title: Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development (RNA-seq)

status: Public on Aug 31 2020

first: Susan

last: Baserga

address: 333 Cedar St., SHM C114

institute: Yale University

summary: We investigated the role of Paired Box 9 in regulating the transcription of mRNAs required for human ribosome biogenesis and craniofacial development.

overall_design: RNA-seq of human MCF10A cells treated with a non-targeting siRNA (siNT) or siRNAs targeting PAX9 (siPAX9) for 72 hours.

first: Katherine

last: Farley-Barnes


title: Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development (RNAPII ChIP-seq)

city: New Haven

middle: J

state: CT

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: RNAPII ChIP-seq of human MCF10A cells treated with a non-targeting siRNA (siNT) or siRNAs targeting PAX9 (siPAX9) for 72 hours.


title: Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: HDAC3 ensures stepwise epidermal stratification via NCoR/SMRT-reliant mechanisms independent of its histone deacetylase activity (HDAC3 NCoRSMRT microarray)

status: Public on Aug 23 2020

city: New York

first: Sarah

middle: E

last: Millar

state: NY

address: Icahn Building, Floor 13 Room 020C, 1425 Madison Ave

department: Developmental, Cell and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary:
Chromatin modifiers play critical roles in epidermal development, but the functions of histone deacetylases in this context are poorly understood. We find that the Class I HDAC, HDAC3, is expressed broadly in embryonic epidermis, and is required for its orderly stepwise stratification. Stability of HDAC3 protein in vivo is reliant on NCoR and SMRT, which function redundantly in epidermal development. However, point mutations in the NCoR and SMRT Deacetylase Activating Domains, which are required for HDAC3’s enzymatic function, permit normal stratification, indicating that HDAC3’s roles in this context are independent of its histone deacetylase activity. HDAC3 functions both in conjunction with, and independent of, KLF4 to repress premature expression of different sets of terminal differentiation genes and suppresses expression of inflammatory cytokines through a RelA-dependent mechanism. These data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition.
We used microarrays to determine transcriptional changes in Hdac3 deleted epidermis compared to control and Ncor1/Ncor2 deleted epidermis compared to control.

overall_design: For the Hdac3 experiment, epidermis was collected from 5 E18.5 controls and 5 E18.5 mutants. For the Ncor1/Ncor2 experiment, epidermis was collected from 4 E18.5 controls and 4 E18.5 mutants.

middle: M

last: Szigety


title: Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification

status: Public on Aug 24 2020

city: Shanghai

first: l

last: y

address: No.138 Xinjun Ring Road, Minhang District

country: China

institute: OE

summary: The coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular trajectories of lineage specification during limb bud development, we used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb.

overall_design: one sample from murine embryonic hindlimb tissue

first: N

middle: H

last: Kelly

middle: P

last: Huynh


title: HDAC3 ensures stepwise epidermal stratification via NCoR/SMRT-reliant mechanisms independent of its histone deacetylase activity (KLF4 microarray)

summary:
Chromatin modifiers play critical roles in epidermal development, but the functions of histone deacetylases in this context are poorly understood. We find that the Class I HDAC, HDAC3, is expressed broadly in embryonic epidermis, and is required for its orderly stepwise stratification. Stability of HDAC3 protein in vivo is reliant on NCoR and SMRT, which function redundantly in epidermal development. However, point mutations in the NCoR and SMRT Deacetylase Activating Domains, which are required for HDAC3’s enzymatic function, permit normal stratification, indicating that HDAC3’s roles in this context are independent of its histone deacetylase activity. HDAC3 functions both in conjunction with, and independent of, KLF4 to repress premature expression of different sets of terminal differentiation genes and suppresses expression of inflammatory cytokines through a RelA-dependent mechanism. These data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition.
We used microarrays to determine transcriptional changes in Klf4 deleted epidermis compared to control.

overall_design: Epidermis was collected from E18.5 from 6 control and 5 mutant embryos derived from two separate litters.


title: Transcriptional profiling of human monocytes separated from patients with end-stage renal disease (ESRD) compared to healthy control (HC)

status: Public on Jul 30 2020

city: Seoul

first: Hee Young

last: Kim

address: 103 Daehak-ro, Jongno-gu,

department: Department of Microbiology and Immunology

country: South Korea

institute: Seoul National University College of Medicine

summary:
End-stage renal disease (ESRD) is the final stage of chronic kidney disease, which is increasingly prevalent worldwide and is associated with the progression of cardiovascular disease (CVD). Despite accumulating evidence that monocytes/macrophages play a pivotal role in the pathogenesis of CVDs in ESRD patients, the current knowledge of transcriptomic signatures of monocytes or macrophages in ESRD patients is very lacking. Therefore, we investigated the transcriptome profiling of monocyte separated from patients with ESRD and HC.
To explore the changes of gene expression in ESRD patient-derived monocytes, compared to monocytes from healthy controls, microarray were performed.

overall_design: The monocytes derived from three ESRD patients and three HCs were used for microarray analysis.

first: Hee

middle: Y

first: Won-Woo

last: Lee


title: HDAC3 ensures stepwise epidermal stratification via NCoR/SMRT-reliant mechanisms independent of its histone deacetylase activity


title: The stress response regulator HSF1 modulates natural killer cell anti-tumour immunity

status: Public on Feb 26 2021

first: Kathryn

middle: Grace

last: Hockemeyer

state: New York

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

summary:
Diverse cellular insults converge on activation of the heat shock factor 1 (HSF1), which regulates the proteotoxic stress response to maintain protein homoeostasis. HSF1 regulates numerous gene programmes beyond the proteotoxic stress response in a cell-type- and context-specific manner to promote malignancy. However, the role(s) of HSF1 in immune populations of the tumour microenvironment remain elusive. Here, we leverage an in vivo model of HSF1 activation and single-cell transcriptomic tumour profiling to show that augmented HSF1 activity in natural killer (NK) cells impairs cytotoxicity, cytokine production, and subsequent anti-tumour immunity. Mechanistically, HSF1 directly binds and regulates the expression of key mediators of NK cell effector function. This work demonstrates that HSF1 regulates the immune response under the stress conditions of the tumour microenvironment. These findings have important implications for enhancing the efficacy of adoptive NK cell therapies and for designing combinatorial strategies including modulators of NK cell-mediated tumour killing.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Iannis

last: Aifantis

first: Nikos

last: Kourtis


title: DIS3 ribonuclease is required for the maintenance of spermatogenic lineage in mice

status: Public on Aug 20 2020

city: Bethesda

first: Zhengpin

last: Wang

state: MD

address: National Institutes of Health, 9000 Rockville Pike

department: Laboratory of Cellular and Developmental Biology

institute: NIDDK, NIH

summary: Spermatogonial stem cells (SSCs) self-renewal and differentiation are the foundation for continious spermatognenesis in mice. Here, we investigate the essential role of DIS3 in maintaining SSC homeostasis and facilitating germ cell differentiation to ensure male fertility. Conditional inactivation of DIS3 in male germ cells have severely impaired SSC self-renewal and differentiation, which results in the failure of spermatogenesis associated with a Sertoli cell-only syndrome and adult sterility. RNA-seq analysis reveales that Dis3 deficiency abolishes its nucleolytic activity and causes significant dysregulation of the expression of transcripts in Dis3 mutant testes. We have also found that the pervasive transcription products described previously, such as Promoter Upstream Transcripts (PROMPTs), accumulate robustly upon DIS3 dysfunction in Dis3 cKO testes. In addition, scRNA-seq analysis indicates that DIS3 mutation significantly impairs germline stem cell development that blocks stem cell proliferation and differentiation. Overall, we show that DIS3 ribonuclease plays a critical role in the maintenance of spermatogenic lineage during spermatogenesis in mice.

overall_design: RNA-seq was performed using postnatal day 4 (P4) testes between control and Dis3 cKO mice in order to identify the differentially expressed genes.

first: Di

last: Wu

first: Guoyun

last: Yu

first: Jurrien

last: Dean


title: Airway-Associated Macrophages in Homeostasis and Repair

status: Public on Dec 30 2020

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: We isolated CD45+ cells after injury (Uninjured, Day1, Day4 and Day7) and CD45+F4/80+ cells from tracheal mesenchyme and dissociated lung, as well as CD45+ cells from peeled tracheal epithelium.

overall_design: Analysis of global transcriptome of airway and lung associated myeloid cells.

first: Anna

last: Engler

first: Alexandra

middle: B

last: Ysasi

first: Jason

middle: R

last: Rock


title: CPD-seq mapping of transcription-coupled DNA repair in yeast

status: Public on Jun 30 2020

city: Albuquerque

first: Peng

last: Mao

state: NM

address: 915 Camino de Salud. NE

institute: The University of New Mexico Comprehensive Cancer Center

summary: Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that responds to RNA polymerase (RNAP) stalling and removes DNA lesions from transcribed genes. Activation of TC-NER requires specific factors, such as human Cockayne syndrome group B (CSB) protein or its yeast homolog Rad26. Mutations in CSB are associated with the severe neurological disorder Cockayne syndrome. However, the genome-wide role of CSB/Rad26 in TC-NER, particularly in the context of chromatin organization, is not fully understood. Here we used single-nucleotide resolution UV damage mapping data to investigate the genome-wide function of Rad26 in TC-NER. Our data shows that Rad26 is critical for TC-NER in transcribed regions downstream of the first (+1) nucleosome; however, Rad26 is largely dispensable for TC-NER in the +1 nucleosome. We further show that the Rad26-independent TC-NER in the +1 nucleosome is correlated with high occupancy of the transcription initiation/repair factor TFIIH. Downstream of the +1 nucleosome, the combination of low TFIIH occupancy and high occupancy of the transcription elongation factor Spt4/Spt5 suppresses TC-NER when Rad26 is dysfunctional. Deletion of SPT4 significantly restores TC-NER in the downstream nucleosomes in a rad26∆ mutant. Collectively, these data indicate that the requirement for Rad26 in TC-NER is modulated by the distribution of TFIIH and Spt4/Spt5, and Rad26 mainly functions in the downstream nucleosomes to remove TC-NER suppression by Spt4/Spt5.

overall_design: UV-induced CPD lesions are mapped using a high throughput method named CPD-seq. CPD-seq data generated in WT, RAD26 deletion, and Rad26 ATPase-dead yeast strains were analyzed to study the genome-wide role of Rad26 in TC-NER.

