title: Weed presence altered biotic stress and light signaling in maize even when weeds were removed early in the critical weed‐free period

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary:
Purpose: This study is designed to identify genes and processes that are differentially regulated in corn when it is grown with or without weeds through the entire critical weed free period (to V8) or when weeds were removed early in the critical weed free period (at V4) and the plants were allowed to recover until V8.
Methods: Corn was grown as described above in field plots near Brookings SD in 2007 and 2008 and RNA was extracted from the top-most leaf tips from four plants per treatment plot. Unidirectional cDNA illumina sequencing libraries were constructed for each sample (pooled leaf tips from the given plot), and were sequenced (some samples were paired end sequenced and some were single end sequenced - all 100 bases for PE and SE reads), quality trimmed, and analyzed using the Tuxedo suite of programs for SE reads of the forward read libraries for each sample.
Results: We identified a small number of genes that were differentially expressed in both years. More importantly, gene set enrichment analysis of the data determined that weeds, when present through the critical weed free period impacted phytochrome signaling, defense responses, photosynthetic processes, oxidative stress responses, and various hormone signaling processes. When weeds were removed at V4 and the plants allowed to recover until V8, the weeds still imprinted impacts on phytochrome signaling, oxidative stress, and defense responses. Thus, it appears that weeds presence through the early portion of the critical weed free period, even after removal, induced processes that reduce corn growth and yield that lasted at least through V8.
Conclusions: This study represents the first investigation of the impact of the lasting effects of weeds during the early critical weed free period on the transcriptome of corn, and provides additional data on the impact of weeds through the critical weed free period that augments and confirms much of what was observed in similar microarray studies.

overall_design: Experimental Design: Samples all collected at the same developmental stage (V8) from three treatments (control, weedy, and weeds removed followed by recovery), in each of two years (2007 and 2008), with two to three biological replicates of each treatment in each year.

first: Stephanie

last: Bruggeman

first: Sharon

last: Clay


title: Disulfiram inhbits M. tuberculosis growth by altering methionine pool and redox balance

status: Public on Mar 08 2021

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

type: Expression profiling by high throughput sequencing

summary: Methionine biosynthetic pathway, essential for the growth of Mycobacterium tuberculosis (Mtb) in the host, represents an attractive target for the development of novel anti-tuberculars. Here, we have biochemically characterized homoserine acetyl transferase (HSAT viz. MetA) of Mtb, which catalyses the first committed step of methionine and S-adenosylmethionine (SAM) biosynthesis. High-throughput screening of a 2300 compound library resulted in identification of thiram, an anti-fungal organosulfur compound, as the most potent MetA inhibitor. Further analysis of thiram analogs led to the identification of orally bioavailable disulfiram (DIS, an anti-alcoholism FDA approved drug) as a novel inhibitor of MetA. Both thiram and DIS restricted the growth of drug-sensitive and drug-resistant Mtb strains in a bactericidal manner. ThermoFlour assay demonstrated direct binding of DIS with MetA. Metabolomic and transcriptomic studies showed DIS mediated perturbation of methionine and redox homeostasis, respectively, in Mtb. In concordance, the effect of DIS on Mtb growth was partially rescued by supplementation with either L-methionine as well as N-acetyl cysteine, suggesting a multi-target killing mechanism. In Mtb-infected mice, DIS administration restricted bacterial growth, increased efficacy of isoniazid, ameliorated lung pathology,  modulated lung immune cell landscape and protective immune response. Taken together, our results demonstrate that DIS can be repurposed for designing an effective anti-tubercular therapy.

overall_design: To compare the transcriptomic profiles of RNA obtained from M. tuberculosis H37Rv exposed to either 1x or 10x MIC99 of disulfiram (TETD). Control M. tuberculosis were treated with DMSO.

first: Deepika

last: Chaudhary

first: Ramandeep

last: Singh

first: Josephine

last: Lum

first: Bernett

last: Lee

first: Amit

last: Singhal


title: Methane-rich water induces bulblet formation of scale cuttings in Lilium davidii var. unicolor by regulating the signal transduction of phytohormones and their levels

city: Lanzhou

last: Qi

state: Anning District

address: Yingmen Village

country: China

institute: Gansu agricultural university

summary: Previous studies have shown that methane (CH4) has promoting roles in the adventitious root (AR) and lateral root formation in plants. However, whether CH4 could trigger the bulblet formation in scale cutting of Lilium davidii var. unicolor has not been elucidated. To gain insight into the effect of CH4 on the bulblet formation, different concentrations (1%, 10%，50% and 100%) of methane-rich water (MRW) and distilled water were applied to treat the scale cuttings of Lilium. We observed that treatment with 100% MRW obviously induced the bulblet formation in scale cuttings. To explore the mechanism of CH4-induced the bulblet formation, the transcriptome of scales was analyzed. A total of 2078 differentially expressed genes (DEGs) were identified. The DEGs were classified into different metabolism pathways, especially phenylpropanoid biosynthesis, starch and sucrose metabolism and plant signal transduction. Of these, approximately 38 candidate DEGs involved in the plant signal transduction were further studied. In addition, the expression of AP2-ERF/ERF, WRKY, GRAS, ARF and NAC transcription factors were changed by MRW treatment, suggesting their potential involvement in bulblet formation. As for hormones, exogenous IAA, GA and ABA could indue the bulblet formation. Additional experiments suggested that MRW could increase the endogenous IAA, GA, and JA levels, but decrease the levels of ABA during bulblet formation, which showed that higher IAA, GA, JA levels and lower ABA content might facilitate bulblet formation. In addition, the levels of endogenous hormone were consistent with the expression level of genes involved in phytohormone signal transduction. Overall, this study has revealed that CH4 might improve the bulblet formation of cutting scales in Lilium by regulating the expression of genes related to phytohormone signal transduction and transcription factors, as well as by changing the endogenous hormone levels.

overall_design: Scales (cutting from the base of scales about 2 cm) of Lilium were harvested after 10 days treatment with 100% methane-rich water and distilled water, and RNA was extracted and sequenced by paired-end sequencing. RNA sequencing reads were aligned against the soybean reference genome and differentially expressed genes between treatments were detected.

first: Nana

first: Xuemei

last: Hou

first: Weibiao

last: Liao


title: miR-378a regulates keratinocyte responsiveness to IL-17A in psoriasis

city: Solna

first: Enikö

last: Sonkoly

state: Stockholm

address: Visionsgatan 18

department: Medicine, Solna

country: Sweden

institute: Karolinska Institutet

summary: In 2019, our group performed small RNA-sequencing on keratinocytes isolated from lesional and non-lesional psoriasis skin as well as from healthy skin, and identified miRNAs with altered levels in psoriasis keratinocytes (Srivastava et al., 2019). One of the miRNAs we identified to be overexpressed in psoriasis keratinocytes was miR-378a-3p. In this study, we aimed to explore the regulation and function of miR-378a in keratinocytes and its potential role in psoriasis. We used microarrays to identify differentially expressed genes upon miR-378a overexpression in primary human keratinocytes as part of the study and gain insights about the modulation of specific pathways.

overall_design: Transfected primary human keratinocytes overexpressing the microRNA miR-378a (treated or not with IL-17A) were collected, RNA was isolated and gene expression profiled by microarray analysis (Affymetrix Human Gene 2.0 ST Array)

first: Ping

last: Xia

first: Lorenzo

last: Pasquali

first: Chen-ying

last: Gao

first: Ankit

last: Srivastava

first: Einar

last: Rosén

first: Bernhard

last: Homey

first: Andor

last: Pivarcsi


title: Next-gen RNA sequencing of normal retina, pretumorigenic retina and tumor retinal

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

country: USA

institute: University of Minnesota

summary: Expression profiling by high throughput sequencing

overall_design: 48 samples were obtained from genetically engineered mice and sorted for GFP signal activated by CRE recombination based on the CHX promoter  sequenced using Illumina HiSeq 2000

middle: L

first: Timothy

last: Hallstrom


title: The Iqgap3-Ras axis drives stem cell proliferation in the stomach corpus during homeostasis and repair

first: Ying

last: Li

state: --- Select a state ---

address: 14 Medical Dr, Singapore

institute: Cancer Science Institute of Singapore

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

overall_design: Refer to individual Series


title: Effect of Cra and carbon sources on global transcription

city: Claremont

first: Daniel

last: Stoebel

state: CA

address: 301 Platt Blvd

department: Biology

institute: Harvey Mudd College

summary: The Gram-negative bacterium Vibrio cholerae adapts to changes in environment by selectively producing the necessary machinery to uptake and metabolize available carbohydrates. The import of the six-carbon sugar fructose by the fructose-specific phosphoenolpyruvate (PEP) phosphotransferase system (PTS) is of particular interest because of its putative connection to biofilms, which have been shown to promote host colonization and cholera pathogenesis. This study focused on the transcriptional response to glucose and fructose, and the role of the Cra protein in this regulatory process.

overall_design: Two replicates of each of wild-type and ∆cra mutant grown with either glucose or fructose were studied by RNA-seq

first: Christina

last: Beck

first: Sayde

last: Perry

middle: M

first: Jane

last: Liu


title: The Iqgap3-Ras axis drives stem cell proliferation in the stomach corpus during homeostasis and repair [RNA-Seq]

summary:
Objective: Tissue stem cells are central regulators of organ homeostasis.  We looked for a protein that is exclusively expressed and functionally involved in stem cell activity in rapidly proliferating isthmus stem cells in the stomach corpus.
Design: We uncovered the specific expression of Iqgap3 in proliferating isthmus stem cells through immunofluorescence and in situ hybridization.  We performed lineage tracing and transcriptomic analysis of Iqgap3+ isthmus stem cells with the Iqgap3-2A-tdTomato mouse model.  Depletion of Iqgap3 revealed its functional importance in maintenance and proliferation of stem cells.  We further studied Iqgap3 expression and the associated gene expression changes during tissue repair after tamoxifen-induced damage.  Immunohistochemistry revealed elevated expression of Iqgap3 in proliferating regions of gastric tumors from patient samples.
Results: Iqgap3 is a highly specific marker of proliferating isthmus stem cells during homeostasis.  Iqgap3+ isthmus stem cells give rise to major cell types of the corpus unit.  Iqgap3 expression is essential for the maintenance of stem potential.  The Ras pathway is a critical partner of Iqgap3 in promoting strong proliferation in isthmus stem cells. The robust induction of Iqgap3 expression following tissue damage indicates an active role for Iqgap3 in tissue regeneration.
Conclusion: IQGAP3 is a major regulator of stomach epithelial tissue homeostasis and repair.  The upregulation of IQGAP3 in gastric cancer suggests that IQGAP3 plays an important role in cancer cell proliferation.

overall_design: RNA expression profile of stomach corpus 48 hr after HDT treated or untreated 6-8 weeks old mice. Total RNA was extracted from the corpus tissue.  Duplicate samples are shown.

