration and regeneration of multinucleated myofibers and pathological activation of a variety of other associated cell types. Here, we describe the creation of a new mouse model of DMD caused by deletion of exon 51 of the dystrophin gene, which represents a prevalent mutation in humans. To understand the transcriptional abnormalities and heterogeneity associated with the nuclei of myofibers, as well as other mononucleated cell types that contribute to DMD disease pathogenesis, we performed single nucleus transcriptomics of skeletal muscle of mice with exon 51 deletion. Our results reveal distinctive and previously unrecognized myonuclear subtypes within dystrophic myofibers and uncover degenerative and regenerative transcriptional pathways underlying DMD pathogenesis. Our findings provide new insights into the molecular underpinnings of DMD, controlled by the transcriptional activity of different types of muscle and nonmuscle nuclei.

overall_design: Nuclei were isolated from TA muscles of 1 month old WT or DMD ∆Ex51 mice, and subjected to single nucleus RNA-seq using 10xGenomics Chromium platform.

first: Francesco

last: Chemello

first: Eric

middle: N

last: Olson


title: Degenerative and Regenerative Pathways Underlying Duchenne Muscular Dystrophy Revealed by Single-nucleus RNA sequencing

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

overall_design: Refer to individual Series


title: 3'READS+RIP defines differential Staufen1 binding to alternative 3'UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association

city: Philadelphia

first: Bin

last: Tian

state: PA

address: 3601 Spruce St

institute: Wistar Institute

summary: Using 3ʹ region extraction and deep sequencing coupled to ribonucleoprotein immunoprecipitation (3’READS+RIP), together with reanalyzing previous STAU1 binding and RNA structure data, we delineate STAU1 interactions transcriptome-wide, including binding differences between alternative polyadenylation (APA) isoforms. Consistent with previous reports, RNA structures are dominant features for STAU1 binding to CDSs and 3ʹUTRs. Overall, relative to short 3ʹUTR counterparts, longer 3ʹUTR isoforms of genes have stronger STAU1 binding, most likely due to a higher frequency of RNA structures, including specialized IRAlus. However, a sizable fraction of genes express transcripts showing the opposite trend, attributable to AU-rich sequences in their alternative 3'UTRs, possibly recruiting antagonistic RBPs and/or destabilizing STAU1-binding RNA structures. Using STAU1-knockout cells, we show that strong STAU1 binding to mRNA 3'UTRs generally enhances polysome association. However, IRAlus have little impact on STAU1-mediated polysome association despite having strong interactions with the protein.

overall_design: 8 3'READS+RIP libraries from STAU1-KO cells (STAU1_IP, GFP_IP, STAU1_Input, GFP_Input in two replicates); 4 3'READS+ libraries from cell frationated samples (KO_C, WT_C, KO_P, WT_P in one replicate)

first: Dinghai

last: Zheng

first: Hanna

last: Cho

first: Wei

first: Xavier

last: Rambout

first: Lynne

middle: E

last: Maquat


title: Metabolic Effects of Air Pollution Exposure and Reversibility

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we modeled early life air pollution exposure using C57BL/6J male mice on a controlled chow diet, exposed to real-world inhaled concentrated PM2.5 (~10x ambient level/ ~60-120g/m3) or filtered air (FA) over 14 weeks.  We investigated PM2.5 effects on phenotype, transcriptome and chromatin accessibility, compared the effects with a prototypical high-fat diet (HFD) stimulus, and examined the effects of cessation of exposure on reversibility of phenotype/genotype.

overall_design: RNA sequencing and ATAC-seq were performed to compare the transcriptome and epigenome of air pollution exposed mice and high-fat diet.

first: Sanjay

last: Rajagopalan

first: Kasper

last: Hansen

first: Shyam

last: Biswal


title: Single cell RNAseq of lung transplant recipient

city: Brisbane

first: Brendan

middle: John

last: O'Sullivan

state: Queensland

address: Level 6, 37 Kent Street Woolloongabba

country: Australia

institute: The University of Queensland Diamantina Institute Translational Research Institute

summary: Single cell RNA sequencing was used to determine cell types in the broncho alveolar lavage (BAL) of a lung transplant recipient.

overall_design: Cryopreserved lung transplant recipient BAL cells were sorted for viable cells and Single-cell sequencing performed using 10X Genomics Single Cell 3′ Chips.

first: Joseph

last: Powell


title: Essential histone chaperones collaborate to regulate transcription and chromatin integrity

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur, Room 239

department: Genetics

summary: Histone chaperones are critical for controlling chromatin integrity during transcription, DNA replication, and DNA repair. We have discovered that the physical interaction between two essential histone chaperones, Spt6 and Spn1/Iws1, is required for transcriptional accuracy and nucleosome organization. To understand this requirement, we have isolated suppressors of an spt6 mutation that disrupts the Spt6-Spn1 interaction. Several suppressors are in a third essential histone chaperone, FACT, while another suppressor is in the transcription elongation factor Spt5/DSIF. The FACT suppressors weaken FACT-nucleosome interactions and bypass the requirement for Spn1, possibly by restoring a necessary balance between Spt6 and FACT on chromatin. In contrast, the Spt5 suppressor modulates Spt6 function in a Spn1-dependent manner. Despite these distinct mechanisms, both suppressors alleviate the nucleosome organization defects caused by disruption of the Spt6-Spn1 interaction. Taken together, we have uncovered a network in which histone chaperones and other elongation factors coordinate transcriptional integrity and chromatin structure.

overall_design: Multiple assays of transcription and chromatin state in spt6 mutants and suppressors of spt6-YW, including transcription start site sequencing (TSS-seq), native elongating transcript sequencing (NET-seq), MNase-seq, and ChIP-seq of Rpb1, Spn1, Spt6, and Spt16.

first: Olga

last: Viktorovskaya

first: James

last: Chuang

first: Dhawal

last: Jain

first: Natalia

middle: I

last: Reim

first: Francheska

last: López-Rivera

first: Magdalena

last: Murawska

first: Dan

last: Spatt

first: L

middle: S

last: Churchman

first: Peter

middle: J


title: Developmental Exposure to Endocrine-Disrupting Chemicals Alters Gene Expression in Myometrium of Exposed Animals

city: AUGUSTA

first: Ayman

last: Al-Hendy

state: Georgia

address: 1120 15th Street

department: Obstetrics and Gynecology

institute: Augusta University

summary: The goal of this study was to compare  NGS-derived murine myometrial progenitor cell transcriptome profiling (RNA-seq) of an animal model of uterine fibroid tumorigenesis in rats exposed during uterine development to an endocrine-disrupting chemical, diethylstilbestrol (DES) versus vehicle (VEH) control, unexposed animals, to determine the pathways and biological processes, whose gene expression may be altered as a result of the exposure.

overall_design: Examination of gene expression in exposed vs. unexposed murine myometrial progenitor cells; myometrial progenitor cells isolated from 5 exposed animals were pooled and compared to that of the same cells isolated from 5 unexposed animals

first: Qiwei

last: Yang

first: Aymara

last: Mas

first: Lauren

last: Prusinski Fernung


title: Emergent metastatic heterogeneity of primary tumor cells is restricted by the Ig-transmembrane protein VSIG II

status: Public on Nov 09 2020

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: Our study prompeted us to assign, through spiked single cell RNAseq, metastatic  function to transcriptomic cluster of colon cancer cells. Interactions between clones also uncover a restrictive anti metastatic influence that act intrinsically and non-cell automomously. We identify VSIG1 as critical mediator of this influence.

overall_design: RNAseq of clones derived from heterogeneous primary Colon Cancer cell culture, in triplicates

first: Carolina

last: Bernal

first: Marianna

last: Silvano

first: Yann

last: Tapponnier

first: Santosh

last: Anand

first: Cecilia

last: Angulo

first: Ariel

last: Ruiz i Altaba


title: Mithramycin A chemogenomic profile

city: Frederick

first: Girma

middle: Moges

last: Woldemichael

institute: National Cancer Institute-Frederick

summary:
Mithramycin A in known to bind DNA but its exact cellular mechanism of action is still unclear.
We used Affymatrix GenFlex_Tag_16K_V2 microarrays to profile sensitivity of genetically barcoded S. cerevisiae gene deletion strains to mithramycin A

overall_design: Two replicates per condition, i.e., two samples each for DMSO and Mithramycin A treatment were used.

middle: M


title: Transcriptome analysis of the TA muscles from WT and Dmd Exon 51 Knockout mice

first: Zhaoning

last: Wang

overall_design: RNA was isolated from TA muscles of 1 month old WT or DMD ∆Ex51 mice. Stranded mRNA-seq was performed to profile gene expression changes upon exon 51 deletion.

first: Francesco

last: Chemello

first: Eric

last: Olson


title: Brd2/4 and Myc regulate alternative cell lineage programs during early osteoclast development [MYC_MAX ChIP-seq]

city: London

first: Anastasios

last: Karadimitris

address: Hammersmith Campus, Du Cane Road

department: Department of Immunology and Inflammation

country: United Kingdom

institute: Imperial College London

summary: Osteoclast development in response to RANKL is critical for bone homeostasis in health and in disease e.g., osteoporosis and cancer. The early and direct chromatin regulatory changes imparted by BET proteins Brd2-4 and osteoclast-affiliated transcription factors (TF) during osteoclastogenesis are not known. Here we show that as early as 4h post-RANKL, osteoclast development entails regulation of two alternative cell fate transcriptional programs, osteoclast vs. macrophage, with repression of the latter following activation of the former. Pharmacological inhibition shows that this requires increased chromatin binding in a non-redundant manner of Brd2 at promoters and Brd4 at enhancers/super-enhancers. Myc, the top RANKL-induced TF, is predicted to regulate early regulatory events in co-operation with Brd2/4 and Max and by establishing negative and positive regulatory loops with other lineage-affiliated TF. These novel insights into the transcriptional regulation of osteoclastogenesis suggest the clinical potential of selective targeting of Brd2/4 to abrogate aberrant OC activation.

overall_design: Monocyte-derived cell line induced to differentiate to OC by addition of RANKL (50ng/ml). The effect of the BET inhibitor (Ibet-500nM) was studied alone or in combination with RANKL. ChIP-seq was performed in crosslinked cells after 4 hrs.