first: John

last: Wyrick


title: A systems approach delivers a functional microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy

status: Public on Jun 10 2020

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are short noncoding RNAs that shape the gene expression landscape, including during the pathogenesis of temporal lobe epilepsy (TLE). In order to provide a full catalog of the miRNA changes that happen during experimental TLE, we sequenced Argonaute 2-loaded miRNAs in the hippocampus of three different animal models at regular intervals between the time of the initial precipitating insult to the establishment of spontaneous recurrent seizures. The commonly upregulated miRNAs were selected for a functional in vivo screen using oligonucleotide inhibitors. This revealed anti-seizure phenotypes upon inhibition of miR-10a-5p, miR-21-5p and miR-142-5p as well as neuroprotection-only effects for inhibition of miR-27a-3p and miR-431-5p. Pathway enrichment analysis on predicted and validated targets of these miRNAs indicated a role for TGFβ signaling in a shared seizure-modifying mechanism. Together, these results identify functional miRNAs in the hippocampus and a pipeline of new targets for seizure control in epilepsy.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: small RNA sequencing of Ago2-loaded miRNAs from three different rodent models across all phases of epilepsy development, two in mouse one in rat. Each model is sequenced in timepoints during epileptogenesis and at chronic phase. Each group is in triplicate.

first: Jorgen

last: Kjems

first: David

middle: C

last: Henshall


title: Control of limb initiation and antero-posterior patterning by cooperation between Meis and Tbx transcription factors [ChIP-seq]

status: Public on May 25 2020

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Meis1 and Meis2 are highly similar homeodomain transcription factors that regulate organogenesis through cooperation with Hox proteins. Overexpression experiments have suggested an essential role for Meis factors in limb proximo-distal patterning; however, loss-of-function experiments supporting this notion have not been reported. Meis1 and Meis2 are coexpressed during limb development, first in the lateral plate mesoderm, before limb induction, and then they become restricted to a proximal domain of the growing limb bud. Here, we report that complete double conditional Meis1/2 inactivation in the lateral plate mesoderm leads to limb agenesis. Meis factors cooperate with Tbx factors in this function, extensively co-binding with Tbx to genomic sites and co-regulating enhancers of fgf10, a critical factor in limb initiation. Limbs with three deleted Meis alleles develop a complete PD set of limb skeletal elements, but show proximal-specific skeletal hypoplasia and agenesis of posterior skeletal elements. This failure in posterior skeletal element specification reveals an early role of Meis factors in establishing the limb AP prepattern required for Shh activation at later stages. Our results uncover novel roles for Meis transcription factors in early limb development and identify their involvement in new molecular interaction networks that regulate organogenesis

overall_design: ChIPSeq was used to determine Meis genome occupancy in WT E10.5 (36 somites approximately) forelimbs and hindlimbs.

first: Irene

last: Delgado

first: Miguel

last: Torres


title: Prox-seq: Simultaneous quantification of proteins, protein complexes and mRNA in single-cells via proximity-sequencing

status: Public on May 16 2020

city: Chicago

first: Hoang Van

last: Phan

state: Illinois

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

summary:
A novel assay based on proximity ligation assay for high-throughput quantification of proteins, protein complexes and mRNA in single cells

Here we present proximity-sequencing (Prox-seq), a method for   simultaneous measurement of an individual cell’s proteins, protein   complexes and mRNA. Prox-seq utilizes deep sequencing and barcoded   proximity assays to measure proteins and their complexes from all   pairwise combinations of targeted proteins, without any prior knowledge   of which proteins can form complexes. The number of measured protein   complexes scales quadratically with the number of targeted proteins,   allowing for unparalleled multiplexing capacity. We developed a   high-throughput experimental and computational pipeline and demonstrated   the potential of Prox-Seq for multi-omic analysis with a panel of 13   proximity probes, enabling the measurement of 91 protein complexes,   along with thousands of mRNA molecules in single T cells and B cells.   Prox-seq is compatible with current single-cell RNA sequencing assays,   such as Drop-seq and Smart-seq2. Prox-seq provides access to an untapped   yet powerful measurement modality for single-cell phenotyping and has   the potential to discover new protein interactions in single-cells.

overall_design:
mRNA and PLA profiling of single Jurkat and Raji cells. PLA profiling of single human PBMCs. PLA profiling of single primary human macrophages after stimulation with LPS, PAM2CSK4, or both for 5 minutes, 2 hours or 12 hours.

Prox-seq profiling of single human PBMCs using 10x pipeline

first: Hoang


title: Nanopore sequencing reveals the roles of spermatozoal DNA N6-Methyladenine modification in mediating transgenerational lipid metabolism disorder induced by folic acid excessive consumption in chicken [RNA-seq]

status: Public on Dec 16 2020

city: Yangling

first: Shengru

address: 22 St.XiNong

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: Increased consumption of folic acid is prevalent due to its beneficial effects to help protecting from genome damage. Growing evidence is emphasizing the side effects pointing to excessive dietary intake. Effects of paternal folic acid excessive consumption on the offspring and its transgenerational inheritance mechanism remain elusive. We hypothesize that the folic acid excessive consumption will alter sperm DNA N6-methyladenine (6mA) and 5-methylcytosine (5mC) methylation, and heritably influence offspring metabolic homeostasis. This is the results of mRNA sequencing part

overall_design: Here, we fed roosters either folic acid-control or folic acid-excess diet throughout life. Paternal chronic folic acid excessive supplementation increased hepatic lipogenesis and lipid accumulation, but reduced lipolysis both in the roosters and their offspring, which was further confirmed to be induced by one carbon metabolism inhibition and gene expression alteration associated with PARR pathway. By nanopore sequencing, the spermatozoal genome-wide DNA (6mA and 5mC) methylation analysis revealed differential methylation pattern of genes implicated in lipid metabolic process. Notably, sperm DNA 6mA methylation could be involved in regulating lipid metabolism related genes expression in offspring chickens.


title: Control of limb initiation and antero-posterior patterning by cooperation between Meis and Tbx transcription factors


title: Transcriptomic profiling of non-alcoholic fatty liver induced by a high-fat and high-sucrose diet in the genetically diverse Collaborative Cross mice.

status: Public on May 05 2020

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

summary: Identification of molecular determinants of the inter-individual and sex variability in the development of nonalcoholic fatty liver disease (NAFLD) is of great importance. Next-generation sequencing (NGS) derived transcriptome profiling (RNA-seq) is a powerful technique to investigate gene transcripts and gene variants for the systems-based analysis of molecular and cellular pathways. The goal of this study was to determine transcriptomic profiles in the livers of male and female Collaborative Cross (CC) mice fed a high-fat and high-sucrose (HF/HS) diet or a control diet for 12 weeks and to identify inter-individual- and sex-specific gene expression differences during the development of NAFLD. Liver mRNA profiles of 10 CC mouse strains (CC003/Unc, CC011/Unc, CC013/GeniUnc, CC019/TauUnc, CC032/GeniUnc, CC040/TauUnc, CC041/TauUnc, CC042/GeniUnc, CC043/GeniUnc, and CC060/Unc) fed an HF/HS diet were generated by deep sequencing, in triplicate, using Illumina NextSeq 500 NGS system. The sequence reads that passed quality filters were analyzed at the transcript level using TopHat followed by Cufflinks. The total number of differentially expressed genes identified by RNA-seq varied between sexes and individual mouse strains and correlated with the severity of liver steatosis. Pathway analysis of differentially expressed genes showed dysregulation of genes involved in lipid metabolism, cell proliferation and death, inflammation, and fibrogenesis pathways in the livers of males and females CC mice. The RNA-seq data were validated and confirmed by qRT-PCR analysis of 27 selected genes associated with lipid metabolism and fibrogenesis using TaqMan assays. Our results show that RNA-seq based transcriptome analysis offers a comprehensive, quantitative, and qualitative evaluation of whole-genome expression that can be used for the identification of unique genes associated with the inter-individual and sex differences in susceptibility to NAFLD at the population level.

overall_design: Liver total RNA profiles of 10 CC mouse strains fed an HF/HS diet were generated by deep sequencing, in triplicate, using Illumina NextSeq 500 NGS system.

first: Rose

middle: A

last: Willett

first: Frederick

last: Beland

first: Ivan

last: Rusyn

first: Igor

last: Pogribny


title: Transcriptome profile of HCT 116p53-/- and HCT 116p53-/- RPL3 KO during Actinomycin (Act D) treatment

status: Public on Apr 13 2020

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To analyse gene expression differences between HCT 116p53-/- and HCT 116p53-/- RPL3 KO and/or during Actinomycin treatment (Act D)

overall_design: Total RNA was extracted from n=3  HCT 116p53-/- and n=3 and HCT 116p53-/- RPL3 KO treated with Act D 5nM for 24h and vehicle control

first: R

first: P

last: Carotenuto


title: Placental Editome Profiling Reveals Widespread RNA-Editing Dysregulation in Preeclampsia

status: Public on Apr 20 2020

city: Guangzhou

first: Xinping

last: Yang

state: Guangdong

address: 1838 N. Guangzhou Ave

institute: Southern Medical University

summary: Dysregulated RNA editing is well documented in several diseases such as cancer. The extent to which RNA editing might be involved in diseases originated in the placenta such as preeclampsia remains unknown, because RNA editing has rarely been studied in the placenta. Here, the RNA editome is systematically profiled on placentae from 9 patients with early-onset severe preeclampsia (EOSPE) and 32 normal controls, and a widespread RNA editing dysregulation in EOSPE has been identified. The mis-edited gene set is enriched with known preeclampsia-associated genes and differentially expressed genes in EOSPE. The “RNA editing events” at two microRNA binding sites in 3’-UTR of the LEP mRNA have been generated, which leads to increased expression level of LEP in trophoblast cells. Upregulation of LEP is also observed in the placentae of PE patients. These results suggest that widespread placental RNA editing may be involved in placental development and dysregulation of RNA editing in the placenta may contribute to the pathogenesis of preeclampsia.

overall_design: Placentae from 9 patients with early-onset severe preeclampsia (EOSPE) and 32 normal controls were used for RNA-sequencing on the Hiseq2500 platform. Sequences were aligned to human transcriptome (hg38). RNA editing sites were detected by GATK and annotated by ANNOVAR. RNA editing levels were calculated from RNA-sequencing reads. Editing levels between EOSPE and normal groups were compared to detect dysregulated RNA editing events. Gene expressions were estimated by htseq-count and differentially expressed genes were detected by comparing expression levels between two groups. Correlation between RNA editing levels and gene expressions were calculated to detect RNA editing events that might associate with expression regulating.

