title: Recognition and fine genetic mapping of the golden pod gene (pv-ye) from the common bean (Phaseolus vulgaris L.)

status: Public on Oct 12 2020

city: Harbin

first: yan

last: yu

address: Nangang District

country: China

institute: Heilongjiang University

summary: The pod is the main edible part of Phaseolus vulgaris L. (common bean). The commercial use of the pods is mainly affected by their color. Consumers seem to prefer golden pods. However, planters suffer economic losses because of pod color instability. The aim of the present study was to identify the gene responsible for the golden pod trait in the common bean. ‘A18-1’ (a golden bean line) and ‘Renaya’ (a green bean line) were chosen as the experimental materials. Genetic analysis indicated that a single recessive gene, pv-ye, controls the golden pod trait. A candidate region of 4.24-Mb was mapped to chromosome A02 using bulked-segregant analysis coupled to whole genome sequencing. In this region, linkage analysis in an F2 population localized the pv-ye gene to an interval of 182.9-kb between the simple sequence repeat markers SSR77 and SSR93. This region comprised 16 genes in this region, comprising 12 annotated genes from the P. vulgaris database, and 4 functionally unknown genes. Combined with transcriptome sequencing, we identified Phvul.002G006200 as the potential candidate gene for pv-ye. Sequencing of Phvul.002G006200 identified a single nucleotide polymorphism (SNP) in pv-ye. This SNP is located in the coding region and is responsible for substituting a glutamic acid with an glutamine at position 416 of the pv-ye protein (E416Q). A pair of primers covering the SNP was designed and the fragment was sequenced to screen 316 F2 plants with the ‘A18-1’ phenotype, based on the different site. Our findings showed that the among the 316 mapped individuals, the SNP cosegregated with the ‘A18-1’ phenotype. The findings presented here could form the basis to reveal the mechanism of the golden pod trait in the common bean at the molecular level.

overall_design:
The present study identified the pv-ye gene, which is responsible for the golden pod trait of line ‘A18-1’ of the common bean.
The pod color of A18-1 changes gradually from green to gold as the tender pods develop into mature commercial pods, and Renaya (R), whose pod color remains green until ripening.
From lines R (Renaya) and A (A18-1), pod walls were collected at 10, 14, and 18 (A10, A14, A18) DAF as RNA-seq materials, with three independent biological repeats.

first: Xiaoxu

last: Yang

first: Chang

last: Liu

first: Dajun

first: Guojun

last: Feng


title: Genome-wide maps of chromatin state in TRIB3Cas9 and control lymphoma cells

status: Public on Oct 10 2020

city: bei jing

first: wang

last: feng

address: nan wei road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College,

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of  RNAPII with promoters in mammalian cells. We performed ChIP sequencing with antibody to total RNAPII in TRIB3Cas9 and CtrlCas9group. Inspection of multiple individual traces and global analyses showed that TRIB3 deletion globally reduced association of RNAPII with promoters.

overall_design: we performed ChIP sequencing with antibody to total RNAPII in TRIB3 deleted group. Inspection of individual traces and global analyses showed that TRIB3 deletion globally reduced association of RNAPII with promoters.

first: Zhuo-wei

last: Hu

first: Ke

last: Li

first: Feng

last: Wang


title: The aureochrome photoreceptor PtAUREO1a is a highly effective blue light switch in diatoms

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

type: Expression profiling by high throughput sequencing

summary: Aureochromes represent a unique type of blue-light photoreceptors that possess a blue-light sensing flavin-binding LOV-domain and a DNA-binding bZIP domain. Therefore, in contrast to other photoreceptors, aureochromes are considered as light-driven transcription factors. As a member of the essential group of marine primary producers, the pennate diatom Phaeodactylum tricornutum possesses four aureochromes (PtAUREO1a, 1b, 1c, 2). We here show a dramatic change in the global gene expression pattern of P. tricornutum cells after a shift from red to blue light. About 75% of the genes show significantly changed transcript levels already after 10 and 60 min of blue light exposure, which includes genes of major transcription factors as well as other photoreceptors. Very surprisingly, in two independent PtAureo1a knockout lines, this light induced regulation of gene expression is almost completely abolished. Such a massive and fast transcriptional change depending on only one single photoreceptor is so far unprecedented. We hence conclude that PtAUREO1a plays a key role in light regulation.

overall_design: Transcriptomes of Phaeodactylum tricornutum wild type (WT) and two independent knock-out mutant clones in PtAUREO1a (1aK8, 1aK9) constantly grown in red light (0min_RL) and shifted for 10 (10min_BL) and 60 min (60min_BL) to blue light (BL). WT samples and 1aK8 samples were sequenced in biological triplicates, 1aK9 samples in biological duplicates. 1aK9 samples were additionally sequenced in two technical replicates.

first: Marcus

last: Mann

first: Manuel

last: Serif

first: Thomas

last: Wrobel

first: Marion

last: Eisenhut

first: Shvaita

last: Madhuri

first: Samantha

last: Flachbart

middle: P

first: Bernard

last: Lepetit

first: Christian

last: Wilhelm

first: Peter

middle: G

last: Kroth


title: Genome-wide maps of chromatin state in Pep2-CM4-treated and control lymphoma cells

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of  RNAPII with promoters in mammalian cells. We performed ChIP sequencing with antibody to total RNAPII in  Pep2-CM4-treated and control group. Inspection of multiple individual traces and global analyses showed that Pep2-CM4-treated cells globally reduced association of RNAPII with promoters.

overall_design: We performed ChIP sequencing with antibody to total RNAPII in UBE3B overexpression or Pep2-CM4-treated and control group and  globally analysed association of RNAPII with promoters.


title: Multi-omics and immune profiling of breast cancers undergoing neoadjuvant chemotherapy identified dynamic cellular and molecular changes associated with clinical response

city: San Diego

first: Zhengyan

last: Kan

state: CA

address: 10770 Science Center Drive

department: Computational Biology, Oncology Research & Development

country: USA

institute: Pfizer

summary: Through multi-dimensional characterization of longitudinally paired breast cancers during NAC treatment, we have identified dynamic changes in the tumor cellular and molecular states and derived insights into the mechanism of action as well as resistance to an important class of therapy.

overall_design: The raw data are available at EGA with accession number EGAS00001003354.

first: Ying

last: Ding

first: Jinho

last: Kim


title: Next Generation Sequencing Facilitates Quantitative Analysis of MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3  cells' Transcriptomes in B cells  lymphoma

first: wang

last: feng

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in  MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3  lymphoma cells  by using NGS-derived lymphoma transcriptome profiling (RNA-seq).
Methods:  MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with  following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including  GO enrichment analysis and KEGG .
Conclusions: Our study represents the first detailed analysis of MYCWT+shCtrl, MYCWT+shTRIB3, MYCT58A+shCtrl and MYCT58A+shTRIB3  cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.


title: RNA-seq of intestinal stem cells

status: Public on Oct 09 2020

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

summary: The impact of Mll1 removal on intestinal stem cells expressing an oncogenic form of beta-catenin (beta-cateninGOF) was analysed in 4 pairs of sorted intestinal stem cells of Lgr5-CreERT2; beta-cateninGOF;Mll1+/- (control) and Lgr5-CreERT2; beta-cateninGOF;Mll1-/- (knockout) at 10 days after tamoxifen-induced mutagenesis. Using 75-base-pair reads, around 30 million reads per sample with comparable unique mapped reads (73-78%) were obtained. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. Differentially expressed genes in beta-cateninGOF; Mll1-/- versus beta-cateninGOF; Mll1+/- stem cells showed both up- and downregulation of genes at a false discovery rate (FDR) of 10%. This included a global increase in the expression of goblet cell-specific genes. Downregulated genes included specific markers of Paneth cells, indicating that ablation of Mll1 shifted the Paneth-like identity of beta-cateninGOF stem cells towards a goblet cell fate. The stem cell transcriptome further revealed that beta-cateninGOF; Mll1-/- stem cells exhibited a decreased expression of several transcription factors and stem cell genes.

overall_design: mRNA profiles of beta-cateninGOF; Mll1+/- (control) and beta-cateninGOF; Mll1-/- (knockout) stem cells were generated by deep sequencing in quadruplicates

first: Johanna

last: Grinat

first: Julian

last: Heuberger

first: Ramon

middle: O

last: Vidal

first: Neha

last: Goveas

first: Frauke

last: Kosel

first: Andrea

last: Kranz

first: Annika

last: Wulf-Goldenberg

first: Diana

last: Behrens

first: Bálint

last: Melcher

first: Sascha

last: Sauer

first: Michael

last: Vieth

first: A

middle: F

first: Walter

last: Birchmeier


title: A pathogen-specific 4mC methyltransferase is critical for epigenetic regulation and virulence of Leptospira interrogans

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Transcriptome analysis of a mutant in an orphan methyltranferase revealed global transcriptional regulation of 100 differentially expressed genes.

overall_design: We used RNA-seq to compare the transcriptomes of wild-type L. interrogans with that of the lomA mutant and complemented strains under ideal culture conditions at mid-log phase.

first: Robert

middle: A

last: Gaultney

first: Antony

middle: T

last: Vincent

first: Céline

last: Lorioux

first: Jean-Yves

last: Coppee

first: Odile

last: Sismeiro

first: Hugo

last: Varet

first: Frederic

middle: J

last: Veyrier

first: Mathieu

last: Picardeau


title: Transcriptome and Retrotranscriptome profiling in HIV infected women with Breast Cancer (RNA-seq)

status: Public on Oct 08 2020

city: New York

first: Matthew

last: Bendall

state: NY

address: Belfer Research Building, Room BB-528, 413 East 69th Street

institute: Weill Cornell Medicine

summary: In order to determine the impact of HIV infection on the breast cancer microenvironment, we sequenced total RNA from formalin-fixed paraffin-embedded (FFPE) breast cancer samples of 10 women (4 HIV-positive: 6 HIV-negative) for studying the transcriptome and retrotranscriptome of those. We performed RNA extraction from samples stored for more than 5 years, cDNA library preparation, total RNA sequencing (RNA-seq) and differentially expressed genes between conditions were analyzed.