first: Junichi

last: Matsuo

first: Daisuke

last: Douchi

first: Khine

last: Myint

first: NaingNaing

last: Mon

first: Akihiro

last: Yamamura

first: Kazuyoshi

last: Kohu

first: Dede

last: Heng

first: Sabirah

last: Chen

first: NurAstiana

last: Mawan

first: Napat

last: Nuttonmanit

first: Supriya

first: Shamaine

middle: H

last: Ting

first: Nicole

middle: Y

last: Lee

first: HongKai

first: Makoto

last: Adachi

first: Atsushi

last: Tamura

first: Jinmiao

first: Henry

last: Yang

first: Ming

last: Teh

first: Jimmy

middle: B

last: So

first: WeiPeng

last: Yong

first: Patrick

last: Tan

first: KhayGuan

last: Yeoh

first: Linda

last: Chuang

first: Sachiko

last: Tsukita

first: Yoshiaki

last: Ito


title: Differential expression analyses in microglial cells from APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– mice treated with tamoxifen vs APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– mice non treated

city: Sevilla

first: María Isabel

middle: Álvarez

last: Vergara

state: Sevilla

address: C/Manuel Siurot, sn

country: Spain

institute: Instituto de Biomedicina de Sevilla

summary:
Microglial cells were isolated by flow citometry using specific markers (CD45+/ CD11b+) and their global gene expression profile was analyzed. This data were used to study the role of HIF1A in microglia associated to Aβ plaques.
In this dataset, we include the expression data obtained in microglial cells from a model of gain of function of HIF1A in APP-PSEN1/+ mice.  (18 moth-old-age) mice model using a specific marker for this cell type (CD31+).  Functional enrichment analyses were carried out through GSEA, where we have included specific categories potentially involved with blood vessel formation.

overall_design: 6 Total samples were analyzed with 3 biological replicates in each condition (APP-PSEN1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– treated with tamoxifen vs the same non treated genetic mouse model).  We generated the following comparison: treated vs non treated APP-PSEN1/+; Cx3cr1-Cre::ERT2/+; Vhl Flox/–).  Data were normalized by using rma algorithm (robust multiarray average) and the normalized matrix that we obtained with this analyses was used such input in the GSEA tool.

first: Rosana

last: March-Diaz

first: Nieves

last: Lara-Ureña

first: Carmen

last: Romero-Molina

first: Antonio

last: Heras-Garvin

first: Clara

last: Ortega-de San Luis

first: Maria

middle: I

last: Alvarez-Vergara

first: Manuel

middle: A

last: Sanchez-Garcia

first: Elizabeth

last: Sanchez-Mejias

first: Jose

middle: C

last: Davila

first: Alicia

middle: E

last: Rosale-Nieves

first: Cristina

last: Forja

first: Victoria

last: Navarro

first: Angela

last: Gomez-Arboledas

middle: V

last: Sanchez-Mico

first: Adrian

last: Viehweger

first: Almudena

last: Gerpe

first: Emma

middle: J

last: Hodson

first: Marisa

last: Vizuete

first: Tammie

last: Bishop

first: Alberto

last: Serrano-Pozo

last: Lopez-Barneo

first: Edurne

last: Berra

first: Antonia

last: Gutierrez

first: Javier

last: Vitorica

last: Pascual


title: Oncostatin M neutralization in E. coli pneumonia

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Oncostatin M (OSM) is an IL-6 family cytokine that is necessary for neutrophil recruitment in pneumonia by inducing STAT3-dependent production of CXCL5. We used microarrays to identify additional pathways affected by OSM neutralization in the lungs during pneumonia.

overall_design: We sought to understand the effect of the cytokine OSM on whole lung RNA in the early stages of E. coli pneumonia. Mice were infected for 6 hours with E. coli plus control or neutralizing anti-OSM antibody.

first: Katrina

last: Traber


title: The Iqgap3-Ras axis drives stem cell proliferation in the stomach corpus during homeostasis and repair [SMART-SeqII]

first: Ying

last: Li

overall_design: Examinination of RNA expression profiles in 2 tdTomato+/EpCAM+ (IQ3pos) and 2 tdTomato-/EpCAM+ (IQ3neg) stomach cell fractions from Iqgap3-2A-tdTomato reporter mice.

first: Junichi

last: Matsuo

first: Daisuke

last: Douchi

first: Khine

last: Myint

first: NaingNaing

last: Mon

first: Akihiro

last: Yamamura

first: Kazuyoshi

last: Kohu

first: Dede

last: Heng

first: Sabirah

last: Chen

first: NurAstiana

last: Mawan

first: Napat

last: Nuttonmanit

first: Supriya

last: Srivastava

first: Shamaine

last: Ting

first: Nicole

last: Lee

first: HongKai

first: Makoto

last: Adachi

first: Atsushi

last: Tamura

first: Jinmiao

first: Henry

last: Yang

first: Ming

last: Teh

first: Jimmy

last: So

first: WeiPeng

last: Yong

first: Patrick

last: Tan

first: KhayGuan

last: Yeoh

first: Linda

last: Chuang

first: Sachiko

last: Tsukita

first: Yoshiaki

last: Ito


title: Systematic evaluation of chromosome conformation capture assays [Hi-C]

city: Worcester

first: Job

last: Dekker

address: 368 Plantation Street, AS5-1049

department: Program in Systems Biology

institute: University of Massachusetts Medical School

summary: Chromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of crosslinkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthening compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results in multiple cell states such as pluripotent and differentiated cells as well as cell cycle stages; Mitosis and G1. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using in situ Hi-C, Micro-C and Hi-C 3.0 for commonly cell lines in the 4D Nucleome Project.

overall_design: 96 Hi-C and Micro-C experiments replicates included. 424 raw files and 292 processed files are used for this paper.

first: Liyan

first: Johan

last: Gibcus

first: Nils

last: Krietenstein

first: Oliver

last: Rando


title: Systematic evaluation of chromosome conformation capture assays [1D]

overall_design: Cut&Run (Janssens et al. 2019), Cut&Tag (Kaya-Okur et al. 2019) and ATAC Seq (Buenrostro JD et al. 2013) Datasets

first: Steven

last: Henikoff

first: Rene

last: Maehr

first: Krishna

last: Mohan Parsi

first: Hui

last: Mao

first: Ryan

last: Geng

first: Marlies

last: Oomen


title: Requisite chromatin remodeling for myeloid and erythroid lineage differentiation from erythromyeloid progenitors

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: The mammalian SWI/SNF chromatin-remodeling BAF (BRG1/BRM associated factor) complex plays an essential role in developmental and pathological processes. We show that the deletion of Baf155 encoding a subunit of BAF complex in the Tie2(+) lineage (Baf155 CKO) leads to defects in the yolk sac myeloid and definitive erythroid (EryD) lineage differentiation from erythromyeloid progenitors (EMPs) and embryonic lethality. Baf155 knock-down in EMP was sufficient to block myeloid and EryD differentiation. Chromatin of the myeloid gene loci in Baf155 CKO EMPs was largely inaccessible and was enriched mostly by the ETS binding motif. BAF155 interacted with PU.1 and was recruited to the PU.1 in target gene loci together with p300 and KDM6a. Treatment of Baf155 CKO embryos with GSK126, an inhibitor of the H3K27me2/3 methyltransferase EZH2, rescued myeloid lineage gene expression. These studies uncover the indispensable BAF mediated chromatin remodeling of the myeloid gene loci at the EMP stage.

overall_design:
Droplet-based 5′ end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from mouse yolk sac and libraries were prepared using Chromium 10x Genomics library construction. The generated scRNAseq libraries were sequenced using HiSeq2500 sequencers.
Equal numbers of mouse E9.5 and E10.5 per genotypes were mixed and dissociated.  Dead cells and Ter119+ cells were excluded by sorting to enrich live and non-erythroid cells that  proceed to sequence.

first: Jun

last: Wu

first: Karen

last: Krchma

first: Hyung

last: Lee

first: Sairam

last: Prabhakar

first: Xiaoli

last: Wang

first: Haiyong

last: Zhao

first: Xiaoyun

last: Xing

first: Rho

last: Seong

first: Daved

last: Fremont

first: Ting

first: Kyunghee

last: Choi


title: Ribosome profiling analysis of aging human skeletal muscle (Ribo-Seq)

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: With advancing age, human muscle loses strength and function, but the molecular causes of these losses are unknown. Skeletal muscle shows an age-dependent decline in the levels of different proteins, but whether such decline is associated with reduced translation has not been studied. To address this gap of knowledge, we used the technique of ribosome profiling to study translation in muscle from middle-aged and old individuals. Using ribosome occupancy as a measure of translation status, several mRNAs showed differential translation with age. Older age was associated with lower translation of myosin and titin isoforms and more broadly with the translation of proteins involved in oxidative phosphorylation encoded by the mitochondrial genome. Based on our findings, we propose that mitochondrial proteins are less translated in old skeletal muscle.

overall_design: A 6-mm Bergström biopsy of 200-400 mg of vastus lateralis skeletal muscle from each of three middle-aged and two old individuals were analyzed  by ribosome profiling.

first: Ravi

last: Tharakan

first: Ceereena

last: Ubaida-Mohien

first: Yulan

last: Piao

first: Myriam

last: Gorospe

first: Luigi

last: Ferrucci


title: Systematic evaluation of chromosome conformation capture assays

first: Job

last: Dekker

first: Liyan

last: Yang

first: Johan

last: Gibcus

first: Nils

last: Krietenstein

first: Oliver

last: Rando


title: Ribosome profiling analysis of aging human skeletal muscle (RNA-Seq)

overall_design: A 6-mm Bergström biopsy of 200-400 mg of vastus lateralis skeletal muscle from each of three middle-aged and two old individuals were analyzed  by paired-end RNAseq.


title: Transcriptome analysis of developmental stages of cocoa pod borer, Conopomorpha cramerella: A polyphagous insect pest of economic importance in Southeast Asia.

city: Kota Kinabalu

first: Chia

middle: Lock

last: Tan

state: Sabah

address: Zon Komersial 1, Taman Perindustrian Kota Kinabalu Selatan, Jalan Norowot, Kota Kinabalu, Sabah, Malaysia

country: Malaysia

institute: Lembaga Koko Malaysia

summary:
Objective: To provide genetic resources for future research on developing RNAi as a strategy for management of this pest
Methods: We sequenced the transcriptome of C. cramerella representing the three stages of development, larva, pupa and adult moth using Illumina NovaSeq6000.  Transcriptome assembly was performed by Trinity for all the samples.
Results: A total number of 147,356,088 high quality reads were obtained.  Of these, 285,882 contigs were assembled.  The mean contig size was 374 bp.  Additionally, we identified a number of genes that are involved in reproduction and development such as genes involved in general function processes in the insect.  Genes found to be involved in reproduction such as porin, dsx, bol and fruitless were associated with sex determination, spermatogenesis and pheromone binding.
Conclusions: The transcriptomes data would be a valuable genetic resource for identification of genes in C. cramerella and the study will provide putative targets for RNAi pest control.

