title: Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain [SmartSeq2]

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.

overall_design: Single cell transcriptomic study of rhesus macaque sensory RDG neurons. This dataset includes 2688 cells using the SmartSeq2 protocol.

first: Dmitry

last: Usoskin

first: Jussi

last: Kupari

first: Daohua

last: Lou

first: Marc

last: Parisien

first: Yizhou

last: Hu

first: Michael

last: Fatt

first: Peter

last: Lönnerberg

first: Mats

last: Spångberg

first: Bengt

last: Eriksson

last: Kharchenko

first: Barkas

last: Nikolaos

first: Karin

last: Loré

first: Samar

last: Khoury

first: Luda

last: Diatchenko

first: Patrik

last: Ernfors


title: Cabozantinib Can Block Tumor Growth by Disrupting Tumor Vasculature in Neuroendocrine Prostate Cancer Patient-Derived Xenografts

status: Public on Jan 27 2021

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

type: Expression profiling by high throughput sequencing

summary: With the advent of potent second-line anti-androgen therapy, we and others have observed an increased incidence of androgen receptor (AR)-null small cell or neuroendocrine prostate cancer (SCNPC) in metastatic castration-resistant prostate cancer (mCRPC).  Additionally, we have detected upregulated expression of MET and RET transcripts in SCNPC metastases relative to adenocarcinoma.  Our study was designed to determine the effect of cabozantinib, a multi-targeted tyrosine kinase inhibitor that inhibits MET, RET and VEGFR2, on SCNPC patient-derived xenografts (PDX) in vivo.  Surveillance of SU2C and University of Washington rapid autopsy mCRPC cohorts through RNA-Seq revealed that increased MET expression significantly correlated with loss of AR expression and activity.  In vitro treatment of SCNPC PDX cells with AMG 337 had no impact on cell viability in LuCaP 93 (MET+/RET+) and LuCaP 173.1 (MET-/RET-), whereas cabozantinib decreased cell viability in LuCaP 93, but not in LuCaP 173.1.  Notably, tumor volume was significantly decreased (p<0.001) with cabozantinib treatment in SCID mice bearing LuCaP 93 and LuCaP 173.1 tumors.  Tissue analysis indicated that tumor cell proliferation was not inhibited by cabozantinib, but that cabozantinib decreased microvessel density (CD31) in LuCaP 93 (p<0.001) and LuCaP 173.1 (p<0.01) tumors.  RNA-Seq and gene set enrichment analysis determined that hypoxia and glycolysis pathways were increased in cabozantinib treated tumors relative to control tumors. Thus, cabozantinib inhibited tumor growth in MET+/RET+ LuCaP 93 and MET-/RET- LuCaP 173.1 tumors in vivo and this activity was independent of MET or RET expression in LuCaP 173.1.  Our data suggest that the most likely mechanism of tumor growth suppression is through disruption of the stromal architecture and cabozantinib may represent a potential therapy for patients with metastatic disease in tumor phenotypes that have a significant dependence on the tumor vasculature for survival and proliferation.

overall_design: RNA sequencing of patient-derived xenograft (PDX) tumors using Illumina TruSeq Library prep and sequenced on Illumina NovaSeq.

first: Mark

middle: P

last: Labrecque

first: Lisha

middle: G

last: Brown

first: Holly

middle: M

last: Nguyen

first: Daniel

middle: W

last: Lin

first: Eva

last: Corey

middle: S

last: Nelson

first: Colm

last: Morrissey


title: Serum exosomal miRNA profiles in fulminant myocarditis patients and healthy controls

city: Wuhu

first: Xueqin

last: Li

address: 2 Western Zheshan Road

country: China

institute: wannan medical college

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: Exosome-derived microRNAs (miRNAs) are potential diagnostic biomarkers. However, little is known about their effectiveness as diagnostic biomarkers of fulminant myocarditis (FM). This study aimed to explore miRNA levels in serum exosomes of patients with FM as potential biomarkers for FM diagnosis.
Methods: 10 samples were screened with a exosomal small RNA sequencing platform (RiboBio). A Mann-Whitney test was performed to discover differentially expressed miRNAs in the two pairwise comparisons: FM versus HC.
Results: From the differentially expressed miRNAs, fourteen candidate miRNAs discovered via small RNA sequencing with P＜0.05 and fold expression change ＞2 were selected for further testing
Conclusions: These data suggested that the miRNA panel in serum-derived exosomes provided excellent diagnostic capability for FM.

overall_design: The miRNA expression profiles of serum exosomes in FM patients and HC were determined using next-generation sequencing, in five replicates, using Illumina HiSeqTM 2500.

first: Kun

last: Lv

first: Yingying

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of B cell Transcriptomes

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

summary: Emergence of IgE antibodies that bind allergens with high affinity is highly correlated with the severity of anaphylaxis. However, the underlying molecular mechanisms by which high-affinity IgE is generated remain poorly understood. To examine function of IL-13 derived from T cells in IgE producing B cell development, we transferred IL-13 sufficient or deficient OT-2 TH2 into IgE reporter (Verigem) mice followed by immunization with NP-OVA. At 7 day post immunization, NP specific IgE producing B cells were sorted and served to single cell transcriptome analysis.

overall_design: NP specific IgE+ B cells of  mice were sorted and analyzed the transcriptome using Illumina NovaSeq 6000.

first: Masato

last: Kubo


title: Expression data from non-tumorous liver from chemically-induced hepatocellular carcinoma of wild-type or G9a deficient mice

city: Bunkyo-ku

first: Takuma

last: Nakatsuka

state: Tokyo

department: Gastroenterology

institute: The University of Tokyo

summary:
Epigenetic gene regulation in various oncogenic pathways is currently an important focus of cancer research. Histone modification plays a pivotal role in human carcinogenesis, but the significance of histone modification in hepatocarcinogenesis remains unknown.
We used microarrays to investigate the oncogenic gene regulation by histone methylase G9a in chemically-induced murine hepatocellular carcinioma model.

overall_design: We investigate the role of a histone methylase G9a in liver tumor development utilizing liver-specific G9a-deficient mice. We obtained the material specimen from non-tumorous liver tissue and analyze it.

first: Keisuke

last: Tateishi


title: Effect of Age on Severity and Recovery of Acute Multiple Sclerosis Attack

city: Ramat Gan

first: Michael

last: Gurevich

address: Tel Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

summary:
Pediatric MS patients suffer from severe first and second relapse but better recovery explained by difference in age-restricted transcriptional profiles associated with antigen-presentation and B-cell activation
Herein, we compared the blood mononuclear cell transcriptome of pediatric and adult MS patients with recovery (PDMS-rec, ADMS-rec) and without recovery (PDMS-norec, ADMS-norec) 6 months after relapse. Healthy pediatric and adult subjects (PDC, ADC) were used as controls.

overall_design: A total of 30 MS patients (14 PDMS-rec and ADMS-rec, 16 PDMS-norec and ADMS-norec , 55 PDC andADC) that met the inclusion criteria were analyzed.

first: Yulia

last: Kavkin

first: Shay

last: Menascu

first: Rina

last: Zilkha-Falb

last: Dolev

first: David

last: Magalashvili

first: Anat

last: Achiron


title: Pathways involved in pony body size development

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: The mechanism of body growth in mammals is poorly understood. Here, we report the regulatory networks involved in body growth through analyzing transcriptomes of pituitary and epiphyseal tissues of Debao ponies and Mongolian horses at juvenile and adult stages. We found that GHR was expressed little in long bones though GH was highly expressed in Debao ponies compared with Mongolian horses. Moreover, m-RAS and ATF3, involved in the GHR pathway, were found to be significantly downregulated in juvenile ponies, which slowed the proliferation of bone osteocytes. However, WNT2 and PLCβ2 were obviously upregulated in juvenile Debao ponies, which led to premature mineralization of bone extracellular matrix. Furthermore, we found that the WNT/Ca2+ pathway may be responsible for the regulation of body growth. We then demonstrated that GHR was lacking in long bones of Debao ponies using RT-qPCR and Western blot. Treatment with WNT antagonist 1 decreased expression of the WNT pathway (P≤0.05) in vitro. The transduction of ATDC5 cells with GHR-RNAi lentivirus decreased expression of the GHR pathway (P≤0.05). Additionally, detection of plasma hormone concentrations showed that the ponies had higher levels of IGF-1 as juveniles and GH in adulthood than Mongolian horses, indicating that the hormone regulation in Debao ponies differs from that in Mongolian horses. Our work provides an insight into the genetic regulation for dwarf growth in mammals and a reference for therapeutic strategy for dwarfism

overall_design: Twenty-four samples were taken and prepared from Six female DPs and six female MHs pituitary and epiphysis tissues.


title: RNA-Sequencing of epithelium and colonoids from patients with pediatric inflammatory bowel disease

city: Philadelphia

first: Kathryn

middle: Elizabeth

last: Hamilton

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary:
Objective: Children with very early onset inflammatory bowel disease (VEO IBD) present with more extensive, severe, and refractory disease than older children and adults with IBD. In the current study, we evaluated functional and transcriptomic differences in epithelial cells from patients with VEO and older onset IBD compared to controls.
Design: We established enteroids and colonoid lines from patients with VEO and older onset IBD and control patients. We evaluated crypt conversion (initial growth efficiency) compared to histopathological and clinical parameters. We performed RNA-sequencing on colonoids followed by validation via qPCR and flow cytometry in additional patients and in colonoids after multiple passages.
Results: Control enteroids and colonoids exhibited consistently high crypt conversion, whereas patients with VEO and older onset IBD exhibited decreased crypt conversion associated with higher inflammation scores. Transcriptomic analysis revealed increased expression of LYZ, reported previously in colonoids from adult patients with ulcerative colitis, as well as antigen presentation genes HLA-DRB1 and HLA-DRA, which persisted after prolonged passaging as verified by flow cytometry.
Conclusion: We present the first functional comparison of enteroids and colonoids from patients with VEO and older onset IBD, a subset of which exhibit poor initial growth. Enhanced and persistent expression of epithelial antigen presentation genes in patient colonoids supports the notion that epithelial cell-intrinsic differences may result from or contribute to disease. Analyses of colonoids from pediatric patients with IBD will contribute to a greater understanding of epithelial cell-autonomous defects in patients with VEO and older onset IBD and will be an important tool for understanding novel disease variants in the future.

overall_design: mRNA profiles from colonoids of 3 patients with older onset IBD, 4 patients with VEO IBD and 7 controls and epithelial tissue of 2 patients with older onset IBD, 3 patients with VEO IBD and 1 control

middle: E

first: Noor

last: Dawany

first: Judith

middle: R

last: Kelsen


title: A census of RNA/protein complexes in a model Gram-positive bacterium reveals exonuclease-mediated sRNA activation in competence regulation

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary: RNA-protein interactions crucially underlie many steps of bacterial gene expression including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast with recent progress in Gram-negative bacteria, knowledge about RNA and protein complexes in Gram-positive species remains scarce. Here, we used Grad-seq to draft a landscape of such complexes in Streptococcus pneumoniae, determining the sedimentation profiles of ~88% of the transcripts and ~62% of the proteins of this important human pathogen. Analysis of in-gradient distributions and subsequent tag-based protein capture identified interactions of the exoribonuclease Cbf1 (a.k.a. YhaM) with sRNAs that control bacterial competence. Contrary to expectation, the nucleolytic activity of Cbf1 stabilized these sRNAs, thereby promoting their function as repressors of competence. These results illustrate how this first RNA/protein complexome resource for a Gram-positive species can be utilized to identify new molecular factors in RNA-based regulation of pathways with relevance to bacterial virulence.

overall_design:
22 total RNA samples from S. pneumoniae wild type resolved on a glycerol gradient resulting in 20 fractions and a pellet fraction. A lysate sample is given as input control.

