title: Microarray Analysis of Striatal Tissue derived RNA isolated from Chronic Levodopa (L-DOPA) treated Parkinsonian and Dyskinetic (LID) Rats as compared to Parkinsonian Disease (PD) Control Rats

city: Omaha

first: SHETTY RAVI

last: DYAVAR

state: NE

address: 4040 EMILE ST

department: Pharmacy Practice and Science

institute: University of Nebraska Medical Center

summary:
We compared differential gene expression between Striatal tissue derived RNA isolated from Chronic Levodopa (L-DOPA) treated (L-Dopa methyl ester plus benserazide were given at 25 mg/kg and 6.25 mg/kg dose) -
Parkinsonian and Dyskinetic Rats  (LID Rats) for 8 days as compared to Parkinsonian Disease Control Rats (PD Control Rats). The hypothesis tested in the present study was that whether Inflammation has any role in Chronic Levodopa Induced Dyskinesia in Rats of Parkinson's disease model-
as compared to Control Rats with Prakinson's disease by performing differential gene expression and pathway analyses.

overall_design: On Day 8 Post Chronic Levodopa treatment, the total RNA was extracted from striatal tissue of Chronic Levodopa (L-DOPA) treated Parkinsonian and Dyskinetic (LID) and Rats with Parkinsonian Disease (PD) Controls.

first: Shetty

first: Stella

last: Papa


title: The contribution of FGFR1 to the development of SCLC is dictated by the cell-of-origin

status: Public on Mar 27 2020

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

type: Expression profiling by high throughput sequencing

summary: Enhanced RAF/MEK/ERK signaling plays an obligatory role in many different types of cancer. Although genetic lesions promoting its aberrant activation are found in lung adenocarcinoma (LADC), the biological role of this pathway is not well documented in small cell lung cancer (SCLC).  Here we explored the role of this pathway in SCLC and the broader class of tumors with neuroendocrine (NE) differentiation by introducing a constitutively active form of Fibroblast growth factor receptor 1 (Fgfr1) together with biallelic inactivation of Rb1 and Trp53 in mouse lung.  Our data show that FGFR1 expression primarily results in LADC but also in NE tumors depending on the cell-of-origin. FGFR1 activation selectively promoted NE bronchial lesions in a novel lung cell subpopulation, whereas it impaired progression of typical central SCLC initiated from CGRP-expressing NE cells, which is believed to be the most prominent cell-of-origin of SCLC.  Strikingly, FGFR1 activation was well tolerated by K14-expressing cells that were efficiently transformed into SCLC and other NE lesions.  Taken together, our results indicate that FGFR1 can serve either as driver or suppressor of distinct lung cancer subtypes depending on the cell-of-origin, which should be taken into account when considering FGFR1 as a therapeutic target.

overall_design: RNAseq samples were derived from 24 mice that developed SCLC. The role of the MAPK-pathway was assessed introducing a constitutively active form of Fibroblast growth factor receptor 1 (Fgfr1) together with biallelic inactivation of Rb1 and Trp53 in mouse lung. Tumors from Fgfr1 mice were compared to tumors from mycl and control mice. Furthermore, multiple adenovirus were tested (Ad5-CMV-Cre, Ad5-CGRP-Cre, Ad5-SPC-Cre). These combinations resulted in differences in histology and location of the tumors in mice.

first: Giustina

last: Ferone

first: Ton

last: Berns


title: Expression analysis of genes modulated after knock-down of lncRNA GUARDIN.

city: hefei

first: sun

last: xuedan

address: daoxiangcun

country: China

institute: ustc

summary: The long non-coding RNA GUARDIN functions to protect genome stability. Inhibiting GUARDIN expression can alter cell fate decisions towards senescence or apoptosis, but the underlying molecular signals are unknown. In this study we knockdown GUARDIN by shRNA and analyze the effect on gene expression in A549 cell line.

overall_design: Gene Expression profile was measured following shRNA mediated knock down of GUARDIN in A549 Cell lines

first: Xuedan

last: Sun

first: Rick

middle: F

last: Thorne

first: Xu

middle: D

last: Zhang

first: Miao

last: He

first: Shanshan

last: Feng

first: Xiaoying

last: Liu

first: Mian

last: Wu


title: Mitochondrial carrier homolog 2 (MTCH2) is necessary for AML survival

status: Public on Mar 25 2020

city: Toronto

first: Dilshad

middle: Hussain

last: Khan

state: Ontario

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Through a CRISPR screen to identify mitochondrial genes necessary for the growth of AML cells, we identified the mitochondrial outer membrane protein MTCH2 (Mitochondrial Carrier Homolog 2).  In AML, knockdown of MTCH2 decreased growth, reduced engraftment potential of stem cells and induced differentiation. Inhibiting MTCH2 altered in AML cells increased nuclear pyruvate and pyruvate dehydrogenase that induced histone acetylation and subsequently promoted the differentiation of AML cells. Thus, we have defined a new mechanism by which mitochondria and metabolism regulate AML stem cells and gene expression.

overall_design:
Examination of H3K27ac histone modification in TEX cells (AML cell line) upon MTCH2 knockdown by shRNA and treatment with or without CBP/p300 inhibitor, C646.
Please note that each processed data was generated from all replicates (R1, R2, R3) and is linked to the corresponding *R1 sample records.

first: Aaron

last: Schimmer

middle: H


title: Transcriptomic effects of insulin Lantus M1 on human internal mammary arteries

city: Oxford

first: Nadia

last: Akawi

address: Headley Way

country: United Kingdom

institute: John Radcliffe Hospital

summary: Internal mammary arteries collected from diabetic and non-diabetic patients were treated with insulin Lantus M1

overall_design: We incubated serial internal mammary artery (IMA) segments from n=6 patients (3 non-diabetic patients & 3 diabetic patients) with insulin 10nM for 6h

first: Ioannis

last: Akoumianakis

first: Chralambos

last: Antoniades


title: Characterization of GJB2 cis-regulatory elements in the DFNB1 locus

status: Public on Mar 26 2020

city: BREST

first: Stéphanie

last: MOISAN

address: 22 avenue Camille Desmoulins

department: Functional Genetics

country: France

institute: INSERM UMR 1078

summary: Although most disease-causing variants are within coding region of genes, it is now well established that cis-acting regulatory sequences, depending on 3D-chromatin organization, are required for temporal and spatial control of gene expression. Disruptions of such regulatory elements and/or chromatin conformation are likely to play a critical role in human genetic disease. Hence, recurrent monoallelic cases of the most common hereditary type of nonsyndromic hearing loss (i.e. DFNB1) carrying out only one identified pathogenic allele, led to strongly suggest the presence of uncharacterized distal cis-acting elements in the missing allele. Herewith, we study the spatial organization of a large DFNB1 locus encompassing the gap junction protein beta 2 (GJB2) gene, the most frequently mutated gene in this inherited hearing loss, with the chromosome conformation capture carbon copy technology (5C). By combining this approach with functional activity reporter assays and mapping of CCCTC-binding factor (CTCF) along the DFNB1 locus by quantitative real-time PCR chromatin immunoprecipitation, we identify a novel set of cooperating GJB2 cis-acting elements and propose a DFNB1 three-dimensional looping regulation model. A loop chromatin forming, allows bringing closer enhancers to the GJB2 promoter, but also avoids GJB2 silencing with an enhancer-blocking insulator activity.

overall_design: We mapped the interaction profile of the GJB2 promoter within the 1025 kb DFNB1 locus with 5C-seq in five HNEC samples isolated from healthy different individuals.

last: Moisan

first: Anaïs

last: Le Nabec

first: Alicia

last: Quillévéré

first: Cédric

last: Le Maréchal

first: Claude

last: Férec


title: Paeonia lactiflora extract suppresses cisplatin-induced muscle wasting via donwnregulations of muscle-specific E3 ubiquitin ligases

status: Public on Mar 28 2020

city: Seoul

first: Minwoo

last: Park

address: 25, Seonyu-ro 13-gil, youngdeungpo-gu

department: Research & Development

country: South Korea

institute: ebiogen

summary: Cisplatin is a broad-spectrum anti-cancer drugs used in diverse types of cancer, however, muscle wasting is one of the most common side effects of cisplatin chemotherapy. This study aimed to elucidate the effects of an ethanol extract of the root of Paeonia lactiflora Pall. (Radix Paeoniae, RP) on cisplatin-induced muscle wasting along with its molecular mechanism.