first: Valentina

last: Caputo

first: Nikolaos

last: Trasanidis

first: Xiaolin

last: Xiao

first: Mark

last: Robinson

first: Alexia

last: Katsarou

first: Kanagaraju

last: Ponnusamy

first: Rab

middle: K

last: Prinjha

first: Nicholas

last: Smithers

first: Aristeidis

last: Chaidos

first: Holger

middle: W

last: Auner


title: TET1 KO affects Sox9 function [cell line]

city: Stanford

first: Nidhi

last: Bhutani

state: California

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

institute: Stanford University

summary:
Ten eleven translocation 1 (Tet1) directs chondrogenic differentiation in the mouse embryonic growth plate. We have characterized the global exon array analysis upon Tet1 knockdown induced by two different shRNAs.
In this dataset, we include the expression data obtained from in vitro differentiation of ATDC5 chondroprogenitor cells for 15 days in presence (non-target) and absence (Tet1 sh1 and Tet1 sh2) of Tet1. These data are used to obtain the genes which are differentially expressed in absence of Tet1 and to identify the altered signaling pathways.

overall_design: Three samples were analyzed, one NT control and two Tet1 knockdowns using different shRNAs. We analyzed the changes in gene expression with Tet1 knockdown; genes with a fold-change ≥ or ≤1.5, with a difference in intensity of >100 and within the lower 90% confidence bound were selected.

first: Sarah

last: Taylor

first: Piera

last: Smeriglio


title: A combination of growth factors and cytokines alter mouse fetal liver and placental gene expression profiles.

city: Parkville

first: Kathryn

last: Gurner

state: VIC

address: Royal Parade

institute: University of Melbourne

summary: This study investigated the effects of preimplantation exposure to combined Growth factors and cytokines in vitro, and their subsequent effects on embryonic and fetal development, including the impact on fetal liver and placental transcriptomes.

overall_design: mRNA profiles of D14.5 murine fetal liver and placental tissues either developed in vitro, or cultured at 5% oxygen in the presence or absence of combined growth factors and cytokines.

middle: H

first: Thi

middle: T

last: Truong

first: Alexandra

last: Harvey

first: David

last: Gardner


title: TET1 KO affects Sox9 function [methylation]

type: Methylation profiling by high throughput sequencing

summary: We report that TET1 mediated 5hmC deposition is necessary for Sox9 function in embryonic cartilage development.

overall_design: 5hmC and 5mC was profiled in progenitor, intermediate and mature ATDC5 differentiation.


title: Overexpression of OsTZF8, a CCCH-Tandem Zinc finger, increases drought tolerance in rice by regulating stress related genes

city: Pyeongchang

first: Jae Sung

last: Shim

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

summary:
Purpose: Next-generation sequencing (NGS) has been utilized for systems-based analysis of rice plants. The goals of this study were to compare the transcriptome  between non-transgenic (NT) control and OsTZF8 overexpressing transgenic plants.
Methods: Total RNAs were extracted from the whole plants of OsTZF8 overexpressing plants (T4 generation, line number #20) and non-transgenic (NT) plant using RNeasy plant mini kit (Qiagen, Germany) according to the manufacturer’s instruction.  cDNA libraries were prepared from total RNAs using TruSeq RNA sample Prep kit (v2) (Macrogen, Korea). Two biological replicates were analyzed by RNA-sequencing analysis. Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequence, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., 2014). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml).
Conclusions: Our study has identified downstream candidate genes regulated  by overexpression of OsTZF8.

overall_design: Non-transgenic (NT) control and OsTZF8 overexpressing trangenic plants were grown in soil for three weeks. Three-week-old plants were harvested and used for RNA-sequencing analysis to identify differentially expressed genes  between NT and OsTZF8 overexpressing transgenic rice plants.

first: Ju-Kon

last: Kim

first: Jae

first: So

last: Seong


title: TBK1-METTL3 axis facilitates antiviral immunity [MeRIP-seq]

status: Public on Nov 04 2020

city: beijing

first: fuping

last: you

address: xueyuan street

institute: Peking University Health Science Center

summary: mRNA m6A modification is involved in regulation of immune system. However, its function in antiviral immunity is controversial, and how immune responses regulate m6A modification is unknown. We here found TBK1, a key kinase of antiviral pathways, phosphorylated the core m6A methyltransferase METTL3 at Serine 67. The phosphorylated METTL3 interacted with translational complex and enhanced proteins translation, including IRF3, and facilitated antiviral responses. TBK1 also promoted METTL3 activation and m6A modification, which is required for stabilizing IRF3 mRNA. Type I IFN induction was severely impaired in METTL3 deficient cells. Mettl3flfl-lyz2-Cre mice were significantly more susceptible to IAV-induced lethality than control mice. Consistently, Ythdf1—/— mice cannot control viral infection and showed higher mortality than control mice due to decreased IRF3 expression. Together, we demonstrated that innate signals activated METTL3 via TBK1, and METTL3 and m6A modification secured antiviral immunity by promoting mRNA stability and protein translation.

overall_design: RNA or m6a modified mRNA profiles of wild type (WT)  and Tbk1 knockout immortalized mouse embryonic fibroblasts (iMEF) cells without any treatment

first: Jingxuan

last: Chen

first: Xuemei

last: Wei

first: Xiao

last: Wang

first: Fuping

last: You


title: The mononuclear phagocyte system contributes to fibrosis in post-transplant Obliterans Bronchiolitis

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Bronchiolitis Obliterans Syndrome (BOS) is a fibrotic disease heavily responsible for high mortality rates after lung transplantation. Myofibroblasts are primary effectors of this fibrotic process, but their origin is still under debate. The purpose of this work was to identify the precursors of mesenchymal cells responsible for post-transplant airway fibro-obliteration.  Lineage-tracing tools were used to track or deplete potential sources of myofibroblasts in the heterotopic tracheal transplantation model. Allografts were analysed by histology, confocal microscopy, flow cytometry or single-cell transcriptomic analysis. BOS explants were evaluated by histology and confocal microscopy. Myofibroblasts in the allografts were recipient-derived. Still, when recipient mice were treated with tacrolimus, we observed rare epithelial-to-mesenchymal transition phenomena and an increase in donor-derived myofibroblasts (P=0.0467), but the proportion of these cells remained low (7%). Hematopoietic cells, and specifically the mononuclear phagocyte system, gave rise to the majority of myofibroblasts found in occluded airways. Ablation of Cx3cR1+ cells decreased fibro-obliteration (P=0.0151) and myofibroblasts accumulation (P=0.0020). Single-cell RNA-sequencing unveiled similarities between myeloid-derived cells from allografts and both murine and human samples of lung fibrosis. Finally, myofibroblasts expressing the macrophage marker CD68 were increased in BOS explants when compared to controls (13% vs 2.3%, P=0.0007). Recipient-derived myeloid progenitors represent a clinically-relevant source of mesenchymal cells infiltrating the airways after allogeneic transplantation. Therefore, therapies targeting the mononuclear phagocyte system could improve long-term outcomes after lung transplantation.

overall_design: 12 mouse samples: 3 cellular sources (Tracheal allograft / Native tracheas / Spleen) x 4 replicates

first: Maria-Pia

last: Di Campli

first: Abdulkader

last: Azouz

first: Assiya

last: Assabban

first: Jessika

last: Scaillet

first: Marion

last: Splittgerber

last: Van Keymeulen

first: Frederick

last: Libert

first: Myriam

last: Remmelink

first: Alain

last: Le Moine

first: Philippe

last: Lemaitre


title: Identification of reproductive performance-related genes in the bovine hypothalamus and pituitary gland and analysis of the regulatory network

city: Changchun

first: YuWen

last: Huang

state: Jilin

address: College of Animal Science

institute: Jilin University

summary: We explored the gene expression patterns of the pituitary gland and hypothalamus of Angus cows at different growth and developmental stages by deep sequencing the transcriptome and identified genes that affect bovine reproductive performance to provide new ideas for improving bovine fertility in production practice. We selected three 6-month-old (weaning period), three 18-month-old (first mating period) and three 30-month-old (early postpartum) Angus cows. The physiological statuses of the cows in each group were the same, and their body shapes were similar. After quality control of the sequencing, the transcriptome analyses of 18 samples yielded 129.18 GB of clean data. Clean data for each sample reached 6.30 GB. The GC content was >47.61%, and the base percentage of Q30 was at least 94.19%. We detected 13280 and 13318 expressed genes in the pituitary gland and hypothalamus, respectively, and screened 35 and 50 differential genes for each, respectively. Differential genes in both tissues were mainly concentrated in metabolism, lipid synthesis, and immune-related pathways in the 18-month-old cows compared with those in the 6-month-old cows. The 30-month-old cows presented more regulated reproductive behavior, and pituitary CAMK4 was the main factor regulating the reproductive behavior during this period via the pathways for calcium signaling, longevity, oxytocin, and aldosterone synthesis and secretion.

overall_design: Nine Angus cattle at the ages of 6, 18 and 30 months from the Changsha Institute of Animal Science were selected and divided into 3 groups according to age, with 3 cows per group.

first: Yuwen

first: Chunjin

last: Li

first: Kangle

last: Yi

first: Xu

last: Zhou


title: DETECTION OF FOUR NOVEL RENAL TUMORS CASES HARBORING RBM10-TFE3 FUSIONS

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

summary: Microphtalmia-associated-transcriptional-factor-family translocation renal cell carcinoma (MiTF-tRCC) currently includes two main subtypes: “TFEB-tRCC” most often characterized by a t(6;11)(p21;q13) that generates a fusion of TFEB with MALAT1 and “TFE3-tRCC” characterized by rearrangements of TFE3 at Xp11.23 (2-3) that produce a variety of fusion genes. FISH is a handy method in routine practice that allows the detection of a rearrangement of TFE3. However, it reaches its limits in cases of micro-inversions or insertions: in fact paracentric microinversions that involve GRIPAP1 (Xp11.23) (23, Classe) or RBM10 (Xp11.3), very close to TFE3 , are most often undetectable.We report the clinical, immunohistological, genomic and molecular description of four novel TFE3-tRCC with RBM10-TFE3 fusion detected by targeted RNASeq analysis that illustrate the difficulties of diagnosis, especially in reason of disconcerting negative TFE3 FISH results.