overall_design: FFPE blocks of breast tissue from 10 women with invasive ductal carcinoma (IDCA) of the female mammary gland (4 HIV-positive: 6 HIV-negative) registered from 2003 to 2014 at the Brazilian National Cancer Institute (INCA) were used in this study.

first: Marcelo

last: Soares


title: Bifidobacterium infantis metabolizes 2´fucosyllactose-derived and free fucose through a common catabolic pathway resulting in 1,2-propanediol secretion

city: Amherst

first: Ezgi

last: Ozcan

state: MASSACHUSETTS

address: 424 Chenoweth Lab, 102 Holdsworth Way

institute: University of Massachusetts Amherst

summary: Human milk oligosaccharides (HMOs) enrich beneficial bifidobacteria in the infant gut microbiome which produce molecules that impact development and physiology. 2´fucosyllactose (2´FL) is a highly abundant fucosylated HMO which is utilized by Bifidobacterium longum subsp. infantis, despite limited scientific understanding of the underlying mechanism. Moreover, there is not a current consensus on whether free fucose could be metabolized when not incorporated in a larger oligosaccharide structure. Based on metabolic and genomic analyses, we hypothesize that B. infantis catabolizes both free fucose and fucosyl oligosaccharide residues to produce 1,2-propanediol (1,2-PD). Accordingly, systems-level approaches including transcriptomics and proteomics support this metabolic path. Co-fermentation of fucose and limiting lactose or glucose was found to promote significantly higher biomass and 1,2-PD concentrations than individual substrates, suggesting a synergistic effect. In addition, and during growth on 2´FL, B. infantis achieves significantly higher biomass corresponding to increased 1,2-PD. These findings support a singular fucose catabolic pathway in B. infantis that is active on both free and HMO-derived fucose and intimately linked with central metabolism. The impact of fucose and 2´FL metabolism on B. infantis physiology provides insight into the role of fucosylated HMOs in influencing host-  and microbe-microbe interactions within the infant gut microbiome.

overall_design: Gene expression of B. infantis ATCC 15697 while growing on different concentrations of 2fucosyllactose

first: Liv

middle: R

last: Dedon

last: Özcan

first: Asha

last: Rani

first: David

last: Sela


title: Separable functions of Tof1/Timeless in intra-S-checkpoint signalling, replisome stability and DNA topological stress

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

summary: The highly conserved Tof1/Timeless proteins minimise replication stress and promote normal DNA replication. They are required to mediate the DNA replication checkpoint (DRC), the stable pausing of forks at protein fork blocks, the coupling of DNA helicase and polymerase functions during replication stress (RS) and the preferential resolution of DNA topological stress ahead of the fork. Here we demonstrate that the roles of the Saccharomyces cerevisiae Timeless protein Tof1 in DRC signalling and resolution of DNA topological stress require distinct N and C terminal regions of the protein, whereas the other functions of Tof1 are closely linked to the stable interaction between Tof1 and its constitutive binding partner Csm3/Tipin. By separating the role of Tof1 in DRC from fork stabilisation and coupling, we show that Tof1 has distinct activities in checkpoint activation and replisome stability to ensure the viable completion of DNA replication following replication stress.

overall_design:
ChIP-seq experiments: In the absence of Tof1 or Mrc1 the helicase advances beyond the point of nascent DNA incorporation, indicating uncoupling of helicase and polymerase activities in the replisome. This uncoupling is predicted to lead to increased binding of the single stranded DNA binding protein, RPA1, to the single stranded regions generated by uncoupled helicase action. We have experimentally confirmed this prediction using RPA1 ChIP-SEQ in HU treated wildtype, tof1 and mrc1 cells and compared to various tof1 mutants.

Sync-seq experiments:  We used sync-seq technique follow DNA replciation restart after HU arrest in various tof1 mutants by comparing relative DNA copy numbers from cells in G1, 60 min HU treated and 80 min after HU release.

first: Rose

last: Westhorpe

first: Nicola

middle: E

last: Minchell

last: Jones

first: Jonathan

last: Baxter


title: Genome-wide expression profiling of Candida albicans transcription factor Rme1p

status: Public on Oct 07 2020

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

summary: Rme1, a conserved transcription factor among members of the ascomycete lineage, regulates meiosis and pseudohyphal growth in baker’s yeast. The genome of the meiosis-defective fungal pathogen Candida albicans encodes a Rme1 homolog, which we previously mapped within a transcriptional circuitry that controls hyphal growth. To delineate a possible role of Rme1 in C. albicans morphogenesis, we combined genome-wide expression and location analyses of Rme1. Strikingly, Rme1 bound upstream and activated the expression of markers of chlamydosporulation, a process leading to formation of large, spherical, thick-walled cells during nutrient starvation. RME1 deletion abolished chlamydosporulation in three chlamydospore-forming Candida species, whereas its overexpression bypassed the requirement for chlamydosporulation cues and regulators, indicating that Rme1 is central to chlamydospore development. Moreover, RME1 expression levels correlated with chlamydosporulation efficiency among clinical isolates, further highlighting Rme1 importance in this process. Interestingly, RME1 displayed a biphasic pattern of expression, with a first phase independent of Rme1 function and dependent on chlamydospore-inducing cues, and a second phase depending upon Rme1 function and independent of chlamydospore-inducing cues. We suggest that Rme1 function spans from the regulation of meiosis in sexual yeasts to the control of an epigenetic switch necessary for asexual spore formation in meiosis-defective Candida species.

overall_design: Two-condition experiments: 1) Samples 1-6: untreated (-Dox, Cy3-labeled) and Dox-treated (+Dox, Cy5-labeled, 40 µg/mL) during 2h and 4h in Yeast Peptone Dextrose medium, 30C, 3 biological replicates for each time-point; 2) Samples 7-9: Comparison of a Candida albicans wild-type clinical isolate (CEC2018, Cy3-labeled) to an rme1-/- mutant derivative (Cy5-labeled) both grown overnight at 30ºC in YPD medium, then diluted to an OD600 nm of 0.2 in 10 mL of PCB (10% potato/carrot extract and 1.5% dehydrated fresh bile) liquid medium and cultured at 25ºC in the dark and under microaerophilic conditions during 24h.

last: Znaidi


title: Genome-wide location of Candida albicans transcription factor Rme1p

type: Genome binding/occupancy profiling by genome tiling array

overall_design: A total of 2 samples are included, corresponding to 2 biological replicates : samples RME1_ChIP_Upper array and RME1_ChIP_Lower array.


title: Genome-wide maps of chromatin state in WT c-Myc and K427R mutant lymphoma cells

first: wang

last: feng

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of  c-Myc with core promoters of its target genes  in mammalian cells. We performed ChIP sequencing with antibody to total c-Myc with core promoters of its target genes in WT c-Myc and K427R mutant group. Inspection of multiple individual traces and global analyses showed that the K427R mutant globally reduced association of c-Myc with core promoters of its target genes.

overall_design: we precipitated chromatin with tag antibody to WT c-Myc and K427R mutant, and sequenced the precipitated material. K427 mutation increased association of c-Myc with core promoters of its target genes

first: Zhuo-wei

last: Hu

first: Ke

last: Li

first: Feng

last: Wang


title: Transcriptomic profiling of adipose tissue in periparturient dairy cows

city: East Lansing

middle: Rodrigo

last: Salcedo-Tacuma

state: Mi

address: 567 Wilson road

department: Physiology

institute: Michigan State University

summary: Periparturient cows rely on adipose tissue fatty acid reserves released by lipolysis to offset the negative energy balance induced by physiological changes related to  parturition and the onset of lactation. However, lipolysis causes inflammation and structural remodeling in excess predisposes cows to disease. The objective of this study was to determine effects of the periparturient period on the transcriptomic profile of AT using NGS RNAseq

overall_design: mRNA profile of 12 mammary glands from cows  before and at two time points after parturition. Subcutaneous adipose biopsies were collected on day -11, day 6 and day 13 relative to parturition

first: Jair

last: Parales

first: Crystal

last: Prom

first: Miguel

last: Chirivi

first: Juliana

last: Laguna

first: Adam

middle: L

last: Lock

first: G

last: Contreras


title: Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Cx3cr1+;NT+ Hippocampus RNA-Seq Data

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Studies of neuroepigenetic mechanisms in health and disease are hindered by a lack of approaches to analyze both the transcriptome and epigenome of specific cell types isolated from the complex milieu of the CNS. Cell isolation by cell surface markers is complicated by preparation artifacts, changes in markers with experimental conditions, and lack of specific markers. This study validates a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach with tamoxifen (Tam) inducible cell-type specific cre recombination to allow the parallel interrogation of the epigenome and the transcriptome in astrocytes (Aldh1l1-creERT2) or microglia (Cx3cr1-creERT2). The recombined NuTRAP construct labels, in a cell-type specific manner, nuclei (RanGAP1) with biotin and mCherry, and the ribosomes (L10a) with EGFP, enabling INTACT isolation of DNA and TRAP isolation of RNA. Validation experiments by flow cytometry and imaging demonstrate cell-type specific induction of the NuTRAP construct. Transcriptomic studies demonstrate isolation of highly enriched RNA by TRAP and oxidative bisulfite studies of INTACT-isolated DNA demonstrate differential DNA modification patterns in microglia and astrocytes. LPS administration in Cx3cr1 NuTRAP mice demonstrates that microglia-specific transcriptome and epigenome changes are revealed that cannot be detected with tissue-level samples. These experiments demonstrate that the NuTRAP approach can be applied to CNS cell populations and that INTACT approaches can be used to study DNA modifications.  These results also provide an approach for generation and validation of NuTRAP neuroscience models crossed to any relevant cell-type specific cre line.