overall_design: C57BL/6 mice (4 weeks old, female) were used to induce muscle wasting by intraperitoneal injection of 3mg/kg cisplatin without or with oral admininstration of 100 mg/kg RP. Gastrocnemius muscle tissues were collected from the untreated group (designiated as Normal) and cisplatin-treated  group (designated as Cisplatin), and cisplatin and RP-treated group (designiated as RP). RNAs extracted from the gastrocnemius muscle tissues were analyzed via RNAseq

first: Yoosik

last: Yoon

first: Jaewoong

last: Jang


title: The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains II (re-analysis)

city: Baltimore

first: Karen

last: Reddy

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

country: USA

institute: Johns Hopkins University

type:
Other
Third-party reanalysis

summary: Three-dimensional (3D) genome organization is thought to be important for regulation of gene expression. Chromosome conformation capture-based studies have uncovered ensemble organizational principles such as active (A) and inactive (B) compartmentalization. In addition, large inactive regions of the genome associate with the nuclear lamina, the Lamina Associated Domains (LADs). Here we investigate the dynamic relationship between A/B-compartment organization and the 3D organization of LADs. Using refined algorithms to identify active (A) and inactive (B) compartments from Hi-C data and to define LADs from DamID, we confirm that the LADs correspond to the B-compartment. Using specialized chromosome conformation paints, we show that LAD and A/B-compartment organization are dependent upon chromatin state and A-type lamins. By integrating single-cell Hi-C data with live cell imaging and chromosome conformation paints, we demonstrate that self-organization of the B-compartment within a chromosome is an early event post-mitosis and occurs prior to organization of these domains to the nuclear lamina.

overall_design:
Hi-C data were mapped using BWA mem followed by processing, normalization, and analysis using HiFive. DamID data were segmented using LADetector.
------------------------------
Hi-C data were aligned using BWA mem. Hi-C data paired ends were aligned independently. All reads were mapped using default parameters.
Hi-C data were analyzed using HiFive v1.4. Fragments were filtered to include only those with at least one interaction. Counts were normalized using the Binning algorithm, normalizing for GC content, fragment length, and mappability using 20, 20, and 10 bins, respectively. GC content and fragment length parameters were split into evenly sized bins and optimized while mappability was split into fixed bin sizes and seeded but not optimized. Seed compartment states were generated using a bin size of 10 kb, dynamically binning with a minimum read count of 3 and finding the sign of the first eigenvector of the log of the observed over expected bin values. Likelihood compartment scores were calculated using a burnin period of 20 iterations and going to a maximum of 200 iterations. Only interactions of 500 Kb or greater were used and fragments were filtered to have at least five interactions greater than 500 Kb. The minimum reads for modeling the distance curve was 10,000 and each iteration the top scoring 50% of state-changing bins were updated.
ES LAD calls were found using the original analysis log2 ratio scores. LADs were determined using the LADetector (https://github.com/thereddylab/pyLAD) segmentation module with default parameters.
DamID-array data were processed using LADetevtor v1 (Harr et al., doi: 10.1083/jcb.201405110) where they were quantile normalized (preprocessCore R package), smoothed and segmented (DNAcopy R package). Segmentation was consolidated, further refined and LADs were returned. LADs from individual arrays were merged. non-LADs were defined as complement regions to LADs.
mm8, mm9
BigWig files were generated using the UCSC bedGraphToBigWig converter tool. Compartment scores were created using HiFive. Bed file was created using LADetector. .LADs and .nonLADs bed files were defined by LADetector v1 and complement nonLAD regions were defined by Galaxy tool "Complement intervals of a dataset".
---------------------------------
GSM2026269, GSM202670, GSM2026271: MEF_mm9_boundary_10K.bw
GSM426758: mm9_LaminB1.bed
GSM1372713, GSM1372714: MEF_Chr11_Chr12_mm8.LADs.txt, MEF_Chr11_Chr12_mm8.nonLADs.txt

first: Teresa

middle: R

last: Luperchio

first: Michael

middle: G

last: Sauria


title: Expression data from rat vocal fold at different periods after vocal fold injury (miRNA)

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Vocal cord healing is a dynamic process, and many genes and proteins are involved, which play varying roles at different regeneration stages after injury. Previous studies have shown that inflammatory responses occur at the early stage of vocal cord injury, where the fibroblasts proliferate exuberantly with intensive secretion and deposition of ECM. These activities reach the peak at 3-7 days and their intensity begins to decline 15 days later. A study based on the dermal system has shown that ECM remodeling during the repair of injury can last for several months. However, few studies have been conducted as to the dynamic changes of gene and microRNA expressions during the healing process of vocal cord injury. Plotting these changes will facilitate the understanding about the physiological changes during healing and the identification of key time points and target genes and microRNAs in fibrosis formation.

overall_design: 20 animals were randomly divided into 4 experimental groups based on time of sacrifice: uninjured control, and 1, 4 and 8 weeks after injury. Following sacrifice, the larynx was harvested, and the bilateral vocal folds were dissected under magnification.

first: Haizhou

last: Wang

first: Wen

last: Xu


title: The effects on oncogenic pathway, signaling, by RSK2 N-terminal kinase inhibitor (BI-D1870) in Mantle cell lymphoma-derived cell lines.

city: Kyoto

first: Junya

last: Kuroda

address: 465 Kajii-cho Kamigyo-ku

department: Division of Hematology and Oncology

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: RSK2 is a serine/threonine kinase downstream signaling mediator in the RAS/ERK signaling pathway and may be a therapeutic target in mantle cell lymphoma (MCL). RSK2-Ser227 in the N-terminal kinase domain (NTKD) of RSK2 was found to be ubiquitously active in five MCL-derived cell lines and in tumor tissues derived from five MCL patients. BI-D1870, an inhibitor specific to RSK2-NTKD, caused RSK2-Ser227 dephosphorylation, and thereby, induced dose-dependent growth inhibition via G2/M cell cycle blockade and apoptosis. Comparative gene expression profiling of the MCL-derived cell lines showed that inhibition of RSK2-Ser227 by BI-D1870 caused downregulation of oncogenes, such c-MYC and MYB; anti-apoptosis genes, such as BCL2 and BCL2L1; genes for B cell development, including IKZF1, IKZF3 and PAX5; and genes constituting the B cell receptor signaling pathway, such as CD19, CD79B and BLNK. These findings show that targeting of RSK2-Ser227 enables concomitant blockade of pathways that are critically important in B cell tumorigenesis.

overall_design: Mantle cell lymphoma-derivedcell lines (Jeko-1 and KPUM-YY1 cells) were treated with BI-D1870 at IC80 for each cell line. After 6 hours of culture, total RNA was isolated and hybridized on microarrays with Clariom S array (Affymetrix, Santa Clara, CA), a GeneChip WT Plus Reagent Kit (Thermo Fisher Scientific, Waltham, MA) and a GeneChip Scanner 7G (Affymetrix).

first: Yayoi

last: Matsumura-Kimoto

first: Taku

last: Tsukamoto

first: Katsura

last: Mizushima


title: Transcriptome analysis of SRD5A1 knockdown (Dox) and control (KD) in colorectal cancer

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

summary: Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expression in colon cancer cells when SRD5A1 was knocked down.

overall_design: Examination of  two cell types

first: Rongfang

first: Mengjie

last: Guo


title: CsFUL1 and auxin participate in the CsCLV3-CsWUS mediated carpel number variation in cucumber (Cucumis sativus L.)

