title: Single-cell RNA-sequencing of adventitial and medial/intimal cells in 8-12-week-old wildtype and ApoE-/- mice

status: Public on Mar 31 2020

city: London

first: Jiacheng

last: Deng

state: Not Applicable

address: James Black Centre, 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

type: Expression profiling by high throughput sequencing

summary: We reported the cellular heterogeneity in the whole aorta (adventitial and medial/intimal layers).

overall_design: This entry contains 10X Single-cell RNA-seq data of vascular cells from the adventitial (ADV) and medial/endothelial (ME) layers of 8-12-week-old wiltype and Apoe-/- mice.

first: Zhichao

last: Ni

first: Wenduo

last: Gu

first: Qingbo

last: Xu


title: Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of long noncoding RNA derived from HNF4A gene (HNF4A-AS1)

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

summary: Long noncoding RNAs (lncRNAs), one type of endogenous RNA longer than 200 nucleotides, play emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of lncRNAs in regulating neuroblastoma progression still remain elusive. We identify HNF4A antisense RNA 1 (HNF4A-AS1), a lncRNA derived from upstream region of hepatocyte nuclear factor 4 alpha (HNF4A), as a novel driver of neuroblastoma progression. To investigate the mechanisms underlying the oncogenic functions of HNF4A-AS1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma SH-SY5Y cells in response to stable over-expression of HNF4A-AS1. The results showed that stable over-expression of HNF4A-AS1 led to altered expression of 4296 human mRNAs, including 2169 up-regulated genes and 2127 down-regulated genes. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to HNF4A-AS1 over-expression in human tumor cells, and these findings will help us understand the pathogenesis of tumor progression.

overall_design: Total RNA of cells stably transfected with empty vector or HNF4A-AS1 was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Liduan

last: Zheng


title: PHF19 Promotes Cell Growth and Confers Drug Resistance through EZH2 Phosphorylation in Multiple Myeloma

city: Xi'an

first: Xiaoke

last: Ma

state: Shaanxi

address: No.2 South TaiBai Road

institute: Xidian University

summary:
To determine the effect of overexpression PHF19 in ARP1  myeloma cells
Drug resistance is a major reason for the recurrence of multiple myeloma (MM). In addition to genetic mutations, epigenetic abnormalities are involved in the whole process of MM relapse and drug resistance. In this study, we investigate the roles of polycomb like protein 19 (PHF19), a critical gene involved in the epigenetic regulation of gene expression, in the development of MM. The gene expression profiling (GEP) data shows that PHF19 is significantly up-regulated in MM cells and associated with shortened progression-free survival and overall survival in MM patients. PHF19 promotes MM cell growth both in vitro and in a subcutaneous xenograft mouse model. Up-regulated PHF19 is also associated with the development of resistance to multiple drugs, including bortezomib, in MM cells. Moreover, miR-15a can directly target PHF19 by binding to its 3'-UTR. Since miR-15a is down-regulated in MM cells, PHF19 is considered to be up-regulated due to loss of the suppression by miR-15a. The mechanistic investigations indicate that PHF19 can activate AKT which in turn leads to an increase in the phosphorylation of EZH2, a core component of PRC2 that mediates the histone H3K27 methylation. Subsequently suppresses histone H3K27 methylation and causes up-regulated expression of several anti-apoptotic genes, including BCL-xL, MCL-1 and HIF-1alpha. Moreover, PDK1 activation is significantly increased in PHF19 overexpressing MM cells.

overall_design: ARP1 cells were transfected by lenti-virus plasmids with PHF19  ORF, then PHF19 overexpressed cells  were sorted. And RNA was extracted.

first: Tengteng

last: Yu

first: Mu

last: Hao


title: SAG/Rbx2-Dependent Neddylation Regulates T-cell Responses

city: Ann Arbor

first: Nathan

middle: Daniel

last: Mathewson

state: MI

address: 1500 E. Medical Center Dr.

department: Internal Medicine

country: USA

institute: University of Michigan

summary: We used microarrays to detail the global program of gene expression underlying SAG-dependent neddylation and identified distinct classes of disparate genes during this process.

overall_design: T cells from WT and SAG-deficient (KO) mice were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare the disparate transcripts in naive T cells.

middle: D

first: Pavan

last: Reddy


title: Hepatic microRNA signatures in experimental nonalcoholic steatohepatitis

status: Public on Mar 30 2020

city: kansas city

first: Yuxia

last: Zhang

state: KS

address: 3901 Rainbow Blvd, Hemenway 4001

department: Pharmacology, Toxicology, and Therapeutics

institute: University of Kansas Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Two-month-old C57BL/6J male mice were placed on chow diet or a diet enriched in high fat, cholesterol, and fructose (Research diet D09100301: 40 kcal% fat, 2% cholesterol, 20 kcal% fructose, HFCF diet) for 1 or 3 months. Liver RNA was isolated and submitted for small RNA sequencing.

overall_design: Total RNA for Illumina sequencing was extracted from mouse liver tissues using a Direct-zol RNA kit. During RNA isolation, DNA was removed by treating the samples with RNase-free DNase to avoid DNA contamination. Three biological replicates in each group for a total of 12 samples were submitted for RNA sequencing. cDNA libraries were prepared using the Illumina TruSeq stranded RNA kit with Ribo-Zero Gold. Fifty-cycle single-read sequencing was performed with an Illumina HiSeq 2500.

first: Nancy

middle: S

last: Magee


title: Activation of Interferon and Complement Pathways in Thrombotic Microangiopathy

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Transplant-associated thrombotic microangiopathy (TA-TMA) is a significant cause of mortality after hematopoietic stem cell transplant (HSCT). Complement blockade is an effective therapeutic strategy for TA-TMA, but some patients with severe disease lack a complete response, prompting a search for additional targetable endothelial injury pathways. We performed transcriptome analysis of peripheral blood mononuclear cells collected prior to HSCT and at onset of TA-TMA and observed significant up-regulation of classical and alternative complement pathways during active TA-TMA. At resolution of TA-TMA after eculizumab therapy, essentially all up-regulated genes and pathways returned to baseline expression levels, supporting the clinical practice of successfully discontinuing complement blockade after resolution of TA-TMA. Further analysis of the global transcriptional regulatory network showed a notable interferon signature associated with TA-TMA with increased STAT1 and STAT2 signaling. To confirm our observations, we documented a high incidence of clinically significant TMA in children with hemophagocytic lymphohistiocytosis (HLH), an interferon gamma-driven disease, outside the setting of transplantation. We also confirmed increased interferon signaling in a separate cohort of patients by measuring CXCL9 and CXCL10 in urine. Our data suggest a key relationship between increased interferon signaling, complement activation, and TMA in two distinct clinical settings, HLH and TA-TMA. Combined anti-complement and anti-interferon treatment may facilitate disease control in patients with refractory TA-TMA. These data cast light on the occurrence of TMA in persons receiving therapeutic interferons, and possibility of TMA in other interferon-driven diseases where interferon may be a novel therapeutic target.

overall_design: We examined seven children of similar age receiving aHSCT for neuroblastoma after an identical preparative regimen of carboplatin, etoposide, and melphalan, a regimen associated with a high-risk of TA-TMA. Four of the seven children developed TA-TMA and three did not. Peripheral blood mononuclear cells (PBMCs) and blood samples were collected prospectively weekly for all children, mRNA was extracted and profiled with RNA-seq.

first: Sonata

last: Jodele

last: Luebbering

first: Christopher

middle: E

last: Dandoy

first: Nicholas

middle: J

last: Gloude

first: Michael

middle: B

last: Jordan

first: Daniella

middle: L

last: Erez

first: Benjamin

last: Laskin

first: Jenny

last: Chen

first: Stella

middle: M

last: Davies


title: Transcriptomic and metabolomic profiling of long-lived growth hormone releasing hormone knock-out mice: Evidence for altered mitochondrial function and amino acid metabolism

first: William

middle: R

last: Swindell

address: 1500 E. Medical Center Drive

department: Dermatology

summary: Numerous genetic manipulations that extend lifespan in mice have been discovered over the past two decades, the most robust of which has arguably been the down regulation of growth hormone (GH) signaling. However, while decreased GH signaling has been associated with improved health and lifespan, many of the underlying physiological changes and molecular mechanisms have yet to be elucidated. To this end, we have completed the first transcriptomic and metabolomic study on long-lived growth hormone releasing hormone knockout (GHRH-KO) and wild-type mice in brown adipose tissue (transcriptomics) and blood serum (metabolomics). We find that GHRH-KO mice have increased transcript levels of mitochondrial and amino acid genes with decreased levels of extracellular matrix genes. Concurrently, mitochondrial metabolites are differentially regulated in GHRH-KO. Furthermore, we find a strong signal of genotype-by-sex interactions, suggesting the sexes have differing physiological responses to GH deficiency. Overall, our results point towards a strong influence of mitochondrial metabolism in GHRH-KO mice which potentially is tightly intertwined with their extended lifespan phenotype.

overall_design: Brown adipose tissue was analyzed from GHRH-KO mice (n = 4 total; 2 males and 2 females) and WT control mice (n = 5; 3 females and 2 males).

first: Jessican

last: Hoffman

first: Liou

middle: Y

last: Sun


title: Sudden reduction of miRNAs during embryonic development-- cohort, buffered regulation of miRNA in Dorsal Root Ganglion

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

summary: Micro RNAs (miRNA) are short, endogenous non-coding RNAs, they function via base pairing with complementary sequences with their targets. With the current advance in modern technologies including Next Generation Sequencing, miRNAs have rapidly emerged as important regulators in various functions in cell proliferation, differentiation, cell death and metabolisms. miRNAs showed specifically important roles in central nerve system development with specific temporal spatial regulation, such as neuronal cell proliferation, neuronal differentiation, cell fate determination, axon outgrowth, dendritogenesis, synaptogenesis, and gliogenesis, neuronal guidance to form neuronal circuits. In this study, we will first focus on how microRNA regulates neuronal specification, proliferation and differentiation by investigating microRNA profiling in Dorsal Root Ganglion (DRG) at different embryonic stages both in chickens and mice. Second, we will investigate how the microRNA expression correlates with important transcription factors and neurotrophic factor receptors during the neuron cell specification, such as Runx3, TrkC. Third, we study the regulated miRNA targets and their impact on neurogenesis and development.  Last, we will study how conserved roles of miRNA between mouse and chicken in the neuro-specification. We found dramatic reduction of large amount miRNA during specific embryonic stage. Their target genes overrepresent dentrites, synaps and neurogenesis genes, as well as genes largely involved in transcription. The study shows the importance of miRNA in neuronal development, and they function in cohort, buffered, flexible manner.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: Spartial and temopary expression of  miRNA of Dorsal Root Ganglion at embryonic devlopmental stages, and the expression of miRNA after treatment with different neurotrophins, transcription activators and neurontransmitters.