overall_design: Hippocampi isolated from Cx3cr1-cre/Ert2+; NuTRAP+ mice; RNA isolated via TRAP methods- Input and Positive fractions were sequenced; 3 biological replicates

first: Ana

last: Chucair-Elliott

first: Sarah

last: Ocanas

last: Stanford

first: Victor

last: Ansere

first: Kyla

middle: B

last: Buettner

first: Hunter

last: Porter

first: Nicole

last: Eliason

first: Amanda

last: Sharpe

last: Beckstead

first: Arlan

last: Richardson

first: Willard

middle: M

last: Freeman


title: Epistatic regulation of complex traits and gene expression in mice

status: Public on Oct 05 2020

city: Cleveland

first: Anna

last: Miller

state: Ohio

address: 2109 Adelbert Rd

institute: Case Western Reserve University

summary: The genetic contribution of additive versus non-additive (epistasis) effects in the regulation of hematologic and other complex traits is unclear. While genome-wide association studies typically ignore gene-gene interactions, in part because of the lack of statistical power for detecting them, mouse chromosome substitution strains (CSSs) represent an alternate and powerful model for detecting epistasis given their limited allelic variation. Therefore, we utilized CSSs to identify and map both additive and epistatic loci that regulate a range of hematologic- and metabolism-related traits, as well as hepatic gene expression. Quantitative trait loci (QTLs) were identified using a modified backcross strategy involving the segregation of variants on the A/J-derived substituted chromosomes 4 and 6 on an otherwise C57BL/6J genetic background. By analyzing the transcriptomes of offspring from this cross, we identified and mapped additive QTLs regulating the expression of 768 genes, and epistatic QTLs for 519 genes. Similarly, we identified additive QTLs for fat pad weight, platelets, and percentage of granulocyte in the blood as well as epistatic QTLs controlling the percentage of lymphocytes in the blood and red cell distribution width. The variance attributed to the epistatic QTLs was approximately equal to that of the additive QTLs, demonstrating the importance of identifying genetic interactions to understand the genetic basis of complex traits. Of particular note, even the epistatic QTLs identified that accounted for the largest variances were undetected in our single loci GWAS-like association analyses, highlighting the need to account for epistasis in association studies.

overall_design: Genomic DNA from the liver of F2 generation mice were isolated for RNA Sequencing. All of the mice are male and were used for mapping; therefore there is no differentiating characteristic between mice

middle: K


title: Combinatorial action of temporally-segregated transcription factors

status: Public on Oct 06 2020

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary: Combinatorial action of transcription factors(TFs) with partially-overlapping expression is a widespreadstrategyto generate novel gene-expression patternsand thuscellular diversity. Known mechanisms underlying combinatorialactivityrequireco-expression of TFswithin the same cell. Here, we describe themechanismby which twoTFsthat are never co-expressed, generate a new, intersectional expression pattern in C. elegans embryos:lineage-specific priming of a gene by a transiently-expressedTFgeneratesa uniqueintersectionwith a second TF acting on the same gene four cell divisions later;the second TF is expressed in multiple cells butonly activatestranscription in those where priming occurred.Early induction of active transcription is necessary and sufficient to establish a competent state that is maintained by broadly-expressed regulators in absence of theinitial trigger. We further uncover new cells diversified through this mechanism. Our findings define anovel mechanism forcombinatorial TF activity with important implications for generation of cell-type diversity in vivo and in vitro.

overall_design: 6 ChIP-seq libraries and 32 ATAC-seq libraries from C. elegans embryos to assess TBX-37/38-bound genomic regions and their differential accessibility over time in sorted cells from the ABa and ABp lineages and mature ASEL/ASER neurons.

first: Julien

last: Charest

first: Thomas

last: Daniele

first: Aleksandr

last: Bykov

first: Ariane

last: Mandlbauer

first: Luisa

last: Cochella


title: Enhancing calmodulin binding to cardiac ryanodine receptor completely inhibits pressure-overload induced hypertrophic signaling

city: Ube,Yamaguchi

first: Shigeki

last: Kobayashi

country: Japan

institute: Yamaguchi university

summary:
Purpose: Cardiac hypertrophy is a well-known major risk factor for poor prognosis in patients with cardiovascular diseases. Dysregulation of intracellular Ca2+ is involved in the pathogenesis of cardiac hypertrophy. However, the precise mechanism underlying cardiac hypertrophy remains elusive. Here, we investigated whether pressure-overload induced hypertrophy can be induced by destabilization of cardiac ryanodine receptor (RyR2) through calmodulin (CaM) dissociation and subsequent Ca2+ leakage, and whether it can be genetically rescued by enhancing the binding affinity of CaM to RyR2.
Methods: To examine the role of CaM-RyR2 complex in the development of pressure-overload induced cardiac hypertrophy, whole transcriptome analysis using RNA-seq analysis in the hearts from WT and homozygous RyR2V3599K/V3599K (V3599K) mice with or without transverse aortic constriction (TAC) was performed to elucidate the RyR2 signaling pathway in the heart.
Results: Gene expression increased in WT (+TAC) hearts compared to WT (-TAC) hearts; however, this increase was not observed in V3599K (+TAC) hearts.
Conclusions:  Enhanced CaM binding to RyR2 decreased expression of hypertrophy-related genes.

overall_design: Heart mRNA profiles of  wild type  and V3559K mice with or without TAC.

first: Michiaki

last: Kohno

first: Takeshi

last: Yamamoto

first: Ryosuke

last: Yoshitomi

first: Toshiro

last: Kajii

first: Shohei

last: Fujii

first: Yoshihide

last: Nakamura

first: Takayoshi

last: Kato

first: Hitoshi

last: Uchinoumi

first: Tetsuro

last: Oda

first: Shinichi

last: Okuda

first: Kenji

last: Watanabe

first: Yoichi

last: Mizukami

first: Masafumi

last: Yano


title: 3D genome landscapes of primary effusion lymphoma cell lines link super-enhancers to dependency factors

city: Tampa

first: Mingxiang

last: Teng

state: FL

address: 12902 Magnolia Dr

department: Department of Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center and Research Institute

summary: H3K27ac HiChIP and ChIP-seq to identify super enhancers inprimary effusion lymphoma cell lines (PEL)

overall_design: We performed HiChIP and ChIP-seq in 4 different PEL cell lines (BC3, BCBL1, JSC and BC1) and used CRISPRi to validate those function links.

first: Chong

last: Wang

first: Bo

last: Zhao


title: AdipoR1/AdipoR2 dual agonist recovers nonalcoholic steatohepatitis and related fibrosis via endoplasmic reticulum-mitochondria axis

status: Public on Oct 03 2020

city: guangzhou

first: Xianxing

last: Jiang

state: guangdong

address: 132 east outer ring road

institute: Sun Yat-Sen University

summary: Nonalcoholic steatohepatitis (NASH) and associated liver fibrosis have limited therapy options. We report a novel adiponectin-based dual agonist for adiponectin receptors 1 and 2 with a longer half-life, and show that it ameliorates NASH and liver fibrosis in mouse models.

overall_design:
Mice liver mRNA profiles of control, NASH, and NASH with JT003 treatment mice; oil-treated control, fibrosis with CCl4 or JT003 treatment mice.
Submitter declares raw data files are unavailable for the oil-treated control, fibrosis with CCl4 or JT003 treatment mice.


title: Germline Copy Number Variants are Associated with Methylation Variation in the Genome

city: Boston

first: Sunita

last: Setlur

address: 221 Longwood Avenue

institute: Brigham and Women's Hospital

summary: Illumina methylation 27 array (Illumina) analysis was performed on 24 HapMap individuals including one CEU trio (family 1463 including NA12878, NA12891, NA12892) and one YRI trio (family Y117 including NA19240, NA19238, NA19239)

overall_design: Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2


title: Genome-wide maps of chromatin state in Ad-UBE3B and control lymphoma cells

first: wang

last: feng

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of  RNAPII with promoters in mammalian cells. We performed ChIP sequencing with antibody to total RNAPII in UBE3B overexpression and control group. Inspection of multiple individual traces and global analyses showed that UBE3B overexpression globally reduced association of RNAPII with promoters.

overall_design: We performed ChIP sequencing with antibody to total RNAPII in UBE3B overexpression and control group and  globally analysed association of RNAPII with promoters.

first: Zhuo-wei

last: Hu

first: Ke

last: Li

first: Feng


title: CD45- sorted tumor cells from RANK+/+ and RANK-/- MMTV_PYMT late carcinomas

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge

summary: Transcriptional profile of either RANK+/+ or RANK-/- MMTV-PyMT late carcinomas, orthotopically injected in syngeneic RANK+/+ mice. Once host mice developed tumors, CD45- tumor cells were sorted by flow cytometry in order to compare changes on tumor gene expression caused by the absence of RANK protein.

overall_design: Two-condition experiment: RANK+/+ (WT) vs. RANK-/- (KO) MMTV_PYMT CD45- sorted tumor cells. Biological replicates: 3 RANK-/-  replicates, 3 RANK-/- replicates. Two technical replicates from each sample (A and B).

first: Guillermo

last: Yoldi Salinas

last: González Suárez


title: Cohesin depleted cells rebuild active and inactive nuclear compartments after mitosis

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Nuclear functions are essentially linked to nuclear compartmentalization. This study demonstrates that cohesin rings as anchors of chromatin loops are dispensable to rebuild a functional nuclear compartmentalization in cohesin depleted cells after passing through mitosis and formation of one daughter cell with a multilobulated nucleus (MLN). Super-resolved microscopy reveals co-aligned active and inactive nuclear compartments (ANC/INC) in these postmitotic nuclei, likely corresponding to A and B compartments, detected with Hi-C. MLN carry chromosome territories, built from chromatin domain clusters, pervaded by a system of interchromatin channels harboring splicing speckles. Channels are lined by transcriptionally competent chromatin, whereas repressed chromatin with higher compaction locates in the interior of chromatin clusters. MLN pass through S-phase with typical early and mid-to-late replication patterns. Sites of DNA synthesis become physically larger, consistent with a model where cohesin dependent loop extrusion tends to compact intervals of replicating chromatin, whereas their genomic boundaries are associated with compartmentalization.