city: Shanghai

first: Hailing

last: Zi

address: Chenhua road3888

institute: Shanghai center for plant stress biology

summary: The carpel number (CN) is an important fruit trait affecting fruit shape, size, and internal quality in cucumber. CsCLAVATA3 (CsCLV3) was previously showed to be the simply inherited gene responsible for carpel number variation in cucumber, but the molecular mechanism of CsCLV3 regulating carpel number remains elusive. Here, we found that the expression of CsCLV3 was negatively correlated with carpel number variation in different cucumber lines. Knock down of CsCLV3 by RNAi led to increased number of petals and carpels, suggesting that CsCLV3 functions as a negative regulator for floral organ number in cucumber. WUSCHEL (WUS) has been well characterized to promote CLV3-expressing stem cell activity in a non-cell autonomous manner to regulate meristem maintenance and floral organ number. However, here we found the expression region of CsCLV3 overlaps with CsWUS in the basal domain of meristem, and CsCLV3 interact with CsWUS at the protein level through binding to the WUS-box motif. Overexpression of CsFUL1, a FRUITFULL-like MADS-box gene involved in fruit length regulation, resulted in increased number of floral organs in cucumber. Biochemical analyses indicated that CsFUL1 can directly bind to CsWUS promoter to stimulate its expression. Further, we found that auxin participates in carpel number variation in cucumber through physical interaction of AUXIN RESPONSE FACTOR 14 (CsARF14) and CsWUS. Therefore, CsFUL1 and CsARF14 are two new players in the WUS-CLV pathway in determining carpel number variation in cucumber.

overall_design: Fruits at anthesis day of 32X and GFC cucumber plants were used for RNA-seq analysis. Three biological replicates were performed for each sample.

first: Gen

last: Che

first: Jianyu

last: Zhao

first: Xiaofeng

last: Liu

first: Ran

last: Gu

first: Zhihua

last: Cheng

first: Junjun

last: Shen

first: Zhongyi

first: Xiaofei

last: Song

first: Liying

last: Yan

first: Yiqun

last: Weng

first: Renyi

first: Xiaolan

last: Zhang


title: Comparative study of gene expression in lower and upper first molar cap stage tooth germs of DUHi and FVB mice

city: Lyon

first: Sophie

last: PANTALACCI

address: 46 Allée d'Italie

department: Ecole Normale Supérieure de Lyon

institute: LBMC

summary: The dataset aims at comparing gene expression in the developing lower and upper first molars of two mouse strains: DUHi and FVB. We studied molar tooth germ an early cap stage, looking for differences in activation-inhibition mechanisms that promote tooth formation. 19202 genes are in common between FVB and reference strain C57B6 and have a MGI annotation. Out of these genes, 2234 genes (11.6%) presented a significant difference of expression between the mapping on the reference strain C57B6 and the mapping on FVB strain (DESeq2, adjusted P value < 0.05, considering the mapping effect that is with 12 replicates). This is presumably a mapping artifact, due to the sequence divergence between mouse strains. These genes were removed, and the remaining 16,968 genes were retained for further analysis. 3619 genes were found to be differentially expressed between the two strains in the lower and upper molar (jaw+strain)

overall_design: The dataset comprises 3 samples per condition: lower FVB germ, upper FVB germ, lower DUHi germ, upper DUHi germ. For each strain, we obtained 3 embryos taken from the same litter and ordered according to their body weight: 196, 219 and 239mg for DUHi embryos, 195, 215 and 233 mg for FVB embryos. Lower and upper molar germs were taken from the same embryo. Thus, we have 3 replicates for each condition. These replicates can also be viewed as tight timeseries. 3619 genes were found to be differentially expressed between the two strains in the lower and upper molar (jaw+strain)

last: Pantalacci

first: Marie

last: Sémon

first: Luke

last: Hayden

first: Maurine

last: Vilcot


title: Differentially expressed genes in the livers of mice exposed to microcystin-LR (MC-LR)

first: Yanyan

address: 73 East Beijing Road, Nanjing 210008, P.R. China

institute: Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences

summary: To explore the molecular mechanisms involved in the toxicity in the livers exposed to MC-LR at the environmental level, the hepatic transcriptome was performed.  A total of 210 genes were differentially expressed (P<0.05, |fold change|≥2) in response to MC-LR exposure; among them, 143 genes were significantly upregulated, and 67 genes were downregulated. Pathway enrichment analysis identified the top biological functions associated with the genes differentially expressed in response to MC-LR exposure, which were circadian regulation of gene expression, negative regulation of glucocorticoid receptor signaling pathway, the epoxygenase P450 pathway, regulation of insulin secretion, lipid metabolic process, and cell cycle pathway.

overall_design: Six-week-old male BALB/c mice were assigned randomly to two groups (one control and one treatment). Mice in treatment were exposed to 100 μg/L microcystin-LR through drinking water for 12 months. The control mice were given normal sterile water. At the end of exposure time, three liver samples from independent mice in each group were obtained to analyze the gene expression by microarray assay. Total RNA was extracted, amplified and labeled using a One-Color LowInput Quick Amp Labeling Kit (Agilent, Santa Clara, CA, USA). Labeled cRNA was purified with an RNeasy Mini Kit (Qiagen, Hilden, Germany). The slides were then hybridized with Cy3-labeled cRNA using Gene Expression Hybridization Kit in a hybridization oven (Agilent, Santa Clara, CA, USA), followed by washing in staining dishes (Thermo, Waltham, MA, USA) with Gene Expression Wash Buffer Kit (Agilent, Santa Clara, CA, USA). An Agilent Microarray Scanner was used to scan the slides. Data were extracted by the Feature Extraction software and normalized by the Quantile algorithm of Gene Spring software.

first: Yunjun

first: Yaojia

last: He

first: Lixiao

last: Wang


title: SIRP-α triggers tolerogenic training of resident alveolar macrophages after inflammation, leading to immune paralysis and increased susceptibility to secondary pneumonia

city: Nantes

first: Alice

last: Mollé

address: 30 bd Jean Monnet

institute: University of Nantes

summary: The reprogramming of alveolar macropahges (AM) in mice after resolution of primary bacterial or viral pneumonia induced poor phagocytic capacity for several weeks. The tyrosine kinase-inhibitory receptor, SIRP-α, played a critical role in the establishment of the microenvironment that induced tolerogenic training.

overall_design: Transcriptomic and epigenetic analyzes were made on uninfected mice (WT and SIRP-α KO) and 7 days after the infection was cured.

first: Antoine

last: Roquilly

first: Cedric

last: Jacqueline

first: Marion

last: Davieau

last: Molle

first: Abderrahmane

last: Sadek

first: Cynthia

last: Fourgeux

first: Paul

last: Rooze

first: Alexis

last: Broquet

first: Barbara

last: Misme-Aucouturier

first: Tanguy

last: Chaumette

first: Mickael

last: Vourc'h

first: Raphael

last: Cinotti

first: Nadege

last: Marec

first: Vanessa

last: Gauttier

first: Hamish

middle: E

last: McWillliam

first: Frederic

last: Altare

first: Jeremie

last: Poschmann

first: Jose

middle: A

last: Villadangos

first: Karim

last: Asehnoune


title: Functional analysis of maize Plant Elicitor Peptide-mediated immune signaling

city: La Jolla

first: Alisa

last: Huffaker

state: CA

address: 9500 Gilman Dr.

department: Cell & Developmental Biology

institute: U.C. San Diego

summary: Plant Elicitor Peptides (Peps) are conserved regulators of defense responses across diverse plant species and are multigene families in most species.  However, the functional relevance of Peps as multigene families remains largely undefined.  While Arabidopsis Peps appear largely redundant in function, previous work examining Pep-induced responses in maize implied specificity of function.  To better define function of individual ZmPeps, activities of each peptide were examined by assessing changes in defense-associated phytohormones, specialized metabolites and global gene expression patterns.  In addition to delineating individual ZmPep and ZmPEPR activities, these experiments led to a number of new insights into Pep signaling.  ZmPROPEP precursors were found to harbor multiple ZmPeps, a phenomenon not previously observed.  In all, seven new ZmPeps were identified and together the family members were found to have specific activities defined by relative magnitude of response output rather than uniqueness.   A striking correlation between ZmPep-elicited changes in levels of jasmonic acid and ethylene and the magnitude of induced defense responses was observed, indicating that ZmPeps regulate immune output through rheostat-like regulation of phytohormone levels.  Peptide structure-function studies and ligand-receptor modeling revealed structural features critical to ZmPep signaling function.  Structural analysis also led to identification of ZmPep5a as a potential antagonist peptide able to competitively inhibit activity of other ZmPeps, a regulatory mechanism not previously observed for this family.  Using heterologous expression assays, endogenous gene expression patterns and analysis of CRISPR/Cas9 generated knockout plants, ZmPEPR1 was found to be the dominant receptor regulating ZmPep-mediated anti-herbivore defenses in planta.