first: Yongtao

last: Xue-Franzén

first: Indranil

last: Sinha

first: Francois

last: Lallemend


title: Comparative analysis of transcriptional profiles of Schistosoma japonicum from SCID mouse and BALB/c mouse

first: Rong

last: Liu

address: 185 East Lake Road

department: School of Basic Medical Sciences

institute: Wuhan University

summary:
Background: In immunodeficient mice, the growth and egg laying of schistosome were significantly retarded or inhibited, and their virulence on the host was also weakened. Some studies have suggested that host factors including endocrine and immune signals can modulate the parasite’s development and maturation. However, it is still not clear for the molecular mechanisms underlying the growth and maturation regulation of schistosome.
Methodology/Principal results: We isolated the total RNAs of female and male schistosome from immunodeficient SCID mice and immunocompetent BALB/c mice (labeled as S_F, S_M, B_F and B_M) obtained at five weeks post infection with cercariae, and constructed cDNA libraries for RNA deep sequencing on an Illumina (Solexa) platform. In the results, the mRNAs were distinguished from long non-coding RNAs after blast to the reference Schistosoma japonicum genome, assemble and assessment of coding potential of the clean reads between S_F and B_F, and between S_M and B_M. The RNA-Seq yielded 90 to 142 million raw reads and 84 to 134 million clear reads per sample for the four schistosome samples. There are 56% to 65% of the clean reads mapped to the reference S. japonicum genome data. Given P-value <0.05, 298 differentially expressed genes (DEGs, mRNAs) for pairwise comparison of the above schistosome samples were identified. In detailed, 240 DEGs were identified in S_F vs B_F, of which 152 DEGs were up-regulated (147 DEGs were present in S_F worms but absent or undetected technically in B_F worms) and 88 were down-regulated (83 DEGs were present in B_F worms but absent or undetected technically in S_F worms). 62 DEGs were identified in S_M vs B_M, of which 39 were up-regulated (29 DEGs were present in S_M worms but absent or undetected technically in B_M worms) and 23 were down-regulated (22 DEGs were present in B_M worms but absent or undetected technically in S_M worms). Four differentially expressed mRNAs were shared among the two comparisons (present both in female and male worms), which were Sjp_0117620 (26S proteasome subunit P28-related), Sjp_0127870 (leucine zipper-EF-hand-containing transmembrane protein 1, mitochondrial precursor), Sjp_0130040 (putative dynein heavy chain) and Sjp_0094540 (hypothetical protein containing proteinase inhibitor I25, cystatin domain，SJCHGC07500 protein, partial). There were other 236 DEG specific in the comparison of S_F and B_F, and 58 DEG specific in the comparison of S_M and B_M. GO analysis was performed to summarize and explore the major GO categories of the DEGs which may be susceptible to host environments. The above DEGs of female comparison and male comparison were annotated with GO terms in three independent categories: biological processes (400 GO terms were hit for annotation of DEGs of female comparison and 287 GO terms were hit for annotation of DEGs of male comparison), molecular functions (231 GO terms were hit for annotation of DEGs of female comparison and 163 GO terms were hit for annotation of DEGs of male comparison), and cellular components (88 GO terms were hit for annotation of DEGs of female comparison and 75 GO terms were hit for annotation of DEGs of male comparison). The biological processes analysis revealed the predominant DEGs of female worms were involved in response to microtubule-based process, while predominant DEGs of male worms were involved in response to response to DNA damage stimulus, oxidation-reduction process and cellular response to stress. The molecular functions, some DEGs of female and male worms were annotated with calcium-dependent phospholipid binding activities in common. Notably, genes coding for microtubule associated complex, cytoskeletal part, cytoskeleton and microtubule cytoskeleton accounted for large portion of annotated DEGs of female worms in the cellular components analysis, while gene coding for nucleoplasmic THO complex of male worms were identified in the cellular components analysis. The KEGG pathway analysis showed many of the DEGs of female worms were involved in purine metabolism, RNA polymerase, fatty acid biosynthesis, fatty acid degradation and pyrimidine metabolism. Many of the DEGs of male worms were involved in oxidative phosphorylation, riboflavin metabolism and tyrosine metabolism.
Conclusions/Significance: This study provides a comparative gene expression profiles of schistosomes derived from SCID mice and immunocompetent BALB/c mice. A number of genes potentially regulating the development of schistosomes were identified. These findings lay the foundation for schistosomiasis research in parasite-host interaction at the transcriptional level and provide a valuable resource for screening antischistosomal intervention targets or vaccine candidates.

overall_design: Examination of Schistosoma japonicum worms from SCID mouse and BALB/c mouse

first: Hui-fen

last: Dong


title: Expression data of transfected SKOV-3 cells before and after cisplatin treatment

city: Bonn

first: Ganna

last: Kalayda

address: An der Immenburg 4

department: Clinical Pharmacy

country: Germany

institute: University of Bonn

summary: Sensitivity to cisplatin is increased in SKOV-3 cells after transfecting the cells with unphosphorylatable PEA-15 (PEA-15AA) but not in cells transfected with the empty vector and phosphomimetic PEA-15 (PEA-15DD). In order to investigate the regulation of the underlying genes that increased the sensitivity to cisplatin after transfection with PEA-15AA, a small and well-annotated Clariom S gene microarray was performed.

overall_design: SKOV-3 cells were transfected with PEA-15-HA- (empty vector, EV), PEA-15AA- or PEA-15DD-containing plasmids. Twenty-four hours after transfection, cells were treated with 15 µM cisplatin (EC50 of cisplatin for EV-transfected cells over 48 hours) for 24 hours and then the total RNA of the cells was extracted. ClariomS assay was performed by Life and Brain GmbH, Bonn, Germany.

first: Shahana

last: Dilruba

middle: V


title: Genomic Landscape of Young-Onset Bladder Cancer and Its Prognostic Implication on Adult Bladder Cancer

city: Jongno-gu

first: Sun-Wha

last: Im

state: Seoul

address: 103, Daehak-ro

department: Genomic Medicine Institute, Medical Research Center

country: South Korea

institute: Seoul National University

summary: Bladder cancer is common in elderly men, and it is a highly mutated tumor with frequent TP53 and FGFR3 mutation. Young-onset bladder cancer (YBC) is extremely rare; therefore, its genomic characteristics are unknown and appropriate management strategy is yet to be defined. Through a nation-wide search for bladder cancer diagnosed at 20 years or younger, 29 cases of biopsy-proven YBCs were collected. Whole exome sequencing and RNA sequencing were performed on 21 and 11 cases, respectively, and the results were compared with those of adult bladder cancer (ABC) retrieved from public database. Almost all YBCs were low grade, non-invasive papillary tumors. YBC had low mutation burden and less complex copy number alterations. Driver mutations were found in all cases. Common mutations included HRAS mutations (10 cases) with a preference in exon 5 and FGFR3 gene fusions (7 cases) with various partner genes, which occurred in a mutually exclusive manner. Other alterations included KRAS mutations (2 cases), arm-level deletion of chromosomes 4p and 10q (1 case), and ERCC2 mutation (1 case). TP53 and FGFR3 point mutations were not found. The gene expression profiles of YBC corresponded to those of the good prognostic group of ABC. No YBC cases had progressed to muscle-invasive tumor during follow-up. In addition, ABCs with YBC-like mutations also showed no progression to muscle-invasive tumor. In conclusion, YBC had distinct driver genetic alterations such as HRAS mutation and FGFR3 gene fusion and showed good prognosis. YBCs and ABCs with YBC-like mutations may be managed with less aggressive surveillance.

overall_design:
RNA expression matrix (FPKM values) derived from RNA sequencing of 11 young-onset bladder cancers
Submitter note: According to my review of our national law and research IRB, my raw data disclosure is not allowed.

first: Yong

last: Cho


title: Major Latex Protein MdMLP423 Is a Negative Regulator to Resist Fungus Infection in Apple

city: Zhengzhou

first: Gaopeng

last: Yuan

state: Henan

address: Weilai Road Nanduan

institute: CAAS

summary: Major latex proteins (MLPs) play critical roles in defense and stress responses in plants. However, the functions of MLPs from the apple (Malus × domestica) have not been clearly characterized. Here, we focused on the biological function of MdMLP423, which was previously identified as a potential pathogenesis-related gene. Phylogenetic analysis and conserved domain analysis revealed that MdMLP423 was a protein with a `Gly-rich loop' (GXGGXG) domain and belonged to the Bet v_1 subclass. Gene expression profile revealed that MdMLP423 was predominantly expressed in the flower. Additionally, the expression of MdMLP423 was significantly inhibited by Macrophoma kawatsukai and Alternaria alternata apple pathotype (AAAP) infection. To verify the function of MdMLP423, we generated its overexpressing transgenic lines in apple callus. The MdMLP423-overexpressing callus exhibited lower resistance to Macrophoma kawatsukai and AAAP infection, as evidenced by the lower expression of resistance-related genes, higher degree and faster speed of the disease than those of non-transgenic callus. RNA-seq analysis for MdMLP423-overexpressing callus and non-transgenic callus was constructed, and the expression analysis indicated that MdMLP423 regulated the expression of a series of differential expression genes (DEGs) and transcription factors, including DEGs involved in phytohormone signaling pathways, cell wall reinforcement, defense-related proteins, AP2-EREBP, WRKY, MYB, NAC, Zinc finger protein and ABI3. Taken together, our results demonstrate that MdMLP423 plays negative regulation on Macrophoma kawatsukai and AAAP resistance through inhibiting the expression of cooperating with defense- and stress-related genes and transcription factor.

overall_design: mRNA profiles of transgenic callus (T)and non-transgenic callus (CK), in apple, using BGISEQ-500

first: Shanshan

last: He

first: Shuxun

last: Bian

first: Xiaolei

last: Han

first: Kai

first: Peihua

last: Cong

first: Caixia

last: Zhang


title: mRNA array of CRISPR-Cas9 medicated ATRX gene editing in glioma cells

city: harbin

first: Han

last: Bo

state: heilongjiang

address: nangang district haerbin medical university

institute: HMU

summary:
Glioma is the most common primary malignant brain tumor in adults. Chemo resistance of temozolomide (TMZ), the first-line chemotherapeutic agent, is a major issue in the management of patients with glioma. Alterations of ATRX constitute one of the most prevalent genetic abnormalities in gliomas.  Therefore, it is urgent to further elucidate the role of ATRX contributing to TMZ resistance in glioma.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated and down-regulated genes after ATRX knockout.