Fraction numbers are sequential: 1 is the fraction with the low molecular weight complexes and with increasing sample number the molecular weight of the complexes increases.

first: Jens

last: Hör

first: Geneviève

last: Garriss

first: Silvia

last: Di Giorgio

first: Lisa-Marie

last: Hack

middle: T

last: Vanselow

middle: U

first: Andreas

last: Schlosser

first: Birgitta

last: Henriques-Normark

first: Jörg

last: Vogel


title: Transcriptomic profiling of wild-type C2C12 cells and C2C12 cells with Myod1 gene knockout by RNA-sequencing

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

summary: C2C12 is a myoblast cell line usually used for study of muscle differentiation. Myod1 is a pro-differentiation factor for myogenesis. We found that CRISPR/Cas9-mediated Myod1 gene knockout in C2C12 cells led to the loss of myoblast identity and gain of neural properties.

overall_design: Myod1 gene was knocked out with CRISPR/Cas9. Wild type C2C12 cells (C2C12(WT)) and gene knockout cells (C2C12(Myod1-/-)) showed different phenotypes when cultured in serum-free medium. Each three samples of C2C12(WT) and C2C12(Myod1-/-) were collected and subjected to RNA-sequencing.

first: Min

last: Zhang


title: RNA-seq analysis of the effects of forskolin treatment on human primary adipocytes

city: Leeds

first: Lee

last: Roberts

state: Yorkshire

address: Level 7 LIGHT Laboratories, University of Leeds

department: LICAMM

country: United Kingdom

institute: University of Leeds

summary: Analysis of forskolin-stimulated cAMP signalling on adipocyte metabolism at gene expression level. Results provide important information of the response of adipocytes to cAMP signaling (a cold-conditioned mimc), such as specific metabolic genes, up- or down-regulated that control expression of putative adipokines.

overall_design: Human white primary preadipocytes (PromoCell, Heidelberg, Germany) were seeded (10,000-15,000 cells/cm2) and grown to confluence (37°C, 5% CO2) in preadipocyte growth medium (0.05ml/ml fetal calf serum, 0.004ml/ml endothelial cell growth supplement, 10ng/ml epidermal growth factor, 1µg/ml hydrocortisone, 90µg/ml heparin). Preadipocytes were differentiated according to supplier’s instructions. Briefly, growth medium was replaced by differentiation media (8µg/ml d-biotin, 0.5µg/ml insulin, 400ng/ml dexamethasone, 44µg/ml isobutylmethylxanthine, 9ng/ml L-thyroxine, 3µg/ml ciglitazone) for 48 hours. Differentiation medium was replaced with adipocyte nutrition media (0.03ml/ml fetal calf serum, 8µg/ml d-biotin, 0.5µg/ml insulin, 400ng/ml dexamethasone) for 12 days until cells were fully differentiated. Media was changed every 48 hours. Human white primary adipocytes were treated with 1 μM forskolin on days 10 - 12 of differentiation or remained untreated (control). Total RNA was then isolated.

middle: D


title: Fos licenses early events in stem cell activation promoting skeletal muscle regeneration

city: Los Angeles

first: Albert

middle: Ernesto

last: Almada

state: CA

address: 1450 Biggy Street

department: Orthopaedic Surgery and Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

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

overall_design: Refer to individual Series


title: Fos licenses early events in stem cell activation promoting skeletal muscle regeneration [RNA-seq]

summary: Muscle stem cells, also known as satellite cells, are largely non-proliferative in uninjured skeletal muscle but transition at sites of injury into rapidly dividing progenitors that mediate muscle repair. As early events in satellite cell activation are rate-limiting for recovery from muscle damage, there is substantial interest in discovering their molecular driver(s). Using a comparative transcriptomic approach, we identified a prominent Fos signature in recently activated muscle satellite cells, which was rapidly and transiently induced by muscle damage. Functional interrogation using complementary genetic mouse models revealed that FOS is required for efficiently initiating key stem cell functions, including cell cycle entry, stem/progenitor cell expansion, and regeneration of muscle after injury. Transcriptional profiling further revealed that FOS activates critical gene circuits that stimulate cell migration, proliferation, and differentiation while simultaneously repressing quiescence-promoting gene signatures. Pharmacological and genetic disruption of one of these FOS-activated target genes, mono-ADP Ribosyl-Transferase 1 (Art1), in freshly isolated satellite cells substantially diminished cell cycle entry and expansion of the pool of regenerative stem cells. Together, these data implicate FOS as a crucial inducer of early-acting, pro-regenerative gene targets and highlight new transcriptional and post-translational modification events necessary for optimal injury-activated muscle stem cell regenerative responses.

overall_design:
RNA-Seq dataset 1: Fresh SCs were isolated via FACS from resting skeletal muscle (hind-limbs, pectoral, and triceps) of 4-month old FosGFP animals (n=4 mice). RNA was extracted from 1000 FosGFP+/B1-Integrin+/CXCR4+/CD45-/CD31-/CD11b-/Ter119-/Sca1- Fresh SCs and 1000 FosGFP-/B1-Integrin+/CXCR4+/CD45-/CD31-/CD11b-/Ter119-/Sca1- Fresh SCs (Samples 1-8).
RNA-Seq data set 2: Fresh SCs were isolated via FACS from resting skeletal muscle (hind-limbs, pectoral, and triceps) of 6-month old FoscKO and Control animals (n=3 mice). RNA was extracted from 1000 FosGFP+/B1-Integrin+/CXCR4+/CD45-/CD31-/CD11b-/Ter119-/Sca1- Fresh SCs and 1000 FosGFP+/B1-Integrin+/CXCR4+/CD45-/CD31-/CD11b-/Ter119-/Sca1- Fresh SCs (Samples 9-14).

first: A

first: N

last: Horwitz

first: F

last: Price

last: Gonzalez

first: M

last: Ko

last: Sinha

first: L

middle: L

last: Rubin

middle: J

last: Wagers


title: Expression dada in  adult mouse cardiomyocytes with knockdown of Hoxa5 (ID:15402) or not and treated with  phenylephrine (100μM)

status: Public on Jan 26 2021

first: Zhiguang

last: Shi

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: HOXA5 is important in overload-induced cardiac hypertrophy. We uesd RNA-Seq to detail global expression program alterations in adult mice cardiomyocytes transfected with Small interfering RNA (siN or siHoxa5 )and treated with  phenylephrine(100μM) . Comparisons consisted of identifying Hoxa5-affected gene expression patterns.

overall_design: Adult mouse cardiomyocytes were isolated and cultured, and transfected with Small interfering RNA targetting to Negtive control or Hoxa5. After  24 hours later, cardiomyocytes were treated  with phenylephrine(100μM) for 24 hours

first: Yan

first: Qiang

last: da

first: Wei

last: Wu


title: A Machine-learning approach to define and predict the therapeutic landscape of pan-cancer Hippo pathway dependency (ATAC-seq)

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

type: Genome binding/occupancy profiling by high throughput sequencing

summary: One challenge of cancer precision medicine is the heterogeneity of genetic and non-genetic alterations that result in dysfunctional molecular pathways. As an emerging drug discovery effort, dysregulation in Hippo pathway signaling is known to drive oncogenesis across numerous cancer types but lacks recurrent mutation(s) that are often found in other canonical signaling pathways. Here, we use first principles approach to develop a machine-learning framework to identify a robust, lineage-independent gene expression signature to quantify Hippo pathway dependency in cancers. Through integrating data from multi-omics platforms, this data-driven approach has enabled identifying a proposed combination with MAPK inhibition for direct targeting of Hippo pathway dependent cancers for which we then elucidate the underlying molecular mechanism. The results underscore how a multifaceted approach, computational models combined with laboratory efforts, can accelerate precision medicine efforts toward co-targeting Hippo and MAPK pathways, an approach that can be generalized to other key cancer signaling pathways to define therapeutic strategies.

overall_design: ATAC-seq of siNTC and siYAP/TAZ of PATU 8902 and Detroit 562

first: Anwesha

last: Dey

first: Matthew

last: Chang

first: Trang

last: Pham

first: Jason

last: Li

first: Thijs

last: Hagenbeek


title: A Machine-learning approach to define and predict the therapeutic landscape of pan-cancer Hippo pathway dependency


title: Transcriptome evidence provides insight into Hox gene regulating rolling behavior in oniscidea

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

summary: Behavior of rolling in oniscidea species had been reported as a sign to protect themselves to increase their survival rates, but the molecular mechanisms of rolling behaviors were still largely unknown. So we deeply characterized the molecular differences in rolling oniscidea samples and stretching oniscidea samples by transcriptome sequencing strategy (RNA-seq). Bulk RNA sequencing was performed with rolling and streching oniscidea samples. And our study suggests that Hox genes' expression levels could play an essential role in regulating neuron system development in oniscidea animals.

overall_design: Bulk RNA-seq of rolling samples and stretching samples in oniscidea.

first: Jujie

last: Chen

first: Xuelan

first: Manli

last: Wang

first: Hongyu

last: Liu

first: Lei

last: Zhao

first: Xiangyu

last: Pan


title: RNA-sequencing of Smoothened Agonist (SAG)- versus solvent-treated (DMSO) TtT/GF cells

city: Goettingen

first: Nadine

last: Brandes

address: Heinrich-Düker-Weg 12

department: Institute of Human Genetics

institute: University Medical Center Goettingen

summary: We analysed the transcriptional changes in the murine folliculostellate cell line TtT/GF after treatment with the Hedgehog signaling activator SAG or its solvent control DMSO, respectively. After activation of the Hedgehog signalling cascade the TtT/GF cells start to transcribe genes that are implicated in extracellular matrix formation and some neuropeptides are transcribed. Partially these genes are described to alter the hormone status in endocrine cells. Therefore, our data implicate that Hedgehog signalling can control hormone secretion in the pituitary gland in an indirect way via folliculostellate cells.

overall_design: mRNA profiles of Smoothened Agonist (SAG)- versus solvent-treated (DMSO) TtT/GF cells were generated by RNA-sequencing

first: Anja

last: Uhmann

first: Dominik

last: Botermann


title: SIX2 and SIX3 coordinately regulate functional maturity and fate of human pancreatic β cells

city: Stanford

first: Romina

last: Bevacqua

address: 279 Campus Drive W

department: Developmental Biology

institute: Stanford University

summary:
Transcriptomic profiling by high-throughput sequencing of primary human Beta cells following SIX2 or SIX3 loss of function. SIX2 genome-binding profiling by CUT&RUN and high-throughput sequencing.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Profiling FACS-purified human pancreatic SIX2 or SIX3 shRNA-mediated knockdown GFP+ Beta cells by RNA-Seq, compared to a non-targeting shRNA control/donor. We analyzed the genomic targets of SIX2 by SIX2-Flag overexpression and CUT&RUN compared to a non-antibody control.