overall_design: Microscopy, Hi-C, and Repli-Seq in HCT-116 cmvOsTir1 RAD21-mAC cells


title: Evolution of regulatory signatures in primate cortical neurons at cell-type resolution [RNA-Seq]

city: Bronx

first: Stella

last: Dracheva

state: New York

address: James J. Peters VA Medical Center,130 W Kingsbridge Rd

department: Dept. of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary: The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type–specific regulatory landscapes in the cortex re- main largely unexplored. Here we report epigenomic and tran- scriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. Using genome- wide profiling of the H3K27ac histone modification, we identify neuron-subtype–specific regulatory elements that previously went undetected in bulk brain tissue samples. Human-specific regula- tory changes are uncovered in multiple genes, including those as- sociated with language, autism spectrum disorder, and drug addiction. We observe preferential evolutionary divergence in neuron subtype-specific regulatory elements and show that a sub- stantial fraction of pan-neuronal regulatory elements undergos subtype-specific evolutionary changes. This study sheds light on the interplay between regulatory evolution and cell- type–dependent gene-expression programs, and provides a re- source for further exploration of human brain evolution and function.

sample_organism:
Macaca mulatta
Pan troglodytes

platform_organism:
Macaca mulatta
Pan troglodytes

overall_design:
Total RNA was isolated and RNA-seq analysis performed on sorted nuclei of glutamatergic and MGE-derived GABAergic neurons, obtained from prefrontal cortex of chimpanzees, rhesus macaques and humans.
Raw data (fastq) for human samples were taken from: Kozlenkov et al, 2018, Science Advances, 4(9):eaau6190

first: Alexey

last: Kozlenkov


title: Evolution of regulatory signatures in primate cortical neurons at cell-type resolution

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

overall_design: Refer to individual Series


title: Osteoporosis is characterized by altered expression of exosomal long noncoding RNAs

city: WuHan

first: Guosong

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Osteoporosis is a metabolic bone disease characterized by a decrease in bone mass and degradation of the bone microstructure, which increases bone fragility and risk of fracture. However, the molecular mechanisms of osteoporosis remain unclear. The current study attempts to elucidate the role of exosomal long noncoding RNA in the pathology of osteoporosis. Peripheral blood was collected from persons with (OP) or without (NC) osteoporosis, and the serum exosomes were extracted using ultra centrifugation process. Total RNA of exosomes was isolated, and the lncRNAs profiling was done using RNA-Seq experiments. In silico analysis resulted in identification of 393 differentially expressed (DE) lncRNAs in OP vs NC, with 296 that were up-regulated and 97 were down-regulated. Bioinformatics analysis of potential target mRNAs of lncRNAs with cis-acting mechanism showed that mRNAs co-located with  DE  lncRNAs were highly enriched in osteoporosis-related pathways, including regulation of insulin secretion, activation of MAPK activity, cellular response to metal ions, fucosylation and proteolysis. Together these results suggest that lncRNAs of serum exosomes could play a significant role in development of osteoporosis and such information may be helpful in developing diagnostic markers and therapeutic modules for osteoporosis.

overall_design: RNA-seq profiles of serum exosomes from persons with (OP) or without (NC) osteoporosis generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Zhaowei


title: Next Generation Sequencing Facilitates Quantitative Analysis of Msx1-overexpressed and Control C2C12 Cells Transcriptomes

status: Public on Oct 02 2020

city: Shanghai

first: Gang

address: 2005 Songhu Rd

department: School of life sciences

institute: Fudan university

summary:
Purpose: RNA-seq analysis to evaluate the impact of Msx1-overexpression on the transcriptome of C2C12 cells.
Methods: Total RNA was isolated with TRIzol from Msx1-overexpressing C2C12 cells (n = 3) or control cells (n = 3). cDNA sequencing libraries were prepared with an NEBNext® Ultra™ RNA Library Prep Kit for Illumina. The RNA-Seq FASTQ raw data were trimmed to remove low-quality reads and adapters using Trimmomatic. The trimmed reads were aligned to the mouse reference genome UCSC GRCm38/mm10 with HISAT2. Gene and transcript quantification was performed using StringTie. The results of the mapping of the RNA-seq reads, transcript assembly and abundance estimation were reported as fragments per kilobase of exon per million fragments mapped (FPKM).

overall_design: mRNA profiles of  Msx1-overexpressing C2C12 cells (n = 3) or control cells (n = 3).

first: Yenan

last: Yang

first: Xiaoli

last: Zhu

first: Wanwan

last: Hou


title: Genome-wide maps of chromatin state in Ad-ube3b and control lymphoma cells

city: bei jing

address: nan wei road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College,

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of  p-RNAPII(ser2) with promoters in mammalian cells. We performed ChIP sequencing with antibody to total p-RNAPII(ser2) in UBE3B overexpression and control group. Inspection of multiple individual traces and global analyses showed that UBE3B overexpression globally reduced association of p-RNAPII(ser2) with promoters.

overall_design: We performed ChIP sequencing with antibody to total p-RNAPII(ser2) in UBE3B overexpression  and control group and  globally analysed association of p-RNAPII(ser2)with promoters.


title: Genome-wide maps of chromatin state in WT c-Myc and K427R mutant lymphoma cells

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of  c-Myc with core promoters of its target genes  in mammalian cells. We performed ChIP sequencing with antibody to total c-Myc with core promoters of its target genes in WT c-Myc and K427R mutant group. Inspection of multiple individual traces and global analyses showed that the K427R mutant globally reduced association of c-Myc with core promoters of its target genes.

overall_design: we precipitated chromatin with tag antibody to WT c-Myc and K427R mutant, and sequenced the precipitated material. K427 mutation reduced association of c-Myc with core promoters of its target genes


title: Genome-wide maps of chromatin state in ad-ube3b or Pep2-CM4-treated and control lymphoma cells

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of  RNAPII with promoters in mammalian cells. We performed ChIP sequencing with antibody to total RNAPII in UBE3B overexpression or Pep2-CM4-treated and control group. Inspection of multiple individual traces and global analyses showed that UBE3B overexpression globally reduced association of RNAPII with promoters.

overall_design: We performed ChIP sequencing with antibody to total RNAPII in UBE3B overexpression or Pep2-CM4-treated and control group and  globally analysed association of RNAPII with promoters.


title: Next Generation Sequencing Facilitates Quantitative Analysis of control and Pep2-CM4-treated cells' Transcriptomes in lymphoma

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in  control and Pep2-CM4-treated  lymphoma cells  by using NGS-derived lymphoma transcriptome profiling (RNA-seq).
Methods:   Control and Pep2-CM4-treated cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with  following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including  GO enrichment analysis and KEGG .
Conclusions: Our study represents the first detailed analysis of  Control and Pep2-CM4-treated cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.


title: RNA-Seq of Myf6-knockout versus Wild-type satellite cells

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

country: Canada

institute: McGill University

summary: In metazoans, skeletal muscle evolved to contract and produce force.  Recent experimental evidence, however, suggests  that  skeletal muscle has also acquired  endocrine functions and produces a vast array of muscle-derived cytokines  and growth  factors, collectively  called myokines. The mechanisms that regulate myokine production and their effect on the resident stem cell population inskeletal muscle remain unknown. Here, we report that in adult skeletal muscle,  Myf6/MRF4  is a major regulator of myokine expression. Genetic  deletion  of  Myf6  in skeletal  muscle leads  to reduction of the muscle stem  cell (MuSCs)  pool  in  adult  mice  in  a myokine-dependent  manner  but,  surprisingly,  does  not  disrupt  muscle differentiation. Using ChIP-Seq and gene expression analyses of myogenic factors, we show that Myf6/MRF4 is a direct regulator of many myokines  and muscle-secreted  proteins,  including ligands  for  canonical signaling pathways such as EGFR and VEGFR.  Consequently, in Myf6-deficient animals,MuSCs increasingly break quiescence, but can nevertheless undergo differentiation. Lastly, we show that Myf6 and its gene network rapidly respondto aerobic and anaerobic exercise. Together, these findings indicate that control of myokine signaling by Myf6 is critical to maintain muscle stem cell pool and skeletal muscle function via myokine signaling.

overall_design: Satellite cells from two 10 month-old female wild-type mice, two 10 month-old female Myf6-knockout mice and three 4 week-old male wild-type mice were analyzed.


title: Next Generation Sequencing Facilitates Quantitative Analysis of lymphoma cells‘ Transcriptomes from the lymph node tissues  of Myc-E and Myc-ECreCD19Trib3F/+ mice

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in  Myc-E and Myc-ECreCD19Trib3F/+ mice‘ lymphoma cells   by using NGS-derived lymphoma transcriptome profiling (RNA-seq).
Methods: The Myc-E and Myc-ECreCD19Trib3F/+ mice' lymphoma cells were isolated, then these cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with  following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including  GO enrichment analysis and KEGG .
Conclusions: Our study represents the first detailed analysis of Myc-E and Myc-ECreCD19Trib3F/+ mice lymphoma cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: The Myc-E and Myc-ECreCD19Trib3F/+ mice' lymphoma cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

last: Wang


title: Lung transcriptome sequencing anlysis in Male Sprague-Dawley rats

status: Public on Oct 01 2020

city: Beijing

first: qianqian

last: li

address: No. 11, Bei San Huan Dong Lu, Chaoyang District

department: School of Traditional Chinese Medicine

institute: Beijing University of Chinese Medicine

summary:
Lung transcriptome sequencing anlysis in LPS-induced ALI model rats (Male Sprague-Dawley rats) after treatment with Ma Xing Shi Gan Decoction, In summary, our study suggests that MXSG inhibits viral invasion, proliferation, and mitigation of virus-induced lung injury, which may be a key mechanism of its therapeutic effect on COVID-19. These results provide experience for the treatment of infectious diseases and lung injury.
we dissected the chemical components of MXSG by liquid chromatography-mass spectrometry (LC-ESI-MS/MS) and analyzed the intervention pathways of MXSG based on components detected through network pharmacology. At the same time, the therapeutic effect of MXSG on COVID-19 was explained through published articles, and the relevant regulatory mechanism was proposed. Then, in this study, the regulatory effect of MXSG on inflammatory lung injury was explorated through transcriptome results.