first: Xiaoxue

first: Jing

first: Xiaozhen

last: Liang

first: Qian

last: Chen

first: Sijia

last: Jiang

first: Haihua

last: Liu

first: Yue

last: Gao

first: Zhonglu

last: Ren

first: Yi-Wu

last: Shi

first: Sheng

last: Li

first: Yanhong

last: Yu

first: Mei

last: Zhong


title: Myeloid-derived suppressor cell subsets drive glioblastoma growth in a sex-specific manner

status: Public on Apr 11 2020

city: Jacksonville

first: Tae Hyun

last: Hwang

state: FL

address: 4500 San Pablo Rd S

department: Department of Artificial Intelligence and Informatics

institute: Mayo Clinic

summary: We report that monocytic (mMDSC) and granulocytic (gMDSC) MDSC susbsets have distinct expression profiles with ~300-1200 genes uniquely expressed on each subset. We further used these genes for pathway annotation. Our findings identified that mMDSC and gMDSC have unique pathway associations that can be targeted via distinct drug candidates.

overall_design: Examination of monoytic MDSC, granulocytic MDSC and nonMDSC populations from six biological replicates.

first: Defne

last: Bayik

first: Yadi

last: Zhou

first: Chihyun

last: Park

first: Changjin

last: Hong

first: Daniel

last: Silver

first: Adam

last: Lauko

first: Gustavo

last: Roversi

first: Dionyosios

last: Watson

first: Alice

last: Lo

first: Tyler

last: Alban

first: Mary

last: McGraw

first: Mia

middle: D

last: Sorensen

first: Matthew

last: Grabowski

first: Balint

last: Otvos

first: Michael

last: Vogelbaum

first: Craig

last: Horbinski

first: Bjarne

middle: W

last: Kristensen

first: Ahmad

last: Khalil

first: Tae

first: Manmeet

middle: S

last: Ahluwalia

first: Feixiong

last: Cheng

first: Justin

last: Lathia


title: HDAC3 ensures stepwise epidermal stratification via NCoR/SMRT-reliant mechanisms independent of its histone deacetylase activity (HDAC3_KLF4_ChIPseq)

first: Sarah

last: Millar

summary: Chromatin modifiers play critical roles in epidermal development, but the functions of histone deacetylases in this context are poorly understood. We find that the Class I HDAC, HDAC3, is expressed broadly in embryonic epidermis, and is required for its orderly stepwise stratification. Stability of HDAC3 protein in vivo is reliant on NCoR and SMRT, which function redundantly in epidermal development. However, point mutations in the NCoR and SMRT Deacetylase Activating Domains, which are required for HDAC3’s enzymatic function, permit normal stratification, indicating that HDAC3’s roles in this context are independent of its histone deacetylase activity. HDAC3 functions both in conjunction with, and independent of, KLF4 to repress premature expression of different sets of terminal differentiation genes and suppresses expression of inflammatory cytokines through a RelA-dependent mechanism. These data identify HDAC3 as a hub coordinating multiple aspects of epidermal barrier acquisition.

overall_design: Examination of HDAC3 and KLF4 genomic binding sites in E18.5 embryonic epidermis

first: Katherine

last: Szigety


title: Next Generation Sequencing of expression profile from synchronized WT and BRD4 KO MEFs cells at different time point

status: Public on Apr 08 2020

city: Frederick

first: Jack

last: Chen

address: SAIC-Frederick Miller Dr

institute: NIH

summary: Brd4f/f ERT2Cre MEFs are a type of fibroblast prepared from Brd4f/f ERT2Cre/- mouse embryo.  MEFs are widely used in life science researches, especially in stem cell biology. Using RNAseq  it was shown that many of cell cycle  genes were under control of BRD4.  Purpose of this study was to assess the effect of BRD4 KO in NGS derived transcriptome profiles of both WT and BRD4KO cells.

overall_design:
RNA-seq from synchronized WT and BRD4 KO MEFs cells at different time point. Brd4f/f ERT2Cre MEFs were prepared from Brd4f/f ERT2Cre/- mice.
mRNA profiles were generated from paired-end sequencing of duplicate samples using Illumina  Hiseq 2000.

first: Tiyun

last: Wu

first: Xiongfong

first: Keiko

last: Ozato


title: Dynamic cohesin is required for lineage specific distal gene regulation

status: Public on Oct 15 2020

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

summary: The cohesin complex plays essential roles in sister chromatin cohesin, chromosome organization and gene expression. The role it plays in the regulation of genes is incompletely understood. Here, we report that the cohesin release factor WAPL in mouse embryonic stem cells is crucial for maintaining a pool of dynamically bound cohesin to regions in the genome that are associated with lineage specific genes. These regions are enriched for active enhancer marks and transcription factor binding sites. Stabilization of cohesin, which leads to a loss of dynamic cohesin from these regions does not affect transcription factor binding or active enhancer marks, but does result in changes in promoter-enhancer interactions and downregulation of genes. Acute cohesin depletion can phenocopy the effect of WAPL depletion, showing that cohesin plays a crucial role in maintaining expression of lineage specific genes. The binding of dynamic cohesin to chromatin is dependent on the pluripotency transcription factor OCT4, but not NANOG. Finally, sites of dynamic cohesin binding sites are also found in differentiated cells, suggesting that they represent a general regulatory principle. We propose that the binding of dynamic cohesin to regulatory sites creates a favorable spatial environment in which promoters and enhancers can communicate to ensure proper gene expression.

overall_design: Acute depletion of WAPL, RAD21, SOX2, OCT4 and NANOG using degron techniques, followed by multiple molecular readouts using different sequencing techniques

first: Elzo

last: de Wit


title: Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation I

status: Public on Mar 06 2020

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

summary: The CCCTC-binding factor (CTCF) is widely regarded as a key player in chromosome organization in mammalian cells, yet direct assessment of its role in genome architecture and gene regulation has been difficult. Here, we use auxin-inducible degron techniques to acutely deplete CTCF to determine how loss of CTCF affect chromatin organization and gene expression. In mouse embryonic stem cells, depletion of CTCF results in rapid loss of chromatin loops anchored at CTCF-binding sites without major disruption to chromatin compartments and topological domains. In the absence of CTCF, many lineage-specific genes fail to express properly during differentiation to neural precursor cells, but transcriptional regulation of most genes is unaffected. Genes dependent on CTCF for induction are generally bound by the factor at promoters, which are connected to distal enhancers via CTCF-dependent chromatin loops. By contrast, CTCF-independent genes generally lack CTCF binding at the promoter and are generally closer to enhancers. These results refine our understanding of CTCF function in chromatin organization and gene regulation.

overall_design: PLAC-seq. Hi-C, mRNA-seq and ChIP-seq experiments in CTCF depleted mouse embryonic stem cells and during neural progenitor cell differentiation.

first: Naoki

last: Kubo


title: Sterol Regulatory Element-Binding Protein Sre1 regulates carotenogenesis in the red yeast Xanthophyllomyces dendrorhous.

status: Public on Sep 29 2020

city: Santiago

first: Melissa

last: Gómez

address: Las Palmeras 3425

department: Ciencias Ecológicas

country: Chile

institute: Universidad de Chile

summary: Xanthophyllomyces dendrorhous is a basidiomycete yeast that produces carotenoids, mainly astaxanthin. Astaxanthin is an organic pigment of commercial interest due to its antioxidant and coloring properties. X. dendrorhous has a functional Sterol Regulatory Element-Binding Protein (SREBP) pathway, and the Sre1 protein is the SREBP homolog in this yeast. However, how Sre1 is promoting the biosynthesis of sterols and carotenoids in X. dendrorhous is unknown. In this work, comparative RNA-seq analysis between modified X. dendrorhous strains that have an active Sre1 protein and the wild-type was performed to identify Sre1-dependent genes. In addition, Sre1 direct target genes were identified through chromatin immunoprecipitation combined with lambda exonuclease digestion (ChIP-exo) assays. SRE motifs were detected in the promoter regions of several Sre1 direct target genes and were consistent with the SREs described in other yeast species. Sre1 directly regulates genes related to ergosterol biosynthesis as well as genes related to the mevalonate pathway, which synthesizes the building blocks of isoprenoids, including carotenoids. Two carotenogenic genes, crtE and crtR, were also identified as Sre1 direct target genes. Thus, carotenogenesis in X. dendrorhous is regulated by Sre1 through the regulation of the mevalonate pathway and the regulation of the crtE and crtR genes. As the crtR gene encodes a cytochrome P450 reductase, Sre1 regulates pathways that include cytochrome P450 enzymes, such as the biosynthesis of carotenoids and sterols. These results demonstrate that Sre1 is a sterol master regulator that is conserved in X. dendrorhous.

overall_design: The wild-type strain CBS 6938, the mutants strains FLAG.Sre1-tagged (CBS.FLAG.SRE1N and CBS.cyp61-.FLAG.SRE1) and the mutant CBS.sre1- of Xanthophyllomyces dendrorhous were grown under standard culture conditions, until the late exponential phase of growth for the extraction of RNA for RNA-seq assays and the performance of ChIP-exo assays. For each assay, three biological replicates of each strain were included. For the RNA-seq assays, RNA samples were shipped to Macrogen (Macrogen Inc., Seoul, South Korea) for library preparation and sequencing. For the ChIP-exo assays, formaldehyde-cross linked cell pellets were prepared and shipped to Peconic LLC (State College, PA, USA) for the library preparation and sequencing. Paired-end reads of the RNA-seq and ChIP-exo assays were mapped to the genome assembly of X. dendrorhous included in the BioProject ID: PRJNA637109.

first: Sebastián

last: Campusano

first: María

last: Gutiérrez

first: Dionisia

last: Sepúlveda

first: Salvador

last: Barahona

first: Marcelo

last: Baeza

first: Víctor

last: Cifuentes

first: Jennifer

last: Alcaíno


title: Genomic characterization of Chinese clear cell renal cell carcinoma

status: Public on Feb 22 2020

city: Suzhou

first: Sheng

last: Guo

state: Jiangsu

address: Xinghu Street 218 BioBay A6

institute: Crown Bioscience Inc.

summary: Large-scale initiatives like The Cancer Genome Atlas (TCGA) performed omics studies on hundreds of kidney cancer patients, but predominantly on Caucasians. We now investigated genomics of Chinese clear cell renal cell carcinoma (ccRCC) patients.

overall_design: Transcriptome sequencing and genomic analysis were performed on 55 tumor tissues and 11 matched normal tissues from Chinese ccRCC patients.