Refer to individual Series

first: Seung

middle: K

last: Kim


title: SIX2 and SIX3 coordinately regulate functional maturity and fate of human pancreatic β cells [RNA-seq]

summary: Transcriptomic profiling by high-throughput sequencing of primary human Beta cells following SIX2 or SIX3 loss of function.

overall_design: Profiling FACS-purified human pancreatic SIX2 or SIX3 shRNA mediated knockdown GFP+ adult Beta cells by RNA-Seq, compared to a non-targeting shRNA control/donor. Profiling FACS-purified human pancreatic SIX3 overexpressing Flag+ juvenile Beta cells by RNA-Seq, compared to an empty overexpressing construct.


summary: SIX2 genome-binding profiling by CUT&RUN and high-throughput sequencing.

overall_design: Analysis of the genomic targets of SIX2 by SIX2-Flag overexpression in adult primary human islets and CUT&RUN with anti-Flag antibody compared to a non-antibody control. 4 replicates.


title: A Machine-learning approach to define and predict the therapeutic landscape of pan-cancer Hippo pathway dependency (RNA-seq)

first: Robert

last: Piskol

overall_design: RNA sequenced from siNTC and siYAP/TAZ treatment of 7 cell lines

first: Anwesha


title: Prolactin Drives a Dynamic STAT5A/HDAC6/HMGN2 Cis-Regulatory Landscape Exploitable in ER+ Breast Cancer

city: Richmond

first: Justin

middle: Michael

last: Craig

state: Virginia

address: 1201 E Marshall St

department: Massey Cancer Center

institute: Virginia Commonwealth University

summary: The hormone, prolactin, has been implicated in breast cancer pathogenesis and regulates chromatin engagement by the transcription factor, STAT5A. STAT5A is known to inducibly bind  promoters and cis-regulatory elements genome wide, though the mechanisms by which it exerts specificity and regulation of target gene expression remain enigmatic. We previously identified HDAC6 and HMGN2 as cofactors that facilitate prolactin induced, STAT5A mediated gene expression. Here, multi-condition STAT5A, HDAC6, and HMGN2 ChIP-seq with parallel condition RNA-seq are utilized to reveal the cis-regulatory landscape and cofactor dynamics underlying prolactin stimulated gene expression in breast cancer. We find that prolactin regulated genes are significantly enriched for cis-regulatory elements bound by HDAC6 and HMGN2, and that inducible STAT5A binding at enhancers, rather than promoters, conveys specificity for prolactin regulated genes. The selective HDAC6 inhibitor, ACY-241, blocks prolactin induced STAT5A chromatin engagement at cis-regulatory elements as well as a significant proportion of prolactin stimulated gene expression. We identify functional pathways known to contribute to the development and/or progression of breast cancer that are activated by prolactin and inhibited by ACY-241. Additionally, we find that the DNA sequences underlying shared STAT5A and HDAC6 binding-sites at enhancers are differentially enriched for estrogen response elements (ESR1 and ESR2 motifs) relative to enhancers bound by STAT5A alone. Gene set enrichment analysis identifies significant overlap of ERα regulated genes with genes regulated by prolactin, particularly prolactin regulated genes with promoters or enhancers co-occupied by both STAT5A and HDAC6.

overall_design: High quality STAT5A, HDAC6, and HMGN2 ChIP-seq datasets were generated in full accordance with guidelines and quality standards established by the ENCODE consortia. Of primary importance, the antibodies utilized here were rigorously tested for specificity, confirmed by knockdown of each targeted protein. To investigate hormone stimulated binding dynamics and the influence of pharmacological HDAC6 inhibition, the chromatin of MCF-7 human breast cancer cells was harvested for ChIP before and after exposure to prolactin (30 minutes; 250 ng/mL) and/or ACY-241 [Citarinostat] (120 minutes; 2 µM). To enable the most informative comparisons across ChIP targets, for each experimental condition (and biological replicate), pooled chromatin was aliquoted for incubation with each antibody immediately prior to immunoprecipitation, ensuring sampling from an identical cell population. Sequencing depth, read quality, and read duplication rates were all well within ideal specifications for mammalian point-source transcription factors. Reads mapping to ENCODE blacklist regions were removed before union peaksets of non-overlapping, robust (MACS2 FDR<0.01) peaks were identified for each factor (88,709 STAT5A peaks; 12,815 HDAC6 peaks; 102,661 HMGN2 peaks). In parallel experiments, we generated matching condition RNA-seq expression data identifying significant (FDR<0.05), differentially expressed genes following prolactin stimulation and/or ACY-241 treatment.

first: Charles

middle: V

last: Clevenger


title: Identification and characterization of pleiotropic high-persistence mutations in the beta subunit of the bacterial RNA polymerase

city: St. Paul

first: Arkady

last: Khodursky

address: 1479 Gortner Ave

institute: University of Minnesota

summary: We report identification and characterization of antibiotic persister mutants carrying characteristic mutations in the Escherichia coli rpoB gene

overall_design: Independently grown colonies of the rpoB encoding a substitution in 1304 aa residue of RpoB have been compared to the wild-type control


title: The expansion of unconventional CD56dim CD16neg cells is a hallmark of the natural killer cell population in COVID-19

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

country: South Korea

institute: KAIST

summary: Natural killer (NK) cells of healthy donors and COVID-19

overall_design: Compare gene expression patterns of NK cells between healthy donors and COVID-19 patients

first: Eui-Cheol

last: Shin


title: UUO-rUUO small RNA seq, Denby lab 2019

city: Edinburgh

first: Oliver

last: Teenan

state: Midlothian

address: 47 Little France Crescent

department: Cardiovascular Sciences

institute: University of Edinburgh

summary: Small RNA sequencing of sorted cell type, mice kidneys, after unilateral ureteral obstructive (UUO) surgery after 2 days, 7 days and a reversible (rUUO) 14 day model with corresponding sham operated mice. The goal of the study is to identify micro-RNA dysregulation of expression between different cell types corresponding with kidney injury, in order to identify and assess biomarkers which could be translated into the clinical setting.

overall_design: Each group was sequenced from 4 mice, and 4 cell types. 2 day UUO kidneys were sorted into PDGFRβ+, F480+, LTL+ and CD31+  cell types before the RNA was extracted and small RNA sequenced for 4 mice. The same protocol was followed for 7 day UUO mice, rUUO mice, as well as sham operated mice for reference.

first: Katie

last: Connor

first: Laura

last: Denby

first: Bryan

last: Conway

first: Jeremy

last: Hughes

first: Carmel

last: Moran


title: TCF7L2 silencing results in altered gene expression patterns accompanied by local genomic reorganization

city: Bethesda

first: Markus

middle: Alexander

last: Brown

state: Maryland

address: 50 South Drive, Room 1408

department: Center for Cancer Research

institute: National Institutes of Health

summary: Canonical Wnt signaling is crucial for intestinal homeostasis as TCF4, the major Wnt signaling effector in the intestines, is required for stem cell maintenance. The capability of TCF4 to maintain the stem cell phenotype is contingent upon β-catenin, a potent transcriptional activator, which interacts with histone acetyltransferases and chromatin remodeling complexes. We used RNAi to explore the influence of TCF4 on chromatin structure (Hi-C) and gene expression (RNA sequencing) across a 72-hour time series in colon cancer. We found that TCF4 reduction results in a disproportionate up-regulation of gene expression, including a powerful induction of SOX2. Integration of RNA sequencing and Hi-C data revealed a TAD boundary loss, which occurred concomitantly with the over-expression of a cluster of CEACAM genes on chromosome 19. We identified EMT and E2F as the two most deregulated pathways upon TCF4 depletion and LUM, TMPO, and AURKA as highly influential genes in these networks using measures of centrality. Results from gene expression, chromatin structure, and centrality analyses were integrated to generate a list of candidate transcription factors crucial for colon cancer cell homeostasis. The top ranked factor was c-JUN, an oncoprotein known to interact with TCF4 and β-catenin, confirming the usefulness of this approach.

overall_design: Eight RNA sequencing samples from the SW480 colon cancer cell line are submitted. The sample set is comprised of two replicates for four time points (0, 24, 48, and 72 hours). The 24, 48, and 72 hour time points where treated with siRNA targeting TCF7L2 transcripts, while the 0 hour time point was treated with negative control siRNA.

middle: A

first: Gabrielle

last: Dotson

first: Indika

last: Rajapakse

first: Thomas

last: Ried


title: KDM5C represses FASN-mediated lipid metabolism to exert tumor suppressor activity in intrahepatic cholangiocarcinoma

city: Shanghai

first: Shanhe

last: Yu

address: 197# Rui Jin Road II

institute: Shanghai Institute of Hematology，Rui Jin Hospital

summary: Next Generation Sequencing Facilitates Quantitative Analysis of HCCC9810 cells transduced with control or KDM5C-expression vector.

overall_design: mRNA profiles of HCCC9810 cells were generated by deep sequencing, in triplicate, using HiSeq X Ten.

first: Bo

last: Zhang


title: Pax3 plays a role in Neuro-2a cells proliferation and neurite outgrowth

city: Shenzhen

first: Huo

last: Bingqing

state: Guangdong

address: Lianhua Road

institute: Shenzhen PKU-HKUST Medical Center

summary: Our fingdings suggested that Pax3 not only inhibited the cell viability and proliferation, but also affected the cell cycle and the neurite outgrowth of Neuro-2a cells.RNA sequencing analysis showed upregulated genes in Pax3 overexpressed group were involved in cell cycle machinery, which may reveal the potential mechanism of proliferation.