overall_design: Transcriptome analysis of three developmental stages of cocoa pod borer, Conopomorpha cramerella  were done by deep sequencing using Illumina NovaSeq6000.  Transcriptome assembly was performed by Trinity for all the samples. Protein coding sequence (CDS) was extracted from the reconstructed transcripts by TransDecoder.  Subsequently, BlastX and InterProScan were applied for homology search to make a prediction of the function of CDS in unigene.

first: Rosmin

last: Kasran

first: Wei

middle: W

last: Lee

first: Wai

last: Leong


title: Ribosome profiling analysis of aging human skeletal muscle


title: Canine osteosarcoma tissues vs. normal bone

city: Toronto

first: Jinchang

last: Lu

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre, University of Toronto

type: Genome variation profiling by genome tiling array

summary: Leveraging the conserved cancer genomes across mammals has the potential to transform driver gene discovery in orphan cancers. Here, we combine cross-species genomics with validation across human-dog-mouse systems to uncover a new osteosarcoma driver genes. This widely applicable cross-species approach serves as a platform to expedite search of cancer drivers in rare human malignancies offering new targets for cancer therapy.

overall_design: Nine tumor samples compared with matched normal tissues

first: Yang

last: Shao

first: Geoffrey

last: Wood

first: Rama

last: Khokha


title: Canine osteosarcoma tissues with DLG2 deletion vs. DLG2 wild type

summary: Microarrays was performed in 7 aCGH-matched canine primary tumors (4 DLG2 deleted, 3 DLG2 wild type) to investigate the gene expression profiles associated with DLG2 deletion in canine osteosarcoma.

overall_design: 4 DLG2 deletion vs. 3 DLG2 wild type


title: Epigenome‑wide association study on asthma and chronic obstructive pulmonary disease overlap reveals aberrant DNA methylations related to clinical phenotypes

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary:
Genome wide DNA methylation profiling of Chronic Obstructive Pulmonary Disease (COPD) patients and healthy subjects. The Illumina Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across in peripheral blood mononuclear cell samples.
Samples included 6 normal subjects and 12 COPD patients among which 3 of them have 2nd samples from follow-up examination.

overall_design: Bisulphite converted DNA from the 21 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip

first: Yung-Che

first: Ting-Wen


title: Analysis of THP-1 cell transcriptome changes induced by Phenylpyruvate, 4-Hydroxyphenylpyruvate and Indole-3-pyruvate

status: Public on Mar 07 2021

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

summary: We analyzed the mRNA changes iduced by the alpha keto acids Phenylpyruvate (PP), 4-Hydroxyphenylpyruvate (4HPP) or Indole-3-pyruvate (I3P) in THP-1 cells.

overall_design: mRNA sequencing of THP-1 cells treated with 200 µM Phenylpyruvate, 4-Hydroxyphenylpyruvate and Indole-3-pyruvate

first: Leonie

last: Zeitler

first: Rinho

last: Kim

first: Peter

last: Murray


title: miRNA expression during BMSCs from human jaw in Type 2 diabetics.

status: Public on Mar 06 2021

city: Beijing

first: LIngxiao

last: Wang

address: Tian Tan Xi Li No.4

institute: School of Stomology, Capital Medical University

summary: The association between T2 DM and BMSCs osteogenic differentiation has been documented in experimental settings. We examine miRNA expression specific for BMSCs from human jaw in Type 2 diabetics.

overall_design: 3 Type 2 diabetes (T2 DM) and 3 non-T2DM were enrolled. All basic information, including age, sex, general health condition, DM type, implant system and implant position, was matched to avoid the influence of other factors. According to the ICSI (Institute for Clinical Systems Improvement) guideline for T2DM in adults, the glycemic control standard for T2DM in this study was HbA1c less than 8%. The match for each T2DM patient was completed immediately after the implant surgery. Implant sites were left to heal for at least three months after tooth extraction. Subjects with implants inserted with guided bone regeneration were excluded from the study. Patients with contraindications for implant surgery, such as cardiovascular disorders, renal diseases or uncontrolled periodontitis, were excluded. The STROBE (Strengthening the Reporting of Observational studies in Epidemiology) guidelines were followed to ensure the rigor of our study. Bone chips were harvested during implant socket preparation and were reserved in phosphate-buffered saline (Gibco, Grand Island, NY, USA) with antibiotics (10,000 U/ml penicillin and 10 mg/ml streptomycin; Gibco). After being centrifuged at 1,100 rpm, the bone chips were resuspended in mesenchymal stem cell medium (MSCM; ScienCell, Carlsbad, CA, USA), then seeded in dishes, and cultured in a humidified cell incubator with 5% CO2 at 37°C without movement for seven days. A 70-μm pore-size strainer (Falcon, BD Labware, Wilmington, DE, USA) was used to obtain single-cell suspensions, which were then cultured in MSCM. The medium was replaced every three days. The fourth-passage BSCMs were used for subsequent experiments.

first: Lingxiao

first: Jun

last: Li

first: Jian

first: Changying

last: Liu

first: Chao

last: Liang

first: Xiao

last: Lin

first: Yafang

last: Jiang


title: The mitochondrial-encoded MOTS-c prevents pancreatic islet destruction in autoimmune diabetes

city: Seoul

first: ByungSoo

last: Kong

address: Yeongundong 128

country: South Korea

institute: Seoul National University Hospital

summary: Mitochondria are principal metabolic organelles that are increasingly unveiled as immune regulators. However, it is currently not known whether mitochondrial-encoded peptides modulate T cells to induce changes in phenotype and function. Here, we found that MOTS-c prevented autoimmune β-cell destruction via phenotypical and functional changes of T cells in NOD mice, a type 1 diabetes (T1D) animal model. MOTS-c ameliorated the development of hyperglycemia and reduced islet-infiltrating immune cells. Furthermore, adoptive transfer of T cells from MOTS-c-treated NOD mice significantly decreased the incidence of diabetes in NOD-SCID mice. Metabolic and genomic analysis revealed that MOTS-c modulated T cell phenotype and function by regulating TCR/mTORC1 pathway. We observed that T1D patients had a lower serum MOTS-c level than healthy controls. Furthermore, MOTS-c reduced T cell activation by alleviating T cells from the glycolytic stress in T1D patients suggesting a potential therapeutic implication. Our findings indicate that the MOTS-c acts as a regulator of T cell phenotype and function in autoimmune diabetes.

overall_design: NOD mice were treated with either vehicle (non-specific scrambled MOTS-c peptide) or MOTS-c (0.5 mg/kg/day; IP) daily in the morning up to 18 or 30 weeks of age. Random blood glucose (RBG) level and body weights were measured in the morning twice every week for all types of mice (Accu-Chek).

first: Byung

middle: S

first: Young

last: Cho

first: Chang

last: Lee

first: See

last: Min


title: Super Enhancer Regulation of Cytokine-Induced Chemokine Production in Alcoholic Hepatitis [ChIP-Seq 3]

city: Rochester

first: Aditya

last: Bhagwate

address: 200 1st Street SW

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Super enhancer in liver propagates inflammatory signaling by super enhancer-mediatedinducing chemokine expression and is the therapeutic potential of BET inhibition in Alcoholic hepatitis(AH) treatment.

overall_design: For human liver sinusoid endothelial cell (LSEC) ChIP-Seq analyses, control and TNF treated LSECs are collected to perfrom ChIPseq with anti H3k27ac and NFKB antibodies respectively.

first: Vijay

last: Shah

first: Sheng

last: Cao

first: Mengfei


title: small RNA sequencing from leaf of Arabidopsis to identify tsRNA

city: Guangzhou

first: Zhicheng

last: Dong

state: Guangdong

address: 230 Wai Huan Xi Road,Guangzhou Higher Education Mega Center

department: School of Life Sciences

institute: Guangzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: tsRNA is newly found small non-coding RNA with important biological function. However, the knowlede of diversity, biogeneis and function of tsRNA in plant is still lacking. Here, we selected 10-60 nt small RNA for high-throughput sequencing and uncovered the diversity,biogenesis and potentical function of tsRNA in Arabidopsis.

overall_design: Col-0, dcl1-7 and PTH-AGO1 transgenic plants were grown under long-day (16h light) condition at 23°C. Leaves of four week old plants were harvested 3 h after wounding, or as control leaves without wounding. One gram of wild type (WT-IP) or PTH-AGO1 (AGO1-IP) transgenic plant leaves was ground in liquid nitrogen and dissolved in 5 mL lysis buffer (50mM Tris-HCl at pH 7.5, 150 mM NaCl, 5 mM MgCl2, 0.5% NP-40, 5 mM DTT and protease inhibitor). After centrifugation, supernatants were incubated with IgG Sepharose 6 Fast Flow agarose beads (GE Healthcare) and rotated for 1 h at 4 °C. The beads were washed five times with lysis buffer. RNA in the immunoprecipitates was recovered with TRIzol reagent (Ambion). Total RNA or IP RNA was fractionated by electrophoresis. RNA from 10 to 60 nt was sliced and recovered. The purified small RNA was subjected to adapter ligation, reverse transcription, PCR amplification with NEXTflex Small RNA Sequencing Kit (Bioo Scientific), and the resulting libraries sent for deep sequencing by Illumina HiSeq2000. For total RNA from wild type and dcl1-7 plants, small RNA libraries were made independently from two biological replicates. WT-IP, AGO1-IP, and its input libraries were made independently from three biological replicates.

first: Lei

last: Zhu

first: Xiaobin

last: Liug


title: De novo Transcriptome Assembly of the Fresh-cut White Husk of Juglans cathayensis

city: Zhengzhou

first: Gao-Pu

state: Henan

address: No. 3, Weiwu Road

department: Non-timber Forest Research and Development Center

institute: Chinese Academy of Forestry

summary: In the present study, we found a new walnut germplasm from wild Juglans cathayensis population, which presented white husk that did not brown. We compared the transcriptome between the fresh-cut browning (control) and white husks of the Chinese walnut using Illumina HiSeq 4000 platform

overall_design: Seq-RNA of  2 different fresh-cut colorJuglans cathayensis varieties to provide insight into enzymatic browning

first: Gaopu

first: Shulin

last: Zhang


title: Anti-aging effects of Vicatia thibetica de Boiss root extract on Caenorhabditis elegans and doxorubicin-induced mice via promoting collagen and stress resistance

city: Shanghai

first: Liu

last: Wenwen

address: 130 Meilong Road

institute: East China University of Science and Technology

summary: The root of Vicatia thibetica de Boiss is a Chinese herb medicine with homology of medicine and food. We first report that HLB01 (the extract of Vicatia thibetica de Boiss root) extends lifespan and promotes healthy parameters in Caenorhabditis elegans (C. elegans). In doxorubicin-induced senescent mice, HLB01 counteracts senescence associated biomarkers significantly, including AST, ALT, p21 and γH2AX. Interestingly, HLB01 promotes the level of collagen in C. elegans and mammalian cell systemically, which might be one of the essential factors to exert anti-aging effects of HLB01. In addition, HLB01 can scavenge free radical to perform antioxidant ability. Lifespan extension of HLB01 also dependent on DAF-16 and HSF-1 to perform oxidative stress resistance and heat stress resistance. Taken together, these data indicate that HLB01 extends lifespan and healthspan of C. elegans, resists doxorubicin‐induced senescence in mice via collagen promoting, antioxidant and stress resistance.