first: Qiang

last: Zhao

first: Jia

last: Xue

first: Wubin

last: Qian

first: Tiezhu

first: Bin

last: Fan

first: Jie

last: Cai

first: Yongpeng

last: Ji

first: Yong

last: Yang

first: Qi-Xiang

last: Li

first: Ning

last: Zhang


title: Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation IV

first: Bing

last: Ren

first: Naoki

last: Kubo


title: Differential gene expression profile between two sunflower inbred lines with different ability to tolerate water stress

status: Public on Jan 15 2020

city: Río Cuarto

first: Sergio

middle: Gabriel

last: Alemano

state: Cordoba

address: Ruta 36. Km 601

department: Ciencias Naturales

country: Argentina

institute: Universidad Nacional de Río Cuarto

summary: This study characterizes and compares the gene expression profiles between aerial part and roots of two sunflower inbred lines with contrasting response to water stress: B59 (sensitive) and B71 (tolerant) under non-stress and water stress mimicked by mannitol application. The results allowed us to evaluate the response of the primary and secondary metabolism as studies of the hormonal pathways of jasmonic, salicylic and abscisic acid such as gibberellins and auxins among others.

overall_design: Analysis of global changes in gene expression profiles in response to water deficit, 44K Agilent one color array

first: Maximiliano

last: Escalante

first: Ana

last: Vigliocco

first: Sebastián

last: Moschen

first: Paula

last: Fernández

first: Ruth

last: Heinz

first: Francisco

last: Garcia-Garcia

first: Julio

last: Di Rienzo

first: Andrea

last: Andrade


title: Construction of A Human Cell Landscape by Single-cell mRNA-seq

status: Public on Feb 10 2020

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

summary: We used single-cell RNA sequencing to determine the cell type composition of all major human organs and construct a basic scheme for the human cell landscape (HCL). We reveal a single-cell hierarchy for many tissues that have not been well characterized previously. We present a “single-cell HCL analysis’’ pipeline that accurately defines human cell types and exemplify its utility in stem cell biology. Finally, we perform single-cell comparative analysis of the human and mouse cell atlases to reveal the conserved genetic networks in the mammalian system.

overall_design: Microwell-seq analyses of 60 types of human tissues and supplementary datasets  for the Mouse Cell Atlas data.

first: Xiaoping

last: Han

first: Ziming

last: Zhou

first: Lijiang

last: Fei

first: Huiyu

last: Sun

first: Renying

last: Wang

first: Jingjing

first: Haide

last: Chen


title: Single cell analysis of immune cell populations in mammary glands from 10-week-old mice

status: Public on May 31 2020

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

summary: Single cell RNA- sequencing analysis was performed on CD45+ cells isolated from mammary glands of 10-week-old mice. The purpose of this study was to identify and characterize macrophages in the normal mammary gland.

overall_design: Mammary glands were harvested from mice in diestrous and CD45+ immune cells were enriched using microbeads and subjected to single cell analysis.

first: Heather

last: Machado

first: Kathryn

last: Schwertfeger


title: Next generation sequencing facilitates lineage identity of RA-induced and RA/CHIR-induced ESCs

status: Public on Dec 10 2019

city: Hangzhou

first: Shihao

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: To uncover the mechanism that Wnt signaling modulates RA-induced ESC differentiation, we conducted time course RNA-seq analysis during the differentiation. Transcriptome profiles of RA-induced and RA/CHIR-induced ESC differentiation were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The RNA-seq data revealed a significant decrease in mesoderm (one of the major source of vascular SMCs) markers and increase in PrE markers in CHIR treated samples, while other lineage markers showed no significant expression, implying a diverging to PrE fate by Wnt activation. Subsequent hierarchical clustering analysis also showed that the gene expression profiles of cells derived from RA induction alone clustered with adult SMCs, while cells derived from RA/CHIR induction gradually clustered to XEN cells with differentiation and was very close to XEN cells at day 16, suggesting that RA/CHIR-induced ESCs differentiated into PrE lineage. This study provided new insights into the importance of RA/Wnt crosstalk in the lineage differentiation of ESCs.

overall_design: mRNA profiles of RA-induced and RA/CHIR-induced ESCs were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 system.

first: Liangbiao


title: RNA-Seq comparison between BrafCA;Cdkn2af/f control and BrafCA;Cdkn2af/f; Arf6Q67L mouse tumors

status: Public on Jul 01 2019

city: Salt Lake City

first: Allie

last: Grossmann

state: Utah

address: 2000 Circle of Hope

institute: University of Utah

summary: We analyzed transcriptomes from BRAFV600E/CDKN2ANull + ARF6Q67L mouse melanoma tumors to identify novel ARF6-regulated target genes and pathways. A unique gene expression signature in the ARF6Q67L tumors included upregulated genes related to known ARF6-dependent cell functions in trafficking, cell adhesion, motility, providing an internal positive control that helps to validate the utility of RNA sequencing as a discovery tool for ARF6.  Interestingly, mTOR signaling components were upregulated in ARF6Q67L tumors, including Pik3r1, which encodes the p85 regulatory subunit of PI3 kinase (PI3K). This finding is provocative because the PI3K pathway is strongly linked to melanoma disease progression and because our ARF6Q67L mice showed a comparable metastatic phenotype to mice with PTEN loss. Transcript levels of Pik3r1 were increased in ARF6Q67L tumors compared to BrafCA;Cdkn2af/f  controls.

overall_design: Comparison of gene expression between 6 Arf6Q67L tumors to 4 control tumors

first: Jae

last: Yoo


title: Molecular fingerprint of in vitro produced bovine embryos with high competence to establish pregnancy

status: Public on Aug 31 2019

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

institute: Utrecht University

summary: The objective of the current experiment was to identify the transcriptome profile of in vitro-derived embryos with high competence to establish and maintain gestation and in vitro-derived embryos treated with CSF2. Using P < 0.01 and a fold change > 2-fold or < 0.5 fold as cut-offs, there were 617 differentially expressed genes (DEG) between embryos that survived to day 30 vs those that did not, 470 DEG between embryos that survived to day 60 and those that did not, 432 DEG between embryos that maintained pregnancy from day 30 to day 60 vs those where pregnancy failed after day 30, and 635 DEG regulated by CSF2, regardless of pregnancy outcome. For each comparison, pathways and ontologies in which DEG were overrepresented included many related to cellular responses to stress and cell survival.

overall_design: Embryos produced with X-sorted sperm were cultured from day 5 to day 7 in serum-free medium containing 10 ng/ml recombinant bovine CSF2 or vehicle. The CSF2 was administered because this molecule can increase blastocyst competence for survival after embryo transfer. Blastocysts were harvested on day 7 of culture and manually bisected. One demi-embryo from a single blastocyst was transferred into a synchronized recipient and the other half was used for RNA-seq analysis by Illumina next-seq. Recipients were diagnosed for pregnancy at day 30 and 60 of gestation.

first: Adriana

last: Zolini

first: Jeremy

last: Block

first: Paula

last: Tribulo

first: Michael

last: Hoelker

first: Gonzalo

last: Rincon

first: John

last: Bromfield

first: Peter

last: Hansen


title: mRNA sequencing of SOD1 mice identifies differentially expressed genes in disease and after shRNA treatment

status: Public on Aug 08 2019

first: Samuel

middle: L

last: Pfaff

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: We report the transcriptome of cervical and lumbar spinal cords from SOD1 G37R ALS model mice in untreated animals and after shRNA treatment.

overall_design: Transcriptome data from wild type, SOD1 G37R untreated, sham treated, and shRNA-treated SOD1 G37R mice are reported.  Time points include end-stage disease animals, as well as mid-stage disease animals.

first: Martin

last: Marsala

first: Shawn

last: Driscoll


title: Identification of a mesenchymal progenitor cell hierarchy in adipose tissue (Bulk RNA-seq)

status: Public on May 01 2019

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: Smilow Center 3400 Civic Center Blvd. 1

institute: University of Pennsylvania

summary: The healthy growth of adipose tissue depends on the capacity of progenitor cells to undergo denovo adipogenesis. However, the cellular hierarchy and mechanisms governing adipocyteprogenitor differentiation are incompletely understood. Here, we identify a lineage hierarchy25 consisting of distinct mesenchymal cell types present in mouse and human adipose tissue. Cellsmarked by Dpp4 expression are highly proliferative, multipotent progenitors that give rise toIcam1+ committed pre-adipocytes and a related adipogenic population marked by Clec11a andCd142 expression. TGFβ maintains DPP4+ cell identity and inhibits adipogenic commitment ofDPP4+ and CD142+ cells. Intriguingly, DPP4+ progenitors reside in the reticular interstitium that30 envelope many organs including adipose depots. Altogether, this study defines the adipose lineagehierarchy and identifies a new anatomical niche for multipotent mesenchymal progenitors.

overall_design: mRNA profiles of 12-day old DPP4+, ICAM1+, and CD142+ cells from wild type (WT) mice were generated by deep sequencing, in triplicate. Followed by DESeq2 analysis with outputs of pairwise comparisons of differential expression in the three cell types.

first: David

last: Merrick

first: Alexander

last: Sakers


title: Identification of a mesenchymal progenitor cell hierarchy in adipose tissue (scRNA-seq)

overall_design: Single cell sequencing of pools of stromal-vascular-cells derived from subcutaneous adipose tissue from either developing mice (p12), adult mice housed at 30C for their entire lives (ScAdult), or from the abdominal subcutaneous adipose tissue of a 31 y.o. human female. For both mouse and human studies stromal vascular cells were isolated and flow sorted with gating to isolate single cells away from debris, doublets, and dead cells.  For the p12 pups (pooled male and female C57BL/6) and human single cell study, the cells were further gated against CD45 to exclude leukocytes.  For the adult mouse thermoneutral (pooled male 129S6/SvEvTac) sample CD45 cells were segregated and remixed with the SVC cells at a ratio of approximately 20% of the total cells. The sorted cells were loaded onto a GemCode instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell barcoded droplets (GEMs) according to the manufacture’s protocol using the 10x Single Cell 3’ v2 chemistry. The resulting libraries were sequenced on an Illumina HiSeq2500 instrument with the HiSeq Rapid SBS kit.  The resulting reads were aligned and gene level unique molecular identifier (UMI) counts obtain using the Cell Ranger (Pipeline).


title: Identification of genes associated with endometrial cell aging.