overall_design: screening of 3 cases of TFE3 translocated renal cell carcinomas by SNP array with affymetrix platform

first: Ilaria

last: DI MAURO

first: Bérengère

last: DADONE-MONTAUDIE

first: Mathilde

last: SIBONY

first: Damien

last: AMBROSETTI

first: Vincent

last: MOLINIE

last: DECAUSSIN-PETRUCCI

last: BLAND

first: Claire

last: ARBAUD

first: Béatrice

last: CENCIU

first: François

last: ARBIB

first: Pierre-Alexandre

last: JUST

first: Nathalie

last: RIOUX-LECLERCQ

first: Florence

last: PEDEUTOUR


title: Genome-wide study reveals the function of transcription factor TREE1 in ethylene signaling

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

summary: Purpose: Next-generation sequencing (NGS) has been used to study the gene expression in Arabidopsis seedlings under air and ethylene treatment. The goal of this study is to uncover how TREE1 and its homologous gene DAZ3 are involved into gene expression regulation in response to ethylene.

overall_design:
Whole seedling mRNA profiles of 3-day old daz3 tree1 was generated by sequencing, in 2 replications, using Illumina HiSeq 2000

Gene accession ID for TREE1: AT4G35610

first: Likai

last: Wang


title: SCL15 is a critical regulator for plant development, germination, seed dormancy and seed vigor in Arabidopsis thaliana

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Seed maturation, dormancy and germination are distinct physiological processes. Transition from maturation to dormancy, and from dormancy into germination are not only critical developmental phases in the plant life cycle but are also important agricultural traits. These developmental processes and their phase transitions are fine determined and coordinately regulated by genetic makeup and environmental cues. SCARECROW-LIKE15 (SCL15) has been demonstrated to be essential for repressing the seed maturation programme in vegetative tissues (Gao et al., Nat Commun, 2015, 6:7243). Here we report that SCL15 is also important for seed dormancy maintenance, germination timing and seed vigor performance based on the effects of SCL15 mutation on plant germination, growth and reproduction when compared with wild type Arabidopsis and over-expression lines 35S:SCL15 and Napin:SCL15. Seed dormancy is enhanced by the mutation of SCL15 in a GA signaling dependent way, indicating that SCL15 plays a negative role for primary dormancy release. Seed germination is positively regulated by SCL15 through interaction with ABA, GA and auxin signaling. SCL15 acts as positive regulator of seed vigor and effect of SCL15 mRNA abundance on seed reserve accumulation and seed development during late embryogenesis may contribute to the seed vigor performance.

overall_design: We compared gene expression in three plant lines:  Wild type, Scl15 knockout, and Scl15 seed-specific overexpression.  For each line we sequenced 3 biological replicates.

first: Ming-Jun

last: Gao

first: Cathy

last: Coutu


title: Mapping endothelial-cell diversity in cerebral cavernous malformations at single cell resolution

city: Uppsala

first: Elisabetta

last: Dejana

address: Dag Hammarskjolds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary: Cerebral cavernous malformation (CCM) is a rare neurovascular disease that is characterized by enlarged and irregular blood vessels that often lead to cerebral hemorrhage. Loss-of-function mutations to any of three genes results in CCM lesion formation; namely, CCM1, CCM2, and CCM3. Here, we report for the first time in-depth single-cell RNA sequencing, combined with spatial transcriptomics and immunohistochemistry, to comprehensively characterize subclasses of brain endothelial cells under both normal conditions and after deletion of Ccm3 in a mouse model of CCM. Integrated single-cell analysis identifies arterial endothelial cells as refractory to CCM transformation. Conversely, a subset of angiogenic venous capillary endothelial cells and respective resident endothelial progenitors is at the origin of CCM lesions. These data are relevant for the understanding of the plasticity of the brain vascular system and provide novel insights into the molecular basis of CCM disease at the single cell level.

overall_design: Single cell RNA-seq of brain endothelial cells from Ccm3 ko and Ccm3 wt mice, in duplicate

first: Fabrizio

last: Orsenigo

first: Lei

middle: L

last: Conze

first: Suvi

last: Jauhiainen

first: Monica

last: Corada

first: Francesca

last: Lazzaroni

first: Matteo

last: Malinverno

first: Veronica

last: Sundell

first: Sara

last: Cunha

first: Johan

last: Brännström

first: Maria

last: Globish

first: Claudio

last: Maderna

last: Lampugnani

first: Peetra

middle: U

last: Magnusson


title: Cohesin residency determines chromatin loop patterns

city: Berkeley

first: lorenzo

last: costantino

state: CA

address: 16 Barker Hall # 3202

department: MCB

institute: university of california, berkeley

summary: The organization of chromatin into higher-order structures is essential for chromosome segregation, the repair of DNA damage, and the regulation of gene expression. These structures are formed by the evolutionarily conserved SMC (structural maintenance of chromosomes) complexes. By analyzing synchronized populations of budding yeast with Micro-C, we observed that chromatin loops are formed genome-wide, and are dependent upon the SMC complex, cohesin. We correlated the loop signal with the position and intensity of cohesin binding to chromosomes in wild-type and cells depleted for the cohesin regulators Wpl1p and Pds5p. We generate a model to explain how the genomic distribution and frequency of loops are driven by cohesin residency on chromosomes. In this model a dynamic pool of cohesin with loop extrusion activity stops when encounters two regions occupied by stably bound cohesin, forming a loop. Different regions are occupied by cohesin in different cells, defining different patterns of chromatin loops.

overall_design: examination of genome-wide localization of 2 proteins in 3 genetic background

first: Lorenzo

last: Costantino

first: Tsung-Han

last: Hsieh

first: rebecca

last: lamothe

first: Xavier

last: Darzacq

first: douglas

last: koshland


title: RNA-seq analysis of developing rice seeds under combined heat and drought stress

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

country: Germany

institute: MPI of Molecular Plant Physiology

summary: A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.

overall_design: Investigation of mRNA profiles of developing seeds for the rice cultivar N22 during early grain filling under control and combined heat and drought stress in the field with three replicates per treatment

first: Lovely

middle: F

last: Lawas

first: Stephanie

last: Schaarschmidt

first: Xia

last: Li

first: S

middle: V

last: Jagadish

first: Dirk

last: Hincha


title: Effect of acute ischemia stroke on circular RNAs

city: Nanjing

first: Lei

last: Zuo

address: Dingjiaqiao 87th

institute: Southeast University

summary: To explore circulating circRNAs associated with acute ischemia stroke(AIS), their utility as an early diagnostic marker and their significance in predicting stroke outcomes.

overall_design: Ischemia induced circular RNA expression in AIS  was measured, and their expression in healthy controls were set as comparison. Three independent samples from AIS group and three independent samples from control group were employed in Arraystar Mouse circRNA Array (8x15K, Arraystar) analysis.

first: Honghong

last: Yao


title: SAM68 promotes Lung adenocarcinoma tumorigenesis by regulating cancer metabolic conversion through alternative splicing

city: guangzhou

first: jizhong

last: wang

address: 63 Duobao Road

institute: Guangzhou Medical University

summary: The metabolic conversion of oxidative phosphorylation to glycolysis provides tumor cells with energy and biosynthetic substrates, thereby promoting tumorigenesis and malignant progression. However, the mechanisms controlling the tumor metabolic switch is still not entirely clear. Here we demonstrate that SAM68 (gene name: KHDRBS1) as a splicing regulatory factor is frequently overexpressed in Lung adenocarcinoma (LUAD) and negatively correlated with the prognosis of LUAD patients. we find SAM68 promotes LUAD cells tumorigenesis and metastasis both in vitro and in vivo by regulating cancer metabolic switch. SAM68 drives cancer metabolism by mediating alternative splicing of Pyruvate kinase (PKM) pre-mRNAs, finally promoting the formation of PKM2. Mechanically, Sam68 interacted with the splicing repressor hnRNP A1, and depletion of hnRNP A1 or mutations that impair this interaction attenuated the PKM splicing regulation. Together, our work demonstrates key roles of SAM68 in the cancer metabolic conversion by regulating alternative splicing and SAM68 may be a promising therapeutic target for treating LUAD.This project looks into how SAM68 levels affect cancer cell phenotype in vitro

overall_design: Overexpression of SAM68 by plasmid transfection followed by examining alternative splicing changes by RNA-seq or examining cancer phenotype by established assays.

first: Song

last: Zhu

first: Dongbo

last: Tian


title: TREE1-EIN3 mediated transcriptional repression inhibits shoot growth in the response to ethylene in the Histone H3K23 acetylation- and EIN3- mediated ethylene response

first: Hong

last: Qiao

summary: We report that ethylene enhances the TREE1 binding. We perform ChIP-sequencing of TREE1 using chromatins isolated from 3-day old etiolated pTREE1:TREE1-GFP seedlings treated with ethylene or air gas. Results show that ethylene enhances TREE1 binding in ethylene down regulated genes.

overall_design: Examination of TREE1 protein binding in 1 Arabidopsis line under 2 different treatments.

first: Likai

last: Wang


title: An allosteric/intrinsic mechanism supports termination of snRNA transcription.