overall_design: Briefly, LN229R was infected with viruses containing the CAS9 gene and selected with 10 mg/ml puromycin for 7 days. The cells were subsequently infected with virus carrying small guide (sg) RNAs designed for ATRX. The infection proceeded for 24 h and ATRX gene expression and KO was confirmed by western blot. ATRX-NC and ATRX-KO cells were used for mRNA microarray

first: Jinquan

last: Cai


title: Serum miRNA expression profile of nasopharyngeal carcinoma with different radiosensitivity

city: Nanning

first: Kaiguo

last: Li

state: Guangxi Zhuang Autonomous Region

address: 71 Hedi Road

department: Department of Radiation Oncology

institute: Guangxi Medical University Cancer Hospital

summary: Nasopharyngeal carcinoma is a squamous cell carcinoma arising from the nasopharynx epithelium. So far, there have been no effective biomarkers to predict the radiosensitivity of NPC. Based on miRNA profile screened out from NPC patients with different radiosensitivity, this study was conducted to explore the correlation between serum miRNAs and radiotherapy response in NPC, and to identify biomarkers for predicting the radiosensitivity of NPC.

overall_design: Total RNA containing small RNA was extracted from the serum specimens of 12 NPC patients with different radiosensitivity (including 7 radiosensitive NPC patients and 5 radioresistant NPC patients).

first: Song

last: Qu


title: Fragile X urine microRNA profiling

city: Helsinki

first: Maija

last: Castrén

state: Helsinki

address: P.O.BOX 63

department: Faculty of Medicine/Physiology

country: Finland

institute: University of Helsinki

summary: MicroRNA (miRNA) biomarkers for fragile X syndrome were searched by urine microRNA (miRNA) profiling using deep sequencing. The urine miRNA profile of twin boys who shared the same environment but one had a FXS full mutation and the other carried a premutation allele was compared based on the similar sequence reads. The urine of twin boys showed 28 differentiatially regulated miRNAs when 219 reliable identified miRNAs were compared.

overall_design: urine microRNA profiles of compared

first: Asta

last: Laiho


title: Microarray expression data from P50 mouse full thickness back skin of C57BL/6 mice - various durations of IMQ treatment and timepoints.

city: irvine

first: Elyse

middle: Noelani

last: Greenberg

state: California

address: 839 medical sciences court, sprague hall rm. 250

institute: UC Irvine

summary:
Imiquimod (IMQ) is a topical therapeutic immune activator that causes psoriasiform inflammation in mice. To determine if IMQ-induced inflammation and gene expression changes depended on the time of day in which treatment is administered, we performed gene expression profiling of dorsal mouse back skin by microarray after different durations of topical 1% IMQ treatment (control = no treatment, 6 hr, 24 hr, and 5 days of IMQ treatment) at different times of day (ZT01, ZT07, ZT09 = day-time treatment; ZT13 and ZT19 = night-time treatment). We also performed a time course after IMQ treatment by collecting mouse back skin after 0 (no treatment), 1, 2, 4, 6, and 24 hours post-treatment. Lastly, we determined gene expression changes in response to IMQ in mice deleted for the core circadian clock gene, Bmal1, after 0 (no treatment) and 24 hours post-1% IMQ compared to Wt (both treated and collected during the daytime at ZT09). The results of this study are important as they show that IMQ-induced activation of interferon sensitive genes are diurnal in Wt mice after 6 hours and 24 hours but not after 5 consecutive treatments. Furthermore, we find that interferon sensitive genes are induced more robustly in the skin of Bmal1 KO mice after 24 hr IMQ compared to Wt mice. These results are important for further understanding how the circadian clock regulates immune activation in response to the theraputic agent IMQ.
In this dataset, we include the expression data obtained from 28 microarray samples, all of which were generated from whole back skin RNA samples pooled from 5-7 mice per sample.

overall_design: 28 Total samples were analyzed. We performed the following analyses: 1) GSEA was performed on samples after both 1 dose or 5 consecutive doses of 1% IMQ, compared to control. To distinguish genes of interest, False-Discovery Rate (FDR) with Q-value of < 0.25 and nominal (NOM) P-value was ≤ 0.05 was utilized to decrease the number of false positive “discovered” genes. 2) Chi-squared test comparing gene expression across different groups. 3) With selected interferon-responsive genes, one-way ANOVA was used to determine if there was a significant difference across timepoints.

first: E

middle: N


title: Differentially expressed genes after mir-7 over-expression

city: Padova

first: Natascia

last: Tiso

address: via Ugo Bassi 58/B

department: Department of Biology

country: Italy

institute: University of Padova

summary: Analysis of differentially expressed genes after mir-7 over-expression in human neural progenitor cells ReNVM

overall_design: Total RNA retro-transcribed as cDNA, then labeled and hydridized to Illumina HT-12 v4 BeadChip. Four replicates from 3 conditions: (negative) control, 50 mM  and 80 mM mir-7 transfected ReNVM cells

first: Lavanya

last: Adusumilli

first: Henry

last: Yang

first: Stefano

last: Campanaro


title: Expression data from gastric cancer cell line SGC-7901

city: Nanjing

first: huawei

last: ni

state: jiangsu

address: No.24, Tongjiaxiang, Gulou District,

institute: China Pharmaceutical University

summary:
miR-375 plays an irreplaceable role in regulation of neoplastic progression in gastric cancer. In order to study the mechanism by which miR-375 inhibits the stemness of gastric cancer cell lines, we need to explore the genetic program controlled by miR-375.
We used microarrays to detail the global program of gene expression underlying miR-375 up-regulation and identified distinct classes of regulated genes during this process.

overall_design: A miR-375 stably overexpressing gastric cancer cell line was constructed by lentivirus infection for RNA extraction and hybridization on Affymetrix microarray. The experimental group and the control group were repeated three times each.

first: Haiwei

last: Ni


title: Abrogation of esophageal carcinoma development by miR-31 genetic knockout

city: Parma

first: Guidantonio

last: Malagoli Tagliazucchi

address: Via Gramsci 14

department: Division of Research and Innovation

institute: Hospital of Parma

summary: Transcriptomics analyses in these Zn-deficient rats revealed the molecular basis of ESCC abrogation by miR-31 knockout: Egln3, a negative regulator of NF-FB, was shown to be a direct miR-31 target; miR-31 inhibition/deletion resulted in suppression of miR-31-associated-EGLN3-NF-KB controlled inflammatory pathways.

overall_design: Genome-wide expression profiling and the analysis of genes with derepressed transcript levels in response to antimiR-31 delivery in vivo. The experimental design consist of rats  that received antimirR over the 5 weeks (ZD-antimir31 5weeks), 20 weeks (ZD-antimir31 20 weeks) and untreated rats (ZD:CTRL, ZS: CTRL).  Transcriptome profiling was also performed from group of rats with  constitutive miR-31 KO (ZD-mir31KO, ZS-mir31KO).

first: Louise

last: Fong

first: Cristian

last: Taccioli

first: Alexey

last: Palamarchuk

last: Tagliazucchi

first: Ruiyan

last: Jing

first: Karl

last: Smalley

first: Sili

last: Fan

first: Joseph

last: Altemus

first: Oliver

last: Fiehn

first: Kay

last: Huebner

first: John

last: Farber

first: Carlo

last: Croce


title: Effect of biogas slurry combined with biochar on soil microbial function gene

first: Feng-Jie

last: Jin

address: 159 Longpan Road

institute: Nanjing Forestry University

summary: The functional diversity of soil microbial communities was explored for a poplar plantation, which was treated solely with biogas slurry, or combined with biochar at different fertilization intensities over several years.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Our experiment was set up in the forest farm in a poplar plantation of Jiangsu Province, in Eastern China.  This area had been fertilized solely with biogas slurry, or in combination with biochar, at different concentrations for 5 years.  The effects of biogas slurry and biochar on the functional structures and gene diversity of soil microbial communities were explored.

first: Jin

last: Feng-Jie


title: LY75 ablation mediates mesenchymal-epithelial transition (MET) in epithelial ovarian cancer (EOC) cells associated with aberrant DNA methylation alterations implicated in EOC dissemination

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

country: France

institute: UMR1078 - Université de Bretagne Occidentale

type: Methylation profiling by high throughput sequencing

summary: In epithelial ovarian cancer (EOC), acquisition of invasiveness is accompanied by the loss of the epithelial features and the gain of a mesenchymal phenotype, a process known as epithelial-mesenchymal transition (EMT). Understanding the regulation of cell behavior during EMT is crucial for identifying the molecular mechanisms of EOC dissemination. Previously we identified the mannose receptor LY75 as the cellular phenotype modulator. LY75 suppression induces the mesenchymal to epithelial transition (MET) in EOC cell lines with mesenchymal phenotype. In this study, we used the Reduced Representation Bisulfite Sequencing (RRBS) technology for a comprehensive analysis of DNA methylation alterations during LY75-mediated EMT in EOC cells. Three different comparison (M vs E) combinations were used for RRBS analysis, as further analysis of the sequencing data based on differentially methylated regions (DMRs) covering genes’ exons and promoter regions was indicative for about 10,000 genes displaying DMRs for each of the three experimental combinations. Consecutive Venn diagram analysis of the DMRs data from the of the three experimental combinations revealed 6666 genes, displaying common altered DMRs in their exons/promoter regions, following LY75-mediated EMT alterations in EOC cells. Based on the 6666 gene list, we further proceeded with a more stringent selection of genes displaying rather high degree (>70%) of methylation in their promoter regions and previously shown to be implicated in cancer-related EMT signaling. Our stringent selection retained 45 genes (see Supplemental Table 1E), as the DNA methylation status of the promoter regions of most of these genes was further validated by an alternative approach (BSP sequencing). Ten genes were finally selected, whose promoter DNA methylation pattern coincided with their mRNA and protein expression levels. Further in vitro and in vivo studies are warranted to more completely elucidate the functional implications of these 10 genes in ovarian tumorigenesis.

overall_design: Examination and comparison of DNA methylation profiles in SKOV3 cells with mesenchymal phenotype (M) (sh-control)  versus SKOV3 cells with epithelial phenotype (E)  (following LY75 gene ablation)

first: Dimcho

last: Bachvarov


title: MicroRNA dynamics during retinal development

city: Wenzhou

first: Zai-Long

last: Chi

state: Zhejiang

address: 270 Xueyuan Road

department: School of Opthalmology & Optometry

institute: Wenzhou Medical University

summary: The mature mammalian retina results from a complex series of developmental events. A lot of work now exists on the organization, function, and development of mouse retina, and the high-throughput technologies for gene expression analyses have helped us to obtain deep insight into the mechanism about the genes that control the retinal neurogenesis and vasculogenesis. MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs that inhibit protein translation through binding to target mRNAs. miRNAs have been reported to be involved in regulating multiple physiological and pathological activities, such as ontogenesis, organogenesis, immunoprotection, and tumorigenesis. To identify miRNAs that are specifically regulated in retinal development, total RNAs isolated from retinas isolated from mice in different developmental periods were used for high-throughput sequencing. The data presented here reveals the spatiotemporal miRNA expression patterns which occur during mice retina development and provides a foundation to further investigate how miRNAs contribute to retinal neurogenesis and vasculogenesis.

overall_design: miRNA profiles of retinas from mice at postnatal day 1 (P1), P7, and P17 were generated by deep sequencing.