overall_design: Examination of HLB01-treated and control group in C. elegans by RNA-seq, in triplicate

first: Xia

last: Conglong

first: Hu

last: Zelan

first: Li

last: Jian


title: RNA-seq of PTEN knockdown in GL261 cells

city: Shenzhen

first: Ping

last: Li

address: Gongchang Road

department: School of Medicine

institute: Sun Yat-sen University

summary: PTEN deficiency is known to lead to tumor-intrinsic resistance to immune checkpoint blockade (ICB) treatment, especially in glioblastoma (GBM). We used RNA sequence to study the global gene expression and identified differentially expressed genes in PTEN knockdown GL261 cells, aiming to identify genes and pathways that are regulated by PTEN.

overall_design: PTEN knockdown GL261 cells were generated by shRNA using lentivirus transfecting. The cells were selected with puromycin for 10 days to establish stably expressing cell lines (GL261-shNC and GL262 -shPTEN). The samples used in the RNA sequence analysis were in triplicates.

first: Fan

last: Xing


title: Next Generation Sequencing facilitates the identification of differential gene expression between MNT-1 expressing control or shABCB6.

city: WUHAN

first: Qiuyun

last: She

address: No.13, Qingnian Road

institute: Huazhong University of Science and Technology

summary: The goal of this study is to investigate the effect of ABCB6 inhibition on the transcriptome level of melanoma cell line MNT-1. We performed next-generation sequencing (NGS) on both ABCB6 depleted MNT-1 cells (shABCB6) and unknocked control cells (CTRL). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2500 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest the key role of ABCB6 in modulating melanocyte development.

overall_design: Differential gene expression between MNT-1 cells expressing shcontrol or shABCB6

first: Yunhua

last: Deng


title: Healing human gingiva

city: Columbus

first: Dimitris

last: Tatakis

state: OH

address: 305 W. 12th ave

department: Periodontology

institute: The Ohio State University

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

overall_design: Refer to individual Series


title: The mitochondrial protease LonP1 promotes proteasome inhibitor resistance in multiple myeloma.

city: Houston

first: Andre

last: Catic

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
Purpose: We report the NGS-derived transcriptome profiling (paired-end RNA-seq) following proteasome inhibition in the multiple myeloma cell line MM.1S.
Methods: MM.1S cells were treated for six hours with the synthetic proteasome inhibitor lactacystin or clinically-approved proteasome inhibitor bortezomib and RNA expression changes were quantified and compared to DMSO control-treated cells by RNA-sequencing.

overall_design: MM.1S myeloma cells were profiled for gene expression after 6h of growth in the presence or the absence of lactacystin (6µM) or bortezomib (60 nM), using Illumina HiSeq 2500 high-throughput sequencing system.

first: Laure

last: Maneix


title: RNAseq analysis of tissue and primary cell transcriptomes from wild type and Beclin 2 KO mice.

first: Motao

state: Texas

address: 6670 Bertner Ave

department: Center for Inflammation and Epigenetics

institute: Houston Methodist Research Institute

summary: Our study represents the first detailed analysis of WT vs Beclin 2 KO cell/tissue transcriptomes, with biologic replicates, generated by RNA-seq technology. RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: The mRNA profiles of primary bone marrow derived macrophages (stimulated by LPS for 3 hours), splenic T cells and B cells from 8-week old wild type (WT) and Beclin 2 KO mice were generated in duplicate using Illumina HiSeq. The mRNA profiles of tumor samples from Beclin 2 KO mice, and lymph nodes from both WT and Beclin 2 KO mice were also generated in duplicate.

first: Rongfu

last: Wang


title: Plant-derived soybean peroxidase stimulates osteoblast collagen biosynthesis and matrix mineralization

status: Public on Mar 05 2021

city: Adelaide

first: Vasilios

last: Panagopoulos

state: SA

address: North Terrace,

department: Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

summary: Bone defects arising from fractures or disease represent a significant problem for surgeons to manage and are a substantial economic burden on the healthcare economy. Recent advances in the development of biomaterial substitutes provides an attractive alternative to the current “gold standard” autologous bone grafting. Despite on-going research, we are yet to identify cost effective biocompatible, osteo-inductive factors that stimulate controlled, accelerated bone regeneration.We have recently reported that enzymes with peroxidase activity possess previously unrecognised roles in extracellular matrix biosynthesis, angiogenesis and osteoclastogenesis, which are essential processes in bone remodelling and repair.  Here, we report for the first time, that plant-derived soybean peroxidase (SBP) possesses pro-osteogenic ability by promoting collagen I biosynthesis and matrix mineralization of human osteoblasts in vitro. Mechanistically, SBP regulates osteogenic genes responsible for inflammation, extracellular matrix remodelling and ossification, which are necessary for normal bone healing. Furthermore, SBP was shown to have osteo-inductive properties, that when  combined with commercially available biphasic calcium phosphate (BCP) granules can accelerate bone repair in a critical size long bone defect ovine model. Micro-CT analysis showed that SBP when combined with commercially available biphasic calcium phosphate (BCP) granules significantly increased bone formation within the defects as early as  4 weeks compared to BCP alone. Histomorphometric assessment demonstrated accelerated bone formation prominent at the defect margins and surrounding individual BCP granules, with evidence of intramembranous ossification. These results highlight the capacity of SBP to be an effective regulator of osteoblastic function and may be beneficial as a new and cost effective osteo-inductive agent to accelerate repair of large bone defects.

overall_design: 2 samples with 3 replicates each: Human osteoblast cells stimulated with or without SBP for 12 days

first: Andreas

last: Evdokiou


title: Effect of Jmjd6 knockout on gene expression and mRNA splicing in Lin-Sca+Kit+ haematopoietic cells

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary University of London

summary: The 2-oxoglutarate dependent protein JMJD6 acts as a lysyl hydroxylase on specific residues of the splicing factor U2AF2.  To understand the molecular roles of JMJD6 in normal haematopoiesis and identify any role of JMJD6 in splicing, we performed RNA-sequencing on Lin-Sca1+Kit+ (LSK) haematopoietic stem and progenitor cells (HSPCs) derived from young mice.

overall_design: One sample per mouse was taken from 4 WT vs 4 KO mice.

first: Louie

middle: N

last: van de Lagemaat

first: Catarina

last: Sepulveda


title: Expression profiles of EMs-related infertility and tubal factor infertility granulosa cells revealed by RNA-seq

city: Xiamen

first: Junzui

address: Xiamen University

institute: Xiamen University

summary: Granulosa cells are essential to the growth, development, and maturation of oocytes and follicles. In patients with EMs-related infertility, follicle maturation disorders, poor oocyte quality may be closely related to GCs in the follicle. However, the molecular biological mechanism of GCs in EMs-related infertility has not been reported.  Therefore, we tried to explore the possible causes of EMs-related infertility through the study of ovarian GCs in patients with EMs-related infertility and tubal factor infertility.

overall_design: mRNA and lncRNA profiles of EMs-related infertility and tubal factor infertility granulosa cells

first: Rongfeng

last: Wu

first: Qionghua

last: Chen


title: Identification of intrinsically immunogenic small cell lung carcinoma (SCLC) subpopulations

city: Boston

first: Michael

last: Tolstorukov

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Identification of intrinsically immunogenic small cell lung carcinoma (SCLC) subpopulations [Cell line]

summary: SCLC is molecularly and immunologically heterogenous. Here, using transcriptional and epigenomic profiling of plastic SCLC states in human and mouse cell lines, and patient samples, we define the phenotype of a SCLC population marked by increased MHC Class I antigen presentation.

overall_design: Examination of paired transcriptome and H3K27Me3 in isogenic SCLC cell lines, and transcriptomes of MHC Class I high vs. low SCLC cell lines and patient samples

first: Navin

last: Mahadevan

first: David

last: Barbie


title: PRKN mutations disrupt mitochondrial biogenesis pathways in patient-derived neurons

city: Berlin

first: Malte

last: Spielmann

address: Ihnestraße 63

institute: Max Planck Institute for Molecular Genetics

summary: Mutations in the E3 ubiquitin ligase Parkin cause autosomal recessive Parkinson’s disease. In concert with PINK1, Parkin regulates the clearance of dysfunctional mitochondria via lysosomes. In response, new mitochondria are generated through an interplay of nuclear- and mitochondrial-encoded proteins. Mouse and overexpression models suggests that Parkin also influences these processes, both in the nuclear cascade and at the level of the mitochondrial genome. Additionally, Parkin has been shown to prevent mitochondrial membrane permeation, impeding the escape of mitochondrial DNA (mtDNA). In line with this, serum from Parkin mutation carriers showed higher levels of circulating cell-free mtDNA (ccf-mtDNA) and inflammatory cytokines – a result of the innate immune response - which can be triggered by cytosolic mtDNA. However, Parkin’s relationship with the mitochondrial genome and the mitogenesis pathway has not been explored in patient-derived neurons. To investigate this aspect of Parkin’s cellular function endogenously, we generated induced pluripotent stem cell (iPSC)-derived midbrain neurons from Parkin mutation carriers and healthy controls. In Parkin-deficient cells, several factors in the mitochondrial biogenesis pathway were significantly reduced, resulting in impaired mtDNA homeostasis - a phenomenon that was exacerbated in dopaminergic neurons. Moreover, in response to a lack of freely accessible NAD+, the energy sensor Sirtuin 1, which simultaneously controls mtDNA maintenance processes and mitophagy, was downregulated in Parkin-deficient neurons. However, while impaired lysosomal degradation of mitochondria was only detectable in oxidative conditions, biogenesis defects were already apparent in untreated patient neurons. This may suggest that mitophagy disruption occurs in response to acute stress. By contrast, the biogenesis pathway may be continually impaired in Parkin-associated Parkinson’s disease. Next, using a mutagenic stress model in combination with Parkin knockdown, we detected an increase in ccf-mtDNA and the cytosolic DNA sensor cGAS. To explore if ccf-mtDNA can act as damage-associated molecular pattern in the brain, we used postmortem tissue from a Parkin mutation carrier and performed single-cell RNA sequencing. In the midbrain lacking Parkin, we found a higher percentage of microglia along with an upregulation of proinflammatory cytokines in these cells. Together, our findings suggest a role for Parkin in the control of mitochondrial biogenesis and mtDNA maintenance, which protects midbrain neurons from neuroinflammation-induced degeneration. Future research in iPSC-derived neuron-microglia co-culture systems could aim at developing PD treatment approaches that target the neuronal release or microglial uptake of ccf-mtDNA.