overall_design: Leaf 5 of V3 stage maize plants was excised and placed in glass vials containing either water or 5 micromolar solutions of ZmPeps; tissue was collected 12 hours post-treatment. For each treatment four biological replicates were generated. Microarray sample preparation and analysis was performed by the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR) gene expression core.

first: Elly

last: Poretsky


title: Genome-wide ATAC-seq maps in human CD4+ T cells stimulated or unstimulated in vitro

first: David

last: Flores Santa Cruz

state: Oxfordshire

address: Roosevelt Drive

department: Diabetes and Inflammation Laboratory

institute: Wellcome Centre for Human Genetics

summary: We report the application of ATAC-seq to CD4+ T cells stimulated with anti-CD3/CD28 T activator beads for four hours in culture versus CD4+ T cells cultured in medium alone.

overall_design: CD4+ T cells were enriched from whole blood using the RosetteSep human CD4+ T cell enrichment kit. Enriched cells were stimulated with anto-CD3/CD28 beads at a ratio of 0.3 beads / cell for four hours in X-VIVO + 1% human AB serum and penicillin/streptomycin antibiotic. Non-activated CD4+ T cells were cultured in medium alone for four hours. Nuclei from 50,000 CD4+ T cells were prepared and ATAC-seq libraries generated fo sequencing. Blood was obtained from two unrelated healthy donors recruited through the Cambridge BioResource.

first: John

last: Todd

first: Antony

middle: J

last: Cutler


title: Cancer associated fibroblasts from localised prostate cancer have a distinctive DNA methylation profile [Illumina EPIC]

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

summary: The current methods to distinguish slow-growing from aggressive localised prostate cancer at diagnosis are imprecise so aggressive tumours can sometimes be missed. In this study we examined whether the changes in the features of cancer associated fibroblasts (CAFs) from the surrounding tumour microenvironment can help identify high risk tumours. We show that CAFs have a distinct methylation profile versus non-malignant prostate fibroblasts (NPFs) including specific differentially methylated regions that distinguish higher grade prostate cancer.

overall_design: DNA methylation microarrays were used to interrogate human prostate fibroblasts from subjects with benign prostate hyperplasia and subjects with prostate cancer with different Gleason grades.

first: R

first: M

last: Lawrence


title: KLK6 expression in skin induces PAR1-mediated psoriasiform dermatitis and inflammatory joint disease

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: Kallikrein-related peptidase 6 (KLK6) is a secreted serine protease hypothesized to promote inflammation via cleavage of protease-activated receptors (PAR)1 and PAR2. KLK6 levels are elevated in multiple inflammatory and autoimmune conditions, but no definitive role in pathogenesis has been established. Here, we show that skin-targeted overexpression of KLK6 causes generalized, severe psoriasiform dermatitis with spontaneous development of debilitating psoriatic arthritis-like joint disease. The psoriatic skin and joint phenotypes are reversed by normalization of skin KLK6 levels and attenuated following genetic elimination of PAR1 but not PAR2. Conservation of this regulatory pathway was confirmed in human psoriasis using vorapaxar, an FDA-approved PAR1 antagonist, on explanted lesional skin from psoriasis patients. Beyond defining a critical role for KLK6-PAR1 signaling in promoting psoriasis, our results demonstrate that KLK6-PAR1-mediated inflammation in the skin alone is sufficient to drive inflammatory joint disease. Further, we identify PAR1 as a promising cytokine-independent target in therapy of psoriasis and psoriatic arthritis.

overall_design: RNA-seq was performed to identify genes with altered expression in skin from Klk6+ transgenic mice (n = 3 males, n = 2 females) as compared to WT mice (n = 3 males, n = 2 females).

first: Allison

middle: C

last: Billi

first: Johann

last: Gudjonsson

first: Nicole

middle: L

last: Ward


title: The lncRNA microarray analysis in EZH2-overexpressing breast cancer cell MCF7

first: Yu

last: Yu

state: Hai Dian

institute: Peking University Health Science Center

summary: To explore the potential target lncRNAs of EZH2 in breast cancer cells, we determined the lncRNA expression profiles in MCF7-control and MCF7-EZH2 overexpressing cells using lncRNA Microarray.

overall_design: EZH2-overexpressing breast cancer cells MCF7 were used for treatment group. Empty vector was transfected into MCF7 cells using for control group. Then, total RNAs were extracted for lncRNA chip preparation and analysis.

first: Hongquan

last: Zhang


title: Mutation of STERILE APETALA, a transcriptional regulator, is involved in pistil abortion and organ size in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

city: Shenyang

first: Shengnan

last: Huang

address: 120 Dongling Road Shenhe District Shenyang P.R. China

institute: Shenyang Agricultural University

summary: Pistil development is a complicated process in plants, and female sterile mutant is an ideal material for screening and cloning the pistil development-related genes. In our previous study, a female sterile mutant fsm (namely fsm1 here) was obtained from a Chinese cabbage DH line ‘FT’ using a combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. BraA04g009730.3C was predicted as the candidate gene for mutant fsm1. BraA04g009730.3C encoded STERILE APETALA (SAP), a transcriptional regulator, which played a role in regulating floral organ development. In this study, another female sterile mutant (namely fsm2) was derived from a population combining EMS mutagenesis and germinating seeds of ‘FT’. The phenotype of mutant fsm2 was consistent with that of fsm1, exhibiting pistil abortion, and smaller floral organs. Genetic analysis indicated that the phenotype of mutant fsm2 was controlled by a single recessive nuclear gene. Allelism testing showed that the mutant genes of fsm1 and fsm2 were allelic, named as Brfsm. A single-nucleotide mutation (G-to-A) in the first exon of BraA04g009730.3C caused a missense mutation from GAA (glutamic acid) to GGA (glycine) in mutant fsm2. Comparative transcriptome analysis on the pistils of wild-type ‘FT’ and mutant fsm1 revealed that a total of 3,855 differentially expressed genes (DEGs) were obtained, among which 29 genes related to ovule development and 16 genes related to organ size were identified. Based on the validation of qRT-PCR, we proposed the possible regulatory pathways whereby SAP may mediate pistil development in the fsm mutant. The mutation of BraA04g009730.3C in fsm plants was involved in the pistil abortion and smaller floral organ in Chinese cabbage. These results lay a solid foundation for elucidating the molecular mechanism of pistil development in Chinese cabbage.

overall_design: The RNA from the pistils of a female sterile mutant fsm1 and its wild type‘FT’at the full-bloom stage in Chinese cabbage were sequenced by RNA-Seq, in triplicate.

first: Wenjie

last: Liu

first: Junjie

last: Xu

first: Zhiyong

first: Hui

last: Feng


title: Nuclear aconitase regulates heterochromatin formation by interacting with Chp1

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

summary: Aconitase is a highly conserved metabolic enzyme for TCA cycle. In Schizosaccharomyces pombe, an aconitase (Aco2) is localized in both mitochondria and the nucleus, apart from an exclusively mitochondrial one (Aco1). We investigated the role of nuclear Aco2, and present evidences that it interacts with Chp1, a heterochromatin-associated HP1 protein, and acts as an anti-silencing factor. Nuclear depletion of Aco2 by deleting nuclear localization signal (aco2ΔNLS) suppressed the gene-silencing defects of RNAi mutants Δago1 and Δdcr1 at the centromere, where RNAi-mediated heterochromatin formation prevails. The aco2 mutation caused an increase in Chp1 binding to the centromeric repeats, with concomitant increase in the level of dimethylated histone H3K9, reflecting restoration of heterochromatin formation. Co-precipitation revealed that Aco2 interacted directly with Chp1 via the N-terminal region (1-235 aa), where the chromodomain (20-75 aa) that recognizes methylated H3K9 is located. Genome-wide analysis revealed that the aco2ΔNLS mutation caused elevation in the level of H3K9me2 not only at heterochromatic but also at euchromatic regions in the Δago1 mutant background. We also found that the single aco2ΔNLS mutation caused aberrant gene silencing at sub-telomeric and some euchromatic coding genes. These results demonstrate that Aco2 inhibits heterochromatin assembly over a wide range, by interfering with Chp1. Its contribution is prominent in the RNAi-independent heterochromatic region or in the absence of RNAi effector complex RITS that holds Chp1. Taken together, this work shows a clear example of a metabolic enzyme that can function in the nucleus as an epigenetic modulator of gene expression.