first: chen

last: bai


title: Next Generation Sequencing Facilitates Quantitative Analysis of ad-control and ad-ube3b cells' Transcriptomes in lymphoma

first: wang

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in  ad-control and ad-ube3b  lymphoma cells  by using NGS-derived lymphoma transcriptome profiling (RNA-seq).
Methods:   Ad-con and Ad-ube3b cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with  following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including  GO enrichment analysis and KEGG .
Conclusions: Our study represents the first detailed analysis of  Ad-con and Ad-ube3b cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Zhuo-wei


title: Genome-wide maps of chromatin state in TRIB3-shRNA and control lymphoma cells

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of  RNAPII with promoters in mammalian cells. We performed ChIP sequencing with antibody to total RNAPII in TRIB3-cas9 and control group. Inspection of multiple individual traces and global analyses showed that TRIB3 deletion globally reduced association of RNAPII with promoters.

overall_design: we performed ChIP sequencing with antibody to total RNAPII in TRIB3 deleted group. Inspection of individual traces and global analyses showed that TRIB3 deletion globally reduced association of RNAPII with promoters.

first: Ke

first: Feng


title: SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability

city: La Jolla

first: Frank

last: Furnari

state: California

address: 9500 Gilman Drive

institute: UC San Diego

summary: We conducted  RNA sequencing of control and SMARCB1 knockdown cells at various neural differentiation states

overall_design: RNA sequencing of control and SMARCB1 knockdown cells by shRNA or CRISPRi knockdown at iPS, neural progenitor and neuron state induced with knockdown during the differentiation process or post-differentiation.

first: Alison

last: Parisian


title: Transcriptional Profiling of Leukocytes in Critically Ill COVID19 Patients

city: London

first: David

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

institute: Robarts Research Institute

summary:
Objective: COVID19 is caused by the SARS-CoV-2 virus and has been associated with severe inflammation leading to organ dysfunction and mortality. Our aim was to profile the transcriptome in leukocytes from critically ill ICU patients positive for COVID19 vs. those negative for COVID19 to better understand the COVID19 associated host response.
Design: Transcriptome profiling of buffy coat cells via ribonucleic acid sequencing (RNAseq) at the time of admission to the ICU.
Setting: Tertiary care ICU and academic laboratory.
Subjects: All patients admitted to the ICU suspected of being infected with SARS-CoV-2, using standardized hospital screening methodologies, had blood samples collected at the time of admission to the ICU.
Interventions: None.
Measurement and Main Results: Age- and sex-matched ICU patients that were either COVID19+ (PCR positive, 2 genes) or COVID19- (PCR negative) were enrolled. Cohorts were well-balanced with the exception that COVID19- patients had significantly higher total white blood cell counts and circulating neutrophils and COVID19+ patients were more likely to suffer bilateral pneumonia compared to COVID19- patients. Further, the mortality rate for this cohort of COVID19+ ICU patients was 29%. Transcriptional analysis revealed that when compared to COVID19- patients, the altered transcriptional responses of leukocytes in critically ill COVID19+ ICU patients appeared to be associated with multiple interrelated outcomes, including but not limited to robust interferon (IFN)-associated transcriptional responses, a marked decrease in the transcriptional activity of genes contributing to protein synthesis and the dysregulated expression of genes that contribute to coagulation, platelet activation, Toll-like receptor activation, neurotrophin signaling, and protein SUMOylation/ubiquitination.
Conclusions: COVID19+ patients on day 1 of admission to the ICU display a unique leukocyte transcriptional profile that distinguishes them from COVID19- patients. Identification of this profile provides guidance for future targeted studies exploring novel prognostic/therapeutic aspects of COVID19.

overall_design: A total of 14 buffy coat samples were analyzed from COVID19+ and COVID19- ICU patients.

first: Sean

last: Gill

first: Claudia

middle: C

last: dos Santos

last: O'Gorman

first: Eric

last: Patterson

first: Marat

last: Slessarev

first: Claudio

last: Martin

first: Mark

last: Daley

first: Michael

last: Miller

first: Gediminas

last: Cepinskas

first: Douglas

middle: D

last: Fraser


title: Genomic Investigations of Acute Munitions Exposures on the Health and Skin Microbiome Composition of Leopard Frog (Rana pipiens) Tadpoles

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: Abstract:  Natural communities of microbes inhabiting amphibian skin, the skin microbiome, are critical to supporting amphibian health and disease resistance.  To enable the pro-active health assessment and management of amphibians on Army installations and beyond, we investigated the effects of acute (96h) munitions exposures to Rana pipiens (leopard frog) tadpoles and the associated skin microbiome, integrated with RNAseq-based transcriptomic responses in the tadpole host.  Tadpoles were exposed to the legacy munition 2,4,6-trinitrotoluene (TNT), the new insensitive munition (IM) formulation, IMX-101, and the IM constituents nitroguinidine (NQ) and 1-methyl-3-nitroguanidine (MeNQ).  The 96h LC50 values and 95% confidence intervals were 2.6 (2.4, 2.8) for ΣTNT and 68.2 (62.9, 73.9) for IMX-101, respectively.  The NQ and MeNQ exposures caused no significant impacts on survival in 96h exposures even at maximum exposure levels of 3,560 and 5,285 mg/L, respectively.  However, NQ and MeNQ, as well as TNT and IMX-101 exposures, all elicited changes in the tadpole skin microbiome profile, as evidenced by significantly increased relative proportions of the Proteobacteria with increasing exposure concentrations, and significantly decreased alpha-diversity in the NQ exposure.  The potential for direct and indirect effects of munitions exposures on the skin microbiome were observed.  A direct effect of munitions on microbial flora included the observation of increased relative abundance of the munitions-tolerant, Aeromonadaceae and Pseudomonadaceae, in the NQ exposure.  Potential indirect effects on the tadpole skin microbiome resulting from tadpole-host responses to munitions included transcriptional responses indicative of potential changes in skin mucus-layer properties as well as altered production of antimicrobial peptides and innate immune factors.  Additional insights into the tadpole host’s transcriptional response to munitions exposures indicated that TNT and IMX-101 exposures each elicited significant enrichment of pathways involved in type-I and type-II xenobiotic metabolism mechanisms where dose-responsive increases in expression were observed.  Significant enrichment and increased transcriptional expression of heme and iron binding functions in the TNT exposures was likely connected with known mechanisms of TNT toxicity including hemolytic anemia and methemoglobinemia.  The significant enrichment and dose-responsive decrease in transcriptional expression of cell cycle pathways in the IMX-101 exposures was consistent with previous observations in fish, while significant enrichment of immune-related function in response to NQ exposure indicated potential immune suppression at the highest NQ exposure concentration.  Finally, the MeNQ exposures elicited significantly decreased transcriptional expression of keratin 16, type I, a gene likely involved in keratinization processes in amphibian skin.  Overall, munitions showed the potential to alter tadpole skin microbiome composition and affect transcriptional profiles in the amphibian host, some indicative of potentially impacted host health and immune status, each of which suggest potential implications for munitions exposure on disease susceptibility.

overall_design: The duration of the TNT, NQ, MeNQ and IMX-101 acute exposures was 96 h.  Target treatment levels for the TNT exposure were 1.5, 2.3, 3.4, and 5.1 mg/L.  Target treatment levels for the NQ exposure were 30, 170, 750, and 3750 mg/L; targets for the MeNQ exposure were  34, 150, 851 and 4255 mg/L; and targets for the IMX-101 exposure were 10, 20, 40 and 80 mg/L.  The target concentrations series for NQ and MeNQ were identical on a molar basis (0.3, 1.4, 7.2, 36 mmol/L).  Acute exposures were performed in 1 L beakers with a test solution volume of 500 ml.  Ten tadpoles were exposed in each beaker and 4 replicate beakers were tested per treatment.  Water renewal was performed on day 2 by replacing approximately 75% of the exposure water with spiked exposure water.  The tadpoles were fed frog brittle ad libitum at experiment initiation and on day 2, when food was added to the beakers 2 h before water renewal in order to minimize the effect of food on aqueous concentrations of the energetic compounds.  Aeration was provided to each beaker using an airstone.  Exposures were conducted in environmentally controlled chambers (Darwin Chambers Company, St. Louis, MO, USA) with a 16:8 light:dark cycle at a target temperature of 23°C.

first: Karl

last: Indest

first: Guilherme

last: Lotufo

first: Steven

last: Everman

first: Carina

last: Jung

last: Ballentine

first: Allison

last: Hoke

first: Bintu

last: Sowe

first: Aarti

last: Gautam

first: Rasha

last: Hammamieh

first: Ji

last: Qing

first: Natalie

last: Barker


title: Changes in DNA methylation accompany changes in gene expression during chondrocyte hypertrophic differentiation in vitro.

city: NEW YORK

first: Piali

last: Mukherjee

department: Medicine

institute: Weill Cornell Medicine

type: Methylation profiling by high throughput sequencing

summary: BACKGROUND: During osteoarthritis (OA), articular chondrocytes undergo phenotypic changes that resemble developmental patterns characteristic of growth plate chondrocytes. These phenotypic alterations lead to a hypertrophy-like phenotype characterized by altered production of extracellular matrix constituents and increased collagenase activity, which in turn results in cartilage destruction in OA disease. PURPOSE: To identify transcriptomic and epigenomic changes in murine primary articular chondrocytes undergoing hypertrophy-like differentiation in vitro. METHODS: We paired an in vitro 3D/pellet culture system that mimics chondrocyte hypertrophy with RNA sequencing (RNA-Seq) and enhanced reduced representation of bisulfite sequencing (ERRBS). RESULTS: We identified hypertrophy-associated changes in DNA methylation patterns in vitro. Integration of RNA-Seq and ERRBS datasets identified associations between changes in methylation and gene expression. CONCLUSION: Our integrative analyses showed that hypertrophic differentiation of articular chondrocytes is accompanied by transcriptomic and epigenomic changes in vitro.