overall_design: We use Pax3 overexpression adenoviral to infect Neuro-2a cells. to detect the function of proliferation,cell cycle and neurite outgrowth.We use Transcriptome sequencing to detect the expression level of mRNA in infected Neuro-2a cells.

first: Wei

first: Bingqing

last: Huo


title: Beyond flowering time: diverse roles of an APETALA2‐like transcription factor in shoot architecture and perennial traits

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

institute: University of Cologne

summary:
Polycarpic perennials maintain vegetative growth after ﬂowering. PERPETUAL FLOWERING 1 (PEP1), the orthologue of FLOWERING LOCUS C (FLC) inArabis alpina regulates ﬂowering and contributes to polycarpy in a vernalisation-dependent pathway. pep1 mutants do not require vernalisation to ﬂower and have reduced return to vegetative growth as all of their axillary branches become reproductive.
To identify additional genes that regulate ﬂowering and contribute to perennial traits we performed an enhancer screen of pep1. Using mapping-by-sequencing, we cloned a mutant (enhancer of pep1-055, eop055), performed transcriptome analysis and physiologically characterised the role it plays on perennial traits in an introgression line carrying the eop055 mutation and a functional PEP1 wild-type allele.
eop055 ﬂowers earlier than pep1 and carries a lesion in the A. alpina orthologue of the APETALA2 (AP2)-like gene, TARGET OF EAT2 (AaTOE2). AaTOE2 is a ﬂoral repressor and acts upstream of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 5 (AaSPL5). In the wild-type background, which requires cold treatment to ﬂower, AaTOE2 regulates the age-dependent response to vernalisation. In addition, AaTOE2 ensures the maintenance of vegetative growth by delaying axillary meristem initiation and repressing ﬂowering of axillary buds before and during cold exposure.
We conclude that AaTOE2 is instrumental in ﬁne tuning different developmental traits in the perennial life cycle of A. alpina.

overall_design: Main shoot apices from  8-week-old plants vernalized for eight weeks (8wLD+8wV) were collected from wild-type and Aatoe2_IL plants to study the effect of AaTOE2 at the transcriptomic level in the regulation of flowering during vernalization. Also, V3 buds were harvested from 8-week-old plants vernalized for eight weeks from both genotypes to study the role of AaTOE2 in the development of axillary branches.

first: Yanhao

last: Zhou

first: Xiangchao

last: Gan

first: Natanael

last: Viñegra de la Torre

first: Ulla

last: Neumann

middle: C


title: APETALA2‐like transcription factor in shoot architecture and perennial traits

type: Genome variation profiling by high throughput sequencing

overall_design: Refer to individual Series


overall_design: The eop mutants were self-fertilized for two generations to fix the phenotype of interest and then backcrossed to the non-mutagenized progenitor pep1-1 followed by one generation of self-fertilization to create a BC1F2 mapping population. Within this backcross population, only mutagen-induced changes segregate, and the causal and closely linked mutations will be fixed in the mutant pool by selecting plants with the mutant phenotype (James et al., 2013). As a result, lots of putative causal changes will be reduced to improve the accuracy of mapping. Researchers suggested that the backcross population needs high coverage (>25 x) for optimal mapping as the number of markers (or mutations) is relatively lower (James et al., 2013).


title: Nrf2-mediated enhancer activation ameliorates oxidative stress and cystogenesis in autosomal dominant polycystic kidney disease [ChIP-seq]

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

summary: Oxidative stress is emerging as a crucial contributor to the pathogenesis of autosomal dominant polycystic kidney disease (ADPKD), but the molecular mechanisms underlying the disturbed redox homeostasis in cystic cells remain elusive. In the present study, we identify impaired activity of Nrf2 antioxidant pathway as a driver mechanism for oxidative damage and ADPKD progression. Using a quantitative proteomic approach, together with biochemistry analyses, we find that Nrf2 antioxidant pathway is suppressed due to increased degradation of Nrf2 protein in ADPKD kidneys. In a cohort of ADPKD patients, reactive oxygen species (ROS) levels are frequently elevated, and the ROS levels inversely correlates with Nrf2 abundance and positively correlates with disease severity. Genetic deletion of Nrf2 further increases ROS generation and promotes cyst growth in an orthologous ADPKD mouse model, while pharmacological induction of Nrf2 reduces ROS levels and retards cystogenesis and disease progression. Mechanistically, pharmacological induction of Nrf2 remodels enhancer landscapes and activates Nrf2-bound enhancer-associated genes in ADPKD cells. The activation domain of Nrf2 forms phase-separated condensates with Mediator subunit MED16 in vitro, and Nrf2 is required for optimal Mediator recruitment to target genomic loci in vivo. Taken together, these findings indicate that Nrf2 remodels enhancer landscapes and activates its target genes through a phase-separation mechanism, and that activation of Nrf2 represents a promising strategy for restoring redox homeostasis and combatting ADPKD.

overall_design: We performed ChIP-Seq analysis of H3K27ac, H3K4me1, H3K4me3, Nrf2, MED1 and p300 in WT 9-12 cells treated with vehicle or SFN.

first: Yupeng

last: Chen


title: Targeting of DNMT3A hotspot mutations in Clonal Hematopoiesis  and Acute Myeloid Leukemia

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

summary: Somatic mutations in DNA Methyltransferase 3A (DNMT3A) with a hotspot in exon 23 at Arginine 882 (DNMT3AR882mut) are the most frequent single mutations in clonal hematopoiesis. Here we analyze the expression of genes and endogenous retrovirus (ERV) sequences in a murine model carrying human DNMT3A-R882H mutation in one allele of the endogenous DNMT3A with respect to normal condition and azacitidine treatment.

overall_design: Lineage- Sca1+ Kit + (LSK) sorted bone marrow cells from WT DNMT3A and mice habouring a human DNMT3A R882H mutant allele in the endogenous locus were subject to transcriptomic sequencing under normal and azazytidine treatment condition. Expression levels of genes as well as repetitive elements were investigated.

first: Marina

last: Scheller

first: Carsten

last: Müller-Tidow


title: Single cell transcriptomics of primate sensory neurons identifies cell types associated with human chronic pain

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

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


title: Nrf2-mediated enhancer activation ameliorates oxidative stress and cystogenesis in autosomal dominant polycystic kidney disease [RNA-seq]

overall_design: We performed gene expression analysis on mRNA from normal and Nrf2 knockout WT 9-12 cells treated with vehicle or SFN.


title: Transcriptom analysis of MCF10A before and after H-RAS transformation [RNA-seq]

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

institute: Bar-Ilan University

summary: Gene transcription is substantially regulated by distant regulatory elements via combinatorial binding of transcription factors. It is more and more recognized that alterations in chromatin state and transcription factor binding in these distant regulatory elements may have key roles in cancer development. Here we focused on the first stages of oncogene induced carcinogenic transformation, and characterized the regulatory network underlying transcriptional reprogramming associated with this process. Using Hi-C data, we couple between differentially expressed genes and their differentially active regulatory elements and reveal two candidate transcription factors, p53 and CTCF, as major determinants of transcriptional reprogramming at early stages of HRas-induced transformation. Strikingly, the malignant transcriptional reprograming is promoted by redistribution of chromatin binding of these factors without major variation in their expression level. Our results demonstrate that alterations in the regulatory landscape have a major role in driving oncogene-induced transcriptional reprogramming.

overall_design: RNA seq in MCF10A cell type before and after H-RAS transformation

first: Michal

last: Schwartz

first: Avital

middle: S

last: Portugez

first: Bracha

middle: Z

last: Attia

first: Miriam

last: Tannenbaum

first: Olga

last: Loza

first: Aliza

last: Chase

first: Yousef

last: Turman

first: Tommy

last: Kaplan

first: Zaidoun

last: Salah


title: Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain [Wafergen]

summary: Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.

overall_design: Single cell transcriptomic study of rhesus macaque sensory DRG. This dataset includes 4742 cells from three individuals using the Wafergen protocol

first: Dmitry

last: Usoskin

first: Jussi

last: Kupari

first: Daohua

last: Lou

first: Marc

last: Parisien

first: Yizhou

last: Hu

first: Michael

last: Fatt

first: Peter

last: Lönnerberg

first: Mats

last: Spångberg

first: Bengt

last: Eriksson

last: Kharchenko

first: Barkas

last: Nikolaos

first: Karin

last: Loré

first: Samar

last: Khoury

first: Luda

last: Diatchenko

first: Patrik

last: Ernfors


title: Elevated intracellular cyclic-di-GMP level in Shewanella oneidensis increases expression of c-type cytochromes

city: Oxford

first: Chun Kiat

last: Ng

address: Parks Road

department: Engineering Science

institute: University of Oxford

summary: Transcriptomic analysis used to understand the influence of elevated intracellular cyclic-di-GMP in Shewanella oneidensis on expression of c-type cytochrome at transcript level.

overall_design: RNA were extracted from S. oneidensis MR-1 WT and pYedQ2 cultures using the RNeasy mini Kit (Qiagen, Germany), with the DNA being depleted using RNase-free DNase set (Qiagen, Germany), sequenced using Illumina HiSeq2500.

first: Chun


title: Nrf2-mediated enhancer activation ameliorates oxidative stress and cystogenesis in autosomal dominant polycystic kidney disease

first: Zhiheng

last: Liu


title: Regulatory regions of MCF10A before and after H-RAS transformation [ATAC-seq]

first: Ofir

last: Hakim

overall_design: ATAC seq in MCF10A cell type before and after H-RAS transformation

first: Michal

last: Schwartz

first: Avital

last: Portugez

first: Bracha

last: Attia

first: Miriam

last: Tannenbaum

first: Olga

last: Loza

first: Aliza

last: Chase

first: Yousef

last: Turman

first: Tommy

last: Kaplan

first: Zaidoun

last: Salah


title: Expression data from P4H-TM knockout mouse cortexes

city: Oulu

first: Nadiya

last: Byts

address: Aapistie 7C

department: FBMM

country: Finland

institute: Biocenter Oulu

summary: Genetic deletion of transmembrane prolyl-4-hydroxylase (P4H-TM) in mice leads to changes in calcium signaling  accompiened by attenuation of calcium agonist-induced gliotransmission and redistribution of mitochondria in primary astrocytes

overall_design: Cortexes from wild-type (WT) and P4H-TM knockout (KO) mice were collected for further mRNA extraction and microarray analysis.  mRNA from 4 individual mice were pooled per experimental condition. Comparison was done between two experimental conditions: WT and KO.