first: Ji-Tian

last: Guan

first: De-Wei

last: Peng


title: Hypercholesterolemia induces vascular immune responses to accelerate atherosclerosis progression in high fat diet-fed Tibetan minipigs

city: Hangzhou

first: Yongming

last: Pan

address: No. 548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

summary: We used transcriptomics to identify vascular gene expression profiles of high-fat-fed Tibetan minipig induced-hypercholesterolemia and atherosclerotic models, to verify the hypothesis that hypercholesterolemia induces innate and adaptive immune responses to accelerate atherosclerosis. Results showed that hypercholesterolemia and atherosclerosis models occurred in the high-fat fed minipigs at 8 and 24 weeks. GSEA analysis showed that the changes of hypercholesterolemia accelerated atherosclerosis were focused on immunity inflammation and lipid metabolism, immune cells such as NK cells and T cells participated in the biological processes. 4 significant modules of 344 overlapping DEGs were identified by STEM analysis. 6 hub genes (ITGB2, TYROBP, LCP2, PTPRC, C5AR1, and PTPN6) and two immune-related pathways (Natural killer cell-mediated cytotoxicity and T cell receptor signaling pathway) were identified by CytoHubba plugin and KEGG analysis. Correlation analysis showed that hub genes were significantly correlated with lipid deposition, IMT, WBC, CD4, and CD8, which was consistent with RT-PCR validation results. From above, this study reveals that hypercholesterolemia accelerate atherosclerosis progression by inducing innate and adaptive immune responses.

overall_design: Examination of the changes of vascular gene expression profiles in hypercholesterolemia and atherosclerosis models induced by high-fat diet in Tibetan minipigs   and compared with normal control group

first: Chen

last: Yu

first: Junjie

last: Huang

first: Yili

last: Rong

first: Jiaojiao

last: Chen

first: Minli


title: scRNAseq of mouse epidermis with and without 6h of IMQ treatment

first: Elyse

last: Greenberg

summary: We report the application of single-cell-RNA sequencing technology for high-throughput profiling of primary mouse epidermal cells. We use a topical toll-like receptor 7 agonist, Imiquimod (IMQ) to activate the skin immune system. We find that the proportion of most of the cell types are conserved after IMQ treatment. We identify many interferon-sensitive genes that are induced after 6 hours of IMQ treatment. This study provides a deeper understanding of the cell type-specific anti-viral gene expression response to chemical modulators such as IMQ.

overall_design: Examination of 2 treatment conditions (control shaved vs 6 hr of 1 % IMQ treatment applied topically onto shaved mouse dorsal back skin)

first: E

first: B

middle: A

last: Andersen


title: EDEM3 modulates plasma triglyceride level through its regulation of LRP1 expression

city: Boston

first: Yu-Xin

last: Xu

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Human genetics studies have uncovered genetic variants that can be used to guide biological research and prioritize molecular targets for therapeutic intervention for complex diseases and metabolic conditions. We have identified a missense variant (P746S) in EDEM3 associated with lower blood triglyceride (TG) levels in >300,000 individuals. Functional analyses in cell and mouse models show that EDEM3 deficiency strongly increased the uptake of very low-density lipoprotein and thereby reduced the plasma TG level, as a result of up-regulated expression of LRP1 receptor. We demonstrate that EDEM3 deletion up-regulated the pathways for RNA and ER protein processing and transport, and consequently increased the cell surface mannose-containing glycoproteins, including LRP1. Metabolomics analyses reveal a cellular TG accumulation under EDEM3 deficiency, a profile consistent with individuals with carrying EDEM3 P746S. Our study identifies EDEM3 as a regulator of blood TG, and targeted inhibition of EDEM3 may provide a complementary approach for lowering elevated blood TG concentrations.

overall_design: 6 HepG2 samples (3 WT, 3 EDEM3 KO)

first: Sekar

last: Kathiresan


title: Analysis of transcriptomic regulation mechanisms underlying cucumber (Cucumis sativus L.) embryogenesis during ovary culture

city: Guiyang

first: LU

last: YUXI

address: Guizhou Academy of Agricultural Sciences

institute: Institute of Horticulture

summary:
Background. Ovary culture has been a useful way to generate double haploid (DH) plant in cucumber (Cucumis sativus L.). However, the rate of embryo induction and the ability for induced embryo to grow into normal embryo are quite low. Moreover, the s mechanism of cucumber embryogenesis remains ambiguous. In this study, the molecular basis for cucumber embryogenesis was explored to set up basis for a more efficient ovary culture method. Differentially expressed genes during embryogenesis process, including the early stages of embryo formation, embryo maturation and shoot formation, were investigated using transcriptomic sequencing.
Methods. Based on the cytological observation of cucumber ovary culture, the ovary culture can be divided into three stages:early embryo development, embryo maturation (from pre-embryos to cotyledon embryos) and the shoot formation stage. six key time points were selected for transcriptome sequencing and analysis.
Results. We firstly conducted cytological observations which suggest that cell enlargement is the symbol for gametophytes to switch to sporophyte development pathway during early embryogenesis stage. In this stage, RNA-seq revealed 3468 up-regulated genes, including hormone signal transduction genes, hormone response genes and stress-induced genes. The reported embryogenesis-related genes BBM, HSP90 and AGL were also actively expressed during this stage. The total 480 genes that function in protein complex binding, microtubule binding, tetrapyrrole binding, tubulin binding and other microtubule activities were continuously up-regulated during the embryo maturation stage, indicating that the cytoskeleton structure was continuously being built and maintained by the action of microtubule-binding proteins and enzyme modification during embryo development. In shoot formation stage, 1383 genes were up-regulated, which were mainly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, phenylalanine metabolism, and starch and sucrose metabolism. The shoot formation stage might be regulated by 6 transcription factors that contained a B3 domain, 9 genes in the AP2/ERF family and 2 genes encoded WUS homologous domain proteins.
Conclusions. These findings offer a valuable framework for explaining the transcriptional regulatory mechanism underlying embryogenesis during cucumber ovary culture.

overall_design: samples were collected from six time-points of ovary culture and used three biological replicates for RNA-Seq analysis

first: Ying

last: Deng

first: Wenyuan

last: Fu


title: A novel mouse model for human synovial sarcoma expressing SS18-SSX1

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

summary:
SS18-SSX fusion proteins play a central role in synovial sarcoma development, however, genetic network and mechanisms of synovial sarcomagenesis remain largely unknown. To clarify such unknown mechanisms, we have established a new ex vivo mouse model for synovial sarcoma, using retrovirus-mediated gene transfer of SS18-SSX1 to mouse embryonic mesenchymal cells followed by subcutaneous transplantation into nude mice. This approach successfully induced subcutaneous tumors in 100% of recipients, showing invasive proliferation of short spindle tumor cells with occasional biphasic appearance. Cytokeratin expression was observed in epithelial components in tumors and expression of TLE1 and BCL2 was also shown. Gene expression profiling indicates modulation of the SWI/SNF pathway by introduction of SS18-SSX1 into mesenchymal cells, and upregulation of Tle1 and Atf2 in tumors. Collectively, these findings indicate the model exhibits typical phenotypes of human synovial sarcoma. Retroviral tagging of the tumor identified 15 common retroviral integration sites with the Dnm3 locus as the most frequent in 30 mouse synovial sarcomas. Up-regulation of micro RNAs miR-199a2 and miR-214 within the Dnm3 locus was observed. Co-introduction of SS18-SSX1 and miR-214 indeed accelerated sarcoma onset, indicating that miR-214 is a cooperative onco-miR in synovial sarcomagenesis. miR-214 functions in the cell non-autonomous manner, promoting cytokine gene expression such as Cxcl15/IL8. We have succeeded to generate a novel mouse model for human synovial sarcoma. As miR-214 overexpression in human synovial sarcoma was reported, our results underscore the important role of miR-214 in tumor development and disease progression.
We used microarrays to detail the global program of gene expression in mouse synovial sarcoma and embryonic mesenchymal cells

overall_design: Murine synovial sarcoma cells and sarcoma tissue, and murine embryonic mesenchymal cells with or without SS18-SSX1 were examined.

first: Miwa

last: Tanaka


title: Responses of Acidobacteria Granulicella sp. WH15 to carbon stress revealed by integrated omics analyses

city: Wageningen

first: Eiko

last: Kuramae

state: Gelderland

address: Droevendaalsesteeg 10

department: Microbial Ecology

country: Netherlands

institute: NIOO-KNAW

summary: We used transcriptome analysis to evaluate the responses of one strain of Acidobacteria group 1, Granulicella sp WH15, to high quantities of carbon (3%) in culture medium.

overall_design: Transcriptome in 2 conditions = 0.025% and 3% of cellobiose


title: Blood test using serum microRNAs can discriminate lung cancer from non-cancer

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

summary: A serum miRNA combination could be a powerful classifier for the detection of patients with lung cancers.

overall_design: Circulting microRNA profiles of 3924 samples consisted of 1566 preoperative lung cancer, 180 postoperative lung cancer and 1774 non-cancer controls.

first: Keisuke

last: Asakura

first: Tsukasa

last: Kadota

first: Juntaro

last: Matsuzaki

first: Yukihiro

last: Yoshida

first: Yusuke

last: Yamamoto

first: Kazuo

last: Nakagawa

first: Makiko

last: Ichikawa

first: Yoshiaki

last: Aoki

first: Hiromi

last: Sakamoto

first: Ken

last: Kato

first: Shun-ichi

last: Watanabe

first: Takahiro

last: Ochiya


title: RNA-seq based transcriptomic profiling of GBM44 glioma cell line with BAT1 shRNA knockdown

city: Chicago

first: Bakhtiar

last: Yamini

address: 900 E 57th St

department: Department of Surgery

institute: University of Chicago

summary:
Purpose: We found that BAT1 plays key role in the regulation of immune related factors, we aim to characterize the genes changed after BAT1 knockdown
Methods: Gene expression profile of GBM44 control and BAT1 knockdown were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000
Results: Using an optimized data analysis pipeline(HISAT2/HT-Seq/DESeq2),   5209 differentially expression protein-coding and noncoding genes (cut-off adjusted P <0.01) were identified in response to BAT1 knockdown.
Conclusions: After BAT1 knockdown, thousands of genes are differentially regulated, and these genes participate in immuse defense, Inflammatory response as well as cell migration and proliferation (GO pathway analysis).

first: Szymon

last: Szymura

first: Longtao

last: Wu


title: RNA-seq of the cultured testis sample of ICR mice treated with busulfan and/or Alginate Oligosaccharides (AOS)

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We profiled a RNA-seq on ICR mouse testis.  We found that AOS can improve the expression of the genes important for spermatogenesis in the cultured testis.