status: Public on Jun 19 2019

city: Fukuoka

first: Teruhiko

last: Kawamura

address: Maidashi 3-1-1,  Higashi-ku

department: Obstetrics and Gynecology, Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

summary: Aging of the uterine endometrium is a critical factor that affects reproductive success, but the mechanisms associated with uterine aging are unclear. In this study, we conducted a qualitative examination of age-related changes in endometrial tissues and identified candidate genes as markers for uterine aging. Gene expression patterns were assessed by twice RNA sequencing of uteri tissues from wild type (WT) C57BL/6 mice. First experimental samples were obtained from 5, 8 and 60-75 (aged) week-old WT (n=2, each). Second experimental samples were obtained from 5, 8 and 79 (aged) week-old WT (n=5, each). Gene expression data obtained by RNA-sequencing were validated by real-time PCR. Genes expressing the pro-inflammatory cytokines Il17rb and chemokines Cxcl12 and Cxcl14 showed differential expression between a group, which was composed of 5-week-old WT and 8-week-old WT (young), and aged WT mice. Protein expression levels of the above genes and IL-8, which functions downstream of IL17RB, were analyzed by quantitative immunohistochemistry of healthy human endometrium tissue samples from patients in their 20?s and 40?s (10 cases each). In these secretory phase samples, 3,3?- diaminobenzidine (DAB) staining intensity of IL17RB, CXCL12 and CXCL14 for patients in their 40?s was significantly higher than that for patients in their 20?s, as detected by a Mann Whitney U test. These results suggest that these genes are candidate markers for endometrial aging and for prediction of age-related infertility, although confirmation of these findings is needed in larger studies involving fertile and infertile women.

overall_design: Uterus mRNA profiles of 5 weeks, 8 weeks, 60-75 weeks and 79 weeks of age  wild type (WT) mice were generated by deep sequencing, using Illumina HiSeq1500 or NovaSeq 6000.

first: Hiroyuki

last: Tomari

first: Ichiro

last: Onoyama

first: Hiromitsu

last: Araki

first: Masafumi

last: Yasunaga

first: Cui

last: Lin

first: Keiko

first: Natsuko

last: Yokota

first: Sachiko

last: Yoshida

first: Hiroshi

last: Yagi

first: Kazuo

last: Asanoma

first: Kenzo

last: Sonoda

first: Katsuko

last: Egashira

first: Takashi

last: Ito

first: Kiyoko

last: Kato


title: Generating automated kidney transplant biopsy reports combining molecular measurements with ensembles of machine learning classifiers

status: Public on Nov 07 2019

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

summary: We previously reported a system for assessing rejection in kidney transplant biopsies using microarray-based gene expression data, the Molecular Microscope® Diagnostic System (MMDx). Ensembles generated diagnoses that were both more accurate than the best individual classifiers, and nearly as stable as the best, consistent with expectations from the machine learning literature. Human experts had ~93% agreement (balanced accuracy) signing out the reports, and random forest-based automated sign-outs showed similar levels of agreement with the human experts (92% and 94% for predicting the expert MMDx sign-outs for T cell-mediated (TCMR) and antibody-mediated rejection (ABMR) respectively). In most cases disagreements, whether between experts or between experts and automated sign-outs, were in biopsies near diagnostic thresholds. Considerable disagreement with histology persisted. The balanced accuracies of MMDx sign-outs for histology diagnoses of TCMR and ABMR were 73% and 78% respectively. Disagreement with histology is largely due to the known noise in histology assessments (ClinicalTrials.gov NCT01299168).

overall_design: The present study was designed to optimize the accuracy and stability of MMDx diagnoses by replacing single machine learning classifiers with ensembles of diverse classifier methods. We also examined the use of automated report sign-outs and the agreement between multiple human interpreters of the molecular results.


title: Graded regulation of cellular quiescence depth between proliferation and senescence by a lysosomal dimmer switch

status: Public on Oct 11 2019

city: Beijing

first: ruoyan

last: Li

address: Yiheyuan street

institute: Peking University

summary: The reactivation of quiescent cells to proliferate is fundamental to tissue repair and homeostasis in the body. Often referred to as the G0 state, quiescence is however not a uniform state but with graded depth. Shallow quiescent cells exhibit a higher tendency to revert to proliferation than deep quiescent cells, while deep quiescent cells are still fully reversible under physiological conditions, distinct from senescent cells. Cellular mechanisms underlying the control of quiescence depth and the connection between quiescence and senescence are poorly characterized, representing a missing link in our understanding of tissue homeostasis and regeneration. Here we measured transcriptome changes as rat embryonic fibroblasts moved from shallow to deep quiescence over time in the absence of growth signals. We found that lysosomal gene expression was significantly upregulated in deep quiescence, and partially compensated for gradually reduced autophagy flux. Reducing lysosomal function drove cells progressively deeper into quiescence and eventually into a senescence-like irreversibly arrested state; increasing lysosomal function, by lowering oxidative stress, progressively pushed cells into shallower quiescence. That is, lysosomal function modulates graded quiescence depth between proliferation and senescence as a dimmer switch. Lastly, we found that a gene expression signature developed by comparing deep and shallow quiescence in fibroblasts can correctly classify a wide array of senescent and aging cell types in vitro and in vivo, suggesting that while quiescence is generally considered to protect cells from irreversible arrest of senescence, quiescence deepening likely represents a common transition path from cell proliferation to senescence, related to aging.

overall_design: Gene expression profiling of rat embryonic fibroblasts undergone different durations (0-16 days) of serum starvation, with 3 biological replicates at each time point.

first: Fan

last: Bai

first: Guang

last: Yao


title: Sequencing of metabolically labeled transcripts in single cells from RPE1-FUCCI cells and murine intestinal organoids.

status: Public on Mar 05 2020

first: Nico

last: Battich

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Measurements of metabolically labeled transcripts in single cells for estimation of mRNA synthesis and degradation rates throughout the cell cycle and intestinal organoid differentiation.

overall_design: Sequencing of metabolically labeled transcripts in single cells from RPE1-FUCCI cells (cell cycle), K562 cells (heat shock), and murine intestinal organoids (differentiation).

first: Joep

last: Beumer

first: Buys

last: de Barbanson

first: Lenno

last: Krenning

first: Chloé

last: Baron

first: Marvin

middle: E

last: Tanenbaum

first: Hans

last: Clevers

first: Alexander

last: van Oudenaarden


title: Total RNA-seq in patients with hematological malignancy

status: Public on Aug 13 2019

city: Chikusa-ku

first: Hitoshi

last: Ohtani

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary: Immune response and leukocyte activation genes are upregulated following 5-azacitidine treatment

overall_design: Total RNA-seq were performed in RNA samples taken before, during, and after treatment with the DNMTi 5-azacitidine.

first: Peter

last: Jones


title: LncRNA and mRNA expression in paired liver tissues (periparasitic liver tissues versus distal liver tissues) from alveolar echinococcosis (AE) patients

status: Public on Dec 27 2018

city: Urumqi

first: Chuanshan

last: Zhang

state: Xinjiang

address: No. 137 Liyushan Road

department: Clinical Medicine Institute

institute: The First Affiliated Hospital of Xinjiang Medical University

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

summary: To determine the LncRNA and mRNA expression profile in periparasitic liver tissues and matched distal-liver tissues, we used LncRNA microarray analysis from Arraystar to examine the expression of LncRNAs and mRNAs in periparasitic liver tissues and matched distal-liver tissues.

overall_design: Paired liver tissues from six AE patients surgery were distributed into two experimental groups: periparasitic liver tissue group and matched distal-tissue group, then perform LncRNAs chips by Arraystar Human LncRNAs chip (Arraystar)


title: Dual RNA-seq of Neisseria gonorrhoeae and human neutrophils

status: Public on Dec 07 2018

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Deep sequencing of cDNA from Neisseria gonorrhoeae bacteria and human neutrophils, alone and after coincubation.

sample_organism:
Neisseria gonorrhoeae
Homo sapiens

platform_organism:
Neisseria gonorrhoeae
Homo sapiens

overall_design: Total RNA was isolated from Neisseria gonorrhoeae and adherent primary human neutrophils, alone and after co-culture over time. Bacteria were of strain FA1090 ?opa ("Opaless"; 130), FA1090 ?opa with H041 penA, penB, and mtrR resistance alleles (3x130), or H041. Bacteria were untreated or treated with experimentally determined sublethal concentrations of selected antibiotics 1 hour prior to and during co-culture. Ribosomal RNA was depleted and the remaining RNA was reverse-transcribed into a cDNA library for Illumina sequencing. Reads were mapped to the FA1090, H041 and/or human genomes.

first: Alison

last: Criss

first: Mary

last: Gray

first: Vonetta

last: Edwards

first: Adonis

last: D'mello

first: Eli

last: McComb

first: Herve

last: Tettelin


title: TFEB controls vascular development by regulating the proliferation of endothelial cells

status: Public on Nov 20 2018

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

summary: The role of the transcription factor EB (TFEB) in the control of cellular functions, including in vascular bed, is mostly thought to be the regulation of lysosomal biogenesis and autophagic flux. While this is its best-known function, we report here the ability of TFEB to orchestrate a non-canonical program involved in the control of cell-cycle and VEGFR2 pathway in the developing vasculature. In endothelial cells, TFEB deletion halts proliferation by inhibiting the CDK4/Rb pathway, which regulates the cell cycle G1-S transition. In an attempt to overcome this limit, cells compensate by increasing the amount of VEGFR2 on the plasma membrane through a microRNA-mediated mechanism and the control of its membrane trafficking. TFEB transactivates the miR-15a/16-1 cluster, which limits the stability of the VEGFR2 transcript, and negatively modulates the expression of MYO1C, which regulates VEGFR2 delivery to the cell surface. In TFEB knocked-down cells, the reduced and increased amount respectively of miR-15a/16-1 and MYO1C result in the overexpression on plasmamembrane of VEGFR2, which however shows low signaling strength. Using endothelial loss-of-function Tfeb mouse mutants, we present evidence of defects in fetal and newborn mouse vasculature caused by the reduced endothelial proliferation and by the anomalous function of VEGFR2 pathway. Thus, this study revealed a new and unreported function of TFEB that expands its role beyond the regulation of autophagic pathway in the vascular system.

overall_design: This SuperSerie is composed of the SubSeries listed below. In the first experiment we report the ChIP-seq of the TFEB transcription factor in a model of HUVEC cells. In the second one, we study the effect of the down-modulation of the TFEB transcription factor, in the same model.