first: Johanna

last: Myllyharju


title: Bach2 deficiency leads to spontaneous expansion of IL-4-producing T follicular helper cells and autoimmunity

first: Heng

last: Zhang

address: No.227 Sounth Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: The transcription factor Bach2 is a critical negative regulator of Tfh cell differentiation, especially IL-4 subset. Tfh cells from the mesenteric lymph nodes of WT and Bach2 CD4 conditional KO mice were collected to process the Rna-seq. Mechanistically, Bach2 may limit abnormal IL-4-produicng Tfh cell formation by repressing c-Maf, CXCR5 and IL-4.

overall_design: 10000-30000 Tfh Cells (CD4+B220-CD44+PD-1+CXCR5+) were sorted from the MLNs of WT and Bach2fl/flCd4-cre mice. cDNA was synthesized and amplified using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech). The library for mRNA sequencing was generated using Illumnia TruSeq Preparation Kit (RS-122-2001) and sequenced using Illumnia Nextseq500 sequencer.

first: Chuanxin

last: Huang

first: Min


title: Neutrophil oxidative stress mediates obesity-associated vascular inflammation and metastatic transmigration

status: Public on Jan 25 2021

city: Montreal

first: Logan

middle: A.

last: Walsh

state: QUEBEC

address: 1160 Pine Avenue, Box 532

country: Canada

institute: MCGILL UNIVERSITY


title: Neutrophil oxidative stress mediates obesity-associated vascular inflammation and metastatic transmigration (Neutrophils_RNA-seq)

summary: Obesity is linked to greater cancer incidence and mortality across multiple tumor types. In breast cancer, metastasis is the leading cause of cancer-related deaths, and epidemiological studies have shown that obesity is associated with increased breast cancer metastasis to lung and liver. Using both diet-induced and genetic preclinical models of obesity, it was previously shown that obese adipose tissue systemically induces lung neutrophilia, which is associated with enhanced breast cancer metastasis to this site. Here we performed RNAseq on neutrophils isolated on the lungs from lf vs hf mice.

overall_design: Neutrophils (CD45+ CD11b+ Ly6Clo Ly6G+) were FACS-purified from lungs of LF (n=3) or HF (n=4) mice. RNA-sequencing and quality control was performed at GENEWIZ, NJ.

first: Benoit

last: Fiset

first: Daniela

middle: F

last: Quail


title: Neutrophil oxidative stress mediates obesity-associated vascular inflammation and metastatic transmigration (Endothelial_Cells_RNA-seq)

overall_design: Endothelial cell (CD45- CD31+) were FACS-purified from lungs of LF (n=4) or HF (n=4) mice. RNA-sequencing and quality control was performed at GENEWIZ, NJ.


title: Fos licenses early events in stem cell activation promoting skeletal muscle regeneration [array]

city: Los Angeles

first: Albert

last: Almada

address: 1450 Biggy Street

institute: University of Southern California

summary: Muscle stem cells, also known as satellite cells, are largely non-proliferative in uninjured skeletal muscle but transition at sites of injury into rapidly dividing progenitors that mediate muscle repair. As early events in satellite cell activation are rate-limiting for recovery from muscle damage, there is substantial interest in discovering their molecular driver(s). Using a comparative transcriptomic approach, we identified a prominent Fos signature in recently activated muscle satellite cells, which was rapidly and transiently induced by muscle damage. Functional interrogation using complementary genetic mouse models revealed that FOS is required for efficiently initiating key stem cell functions, including cell cycle entry, stem/progenitor cell expansion, and regeneration of muscle after injury. Transcriptional profiling further revealed that FOS activates critical gene circuits that stimulate cell migration, proliferation, and differentiation while simultaneously repressing quiescence-promoting gene signatures. Pharmacological and genetic disruption of one of these FOS-activated target genes, mono-ADP Ribosyl-Transferase 1 (Art1), in freshly isolated satellite cells substantially diminished cell cycle entry and expansion of the pool of regenerative stem cells. Together, these data implicate FOS as a crucial inducer of early-acting, pro-regenerative gene targets and highlight new transcriptional and post-translational modification events necessary for optimal injury-activated muscle stem cell regenerative responses.

overall_design: B1-Integrin+/CXCR4+/CD45-/CD31-/CD11b-/Ter119-/Sca1- Fresh satellite cells (Fresh SCs) were isolated via FACS from resting skeletal muscle (hind-limbs, abdominal, and triceps) of 2-month old C57BL/6J (n=3 mice) adult animals. RNA was extracted from Fresh and Cultured (5-days) SCs and prepared for microarray analysis.

first: A

middle: E

first: N

last: Horwitz

first: F

last: Price

last: Gonzalez

first: M

last: Ko

last: Sinha

first: L

last: Rubin

last: Wagers


city: harbin

first: gao

last: junxin

state: hei longjiang

address: haping street

institute: junxingao

summary: We used the high-throughput sequencing and inhibitors to screen microRNAs that play the role in anti-porcine reproductive and respiratory syndrome virus (PRRSV) responses in porcine alveolar macrophages (PAMs).

overall_design: Next Generation Sequencing of miRNA in PRRSV-infected PAMs of pigs. The miRNA library construction and sequencing were conducted with Illumina sequencing technology (BGI-Wuhan, China), and qualified sequence data were analyzed by GBI (Wuhan, China). In brief, only miRNAs represented by > 20 reads were selected for differential expression testing.

first: Yue

last: Wang


title: Novel insights into the mode of action of 1,4 dioxane

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

summary: 1,4-Dioxane (1,4-DX) is an environmental contaminant found in drinking water throughout the United States (US). While it is a suspected liver carcinogen, there is no federal or state maximum contaminant level for 1,4-DX in drinking water. Very little is known about the mechanisms by which this chemical elicits liver carcinogenicity. In the present study, we performed chronic and short-term dosing studies in female BDF-1 mice to explore the toxic effects of 1,4-DX. Histopathology studies and a multi-omics approach (transcriptomics and metabolomics) were performed to investigate potential mechanisms of toxicity. Mice were exposed to various concentrations of 1,4-DX (0, 50, 500 and 5,000 mg/L) in their drinking water for one or four weeks. Immunohistochemical analysis of the liver revealed an increase in the number of H2AXγ-positive hepatocytes (a marker of DNA double strand breaks) in mice exposed to 5,000 mg/L 1,4-DX for one and four weeks. In addition, an expansion of precholangiocytes was observed after four weeks of 5,000 mg/L 1,4-DX exposure, as reflected by CK-7 immunostaining. An increase in these markers reflect both DNA damage and repair mechanisms. Liver transcriptomics profiling showed that exposure to 5,000 mg/L 1,4-DX for four weeks resulted in the differential expression of 65 genes compared to controls. Pathway analysis of the transcriptomic data revealed 1,4-DX-induced perturbations in multiple signaling pathways in the liver, including those involved in xenobiotic metabolism, nicotine degradation and glutathione-mediated detoxification. Changes to these pathways as a result of 1,4-DX exposure reflect would be predicted to impact the oxidative stress response, detoxification, and DNA damage. Liver, kidney, stool and urine metabolomics profiling revealed no effect of 5,000 mg/L 1,4-DX exposure for one or four weeks on metabolites. We speculate that this may be reflective of DNA damage being counterbalanced by the repair response, with the net result being a null overall effect on the systemic biochemistry of the exposed mice. Our results show a novel approach for the investigation of environmental chemicals that do not elicit cell death, but have activated the repair systems in response to 1,4-DX exposure

overall_design: Three week old female BDF1 mice treated with 1,4-Dioxane (50, 500 or 5,000 mg/L) in drinking water

first: Vasilis

last: Vasiliou

first: Georgia

last: Charkoftaki


title: Transcriptional profiles of human islet and exocrine endothelial cells in subjects with or without impaired glucose metabolism

city: Uppsala

first: Anders

middle: Roger

last: Hedin

state: Uppland

address: Dag Hammarskjölds väg 20.

department: Clinical immunology

institute: Uppsala University

summary: We report the application of RNA sequencing to quantify the global transcriptome of sorted endothelial cells from the endocrine and exocrine pancreas in normoglycemic and impaired glucose metabolism(IGM) human donors.

overall_design:
Examination of gene transcription in endothelial cells from human pancreatic islets and the exocrine pancreas purified using FACS from 8 normoglycemic and 5 IGM donors.
NOTE: Raw data is not included because the files were deleted by the sequencing center.

first: Olle

last: Korsgren

first: Alexander

last: Jonsson

first: Oskar

last: Skog


title: Single-Cell RNA-Seq Analysis of cells from human urine

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

summary: Urine passes through the entire kidney and urinary tract system starting from the glomerulus and ending to the urethra. Cells in the kidney and urinary tract could be exfoliated from the epithelium into the urine, while leukocyte could infiltrate from the local tissue into the urine, which makes the urine a useful subject for clinical evaluation of relevant diseases. We performed scRNA-seq on voided urine samples. 50–100 mL middle stream urine samples were collected from 12 Chinese healthy adults and combined for droplet-based single-cell RNA sequencing after flow cytometric sorting of live cells. We presented the first single-cell atlas of adult human urine and identified multiple previously unrecognized cell types. Based on our scRNA-seq analysis data, a SOX9+ cell population was identified in adult human urine which we speculated to have progenitor potential.

overall_design: For scRNA-seq analysis, urine samples were collected from healthy adult volunteers. Midstream of voided urine specimen was collected for each donor. Samples were centrifuged immediately at the speed of 390 ×g and combined for droplet-based single-cell RNA sequencing after flow cytometric sorting of live cells.

first: Daniel

middle: W

last: Henry


title: RNA-seq analysis of Arabidopsis plants overexpressing Sclerotinia sclerotiorum effector SsE1-GFP

city: Pullman

first: Hao

last: Peng

state: WA

department: Crop and Soil Sciences

institute: Washington State University

summary: Ten-day old seedlings of Arabidopsis wildtype Col-0, and SsE1-overexpressing lines SsE1-GFP-5 and SsE1-GFP-8 were collected for total RNA extraction. Three biological replicates were prepared for each genotype.

overall_design: Examination of differentially expressed genes in SsE1-GFP-5 and SsE-GFP-8 when compard to Col-0

last: Wei

first: Weidong

last: Chen


title: Chronic cadmium exposure induces differential methylation in mice spermatozoa

city: Lexington

first: Wesley

middle: N

last: Saintilnord

state: KY

address: 741 South Limestone, Biological Biomedical Sciences Research Building

department: Molecular and Cellular Biochemistry

institute: University of Kentucky College of Medicine

type: Methylation profiling by high throughput sequencing

summary: We used Reduced Representation Bisulfite Sequencing (RRBS) to comprehensively investigate the impact of chronic, low-dose Cd exposure on mice spermatozoa DNA methylation. Adult male C57BL/J6 mice were provided water with or without cadmium chloride. We purified genomic DNA from sperm samples collected after nine weeks of treatment. We found 1,788 differentially methylated sites present at regulatory regions in sperm of mice exposed to chronic, low-dose of Cd compared to vehicle (control) mice. Our results present a comprehensive analysis of the sperm methylome in response to chronic Cd exposure

overall_design: DNA methylation profile of mice spermatozoa was generated using RRBS.