overall_design: The mice were treated with one dose of busulfan at 3 weeks of age. After two weeks, the testes were collected and cultured in the medium with or without Alginate Oligosaccharides (AOS) at concentration 10 mg/kg bodyweight (BW) or 50 mg/kg BW for 2 days (48h). Then total RNA was isoltated from the cultured testes and the cDNA library was constructed and the samples were subjected to do RNA-seq.

first: Pengfei

last: Zhang

first: Wei

last: Shen

first: Hongfu


title: Bulk DNA sequencing of A375, BT549, SKBR3 and 315A cell lines [cell line bulk DNA-seq]

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: We first validated the robustness and high throughput capability of the GTO protocol in multiple cell lines. The key step to success of GTO is determining the optimum number of cycles for first amplification of cDNA. This step needs to be result in a balance between cDNA and gDNA reads so that the gene expression profiles generated are good while not comprimising on the CNA profile quality. This validation was done in SKBR3, A375 and BT549 cell lines. They were then compared to 315A control diploid cell line also processed by the GTO method. The scRNAseq and scDNAseq data generated by GTO was alsocompared to bulk RNAseq and DNAseq data generated in triplicates for each cell line by traditional methods. After the method was tested in cell lines, we next applied the method to mouse models to understand tumor biology. The mouse model we used here is an orthotopic transplantation model of pancreatic cancer in syngenic mice. EGFP positive KPC 1199 tumor cells were injected into the pancreas of adult wild-type mice to generate primary tumors in pancreas and metastases in liver, spleen, peritoneum and kidneys. These primary tumors and mets were then extracted and dissociated into single cell suspensions. The single cell suspensions were analyzed by flow cytometry with antibodies against CD45, Epcam and for endogeneous GFP to isolate single stromal and tumor cells. These cells were then processed by GTP protocol to analyze gDNA by CNV profiles and RNA through read counts from the same cell. To validate our data and also have controls, we generated scRNAseq gene expression data and scDNAseq CNA profiles from the 2D cells at the same passage number at which they were injected into the mice. The scRNAseq data was generated using Fluidigm C1 machine on theie medium IFC for mRNA seq according to user manual instructions. The scDNAseq data for CNA profiles was generated by sorting single nuclei into PCR plates and then using SeqXE kit from Sigma Aldrich for Whole genome amplification using their instructions again. The data analysis was done similar to scRNAseq or scDNAseq data from GTO.

overall_design:
In this study we describe a new method for GTO (Genomics Transcriptomics One-Tube) that allows for simeltaneous sequencing of RNA and DNA from a single cell in the same tube. This method relies on dual amplification. The first amplification is done immediately after the mRNA is transcribed to cDNA using SMART-Seq2 protocol (Picelli et al., 2014) to increase the level of cDNA to that comparable to gDNA. The second amplification with universal primers from SeqXE kit for whole genome amplification (from Sigma Aldrich) amplifies the cDNA and gDNA fragments to amounts required for library preparation. The reads generated from this mixed library are separated bioinformatically to exonic and nonexonic reads depending on where they align in the reference genome to generate the RNAseq and DNAseq data respectively. We present data generated from single in-vitro cells of multiple cell lines (A375, BT549, SKBR3, 315A) and also from single in-vivo cells isolated from tumors of an orthotopic tranplantation mouse model of pancreatic cancer (using KPC1199-EGFP cell line).
single cell whole genome sequencing of A375 DNA

first: Naishitha

last: Anaparthy


title: Single cell whole genome sequencing (WGS) of mouse KPC1199EGFP cell line [mouse WGS]

overall_design:
In this study we describe a new method for GTO (Genomics Transcriptomics One-Tube) that allows for simeltaneous sequencing of RNA and DNA from a single cell in the same tube. This method relies on dual amplification. The first amplification is done immediately after the mRNA is transcribed to cDNA using SMART-Seq2 protocol (Picelli et al., 2014) to increase the level of cDNA to that comparable to gDNA. The second amplification with universal primers from SeqXE kit for whole genome amplification (from Sigma Aldrich) amplifies the cDNA and gDNA fragments to amounts required for library preparation. The reads generated from this mixed library are separated bioinformatically to exonic and nonexonic reads depending on where they align in the reference genome to generate the RNAseq and DNAseq data respectively. We present data generated from single in-vitro cells of multiple cell lines (A375, BT549, SKBR3, 315A) and also from single in-vivo cells isolated from tumors of an orthotopic tranplantation mouse model of pancreatic cancer (using KPC1199-EGFP cell line).
single cell whole genome sequencing of KPC1199EGFp nuclei


title: HLH-30/TFEB is a master regulator of reproductive quiescence

city: Koln

first: Jorge

last: Boucas

address: Joseph-Stelzmann-Str. 9b

department: Bioinformatics

institute: Max Planck Institute for Biology of Ageing

summary: All animals have evolved the ability to survive nutrient deprivation, and nutrient signaling pathways are conserved modulators of health and disease. In C. elegans, late-larval starvation provokes adult reproductive diapause (ARD), a long-lived quiescent state that enables animals to survive months without food, yet underlying molecular mechanisms remain unknown. Here, we show that ARD is distinct from other forms of diapause, and shows surprisingly little requirement for canonical longevity pathways, autophagy and fat metabolism. Instead ARD depends dramatically on HLH-30/TFEB transcription factor to promote morphologic and metabolic remodeling involved in ARD entry, survival, and recovery, suggesting it is a master regulator of reproductive quiescence. TFEB transcriptome and genetic analyses reveal that Max-like HLH factors, mTOR, AMP-kinase, protein synthesis, and mitochondrial fusion are target processes that promote ARD longevity. Evidently reproductive quiescence rewires metabolism in unique ways to ensure long-term survival, and could illuminate similar mechanisms acting in latent tumorigenesis, and long-term fasting.

overall_design: Trancsriptome of C. elegans wild type and hlh-30 under ad libitum bacteria conditions and 24 hours of ARD starvation.

first: Birgit

last: Gerisch

first: Adam

last: Antebi


title: Bulk DNA seq, GTO-seq, and RNA-seq with murin and human cell lines

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Effects of fructose on liver gene expression profile in DEN-induced HCC model.

city: Darlinghurst

first: Saskia

last: Reibe

state: NSW

address: 384 Victoria Street

department: Diabetes & Metabolism

country: Australia

institute: Garvan Institute of Medical Research

summary: Excessive fructose consumption causes fatty liver disease and steatohepatitis, conditions that elevate liver cancer risk. Although fructose was documented to cause metabolic abnormalities and microbial dysbiosis, whether and how it triggers liver tumorigenesis was unknown. We now describe a mouse model in which fructose acts as a carcinogen, giving rise to intestinal dysbiosis and translocation of inflammation-evoking microbial products that reach the liver via the portal circulation. These inflammatory stimuli initiate hepatocellular carcinogenesis. Genetic enhancement of epithelial barrier integrity and microbiota depletion with broad spectrum antibiotics prevent fructose-induced steatosis and liver cancer.

overall_design: Using DEN-induced and MUP-uPA HCC mouse models we investigated effects of diets rich in corn starch or fructose on intestinal barrier integrity, NASH development and hepatocarcinogenesis.

first: J

last: Todoric

first: M

last: Febbraio

last: Karin


title: Teriparatide changes the gene expression of dorsal root ganglia in ovariectomized rats

city: Shizuoka

first: Tomoya

last: Tanaka

address: 632-1 Mifuku, Izunokuni

institute: Asahi Kasei Pharma

summary: Twelve-week-old rats underwent bilateral ovariectomy (OVX) or sham surgery. Four weeks after surgery, the animals underwent the following treatments for 4 weeks: subcutaneous injection of teriparatide (TPTD) or saline 3 times weekly. All rats were anesthetized and sacrificed at the end of the experimental period. The L4-5 dorsal root ganglia (DRG) were harvested.

overall_design: mRNA profiles of DRG collected from OVX rats were treated with TPTD using Illumina Hiseq

first: Tadahiro

last: Iimura


title: Modulation of LTR-retrotransposons expression in mHLA-DR stratified septic shock patients: a pilot study [IS]

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

summary:
Background: Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection. To date, no biomarker has shown sufficient evidence and ease of application in clinical routine to monitor the complexity of the sepsis-related immune alterations. Multiple levels of interaction of human endogenous retroviruses (HERVs) with the immune response led us to hypothesize that they may be relevant candidates both to contribute to the physiopathology of sepsis and to be part of a molecular signature. In this study, we used a recently described high-density microarray which allows exploring HERVs/MaLRs transcriptome in septic shock patients.

Results: About 6.9% of the HERVs/MalRs repertoire is transcribed in whole blood. Concerning the functionality of LTRs, the majority of LTRs are silent (62.9%), 7.5% of LTRs present a putative constitutive promoter or polyA functions, while 20.4% of them may shift from silent to active. Evidence was given that a subset of HERVs/MaLRs and genes were modulated in septic shock patients according to the monocyte HLA-DR (mHLA-DR) expression level measured by flow cytometry, as a proxy of immunosuppression. We then identified a large signature consisting of 193 differentially expressed HERVs/MaLRs probesets  further reduced to a smaller 10 HERVs/MaLRs signature. Both signatures, validated in an independent septic shock cohort, identified two groups of patients with different severity features including clinical criteria and the CD74 and CX3CR1 sepsis severity molecular markers.

Conclusion: This microarray-based approach unveiled the expression of about 87,912 distinct HERV probesets and identified 764 putative promoter LTRs and 642 putative polyA LTRs in whole blood. HERV/MaLR expression was shown to be tightly modulated in septic shock patients according to mHLA-DR expression. We identified a set of potential molecular biomarkers in septic shock patients partially overlapping immunosuppression (mHLA-DR), and the risk of Health Care associated Infections (HAI) (CD74 ratio), complementary to existing molecular markers of a sepsis patients stratification. We identified a HERV/MaLR signature discriminating patients based on their immunosuppression state and severity.

overall_design: 10 septic shock patients at D1 and D3-4 after ICU admission presenting with features of sepsis-induced immunosuppression or not (HLA-DR low/high), and compared to 4 healthy controls

first: Marine

last: Mommert

first: Olivier

last: Tabone

first: Audrey

last: Guichard

first: Guy

last: Oriol

first: Elisabeth

last: Cerrato

first: Mélanie

last: Denizot

first: Alexandre

last: Pachot

first: Alain

last: Lepape

first: Guillaume

last: Monneret

first: Fabienne

last: Venet

first: Karen

last: Brengel-Pesce

first: François

last: Mallet


title: Single cell RNA sequencing of KPC1199 cell line [mouse scRNA-seq]

first: Yu-Jui

last: Ho

summary: In this study we describe a new method for GTO (Genomics Transcriptomics One-Tube) that allows for simeltaneous sequencing of RNA and DNA from a single cell in the same tube. This method relies on dual amplification. The first amplification is done immediately after the mRNA is transcribed to cDNA using SMART-Seq2 protocol (Picelli et al., 2014) to increase the level of cDNA to that comparable to gDNA. The second amplification with universal primers from SeqXE kit for whole genome amplification (from Sigma Aldrich) amplifies the cDNA and gDNA fragments to amounts required for library preparation. The reads generated from this mixed library are separated bioinformatically to exonic and nonexonic reads depending on where they align in the reference genome to generate the RNAseq and DNAseq data respectively. We present data generated from single in-vitro cells of multiple cell lines (A375, BT549, SKBR3, 315A) and also from single in-vivo cells isolated from tumors of an orthotopic tranplantation mouse model of pancreatic cancer (using KPC1199-EGFP cell line).