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

institute: University of Exeter

summary: Termination of protein-coding gene transcription by RNA polymerase II (Pol II) depends on endonucleolytic cleavage at the poly(A) site and the activity of a 5’->3’ “torpedo” exoribonuclease. Other Pol II transcripts also undergo endonucleolytic cleavage suggesting common themes for its termination. Nevertheless, many RNA polymerases employ intrinsic/allosteric termination that directly defines transcript 3’ ends. We have analysed termination of snRNA transcription in humans, which utilises the endoribonucleolytic integrator complex. Integrator is involved, but termination continues after its depletion. This implicates additional mechanisms and shows that endo- and 5’->3’ exonuclease activities are not necessarily a basis for all Pol II termination. Although the alternative process acts as a failsafe in the absence of integrator it contributes significantly to snRNA termination in the natural situation. Long-read sequencing reveals its products to have stochastic 3’ ends that are terminated before integrator cleavage, ruling out 5’->3’ exonuclease contribution(s) and supporting an allosteric/intrinsic mechanism. Termination of some snRNA transcription occurs at T-runs further indicating common principles between this mechanism and those used by other RNA polymerases.

overall_design: Nuclear and sub-nuclear selected RNA was isolated auxin-indubile degron (AID) tagged HCT116 cell lines treated with or without auxin, and sequenced using a combination of library approaches and short- or long-read technologies to study the termination of snRNA gene transcription temination. RNA Polymrease II associated DNA fragmnts were also analysed in the form of a ChIP-Seq experiment. We integrated an in-frame insertion of AID tag, P2A cleavage site, antibiotic resistance marker and SV40 polyA site to the 3' end of three proteins: DIS3-AID, CPSF73 or FUS. Modified DIS3-AID and FUS-AID cells also ectopically expressed TIR1 from a sleeping beauty transposon integrated cassette. The CPSF73-AID cell line was additionally modified at the AAVS1 safe-habour locus by ectopic integration of a doxycycline-inducible TIR1 gene using a pMK243 repair template plasmid (addgene #72835) via CRISPR/Cas9. In all cell lines, TIR1 protein is the E3 ubiquitin ligase required to induce degradation of AID containing proteins in the presence auxin however, CPSF73-AID cells were not treated with auxin but were instead used to RNAi deplete the INTS1 protein. Using a similar approach, we replaced the AID tag repair cassette with a Small Molecule-Assisted Shutoff (SMASh) inducible protease degron tag which was the inserted at the 3'-end of INTS11 to induce protein depletion (isolated from pCS6-YFP-SMASh (Addgene Plasmid #68853). Nuclear RNA was extracted from INTS11-SMASh cells treated with asunaprevir or not.

first: Lee

last: Davidson

first: Laura

last: Francis

first: Joshua

middle: D

last: Eaton

first: Steve


first: Xavier

last: Darzacq

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

overall_design: We mapped the 3D genome organization of mitotic chromatin in budding yeast (A364 background) by using Micro-C.  We performed two replicates of Micro-C experiments for wild-type, Mcd1-AID, Brn1-AID, Wpl-AID, and one replicate for Pds5-AID cells. Time-course experiments were done in two replicates at 23°C and 30°C, respectively. The Micro-C contact matrices were stored into the formats for HiGlass (.mcool) or Juicer  (.hic) 3D genome browsers.

first: Tsung-Han

last: Hsieh

first: Lorenzo

last: Costantino

first: Rebecca

last: Lamothe

first: Douglas

last: Koshland


title: Ubiquitylated H2A.Z nucleosomes are associated with nuclear architectural proteins and global transcriptional silencing

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

summary: H2A.Z mono-ubiquitylation has been linked to transcriptional repression, but the mechanisms involved are not well understood. To address this, we developed a biotinylation-based approach to purify ubiquitylated H2A.Z (H2A.Zub) mononucleosomes for biochemical and genomics analyses. We observe that H2A.Zub nucleosomes are enriched for the repressive histone post-translational modification H3K27me3, but depleted of H3K4 methylation and other modifications associated with active transcription. ChIP-Seq analyses reveal that H2A.Zub-nucleosomes are enriched over non-expressed genes, and suggest that it is the relative ratio of ubiquitylated to non-ubiquitylated H2A.Z, rather than absolute presence or absence of H2A.Z ubiquitylation, that correlates with gene silencing. Finally, we observe that H2A.Zub-eniched mononucleosomes preferentially co-purify with transcriptional silencing factors as well as proteins involved in higher order chromatin organization such as CTCF and cohesin. Collectively, these results suggest an important role for H2A.Z ubiquitylation in mediating transcriptional regulation through its recruitment of transcriptional silencing factors and nuclear architectural proteins.

overall_design: ChIP-Seq of Avi-ubiquitylated and total BirA-Flag-tagged histone H2A.Z with control histone H3 ChIP-Seq

first: Marlee

last: Ng

first: Benjamin

last: Blencowe

first: Peter

last: Cheung


title: Coordinated regulation of starch synthesis by microRNAs and DNA methylation [miRNA-seq]

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. Expression pattern analysis establishes a comprehensive network between starch synthesis genes and transcription factors. MiRNAs negatively regulating TF expression were extensively downregulated during maize endosperm development. We showed that TF ZmMYB33 and ZmMYB65 promotes the transcription of the GUS reporter under the control of Wx and Sbe2b/Bt2 gene promoters containing their binding motifs, respectively. We further showed that the abundantly expressed miR159k-3p negatively regulate the expression of these two transcription factors, suggesting that miRNAs are important regulators of starch synthesis. In addition, we showed that both starch synthesis genes and miRNAs are globally repressed by DNA methylation, while transcription factors are not. Taken together, the presented results establish the regulatory functions of miRNAs and DNA methylation in starch synthesis, and indicates DNA methylation as the master switch.

overall_design: Maize miRNA profiles of two stages of whole kernels (3 and 5 DAP) and eight stages of isolated endosperm (7, 9, 10, 11,13, 15, 20 and 25 DAP) of the Mo17 inbred line were generated by Illumina NextSeq 500, 13 DAP ear leaf was selected as a control.

first: Yubi

last: Huang

first: Yu-Feng

last: Hu

first: Hanmei

last: Liu

first: Junjie

last: Zhang

first: Yang-Ping

last: Li


title: Coordinated regulation of starch synthesis by microRNAs and DNA methylation [RNA-seq]

overall_design: Maize mRNA profiles of two stages of whole kernels (3 and 5 DAP) and eight stages of isolated endosperm (7, 9, 10, 11,13, 15, 20 and 25 DAP) of the Mo17 inbred line were generated by Illumina NextSeq 500, 13 DAP ear leaf was selected as a control.


title: Genomic validation of the revised Bethesda criteria in terms of pathogenesis and oncologic significance

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: To know genomic alterations of the respective situation of the revised Bethesda criteria, we investigated the impact of somatic variants and gene expression using colorectal tumor tissues. Using Exome-seq and RNAseq analysis, we identified novel somatic variants that are significantly associated with Bethesda criteria. Using the markers, we predicted the the therapeutic target of familial colorectal cancer.  This series includes only the RNA-seq data.

overall_design: RNA-seq of 98 colorectal tumor tissues

first: Jin

middle: C

first: Jong-Hwan

first: Seon-Kyu

first: Yong

first: Seon-Young


title: Peronospora belbahrii infected Sweet Basil transcriptome timecourse

city: Amherst

first: Gregory

middle: Alan

last: DeIulio

address: 240 Thatcher Road

department: Biochemistry and Molecular Biology

institute: Umass Amherst

summary: Basil downy mildew (BDM) caused by Peronospora Belbahrii leads to losses in sweet basil cultivation across the world. Though resistant cultivars of basil exist, the formation of sterile offspring and the introduction of unwanted phenotypic and chemotypic traits slows breeding. Previous work by the Simon lab at Rutgers University identified pair of sweet basil cultivars; one resistant to BDM, MRI, and one susceptible, SB22. They predicted that three genes in MRI confer increased BDM resistance. RNA from infected MRI and SB22 plants was harvested during the first 3 days of infection at 4 timepoints in order to capture as many early phases of plant-pathogen interaction as possible. The goal is to develop resistance markers for use in breeding experiments.

sample_organism:
Ocimum basilicum
Peronospora belbahrii

platform_organism:
Ocimum basilicum
Peronospora belbahrii

overall_design: Two basil cultivars sequenced. Each cultivar was sequenced 12 hours post mock innoculation as well as 12, 24, 48, and 72 hours post innoculation with peronospora belbahrii. Additionally sporangia from P. belbahrii were sequenced as a pathogen control. Every datapoint was sequenced in triplicate including the sporangia control.

first: Greg

middle: A

first: Li-Jun

last: Ma

first: Li

last: Guo

first: James

last: Simon

first: Robert

last: Pyne


title: Coordinated regulation of starch synthesis by microRNAs and DNA methylation [BiSulfite-seq]

first: dong

overall_design: Maize global genomic methylation profiles of two stages of whole kernels (3 and 5 DAP) and eight stages of isolated endosperm (7, 9, 10, 11,13, 15, 20 and 25 DAP) of the Mo17 inbred line were generated by Illumina HiSeq 2000, 13 DAP ear leaf was selected as a control.

first: Yubi


title: Coordinated regulation of starch synthesis by microRNAs and DNA methylation

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

overall_design: Refer to individual Series


title: IDENTIFYING KEY DRIVER GENES OF INNATE IMMUNE PATHWAYS AS NOVEL THERAPEUTIC TARGETS IN RENAL ALLOGRAFT REJECTION

status: Public on Nov 03 2020

city: New York

first: Weijia

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: Acute rejection (AR) in renal transplantation is an established risk factor for reduced allograft survival, and still occurs in 10-20% of allograft recipients despite standard of care immunosuppression. This suggests molecular pathways exist which are inadequately suppressed by current therapy. We describe for the first time, integrative network- based computational strategies incorporating genotyping data to identify key driver genes (KDGs) amongst networks of perturbed transcripts in AR, which may serve as therapeutic targets.

overall_design: A microarray set (N=52) was used for discovery of meta-gene sigantures associated with acute rejection.

first: Zhengzi

last: Yi

first: Karen

last: Keung

first: Barbara

last: Murphy


title: β-catenin drives distinct transcriptional networks in proliferative and non-proliferative cardiomyocytes

city: Brisbane

last: Hudson

state: QLD

address: 300 Herston Rd

institute: QIMR Berghofer Medical Research Institute

summary: The inability of the adult mammalian heart to regenerate represents a fundamental barrier in heart failure management. In contrast, the neonatal heart retains a transient regenerative capacity, but the underlying mechanisms are not fully understood. Wnt/β-catenin signaling has been suggested as a key cardio-regenerative pathway. Here, we show that Wnt/β-catenin signaling potentiates neonatal mouse cardiomyocyte proliferation in vivo and immature human pluripotent stem cell-derived cardiomyocyte (hPSC-CM) proliferation in vitro. In contrast, Wnt/β-catenin signaling in adult mice is cardioprotective but fails to induce cardiomyocyte proliferation. Transcriptional profiling of neonatal mouse and hPSC-CM revealed a core Wnt/β-catenin-dependent transcriptional network governing cardiomyocyte proliferation. In contrast, β-catenin failed to re-engage this proliferative gene network in the adult heart, which instead reverted to a neonatal-like glycolytic program. These findings suggest that Wnt/β-catenin drives distinct transcriptional networks in regenerative and non-regenerative cardiomyocytes, which may contribute towards the inability of the adult heart to regenerate following injury.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
2D cardiac cells were treated with either 0.05% DMSO or 5 µM CHIR99021 for 24 hours and then sorted by FACS into cardiomyocyte (CD90-) and non-cardiomyocyte (CD90+) cell populations. Isolated cardiomycoytes from myocardial infarcted mice with AAV6 intramyocardial injections
2D cardiac cells were treated for 24 hours with 5 µm CHIR. hPSC-CMs were fixed for 10 minutes at room temperature with 1% paraformaldehyde (PFA). Cross-linking was stopped by addition 0.125M glycine for 5 minutes and ChIP-seq was performed

last: Quaife-Ryan

first: Enzo

middle: R

last: Porrello

middle: E


title: MiR-29 coordinates age-dependent plasticity brakes in the adult visual cortex