first: Saray

last: Tenlep

first: Josh

last: Preston

first: Jason

last: DeRouchey

last: Unrine

first: Kevin

last: Pearson

first: Yvonne

last: Fondufe-Mittendorf


title: Adaptation of Bacillus subtilis tat and S313 mutant cells to growth in Lysogeny Broth (LB) lacking NaCl

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary: In B. subtilis, the Tat secretion system is essential for effective growth in media lacking iron or NaCl, which is related to the Tat-dependent export of the heme peroxidase EfeB. In Lysogeny Broth (LB) without NaCl, tat mutant bacteria undergo cell lysis in the early exponential growth phase. Part of the population of mutant bacteria then adapts to the salt-deprived condition and resumes growth. The absence of sRNA S313, which has a predicted role in modulating the expression of the efeUOB operon, also leads to a lysis-recovery phenotype. In this study, the transcriptomes of B. subtilis wild type, tat mutant and S313 mutant were analyzed during lysis and recovery phase in order to elucidate the reasons for lysis of mutant bacteria  in the absence of NaCl and subsequent adaptation to this condition. It was, e.g., shown that tat mutant cells suffer from severe oxidative stress and starvation.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
B. subtilis 168 wild-type, Δtat and ΔS313 mutants were grown aerobically at 37 °C in Lysogeny Broth (1 % tryptone, 0.5 % yeast extract, without NaCl). Samples were taken at two time points. The first was when the lysis of the Δtat mutant started (OD at 600 nm of ~0.9) and the second was the recovery phase (OD at 600 nm of 2).
Microarray hybridizations were performed with RNA from three biological replicates. The samples were labeled with Cy3.

first: Hermann

last: Rath

first: Bimal

last: Prajapati

first: Leif

last: Steil

first: Jan

last: Maarten van Dijl


title: Differential expression of genes cultured on extracellular matrix from control or irradiated astrocytes

city: Lund

first: Alexander

last: Pietras

address: Medicon Village 404:C3, Scheelevägen 2

department: Division of Translational Cancer Research

institute: Lund University

summary: U3082 human glioma cells were cultured on cell-derived extracellular matrix from primary human astrocytes that had been treated with either 0 Gy or 10 Gy radiation.

overall_design:
4 samples of U3082 were plated on four different samples of astrocyte derived matrix for 48 hours followed by RNA collection for RNAseq

**Raw data not available due to patient privacy concerns**

first: Tracy

last: Berg

first: David

last: Lindgren


title: Treatment of primary human astrocytes with 0 Gy or 10 Gy radiation

summary: Cultured primary human astrocytes were maintained in HA media (SciCell) treated with 0 Gy or 10 Gy radiation to identify changes to gene sets after irradiation.

overall_design: 4 repetitions of control and irradiated astrocytes were harvested for RNAseq

first: Kristoffer

last: von Stedingk


title: Whole exome sequencing of human primary uveal melanomas

city: Valbonne - Sophia-Antipolis

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Primary uveal melanomas show multiple genetic alterations. To determine mutational status of six human primary uveal melanomas, we performed whole exome sequencing (WES) and called Single Nucleotide Polimorphism (SNPs) to identify somatic mutations in these human primary uveal melanomas.

overall_design: Primary uveal melanomas from six patients were analyzed by whole exome sequencing

first: C

last: Pandiani

first: N

last: Nottet

first: R

last: Ballotti

last: Bertolotto


title: Single-cell RNA-seq reveals intratumoral heterogeneity in primary uveal melanomas and discloses new targetable vulnerability

summary: Lack of specific markers for invasive uveal melanoma cells prevents early diagnosis of metastasis, while no systemic treatment options are available for patients with disseminated uveal melanomas. Intra-tumor heterogeneity has been recognized in numerous cancers as the main cause of metastasis development and therapy resistance. However, in uveal melanomas the specific subpopulations and their biological function which influence tumor behavior remained unknown.  Here, using scRNA-seq analysis of six different primary uveal melanomas, we uncovered previously unrecognized intratumor heterogeneity. We localized diverse tumor-associated populations and transcriptional states in primary uveal melanomas. We also unraveled a gene regulatory network underlying a poor prognosis melanoma state. Heterogeneity was demonstrated in uveal melanoma tissue using the RNAscope assay.   Thus, single-cell analysis offers an unprecedented view of intratumor heterogeneity in primary uveal melanoma, identified bona fide biomarkers for metastatic cells in the primary tumor, and unravel targetable modules driving metastase formation and growth, with critical implications for prognosis and therapeutic opportunity.

overall_design: Single-cell RNA-seq of uveal melanoma cells from six patients.

first: K

first: P

last: Barbry


title: Single-cell RNA-seq reveals intratumoral heterogeneity in primary uveal melanomas

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: SETD4 marks Quiescent Cancer Stem Cells with Chemoradiotherapy Resistance in Breast Cancer of MMTV-PyMT Mouse

status: Public on Jan 24 2021

city: Hangzhou

last: Lu

address: Yuhangtang street 866

institute: Zhejiang university

summary: We isolated quiescent CSCs using chemoradiotherapy resistance assays on tumors of MMTV-PyMT transgenic (specific breast cancer model) mice. We found that quiescent CSCs specifically expressed SETD4 without exception, and beyond activation exhibited high capacity of tumor-initiation in vivo and tumorsphere formation in vitro. Quiescent CSCs expressed high levels of ALDH1 and CD44 and low levels of CD24, that corresponds with their use as breast CSCs markers. Quiescent CSCs were showed to be resistant and able to survive under chemoradiotherapy treatment in either in vivo or in vitro models. Similarly, SETD4 overexpression caused cells extracted from tumors to exhibit clear chemoradiotherapy resistance. Transcriptomic analysis revealed that the molecular processes associated with cellular quiescence included those of DNA damage response and the Wnt/β-catenin signaling pathway. Together with our previous results, these findings showed that SETD4 marks quiescent CSCs and suggest that SETD4-marked quiescent CSCs could be used as key targets in clinical treatment for multiple cancers.

overall_design: RNA sequencing was performed in quiescent CSCs and activated CSCs. Transcriptome profiles of three replicates in each group were compared.

first: Qian-Yun

first: Yao-Shun

last: Yang

first: Xi-Zheng

last: Jia


title: Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses

city: Beijing

first: Jian

last: He

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

summary: Mapping the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution during limb bud and primary ossification center (POC) formation. We found significant heterogeneity of stromal cells within the limb bud mesenchyme that specified proximal-distal and anterior-posterior patterning. Embryonic skeletal stem and progenitor cells first appeared during POC formation, which were highly enriched by CADM1 expression and could differentiate into osteoblasts, chondrocytes and periosteal mesenchymal stromal cells.

overall_design: We performed droplet-based scRNA-seq of 42,857 cells to firstly construct a molecular landscape of skeletogenesis in human embryos

first: Jing

last: Yan

first: Jianfang

last: Wang

first: Liangyu

last: Zhao

first: Heng

last: Zhu

first: Bing

last: Liu

first: Rui

last: Yue


title: Array CGH analysis of human uveal melanomas

first: Kevin

type: Genome variation profiling by genome tiling array

summary: Primary uveal melanomas show multiple chromosomal aberrations. To identify genome variation in six human primary uveal melanomas, genome wide copy number variation (CNV) analyses were carried out in human primary uveal melanoma samples using array comparative genome hybridization.

overall_design: Uveal melanoma tumors obtained from six patients were analyzed using Agilent CGH microarray

first: F

last: Pedeutour


title: Protein arginine methyltransferase 6 drives endocrine resistance in breast cancer: ERα and NFkB signalling directly regulate PRMT6 expression

city: San Diego

first: Tae Gyu

last: Oh

address: North Torrey Pines Road

institute: Salk Institute

summary: Gain- and Loss-of-function coupled with RNA-seq revealed that PRMT6 is involved in pathways drives breast carcinogenesis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mammary specific PRMT6 mice and PRMT6 knockdowned MCF-7 and MDA-231 cells were investigated using NEXTseq

first: Tae

middle: G

first: George

last: Muscat


title: Next Generation Sequencing Facilitates Quantitative Analysis of IgG or IgE producing B cells

status: Public on Jan 23 2021

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

summary: Emergence of IgE antibodies that bind allergens with high affinity is highly correlated with the severity of anaphylaxis. However, the underlying molecular mechanisms by which high-affinity IgE is generated remain poorly understood. We examined the effects of cytokines in IgE class switch using in-vitro B cell activation system

overall_design: B cells from spleen of IgE reporter mice (Verigem) were cultured on the CD154+ fibroblast cell line expressing CD40L and BAFF, NB21.2D9 feeder cells in the presence of recombinant murine IL-4, or IL-21 and/or IL-13. IgG+ or IgE reporter positive B  cells were sorted and analyzed the transcriptome using Illumina HiSeq1500.

first: Masato

last: Kubo


title: Heart fields auto-regulate second heart field cell fate via Wnt secretion

city: Baltimore

first: Suraj

last: Kannan

state: MD

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

summary: The purpose of this study was to identify the source of Wnt signals that lead to development/proliferation of the heart fields, particularly the second heart field. To this end, we knocked out Wntless (Wls), which is necessary for Wnt secretion, in Mesp1+ lineage cells. We performed single cell RNA-seq to better identify the source of Wnt signals and the effects of the loss of Wnt secretion in mesoderm.

overall_design: We isolated Mesp1+ cells from Mesp1-Cre; Ai9; Wlsfl/+ and Wlsfl/fl mice at three developmental timepoints (E8.0, E8.5, and E9.5) and performed scRNA-seq. As separating control and mutant cells into separate capture runs can lead to potential downstream batch effects, we multiplexed and pooled samples using lipid-tagged indices through MULTI-seq. We subsequently performed fluorescence-activated cell sorting to isolate RFP+ cells, and generated sequencing libraries through the 10x Chromium platform.

first: S

first: M

last: Miyamoto

first: C

last: Kwon


title: Next Generation Sequencing Facilitates Quantitative Analysis of lung resident cells cell Transcriptomes

summary: To examine reaction in lung residential cells to influenza viral infection, lung epithelial cells (AEC), clara cells, DC, Mast cells, macrophages, eosinophil, and neutrophils were isolated from lung of mice infected with influenza viruses at 3 day postinfection.

overall_design: AEC, Clara cells, DC, Mast cells, macrophages, eosinophil, and neutrophils of mice lung were sorted and analyzed the transcriptome using Illumina HiSeq1500.