overall_design: Chondrocytes were isolated from articular cartilage obtained from 5-to-6 days old C57BL/6J mice. 3D/pellet culture systems were used to drive chondrocyte hypertrophy in vitro. Pellets were harvested at 7 and 21 days for RNA (n=3 per time-point) or DNA isolation (n=3 per time-point). Total RNA was used for RNAseq, and DNA was used for Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) at the Epigenomics Core at Weill Cornell Medical College. CpG sites in the resulting ERRBS data were interrogated for methylation patterns and differential methylation using methylKit. The differential methylation data was queried for differentially methylated regions using eDMR. RNA-Seq reads passing Illumina’s purity filter were adapter trimmed using FLEXBAR barcode and adapter processing tool. The trimmed reads were aligned to the Gencode mm10/ GRC38.p3 build of the mouse genome using STAR aligner with default parameters. Read counts for RefSeq (NCBI) transcripts were then quantified from the alignments using the feature Counts software package. Significant differential expression (adjusted p-value < 0.05) was assessed between the read counts for the control and DMM sample groups using the DESeq2 R Bioconductor package. Gene Ontology (GO) enrichment analysis for Biological Processes and Molecular Functions was performed for differentially expressed genes and genes associated with differentially methylated regions using the clusterProfiler Biocondutor R package.

first: Purva

last: Singh

first: Samantha

last: Lessard

first: Brennan

last: Rourke

first: Miguel

last: Otero


title: Kindlin-2 modulates PTH1R to regulate bone mass and PTH actions in bone

city: Shen Zhen

first: Guozhi

last: Xiao

state: Guang Dong

address: No. 1088, Xueyuan Road

department: Biology

institute: Southern University of Science and Technology

summary: To investigation the role of PTH and Kindlin-2 in bone development, we performed single-cell RNA-sequencing. From Con-veh, Con-PTH, cKO-veh, cKO-PTH, we profiled more than 20k single cells, including multi-potent mesenchymal stromal cells (MSC), osteoprogenitors, osteoblasts, chondrocytes, fibroblasts, endothelial cells, smooth muscle cells, skeletal muscle cells, pericytes, and schwann cells. We found proportion of part of these cells were significant altered by PTH or Kindlin-2 loss, especially for MSC, osteoblast, chondrocyte, and fibroblast. Transcriptomic analysis revealed gene expression was dramatically regulated by PTH or Kindlin-2 loss.

overall_design: 3-month-old Kindlin-2f/f (control, n=6) and Dmp1-Cre; Kindlin-2f/f  (cKO, n=6) mice were treated with or without PTH daily continuously for 28d. Mice were sacrificed after the last PTH injection. Non-hematopoietic cells from bone marrow were extracted for single-cell RNA-sequencing

first: XueKun

last: Fu

first: Bo

last: Zhou

first: GuoZhi


title: Functional precision medicine identifies new therapeutic candidates for medulloblastoma (expression dataset)

first: Edwin

middle: Francisco

last: Juarez

address: 9500 Gilman Dr

institute: University of California San Diego

summary: Medulloblastoma (MB) is among the most common malignant brain tumors in children. Recent studies have identified at least four subgroups of the disease that differ in terms of molecular characteristics and patient outcomes. Despite this heterogeneity, most MB patients receive similar therapies, including surgery, radiation and intensive chemotherapy. Although these treatments prolong survival, many patients still die from the disease, and survivors suffer severe long-term side effects from therapy. We hypothesize that each MB patient is sensitive to different therapies, and that tailoring therapy based on the molecular and cellular characteristics of patients’ tumors will improve outcomes. To test this, we have assembled a panel of orthotopic patient-derived xenografts (PDXs) and subjected them to DNA sequencing, gene expression profiling and high-throughput drug screening. Analysis of DNA sequencing suggests that most MBs do not have actionable mutations that point to effective therapies. In contrast, gene expression and drug response data provide valuable information about potential therapies for every tumor. For example, drug screening demonstrates that actinomycin D – which is used for treatment of sarcoma but rarely for MB – is active against PDXs representing Group 3 MB, the most aggressive form of the disease. Finally, we show that functional analysis of tumor cells can be used in a clinical setting to identify more treatment options than sequencing alone. These studies suggest that it should be possible to move away from a one-size-fits-all approach and begin to treat each patient with therapies that are effective against their tumor.

overall_design: We analyzed RNA from 20 PDX samples and 7 primary tumors. Array data was processed by  No techinical replicates were performed.

first: Jessica

last: Rusert

first: Sebastiam

last: Brabetz

first: Marcel

last: Kool

first: Jill

last: Mesirov

first: Robert

last: Wechsler-Reya


title: Evolution of regulatory signatures in primate cortical neurons at cell-type resolution [ChIP-Seq]

first: Stella

last: Dracheva

summary: The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type–specific regulatory landscapes in the cortex re- main largely unexplored. Here we report epigenomic and tran- scriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. Using genome- wide profiling of the H3K27ac histone modification, we identify neuron-subtype–specific regulatory elements that previously went undetected in bulk brain tissue samples. Human-specific regula- tory changes are uncovered in multiple genes, including those as- sociated with language, autism spectrum disorder, and drug addiction. We observe preferential evolutionary divergence in neuron subtype-specific regulatory elements and show that a sub- stantial fraction of pan-neuronal regulatory elements undergos subtype-specific evolutionary changes. This study sheds light on the interplay between regulatory evolution and cell- type–dependent gene-expression programs, and provides a re- source for further exploration of human brain evolution and function.

overall_design:
ChIP-seq Histone 3 Lysine 27 acetylation (H3K27ac) profiling was performed on sorted nuclei of glutamatergic and MGE-derived GABAergic neurons, obtained from prefrontal cortex of chimpanzees, rhesus macaques and humans.
Raw data (fastq) for human samples were taken from: Kozlenkov et al, 2018, Science Advances, 4(9):eaau6190

first: Alexey

last: Kozlenkov


title: Rapid and efficient conversion of common marmoset fibroblasts into mature and functional neurons by overexpression of ASCL1 and microRNA-9/9*-124

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary: The common marmoset (marmoset; Callithrix jacchus) has been attracting much attention especially in the research fields of biomedical science and neuroscience, because of its potential to recapitulate the complex and multidimensional phenotypes of human diseases. Taking these advantages, several transgenic models have been reported so far. However, there remain several issues such as (i) it takes years to generate the late-onset disease models, and (ii) the onset age and severity of phenotypes can vary among individual animals due to their differences in the genetic background. In the present study, we established an efficient and rapid direct neuronal induction method (induced Neuron; iN) from embryonic and adult marmoset fibroblasts. This iN method is a minimally invasive approach to investigate cellular-level phenotypes in the marmoset brain. We overexpressed microRNA-9/9*-124 and a transcription factor ASCL1 in fibroblasts with a small molecule cocktail that ameliorates neuronal induction. The resultant iN cells from both embryonic and adult marmoset fibroblasts showed standard neuronal characteristic within 2 weeks, including neuronal specific gene expression and neuronal membrane spontaneous firing activity. Thus, this novel neuronal induction method may offer a new tool for investigating neurological phenotypes in vitro without collecting living brain tissue in non-human primate neurological disease models.

overall_design: RNA seq of marmoset fibroblasts and iNs

first: Akisa

last: Nemoto

first: Hideyuki

last: Okano


title: Biological effects of inhaled hydraulic fracturing sand dust in rats

city: Morgantown

first: Christina

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

summary: The pulmonary inflammatory response to inhalation exposure to fracking sand dust (FSD) was investigated in a rat model.  Adult male Sprague-Dawley rats were exposed by whole-body inhalation to air or an aerosol of FSD at concentrations of 10 or 30 mg/m3, 6 hours/day for 4 days.  The control and FSD-exposed rats were euthanized at post-exposure time intervals of 1, 7 or 27days and pulmonary inflammatory, cytotoxic and oxidant responses were determined.  Deposition of FSD particles was detected in the lungs of all the FSD-exposed rats.  Analysis of bronchoalveolar lavage parameters of toxicity, oxidant generation, and inflammation did not reveal any significant persistent pulmonary toxicity in the FSD- exposed rats.  Similarly, the lung histology of the FSD-exposed rats showed only minimal changes in influx of macrophages following the exposure.  Determination of global gene expression profiles detected significant differential expressions of only six and five genes in the 10 mg/m3, 1 day post-exposure, and the 30 mg/m3, 7-day post-exposure FSD groups, respectively.  Taken together, data obtained from the present study demonstrated that FSD inhalation exposure resulted in minimal/no toxicity or gene expression changes in the lungs of the rats.

overall_design: The rats were exposed by inhalation to filtered air or fracking sand dust (10 or 30 mg/m3, 6 hours/day for 4 days). At post exposure time intervals of 1, 7, and 27 days, the air and fracking sand dust exposed rats were euthanized and lung samples (n=5 for the 10 mg/m3 post exposure intervals 1 and 7 days; n=4 for 10 mg/m3 post exposure interval 27 days, and n=6 for the 30 mg/m3 fracking sand dust at all post exposure intervals) were used to determine gene expression profiles by RNA sequencing.

first: Tina

last: Sager

first: Pius

last: Joseph


title: Transcriptomic analyses in brains of exposed F0 zebrafish and their unexposed F2 offspring after exposure to a mixture of PCBs and PBDEs

city: Palavas

first: Mélanie

last: Blanc

address: Route de Maguelone

department: UMR MARBEC

institute: INRAE

summary: Polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) are persistent organic pollutants still present in aquatic environments despite their total or partial ban. Previously, we observed that an environmentally realistic mixture of these compounds affects energy balance, growth, and reproduction in exposed zebrafish (F0), and behavior in their unexposed offspring (F1-F4). In the present work, we performed lipidomic and transcriptomic analyses on brains of zebrafish (F0-F2) from exposed and control lineages to identify molecular changes that could explain the observed phenotypes. The use of both technologies highlighted that F0 zebrafish displayed impaired mitochondrial function and lipid metabolism dysregulation (depletion in triacylglycerols and phospholipids) which can explain disruption of energy homeostasis. A subset of the dysregulated biological pathways (Gene Ontology and Reactome databases) related to energetic metabolism and neurotransmission were inherited in F2. In addition, there were increasing effects on epigenetic pathways from the F0 to the F2 generation. Altogether, we show that the effects of an environmental exposure to PCBs and PBDEs on energetic metabolism as well as neurotransmission extend over 2 generations of zebrafish, possibly due to transgenerational epigenetic inheritance.