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: Visual cortical circuits show profound plasticity during early life and are later stabilized by molecular "brakes" limiting excessive rewiring beyond a critical period. The mechanisms coordinating the expression of these factors during the transition from development to adulthood remain unknown. We found that miR-29a expression in the visual cortex dramatically increases with age, but it is not experience-dependent. Precocious high levels of miR-29a blocked ocular dominance plasticity and caused an early appearance of perineuronal nets. Conversely, inhibition of miR-29a in adult mice using LNA antagomirs activated ocular dominance plasticity, reduced perineuronal nets and restored their juvenile chemical composition. Activated adult plasticity had the typical functional and proteomic signature of critical period plasticity. Transcriptomic and proteomic studies indicated that miR-29a manipulation regulates the expression of plasticity brakes mainly affecting parvalbumin-positive interneurons. These data indicate that miR29a is a master regulator of the plasticity brakes promoting age-dependent stabilization of visual cortical circuits.

overall_design: RNA-seq was performed on the visual cortex of adult mice intracortical injected with 1) LNA oligonucleotide with scrambled sequence (control), number of replicates = 4; or 2) intracortical injected with LNA oligonucleotide complementary to miR-29a (miR-29a), treated samples, number of replicates = 4.

first: Debora

last: Napoli

first: Leonardo

last: Lupori

first: Raffaele

last: Mazziotti

first: Giulia

last: Sagona

first: Sara

last: Bagnoli

first: Muntaha

last: Samad

first: Erika

last: Kelmer Sacramento

first: Johanna

last: Kirkpartick

first: Elena

last: Putignano

first: Eva

last: Terzibasi Tozzini

first: Paola

last: Tognini

first: Pierre

last: Baldi

first: Jessica

last: Kwok

first: Alessandro

last: Cellerino

first: Tommaso

last: Pizzorusso


title: Critical Regulation of a NDIME/Mef2c Axis in Embryonic Stem Cell Neural Differentiation and Autism

city: shanghai

first: Mingliang

last: Bai

state: shanghai

address: siping road

institute: tongji university

summary: Recent studies revealed that microdeletion of human chromosome 5q14.3 leads to the occurrence of neurodevelopmental disorders such as autism and intellectual disability, and have identified Mef2c haploinsufficiency as a main cause. Here, we found that a brain-enriched long non-coding RNA, termed NDIME, is located near the Mef2c locus and is required for normal neural differentiation of mouse embryonic stem cells (mESCs). Mechanistic studies showed that exons 1-3 of NDIME interacts with the major component of polycomb repressive complex 2 (PRC2) EZH2, blocking EZH2-mediated trimethylation of histone H3 lysine 27 (H3K27me3) at the Mef2c promoter, ensuring Mef2c transcription. Moreover, both the expression levels of NDIME and Mef2c were significantly downregulated in the hippocampus of autism model mice, while adeno-associated virus (AAV)-mediated expression of NDIME significantly increased the Mef2c expression and ameliorated autism-like behaviors. Collectively, our findings reveal an epigenetic mechanism of NDIME regulating Mef2c transcription and neural differentiation, and the potential effects and application of the NDIME/Mef2c axis in autism.

overall_design: mRNA profiles of  wild type (WT), LincNDIME_KO, shCtrl, and shMef2c  46C cells at day 0 and day 5 were generated by deep sequencing.


title: Transcriptome of lesional skin of patients suffering from Acne inversa

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Transcriptome of skin from Acne inversa lesions show specific alterations compared to healthy donor skin.

overall_design: Skin biopsies were taken from 4 healthy donors and 3 patients with Acne inversa. RNA was extracted. Transcriptome analysis was performed using RNA sequencing (Illumina).

first: Ellen

last: Witte-Händel

first: Orr

last: Shomroni

first: Kerstin

last: Wolk

first: Robert

last: Sabat


title: Long noncoding RNA glycoLINC assembles a lower glycolytic complex essential for cellular adaptation to serine starvation

city: Beijing

first: Fengyang

last: Jing

address: xueyuan road #38

institute: Peking university

summary: Here we show that a c-Myc-responsive long noncoding RNA (lncRNA) that we name glycoLINC (gLINC) acts as a backbone for metabolon formation between all four glycolytic pay-off phase enzymes (PGK1, PGAM1, ENO1 and PKM2) along with LDHA.

overall_design: LncRNA profiles of shCtrl and shC-myc in HepG2 cell line.

first: Mian

last: Wu

first: Youming

last: Zhu

first: Lei

last: Jin


title: Transcriptional profile of male and female embryonic day 18 (E18) C57Bl6/J mouse dorsal forebrain after chronic maternal infusion with arginine vasopression (AVP) or saline throughout gestation.

city: Iowa City

first: Serena

last: Gumusoglu

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

summary: This experiment assessed transcriptional changes in embryonic dorsal forebrain in male and female offspring to determine the sex-specific mechanism(s) by which chronic gestaitonal exposure to arginine vasopression (AVP), a mouse model of the hypertensive gestational disorder preeclampsia, alters neurodevelopment.

overall_design: RNA was isolated from male and female E18 dorsal forebrain following maternal infuson throughout gestation with vasopressin or saline via a subcutaneous osmotic minipump.

first: S

middle: B

first: B

last: Hing

first: H

last: Stevens


title: TREE1-EIN3 mediated transcriptional repression inhibits shoot growth in the response to ethylene

city: Austin

first: Hong

last: Qiao

address: 2506 speedway, NMS5.324

institute: The University of Texas at Austin

summary: Purpose: Next-generation sequencing (NGS) has been used to study the gene expression in different samples under air and ethylene treatment. The goal of this study is to uncover how TREE1 repress expression of genes that bound by transcriptional activitor EIN3 after ethylene treatment.

overall_design:
Seedling mRNA profiles of 3-day old TREE1ox (in COL background) were generated by sequencing, in 2 replications, using Illumina HiSeq 2000

Wildtype control samples were re-analyzed samples: GSM2209777 and GSM2209778.

first: Likai

last: Wang


title: Effect of IL-1b on primary human skin-relevant cells

summary: Analyses of IL-1b-induced transcriptome in various skin-relevant cell types (keratinocytes, dermal fibroblasts, dermal microvascular endothelial cells, mononuclear immune cells) by RNASeq method disclosed an overlap of upregulated molecules among the different cell types. Matching cellular IL-1 receptor levels, dermal fibroblasts showed both the strongest and broadest IL-1b response.

overall_design: Primary human keratinocytes, fibroblasts and microvascular endothelial cells derived from human healthy skin as well as mononuclear immune cells separated from the blood of healthy donors were cultured in the absence (control) or presence of recombinant human IL-1b for 24h.


title: Role of the histone methylase G9a in pancreatic carcinogenesis

city: Tokyo

first: Keisuke

last: Tateishi

address: Bunkyo-ku, Hongo7-3-1

country: Japan

institute: University of Tokyo

summary: Accumulating evidences propose the importance of epigenetic regulation in pancreatic carcinogenesis, but the mechanistic insights of a variety of histone modification process still remains to be elucidated. G9a functions as a transcriptional repressor via the methylating activity specific for histone H3 lysine9. We identified G9a as a critical factor in the development of murine pancreatic oncogenesis.

overall_design: Comparison of gene expression in P48-Cre; KrasG12D and P48-Cre; KrasG12D; G9a flox/flox Pancreas

first: KEISUKE

last: TATEISHI


title: RNA sequencing of Bos indicus testicular samples (adult and fetus) and liver samples (adult) [total RNA]

first: Marina

last: Fortes

state: Queensland

address: SCMB, room 454 bld 76

department: School of Chemistry and Molecular Biosciences

institute: The University of Queensland

summary: We report the raw data in fastq format of the sequencing of total and small RNA from testis and liver of Bos indicus cattle

overall_design:
examination of total RNA sequences from tissue biopsies of Bos indicus cattle (5 individual liver samples, 5 individual testicular samples, 5 individual fetus samples)

These samples are part of the Functional Annotation of Animal Genomes (FAANG)  project https://www.animalgenome.org/community/FAANG/

EBI BioSample Group: SAMEG329764

first: Laercio

last: Porto Neto


title: RNA sequencing of Bos indicus testicular samples (adult and fetus) and liver samples (adult) [small RNA]

overall_design:
examination of total and small RNA sequences from tissue biopsies of Bos indicus cattle (5 individual liver samples, 5 individual testicular samples, 5 individual fetus samples)

These samples are part of the Functional Annotation of Animal Genomes (FAANG)  project https://www.animalgenome.org/community/FAANG/

EBI BioSample Group: SAMEG329764


title: RNA sequencing of Bos indicus testicular samples (adult and fetus) and liver samples (adult)


title: Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation

status: Public on Nov 02 2020

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health


title: Limiting Self-Renewal of the Basal Compartment Induces Differentiation and Alters Evolution of Mammary Tumors

city: Bengaluru

first: Mohamed Ashick

last: Mohamed Saleem

state: Karnataka

address: #1519/10, 8Th A Main, 'Akshaya', Sahakaranagar

country: India

institute: LifeBytes India Pvt Ltd

summary:
The goal of the study was to assess the role of PKA activation in mammary development and the development and progression of mammary tumors. The scRNA-Seq experiment was specifically designed to plot the evolution of cell subpopulations within mammary glands from the hyperplasia stage as they progress to fully-blown tumors.
Results: PKA activation resulted in tumors that were more benign, exhibited reduced metastatic propensity, loss of tumor-initiating potential and increased sensitivity to chemotherapy. Longitudinal single cell profiling at the hyperplasia and tumor stages uncovered an altered path of tumor evolution whereby PKA curtails the emergence of aggressive subpopulations.