overall_design: Single-cell transcriptome of postmortem midbrain of one Parkin mutation carrier and two control individuals (GSM4774937 and GSM4774938)

first: Kobi

last: Wasner

first: Semra

last: Smajic

first: Cesar

last: Prada-Medina

first: Christopher

middle: M

last: Morris

first: Anne

last: Grünewald


title: Neural lineage cells derived from dental pulp stem cells generate Schwann cells via oligodendrocyte progenitor cells in peripheral nerve regeneration

city: Tsukuba

first: Shohei

last: Takaoka

state: 茨城県

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

summary: The current understanding is that Schwann cell transplantation is ideal strategy for peripheral nerve regeneration instead of autograft. It is difficult to obtain the required amount of Schwann cells which are best transplant condition, and central nervous cells have been gained attention in recent years, but its regenerative mechanism remain unknown. Neural stem/progenitor cells (NSPC) can generate various type of neural lineage cells (NLCs), and NSPCs derived from pluripotent stem cells are promising cells for cell therapy for neurodegenerative diseases. However, more safe and accessible cell source of NSPCs are required. In this study, we aim to provide NLCs derived from human dental pulp stem cells (DPSCs), and reveal the mechanism involved in regeneration after NLCs transplantation into peripheral nerve defect. Here, characterization of NLCs, paracrine effects for endothelial cells and Schwann cells, in xenotransplant for rat 10mm sciatic nerve defect, the differentiation, the survival, and outcome of nerve regeneration were investigated. Induced NLCs consisted of neuronal lineage cells, astrocyte lineage cells, oligodendrocyte lineage cells, and neural crest lineage cells. Considering retrospectively, NLCs were possible derived from NSPCs. Microarray analysis revealed neural markers of primary embryological development were up-regulated in induced NLCs compared to DPSCs. Moreover, NLCs enhanced the activity of endothelial cells and Schwann cells by paracrine effects in vitro. Two weeks after transplantation, many transplanted NLCs differentiated into platelet-derived growth factor receptor alpha (PDGFRa) + oligodendrocyte progenitor cells (OPCs), and PDGFRa+/p75 neurotrophin receptor + Schwann cells derived from OPCs were observed. Twelve weeks after transplantation, NLCs promoted functional repair of peripheral nerve. A few human Schwann cells survived, but did not myelinate axon. These findings suggest that some of mechanism promoting for peripheral nerve regeneration by transplanted NLCs. Transplantation of NLCs derived from DPSCs into partial peripheral nerve defect may be widely used for further experiments.

overall_design: Expression profiling of dental pulp stem cells and neural lineage cells derived from dental pulp stem cells.

first: Fumihiko

last: Uchida

first: Hiroshi

last: Ishikawa

first: Junko

last: Toyomura

first: Akihiro

last: Ohyama

first: Miho

last: Watanabe

first: Hideaki

last: Matsumura

first: Aiki

last: Marushima

first: Seiichiro

last: Iiuzmi

first: Satoshi

last: Fukuzawa

first: Naomi

last: Kannno

first: Kenji

last: Yamagata

first: Toru

last: Yanagawa

first: Hiroki

last: Bukawa


title: Validation of Differentially Expressed Immune Biomarkers in Latent and Active Tuberculosis by Real-Time PCR

city: Salisbury

first: Karen

middle: Elizabeth

last: Kempsell

state: Wiltshire

address: Porton Down

department: Science Group

institute: UK Health Security Agency

summary:
72 candidate biomarkers evaluated for TB diagnosis using mRNA purified from whole blood of Active TB patients recruited in the UK and India, LTB and two groups of controls from the UK (i) from a low incidence region and (ii) individuals variably domiciled in the UK and India.
Tuberculosis (TB) remains a major global threat and diagnosis of active TB ((ATB) both  extra-pulmonary (EPTB) and pulmonary (PTB)) and latent TB (LTBI) remains challenging,  particularly in high-burden countries which still rely heavily on conventional methods.  Although molecular diagnostic methods are available, e.g., Cepheid GeneXpert, they are  not universally available in all high TB burden countries. There is intense focus on immune  biomarkers for use in TB diagnosis, which could provide alternative low-cost, rapid  diagnostic solutions. In our previous gene expression studies, we identified peripheral  blood leukocyte (PBL) mRNA biomarkers in a non-human primate TB aerosol-challenge  model. Here, we describe a study to further validate select mRNA biomarkers from this  prior study in new cohorts of patients and controls, as a prerequisite for further  development. PBL mRNA was purified from ATB patients recruited in the UK and India,  LTBI and two groups of controls from the UK (i) a low TB incidence region (CNTRLA) and  (ii) individuals variably-domiciled in the UK and Asia ((CNTRLB), the latter TB high  incidence regions). Seventy-two mRNA biomarker gene targets were analyzed by  qPCR using the Roche Lightcycler 480 qPCR platform and data analyzed using  GeneSpring™ 14.9 bioinformatics software. Differential expression of fifty-three  biomarkers was confirmed between MTB infected, LTBI groups and controls,  seventeen of which were significant using analysis of variance (ANOVA): CALCOCO2,  CD52, GBP1, GBP2, GBP5, HLA-B, IFIT3, IFITM3, IRF1, LOC400759 (GBP1P1),  NCF1C, PF4V1, SAMD9L, S100A11, TAF10, TAPBP, and TRIM25. These were  analyzed using receiver operating characteristic (ROC) curve analysis. Single  biomarkers and biomarker combinations were further assessed using simple arithmetic  algorithms. Minimal combination biomarker panels were delineated for primary diagnosis of ATB (both PTB and EPTB), LTBI and identifying LTBI individuals at high risk of  progression which showed good performance characteristics. These were assessed for  suitability for progression against the standards for new Tuberculosis diagnostic tests  delineated in the published World Health Organization (WHO) technology product  profiles (TPPs)

overall_design: RNA was extracted from blood collected in Paxgene and Tempus tubes using PAXgene Blood RNA and Tempus spin RNA kits following manufacturer's instructions. cDNA obtained using First Strand cDNA sytthesis kit following manifacturer's instructions. Analysis performed in duplicate using Roche Lightcycler 480 platform and Roche Real-Time Ready qPCR assays and TagMan PCR Prove Master mix using the following cycling conditions: 95C for 10 minutes followed by 45 cycles of 95C for 10 seconds and 60C for 30seconds, 72C for 1 second. Cooling to 40C for 10 seconds.


title: A neuroprotective locus modulates ischemic stroke infarction independent of collateral vessel anatomy

city: Durham

first: Han Kyu

last: Lee

state: NC

address: 213 Research Dr. PO box #3175

institute: Duke University Medical Center

summary: The strains, C57BL6/J, C3H/HeJ, and WSB/EiJ, show a similar collateral vessel anatomy but differ infarct volume after ischemic stroke induction. To identify a gene(s) exhibiting differential gene expression, we performed RNA seq experiment within these mouse strains.

overall_design: Strain-specific differential expressed genes were examined from adult brain cortex of the strains ( 8-12 weeks old).

first: Han

middle: K

first: Sarah

last: Wetzel-Strong

first: David

middle: L

last: Aylor

first: Douglas

last: Marchuk


title: Bromodomain testis-specific protein BRDT directs ΔNp63 function and super enhancer activity in a distinct subset of esophageal squamous cell carcinomas [HiChIP]

first: Xin

last: Wang

address: 1068, Xueyuan Road

department: Institute of Synthetic Biology

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

summary: Using an unbiased method, we found a testis-specific epigenetic reader protein BRDT to be expressed and functional active in a significant portion of ESCC patients. Mechanistically, BRDT co-localizes with ΔNp63, a defining transcription factor for squamous subtype, at selected super-enhancers to regulate ΔNp63-dependent transcription programs to promote cell migration. Pharmacologically depleting BRDT resembles the effects of knock-down of BRDT, thus providing a promising clinical approach for precision medicine in a subset of ESCC.

overall_design: Examination of H3K27ac-associated chromatin interaction in ESCC.

first: Steven

last: Johnsen

first: Ana

middle: P

last: Kutschat


title: Stable DNMT3L Overexpression in SH-SY5Y Neurons Recreates a Facet of the Genome-Wide Down Syndrome DNA Methylation Signature

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

type: Methylation profiling by high throughput sequencing

summary:
Background: Down syndrome (DS) is characterized by a genome-wide profile of differential DNA methylation that is skewed towards hypermethylation in most tissues, including brain, and includes pan-tissue differential methylation. The molecular mechanisms involve the overexpression of genes related to DNA methylation on chromosome 21. Here, we stably overexpressed the chromosome 21 gene DNA methyltransferase 3L (DNMT3L) in the human SH-SY5Y neuroblastoma cell line and assayed DNA methylation at over 26 million CpGs by whole genome bisulfite sequencing (WGBS) at three different developmental phases (undifferentiated, differentiating, and differentiated).
Results: DNMT3L overexpression resulted in global CpG and CpG island hypermethylation as well as thousands of differentially methylated regions (DMRs). The DNMT3L DMRs were skewed towards hypermethylation and mapped to genes involved in neurodevelopment, cellular signaling, and gene regulation. Consensus DNMT3L DMRs showed that cell lines clustered by genotype and then differentiation phase, demonstrating sets of common genes affected across neuronal differentiation. The hypermethylated DNMT3L DMRs from all pairwise comparisons were enriched for regions of bivalent chromatin marked by H3K4me3 as well as differentially methylated sites from previous DS studies of diverse tissues. In contrast, the hypomethylated DNMT3L DMRs from all pairwise comparisons displayed a tissue-specific profile enriched for regions of heterochromatin marked by H3K9me3 during embryonic development.
Conclusions: Taken together, these results support a mechanism whereby regions of bivalent chromatin that lose H3K4me3 during neuronal differentiation are targeted by excess DNMT3L and become hypermethylated. Overall, these findings demonstrate that DNMT3L overexpression during neurodevelopment recreates a facet of the genome-wide DS DNA methylation signature by targeting known genes and gene clusters that display pan-tissue differential methylation in DS.

overall_design: DNA methyltransferase 3L (DNMT3L) was stably overexpressed in the human SH-SY5Y neuroblastoma cell line and DNA methylation was assayed by whole genome bisulfite sequencing (WGBS) three different developmental phases (undifferentiated, differentiating, and differentiated) in cells overxpressing DNMT3L+GFP or only GFP.

first: Jose

last: Gomez

first: Janine

last: LaSalle


title: Bromodomain testis-specific protein BRDT directs ΔNp63 function and super enhancer activity in a distinct subset of esophageal squamous cell carcinomas


title: The memory B cell response to influenza vaccination is impaired in older persons