overall_design: RNA-sequencing was performed on F0 male fish from the F0 generation (6 replicates treatment, 6 replicates control), on F2 female fish (4 replicates treatment, 4 replicates control) and on F2 male fish (2 replicates treatment, 2 replicates control).

first: Xavier

last: Cousin


title: Re-assessment of the involvement of Snord115 in the serotonin 2C receptor pathway in a genetically relevant mouse model

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: SNORD115 has been proposed to promote the activity of serotonin (HTR2C) receptor via its ability to base-pair with its pre-mRNA and regulate alternative RNA splicing and/or A-to-I RNA editing. Because SNORD115 genes are deleted in most patients with the Prader-Willi syndrome (PWS), diminished HTR2C receptor activity could contribute to the impaired emotional response and/or compulsive overeating characteristic of this disease. In order to test this appealing but never demonstrated hypothesis in vivo, we created a CRISPR/Cas9-mediated Snord115 knockout mouse. Surprisingly, we uncovered only modest region-specific alterations in Htr2c RNA editing profiles while Htr2c alternative RNA splicing was unchanged. These subtle changes, whose functional relevance remains uncertain, were not accompanied by any discernible defects in anxio-depressive-like phenotypes. Energy balance and eating behaviour were also normal, even after exposure to high fat diet. Our study raises questions concerning the physiological role of SNORD115, notably its involvement in behavioural disturbance associated with PWS.

overall_design: 2 samples were analysed in biological triplicates, in total 6 samples

first: Hebras

last: Jade

first: Marty

last: Virginie

first: Jean

last: Personnaz

first: Pascale

last: Mercier

first: Henrik

last: Nielsen

first: Marion

last: Aguirrebengoa

first: Hervé

last: Seitz

first: Jean-Philippe

last: Pradère

first: Bruno

last: Guiard

first: Cavaillé

last: Jérôme


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

first: wang

last: feng

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in  Ctrl-Cas9 and TRIB3-Cas9  lymphoma cells  by using NGS-derived lymphoma transcriptome profiling (RNA-seq).
Methods:  Ctrl-Cas9 and TRIB3-Cas9 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with  following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including  GO enrichment analysis and KEGG .
Conclusions: Our study represents the first detailed analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Ctrl-Cas9 and TRIB3-Cas9 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina.

first: Zhuo-wei

last: Hu

first: Ke

last: Li

first: Feng

last: Wang


title: Targeting Fibroblast growth factor-23 (FGF23) responsive pathways in the control of renal phosphate and vitamin D metabolism

city: Indianapolis

first: Kenneth

middle: E.

last: White

state: IN

address: 635 Barnhill Dr, MS 5012

institute: Indiana University School of Medicine

summary: FGF23 is a bone-derived hormone that mediates renal phosphate reabsorption and 1,25(OH)2 vitamin D metabolism via its required co-receptor alpha-Klotho (KL).  The functional pathways guiding this hormone’s activity in kidney have not been studied extensively, and whether using other factors with overlapping signaling profiles to produce FGF23-like responses is unclear. To map FGF23-related genes, gene array and single-cell RNA sequencing were utilized on wild type mouse kidneys. After identifying Heparin-binding EGF-like growth factor (HBEGF) as an up-regulated gene in response to FGF23 delivery, KL-null and phosphate-deficient diet fed mouse models and in vitro experiments were utilized to further test HBEGF bioactivity in kidney. Gene array demonstrated that HBEGF was significantly up-regulated following FGF23 delivery to wild type (WT) mice. Next, mice injected with HBEGF had phenotypes consistent with partial FGF23-mimetic activity including robust induction of EGR1, and increased CYP24A1 mRNAs. Single cell RNA sequencing showed overlapping HBEGF and EGFR expression in the proximal tubule (PT), and KL expression in PT and distal tubule (DT) segments. In KL-null mice devoid of canonical FGF23 signaling, HBEGF injections significantly increased EGR1 and CYP24A, and correction of basally-elevated CYP27B1 was observed. In addition, mice placed on a phosphate deficient diet to suppress FGF23 had endogenously increased CYP27B1 mRNA, which was rescued in mice receiving HBEGF. In HEK293 renal epithelial cells, HBEGF and FGF23 increased CYP24A1 mRNA. Targeting pathways known to be downstream of FGF23 in kidney may help to control renal phosphate handling in diseases of altered FGF23 bioactivity.

overall_design: Mice, WT treated and untreated with FGF23 plus Klotho null mice untreated

first: Pu

last: Ni

first: Erica

last: Clinkenbeard

first: Megan

last: Noonan

first: Joseph

last: Richardville

first: Takashi

last: Hato

first: Danielle

last: Janosevic

first: Pierre

last: Dagher


title: Arterialization requires the timely suppression of cell growth

status: Public on Sep 30 2020

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: Arteries are thought to be formed through the induction of a highly conserved arterial genetic programme in a subset of vessels that will later experience an increase in oxygenated blood flow. The initial steps of arterial specification require both VEGF and Notch signalling. Here, we combined inducible genetic mosaics and transcriptomics to modulate and define the function of these signalling pathways in cell proliferation, arteriovenous (AV) differentiation and mobilization. We observed that endothelial cells (ECs) with high VEGF or Notch signalling are intrinsically biased to mobilize and form arteries; nevertheless, they are not genetically pre-determined, and can also form veins. Mechanistically, we found that higher VEGF and Notch signalling in pre-arterial capillaries suppresses Myc-dependent metabolic and cell-cycle activities, promoting the incorporation of ECs in arteries. Mosaic lineage tracing studies revealed that ECs completely lacking the Notch-Rbpj transcriptional activator complex rarely form arteries; however, these cells regained the ability to form arteries when Myc function was suppressed. Thus, arterial development does not require the direct induction of a Notch-dependent arterial differentiation programme, but rather the timely suppression of endothelial cell-cycle progression and metabolism, a process preceding arterial mobilization and complete differentiation.

overall_design: To isolate and profile coronary ECs with normal, half or full loss of Dll4 signalling, we intercrossed Pdgfb-iCreERT2-IRES-EGFP mice with wildtype females (abbreviated here as Wt samples) or Dll4flox/flox Pdgfb-iCre-ERT2-EGFP mice with wildtype (abreviated here as Het samples) or Dll4 flox/flox females (abreviated here as KO samples). Tamoxifen was administered at E13.5 and several litters of independent females were collected at E14.5. Different groups of hearts carrying EGFP expression were obtained: controls (wt), Dll4 heterozygous mutants (het), and Dll4 homozygous mutants (KO). Embryonic hearts were dissected and then filtered through a 70-μm cell strainer, incubated for 30min at 4C with APC rat-anti-mouse CD31, and CD31+GFP+ ECs sorted by FACS. RNA was isolated from the sorted endothelial cells of  embryonic hearts with RNAeasy Micro kit – Qiagen. cDNA amplification (SMART-Seq v4 Ultra Low Input RNA Kit – Clontech-Takara), library preparation (Nextera XT DNA library preparation kit - Illumina) and single read Next generation sequencing (Illumina HiSeq 2500) were performed at the Genomics Unit at Centro Nacional de Investigaciones Cardiovasculares (CNIC).

first: Wen

last: Luo

first: Irene

last: Garcia-Gonzalez

first: Macarena

last: Fernández-Chacón

first: Verónica

last: Casquero-Garcia

first: Maria

middle: S

last: Sanchez-Muñoz

first: Severin

last: Mühleder

first: Lourdes

last: Garcia-Ortega

first: Jorge

last: Andrade

first: Michael

last: Potente

first: Rui

last: Benedito


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

first: wang

last: feng

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in  Ctrl-siRNA and c-Myc-siRNA  lymphoma cells  by using NGS-derived lymphoma transcriptome profiling (RNA-seq).
Methods:  Ctrl-siRNA and c-Myc-siRNA cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with  following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including  GO enrichment analysis and KEGG .
Conclusions: Our study represents the first detailed analysis of Ctrl-siRNA and c-Myc-siRNA cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Zhuo-wei

last: Hu

first: Ke

last: Li

first: Feng

last: Wang


title: Urothelial-to-Neural Lineage Plasticity Drives Progression to Small Cell Bladder Cancer [RNA]

city: Houston

first: David

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

summary: We report a comprehensive molecular analysis of 22 cases of SCC

overall_design: 22 cases of small cell carcinoma (FFPE) profiled by Illumina HumanHT-12 DASL Expression BeadChips. The dataset was used to compare with 80 cases of conventional UCs in GSE128192

first: Guoliang

last: Yang

first: Jolanta

last: Bondaruk

first: Ziqiao

first: Sangkyou

last: Lee

first: June

middle: G

first: Shizhen

last: Zhang

first: Woonyoung

last: Choi

first: Yan

first: Gang

first: Hui

last: Yao

first: Vipulkumar

last: Dadhania

first: Christopher

last: Logothetis

first: Arlene

last: Siefker-Radtke

first: Ashish

last: Kamat

first: Colin

last: Dinney

first: Dan

last: Theodorescu

first: Marek

last: Kimmel

first: Peng

last: Wei

first: Yu

last: Liang

first: Charles

last: Guo

first: John

middle: N

last: Weinstein

last: McConkey

first: Bogdan

last: Czerniak


title: SMARCB1 loss interacts with neuronal differentiation state to block maturation in an organoid model

first: Frank

last: Furnari

summary: We conducted 10X single-cell RNA sequencing of control organoids and organoids differentiated with SMARCB1 knockdown from Day 0 of protocol

overall_design: Single-cell RNA sequencing of control and SMARCB1 knockdown organoids with knockdown during the differentiation process.