overall_design:
We first validated the robustness and high throughput capability of the GTO protocol in multiple cell lines. The key step to success of GTO is determining the optimum number of cycles for first amplification of cDNA. This step needs to be result in a balance between cDNA and gDNA reads so that the gene expression profiles generated are good while not comprimising on the CNA profile quality. This validation was done in SKBR3, A375 and BT549 cell lines. They were then compared to 315A control diploid cell line also processed by the GTO method. The scRNAseq and scDNAseq data generated by GTO was alsocompared to bulk RNAseq and DNAseq data generated in triplicates for each cell line by traditional methods. After the method was tested in cell lines, we next applied the method to mouse models to understand tumor biology. The mouse model we used here is an orthotopic transplantation model of pancreatic cancer in syngenic mice. EGFP positive KPC 1199 tumor cells were injected into the pancreas of adult wild-type mice to generate primary tumors in pancreas and metastases in liver, spleen, peritoneum and kidneys. These primary tumors and mets were then extracted and dissociated into single cell suspensions. The single cell suspensions were analyzed by flow cytometry with antibodies against CD45, Epcam and for endogeneous GFP to isolate single stromal and tumor cells. These cells were then processed by GTP protocol to analyze gDNA by CNV profiles and RNA through read counts from the same cell. To validate our data and also have controls, we generated scRNAseq gene expression data and scDNAseq CNA profiles from the 2D cells at the same passage number at which they were injected into the mice. The scRNAseq data was generated using Fluidigm C1 machine on theie medium IFC for mRNA seq according to user manual instructions. The scDNAseq data for CNA profiles was generated by sorting single nuclei into PCR plates and then using SeqXE kit from Sigma Aldrich for Whole genome amplification using their instructions again. The data analysis was done similar to scRNAseq or scDNAseq data from GTO.
single cell mRNA sequencing using Fluidigm C52

first: Naishitha

last: Anaparthy


title: Modulation of LTR-retrotransposons expression in mHLA-DR stratified septic shock patients: a pilot study


title: Determine genes differentially expressed between Raji cells and a subline which is resistant to APTO-253 (Raji/253R)

city: La Jolla

first: Stephen

last: Howell

state: CA

address: 3855 Health Sciences Drive, #0819, Room 3344

department: School of Medicine and Moores Cancer Center

institute: University of California, San Diego

summary: To obtain further insight into the resistance mechanism, RNA-seq analysis was carried out on 3 independent samples of both the sensitive Raji and resistant Raji/253R cells. A gene-level differential expression analysis was performed by removing all genes with less than 50 reads across all 6 samples as genes with only low level expression can cause irregularities in differential expression analysis. Genes were considered to be differentially expressed if their adjusted p-value was less than the 0.05 level and their fold change was >2 in either direction.  Among the 13,791 evaluable genes there were 1,012 that were significantly up-regulated in the Raji/253R cells and 704 genes that were significantly down regulated relative to the parental sensitive Raji cells. The ATP-binding cassette sub-family member ABCG2 was the most up-regulated gene with more than a thousand-fold increase in transcript level. Genes were considered to be differentially expressed if their adjusted p-value was less than the 0.05 level and their fold change was >2 in either direction.

overall_design: Total cellular RNA was isolated using the RNeasy mini kit (QIAGEN, Valencia, CA) from 3 independent samples for each cell line. Total RNA was polyA selected and libraries were contructed using the Iluumina Tru-seq kit.

first: Cheng-Yu

last: Tsai


title: Histone Demethylation by a Family of UBA Domain-containing Proteins

status: Public on Mar 29 2020

city: Shanghai

first: Charilie

middle: Degui

last: Chen

address: No. 320 YueYang Road

institute: SIBCB

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone methyl groups can be removed by histone demethylases. Although LSD1 and JmjC domain-containing proteins have been identified to be histone demethylases, enzymes responsible for many histone methylation states or sites are not identified. Here, we performed a high-content cell-based screening of a cDNA library containing 2,500 nuclear proteins and identified KDM10A as a histone demethylase specific for histone H4 lysine 20 (H4K20). Ectopic expression of KDM10A reduced the global levels of H4K20me1/2/3 in 293T cells. In vitro, KDM10A specifically demethylated H4K20me1/2/3 and generated formaldehyde. The enzymatic activity required Fe(II) and α-ketoglutarate as cofactors. Domain mapping indicated that the demethylase activity required its UBA domain. We also demonstrated that KDM10B, a protein homologous to KDM10A, had H4K20 demethylase activity in vitro and in vivo. ChIP-seq reveals that KDM10A/B demethylated H4K20 methylation at specific genomic loci in vivo. We further demonstrated that KDM10A/B activated the transcription of coding genes by demethylating H4K20me1 in the gene body, and the transcription of repetitive elements by demethylating H4K20me3 in intergenic regions. NMR analyses demonstrated that an HxxxE motif in the UBA domain is crucial for iron binding, mutation of these two residues abolished iron binding and the demethylase activity. Thus, we identified a family of UBA domain-containing proteins as histone demethylases.

overall_design: Examination of KDM10A/B binding and histone H4K20me1/2/3 modification in control and KDM10A/B double knockdown cells

first: Charli

first: Xiongwen

last: Cao


title: Next Generation Sequencing of sh-control and sh-KDM10A/KDM10B double knockdown HeLa Cells Transcriptomes

overall_design: Examination of differential genes expression in two HeLa cell lines

first: Yanran


title: The mantle exosome and microRNAs of Hyriopsis cumingii involved in nacre color formation

first: Chen

last: xiajun

address: hucheng road 999

institute: shanghai ocean university

summary: The nacre color of shells has an effect on the pearl color in Hyriopsis cumingii, and is an important indicator for its value. However, little exosome and micro (mi)RNA information are available on nacre color formation in mussels. In this study, exosomes of mantles were extracted from white and purple mussels. High-throughput Illumina sequencing was performed on the white and purple mussel mantle exosomes.Moreover, miR-223 negatively regulated hcApo, which plays important roles in the absorption and transport of β-carotene in H. cumingii. These results improve our understanding of the molecular mechanisms of nacre color formation in H. cumingii.

first: Xiajun

first: Zhiyi

last: Bai

first: Jiale

last: Li


title: Next Generation Sequencing Facilitates Quantitative Analysis of Original and RCHO-resistant NU-DUL-1 cell Transcriptomes

first: Jianfeng

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: The goal of this study is to screen the differential genes between original and RCHO-resistant NU-DUL-1 cells, then analyze the significant pathways.

overall_design: The total RNA of each group was pooled from 3 different passages separately. RNA-seq was performed using the proton sequencing process.

first: Weiguo

last: Hu


title: Z-DNA Binding Protein 1 Promotes Osteogenic Differentiation of Mesenchymal Stem Cells

city: chengdu

first: Peng

last: Deng

state: Sichuan

address: No.14 Renmin South Rd 3rd Section

department: West China School of Stomotology

institute: Sichuan University

summary: The aim of this study is to investigate the role of ZBP1 in regulation of osteogenic differentiation of mouse bone marrow derived mesenchymal stem/progenitor cells.

overall_design: mRNA profiles of ZBP1-depleted bone marrow–derived mesenchymal stem/progenitor cells and contorls were generated by deep sequencing.

first: X

last: Zhao

first: H

last: Xu

first: D

first: P


title: Genome-wide lncRNA Expression Profiling in colon cancer patients.

city: LOS ANGELES

first: MARINA

last: KOUTSIOUMPA

address: 650 Charles E. Young Dr South, CHS 33-315

department: MEDICINE

institute: UCLA

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

summary: Transcriptional lncRNAs expression comparing human colon cancer tissues to normal colon tissues using Agilent-062918 Human lncRNA array V4.0.

overall_design: Differential expression profiling of lncRNAs originating from human colon cancer tissues and normal colon tissues.

first: Dimitrios

last: Iliopoulos

first: Marina

last: Koutsioumpa


title: Bulk RNA sequencing of A375, BT549, SKBR3 and 315A cell lines [cell line bulk RNA-seq]

first: Yu-Jui

overall_design: In this study we describe a new method for GTO (Genomics Transcriptomics One-Tube) that allows for simeltaneous sequencing of RNA and DNA from a single cell in the same tube. This method relies on dual amplification. The first amplification is done immediately after the mRNA is transcribed to cDNA using SMART-Seq2 protocol (Picelli et al., 2014) to increase the level of cDNA to that comparable to gDNA. The second amplification with universal primers from SeqXE kit for whole genome amplification (from Sigma Aldrich) amplifies the cDNA and gDNA fragments to amounts required for library preparation. The reads generated from this mixed library are separated bioinformatically to exonic and nonexonic reads depending on where they align in the reference genome to generate the RNAseq and DNAseq data respectively. We present data generated from single in-vitro cells of multiple cell lines (A375, BT549, SKBR3, 315A) and also from single in-vivo cells isolated from tumors of an orthotopic tranplantation mouse model of pancreatic cancer (using KPC1199-EGFP cell line).

first: Naishitha


title: Transcriptome analysis of human colonic IgA+ plasma cell subsets and naïve B cells

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

country: Spain

institute: Vall d'Hebron Institute of Oncology

summary: Immunoglobulin A (IgA) is the most abundant antibody in the intestinal tract. Recent studies show that discrete subsets of gut human plasma cells (PCs) release IgA, which contributes to the maintenance of gut homeostasis. To better characterize the properties of these PC subsets, we performed global transcriptome analysis in naïve B cells as well as immature CD19+IgA+CD138- PCs, mature CD19+IgA+CD138+ PCs and late CD19-IgA+CD138+ PCs after their purification from human colon samples.

overall_design: Control naive (N) CD45+CD10−CD19+IgA−IgM+IgD+ B cells as well as immature CD45+CD10−CD19+IgA+CD38+CD138− PCs (A), mature CD45+CD10−CD19+IgA+CD38+CD138+ PCs (B) and late CD45+CD10−CD19−IgA+CD38+CD138− PCs (D) were FACSorted from histologically normal tissue samples obtained from the ascending colon of four adult donors undergoing right hemicolectomy. The global transcriptome of each of these gut immune cell subsets was dissected by performing microarray analysis.