overall_design: For ChIP-seq experiment (S. pombe): Genome-wide distributions of H3K9me2 in wild-type, aoc2∆N, and ago1∆ x aco2∆N cells. Genome-wide distributions of Chp1 in wild-type cells. For RNA-seq experiment: Strand-specific mRNA-Seq of wild type and aoc2∆N cells

first: Soo-Jin

last: Jung

first: Yoon-Jung

first: Daeyoup

last: Lee

first: Jung-Hye

last: Roe


title: BRCA1 mutational complementation induces synthetic viability

status: Public on Mar 24 2020

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

summary: We report DNA resection length after induced double stranded breaks in specific genomic loci with the expression of the AsisI restriction enzyme

overall_design:
Exponentially AsiSI-expressing MEFs with different Brca1 alleles were treated with 1uM doxocyclin (DOX) for 24 hours and then, for 5 hours with 4-OHT, resulting in the nuclear translocation of AsiSI

BRCA1 alleles used in this study:
CC: Deletion 4287 to 4295
Del 11:  Deletion   874 to 4188

first: Joseph

last: Nacson

first: Andre

last: Nussenzweig

first: Neil

last: Johnson


title: Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis

city: New York

first: Emma

last: Guttman

state: New York

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mt. SInai

summary: Background: Atopic dermatitis (AD) is a prevalent inflammatory skin disease with a complex pathogenesis, involving immune cell and epidermal abnormalities. Despite whole tissue biopsy studies that have advanced the mechanistic understanding of AD, single-cell-based molecular alterations are largely unknown. Objective: To construct a detailed, high-resolution atlas of cell populations, and to assess variability in cell composition and cell-specific gene expression in the skin of AD patients versus controls.  Methods: We performed single-cell RNA-sequencing on skin biopsies from 5 patients with AD (4 lesional samples, 5 non-lesional samples) and 7 healthy control subjects, using 10x Genomics. Results: We created transcriptomic profiles for 39,042 AD (lesional and non-lesional) and healthy skin cells. Fibroblasts demonstrated a novel COL6A5+COL18A1+ subpopulation that was unique to lesional AD, and expressed CCL2 and CCL19 cytokines. A corresponding LAMP3+ dendritic cell (DC) population that expressed the CCL19 receptor CCR7 was also unique to AD lesions, illustrating a potential role for fibroblast signaling to immune cells. Lesional AD samples were characterized by expansion of inflammatory DCs (CD1A+FCER1A+) and tissue resident memory T-cells (CD69+CD103+). The frequencies of type 2 (IL13+)/type 22 (IL22+) T-cells were higher than type 1 (IFNG+) in lesional AD, while this ratio was diminished slightly in non-lesional AD and further in controls. Conclusion: AD lesions were characterized by expanded type 2/type 22 T-cells and inflammatory DCs, and a unique inflammatory fibroblast that may interact with immune cells to regulate lymphoid cell organization and type 2 inflammation.

overall_design: Lesional/non-lesional skin biopsies were taken from the extremities of 5 moderate-to-severe AD patients and 7 matching controls. Biopsies were cryopreserved and processed by 10x Genomics. The library was sequenced on the Illumina HiSeq 2500 platform.

first: Helen

last: He

first: Hemant

last: Suryawanshi

first: Pavel

last: Morozov

first: Jesús

last: Gay-Mimbrera

first: Ester

last: Del Duca

first: Hyun

last: Kim

first: Naoya

last: Kameyama

first: Yeriel

last: Estrada

first: Evan

last: Der

first: James

last: Krueger

first: Juan

last: Ruano

first: Thomas

last: Tuschl

last: Guttman-Yassky


title: Whole-transcriptome quantitative analysis of WT versus Ikzf4-/- CD4+ T cells cultured in Th1-polarizing conditions

city: Columbus

first: Ken

last: Oestreich

state: Ohio

address: 460 W 12th Avenue, 740 Biomedical Research Tower

institute: The Ohio State University

summary: Purpose: To evaluate transcriptome-wide alterations  in CD4+ T cells cultured under Th1-polarizing conditions in the absence of the Ikaros zinc finger transcription factor Eos via RNA-seq analysis.

overall_design: Naïve CD4+ T cells (wild type or Ikzf4-/- (Eos KO)) were stimulated on plate-bound anti-CD3 and anti-CD28 in the presence of Th1-polarizing conditions for 72h. Total RNA was analyzed for alterations in global changes to the transcriptome resulting from the absence of the transcription factor Eos.

first: Michael

last: Powell

first: Bharath

middle: K

last: Sreekumar

first: Patrick

last: Collins


title: iCLIP-Seq analyses of YTHDF3-bound RNAs

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

summary: We found that YTHDF3 work as m1A reader,but the potential substrate RNA remain elusive.

overall_design: iCLIP-Seq analyses of YTHDF3-bound RNAs from normoxia and hypoxia trophoblast cells

first: Qingliang

last: Zheng


title: Pan-HDAC Inhibition Reverses the Warburg Effect and Leads to Metabolic Vulnerabilities

first: Markus

last: Siegelin

institute: Columbia University Medical Center

summary: We report the HDAC inhibiton of glioblastoma cells causes histone H3K27 acetylation and leads to upreguated OXPHOS master regulator PGC1a which then leads to an increase in mitochondrial fusion, mitochondrial biogenesis and higher mitochondrial oxygen consumption rate coupled with increased fatty acid oxidation (FAO).

overall_design: Examination of histone H3K27ac modifications and RNA polymerase accumulating in 3 cell types under control or drug treated condition

first: Yiru

last: Zhang


title: Peritoneal macrophage heterogeneity in decompensated liver cirrhosis

city: Jena

first: Sven

last: Stengel

address: Am Klinikum 1

department: Clinic for Internal Medicine IV

country: Germany

institute: Jena University Hospital

summary:
Peritoneal macrophages (PM) are thought to regulate peritoneal inflammation and control bacterial infections in decompensated liver cirrhosis. The aim of this study was to characterize human PM heterogeneity.
Employing CD206 surface expression, we identified subsets of human large (LPM) and small (SPM) PM, which differed in granularity and maturation states. FACS-sorted LPM from patients with decompensated cirrhosis revealed discrete transcriptome clusters, comprising more than 4000 differentially regulated genes involved in cell cycle, metabolism, and immune signaling.

overall_design: Mononuclear cells from patients with decompensated liver cirrhosis (n=4) were purified from ascitic fluid by Ficoll density gradient centrifugation using Lympholyte-H (Cedarlane). Peritoneal macrophages were enriched using positive magnetic assisted cell sorting (Milteny Biotec). PM subsets (SPMs and LPMs) were sorted by flow cytometry on a FACSAria III (BD Biosciences) using monoclonal antibodies against CD14 (PE) and CD206 (APC or FITC). Sorted cells were seeded in cell culture plates at a density of about 100k cell per cm2 (0.75 – 1.0 mio cells per well) and treated with 10 ng/ml E. coli lipopolysaccharide (LPS) for 3h or left untreated. Total RNA was isolated and microarray analysis was performed by a commercial transcriptomics provider (Aros Applied Biotechnology, Eurofins, Aarhus, Denmark) using the Affymetrix Human Clariom S HT 24 array plate and the WT plus kit for labeling. CHP files were created using Transcriptome analysis concole (TAC, ThermoFisher Scientific). GC Correction, SST (Signal Space Transformation), RMA background and quantile normalization were applied. Differential gene expression between SPMs and LPMs was analyzed in steady state or following LPS stimulation. Before extracting differentially expressed genes, patient dependent differences were eliminated using repeated measure option (pairwise analysis or batch effect removal) of TAC software package.