first: Alison

last: Parisian


title: TRF2-mediated telomere protection is dispensable in pluripotent stem cells

city: Bethesda

first: Eros

last: Lazzerini Denchi

state: MD

address: 9000 Rockville Pike building 37, room 2144B

institute: National Cancer Institute

summary: Transcriptional response to telomere dysfunction in ES and differentiated cells

overall_design: ES cells and differentiated cells derived from ES were analyzed in the presence or absence of OHT

last: Denchi

first: Marta

last: Markiewicz-Potoczny


title: Rapid and efficacious humoral responses are required for recovery from hemorrhagic fever with renal syndrome

city: Taian

first: chuansong

last: quan

state: - Select -

address: yingsheng road 2

department: School of Basic Medical Sciences

institute: shandong first medical university

summary: Hemorrhagic fever with renal syndrome (HFRS) caused by hantaan virus (HTNV) infection displays variable clinical signs. Humoral responses are important players against HTNV infections, however, this process is poorly understood. Herein, we investigated the phenotype, temporal dynamics, and characteristics of B-cell receptor repertoire (BCR) in a patient cohort with HFRS. The serological proﬁle was characterized by low expression level of NP-speciﬁc antibody in severe cases. Importantly, B-cell subsets were activated and proliferated within the first two weeks of symptom onset, and the moderate cases reacted more rapidly. BCR analysis in the recovery phase revealed immunoglobulin gene diversity had dramatical rise and progressed more significant in the moderate group. The transcription of gene sets related to B-cell was lower, but the inflammatory sets were over-activated in severe cases. These data suggested the clinical signs and diseases recovery in HFRS patients were benefitted from rapid and efficacious humoral responses.

overall_design: Clinical specimens were collected from HFRS patients at Baoji central hospital from November 2018 to January 2019. NP-IgM and NP-IgG in serum specimens were detected by serological testing for HTNV diagnosis. According to the diagnostic criteria from the prevention and treatment strategy of HFRS promulgated by the Ministry of Health, People’s Republic of China, the patients were classified into four clinical types: mild, moderate, severe, and critical (Ma et al., 2015). To depict the dynamic changes of humoral response, the consecutive blood samples of HTNV patients with difference clinical types were collected.

first: Yaoni

last: Li

first: Chuansong

last: Quan

first: Weijia

last: Xing

first: Peihan

last: Wang

first: Jiming

last: Gao

first: Zhenjie

last: Zhang

first: Xiaolin

last: Jiang

first: Chuanmin

last: Ma

first: Michael

last: Carr

first: Qian

last: He

first: Lei

first: Yuhai

last: Bi

first: Hua

last: Tang

first: Weifeng

last: Shi


title: Bisphenol A and membrane estrogen receptor activation in the mammalian preimplantation embryo

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

summary:
The goal of this project is to mimic the ART conditions to expose mouse embryos to this kind of plastic devices in order to analyse its consequences on embryo preimplantation development (embryo developmental kinetic, blastocyst rate and quality of the blastocyst), on embryo gene expression (transcriptomic analysis) and epigenetic modulation (LINE-1 Orf2 expression). In parallel, the project aims to demonstrate that BPA is indeed implicated in those observations and to evidence the role of GPER using specific GPER antagonist drugs.
Outbred CD1 Swiss CD1 mice embryos were handled according to 6 different conditions: HC1: manipulation with polycarbonate stripper; HC2: manipulation with glass stripper; HC3: exposure to BPA; HC4: exposure to G15 and manipulation with polycarbonate stripper; HC5: exposure to BPA and G15; HC6: manipulation with glass stripper and use of glass dishes.

overall_design: 15 frozen expanded blastocysts by condition (except HC6: 20 blastocyst), 4 series per condition.

first: Roger

last: Leandri

first: Jessika

last: Moreau

first: Claire

last: Naylies

first: Anthony

last: Emile


title: EZH2-GATA6 axis in Pancreatic ductal adenocarcinoma [ChIP-Seq]

city: GOETTINGEN

first: SHILPA

last: PATIL

state: No further selection needed

address: ROBERT KOCH STRASSE 40

institute: UNIVERSITY MEDICAL CENTER GOETTINGEN

summary: We conducted ChIP-seq experiments to investigate the role of EZH2 in Pancreatic ductal adenocarcinoma

overall_design: ChIP-seq profiles for EZH2 in NKC cells (mouse PDAC cell line carrying pancreas specific-Kras mutation (KrasG12D) and constitutive activation of NFATc1).ChIP-seq profiles for H3K27me3 and H3K4me3 in NKC cells transfected with shRNA control and shRNA EZH2. Three replicated per condition were analysed.

first: Elisabeth

last: Hessmann

first: Shilpa

last: Patil

first: Zhe


title: EZH2-GATA6 axis in Pancreatic ductal adenocarcinoma [RNA-Seq]

summary: We conducted RNA-seq experiments to investigate the role of EZH2 in Pancreatic ductal adenocarcinoma

overall_design: RNA-seq profiles for EZH2 in NKC cells (mouse PDAC cell line carrying pancreas specific-Kras mutation (KrasG12D) transfected with shRNA control and shRNA EZH2. Three replicated per condition were analysed.


title: Df(h15q13)/+ mouse model reveals loss of astrocytes and synaptic-related changes of the excitatory and inhibitory circuits in the medial prefrontal cortex.

city: Aarhus

first: Abdel-Rahman

last: Al-Absi

address: Palle Juul Jensens Boulevard 99

institute: Aarhus University

summary: RNA sequencing is applied to medial preforntal cortex (mPFC) in Df(h15q13)/+ mouse model of the 15q13.3 hemizygous deletion. The overall goal is to identify the transcriptomic signature of the 15q13.3 deletion.

overall_design: RNA sequencing was performed in mPFC of 8-10 weeks male Df(h15q13)/+ mice (n=7) and wild type littermates (n=8) using BGISEQ-500 platform.


title: Highly Efficient, Massively-Parallel Single-Cell RNA-Seq Reveals Cellular States and Molecular Features of Human Skin Pathology

city: Cambridge

first: Ken

last: Dower

state: MA

address: 1 Portland Street

department: Inflammation & Immunology

institute: Pfizer

summary: The development of high-throughput single-cell RNA-sequencing (scRNA-Seq) methodologies has empowered the characterization of complex biological samples by dramatically increasing the number of constituent cells that can be examined concurrently. Nevertheless, these approaches typically recover substantially less information per-cell as compared to lower-throughput microtiter plate-based strategies. To uncover critical phenotypic differences among cells and effectively link scRNA-Seq observations to legacy datasets, reliable detection of phenotype-defining transcripts – such as transcription factors, affinity receptors, and signaling molecules – by these methods is essential. Here, we describe a substantially improved massively-parallel scRNA-Seq protocol we term Seq-Well S^3 (“Second-Strand Synthesis”) that increases the efficiency of transcript capture and gene detection by up to 10- and 5-fold, respectively, relative to previous iterations, surpassing best-in-class commercial analogs. We first characterized the performance of Seq-Well S^3 in cell lines and PBMCs, and then examined five different inflammatory skin diseases, illustrative of distinct types of inflammation, to explore the breadth of potential immune and parenchymal cell states. Our work presents an essential methodological advance as well as a valuable resource for studying the cellular and molecular features that inform human skin inflammation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Profile five different inflammatory skin diseases using scRNA-Seq

first: Marc

middle: H

last: Wadsworth II

first: Travis

last: Hughes

first: Todd

last: Gierahn

first: Robert

last: Modlin

first: J

last: Love

first: Alex

last: Shalek


title: Noise exposures causing hearing loss generate proteotoxic stress and activate the proteostasis network

status: Public on Nov 03 2020

city: Chicago

first: Jeffrey

last: Savas

state: Illinois

address: 303 E. Chicago Avenue, Ward 12-013

department: Neurology

institute: Northwestern University

summary: We investigate how noise insults affect the cochlea with proteomics and functional assays. Quantitative proteomics reveals that exposure to loud noise causes proteotoxicity. We identify and confirm hundreds of proteins that accumulate, including cytoskeletal proteins, and several nodes of the proteostasis network. Transcriptomic analysis reveals that a subset of the genes encoding these proteins also increase acutely after noise exposure, including numerous proteasome subunits.

overall_design: Cochlear mRNA profiles of 60-day old FVB/NCrl mice after 30 minute exposures to 70, 94 and 105 dB SPL noise.

first: Nopporn

last: Jongkamonwiwat

first: Miguel

middle: A

last: Ramirez

first: Seby

last: Edassery


title: GRB10 sustains AR activity by interacting with PP2A in prostate cancer cells

city: Vancouver

first: Yuzhuo

last: Wang

state: BC

address: 2660 Oak Street

department: Vancouver Prostate Centre

institute: University of British Columbia

summary: Prostate cancer (PCa) progression is driven by androgen receptor (AR) signaling. Unfortunately, androgen-deprivation therapy and the use of even more potent AR pathway inhibitors (ARPI) cannot bring about a cure. ARPI resistance (i.e. castration-resistant PCa, CRPC) will inevitably develop. Previously, we demonstrated that GRB10 is an AR transcriptionally-repressed gene that functionally contributes to CRPC development and ARPI resistance. GRB10 expression is elevated prior to CRPC development in our patient-derived xenograft models and is significantly upregulated in clinical CRPC samples. Here, we analyzed transcriptomic data from GRB10 knockdown in PCa cells and found that AR signaling is downregulated. While the mRNA expression of AR target genes decreased upon GRB10 knockdown, AR expression was not affected at the mRNA or protein level. We further found that phosphorylation of AR serine 81 (S81), which is critical for AR transcriptional activity, is decreased by GRB10 knockdown and increased by its overexpression. Luciferase assay using GRB10-knockdown cells also indicated reduced AR activity. Immunoprecipitation coupled with mass spectrometry revealed an interaction between GRB10 and the PP2A complex, which is a known phosphatase of AR. Further validations and analyses showed that GRB10 directly binds to the PP2Ac catalytic subunit with its PH domain. Mechanistically, GRB10 knockdown increased PP2Ac protein stability, which in turn decreased AR S81 phosphorylation and reduced AR activity. Our findings indicate a reciprocal feedback between GRB10 and AR signaling, implying the importance of GRB10 in PCa progression.

overall_design: LNCaP cell was transduced with lentiviral particles delivering control or GRB10 shRNA. Total RNA was extracted from stable cell lines, and applied for gene expression profiling analysis using Agilent SurePrint G3 Human Gene Expression v3 8x60K array.

first: Jun

last: Hao

first: Anne

last: Haegert

first: Dong

last: Lin


title: Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

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

overall_design: Refer to individual Series