overall_design:
MMTV-PyMT WT and PKA activated mice were sacrificed at two time points -  8-9 weeks (hyperplasia) or 22 weeks (tumor). Hyperplastic mammary glands  and tumors within the same mouse were processed for longitudinal assesment of tumor development. Single-cell RNA-Seq was carried out at the hyperplasia and tumor stages of WT tumors and those with activated PKA signaling.
Single cell RNA-seq libraries were be prepared using the Chromium Single Cell 3’ v2 kit (10x Genomics) and sequenced on an Illumina NextSeq500 High Output 26bp x 98bp run to generate an average of 50,000 reads/cell.
Following cell-type specific markers were used for the cells classification, Basal cells: Krt14, Krt5, Snai2; Luminal Mature cells: Pgr, Prlr, Foxa1, Gpx3, Esr1; Luminal Progenitor cells; CD14, Kit, Lalba; Lumino-basal: Krt14, Krt8, CD14; EMT-like: Trim29, Vim, Cldn6, Sox4. We identified and classified cell-types using Monocle2’s classifyCells function. Transition of gene expression kinetics was performed by integrative Pseudotime analysis using Monocle2.

first: Nevena

last: Ognjenovic

first: Meisam

last: Bagheri

first: Gadisti

last: Mohamed

first: Ke

last: Xu

first: Youdinghuan

last: Chen

first: Mohamed

last: Saleem

first: Meredith

middle: S

last: Brown

first: Shivashankar

last: Nagaraj

first: Kristen

last: Muller

first: Scott

last: Gerber

first: Brock

last: Christensen

first: Diwakar

last: Pattabiraman


title: Intra-tumour heterogeneity of Diffuse Large B-cell Lymphoma involves the induction of diversified stroma-tumour interfaces

city: Palermo

first: Claudio

last: Tripodo

address: Corso Tukory 211

department: Department of Health Sciences

country: Italy

institute: University of Palermo School of Medicine

summary: Intra-tumour heterogeneity in lymphoid malignancies encompasses selection of genetic events and epigenetic regulation of transcriptional programs. Clonal-related neoplastic cell populations are unsteadily subjected to immune editing and metabolic adaptations within different tissue microenvironments. How tissue-specific mesenchymal cells impact on the diversification of aggressive lymphoma clones is still unknown. We investigated the intra-tumour heterogeneity and the specific mesenchymal modifications that are associated with  A20 diffuse large B-cell lymphoma (DLBCL) cells seeding of different tissue microenvironments. We found that the tissue microenvironment casts a relevant influence over A20 transcriptional landscape also impacting on Myc and DNA damage response programs. Extending the investigation to mice deficient for the matricellular protein SPARC, a stromal prognostic factor in human DLBCL, we demonstrated a different immune imprint on A20 cells according to stromal Sparc proficiency.

overall_design: A20 lymphoma cells were injected into WT or Sparc-/- recipent mice. Following 5 weeks of injection tumor cells were isolated from the bone marrow, spleen and liver of 5 mice per genotype and subjected to RNA-seq profiling.

first: Sangaletti

last: Sabina

first: Iannelli

last: Fabio

first: Zanardi

last: Federica

first: Cancila

last: Valeria

first: Portararo

last: Paola

first: Botti

last: Laura

first: Vacca

last: Davide

first: Chiodoni

last: Claudia

first: Di

middle: N

last: Arianna

first: Valenti

last: Cesare

first: Rizzello

last: Celeste

first: Vegliante

middle: M

last: Carmela

first: Pisati

first: Gulino

last: Alessandro

first: Ponzoni

last: Maurilio

first: Colombo

last: Paolo

first: Tripodo

last: Claudio


title: Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation [ATAC-Seq]

first: Pedro

last: Rocha

summary: Reversible modification of proteins with linkage-specific ubiquitin chains is critical for intracellular signaling. Yet, information on physiological roles and underlying signaling mechanisms of particular ubiquitin linkages during human development are limited. Here, relying on genomic constraint scores, we identify 10 patients with a novel multiple congenital anomaly disorder caused by hemizygous variants in OTUD5, encoding a K48-/K63-linkage-specific deubiquitylase. By studying these mutations, we find that OTUD5 controls neuroectodermal differentiation through cleaving K48-linked ubiquitin chains to counteract degradation of a select group of chromatin regulators. These include ARID1A/B, HDAC2, and HCF1, mutation of which underlie different developmental disorders that exhibit phenotypic overlap with OTUD5 patients. Consequently, loss of OTUD5 during early differentiation leads to less accessible chromatin at neuroectodermal enhancers and thus aberrant rewiring of gene expression networks. Our study describes a novel developmental disorder we name LINKED (LINKage-specific-deubiquitylation-deficiency-induced Embryonic Defects) syndrome, provides a previously unrecognized mechanistic link between phenotypically related diseases, and reveals linkage-specific ubiquitin cleavage from substrate groups (i.e. chromatin remodelers) as an essential mode of signaling required to coordinate embryonic differentiation pathways.

overall_design: ATAC seq was performed in human stem cells and following three days of neural differentiation. Cells treated with control shRNA were compared against cells treated with shRNA targeting OTUD5. Each condition/timepoint was performed in triplicate.


title: Sexually dimorphic ozone-induced changes in fetal rat hypothalamus

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

summary: IUGR is associated with an increased risk of obesity in offspring, which is likely driven in part by reprogramming of the hypothalamus due to suboptimal nutrition and hypoxia during development. As such, we performed mRNA-seq on whole hypothalamic tissue to identify altered expression of genes in our model of IUGR and to identify major pathways that could be associated with fetal undernutrition near term.

overall_design: Kidneys from 3 naïve adult male Sprague-Dawley rats, 6 months old, were collected and laser capture dissection was used to sample the proximal tubules, glomeruli,  the thick ascending limb (TAL) of the loop of Henle, and collecting duct (CD). Samples were measured for microRNAs using small RNA sequencing on an Illumina HiSeq 2000.

first: Colette

last: Miller


title: Regeneration Defects in Livers of Mice With Mutations in Yap and Taz Caused by Bile Duct Disruption and Cholestasis

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

institute: VIB-KU Leuven

summary: Background and aims:   The Hippo pathway and its downstream effectors YAP and TAZ (YAP/TAZ) are heralded as important regulators of organ growth and regeneration. However, different studies provided contradictory conclusions about their role during regeneration of different organs ranging from promoting proliferation to inhibiting it. Here, we resolve the function of YAP/TAZ during regeneration of the liver, where Hippo’s role in growth control has been studied most intensely.     Methods:   We evaluated liver regeneration after CCl4 toxic liver injury in mice with conditional deletion of Yap/Taz in hepatocytes and/or biliary epithelial cells and measured the behavior of different cell types during regeneration by histology, RNA-sequencing and flow cytometry.    Results:   We found that YAP/TAZ were activated in hepatocytes in response to CCl4 toxic injury. However, their targeted deletion in adult hepatocytes did not noticeably impair liver regeneration. In contrast, Yap/Taz deletion in adult bile ducts caused severe defects and delay in liver regeneration. Mechanistically, we show that Yap/Taz mutant bile ducts degenerated, causing cholestasis which stalled the recruitment of phagocytic macrophages and the removal of cellular corpses from injury sites. Elevated bile acids activated PXR, which was sufficient to recapitulate the phenotype observed in mutant mice.     Conclusions:   Our data show that YAP/TAZ are practically dispensable in hepatocytes for liver development and regeneration. Rather, YAP/TAZ play an indirect role in liver regeneration by preserving bile duct integrity and securing immune cell recruitment and function.

overall_design: mRNA profiles of sorted populations of hepatocytes and macrophages from mouse livers: 1) with BEC-specific Yap/Taz KO, 2) wildtype after 48h of acute CCl4 treatment, 3) with BEC-specific Yap/Taz KO and after CCl4 treatment, 4) wildtype

first: Elisabeth

last: Verboven

first: Iván

last: Moya

first: Leticia

last: Sansores

first: Weronika

last: Kowalczyk


title: Salmonella Typhimurium uses smooth swimming to increase invasion in the mammalian gut

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: The enteric pathogen Salmonella enterica serovar Typhimurium infects humans and animals. Invasion of intestinal epithelial cells is an important step in gut colonization. Both the Salmonella invasion-associated Type III Secretion System 1 (T3SS1) and motility are required for efficient invasion. The master regulator HilD induces expression of T3SS1 and flagella genes, thus coordinating expression of invasion and motility. Here we show that HilD also induces smooth swimming and that this is important for invasion of epithelial cells, in vitro and in vivo. HilD-induced bacteria express the chemotaxis receptor McpC, which suppresses tumbling and increases smooth swimming, even in the absence of exogenous ligands. mcpC is repressed by H-NS binding, which can be displaced by HilD. This is the first time that bacteria have been shown to use the smooth swimming phenotype in order to optimize invasion.

overall_design: RNA-Seq of 2 sample types (3 replicates each) of WT vs HilD overexpressing strain

first: Kendal

last: Cooper

first: Audrey

last: Chong

first: Laszlo

last: Kari

first: Brendan

last: Jeffery

first: Tregei

last: Starr

first: Molly

last: McClurg

first: Victoria

last: Posada

first: Richard

last: Laughlin

first: Canaan

last: Whitfield-Cargile

first: L

middle: G

last: Adams

first: Laura

last: Bryan

first: Sara

last: Little

first: Mary

last: Krath

last: Lawhon

first: Olivia

last: Steele-Mortimer


title: Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation [RNA-Seq]

first: Pedro

last: Rocha

overall_design: RNA-seq was performed in human stem cells and following three days of neural differentiation. Cells treated with control shRNA were compared against cells treated with shRNA targeting OTUD5. Each condition/timepoint was performed in triplicate.


title: The S phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathway

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: Cell cycle is a cellular process that are subject to stringent control. In contrast to the wealth of knowledge of proteins controlling the cell cycle, very little is known about the molecular role of lncRNAs (long noncoding RNAs) in cell cycle progression.  To understand the role of S phase upregulated SUNO1 lncRNA, we performed microarray analyses of control and SUNO1-depleted HCT116 cells.