first: Andrea

last: Cerutti

first: Giuliana

last: Magri

first: Laura

last: Comerma


title: GTO sequencing of Human Cell Lines [cell line GTO-seq]

last: Ho

overall_design:
In this study we describe a new method for GTO (Genomics Transcriptomics One-Tube) that allows for simeltaneous sequencing of RNA and DNA from a single cell in the same tube. This method relies on dual amplification. The first amplification is done immediately after the mRNA is transcribed to cDNA using SMART-Seq2 protocol (Picelli et al., 2014) to increase the level of cDNA to that comparable to gDNA. The second amplification with universal primers from SeqXE kit for whole genome amplification (from Sigma Aldrich) amplifies the cDNA and gDNA fragments to amounts required for library preparation. The reads generated from this mixed library are separated bioinformatically to exonic and nonexonic reads depending on where they align in the reference genome to generate the RNAseq and DNAseq data respectively. We present data generated from single in-vitro cells of multiple cell lines (A375, BT549, SKBR3, 315A) and also from single in-vivo cells isolated from tumors of an orthotopic tranplantation mouse model of pancreatic cancer (using KPC1199-EGFP cell line).
GTO sequencing to analyze RNA and DNA from single cell

last: Anaparthy


title: GTO sequencing of Mouse Tumors In KPC transplantation model [mouse GTO-seq]

overall_design:
In this study we describe a new method for GTO (Genomics Transcriptomics One-Tube) that allows for simultaneous sequencing of RNA and DNA from a single cell in the same tube. This method relies on dual amplification. The first amplification is done immediately after the mRNA is transcribed to cDNA using SMART-Seq2 protocol (Picelli et al., 2014) to increase the level of cDNA to that comparable to gDNA. The second amplification with universal primers from SeqXE kit for whole genome amplification (from Sigma Aldrich) amplifies the cDNA and gDNA fragments to amounts required for library preparation. The reads generated from this mixed library are separated bioinformatically to exonic and nonexonic reads depending on where they align in the reference genome to generate the RNAseq and DNAseq data respectively. We present data generated from single in-vitro cells of multiple cell lines (A375, BT549, SKBR3, 315A) and also from single in-vivo cells isolated from tumors of an orthotopic tranplantation mouse model of pancreatic cancer (using KPC1199-EGFP cell line).
GTO sequencing to analyze RNA and DNA from single cell


title: Modulation of LTR-retrotransposons expression in septic shock patients: a pilot study  [MIP]

first: Julien

last: Textoris

overall_design:
102 septic shock patients at D1, D3 and D6 after ICU admission

contributor: MIP Rea Study Group
contributor: REALISM Study Group

first: Marine

last: Mommert

first: Olivier

last: Tabone

first: Audrey

last: Guichard

first: Guy

last: Oriol

first: Elisabeth

last: Cerrato

first: Mélanie

last: Denizot

first: Alexandre

last: Pachot

first: Alain

last: Lepape

first: Guillaume

last: Monneret

first: Fabienne

last: Venet

first: Karen

last: Brengel-Pesce

first: François

last: Mallet


title: Craniofacial neural crest cell-specific deletion of Ihh causes skeletal malocclusion in mice

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Although our data is providing the evidence that Ihh regulates nasal and mandibular cartilage development to establish facial and masticatory system, the cartilage gene network conducted by Ihh signaling has not been broadly investigated. To establish such gene expression profile, we selected mandibular condylar cartilage to examine differentiating cartilage tissue. The cartilage histologically indicates simple endochondral ossification and mutant sections positive to Tomato staining presented decreased and disrupted cartilage.

overall_design: Condylar cartilages dissected under microscope from both control and mutant groups were processed and the total RNA was subjected to RNA Seq analysis. In parallel, mutant condylar samples were confirmed by Ihh, Cre and Tomato expression analysis.

first: Katsuhiko

last: Amano


title: A molecular network regulating the proinflammatory phenotype of human memory T lymphocytes

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

institute: IRCCS San Raffaele Scientific Institute

summary: Understanding the mechanisms that modulate T helper lymphocyte functions is crucial to decipher normal and pathogenic immune responses in humans. To identify molecular determinants influencing the pathogenicity of T cells, we separated ex vivo-isolated primary human memory T lymphocytes based on their ability to produce high levels of inflammatory cytokines. We found that the inflammatory, cytokine-producing phenotype of memory T lymphocytes was defined by a specific core gene signature and was mechanistically regulated by the constitutive activation of the NF-kB pathway and by the expression of the transcriptional repressor BHLHE40. BHLHE40 attenuated the expression of anti-inflammatory factors, including miR-146a, a negative regulator of NF-kB activation, and ZC3H12D, an RNase of the Regnase-1 family able to degrade inflammatory transcripts. Our data reveal a molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes, with the potential to contribute to disease.

overall_design: Refer to individual Series


title: A hypermethylation strategy utilized by enhancer-bound CARM1 to promote estrogen receptor a-dependent transcriptional activation and breast carcinogenesis  (ChIP-Seq)

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

summary: While protein arginine methyltransferases (PRMTs) and PRMT-catalyzed protein methylation have been well-known to be involved in a myriad of biological processes, their roles in carcinogenesis, particularly in estrogen receptor alpha (ERa)-positive breast cancers, remain incompletely understood. Here we focused on investigating PRMT4 (also called coactivator associated arginine methyltransferase 1, CARM1) due to its high expression and the associated poor prognosis in ERa-positive breast cancers. We first uncovered the chromatin-binding landscape and transcriptional targets of CARM1 in the presence of estrogen in ERa-positive breast cancer cells employing genomic and transcriptomics approaches. CARM1 was found to be predominantly and specifically recruited to ERa-bound active enhancers and essential for the transcriptional activation of cognate estrogen-induced gene transcriptional activation in response to estrogen. Global mapping of CARM1 substrates revealed that CARM1 methylates a large cohort of proteins with diverse biological functions, including regulation of intracellular estrogen receptor signaling, chromatin organization, chromatin remodeling and others. Intriguingly, a number of proteins were hypermethylated exclusively by CARM1 on a cluster of arginine residues. Exemplified by MED12, hypermethylation of these proteins by CARM1 served as a molecular beacon for recruiting coactivator protein, tudor domain-containing 3 (TDRD3), to ensure the full activation of estrogen/ERa target genes. In consistent with its critical role in estrogen-induced gene transcriptional activation, CARM1 was found to promote cell proliferation of ERa-positive breast cancer cells in vitro and tumor growth in mice. Taken together, our study uncovered a “hypermethylation” strategy utilized by CARM1 in gene transcriptional regulation, and suggested that CARM1 can server as a therapeutic target for breast cancer treatment.

overall_design: ChIP-seq performed in this study was designed to understand the molecular mechanisms underlying CARM1 regulation of breast cancer

first: Wen

last: Liu

first: Bing-Ling

last: Peng

first: Jian-Cheng


title: Glycosylation-dependent modulation of the IL-2 signaling axis determines Th17 differentiation and IL-10 production

city: London

first: Leona

last: Gabrysova

address: 1 Midland Road

institute: The Crick Institute

summary: Metabolism plays an essential role in shaping Th cell responses including the production of pro-inflammatory cytokines. However, its effect on the production of the anti-inflammatory cytokine IL-10 has not been investigated. We show here that the glucose analogue 2-deoxyglucose (2DG) specifically inhibited Th1 and Th2 cell differentiation and accompanying IL-10 production. In contrast, 2DG promoted IL-17A production by Th17 cells, even in the presence of IL-2 known to limit Th17 differentiation, whilst simultaneously also abrogating the production of IL-10. Rather than inhibiting glycolysis, 2DG was found to act through the inhibition of glycosylation, itself critical for IL-2Ra surface expression and downstream signaling, explaining the reciprocal effect of 2DG on the Th1 and Th2 versus Th17 differentiation. The essential role of IL-2 for IL-10 production by Th17 cells was confirmed by adding IL-2 or anti-IL-2, neither of which made the cells more pathogenic. The molecular mechanism of the IL-2 driven Th17 IL-10 production may be attributed to the transcription factor c-Maf, whose expression was significantly upregulated in the presence of IL-2 signaling. The overall RNA signature of sorted IL-10+ T cells driven by IL-2, be it IL-17A+ or IL-17A-, was dominated by protein synthesis whereas that of their IL-10- counterparts by cell cycle associated processes suggesting that IL-10 secreting Th17 cells trade off self-renewal for secretory capacity. Our study thus reveals a previously unappreciated, anti-inflammatory role for IL-2 in Th17 cell production of IL-10 and identifies a novel mechanism to limit Th17 pathogenicity.

overall_design: RNA-Seq on in-vitro differentiated Th17 cells in the presence of added IL-2 or anti-IL-2 antibody, all cells or cells sorted into different IL-17A/IL-10 secreting T cells following intracellular cytokine staining

last: Gabryšová

first: Charlotte

last: Whicher

first: Lydia

last: Bradley

first: James

middle: I

last: MacRae

first: Probir

last: Chakravarty

first: Elizabeth

middle: H

last: Mann

first: Catherine

last: Hawrylowicz

first: Dimitrios

last: Anastasiou

first: Anne

last: O’Garra


title: A Functional Allele of CsFUL1 Regulates Fruit Length through Repressing CsSUP and Inhibiting Auxin Transport in Cucumber

status: Public on Mar 28 2020

city: Boston

first: Yanqiang

last: Li

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

summary: Cucumber (Cucumis sativus L.) is an important vegetable crop bearing fleshy pepo fruits that harvested immature. The fruit length is one of the most important agricultural traits that directly determine the fruit yield and affects fruit quality, but the regulatory mechanism of fruit length variation remains elusive. Here we found a FRUITFULL-like MADS-box gene CsFUL1 functions as a key repressor for fruit length regulation in cucumber. The expression of CsFUL1 is highly enriched in male flowers and fruits, and negatively correlated with fruit length in different cucumber lines. Notably, a key SNP in CsFUL1 was selected during cucumber domestication for long fruit. Ectopic expression of CsFUL1 was unable to rescue the indehiscent fruit phenotype of ful-1 in Arabidopsis. Overexpression of CsFUL1 resulted in increased floral organs and reduced fruit length, whereas knockdown of CsFUL1 led to elongated fruit in cucumber. Transcriptome and biochemical analyses showed that CsFUL1 regulates fruit length through two pathways: one by inhibiting the PIN-FORWED (PIN1/7)-mediated auxin transport and thus downregulates auxin related genes in the fruit, and the other by forming a tetramer with other MADS-box genes to repress the CsSUP-mediated cell division and cell expansion. In addition, we found that CsFUL1 promotes locule number variation through the classical CsWUS-CsCLV pathway. Our findings uncover the regulatory commonality and specificity during development of different fruit types, and provide an important candidate gene to customize fruit length during cucumber breeding.

overall_design: Comparative analysis of fruit from two near-isogenic lines, WT(long fruit) and OX-29 (short fruit),  was employed to discover  genes and networks that regulate the fruit length. Two biological replicates were used from each line.