title: TFEB controls vascular development by regulating the proliferation of endothelial cells (sh-TFEB marray)

overall_design: Comparison of gene expression profiles obtained in human endothelial cells infected with pLKO.1-puro non-Mammalian vector (scr-shRNA ECs) or with specific shRNA against TFEB (sh-TFEB ECs)

first: G

last: Doronzo

first: D

last: Cora


title: Identification of a mesenchymal progenitor cell hierarchy in adipose tissue

first: Patrick

last: Seale

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

overall_design: Refer to individual Series

first: David

last: Merrick

last: Sakers


title: Time-course chromatin accessibility and transcriptome in regeneration

status: Public on Oct 11 2018

city: Barcelona

first: Montserrat

last: Corominas

state: Catalonia

address: Diagonal 643

department: Genètica, Microbiologia i estadística

institute: University of Barcelona


title: The Influence of Met Receptor Level on HGF-Induced Glycolytic Reprogramming in Head and Neck Squamous Cell Carcinoma

status: Public on Jan 17 2020

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

summary: Head and neck squamous cell carcinomas (HNSCC) are known to overexpress a variety of receptor tyrosine kinases, such as the HGF receptor Met. Like other malignancies, there is a mutual interaction between the tumor cells and surrounding tissues and cells. We hypothesized that activation of HGF/Met signaling in HNSCC might influence glucose metabolism and therefore substantially changes the tumor microenvironment. To determine the effect of HGF, we used three established HNSCC cell lines and flow cytometry, western blot and RNA sequencing. Dynamic changes in glucose metabolism were measured real-time by an Extracellular flux analyzer. As expected, the cell lines exhibited different levels of Met and responded differently to HGF stimulation. As confirmed by RNA sequencing, the level of Met expression is associated with the number of upregulated HGF-dependent genes. Overall, Met stimulation by HGF leads to increased glycolysis, presumably mediated by higher expression of three key enzymes of glycolysis. These effects appear to be stronger in Methigh expressing HNSCC cells. Collectively our data supports the hypothesized role of HGF/Met signaling in metabolic reprogramming of HNSCC.

overall_design: 3 cell lines, of each one an untreated control and one sample treated with 50 ng/ml HGF for 48 hours, 3 replicates

first: Verena

last: Boschert

first: Thorsten

last: Bischler

first: Stefan

last: Hartmann


title: Time-course transcriptome of regeneration [RNA-Seq]

summary: The ability to regenerate or recover from injuries varies greatly not only between species but also between tissues and organs or developmental stages of the same species. The mechanisms behind these different regenerative capabilities are ultimately dependent on the control of genome activity, determined by a complex interplay of regulatory elements functioning at the level of chromatin. Resetting of gene expression patterns during injury responses is, thus, shaped by the coordinated action of genomic regions (enhancers, silencers) that integrate the activity of multiple sequence-specific DNA binding proteins (transcription factors and cofactors). Using  genome- wide approaches to interrogate chromatin function here we identify the regulatory elements governing tissue recovery in Drosophila wing imaginal discs, which show a high regenerative capacity after genetically induced cell death. Our findings point to a global co-regulation of gene expression and provide evidence for Damage Responding Regulatory Elements (DRRE), some of which are novel whereas others are also used in other tissues or developmental stages.

overall_design: We collected data at different time points (0, 15 and 25h) after apoptosis induction. These time periods were selected because they included the most important transcriptional responses to apoptosis, ranging from the earliest gene expression up to complete re-patterning. Discs kept at the same conditions without inducing cell death were used as controls.

first: Elena

last: Vizcaya

first: Cecilia

last: Klein

first: Florenci

last: Serras

first: Rakesh

last: Mishra

first: Roderic

last: Guigó


title: Time-course chromatin accessibility in regeneration [ATAC-seq]


title: Single-cell transcriptomics reveals distinct microglia signatures under inflammation

status: Public on Sep 10 2018

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Microglia are specialized parenchymal-resident phagocytes of the central nervous system (CNS) that actively support, defend and modulate the neural environment. Dysfunctional microglia responses are believed to worsen CNS diseases, nevertheless their impact during the neuroinflammatory processes remains largely obscure. Here, using a combination of multicolor flow cytometry and single-cell RNA sequencing, we comprehensively profiled microglia in the brain of lipopolysaccharide (LPS)-injected mice. By excluding the contribution of other immune CNS-resident and peripheral cells, we showed that microglia isolated from LPS-injected mice displayed a global downregulation of their homeostatic signature together with an upregulation of inflammatory genes. Notably, we identified distinct microglia activated profiles under inflammatory conditions, which greatly differ from neurodegenerative disease-associated profiles. These results provide insights into microglia heterogeneity and establish a resource for the identification of specific phenotypes in CNS disorders, such as neuroinflammatory and neurodegenerative diseases.

overall_design: Comparison of sorted microglia (CD11b+CD45int cells) between peripherally LPS-injected mice and saline control mice at single-cell resolution. One sample saline control and one sample LPS 24h (from 2 mice per group; 1 female and 1 male)

first: Carole

last: Sousa

first: Suresh

middle: K

last: Poovathingal

last: Kaoma

first: Francisco

last: Azuaje

first: Alexander

last: Skupin

first: Alessandro

last: Michelucci


title: ChIP-seq for active enhancers marks at early regeneration

last: Corominas

summary: The ability to regenerate or recover from injuries varies greatly not only between species but also between tissues and organs or developmental stages of the same species. The mechanisms behind these different regenerative capabilities are ultimately dependent on the control of genome activity, determined by a complex interplay of regulatory elements functioning at the level of chromatin. Resetting of gene expression patterns during injury responses is, thus, shaped by the coordinated action of genomic regions (enhancers, silencers) that integrate the activity of multiple sequence-specific DNA binding proteins (transcription factors and cofactors). Using  genome-wide approaches to interrogate chromatin function, here we identify the regulatory elements governing tissue recovery in Drosophila wing imaginal discs, which show a high regenerative capacity after genetically induced cell death. Our findings point to a global co-regulation of gene expression and provide evidence for Damage Responding Regulatory Elements (DRRE), some of which are novel whereas others are also used in other tissues or developmental stages.

overall_design: We collected data at early stages after apoptosis induction. Discs kept at the same conditions without inducing cell death were used as controls.


title: Definition of Natural Killer cell heterogeneity in humans and mice by high-throughput single-cell RNA sequencing

status: Public on Sep 07 2018

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

country: France

institute: CIML

summary: Natural Killer (NK) cells are innate lymphoid cells (ILCs) involved in antimicrobial and antitumoral responses. Several NK cell subsets have been reported in humans and mice, but their heterogeneity across organs and species remains poorly characterized. We assessed the diversity of human and mouse NK cells by single-cell RNA sequencing on thousands of individual cells isolated from spleen and blood. Unbiased transcriptional clustering revealed two distinct signatures differentiating between splenic and blood NK cells. This analysis at single-cell resolution identified three subpopulations in mouse spleen and four in human spleen, and two subsets each in mouse and human blood. A comparison of transcriptomic profiles within and between species highlighted the similarity of the two major subsets, NK1 and NK2, across organs and species. This unbiased approach provides new insight into the biology of NK cells and establishes a rationale for the translation of mouse studies to human physiology and disease.

overall_design:
Spleen and Blood paired NK cells from 3 individual human brain dead donors (CD45+ CD3– CD14– CD19– CD56+) and 3*5 pooled mice (CD45+ CD3– CD19– NKp46+ NK1.1+) were sorted.
Sample 1 : Frozen live spleen NK cells from donor 1 mixed with fresh live spleen NK cells from mouse group 1.
Sample 2 : Frozen live spleen NK cells from donor 2 mixed with fresh live spleen NK cells from mouse group 2.
Sample 3 : Frozen live spleen NK cells from donor 3 mixed with fresh live spleen NK cells from mouse group 3.
Sample 4 : Frozen live blood NK cells from donor 1 mixed with fresh live blood NK cells from mouse group 1.
Sample 5 : Frozen live blood NK cells from donor 2 mixed with fresh live blood NK cells from mouse group 2.
Sample 6 : Frozen live blood NK cells from donor 3 mixed with fresh live blood NK cells from mouse group 3.

first: Adeline

last: Crinier

first: Pierre

last: Milpied

last: Escalière

first: Christelle

last: Piperoglou

first: Justine

last: Galluso

first: Anaïs

last: Balsamo

first: Lionel

last: Spinelli

first: Inaki

last: Cervera-Marzal

first: Mikaël

last: Ebbo

first: Mathilde

last: Girard-Madoux

first: Sébastien

last: Jaeger

first: Emilie

last: Bollon

first: Sami

last: Hamed

first: Jean

last: Hardwigsen

first: Sophie

last: Ugolini

first: Frédéric

last: Vély

last: Narni-Mancinelli

first: Eric

last: Vivier


title: ATAC-seq analysis of human CD8 T cells specific for the NS4B-214 epitope in the Yellow fever vaccine YFV-17D strain

status: Public on Dec 13 2017

city: Palo Alto

first: Bin

last: Hu

state: California

address: 3801 Miranda Avenue

department: School of Medicine

institute: Stanford University

overall_design: YFV tetramer- positive and naïve CD8 T cells were sorted from PBMC at indicated time points after vaccination and ATAC-seq analysis was performed as described in Buenrostro et al 2015.

first: Rama

last: Akondy

first: Rafi

last: Ahmed

first: Jorg

last: Goronzy


title: tRNA-derived small non-coding RNAs (tDRs) as novel predictive biomarkers for trastuzumab-resistant breast cancer.

status: Public on Jun 30 2018

city: Nanjing

first: Chunxiao

last: Sun

address: Guangzhou Road,300

institute: Nanjing Medical University

summary:
Background: Resistance to trastuzumab remains a common challenge to HER-2 positive breast cancer. Up until now, the underlying mechanism of trastuzumab resistance is still unclear. tRNA-derived small non-coding RNAs (tDRs), a new class of small non-coding RNA (sncRNAs), have been observed to play an important role in cancer progression. However, the relationship between tDRs and trastuzumab resistance is still unknown.
Methods: We detected the levels of tDRs expression in normal breast epithelial cell lines, trastuzumab-sensitive and -resistant breast cancer cell lines using high-throughput sequencing. qRT-PCR was conducted to validate the differentially expressed tDRs in serums from trastuzumab-sensitive and -resistant patients. A receiver operating characteristic (ROC) curve analysis was performed to evaluate the power of specific tDRs. Progression-free survival (PFS) was analyzed using Cox-regression. Furthermore, Gene Ontology (GO) and pathway analyses indicated the potential mechanism underlying tDR-mediated trastuzumab resistance.
Results: Our sequence results showed that tDRs were differentially expressed in the HBL-100, SKBR3, and JIMT-1 cell lines. tDR-1960 and tDR-1969 were found significantly upregulated in trastuzumab-resistant patients compared to sensitive individuals, and the ROC analysis showed that tDR-1960 and tDR-1969 were correlated with trastuzumab resistance. In a multivariate analysis, higher levels of tDR-1960 and tDR-1969 expression were associated with signiﬁcantly shorter PFS in patients with metastatic HER-2 positive breast cancer. Additionally, the GO analysis indicated that tDR-1960 and tDR-1969 were mainly involved in the cellular response to drug, which may partially explain the molecular mechanism underlying trastuzumab resistance in HER-2 positive breast cancer.
Conclusion: we comprehensively analyzed tDRs in trastuzumab-sensitive and -resistant breast cancer. Our results suggest that tDR-1960 and tDR-1969 play important roles in trastuzumab resistance. Patients with high levels of tDR-1960 and tDR-1969 expression benefitted less from trastuzumab-based therapy than those that express lower-levels of these tDRs. tDR-1960 and tDR-1969 may be potential biomarkers and intervention targets in the clinical treatment of trastuzumab-resistant breast cancer.