title: High altitude disease in yearling beef cattle

city: Aurora

first: Dale

middle: R

last: Brown

state: Colorado

address: 12700 East 19th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: This study examined tolerance to hypoxia-induced pulmonary hypertension in yearling beef cattle raised at high elevation (7120 ft/2170m).

overall_design: Animals raised 15 months at high elevation were classified by serial right heart catheterization (mean Pulm Artery Pressure, PAP) and clinical signs as Lo PAP, Pulmonary hypertension - Healthy (PH-Healthy), or Pulmonary hypertension - Right Heart Failure (PH-Failure)

first: R

middle: D

first: Milt

last: Thomas

first: Kurt

last: Stenmark


title: Key metabolism pathways and regulatory mechanisms of high polysaccharide yielding in Hericium erinaceus

status: Public on Jan 22 2021

city: shanghai

first: henan

last: zhang

state: shanghai

address: No. 1000 Jinqi Road

institute: Shanghai Academy of Agricultural Sciences

summary: The genome of H. erinaceus original strain HEA was reported 38.16 Mb, encoding 9,780 predicted genes by single-molecule, real-time sequencing technology. The phylogenomic analysis showed that H. erinaceus had the closest evolutionary affinity with Dentipellis sp. The polysaccharide content in the fermented mycelia of mutated strains HEB and HEC, which obtained by ARTP mutagenesis in our previous study, was improved by 23.25% and 47.45%, and a new β-glucan fraction with molecular weight 1.056×10^6 Da was produced in HEC. Integrative analysis of transcriptome and proteomics showed the upregulation of the carbohydrate metabolism pathway modules in HEB and HEC might lead to the increased production of glucose-6P and promote the repeating units synthesis of polysaccharides. qPCR and PRM analysis confirmed that most of the co-enriched and differentially co-expressed genes involved in carbohydrate metabolism shared a similar expression trend with the transcriptome and proteome data in HEB and HEC. Heatmap analysis showed a noticeably decreased protein expression profile of the RAS-cAMP-PKA pathway in HEC with a highly increased 47.45% of polysaccharide content. The S phase progression blocking experiment further verified that the RAS-cAMP-PKA pathway's dysfunction might promote high polysaccharide and β-glucan production in the mutant strain HEC.

overall_design: In this study, we reported the original strain genome of H. erinaceus using a single molecule, real-time sequencing technology, and multi-omics analysis was carried out between mutant strains obtained by ARTP mutagenesis and the original strain. Multi-omics analysis indicated that the increased carbohydrate metabolism and the production of glucose-6P constitute the basis of high polysaccharide yield in ARTP mutated strain. Furthermore, the RAS-cAMP-PKA pathway's decreased activity might promote high polysaccharide and β-glucan production through the block of S phase progression. The study revealed the mechanism of the increased polysaccharide synthesis induced by ARTP mutagenesis associated with carbohydrate metabolism and glucose signaling regulation dysfunction and provided the critical theoretical and practical basis for polysaccharide production in H. erinaceus.

first: Henan

last: Zhang

first: Yan

last: Yang


title: Development and characterization of vorinostat-resistant cutaneous T cell lymphoma cells

city: Singapore

first: Kizhakeyil

last: Atish

state: Singapore

address: Mandalay road 11

country: Singapore

institute: Nanyang Technological University

summary: We demonstrate that vorinostat-resistant HuT78VR exhibits enhanced invasion characteristics and activation of MAPK signaling.

overall_design: We performed RNAseq analsysis of vorinostat-resistant CTCL cells (HuT78VR) which were developed in-house using dose escalation protocol.

first: Poh

last: Sheng

first: Navin

middle: K

last: Verma


title: Effect of Lenalidomide on human macrophages.

city: Erlangen

first: Heiko

last: Bruns

address: Hartmannstraße 24

institute: University Hospital Erlangen

summary: Lenalidomide, an IMiD® immunomodulatory agent used for the treatment of multiple myeloma (MM),is believed to target the stromal support, but its precise mechanism on the phenotype or the effector functions of macrophages is still unclear. To investigate the effect of lenalidomide on macrophages, M-CSF generated macrophages were treated with Lenalidomide and analyzed by RNA-seq.

overall_design: Macrophages of five different donors were treated with or without Lenalidomide and analyzed by RNA-Seq

first: Michael

last: Rehli

first: Julia

last: Wimmer


title: Exploration of SQC formula effect on Type 2 diabetes mellitus by whole transcriptome profile in rats

city: 成都

first: 旭

middle: 晓

last: 富

state: 四川

address: 十二桥路37号

institute: 成都中医药大学

summary:
Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that has turned up as pandemic dimensions all over the world. In China, some traditional Chinese herbal formulas have enjoyed a high reputation in T2DM treatment for centuries. And ShenQi compound (SQC), a formula has been performed on T2DM clinical therapeutics in China for many years, deserve to study in depth.
Gene microarray experiments were performed to explore the molecular mechanism of SQC treatment. In addition, a western medicine, metformin was employed as a comparison.

overall_design: The rats were divided into four groups including control group(3 rats), model group(3 rats),  metformin group(3 rats) and SQC  group(3 rats,SQC dose:1.44 g/kg*5 per day, once a day for 8 weeks). Then gene microarray experiments were performed.

first: Fu

last: Xiaoxu

first: Zhou

last: xiujuan

first: Xie

last: chunguang


title: Transcriptomic response of Cryptococcus neoformans to ecologically relevant nitrogen concentrations

city: Stellenbosch

first: Caylin

last: Bosch

state: Western Cape

address: JC Smuts Building, Van der Byl road

department: Microbiology

country: South Africa

institute: Stellenbosch University

summary: We examine the transcriptomic response of Cryptococcus neoformans to two different ecologically relevant nitrogen concentrations. Our data revealed that low nitrogen conditions modulate the expression of numerous virulence genes in C. neoformans. Among these were, CTR4 and CGP1, which showed highly significant modulation under low nitrogen conditions. Furthermore, data analysis revealed the upregulation of antifungal tolerance-related genes in low nitrogen conditions, including genes involved in ergosterol biosynthetic processes and cell wall integrity. Overall, our findings provide insight into the survival of C. neoformans in nitrogen-poor ecological niches and suggest that pre-adaptation to these conditions may influence the pathobiology of this yeast.

overall_design: Examination of the C. neoformans transcriptome during growth in high and low nitrogen conditions

first: Zoë

last: Bhana

first: Barbra

last: Toplis

first: Heinrich

last: Volschenk

first: Alfred

last: Botha


title: Adenosine stimulation of normal human epidermal keratinocytes (NHEK)

city: Chapel Hill

first: David

last: Corcoran

state: NC

address: 125 Mason Farm Rd

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Gene expression profile of normal human epidermal keratinocytes treated with adenosine

overall_design: Cultured primary normal human epidermal keratinocytes are treated with vehicle or adenosine and differential expression was measured.

first: Amanda

last: MacLeod


title: Integrated proteomic and transcriptomic analysis reveals wounding-responsive plant hormone signaling and primary metabolism contributing to the biosynthesis of secondary metabolites in harvested broccoli (Brassica oleracea L. var. italica)

city: Dalian

first: Yuge

last: Guan

address: Linggong Road 2, Dalian

institute: Dalian University of Technology

summary: In this study, the annotation of protein in broccoli was used the cds sequence predicted by RNA-Seq De novo assembly. The libraries of RNA extracted from the broccoli were employed for sequencing and analysis. Our results demonstrated that alicylic acid (SA) and ethylene (ET) biosynthesis were more susceptible to being induced by wounding with lower intensities, whereas, jasmonic acid (JA) biosynthesis was more susceptible to being activated by wounding with higher intensities. Some carbohydrate metabolic pathways and amino acid biosynthesis-related pathways such as phenylalanine, cysteine and methionine metabolic pathways were significantly up-regulated, which promotes the precursor levels for phenolic substances and glucosinolate synthesis. Biosynthesis of secondary metabolites was activated by wounding through regulation of critical proteins involved in the corresponding metabolic pathways.

overall_design: RNA profiles of 1 sample of broccoli.

first: Wenzhong

last: Hu


title: Next Generation Sequencing Facilitates Quantitative Analysis of hepacyte steatosis under Ang(1-7) treatment

city: Guangzhou

first: Yijie

last: Zhang

state: Guangdong

address: Nanfang Hospital

institute: Nanfang Hospital

summary: AML12 Cells were pretreated with 100nM Angiotensin(1-7) 30 minutes before Palmitic(200μM) and Oleanic(400μM) stimulation.

overall_design:
there are 3 groups
group1:AML12 control
group2:AML12 PA+OA
group3:AML12 PA+OA+Ang(1-7)


title: RNA sequence of mouse lung after brain exposed to 10Gy or 10Gy*3

city: Suzhou

first: Qiu

last: Chen

address: 199 Renai Road

institute: Soochow University

summary: we reported the lung mRNA change after brain exposed to 10Gy or 10Gy*3 compared to sham ionizing radiation

overall_design: Examination of lung's by-stand effects

first: Ke

first: Fengmei

last: Cui


title: Mitochondrial DNA Alterations Underlie an Irreversible Shift to Aerobic Glycolysis in Fumarate Hydratase-deficient Renal Cancer

city: Bethesda

first: Mayank

last: Tandon

address: 41 CENTER DR, BG 41 RM B620

institute: CCR Collaborative Bioinformatics Resource

summary: Understanding the mechanisms of the Warburg shift to aerobic glycolysis is central to defining the metabolic basis of cancer. Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is an aggressive cancer characterized by bi-allelic inactivation of the gene encoding the Krebs cycle enzyme fumarate hydratase, an early shift to aerobic glycolysis, and rapid metastasis. We observed   of the mitochondrial   in tumors from HLRCC patients. Biochemical and transcriptomics analyses revealed that respiratory chain dysfunction in the tumors was due to loss of expression of mitochondrial DNA (mtDNA)-encoded subunits of respiratory chain complexes, caused by a marked decrease in mtDNA content and increased mtDNA mutations. We demonstrated that accumulation of fumarate in HLRCC tumors inactivated the core factors responsible for replication and proofreading of mtDNA, leading to loss of expression of respiratory chain components, thereby promoting the shift to aerobic glycolysis and disease progression in this prototypic model of glucose-dependent human cancer.

overall_design: Transcriptome profiling was performed on RNA from five primary HLRCC tumors and paired normal tissue, as well as from 16 metastatic tumors, for a total of 26 samples. Expression levels of tricarboxylic acid (TCA) cycle enzymes and both nuclear and mitochondrial genes encoding Complexes I- V components were evaluated for differential expression among the normal, primary, and metastatic samples.  Results were confirmed with qPCR.