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Influenza imparts an age-related increase in mortality and morbidity. The most effective countermeasure is vaccination; however, vaccines offer modest protection in older adults. To investigate how ageing impacts the memory B cell response we tracked haemagglutinin specific B cells by indexed flow sorting and single cell RNA sequencing in twenty healthy adults administered the trivalent influenza vaccine. We found age-related skewing in the memory B cell compartment six weeks after vaccination, with younger adults developing haemagglutinin specific memory B cells with an FCRL5+ “atypical” phenotype, showing evidence of somatic hypermutation and positive selection, which happened to a lesser extent in older persons. We confirmed the germinal center ancestry of these FCRL5+ “atypical” memory B cells using scRNASeq from fine needle aspirates of influenza responding human lymph nodes and paired blood samples. Together, this study shows that the aged human germinal center reaction and memory B cell response following vaccination is defective.

overall_design: Plate based SMART-Seq single cell RNA sequencing of index flow sorted haemagglutinin specific B cells on days 0 and 42 after trivalent influenza vaccination, from 22-36 year old, or 67-86 year old healthy adults

first: Edward

last: Carr

first: Danika

last: Hill

first: Michelle

middle: A

last: Linterman


title: Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis

city: Stanford

last: Liu

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

summary: Adenosine-to-inosine (A-to-I) RNA editing catalyzed by ADAR enzymes occurs in double-stranded RNAs. Despite a compelling need towards predictive understanding of natural and engineered editing events, how the RNA sequence and structure determine the editing efficiency and specificity (i.e., cis-regulation) is poorly understood. We apply a CRISPR/Cas9-mediated saturation mutagenesis approach to generate libraries of mutations near three natural editing substrates at their endogenous genomic loci. We use machine learning to integrate diverse RNA sequence and structure features to model editing levels measured by deep sequencing. We confirm known features and identify new features important for RNA editing. Training and testing XGBoost algorithm within the same substrate yield models that explain 68 to 86 percent of substrate-specific variation in editing levels. However, the models do not generalize across substrates, suggesting complex and context-dependent regulation patterns. Our integrative approach can be applied to larger scale experiments towards deciphering the RNA editing code.

overall_design: To study the effects of mutation on the RNA structure, we used chemical probing of in intro transcribed RNA to infer secondary structure of RNA libraries. Each RNA is barcoded with unique sequences.  Libraries of RNA with designed mutations were made by in vitro transcribed using T7 RNA polymerase and DNA templates. RNA were purified by AMpure RNA beads before chemical treatmentment. RT-PCR reaction are followed to construct sequencing library to count chemically induced mutation rate (called reactivity) to infer the secodnary structure of RNA.

first: Liu

last: Xin

first: Li

last: Jin Billy


title: Delayed colostrum feeding influences ileum transcriptome profile in neonatal calves

city: Edmonton

first: Yang

last: Song

state: Alberta

department: AFNS

institute: University of Alberta

summary: Our study would like to explore the different colostrum feeding time treatment, as well as the influence of host-microbial interaction on transcriptome profile and enriched functions of the two day old dairy calves.

overall_design: RNA sequencing based transcriptome analysis was conducted for ileum tissues collected from twenty-seven male Holstein calves which were randomly assigned to one of three colostrum feeding strategies (immediately after birth (TRT0h); 6 h after birth (TRT6h); 12 h after birth (TRT12h))

first: Michael

last: Steele

first: Le

last: Guan

first: Zhixiong

last: He


title: Kaiso, a critical regulator of spermatogenesis

city: Seoul

first: Man-Wook

last: Hur

address: 134 ShinChon-Dong, SeoDaeMoon-Ku

department: Department of Biochemistry and Molecular Biology and the Institute of Genetic Sciences

institute: Yonsei University School of Medicine

summary: Spermatogenesis is a highly coordinated process by which diploid spermatogonia (2n) differentiate into mature haploid (1n) spermatozoa in the seminiferous epithelium. Here, we show that Kaiso (Zbtb33) is critical to spermatogenesis, via binding to KBEs (Kaiso-binding elements) in the 5’ upstream regulatory regions of Gdnf and Plzf to repress their expression, promoting the differentiation of spermatogonial stem cells (SSCs). In Kaiso-/Y mice, Plzf and Gdnf were derepressed in both SSCs and Sertoli cells, explaining the increased number of SSCs observed in these abnormal mice. We also found that Bcl6, an antiapoptotic spermatocyte survival factor, represses the Crem pathway genes. In particular, Kaiso represses Bcl6 by binding two KBEs in the Bcl6 5’ upstream regulatory region  and first intron, thus indirectly derepressing Crem and Crem pathway genes. In Kaiso-/Y mice, Bcl6 is overexpressed, and these mice lack differentiated post-mitotic cells and consequently, are infertile. Interestingly, epigenetic “marks,” histone post-translational modifications such as lysine methylation, within histone H3 (H3K27me3), of the promoters of Kaiso target genes, were found transgenerationally heritable, prior to “wash out” during generations 1-3 in Kaiso-/Y mice, thus impacting Kaiso target gene expression. Consequently, Kaiso, by repressing Plzf, Gdnf, and Bcl6, indirectly upregulates Crem, and thereby plays a critical role not only in SSC differentiation, but also in post-meiotic events during spermatogenesis.

overall_design: Methylated genomic DNA was isolated from fragmented whole genomic DNA using the methyl-CpG binding domain of mouse MBD2 protein coupled to paramagnetic Dynabeads® labeled with M-280 streptavidin, via a biotin linker. Isolated Methylated DNA sequence was analyzed by NGS technology.

first: Dong-In

last: Koh

first: Hyuk

first: Min-Young

last: Kim

first: Haemin

last: An

first: Ran

last: Lee

first: Won-Young

first: Seo-Hyeon

last: Choi

first: Sun

first: Kyung-Sup


title: Gene Expression Profiling of Estrogen Signaling in Colon Cancer Cell Line [CRC Project_addendum]

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

institute: KTH Royal Institute of Technology

summary: We studied the transcriptional effect of estrogen, G1, and ICI in two colon cancer cell lines SW620 and SW480

overall_design: Cells were treated with estradiol (E2), G1 and ICI for 24 hrs with/without ERB transduction

first: Fahmi

last: Mesmar

first: Linnea

last: Pettersson


title: Role of Hif1alpha in cytokine-induced macrophage gene expression

city: Cleveland

first: Ernest

last: Chan

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Hypoxia-inducible factor 1-alpha (HIF1a) is a basic helix-loop-helix PAS domain-containing protein, and is considered as the master transcriptional regulator of cellular response to hypoxia and inflammatory stimuli. Studies over the year have demonstrated that HIF1a play a critical role in innate immune cell response to infection and injury. Here we isolated bone marrow of 3 mice per group (Lyz2cre and Lyz2cre:HIF1aFl/Fl) and differentiated into macrophages by culturing them in M-CSF containing media. These cells were stimulated with 100ng/ml LPS, 10ng/ml IFNgamma, 10ng/ml IL4 or 10ng/ml IL10 for 18 hours. Total RNA was isolated and subjected to RNAseq analyses.

overall_design: Bone marrow of 3 mice per group (Lyz2cre and Lyz2cre:HIF1aFl/Fl) and differentiated into macrophages by culturing them in M-CSF containing media. These cells were stimulated with 100ng/ml LPS, 10ng/ml IFNgamma, 10ng/ml IL4 or 10ng/ml IL10 for 18 hours. Total RNA was isolated and subjected to RNAseq analyses.

first: Ganapati

middle: H

last: Mahabeleshwar

first: E


title: Identification of intrinsically immunogenic small cell lung carcinoma (SCLC) subpopulations [patient]

first: Michael

last: Tolstorukov

state: MA

first: Navin

last: Mahadevan

first: David

last: Barbie


title: RNA-Seq analysis, transcriptome assembly and gene expression profile analysis for vascular smooth muscle cells with up- or downregulation of CKLF1

city: Nanchang

first: Yanyu

last: Dean

address: Lushanzhong888, Changbei district

institute: Jiangxi Agricultural University

summary: To understand the role of Cklf1 in the proliferation of vascular smooth muscle cells (VSMC), we quantified the whole genome transcriptomes of VSMC that were treated by Cklf1 adenovirus (n=3) or control (n=3) for 24 h using RNA-seq. In total, we obtained over 82 million clean reads from each library after trimming adaptor sequences, low quality reads and multiple mapped reads. The clean reads were mapped to 29330 genes annotated in the rat reference genome (Rattus_norvegicus 6.0). We then identified differentially expressed genes (DEGs) between Cklf1-associated adenovirus and controls by comparing RNA-Seq data between the two groups. A total of 238 DEGs for Ad-GFP vs. Ad-Cklf1 and 468 DEGs for shRNA Scramble vs. shRNA Cklf1 were defined using the thresholds of FDR ≤ 0.05, difference ratio of FPKM (fragments per kilobase of exon model per million mapped fragments) ≥ 2 and diverge probability ≥ 0.8. The increased CKLF1 resulted in 34 up-regulated and 204 down-regulated genes while knockdown of Cklf1 led to 358 up-regulated and 110 down-regulated genes.

overall_design: Vascular smooth muscle cells were obtained from the media of normal thoracic aorta of male Sprague-Dailey rats (100 ± 10 g) using primary explant technique. Cells were incubated with Cklf1 adenovirus (shRNA CKLF1 or CKLF1) and control (shRNA scramble or none) overnight and cultured as described in growth protocol. Total RNA were extracted and generated by deep sequencing, in triplicate, using Illumina X Ten sequencer.

last: Duan

first: Yongbao

last: Zhang

first: Chengjia

last: Qu

first: Weidong

last: Yu

first: Chenyang

last: Shen


title: The Genome-Wide Binding Landscape of Estrogen Receptor β in Human Colon Can-cer Cells Reveals Its Tumor Suppressor Activity

city: Stockholm

first: Rajitha

last: Indukuri

state: Sweden

address: Tomtebodavägen 23a, Solna

institute: Scilifelab

summary: In order to elucidate the mechanism of ERβ in the colon, we validated ERβ antibodies, optimized chromatin-immunoprecipitation (ChIP), and performed ChIP-Seq of CRC engineered cell lines re-expressing ERβ. In addition, we also performed H3K27AC ChIP-Seq to analyse histone marks in presence of ERβ. We present for the first time, the cistrome of nuclear receptor ERβ in different CRC cell lines and corresponding H3K27AC histone marks.

overall_design: Each ChIP was performed three times. For further analysis, we focused on sites present in at least two out of three replicates


title: Gene Expression Profiling of Estrogen Signaling in Colon Cancer Cell Line

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

overall_design: Refer to individual Series


title: Gene knockdown of PBK in the glioblastoma stem-like cell (GSC) culture T59

city: Oslo

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

country: Norway

institute: Oslo University Hospital

summary: Expression of genes in the GSC culture T59 featuring PBK gene knockdown. Expression of genes in the GSC culture T59 over-expressing non-silencing (NS-shRNA) transgenic sequence.