overall_design: Examination of tDRs in trastuzumab-sensitive and -resistant cell lines.


title: Transcriptional Analysis of an Ammonium-Excreting Strain of Azotobacter vinelandii Deregulated for Nitrogen Fixation

status: Public on Jun 01 2017

city: Saint Paul

first: Brett

middle: M

last: Barney

address: 1500 Gortner Avenue

department: Bioproducts and Biosystems Engineering

institute: University of Minnesota

summary: The transcriptional differences found during stationary-phase ammonium accumulation show a strong contrast between the deregulated (nifL disrupted) and wild-type strain, and to what was reported for the wild-type strain under exponential growth related to key processes involved in driving the process of nitrogen fixation in A. vinelandii. These results further illuminate a number of additional genes associated with siderophore synthesis, molybdate transfer and electron transfer that are likely associated with biological nitrogen fixation.

overall_design: Azotobacter vinelandii was grown in standard Burk's media and standard Burk's media containing 20 mM Ammonium sulfate. Azotobacter vinelandii mutant strain deregulated for nitrogen fixation was grown in standard Burk's media. All samples were harvested at various time points, total RNA was extracted and mRNA was enriched. Libraries were constructed, and RNA was sequenced using Illumina paired-end reads.

first: Mary

middle: H

last: Plunkett

first: Velmurugan

last: Natarajan

first: Florence

last: Mus

first: Carolann

last: Kutson

first: John

last: Peters


title: FACS microarray analysis of radially migrating cortical neurons

status: Public on Aug 23 2017

city: Setagaya-ku

first: Chiaki

last: Ohtaka-Maruyama

state: Tokyo

address: 2-1-6 Kamikitazawa

department: Department of brain development and neural regeneration

institute: Tokyo Metropolitan Institute of Medical Science

summary: During the developmental formation of 6-layered neocortical structure of mammalian cerebral cortex, newborn excitatory neurons depart the ventricular zone and migrate toward the pial surface. At a middle stage of cortical development, newly differentiated postmitotic neurons adopt a multipolar shape (MP), and exhibit a random non-directional migration in the intermediate zone (multipolar migration). When these neurons pass through the subplate layer (SP), they convert to a bipolar shape (BP), and then migrate radially toward the pial surface (locomotion).   In order to elucidate the molecular mechanisms of such neuronal migration, we performed a gene expression profiling of newborn excitatory neurons during their migration processes. After in utero electroporation of GFP expressing plasmid into E14 mouse cortex, GFP-positive cells were collected using FACS sorting method after one, two, or three days of electroporation. RNAs of collected GFP-positive cells at each day were purified and applied to microarray analyses. gene-ontology and pathway analyses revealed that genes encoding synaptic proteins, receptors and ECM-related proteins were up-regulated as the migration proceeds. On the other hand, genes encoding cell cycle regulation and immune-related proteins were down-regulated. We will discuss the relationship between the migration mode and the transition of the gene expression.

overall_design: pCAGGS-EGFP was electroporated in utero into the mouse embryonic cortices at E14.5, and the brains were collected at E15.5, E16.5, and E17.5. GFP-positive dorsal cortical areas were dissected out under a dissection microscope with a fluorescent lamp. GFP-positive cortical cells were dissiciated with papain and subjected to FACS cell sorter BD FACS Aria III . Cells prepared from the brains not electroporated with pCAGGS-EGFP were used as the negative controls. We performed FACS sorting 5-9 times independently (9 times for E15.5, 5 times for E16.5, and 7 times for E17.5) to pool approximately 2×105 GFP-positive cells in total for each time point.

first: Chiak

first: Nobuaki

last: Maeda


title: Single cell RNA sequencing of interneurons of the mouse dorsolateral striatum I

status: Public on Aug 22 2018

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: In  this  study  we  performed  single-cell  sequencing  of  striatal   interneurons,  revealing  striatal  populations  as  well  as  the  relation  to  their   telencephalic  counterparts

overall_design: FACS-sorted single cells isolated from the dorso-lateral striatum from either a 5ht3a-EGFP mouse line or a Lhx6-cre mouse crossed onto a R26R-tdTomato reporter mouse line

first: Ana

last: Munoz-Manchado

first: Amit

last: Zeisel

first: Jens

last: Hjerling-Leffler


title: The histone deacetylase inhibitor givinostat (ITF2357) exhibits potent anti-tumor activity against CRLF2-rearranged BCP-ALL.

status: Public on Mar 24 2017

city: Padova

first: Luca

last: Trentin

address: Via Giustiniani, 3

department: Department of Women's and Children's Health

institute: University of Padova

summary: We studied the in vitro and in vivo efficacy of the HDAC inhibitor Givinostat/ITF2357 in BCP-ALL  with CRLF2 rearrangements. We used BCP-ALL CRLF2- rearranged MHH-CALL4 and MUTZ5 cell lines as well as blasts from CRLF2 rearranged BCP-ALL patients and patients’ derived xenograft samples. We conclude that Givinostat may represent a novel and effective tool, in combination with current chemotherapy, to treat this subsets of ALL with poor prognosis and chemotherapy-related toxicity.

overall_design: Gene expression was measured using  Affymetrix platform in 5 pair of BCP-ALL patient derived xenograft samples treated or untreated ex vivo with Givinostat  at 0.2 uM for 6 hours.

first: Angela

last: Savino


title: Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

status: Public on May 01 2018

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine


title: RNA-Seq Analysis of Anacardic Acid Treated MCF7 and MDA-MB-231 Breast Cancer Cell Lines

status: Public on Feb 01 2017

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Anacardic acid (AnAc) is a mixture of 6-alkylbenzoic acid congeners that are produced in a number of plants. Previously, we showed a specific congener AnAc 24:1n5 acts as a nuclear receptor alternate site modulator (NRAM) to inhibit breast cancer cells in an estrogen receptor (ER)-dependent manner by interfering with ER-DNA binding. AnAc 24:1n5 also inhibited the growth of a triple negative breast cancer (TNBC) cell line, through an undefined mechanism. Additional work from our labs  indicated AnAc 24:1n5 inhibits prostaglandin synthase and that inhibition is more specific to COX-2. Reports from other investigators indicate AnAc has a number of interesting potential pharmacological targets. We previously used qRT-PCR to investigate expression changes in endogenous estrogen-regulated genes, i.e., TFF1, CCND1, and CTSD in breast cancer cell lines. However, since AnAc has the capacity of effect multiple molecular targets and since we detected an ER-independent inhibition of breast cancer cell proliferation, we suspect additional unknown molecular targets are affected in breast cancer cells. Identification of such targets using RNA-seq would be quite beneficial in targeting TNBC which primarily affects premenopausal women with a predominance in women of African and Latina ancestry.  The goal of this portion of the project is to use next-generation RNA-SEQ to identify alterations in molecular target sequence levels in ER-positive and -negative breast cancer cell lines treated with AnAc.

overall_design: There are two breast cancer cell lines used in this study, including MCF-7 (invasive breast ductal carcinoma; estrogen receptor positive (ER+); progesterone receptor positive (PR+); human epidermal growth factor 2 negative (HER2-)) and MDA-MB-231 (breast adenocarcinoma; triple negative – ER-; PR-; HER2-).  Each of these cell lines was treated with anacardic acid (AnActrt) with three replicates each, resulting in a total of 12 RNA samples.  One MDA-MB-231 control sample and one MDA-MB-231 AnActrt treated sample were removed after QA/QC determined they were likely contaminated samples.

first: Carolyn

last: Klinge

first: David

middle: J

last: Schultz

first: Brandie

middle: N

last: Radde

first: Xiaohong

last: Li


title: Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells

status: Public on Jun 21 2017

city: Blacksburg

first: Fernando

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: The maturation of an oocyte, the female gamete, during folliculogenesis is highly dependent on the molecular interaction with the somatic cells. Here we generated transcriptome data of single oocytes and the surrounding cumulus cells from antral follicles, and developed an analytical framework to unveil their inter-cellular communication. We identified hundreds of ligand-receptors pairs that can transduce paracrine signaling between oocyte and cumulus. Several of the ligand-coding genes expressed in oocytes and cumulus cells are also functionally associated with regulation of transcription. Ligand-coding genes expressed in oocytes or cumulus showed distinct enrichment for biological functions that are likely associated with a coordinated formation of the transzonal projections from the cumulus that reach the oocyte’s membrane. Finally, there were thousands of gene pairs with non-trivial linear co-expression pattern between oocytes and cumulus cells. Our analyses revealed a complex and functional regulatory circuit between the oocyte and surrounding cumulus cells.

overall_design: Transcriptome data was generated from cumulus cells and oocytes from the same cumulus-oocyte complex


title: TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells  (WGBS)

status: Public on Nov 21 2016

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

type: Methylation profiling by high throughput sequencing

summary: TET proteins oxidize 5-methylcytosine to 5-hydroxymethylcytosine and further oxidation products in DNA. Here we report that simultaneous deletion of Tet2 and Tet3 in mouse double-positive thymocytes resulted in dysregulated development and proliferation of invariant natural killer T (iNKT) cells. Tet2-Tet3-double-deficient (DKO) iNKT cells displayed pronounced skewing towards the NKT17 lineage, with increased DNA methylation and impaired expression of genes encoding the key lineage-specifying factors T-bet and ThPOK. Transfer of purified Tet2-Tet3 DKO iNKT cells into immunocompetent recipient mice resulted in uncontrolled expansion dependent on the nonclassical MHC protein CD1d, which presents lipid antigens to iNKT cells. Our data indicate that TET proteins regulate iNKT cell fate by ensuring proper development and maturation and suppressing aberrant T cell antigen receptor (TCR)-mediated proliferation.