overall_design: We performed the microarray in biologicl duplicates. We used to two time points (36 hrs and 72 hrs post siRNA treatment) to identify the gene sets that showed differential expression during early and late time points post SUNO1 depletion.

first: K

last: Prasanth


title: RNA-seq based in vivo transcriptomes of pine trees inoculated with pinewood nematode under the enhanced resistance state

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

summary: Bursaphelenchus xylophilus (pinewood nematode, PWN) is a causal agent of pine wilt disease and results in economic and environmental losses in pine forests. The establishment of systemic acquired resistance (SAR) provides positive capacities to control PWN. We selected two SAR elicitors, acibenzolar-S-methyl (ASM) and methyl salicylic acid (MeSA), which effectively inhibited disease symptoms on PWN-infected pine trees. To understand dynamic interactions between pine host and PWN under SAR state, we characterized in vivo transcriptomes of pine trees infected by B. xylophilus according to the ASM and MeSA treatment. After distilled water treatment, pine trees infected by B. xylophilus was used as a negative control.

overall_design: To induce systemic acquired resistance (SAR), pine seedlings were treated with the acibenzolar-S-methyl or methyl salicylic acid. As a negative control, pine seedlings were treated with distilled water containing 250 μg/ml Tween 20. One week after treatment, all pine seedlings were inoculated with Bursaphelenchus xylophilus. For each group, three replicates were used.

first: Hyejung

last: Jung

first: Hyun-Hee

last: Lee

first: Namgyu

last: Kim

first: Jin-Cheol

first: Young-Su

last: Seo


title: Ant-leukemic effect of CDK9 inhibition in T-cell prolymphocytic leukemia (microRNA)

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

institute: University Hospital Essen

summary: We investigated the pharmacological effects of the novel highly specific cyclin-dependent kinase 9 (CDK9) inhibitor LDC526 and its clinically used derivate atuveciclib employing primary T-PLL cells in an ex vivo drug sensitivity testing platform. All T-PLL samples were sensitive to CDK9 inhibition at submicromolar concentrations while conventional cytotoxic drugs were found to be largely ineffective. At the cellular level LDC526 inhibited the phosphorylation at serine 2 of the RNA polymerase II C-terminal domain resulting in decreased de novo RNA transcription. LDC526 induced apoptotic leukemic cell death through down-regulating MYC and MCL1 both at the mRNA and protein level. Microarray based transcriptomic profiling revealed that genes down-modulated in response to CDK9 inhibition were enriched for MYC and JAK-STAT targets. By contrast, CDK9 inhibition increased the expression of the tumor suppressor FBXW7 which may contribute to decreased MYC and MCL1 protein levels. The combination of atuvecliclib and the BCL2 inhibitor venetoclax exhibited synergistic anti-leukemic activity, providing the rationale for a novel targeted-agent based treatment of T-PLL.

overall_design: After tumor cell enrichment for T-PLL cells we performed miRNA profiling with GeneChip miRNA 3.0 arrays (Affymetrix, Santa Clara, CA) and Microarray based gene expression profiling (GEP). GEP was performed using high-densitiy oligonucleotide arrays (Clariom S, Affymetrix, Santa Clara, CA, USA).

first: Patricia

last: Johansson

last: Dierichs

first: Ludger

last: Klein-Hitpass

first: Anke

middle: K

last: Bergmann

first: Michael

last: Möllmann

first: Sascha

last: Menninger

first: Peter

last: Habenberger

first: Bert

last: Klebl

first: Jens

middle: T

last: Siveke

first: Ulrich

last: Dührsen

first: Axel

last: Choidas

first: Jan

last: Dürig


title: Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota

summary: The human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNAseq to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of cell types are susceptible to infection, ciliated cells are a predominant cell target for SARS-CoV-2. Remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. We also found that heavily infected epithelial cells demonstrate impaired IFN signaling and express abundant IL-6, a potential mediator of COVID-19 pathogenesis.

overall_design: Basal layer of medium was replaced with infection media (DMEM with 2% FBS, 100 U/mL penicillin and streptomycin, 10 mM HEPES, 0.1 mM nonessential amino acids, 4 mM L-glutamate, and 1mM sodium pyruvate). Wells were left untreated, or treated with 100 ng of IFN-b or 0.1 mM remdesivir in the basal compartment for 1 hr prior to infection. For infection, SARS-CoV-2 strain 2019-nCoV/USA_WA1/2020 (provided by World Reference Center for Emerging Viruses and Arboviruses at the University of Texas Medical Branch) and icSARS-CoV-2-mNG, were added directly to the apical layer of cells for 1 hr at 37°C with rocking every 10 min. The virus was removed from the apical compartment and cells were incubated at 37°C until harvest.

first: Jessica

last: Fiege

first: Josh

last: Thiede

first: Hezkiel

last: Nanda

first: William

last: Matchett

first: Patrick

last: Moore

first: Noe

last: Montanari

first: Beth

last: Thielen

first: Jerry

last: Daniel

first: Emma

last: Stanley

first: Ryan

last: Hunter

first: Vineet

last: Menachery

first: Steven

last: Shen

first: Tyler

last: Bold

last: Langlois


title: Evolutionarily selected overexpression of the cytokine BAFF enhances mucosal immune response against P. falciparum

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: A variant of the TNFSF13B gene (BAFF-var) increases the production of the cytokine BAFF, up-regulating humoral immunity and increasing the risk for certain autoimmune diseases. BAFF-var was evolutionarily advantageous, most likely by increasing resistance to malaria infection.    We assessed experimentally the role of BAFF-var in response to malaria antigens.    Lysates of erythrocytes infected with Plasmodium falciparum (iRBCs) or left uninfected (uRBCs, control) were used to treat PBMCs with distinct BAFF genotypes.    PBMCs purified from BAFF-var donors and treated with iRBCs showed different levels of specific cells, immunoglobulins and cytokines as compared with BAFF-WT.  In particularly a relevant differential effect on mucosal immunity B subpopulations have been observed.    RNA sequencing of total B cells, purified from PBMC treated with iRBCs or uRBCs, identified several transcripts differentially expressed including some that encoded proteins critical for the response to malaria infection.    These findings point to specific immune cells and molecules through which the evolutionary selected BAFF-var may have improved fitness during P. falciparum infection.

overall_design: Lysates of erythrocytes infected with Plasmodium falciparum (iRBCs) or left uninfected (uRBCs, control) were used to treat PBMCs with distinct BAFF genotypes.  PBMC and B cells responce were analyzed.

first: Valeria

last: Lodde

first: Francesco

last: Cucca

first: M

middle: L

last: Idda

first: Myriam

last: Gorospe


title: Landscape of genome-wide DNA methylation profile of colorectal cancer metastasis

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Genome-wide DNA methylation of colorectal cancer patients with lymph node metastases showed global loss of DNA methylation in CG-poor, non-CpG island (CGI) regions. Overall CGI methylation was increased in tumour samples. Differential methylation analysis of CGIs identified 60 putative biomarkers, with >20% increase in DNA methylation in both primary tumour and metastasis samples compared to normal adjacent tissue.

overall_design: Enhanced methyl-seq of matched normal adjacent tissue, primary tumour and lymph node metastasis from 5 colorectal cancer patients was analysed.

first: Carmen

last: Ili

first: Kurt

last: Buchegger

first: Hannah

last: Demond

first: Priscilla

last: Brebi


title: Transcriptomic profiling of micro RNAs in mock-infected cells and an in vitro model of HIV latency before and after activation

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary:
Purpose: The goal of this study is to identify host micro RNAs (miRNAs) whose expression is dysregulated during HIV latency, cell activation and productive infection. This information provides a mechanistic insight into an additional layer of miRNA-mediated regulation of gene expression and cellular pathways that are involved in HIV latency establishment and maintenance.
Methods: An in vitro model of HIV latency and mock-infected cells before and after activation with antiCD3/antiCD28 coated magnetic beads was used for miRNA expression profiling using small RNA sequencing (smRNA-Seq).
Results: Read counts of the 418 miRNAs survived filtering. Differential expression analysis identified 26 miRNAs dysregulated in latency. Messenger RNA (mRNA) targets and cellular pathways enriched for mRNA targets were identified using several analytical methods. Our analyses showed that many protein-coding genes and pathways targeted by dysregulated miRNAs have relevance to regulation of HIV expression or establishment of HIV latency. The p53 signalling pathway was found among pathways that were targeted by dysregulated miRNAs at a greater level than expected by chance.
Conclusions: The present study identifies miRNAs dysregulated during HIV latency and provides a mechanistic insight into regulation of the p53 pathway via miRNAs that may contribute to latency establishment.

overall_design: Transcriptomic profiling of the in vitro model of HIV latency and mock-infected cells before and after activation. The experiment had 4 biological replicates, 4 conditions for each, for a total of 16 samples.

first: Ashley

last: Heinson


title: BMP10 signaling promotes the development of endocardial cells from human pluripotent stem cell-derived cardiovascular progenitors

city: Toronto

first: Gordon

last: Keller

address: 101 College street

department: McEwen Stem Cell Institute

institute: University Health Network

summary: We established a differentiation strategy to generate endocardial-like cells from hPSCs. Endocardial-like cells generated from our protocol display major functional properties of endocardium in developing embryo: they can induce trabecular markers in early hPSC-derived ventricular cardiomyocytes and they can undergo endothelial-to-mesenchymal-trasition under appropriate conditions. Furthermore, the transcriptome of our in vitro generated endocardial cells showed a very high level of correlation to that of primary fetal endocardial cells.  Functional properties and transcriptional profile of hPSC-derived endocardial cells were also compared to those of control (non-endocardial) endothelial cells. For scRNA-seq analysis live cells from bulk endocardial and control endothelial differentiation cultures were labeled with two different sets of anti-human Hashtag antibodies before sequencing. Single cell RNA sequencing was carried out on a sample consisting of 85% bulk endocardial cells (TotalSeq-A0255 anti-human Hashtag 5 antibody, BioLegend) and 15% bulk control endothelial cells (TotalSeq-A0254 anti-human Hashtag 4, Biolegend).

overall_design: Examination of heterogeneity and global transcriptome between hPSC-derived endocardial-like cells and control (non-endocardial) endothelial cells.

first: Alexander

last: Mikryukov


title: Single nuclei RNA-seq of mouse placental labyrinth development

city: San Francisco

first: Bryan

last: Marsh

address: 35 Medical Center Way, RMB 912E, None

institute: University of California, San Francisco

summary:
Single nuclei RNA-sequencing of the mouse placenta at four developmental stages (E9.5, E10.5, E12.5, E14.5).