overall_design: Total RNA isolated from GSC culture T59 featuring PBK gene knockdowns was compared to RNA from non-silencing control GSC culture (NS-shRNA).


title: Pleiotropic Roles for the Plasmodium berghei RNA Binding Protein UIS12 in Anopheles Transmission and Sporogony

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Colonization of the mosquito host by Plasmodium parasites is achieved by sexually differentiated gametocytes. Gametocytogenesis, gamete formation and fertilization are tightly regulated processes, and translational repression is a major regulatory mechanism for stage conversion. Here, we present a characterization of a Plasmodium berghei RNA binding protein, UIS12, that contains two conserved eukaryotic RNA recognition motifs (RRM). Targeted gene deletion results in viable parasites that replicate normally during blood infection, but form fewer gametocytes. Upon transmission to Anopheles stephensi mosquitoes, both numbers and size of midgut-associated oocysts are impaired. As a consequence, no salivary gland sporozoites are formed indicative of a complete life cycle arrest in the mosquito vector. Comparative transcript profiling in mutant and wild-type infected red blood cells revealed downregulation of mRNAs coding for signature gamete-, ookinete- and oocyst-specific proteins in uis12(-) parasites. Together, our findings indicate multiple roles for UIS12 in regulation of gene expression after blood infection in good agreement with the pleiotropic defects that terminate successful sporogony and onward transmission to a new vertebrate host.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent custom whole genome Plasmodium berghei 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Katja

last: Mueller

first: Kai

last: Matuschewski


title: Bromodomain testis-specific protein BRDT directs ΔNp63 function and super enhancer activity in a distinct subset of esophageal squamous cell carcinomas [ChIP-seq]

city: Shenzhen

first: Xin

last: Wang

overall_design: Examination of BRDT, BRD4, p63 and various histone modifications in ESCC.

first: Steven

last: Johnsen

first: Ana

last: Kutschat


title: Mechanisms of drugs-resistance in small cell lung cancer

status: Public on Mar 04 2021

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

summary:
Lung cancer is the leading cause of cancer mortality and is classified by the World Health Organization into two broad histological subtypes. Non–small cell lung cancer (NSCLC), including adenocarcinoma, squamous cell carcinoma, and large cell carcinoma, accounts for ~85% of all lung cancer cases, with the remaining 15% of cases being due to small cell lung cancer (SCLC), which arises from neuroendocrine cells in the lung. Although most SCLC tumors are initially responsive to chemotherapy and radiation, patients often experience relapse, with the tumor acquiring an aggressiveness and therapeutic resistance that lead to a poor clinical outcome. Improvement of overall survival in individuals with SCLC will require the identification of novel therapeutic targets based on a better understanding of the changes in intracellular signaling of aggressive SCLC cells.
The malignant progression of SCLC often occurs concomitantly with the acquisition of chemoresistance, suggesting that phenotypic malignant change is related to adaptation to the stresses induced by chemotherapy. In order to analyze gene expression changes associated with malignant transformation in SCLC, we established a cisplatin-resistant SCLC cell line and performed RNA sequencing.

overall_design: Cisplatin-resistant SBC5 cells were generated by exposing the parental cell lines to stepwise increases in the concentration of cisplatin. RNAs were isolated from parental and cisplatin-resistant SBC5 cells and subjected RNA-sequencing analysis.

first: Kentaro

last: Suina


title: RNAseq analysis of BDAA treatment on YFV infected HEK293 cells

city: Doylestown

first: Jinhong

last: Chang

state: PA

address: 3805 Old Easton Road

institute: Baruch S. Blumberg Institute

summary:
Purpose: to investigate the change in gene expression after BDAA treatment on YFV infected HEK293 cells.
Methods: HEK293 cells were cultured; then cells were non-infected/infected with YFV, and then untreat/treat with BDAA. Total RNA were harvested and sent to RNA sequencing.
Results: we demonstrated that BDAA treatment of YFV infected HEK293 cells at 18 hpi for 2 h increased expression of a total of 39 cellular genes, 33 of which are inflammatory cytokines, chemokines or ISGs, and the remaining are mostly genes related to NFκB, TNF-α and MAPK signal transduction.
Conclusion: BDAA triggers an enhanced activation of RNA sensor-mediated inflammatory cytokine responses, most likely by YFV RNA.

overall_design: There were four experimental groups: HEK293 cells were either uninfected or infected with YFV at MOI of 10 for 1 h. At 18 hours post infection, the cells were then either mock treated with DMSO or treated with 3µM of BDAA for 2 h. Total cellular RNA was extracted by TRIzol reagent, then sent to RNA sequencing.

first: Xuexiang


title: ETTIN regulates genes involved in cell wall modification

city: Lyon

first: Charles

middle: Patrick

last: Scutt

address: 46 allee d'Italie

department: RDP

country: France

institute: ENS de Lyon

summary: ETTIN (ETT) encodes a member of the Auxin Response Factor (ARF) family of transcription factors. The gynoecia of strong ett mutants show a partial breakdown in abaxial-adaxial (internal -external) polarity, and a shift in tissue boundaries along the apico-basal axis of the gynoecium. This latter effect increases the size of the stigma, style and stipe in ett mutants at the expense of ovary tissue. Among the putative direct targets of ETT, we found several genes encoding either pectin methylesterases (PMEs) or their inhibitors. PMEs may function to increase the extensibility of the cell wall and thus contribute directly to cellular growth. The identification of genes encoding PMEs and related molecules as direct targets of ETT therefore suggests this factor to be situated near the end of a hierarchy of genetic regulation acting on growth through cell wall modification. Other putative direct targets of ETT encode two members of the Aux/IAA protein family, which have been found to negatively regulate ARFs as an inverse function of auxin concentration. ETT lacks the protein domains, present in most ARFs, that are necessary for negative regulation by Aux/IAA proteins and its own activity should not therefore be subject to regulation by auxin concentration. However, the regulation of two Aux/IAA proteins by ETT may represent an input of this protein into an auxin-regulated network involving other ARFs.

overall_design: To identify the direct target genes of ETT, we generated transgenic plants in which the translocation to the nucleus of a constitutively produced ETT fusion protein could be induced by exogenous application of the hormone analogue dexamethasone (DEX). Inflorescence tissues of transformed plants were treated either with DEX and cycloheximide (CYC) to modify the transcription of ETT-target genes while blocking protein synthesis, or with CYC alone to provide a reference sample. RNA was harvested 2 h after treatments and processed for expression analyses on CATMA microarrays, representing most of the genes in the A. thaliana genome. Microarray analyses were performed from three completely independent experiments (one pair of dye-swaps for each experiment) and the results of these were compared statistically to derive a list of putative ETT-targets.


title: CRABS CLAW positively regulates genes involved in the establishment of both abaxial and adaxial identity in Arabidopsis

summary: CRABS CLAW (CRC) encodes a transcription factor of the plant-specific YABBY class in the model plant Arabidopsis thaliana. This gene is highly expressed in the abaxial (external) domain of the gynoecium wall and contributes to the establishment of abaxial-adaxial (external-internal) polarity in that tissue. Here we derive a list of putative target genes of CRC, which include AUXIN RESPONSE FACTOR4 (ARF4) and ASSYMETRIC LEAVES1 (AS1), both of which are known to be involved in the establishment of abaxial-adaxial polarity in lateral organs. ETTIN (ETT), which is partially redundant with ARF4, was not identified as a direct target of CRC, and this observation led us to predict that crc/ett double mutants might resemble ett/arf4 double mutants, which show a very strong breakdown of abaxial-adaxial polarity in the gynoecium wall. We have confirmed this prediction by constructing double mutants using several available mutant alleles of crc, ett and arf4. Interestingly, AS1 plays a role in the establishment of adaxial tissue identity in lateral organs, though its expression is not restricted to the adaxial domain. The observed positive regulation of AS1 by CRC may thus occur very early in gynoecium development, before CRC expression becomes polarised, or at later stages of development, specifically in the abaxial domain.

overall_design: To identify the direct target genes of CRC, we generated transgenic plants in which the translocation to the nucleus of a constitutively produced CRC fusion protein could be induced by exogenous application of the hormone analogue dexamethasone (DEX). The transgene construction used in this procedure included a VP16 viral transactivation domain to amplify the effects of CRC fusion protein on transcription, thereby increasing the sensitivity of the analysis. Inflorescence tissues of transformed plants were treated either with DEX and cycloheximide (CYC) to induce the transcription of CRC-target genes while blocking protein synthesis, or with CYC alone to provide a reference sample. RNA was harvested 2 or 4h after treatments and processed for expression analyses on CATMA microarrays, representing most of the genes in the A. thaliana genome. Further experiments were performed without CYC treatment (mock/DEX), permitting the identification of genes regulated indirectly be CRC.


title: LncRNAs and mRNAs profile suggested CCL / CXCL were involved in the reoxygenation reversal of hypoxic pulmonary hypertension in mice

city: Xi'an

first: Shujuan

last: Xing

state: Shaanxi

address: 18 Yudou Road, Yanta District,

institute: Xi’an International University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: The potential roles of mRNAs and lncRNAs in the development and the reoxygenation treatment of reversal of hypoxic pulmonary hypertension are still unknown. 24 healthy adult male C57/BL6 mice were divided into three groups (normoxia group, hypoxia group, hypoxia-normoxia group), lncRNA and mRNA microarray was performed，meanwhile，the changes of right ven-tricular systolic pressure (RVSP) and other physiological indexes were measured in the three groups. The results showed that the index of RVSP, the right ventricular hypertrophy index RV/(LV+S), pulmonary artery walls and the muscularization ratio of pulmonary arterioles were significantly increased after Hypoxia treatment, while they were attenuated after the normoxia condition restored. Moreover, the study revealed there were 62 lncRNAs and 99 mRNAs with significant difference expression were associated with the reversal of hypoxic pulmonary hypertension by reoxygenation in mice. Furthermore, the pathway enrichment and gene ontology analysis of 99 DEGS were performed. Interestingly, the result suggested that chemokine subfamily CCL2/ CXCL played a role in the occurrence, development and reversion of pulmonary hypertension by reoxygenation. This study was the first time to demonstrate the transcriptome profiles of lncRNAs and mRNAs in the lung tissue during the reversal of hypoxic pulmonary hypertension in mice by reoxygenation, which might further broaden the understanding of the pathogenesis and the therapeutic effect of oxygen recovery of hypoxic pulmonary hypertension.