overall_design: In order to address the impact of the loss of Tet2/3 proteins in DNA methylation in iNKT cells we compared by WGBS seq the methylome of wild INKT cells, Tet2/3 DKO iNKT cells and expanded Tet2/3 DKO iNKT cells in congenic recipients.

first: Ageliki

last: Tsagaratou

first: Anjana

last: Rao


title: TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells  (ATAC-Seq)

overall_design: In order to address the impact of the loss of Tet2/3 proteins inchromatin accessibility in iNKT cells we compared by ATACseq thymic wild INKT cells and Tet2/3 DKO iNKT cells


title: Molecular mechanisms underlying the development of Sonic Hedgehog subtype medulloblastoma

status: Public on Dec 31 2016

city: Xi'an

first: Ting

last: Wang

address: Changlexilu Road

department: Biochemistry and Molecular Biology

institute: the Fourth Military Medical University

summary: Medulloblastoma (MB) is a highly malignant primary brain tumor that originates from the cerebellar granule neuron precursors (CGNPs) in the cerebellum or posterior fossa. The overactivation of the Sonic Hedgehog (Shh) signal pathway accounts for the occurrence of 30% clinical cases of MB. Shh engagement with the inhibitory receptor Patched 1 derepresses the second receptor, Smoothened (Smo), and thereby activates the Gli transcriptional factors, allowing for the expression of a cohort of genes involved in cell growth and differentiation. Nevertheless, the mechanisms of Shh signaling-driven carcinogenesis, e.g. the Gli target genes that play pivotal roles in the transformation of CGNPs, remain largely unknown. To screen for the genes involved in the development of Shh subtype MB, we attempt to analyze genes differentially expressed between CGNPs and MB cells, which will hopefully provide clues for the elucidation of key molecular events that mediate the onset of this specific type of nervous system malignancy.

overall_design: In the study presented here, the transgenic mice that express a constitutively active Smo in cerebellar granule cells [C57BL/6-Tg(Neurod2-Smo*A1)199Jols/J, Jackson Laboratory stock #: 008831] were used as a model for MB. The tumors were dissected from 4-month-old mice and cells were dissociated and used as MB samples. Meanwhile, CGNPs were isolated from the same strain of newborn mice (4 to 6-day-old). Three cases of paired MB and CGNP cells were subjected to microarray analysis of gene expression profiles using the Agilent Arraystar Mouse LncRNA Microarray V3.0.

first: Lintao

last: Jia

first: Lei

first: Yimeng

last: Zhang


title: Ketogenesis: An Achilles' heel of starvation-selected persistent mycobacteria

status: Public on Aug 25 2016

city: Cambridge

first: Dunaduan

last: Ma

state: Ma

address: 77 Massachusetts Ave

department: Koch Institute

institute: MIT

summary: Mycobacterial pathogens adapt to environmental stresses such as nutrient deprivation by entering a non-replicative antibiotic-tolerant state of persistence. Using a biochemically-validated data-driven approach, we identified an adaptive metabolic network underlying the mycobacterial response to starvation in M. tuberculosis, M. bovis BCG and M. smegmatis. All three species show a strong Mg+2-dependence for surviving complete nutrient deprivation, accompanied by a broad phenotypic antibiotic resistance. Multivariate analysis of RNA-seq, metabolic phenotyping and biochemical data revealed substantial metabolic remodelling involving a shift to triacylglycerol utilization with adaptation to the consequent ketoacidosis by upregulation of cytochrome P450s. Paradoxically, the ketosis-driven P450 upregulation generated substantial levels of reactive oxygen species (ROS) yet conferred hypersensitivity to killing by hydrogen peroxide-induced inactivation of the P450s that reduced ROS levels. This emergent property of starvation-induced mycobacterial persistence represents a potentially exploitable vulnerability.

sample_organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

overall_design: Profiles of Mycobacterium bovis BCG coding RNA, enriched through the depletion of rRNAs and tRNAs, were generated by deep sequencing, in biological triplicate, using Illumina MiSeq as bacterial cultures were starved and subsequently replenished with nutrients.

first: Peter

last: Dedon

first: Megan

last: McBee

first: Yok

last: Chionh


title: TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells (RNA-Seq)

overall_design: DKO vs. wild type


title: Transcriptional targets of oncogenic RAS proteins that mediate their ability to induce cellular transformation

status: Public on Sep 08 2016

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Mutations in the NRAS oncogene are present in up to 20% of melanoma. Here, we show that interferon alpha-inducible protein 6 (IFI6) is necessary for NRASQ61K-induced transformation and melanoma growth. IFI6 was transcriptionally upregulated by NRASQ61K, and knockdown of IFI6 resulted in DNA replication stress due to dysregulated DNA replication via E2F2. This stress consequentially inhibited cellular transformation and melanoma growth via senescence or apoptosis induction depending on the RB and p53 pathway status of the cells. NRAS-mutant melanoma were significantly more resistant to the cytotoxic effects of DNA replication stress-inducing drugs, and knockdown of IFI6 increased sensitivity to these drugs. Pharmacological inhibition of IFI6 expression by the MEK inhibitor trametinib, when combined with DNA replication stress-inducing drugs, blocked NRAS-mutant melanoma growth. Collectively, we demonstrate that IFI6, via E2F2 regulates DNA replication and melanoma development and growth, and this pathway can be pharmacologically targeted to inhibit NRAS-mutant melanoma.

overall_design: MEL-ST cells expressing either empty vector or mutant oncogenic RAS genes (HRAS v12, KRAS v12, NRAS Q61K) were used to isolate total RNA. The RNA was then used to perform gene expression analyses using the Illumina HumanHT-12 V4.0 Expression BeadChip array.

first: Romi

last: Gupta

first: Matteo

last: Forloni

first: Shaillay

last: Dogra

first: Malik

last: Bisserier

first: Qiahong

last: Yang


title: TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells

first: Sini

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

overall_design: Refer to individual Series


title: Expression data from pancreatic cancers patients and healthy controls

status: Public on Oct 30 2016

city: Seoul

first: Jaehoon

last: Lee

address: 38, Baumoe-ro

institute: LG Electronics

summary:
For the identification of miRNA biomarker of pancreatic cancer,
total RNA containing miRNA was extracted from the serum samples using Affymetrix miRNA 4.0 and the serum miRNA purification kit (Genolution, Seoul, Korea)

overall_design: Blood serum samples were extracted from 88 PC patients, 101 ICC patients, 7 stomach cancer (SC) patients, 5 colorectal cancer (CC) patients, 2 gastrointestinal stromal tumours (GIST) patients, 10 cholelithiasis patients, and 19 healthy subjects who had been clinically classified as so at the time of participation

first: Dawoon

last: Jung

first: Hyung-Seok

last: Choi

first: Siyoung

last: Song


title: TFEB controls vascular development by regulating the proliferation of endothelial cells (TFEB ChIp-seq)

status: Public on Nov 20 2018

city: Candiolo

first: Davide

last: Cora'

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

summary: The role of the transcription factor EB (TFEB) in the control of cellular functions, including in vascular bed, is mostly thought to be the regulation of lysosomal biogenesis and autophagic flux. While this is its best-known function, we report here the ability of TFEB to orchestrate a non-canonical program involved in the control of cell-cycle and VEGFR2 pathway in the developing vasculature. In endothelial cells, TFEB deletion halts proliferation by inhibiting the CDK4/Rb pathway, which regulates the cell cycle G1-S transition. In an attempt to overcome this limit, cells compensate by increasing the amount of VEGFR2 on the plasma membrane through a microRNA-mediated mechanism and the control of its membrane trafficking. TFEB transactivates the miR-15a/16-1 cluster, which limits the stability of the VEGFR2 transcript, and negatively modulates the expression of MYO1C, which regulates VEGFR2 delivery to the cell surface. In TFEB knocked-down cells, the reduced and increased amount respectively of miR-15a/16-1 and MYO1C result in the overexpression on plasmamembrane of VEGFR2, which however shows low signaling strength. Using endothelial loss-of-function Tfeb mouse mutants, we present evidence of defects in fetal and newborn mouse vasculature caused by the reduced endothelial proliferation and by the anomalous function of VEGFR2 pathway. Thus, this study revealed a new and unreported function of TFEB that expands its role beyond the regulation of autophagic pathway in the vascular system.

overall_design: ChIP-seq TFEB and IgG in HUVEC cells

first: Gabriella

last: Doronzo

first: Elena

last: Astanina

first: Francesco

last: Neri

first: Salvatore

last: Oliviero

first: Bussolino

last: Federico


title: Mice produced by mitotic reprogramming of sperm injected into haploid parthenogenotes

status: Public on Jul 22 2016

city: Regensburg

first: Xin

last: Lu

address: Universitätsstraße 31

institute: University of Regensburg

summary: Sperm are highly differentiated and the activities that reprogram them for embryonic development during fertilization have historically been considered unique to the oocyte. We here challenge this view and demonstrate that mouse embryos in the mitotic cell cycle can also directly reprogram sperm for full term development. Developmentally incompetent haploid embryos (parthenogenotes) injected with sperm developed to produce healthy offspring at up to 24% of control rates, depending when in the embryonic cell cycle injection took place. This implies that most of the first embryonic cell cycle can be bypassed in sperm genome reprogramming for full development. Remodeling of histones and genomic 5'- methylcytosine and 5'-hydroxymethylcytosine following embryo injection were distinct from remodeling in fertilization and the resulting 2-cell embryos consistently possessed abnormal transcriptomes. These studies demonstrate plasticity in the reprogramming of terminally differentiated sperm nuclei and suggest that different epigenetic pathways or kinetics can establish totipotency.

overall_design: phICSI vs ICSI

first: A

middle: F

last: Perry


title: TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells (CMS-Seq)

last: Rautio

overall_design: CMS IP vs. input

first: Ageliki

last: Tsagaratou

first: Anjana

last: Rao


title: Dilemma of quiescent HSCs with shorten telomere

status: Public on Dec 02 2014

summary: quiescent HSCs have an elevated tolerance to accumulate genomic alterations in response to telomere shortening but the transmission of these aberrations to the progenitor cell level is prevented by senescence and apoptosis

overall_design: HSC: g3 vs Wt, MPP: g3 vs Wt, Myeloid cell: g3 vs Wt.

first: C

last: Klein

first: K

last: Rudolph