first: Daniel

last: Crooks

first: Nunziata

last: Maio

first: Martin

last: Lang

first: Christopher

middle: J

last: Ricketts

first: Cathy

last: Vocke

first: Sandeep

last: Gurram

first: Sevilay

last: Turan

first: Yun-Young

last: Kim

first: G

middle: M

last: Cawthon

first: Ferri

last: Sohelian

first: Natalia

last: Alda

first: Parthav

last: Jailwala

first: Bao

last: Tran

first: Teresa

last: Fan

first: Andrew

last: Lane

first: Thomas

last: Reid

first: Darawalee

last: Wangsa

first: Ashkan

last: Malayeri

first: Maria

last: Merino

first: Youfeng

last: Yang

first: Jordan

last: Meier

first: Mark

last: Ball

first: Tracey

last: Rouault

first: Ramaprasad

last: Srinivasan

first: Ruth

last: Pfeiffer

first: W

last: Linehan


title: Human endometrial organoids

city: Vienna

first: Paulina

middle: Anna

last: Latos

address: Schwarzspanierstraße 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

summary: Human endometrial organoid cultures were established from the decidual samples. We analyzed the global expression profiles of the endometrial organoids. Next, we determined the global expression patterns upon estrogen treatment and compared them to untreated controls.

overall_design: We employed RNA-seq to analyze the global expression profiles of endometrial organoids (EORG-1, EORG-2, EORG-3, EORG-C; 3 replicates each).  Next, we determined the global expression patterns upon estrogen treatment (3 replicates: EORG-E) and compared them to untreated controls (3 replicates: EORG-C).

last: Burkard

first: Martin

last: Knoefler

first: Sasha

last: Mendjan


title: Blood RNA biomarkers for spinal cord injury

city: San Francisco

first: Nikolaos

last: Kyritsis

state: CALIFORNIA

address: 1001 Potrero Ave

department: Neurological Surgery

institute: University of California San Francisco (UCSF)

summary: Biomarkers of spinal cord injury (SCI) could help determine the severity of the injury and facilitate early critical care decision making. We analyzed global gene expression in peripheral white blood cells during the acute injury phase and identified 197 genes whose expression changed after SCI compared to healthy and trauma controls and in direct relation to SCI severity. Unsupervised co-expression network analysis identified several gene modules that predicted injury severity (AIS grades) with an overall accuracy of 72.7% and included signatures of immune cell subtypes. Specifically, for complete SCIs (AIS ‘A’) ROC analysis showed impressive specificity and sensitivity (AUC: 0.865). Similar precision was also shown for AIS ‘D’ SCIs (AUC: 0.938). Our findings indicate that global transcriptomic changes in peripheral blood cells have diagnostic and potentially prognostic value for SCI severity.

overall_design: There are 58 sequenced samples in total. 10 are from healthy individuals without history of CNS pathology (HC), 10 are non-CNS trauma patients (TC), and 38 are from individuals who suffered a traumatic spinal cord injury (SCI).

first: Nikos

first: Abel

last: Torres-Espín

first: Patrick

last: Schupp

first: J

last: Huie

first: Austin

last: Chou

first: Xuan

last: Duong Fernandez

first: Leigh

middle: H

last: Thomas

first: Rachel

last: Tsolinas

first: Debra

last: Hemmerle

first: Lisa

middle: U

last: Pascual

first: Vineeta

last: Singh

first: Jonathan

last: Pan

first: Jason

last: Talbott

first: William

last: Whetstone

first: John

last: Burke

first: Anthony

last: DiGiorgio

first: Philip

last: Weinstein

first: Geoffrey

middle: T

last: Manley

first: Sanjay

last: Dhall

first: Adam

last: Ferguson

first: Michael

middle: C

last: Oldham

first: Jacqueline

last: Bresnahan

last: Beattie


title: Expression data from human bone marrow-derived mesenchymal cell clones

first: DARIO

last: CAMPANA

address: 14 Medical Drive

department: Pediatrics

institute: National University of Singapore

summary:
The generation of blood cells in the hematopoietic microenvironment requires support from mesenchymal cells. We found that stably growing cell populations derived from individually sorted human bone marrow mesenchymal cells immortalized by enforced expression of hTERT comprised both supportive and non-supportive clones.
We compared gene expression of supportive and non-supportive clones to identify genes associated with the growth supportive capacity of mesenchymal cells
Keywords: Cell type comparison

overall_design: We analyzed global gene expression in five supportive clones (nos. 1, 2, 3, 5 and 6) and compared the profiles with those of two nonsupportive clones (nos. 4 and 7).

first: Dario

last: Campana

first: Keichiro

last: Mihara


title: aCGH analysis of liver tumors generated in C57BL/6J mice with a liver specific loss of Trp53-/- [Agilent-027411]

city: Ulm

first: André

last: Lechel

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine I

institute: University hospital Ulm

summary:
Background and aims: P53 limits the self-renewal of stem cells from various tissue. A Loss of p53 in combination with other oncogenic events results in aberrant self-renewal and transformation of progenitor cells. Here, we investigated whether a loss of p53 as a single genetic lesion is sufficient to induce liver tumor formation.
Methods: AlfpCre mice were crossed with Trp53 conditional knockout mice to achieve a liver-specific loss of Trp53.
Results: The liver-specific loss of Trp53 results in liver tumor formation. A high percentage of the tumors showed a mixed differentiation of hepatocellular carcinoma and intrahepatic cholangiocarcinoma.
Conclusion: The liver-specific deletion of Trp53 is sufficient to induce liver tumor formation.

overall_design: Liver tumors from 4 invidual Trp53-/- mice were analyzed, pooled spleen DNA from 3 sex matched littermates were used as controls.


title: Persistence of mature dendritic cells, Th2A and Tc2 cells characterize clinically resolved atopic dermatitis under IL-4R-alpha blockade

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

summary: Therapeutic options for autoimmune diseases typically consist of broad and targeted  immunosuppressive agents. However, a sustained clinical benefit is rarely achieved, as the  disease phenotype usually returns after cessation of treatment. To better understand this kind of  tissue-resident “immune memory” in human disease, we investigated patients with atopic  dermatitis (AD), who underwent short-term or long-term treatment with the IL-4Rα blocker  dupilumab. Using multi-omics profiling with single-cell RNA sequencing and multiplex  proteomics, we found significant decreases in overall skin immune cell counts, and  normalization of transcriptomic dysregulation in keratinocytes consistent with clearance of  disease. However, we identified specific immune cell populations that persisted for up to a year  after clinical remission, while being absent from healthy controls. These included LAMP3+  CCL22+ mature dendritic cells, CRTH2+ CD161+ T helper (“Th2A”) cells, and CRTAM+  cytotoxic T-cells, which expressed high levels of CCL17 (dendritic cells) and IL13 (T-cells).  Th2A cells showed a unique cytokine receptor constellation of IL17RB, IL1RL1 (ST2) and  CRLF2 expression, suggesting that these are key responders to the AD-typical epidermal  alarmins IL-25, IL-33 and TSLP, respectively. We thus identified characteristic immune cell  populations in resolved AD indicative of a persisting disease memory, facilitating a rapid  response system of epidermal-dermal crosstalk between keratinocytes, dendritic cells and Tcells.  This observation may explain the disease recurrence upon termination of  immunosuppressive treatments in AD, and it identifies cell types that may be targeted to achieve  a more sustained therapeutic response.

overall_design:
Comparison of skin cells from patients without and with short-term (16 weeks) or long-term (1 year) treatment with the IL-4Rα blocker   dupilumab

>>>Raw data are unvailable due to patient privacy concerns<<<

first: Christine

last: Bangert

first: Thomas

last: Krausgruber

first: Natalia

last: Alkon

first: Felix

last: Thaler

first: Tanja

last: Ayub

first: Denis

last: Demirtas

first: Nikolaus

last: Fortelny

first: Vera

last: Vorstandlechner

first: Wolfgang

last: Bauer

first: Tamara

last: Quint

last: Mildner

first: Constanze

last: Jonak

first: Adelheid

last: Elbe-Bürger

first: Johannes

last: Griss

first: Christoph

last: Bock

first: Patrick

last: Brunner


title: Macrophage derived-inflammation for confitioning of mesenchymal stromal cells

status: Public on Jan 21 2021

city: Chicago

first: Ines

last: Maldonado-Lasuncion

state: Illinois

address: 355 E Erie Street

department: Biologics Lab

institute: Shirley Ryan Ability Lab

summary:
The study: Bone marrow-derived mesenchymal stromal cells (MSC) can be triggered to enhance the expression of repair associated factors by certain stimuli. The purpose of this study was to perform a transcriptome-wide analysis of the effect of macrophage-derived inflammation on MSC and evaluate the repair potential of the conditioned cells. To validate the results, we compared the condition of interest to three control conditions, described bellow.
Methods: MSC were cultured in baseline conditions (D10 medium) until reaching passage 4. In parallel, monocytes were differentiated to macrophages and polarized to pro-inflammatory (M1) or non-polarized (M0). After 24h of polarization, the supernatants were collected to produce M1CM and M0CM, respectively. The medium used for macrophage polarization (Pol1) was included in the conditions for MSC culture as a control. The medium of all MSC cultures was changed into fresh D10, M1CM, M0CM or Pol1, and they were cultured for 24h (conditioning). Then, MSC were trypsinized and their RNA was extracted. We worked with Novogene Inc. USA for the RNAsequencing, which they performed based on the Illumina platform. Novogene performed the sequencing, data processing and preliminary analysis. We then did the downstream analysis and data interpretation.
Results: Dowstream analysis, after data processing was completed for all samples and groups, was focused on the comparison M1CM vs D10. This is because the effect of M0CM and Pol1 on MSC was minor compared to the effect of M1CM, based on correlation and Venn diagram analysis. M1CM induced 1721 upregulated DEG and 1487 downregulated DEG in MSC compared to D10. Among those genes, the GO and KEGG analyses showed enrichment in GO terms and pathways associated to the enhancement of angiogenesis, immunomodulation, paracrine cell survival, tissue development and regeneration, indicating increased therapeutic potential. Additionally, genes associated with programmed cell death were upregulated, while cell cycle and motility associated genes were downregulated, indicating compromised cell viability and motility.
Conclusions: We found that macrophage-derived inflammation induces a transcriptomic makeover on MSC, enhancing their reparative potential. These results reveal the possibility to use inflammation as a priming method for MSC before transplantation, which could potentiate the transplant's efficacy. Further pre-clinical studies are necessary to determine the effects of the beneficial outcomes in tissue, as well as the implications of compromised viability and motility.

overall_design: Use of RNAseq for examination of gene expression in rat bone-marrow derived MSC, after 24h of conditioning with the experimental or control media (4 conditions), using 4 biological replicates.

first: Martin

last: Oudega