first: ShuJuan

first: MingQing

last: Dong

first: Fen

last: Liu

first: ShengChao

first: Ying

last: Luo


title: Compare transcriptomes of BMP4 and BMP4 plus Palo treatment in 2H11 cells

city: Houston

first: GUOYU

last: YU

address: 1515 Holcombe Blvd, Houston,

department: Translational Molecular Pathology

institute: MD Anderson Cancer Center

summary: In order to observe palovarotene modulates BMP4-induced transcriptome,2H11 cells treated with BMP4 or BMP4 plus palovarotene for 48 hours were subjected to RNAseq analyses

overall_design: mRNA profiles of BMP4 or BMP4 plus Palovarotene treated for 48 hours in 2H11 cells

first: Guoyu

last: Yu

first: Sue-Hwa

last: Lin

first: Yanggu

last: Shi


title: Systematic analysis of innate lymphoid cells and natural killer cells in context of HIV-1 infection

city: Nanjing

first: Yetao

state: Jiangsu

address: No. 12, Jiangwangmiao street,  Xuanwu District

department: Central Laboratory

institute: Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: We performed bulk and single cell RNA-Seq and ATAC-Seq of CD56-, CD56dim, CD56hi NK cells and innate lymphoid cells, revealed relationship among these developmental related populations, investigated the effect of HIV-1 infection on these innate populations. These findings clarify the interrelatedness of ILC populations disrupted by HIV-1 infection and provide insight into how these functions might be restored.

overall_design: Sorted Lin-CD56-CD127-, Lin-CD56-CD127+, CD56-NK cells (Lin-CD56-CD16+), CD56dimNK cells (Lin-CD56dim), CD56hiNK cells (Lin-CD56hi) and ILCs (Lin-CD56-CD16-CD127+) from CD45+ cells of fresh PBMCs or different culture conditions were subject to bulk-RNA seq (based on CEL-Seq2 protocol), single cell RNA-Seq (based on 10x Genomics instruction, Single Cell 3’ Reagent Kits v2) and ATAC-Seq.

first: Lawrence

last: Lifshitz

first: Jeremy

last: Luban


title: Single cell RNA sequencing of the limb myotendionous junction

city: Sakhnin

first: Wesal

middle: Yaseen

last: Badarne

address: P.O box 2016

department: Department of Genetics and Developmental Biology.

country: Israel

institute: Technion

summary: Vertebrate muscles and tendons are derived from distinct embryonic origins yet they must interact in order to facilitate muscle contraction and body movements. How robust muscle tendon junctions (MTJs) form to be able to withstand contraction forces is still not understood. Using techniques at a single cell resolution we reexamined the classical view of distinct identities for the tissues composing the musculoskeletal system. We identified fibroblasts that have switched on a myogenic program and demonstrate these dual identity cells fuse into the developing muscle fibers along the MTJs facilitating the introduction of fibroblast-specific transcripts into the elongating myofibers. We suggest this mechanism resulting in a hybrid muscle fiber, primarily along the fiber tips, enables a smooth transition from muscle fiber characteristics towards tendon features essential for forming robust MTJs. We propose that dual characteristics of junctional cells could be a common mechanism for generating stable interactions between tissues throughout the musculoskeletal system.

overall_design: We report the single cell RNA sequencing from the region of a P0 myotendinous junction taken from forelimbs

first: Peleg

last: Hasson

last: Yaseen-Badarneh

first: Ortal

last: Kraft-Sheleg

first: Shay

last: Melamed

first: Chengyi

last: Sun

first: Douglas

last: Millay

first: Shelly

last: Zaffryar-Eilot


title: miRNA-seq in ovarian tissues of prenatally androgenized (PNA) mice

city: Minhang district of Shanghai

first: yani

last: Kang

address: Dongchuan Road 800

institute: Shanghai Jiaotong University

summary: To investigate the molecular mechanisms of miRNA-mRNA expression underlying this phenotype, ovarian samples from PNA and control mice were subjected to microRNA-seq and RNA-seq. Differential expression analyses were carried out to identify differentially expressed microRNAs (DEmiRs) and differentially expressed genes (DEGs). Target genes of DEmiRs were predicted by miRTarbase and visualization by Cytoscape. Functional annotation and pathway enrichment analyses for the DEGs and target genes were performed through the DAVID database. Then, to reveal the interactions involved in the pathogenesis of PCOS, the integrated analysis of miRNA-mRNA was performed in PNA mice vs. controls and granulosa cells (GCs) of PCOS women vs. health women. Protein–protein interaction (PPI) networks were established for these negatively regulated pairs via the STRING database. The expression and correlation of potential miRNAs and targets were further validated using RT-qPCR in more PNA mice and clinical human granulosa cells.

overall_design: miRNA-seq combined with RNA-seq analysis to find the regulation network in PCOS

first: Yulan

last: Qin

first: Ting

last: Li

first: Yuhuan

last: Wang

first: Hui

last: Zhao

first: Zhaoxia

last: Yang

first: Yani


title: Comparison of skin and in vitro differentiated human Langerhans cells

city: Strasbourg

first: Henri

last: de la Salle

address: 10 rue Spielmann

institute: EFS Grand-Est

summary: Langerhans cells were prepared from skin or derived from cord blood CD34+ cells

overall_design: Epidermal sheets were digested with dispase. CD1a+ cells were isolated using Myltenyi beads.  CD1a-depleted cells were used to control keratinocyte contamination. CD1a+ Langerhans cells were isolated using Myltenyi beads from human cord blood CD34+ cells purified using Myltenyi beads in the presence of recombinant TGFb, SCF, GM-CSF, FLT3.

first: Daniel

last: Hanau

first: Thomas

last: Bieber


title: Laser capture microdissection and miRNA expression profiling of different tissue morphologies in triple-negative breast cancer

city: Olomouc

first: Jan

last: Bouchal

address: Hnevotinska 3

department: Department of Clinical and Molecular Pathology

country: Czech Republic

institute: Palacky University

summary:
Triple negative breast cancers (TNBC) are a morphologically and genetically heterogeneous group of breast cancers with uncertain prediction of biological behavior and response to therapy. The aim of our study was to analyze miRNAs expression within areas of TNBCs with different cellular morphology. We performed laser capture microdissection with PALM MicroBeam system from Zeiss and subsequent expression profiling with Affymetrix GeneChip miRNA 4.0 Arrays to identify distinct classes of miRNAs deregulated in respective tissue morphologies.
The study was approved by the Ethics Committee of the University Hospital Olomouc and Medical Faculty of Palacky University in compliance with the Helsinki Declaration (Ref No. 111/15). According to the Czech Law (Act. no. 373/11, and its amendment Act no. 202/17), it is not necessary to obtain informed consent in fully anonymised retrospective studies on formalin-fixed paraffin-embedded tissues. At least one tissue block for each patient was retained in the archive to allow future clinical use such as re-evaluation or further studies.

overall_design: We assembled a set of selected 25 TNBC cases to determine miRNA expression levels in relation to present focal carcinoma in situ (CIS), spindle cell, apocrine, invasive and other tumor morphologies within individual TNBCs. We excluded all tumors which were not complete (core-cut biopsies) and which were treated by previous neoadjuvant chemotherapy. Thus, the cohort of tumors were of limited size, varied from 5 to 20 mm (pathological tumor stage pT1a – pT1c), with an average size of 13.4 mm (median 15 mm). Despite the triple negative phenotype, we also excluded the histological tumor types associated with favourable prognosis (adenoid cystic carcinomas).

first: Marketa

last: Koleckova

first: Zdenek

last: Kolar


title: Profiling NSD3-dependent neural crest gene expression reveals known and novel candidate regulatory factors

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: The lysine methyltransferase NSD3 is required for the expression of key neural crest transcription factors and the migration of neural crest cells. Nevertheless, a complete view of the genes dependent upon NSD3 for expression and the developmental processes impacted by NSD3 in the neural crest was lacking. We used RNA sequencing (RNA-seq) to profile transcripts differentially expressed after NSD3 knockdown in chick premigratory neural crest cells, identifying 674 genes. Gene Ontology and gene set enrichment analyses further support a requirement for NSD3 during neural crest development and show that NSD3 knockdown also upregulates ribosome biogenesis. To validate our results, we selected three genes not previously associated with neural crest development, Astrotactin-1 (Astn1), Dispatched-3 (Disp3), and Tropomyosin-1 (Tpm1). Using whole mount in situ hybridization, we show that premigratory neural crest cells express these genes and that NSD3 knockdown downregulates (Astn1 and Disp3) and upregulates (Tpm1) their expression, consistent with RNA-seq results. Altogether, this study identifies novel putative regulators of neural crest development and provides insight into the transcriptional consequences of NSD3 in the neural crest, with implications for cancer.

overall_design: NSD3-dependent gene expression in chick neural folds is profiled by RNA-seq with 5 control and 5 knockdown replicates.

first: Bridget

middle: T

last: Jacques-Fricke

first: Julaine

last: Roffers-Agarwal

middle: D

first: Laura

last: Gammill

first: Amina

middle: O

last: Hussein

first: Kendra

middle: J

last: Yoder


title: Gene Expression Profiling of Estrogen Signaling in Colon Cancer Cell Line [CRC Project]

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

institute: KTH Royal Institute of Technology

summary: We studied the transcriptional effect of estrogen in two colon cancer cell lines SW620 and SW480

overall_design: Cells were treated with estradiol (E2) for 24 hrs with/without ERB transduction

first: Fahmi

last: Mesmar

first: Linnea

last: Pettersson


title: A genome-wide screen for essentiality upon telomerase inhibition identifies a novel p53 regulator, C16ORF72/TAPR1 [TAPR1_KO]

city: Montreal

first: Lea

last: Harrington

state: Quebec

address: 2950 chemin de Polytechnique, Pavillon Marcelle-Coutu

department: Department of Medicine

institute: University of Montreal

summary: Telomere erosion in cells with insufficient levels of the telomerase reverse transcriptase, TERT, contributes to age-associated tissue dysfunction and senescence, and p53 plays a crucial role in this response. We undertook a genome-wide screen to identify gene deletions that sensitized p53-positive human cells to telomerase inhibition. We uncovered a previously unannotated gene, C16ORF72, which we term Telomere Attrition and p53 Response 1, TAPR1, that exhibited a synthetic-sick relationship with TERT loss. A genome-wide screen in TAPR1-disrupted cells also identified TERT as a sensitizing gene deletion. Additional genetic and transcriptome analysis of TAPR1-disrupted cells revealed that TAPR1 tapered p53 activation in response to eroded telomeres, p53 stabilization with nutlin-3a, or DNA damage. Importantly, deletion of TP53 rescued the fitness defect in TAPR1-disrupted cells. These findings identify C16ORF72/TAPR1 as new regulator at the nexus between telomere integrity and p53 regulation.

overall_design: Genome-wide screen to test for gene deletions that affect fitness in cells harboring a homozygous deletion for the C16orf72/TAPR1 gene.

first: Yahya

last: Benslimane

first: María

last: Sánchez-Osuna

first: Jasmin

last: Coulombe-Huntington

first: Thierry

last: Bertomeu

first: Danielle

last: Henry

first: Caroline

last: Huard

first: Éric

last: Bonneil

first: Pierre

last: Thibault

first: Mike

last: Tyers


title: A genome-wide screen for essentiality upon telomerase inhibition identifies a novel p53 regulator, C16ORF72/TAPR1

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

overall_design: Refer to individual Series