first: Zhao

last: Jianyu

first: Jiang

first: Che

last: Gen

first: Hou

last: Yu

first: Li

last: Yanqiang

first: Pan

last: Yupeng

last: Wensheng

first: Ding

last: Lian

first: Yan

last: Shuangshuang

first: Liu

last: Renyi

last: Liying

first: Wu

last: Tao

first: Weng

last: Yiqun

first: Zhang

last: Xiaolan


title: RNA-seq analysis for VCPWT and VCPT76A breast tumor

city: Hong Kong

first: Kaiyuan

last: ZHU

address: Tat Chee Avenue. Kowloon Tong.

institute: City University of Hong Kong

summary: Proper centrosome movement to the bipolar position is a prerequisite for bipolar spindle orientation and genome stability. Polo like kinase 1 (Plk1) is a key mitotic kinase which controls centrosome separation. Here we found that Plk1 phosphorylated residue Thr76 in VCP/p97, an AAA-ATPase mainly involved in protein homeostasis, at centrosome from prophase to anaphase. This phosphorylation recruited VCP to centrosome to regulate centrosome orientation. VCP also exhibited strong co-localization with Eg5, a mitotic kinesin motor for centrosome movement, at mitotic spindle, and dephosphorylation of Thr76 in VCP was required for the enrichment of VCP and Eg5 to the spindle, thus, ensuring proper spindle orientation and chromosome segregation. Since genome instability is the hallmark of cancer and the phosphorylation of Thr76 in VCP is important for proper centrosome movement, spindle orientation, and chromosome segregation, we, thus, knocked down VCP in MDA-MB-231cells by its specific shRNA, and reconstituted the expression of VCP by infecting the cells with lentivirus encoding shRNA-resistant Flag-VCPWT or Flag-VCPT76A. We then implanted VCPWT- or VCPT76A-expressing MDA-MB-231 cells into nude mice and found that the tumor growth in mice implanted with VCPT76A-expressing cells was significantly slower when compared with the mice implanted with the Flag-VCPWT-expressing cells. To better understand the decreased tumor formation ability of Flag-VCPT76A-expressing cells, we isolated the primary breast tumor tissues for the RNA-Seq analysis. Of the 57,905 mapped whole genome genes in the isolated tumors, we identiﬁed 234 differentially expressed genes (DEGs; false discovery rate (FDR) < 0.1).

overall_design: Study the genome wide difference between VCPWT and VCPT76A derived breast tumors

first: Jianbo

last: Yue

last: Zhu


title: Expression data from Ulk1 silencing in mouse liver and AML12 cells

status: Public on Mar 27 2020

city: SINGAPORE

first: SUJOY

last: GHOSH

address: 8 COLLEGE ROAD

department: Cardiovascular & Metabolic Diseases

country: Singapore

institute: DUKE-NUS Graduate Medical School

summary:
This experiments detail the differential gene expressionin hepatic cells in response to Ulk1 silencing both in vivo and in vitro
We used microarrays to detail the global programme of gene expression underlying the loss of ULK1 knockdownin hepatic cells

overall_design: Ulk1 siRNA was administered  in both mouse and AML12 cells in culture and microarray analysis was performed 72 hrs post administration

first: Rohit

last: Sinha

first: Veerabrahma

middle: P

last: Seshachalam

first: Sujoy

last: Ghosh


title: Metformin reverses a precancerous niche featuring cytoplasmic p21WAF1/CIP1-expressing hepatocytes and prevents hepatocellular carcinoma development

city: East Lansing

first: Hua

last: Xiao

state: Michigan

address: 567 WILSON RD, RM 2201

department: Physiology

institute: Michigan State University

summary: Prevention and treatment options for hepatocellular carcinoma (HCC) are presently limited, underscoring the necessity for elucidating molecular mechanisms underlying HCC development and identifying new prevention and therapeutic targets.  We demonstrate a unique precancerous niche that features enhanced p53 pathway, aberrant cytoplasmic p21WAF1/CIP1-expressing hepatocytes, and increased CD8+ T lymphocyte and macrophage infiltration in the livers of Ncoa5+/- mouse model of HCC. Metformin treatment reverses these precancerous features and profoundly reduces tumor incidence. Our data also reveal that a subset of HCC patients with a similar precancerous niche in the adjacent noncancerous livers had a relatively poor prognosis.  Our study suggests a perceptible hepatic niche predisposing to HCC development and uncovers new actions of metformin in the prevention and treatment of HCC.

overall_design: Liver mRNA profiles of a cohort of 20 week old C57BL/6 mice were generated by Illumina HiSeq2500, samples include 4 Ncoa5+/- and 4 wild type mice which were not treated by metformin. Liver mRNA profiles of another cohort of 39 week old C57BL/6 mice were generated by Illumina HiSeq4000. Part of the cohort of 39 week old mice includes 5 Ncoa5+/- mice and 3 wild type mice treated with Metformin through drinking water for 31 weeks, the rest of 39 week old cohort are 5 non-treated Ncoa5+/- mice and 4 non-treated wild type mice.

first: Mark

last: Williams

first: Xinhui

last: Liu

first: Yueqi

last: Zhang

first: Jake

last: Reske


title: BET bromodomain containing epigenetic reader proteins regulate vascular smooth muscle cell proliferation and neointima formation

city: Hannover

first: Simona

last: Weisheit

address: Carl-Neuberg-Strasse 1

department: Cardiology and Angiology

institute: Hannover Medical School

summary:
Recent studies revealed that the bromodomain and extraterminal (BET) epigenetic reader proteins resemble key regulators in the underlying pathophysiology of cancer, diabetes or cardiovascular disease. However, whether they also regulate vascular remodeling processes by direct effects on vascular cells is unknown. In this study we investigated the effects of the BET proteins on neointima formation in response to vascular injury in vivo and on human smooth muscle cell function in vitro.
In this study we showed that the selective inhibition of BETs by the small molecule (+)-JQ1 dose dependently reduced proliferation and migration of SMCs without apoptotic or toxic effects caused by cell cycle arrest in the G0/G1 phase. Whole genome microarray expression profiling analysis revealed a substantial transcriptional regulation of gene sets controlled by the FOXO1-transcription factor. Additional data confirmed that the BET protein BRD4 directly binds to FOXO1 and regulates FOXO1 transactivational capacity.
Inhibition of BET epigenetic reader proteins might represent a promising therapeutic strategy to prevent adverse vascular remodeling.

overall_design: RNA isolation for microarray analysis was prepared 6 h after treating human smooth muscle cells with growth medium or (+)-JQ1. SMCs in basal medium served as control. We analysed four control replicates and three replicates of each growth medium and (+)-JQ treated SMC.

last: Gegel


title: Immunological subtypes of depression: insights from monocyte gene expression II

city: Rotterdam

first: Hemmo

last: Drexhage

address: Dr Molewaterplein 40

department: Immunology

institute: Erasmus MC

summary:
32 genes of a previously established inflammation-related gene signature  were assessed in 197 patients with MDD and 151 controls collected during the EU-MOODINFLAME project. Monocyte gene expression data were related to age, gender, BMI, depression severity, Childhood Adversity (CA), and Suicide Risk (SR)
data studycenter 2

overall_design: qPCR gene expression profiling. Details of patient selection, recording of patient data, laboratory methods can be found in Schiweck C. et al,

first: J

last: Wijkhuijs

first: H


title: Single-cell RNA-seq from primary somatosensory cortical S1L2/3glutamatergic neurons of the mouse

city: Hefei

first: zhi

last: zhang

state: Anhui

address: 443 Huangshan Road

department: School of Life Science

institute: University of Science and Technology of China

summary: We analyzed the gene expression profiles of S1L2/3 glutamatergic neurons  in maternal mice and their offspring by single-cell RNA sequencing (12,671 ± 1,402 genes per neuron). Compared to sham control mice, we identified 513 and 571 differentially expressed genes in CCI offspring and their maternal mice respectively. And 102 overlapped genes were identified between CCI offspring and their maternal mice.

overall_design: Single-cell RNA-seq using SMART-Seq2 method was performed from individual S1 glutamatergic neuron after patch clamp recording. We performed RNA-seq on total 9 neurons from CCI offspring, CCI maternal and sham mice and three replicated neurons for each group.

first: Wenjuan

last: Tao

first: Changmao

last: Chen

first: Yuping

last: Wang

first: Zhi


title: Rice-NaCl or Na2SO4 toxicity

city: Louvain-la-Neuve

first: Willy

last: IRAKOZE

state: Belgium

address: 5 (Bte 7.07.13) Place Croix du Sud

department: Earth and Life Institute-Agronomy

country: Belgium

institute: UCLouvain

summary:
A comparative transcriptomic study of the impact of salt toxicity on rice plant (Oryza sativa L.; cv 'I Kong Pao') after short term (48 hours) exposure to NaCl (200 mM) or Na2SO4 (100 mM).
Twenty five days old rice seedlings were exposed to 0, 200 mM NaCl or 100 mM Na2SO4 for 48 hours in hydroponic culture. Comparison between control and salt-stressed plants were done at the shoot and the root levels. The essays were replicated twice on two independent plant cultures.

overall_design: 12 samples, three condition experiment, control (0 mM NaCl or Na2SO4) vs. salt-treated (200 mM NaCl or 100 mM Na2SO4). Biological replicates: 2 replicates (taking control as reference) for comparison NaCl-stressed shoot, Na2SO4-stressed shoot, NaCl-stressed root, Na2SO4-stressed root and 2 replicates (taking NaCl as reference) for comparison Na2SO4-stressed shoot as well as Na2SO4-stressed root.

last: Irakoze

first: Stanley

last: Lutts

first: Hermann

last: Prodjinoto

first: Gervais

last: Rufyikiri

first: Séverin

last: Nijimbere

first: Muriel

last: Quinet


title: Transcriptional Heterogeneity within the Glucocorticoid Response

status: Public on Mar 26 2020

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

summary: Steroid hormone receptors such as the Glucocorticoid Receptor (GR) mediate the transcriptional response to hormones and are frequently targeted in the treatment of human diseases. Experiments using bulk populations of cells have provided a detailed picture of the global transcriptional hormone response but are unable to interrogate cell-to-cell transcriptional heterogeneity. To examine the glucocorticoid response in individual cells, we performed single cell RNA sequencing (scRNAseq). The transcriptional response to hormone was robustly detected in individual cells and scRNAseq provided additional statistical power to identify over 100 GR-regulated genes that were not detected in bulk RNAseq. scRNAseq also revealed a large degree of cell-to-cell variability in the hormone response. On average, individual hormone-treated cells showed a response at only 30% of the total set of GR target genes. Understanding the basis of this heterogeneity will be critical for the development of more precise models of steroid hormone signaling.

overall_design: Single-cell RNAseq and bulk total RNAseq in A1-2 human breast cancer cells

first: Brian

last: Papas

first: Kevin

middle: W

last: Trotter

first: Trevor

middle: K

last: Archer