Supplementary files include the expression matrices for the integrated datasets containing nuclei from E9.5, E10.5, E12.5, and E14.5 and the clustering annotations for either all nuclei (AllStages_AllNuclei) or subclustered trophoblast nuclei (AllStages_TrophoblastNuclei).

Processed data as R objects for both AllStages_AllNuclei and AllStages_TrophoblastNuclei are available at https://figshare.com/projects/Single_nuclei_RNA-seq_of_mouse_placental_labyrinth_development/92354

overall_design: Four single nuclei sequencing collections from mouse placentas at E9.5, E10.5, E12.5, and E14.5, with an emphasis on the collection from the placental labyrinth.

first: Robert

middle: H

last: Blelloch


title: Ant-leukemic effect of CDK9 inhibition in T-cell prolymphocytic leukemia (mRNA)

first: Rene

last: Scholtysik

first: Patricia

last: Johansson

first: Laura

last: Dierichs

first: Ludger

last: Klein-Hitpass

first: Anke

last: Bergmann

first: Michael

last: Möllmann

first: Sascha

last: Menninger

first: Peter

last: Habenberger

first: Bert

last: Klebl

first: Jens

last: Siveke

first: Ulrich

last: Dührsen

first: Axel

last: Choidas

first: Jan

last: Dürig


title: Zinc effect on mice

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

institute: University of Lille

summary: This study underlines the beneficial use of excess dietary zinc in preventing colitis and inflammatory events. Zn-induced gene expression profiles were analyzed at ileum and colon level. A total number of 101 profiles were found differentially expressed during Zn supplemented diet, with an unbalanced pattern between these two tissues. A largest number of genes were found up-regulated in colon (22 genes), unlike the ileum (6 genes). At the other side, the number of down-regulated genes was higher in ileum (63 genes) against the colon (15 genes). Very few common profiles were detected in these two tissues, 3 up- and 2 down-regulated genes respectively. Genes coding for metallothioneins (Mt1, Mt2) and for phosphatidylinositol-4-phosphate 5-kinase (Pip5k1a) were found commonly up-regulated in ileum and colon, with the highest FC values. Genes coding for the zinc transporter of solute carrier family 39 (Slc39a4) and for lymphotoxin B (Ltb) were found commonly down-regulated with among the lowest FC values. Despite the different patterns, functional clustering of expressed genes converged for substantially the same physiological activities in both ileum and colon: intestinal tissue protection and epithelium reestablishment, immune system regulation as well as digestive and metabolic targeted functions.

overall_design: Three groups of mice were randomized to receive distinct doses of ZnCl2 solutions administered in the drinking water while a control group consisted in standard uncontaminated drinking water. After 15 days of Zn treatment, mice are sacrificed and sections from the median colon and terminal ileum were collected and processed for transcriptomic analyses.

first: Benoît

last: Foligné

first: Catherine

last: Daniel


title: Inhibition of protein translation is a major mechanism for the activity of the pan-PIM kinase inhibitor PIM447 in combination with Pomalidomide-dexamethasone in multiple myeloma

city: Salamanca

first: Teresa

last: Paíno Gómez

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer

summary: The overexpression of PIM kinases in hematologic malignancies, including multiple myeloma, make PIM inhibitors an attractive therapeutic strategy for these diseases. Recent preclinical data from our group demonstrated the anti-myeloma effect of the pan-PIM kinase inhibitor PIM447, along with its synergistic effect with standard of care anti-myeloma agents. Based on those previous data, we have evaluated here the in vitro and in vivo activity of the triple combination of PIM447 + pomalidomide + dexamethasone (PIM-Pd). Our results show that this combination exerts a potent anti-myeloma effect in vitro, even in presence of microenvironment cells, and, in vivo, it markedly delays tumor growth and prolongs survival. Mechanism of action studies suggest that the combination PIM-Pd inhibits protein translation processes through the convergent inhibition of mTORC1, which disrupts the function eIF4E, and c-Myc. As a consequence, cell cycle arrest and disruption of metabolic pathways, including glycolysis and lipid biosynthesis, is induced, inhibiting myeloma cell proliferation. Altogether, these data support the potential future clinical development of the triple combination PIM-Pd for the treatment of patients with MM.

overall_design: Total RNA was isolated using Trizol reagent (Invitrogen) and purified with the RNAeasy Mini Kit (QIAGEN, Hilden, Germany) from three independent experiments of MM1S cells untreated (control) or treated with PIM447 (PIM), Pomalidomide + dexamethasone (Pd) or the triple combination PIM447 + Pomalidomide + dexamethasone (PIM-Pd).

last: Paíno


title: Multi-treatment models for breast cancer

city: Urbana

first: Zeynep

last: Madak-Erdogan

state: Illinois

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Illinois

summary: RNA seq analysis of multiple treatments and their effects on in vitro breast cancer models

overall_design: RNA seq analysis


title: Transcriptome sequencing of laryngeal squamous cell carcinoma and paired adjacent normal mucosa tissues

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer. However, the mechanism underlying the pathogenesis of LSCC remains unclear. To identify dysregulated genes  in LSCC.Transcriptome sequencing were performed was performed on a cohort of 53 LSCC tissues and 53 paired adjacent normal mucosa tissues.

overall_design: Expression of lncRNA, mRNA and circRNA in 53 LSCC tissues and 53 paired adjacent normal mucosa tissues was determined by high throughout sequencing.

first: Wei

last: Gao

first: Binquan

last: Wang

first: Qinli

last: Zhao


title: Impaired AKT signaling and lung tumorigenesis by PIERCE1 ablation in KRAS-mutant non-small cell lung cancer

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

summary: KRAS-mutant non-small cell lung cancer (NSCLC) is one of the main subtypes across lung cancers. Despite the enormous studies on KRAS-mutant NSCLC, new therapeutic targets need to be identified because current therapies are insufficient. Here we show the tumor promoting function of PIERCE1 in the KRAS-mutant NSCLC. Mechanistically, PIERCE1 depletion inhibits cell growth and AKT phosphorylation (pAKT) at S473, particularly in KRAS-mutant lung cancer. Analyses of AKT-related genes show that PIERCE1 negatively regulates gene expression of AKT suppressor TRIB3 through CHOP pathway. Correspondingly, four independent in vivo approaches in lung cancer mouse models related to KRAS mutations reveal the tumor suppressive effect of PIERCE1 depletion suggesting its therapeutic potential. Tissue microarray of human lung cancer showed that PIERCE1 is expressed in 83% of lung cancers and is linked to pAKT expression. This illustrates how PIERCE1 depletion acts as a novel therapeutics against KRAS-mutant NSCLC.

overall_design: The mRNA levels were measured for two biological replicates for each condition: A549 cells transfected with one of three different sequences of siPIERCE1 (siP1 #1, siP1 #2, and siP1 #3) or control (siControl).

first: Han-Woong

last: Lee


title: YAMAT-seq of mature tRNA pools in the bacterium Pseudomonas fluorescens SBW25 and derivatives

city: Ploen

first: Jenna

last: Gallie

address: August-Thienemann Strasse 2

institute: Max Planck Institute for Evolutionary Biology

summary: Mature tRNA pools were measured using an adaptation of Y-shaped Adapter-ligated MAture tRNA sequencing (YAMAT-seq) (Shigematsu et al., 2017) in nine strains derived from the model bacterium, Pseudomonas fluorescens SBW25. The aim of the experiment was to determine the effect on the mature tRNA pool of (i) removing the single-copy serCGA gene by genetic engineering, and (ii) duplicating the serTGA gene during a subsequent, compensatory evolution experiment. We found that (i) results in the loss of tRNA-Ser(CGA) from the mature tRNA pool, and (ii) results in a 2-fold higher expression of tRNA-Ser(UGA). tRNA-Ser(UGA) presumably substitutes for tRNA-Ser(CGA) by wobble base pairing to translate codon 5'-UCG-3'.

overall_design: Three replicates of nine strains: SBW25, delserCGA-1, delserCGA-2, W1-L, M1-L, M2-L, M2-Lop, M3-L, M4-L

first: Gökçe

last: Ayan

first: Hye Jin

last: Park


title: NAIL: an evolutionarily conserved lncRNA essential for coordinating p38 activation and NFκB mediated chromatin remodelling in inflammation

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive,  Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

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

overall_design: Refer to individual Series


title: G-quadruplex roles in transcription deciphered by comparative transcriptomic analyses

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

institute: Institut Imagine

summary: G-quadruplexes (G4) are non-canonical nucleic acid structures that can form at certain DNA or RNA guanine-rich sequences. G4 motifs are dispersed throughout the genome and considerably enriched at promoters, where they flank the transcription start site (TSS) and cluster at the 5’ end of the first intron, which suggests potential regulatory roles of quadruplexes in transcription. To improve our understanding of these roles, we have associated gene expression with the frequency of canonical G4 motifs near gene promoters and characterized perturbations caused by treatment with three G-quadruplex ligands, Pyridostatin and the two bisquinolinium compounds PhenDC3 and PhenDC6. We show that enrichment of G4 motifs characterizes the most actively transcribed genes, challenging the notion that quadruplexes chiefly exert negative regulation by blocking progress of RNA polymerase. G4 ligand-treatment altered splicing of transcripts at genes enriched for G4 motifs at the 5’-end of intron 1, suggesting that G-quadruplexes in the pre-mRNA can regulate splicing. Furthermore, our analysis also revealed some of the effects of G4 ligand treatment that likely reflect quadruplex-dependent replication stress leading to the induction of transcriptional signatures compatible with impaired cell cycle progression. Collectively, our results support the view that G-quadruplexes typically function as positive regulators of transcription, suggesting that quadruplexes may stabilize promoter architecture to enable efficient transcription. This analysis provides strong support for function of quadruplexes near the promoter as regulators of transcription and splicing.

overall_design: RNA-seq data in HT1080-ST fibrosarcoma human cells untreated (DMSO) or treated with G-quadruplex ligands

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