first: Tony

last: Bruns


title: m1A-Seq analyses of trophoblast upon hypoxia or normoxia

summary: N1-methyladenosine (m1A) is one of messenger RNA modification in eukaryotes, but the potential roles of m1A methylated mRNA in trophoblast upon hypoxia remain elusive.

overall_design: m1A-Seq analyses of mRNAs from normoxia and hypoxia trophoblast cells


title: Interpreting an apoptotic corpse as anti-inflammatory involves a chloride sensing pathway

first: Justin

middle: Shaun Arnold

last: Perry

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

summary: Phagocytes in different tissues recognize and remove apoptotic cells via the process of efferocytosis. Although it is well-established that efferocytosis elicits an anti-inflammatory response by phagocytes, the molecules and mechanisms that enforce this response in phagocytes are still being defined. In attempting to decipher gene programs induced after a phagocyte ingests a dying cell, we uncovered a chloride-sensing signaling pathway that controls both the ‘appetite’ of a phagocyte and how a phagocyte responds after corpse uptake. First, we noted that within phagocytes that have ingested a corpse, the solute carrier 12 (SLC12) family members SLC12A2 and SLC12A4 are actively modulated. Interfering with SLC12A2, either genetically or pharmacologically, led to significantly enhanced corpse uptake per phagocyte, while loss of SLC12A4 inhibited corpse uptake. Interestingly, when phagocytes with disrupted SLC12A2 engulfed apoptotic corpses, the typical homeostatic efferocytosis signature was perturbed, characterized by loss of the canonical anti-inflammatory program and replaced by pro-inflammatory and oxidative stress-associated gene programs. In further mechanistic studies, we observed efferocytosis was also regulated by the chloride-sensing pathway upstream of SLC12A2, including the kinases WNK1-OSR1-SPAK, and this involved chloride entry/exit across the plasma membrane of phagocytes during corpse engulfment. We also show that the ‘switch’ to pro-inflammatory sensing of apoptotic cells is specifically due to disruption of the chloride-sensing pathway and not due to corpse overload or poor degradation, and that the pro-inflammatory gene signature can be reversed using a chloride ionophore. Collectively, these data identify the WNK1-OSR1-SPAK-SLC12A2/SLC12A4 chloride-sensing pathway and chloride flux in phagocytes as key modifiers of how a phagocyte interprets an engulfed apoptotic corpse.

overall_design: The first experiment consisted of four conditions: Phagocytes (LR73 cells) alone, treated with cytochalasin-D, co-cultured with apoptotic Jurkat lymphoma cells, or treated with cytochalasin-D and co-cultured with apoptotic Jurkat lymphoma cells. The second experiment consisted of two conditions, wildtype or Slc12a2-deficient LR73 phagocytes. Phagocytes were co-cultured with apoptotic Jurkat cellsfor 2h, then actively engulfing phagocytes (i.e. CypHer5E+) were FACS-sorted prior to RNA isolation. All conditions consisted of four biological replicates.

middle: S

first: Sho

last: Morioka

first: Christopher

middle: B

last: Medina

first: J

last: Iker Etchegaray

first: Brady

last: Barron

last: Raymond

last: Lucas

first: Suna

last: Onengut-Gumuscu

first: Eric

last: Delpire

first: Kodi

last: Ravichandran


title: Examination of gene expression changes after exposure to 29 chemicals in rat primary hepatocytes

city: Research Triangle Park

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

summary: In this study we examined transcriptional responses to 29 ToxCast chemicals in dose-response format. The chemicals were selected because in vitro transcriptional effects could be extrapolated to in vivo effects including liver cancer and steatosis incidences using in vitro to in vivo extrapolation.

overall_design: Rat primary hepatocytes were plated on collagen-coated plates and treated with DMSO (0.1%) or 6 concentrations of chemical (100 or 33.3 uM as the top concentration with a log2 step-down of dose level). Cells were treated for 24 hrs. Purified RNA was examined for gene expression changes using the rat TempO-Seq targeted RNA-Seq platform (BioSpyder, Inc; Carlsbad CA). The following chemicals were examined in dose-response format: Acetochlor, Alachlor, Ametryn, Bensulide, Bisphenol A, Carbaryl, Cyclanilide, Cyproconazole, Cyprodinil, Di-2-ethylhexyl phthalate, Dichlobenil, Dimethenamid, Dithiopyr, Etoxazole, Fludioxonil, Flusilazole, Hexaconazole, Imazalil, Isoxaflutole, Oxadiazon, Perfluorooctanoic acid, Perfluorooctanesulfonate, S-Bioallethrin, Simazine, Tetraconazole, Triadimefon, Triclosan, Triflumizole, Triticonazole. In addition, a number of reference chemicals were examined at one concentration (17beta-estradiol, Dexamethasone, GW4046, Oltipraz, Pregnenolone 16-alpha-carbonitrile, Sulforaphane, TCPOBOP, Testosterone, WY-14,643).

first: N

last: Ryan


title: Long non-coding RNA MANCR is a target of BET bromodomain protein BRD4 and plays a critical role for cellular migration and invasion abilities of prostate cancer

status: Public on Mar 23 2020

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Androgen receptor (AR)-negative castration-resistant prostate cancer (CRPC) is highly aggressive and resistant to current therapies.  BET bromodomain protein BRD4 binds to super-enhancers (SEs) that drive high expression of oncogenes in many cancers.  A BET inhibitor JQ1 has been found to suppress malignant phenotypes of prostate cancer cells, however, the target genes of JQ1 remains largely unknown.  Here we show that SE-associated genes specific for AR-negative CRPC PC3 cells include the genes involved in migration and invasion and that JQ1 impairs migration and invasion of PC3 cells.  We identified the long non-coding RNA MANCR, which is markedly down-regulated by JQ1 and found that BRD4 binds to the MANCR locus.  MANCR knockdown led to a significant decrease in migration and invasion of PC3 cells.  RNA sequencing analysis revealed that expression of the genes involved in migration and invasion is altered by MANCR knockdown.  In summary, our data demonstrate that MANCR has a critical role for cellular migration and invasion abilities of PC3 cells.

overall_design: mRNA profiles of PC3 cells for ctrl and MANCR knockdown were generated

last: Motooka

first: Kosuke

last: Tomimatsu

first: Masayuki

last: Nagasawa

first: Yasutoshi

last: Agata


title: Mapping regulatory networks of Zymomonas mobilis small RNAs Zms4 and Zms6

city: Austin

first: Lydia

middle: M

last: Contreras

state: TX

address: 200 E. Dean Keeton St Stop C0400

department: McKetta Department of Chemical Engineering

institute: University of Texas at Austin

summary: sRNAs represent a powerful class of regulators that influence multiple mRNA targets but remain largely uncharacterized outside of model organisms. Zymomonas mobilis is a natural ethanol-producing bacterium in which multiple small RNAs (sRNAs) have recently been identified, some of which show differential expression in ethanol stress. In this study, we show that sRNAs Zms4 and Zms6 have significant impacts on ethanol tolerance in Z. mobilis. We have conducted multi-omics analyses (including transcriptomics and sRNA-immunoprecipitation) to map gene networks under the influence of their regulation.

overall_design: Regulatory networks of Z. mobilis sRNAs Zms4 and Zms6 were elucidated by sRNA-immunoprecipitation (MS2-affinity purification) and sRNA induction experiments.  Potential directly-interacting targets were identified by sRNA-immunoprecipitation and mechanisms were inferred by expression patterns of these targets in sRNA induction experiments.


title: Impacts of Z. mobilis sRNAs Zms4 and Zms6 overexpression on gene networks

summary: The induction of Z. mobilis sRNAs Zms4 and Zms6 reveals their regulatory impacts on gene networks.

overall_design: RNA-sequencing of total RNA from three Z. mobilis strains: inducible plasmid overexpression of Zms4, inducible plasmid overexpression of Zms6, and the wild type. Transcript abundances were compared before and after induction with biological duplicates.

first: Katie

last: Haning

first: SeungHee

last: Cho

first: Juan

last: Gonzalez-Rivera

first: Bobi

last: Simonsen


title: Prevalent N6-methyldeoxyadenosine methylation in mammalian mitochondrial DNA

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

summary: N6-methyldeoxyadenosine (6mA or m6dA), a well-known prokaryotic DNA modification has recently been shown to exist and play regulatory roles in eukaryotic genomic DNA. However, biological functions of 6mA in mammals remain to be explored largely due to its low abundance in most mammalian genomes. Here, we report a significant enrichment of 6mA in mammalian mitochondrial DNA (mtDNA), and identify METTL4 as a methyltransferase that installs 6mA. The level of 6mA in mtDNA is elevated up to over 0.02%  of the total deoxyadenosines under hypoxia, representing ~7,00-fold enrichment over 6mA in the genomic DNA (gDNA) under normal growth conditions. The presence of 6mA negatively regulates mitochondrial transcription and balances mitochondrial function for cellular adaption to hypoxic stress. While DNA 5-methylcytosine (5mC) is a well-established, prevalent epigenetic mark in mammalian genomic DNA, our study reveals for the first time DNA 6mA methylation as a regulatory mark in mammalian mtDNA.

overall_design: We performed CLIP-exo sequencing for 6mA under normoxia and hypoxia conditions, respectively. Furthermore, the transcriptome-wide changes between wild-type cells and cells with METTL4 knockdown were characterized using RNA-Seq.

first: Ziyang

last: Hao

first: Tong

last: Wu

first: Xiao-Long

first: Chuan

last: He


title: Targeted suppression of ZNF217-induced AKT signaling inhibits tumor growth and metastasis in osteosarcoma

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

summary: We previously identified ZNF217 as an oncogenic driver of a subset of osteosarcomas (OSAs) using the Sleeping Beauty (SB) transposon system. Here, we followed up investigating the role of ZNF217 in OSA and combined these studies with an orthotopic preclinical animal model and culture experiments. We found that targeting ZNF217-induced AKT signaling with a small molecule inhibitor is a promising approach to treating ZNF217+ OSAs. Here, we demonstrate that ZNF217 is involved in numerous facets of OSA transformation including proliferation, cell motility, colony formation, and ultimately promoting OSA growth, progression, and metastasis in part through AKT survival pathway modulation. Preclinical blockade of AKT signaling with nucleoside analogue triciribine (TCN) in ZNF217+ orthotopically-injected OSA cell lines reduced tumor growth, metastasis, and was well-tolerated. TCN treatment was also found to synergize with common broad-spectrum chemotherapeutic doxorubicin. Our data demonstrate that TCN treatment may be a relevant and efficacious therapeutic strategy for OSA patients with ZNF217+ and p-AKTSer473-rich tumors. With the recent revitalization of triciribine for clinical studies in other solid cancers (PTX-200, Prescient Therapeutics), our study provides rationale for further evaluation preclinically with the purpose of clinical evaluation in patients with incurable, ZNF217+ OSA.

overall_design:
This RNA study examined the role of ZNF217 in osteosarcoma through knockdown studies
Control and knockdown samples were performed in duplicate in SJSA-1 osteosarcoma cells


title: Transcriptome analyses of trophoblast upon YTHDF3 knockdown

first: ql

last: zheng

summary: YTHDF3 play important role in regulation of trophoblast activity, we examined the downstream genes of YTHDF3 via transcriptome sequencing

overall_design: Transcriptome analyses of mRNAs from trophoblast cells upon YTHDF3 knockdown

first: Qingliang

last: Zheng


title: MS2-affinity purification coupled to RNA-sequencing (MAPS) reveals targetomes of Z. mobilis sRNAs Zms4 and Zms6

summary: The MS2-affinity purification coupled to RNA-sequencing (MAPS) approach was used to identify RNA targets that physically associate in vivo with Zymomonas mobilis small RNAs Zms4 and Zms6.

overall_design: RNA-sequencing of affinity-purified in vivo regulatory complexes in three Z. mobilis strains containing plasmids expressing MS2-Zms4, MS2-Zms6, and MS2 alone. MS2-Zms4 and MS2-Zms6 were each compared to MS2 alone as a control, each with biological triplicates.


title: Eomes identifies thymic precursors of self-specific memory-phenotype CD8+ T cells

first: Nicholas

last: Socci

state: NY

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Unprimed mice harbor a substantial population of "memory-phenotype" CD8+ T cells (CD8-MP cells) that exhibit hallmarks of activation and innate-like functional properties. Due to the lack of faithful markers to distinguish CD8-MP cells from bona fide CD8+ memory T cells, the developmental origins and antigen specificities of CD8-MP cells remain incompletely defined. Using deep T cell receptor (TCR) sequencing, we found that the TCRs expressed by CD8-MP cells are highly recurrent and distinct from the TCRs expressed by naive-phenotype CD8+ T cells. CD8-MP clones exhibited reactivity to widely expressed self-ligands. T cell precursors expressing CD8-MP TCRs upregulated the transcription factor Eomes during maturation in the thymus, prior to induction of the full memory phenotype, suggestive of a unique program triggered by recognition of self-ligands. Moreover, CD8-MP cells infiltrate oncogene-driven prostate tumors and express high densities of PD-1, suggesting a potential role in anti-tumor immunity and response to immunotherapy.

overall_design: TCRalpha chains were sequenced from FACS-purified CD8-Naïve (CD8+ CD44lo CD122neg) and CD8-MP (CD8+ CD44hi CD122+) T cells from the pooled spleen and lymph nodes of mice expressing a fixed transgenic TCRbeta. Cells were purified from five different 9-week-old male mice on the C57BL/6J (B6) background. In addition, TCRalpha chains were sequenced from FACS-purified CD8+ T cells from the prostate tumors of five 27-week-old TRAMP+/- males expressing the fixed TCRbeta chain.

first: Christine

last: Miller

first: David

last: Klawon

first: Sharon

last: Zeng

first: Victoria

last: Lee

first: Peter

last: Savage


title: Transcriptional control of thermogenesis by early B cell proteins [RNA-seq]

city: Philadelphia

first: Anthony

last: Angueira

state: Pennsylvania

address: 3400 Civic Center Blvd

department: IDOM

institute: University of Pennsylvania

summary: Early B Cell Factor 2 (EBF2) is required for brown adipose tissue basal thermogenic gene expression; however, it was unknown whether chronic cold exposure normalized the expression of thermogenic genes in Ebf2 mutant mice. We examined the transcriptome of Ebf2 WT and mutant brown adipose tissue in mice housed at room temperature or one week of cold exposure.

overall_design: RNASeq was performed in control and Ebf2 mutant brown adipose tissue from adult mice acclimated to room temperature or 1 week of cold exposure.

first: Patrick

last: Seale

first: Hee

middle: W

last: Lim


title: Inflammasome Signaling and Impaired Vascular Health in Psoriasis

first: Michael

middle: Seth

last: Garshick

address: 435 East 30th Street

institute: NYU Langone Health

summary: De-identified RNA sequencing of whole blood in psoriasis and control participants

overall_design: Cross-sectional comparison of disease (psoriasis) vs. control. We report the comparison in the whole blood transcriptome inflammatory signature by RNA sequencing in psoriasis compared to control individuals. We find the inflammasome signaling pathway as the highest differentially expressed.


title: Transcriptional control of thermogenesis by early B cell proteins

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

overall_design: Refer to individual Series


title: Single-cell RNA-seq reveals distinct gene expression profiles underlying the cellular heterogeneity of Shox2-positve palatal cells

city: New Orleans

first: Linyan

last: Wang

state: LA

address: 6400 freret street

institute: Tulane University

summary:
We use single cell RNA-sequencing to profile palatal mesenchyme cells from Shox2Cre/+;R26RmTmG at E13.5.
Haploinsufficiency of MEIS2 is associated with cleft palate in humans and Meis2 inactivation leads to abnormal palate development in mice, implicating an essential role for Meis2 in palate development. However, its functional mechanisms remain unknown. In this study, we found widespread Meis2 expression in the developing palate in mice. Meis2 inactivation by Wnt1Cre in cranial neural crest cells led to the cleft of the secondary palate. Importantly, about half of Wnt1Cre;Meis2f/f mice exhibited submucous cleft, providing an excellent model for studying palatal bone formation and patterning. Consistent with a complete absence of the palatal bones, integrative analyses of Meis2 ChIP-seq, RNA-seq, and ATAC-seq results identified key osteogenic genes that are regulated directly by Meis2, indicating the fundamental role of Meis2 in palatal osteogenesis. De novo motif analysis discovered that the Meis2-bound regions possess highly enriched binding motifs of several key osteogenic transcription factors particularly Shox2. Comparison of Meis2 and Shox2 ChIP-seq analyses further revealed a genome-wide co-occupancy, in addition to their co-localization in the developing palate and physical interaction, suggesting that Shox2 and Meis2 act as partners. However, while Shox2 is required for proper palatal bone formation and is a direct downstream target of Meis2, Shox2 overexpression failed to rescue the palatal bone defects in Meis2 mutant background. These results, together with the facts that Meis2 expression is associated with high osteogenic potential and is required for the chromatin accessibility of osteogenic genes, support a vital function of Meis2 in setting up the ground state for palatal osteogenesis.

overall_design: Single-cell RNA-seq of Shox2-positive cells of E13.5Shox2Cre/+;R26RmTmG

first: YiPing

last: Chen


title: Transcriptional control of thermogenesis by early B cell proteins [ChIP-seq]

summary: Early B Cell Factor 2 (EBF2) is required for brown adipose tissue basal thermogenic gene expression; however, it was unknown whether chronic cold exposure normalized the enhancer landscape of Ebf2 mutant mice. We profiled H3K27Ac binding in Ebf2 WT and mutant brown adipose tissue in mice housed at room temperature or one week of cold exposure.

overall_design: H3K27Ac ChIP-Seq was performed in control and Ebf2 mutant brown adipose tissue from adult mice acclimated to room temperature or 1 week of cold exposure.


title: RNA-Seq profiling of LAQ vs Control mice

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary:
Illumina mRNA-Seq, 18-20 million single end reads/sample with Bioinformatics of LAQ vs Control mice
Laquinimod (LAQ) was initially known as an immunomodulatory agent and was used to treat multiple sclerosis and alleviate demyelination in the mouse models of different diseases. We assumed that it may modulates gene transcription to influence protein function in the mouse brain, based on the previous finding. We therefore performed RNAseq detection of gene expression from the oligodendrocyte-enriched corpus callosum of 3-month-old PLP-150Q mice that had been treated with 5 mg/kg LAQ for two months. The control group was the age-matched PLP-150Q mice treated with purified water.

overall_design: Examination of gene expression in PLP-150Q mouse corpus callosum after LAQ treatment, using 4 LAQ treated and 4 control mice.

first: Peng

last: Yin

first: Shihua

last: Li


title: Transcriptome of wildtype and Meis2 mutant  in the developing palate

summary:
We use RNA-sequencing to profile the different expression genes in the palatal mesenchyme of wildtype and Wnt1Cre;Meis2f/f mice at E12.5.
Haploinsufficiency of MEIS2 is associated with cleft palate in humans and Meis2 inactivation leads to abnormal palate development in mice, implicating an essential role for Meis2 in palate development. However, its functional mechanisms remain unknown. In this study, we found widespread Meis2 expression in the developing palate in mice. Meis2 inactivation by Wnt1Cre in cranial neural crest cells led to the cleft of the secondary palate. Importantly, about half of Wnt1Cre;Meis2f/f mice exhibited submucous cleft, providing an excellent model for studying palatal bone formation and patterning. Consistent with a complete absence of the palatal bones, integrative analyses of Meis2 ChIP-seq, RNA-seq, and ATAC-seq results identified key osteogenic genes that are regulated directly by Meis2, indicating the fundamental role of Meis2 in palatal osteogenesis. De novo motif analysis discovered that the Meis2-bound regions possess highly enriched binding motifs of several key osteogenic transcription factors particularly Shox2. Comparison of Meis2 and Shox2 ChIP-seq analyses further revealed a genome-wide co-occupancy, in addition to their co-localization in the developing palate and physical interaction, suggesting that Shox2 and Meis2 act as partners. However, while Shox2 is required for proper palatal bone formation and is a direct downstream target of Meis2, Shox2 overexpression failed to rescue the palatal bone defects in Meis2 mutant background. These results, together with the facts that Meis2 expression is associated with high osteogenic potential and is required for the chromatin accessibility of osteogenic genes, support a vital function of Meis2 in setting up the ground state for palatal osteogenesis.

overall_design:
Palatal mRNA profiles of wildtype (WT) and Wnt1Cre;Meis2f/f palatal mesenchyme were generated by deep sequencing, in triplicate.
The processed data tabular files are the DEGs between Control and Mutant, for example, the file "1-E12.5_Meis2 cKO_rep1.tabular" is the result of E12.5-WT-rep1 vs. E12.5-Wnt1Cre;Meis2f/f-rep1


title: Genome-wide epistatic interaction networks affecting feed efficiency in Duroc and Landrace pigs

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

type: Genome variation profiling by genome tiling array

summary: Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions amongst causal genes of small effects, and biological pathways could be identified using a network biology approach. The main objective of this study was to determine the genome-wide epistatic variants affecting feed efficiency traits [feed conversion ratio (FCR) and residual feed intake (RFI)] based on weighted interaction SNP hub (WISH-R) method. Herein, we detected highly interconnected epistatic SNP modules, pathways, and potential biomarkers for the FCR and RFI in Duroc and Landrace purebreds considering the whole population, and separately for low and high feed efficient groups. Highly interacting SNP modules in Duroc (1,247 SNPs) and Landrace (1,215 SNPs) across the population and for low feed efficient (Duroc - 80 SNPs, Landrace - 146 SNPs) and high feed efficient group (Duroc - 198 SNPs, Landrace - 232 SNPs) for FCR and RFI were identified. Gene and pathway analyses identified ABL1, MAP3K4, MAP3K5, SEMA6A, KITLG, and KAT2B from chromosomes 1, 2, 5, and 13 underlying ErbB, Ras, Rap1, thyroid hormone, axon guidance pathways in Duroc. GABBR2, GNA12, and PRKCG genes from chromosomes 1, 3, and 6 pointed towards thyroid hormone, cGMP-PKG and cAMP pathways in Landrace. From Duroc low feed efficient group, the TPK1 gene was found involved with thiamine metabolism, whereas PARD6G, DLG2, CRB1 were involved with the hippo signaling pathway in high feed efficient group. PLOD1 and SETD7 genes were involved with lysine degradation in low feed efficient group in Landrace, while high feed efficient group pointed to genes underpinning valine, leucine, isoleucine degradation, and fatty acid elongation. Some SNPs and genes identified are known for their association with feed efficiency, others are novel and potentially provide new avenues for further research. Further validation of epistatic SNPs and genes identified here in a larger cohort would help to establish a framework for modelling epistatic variance in future methods of genomic prediction, increasing the accuracy of estimated genetic merit for FE and helping the pig breeding industry.

overall_design: A total of 109 (59 Danbred Duroc and 50 Danbred Landarace) pigs were genotyped from blood. Feed intake and growth of the pigs was measured during a testing period from ~28kg to ~100kg, spanning 40-70 days. Based on these measurments FCR and RFI was calculated for all pigs.

first: Priyanka

last: Banerjee

first: Victor

last: Carmelo


title: Meis2 sets up the ground state for palatal osteogenesis in mice


title: Gene expression profile of laryngeal squamous cell carcinoma

city: Rio de Janeiro

first: Pedro

last: Nicolau Neto

state: RJ

address: 37 Andre Cavalcanti Street

department: PCM

country: Brazil

institute: INCA

summary: The goal was to identify the differently expressed genes between laryngeal tumor and nonmalignant surrounding mucosa

overall_design: 14 paired LSCC samples and matched nonmalignant mucosa were analyzed

middle: P

last: Nicolau-Neto

first: Paulo

last: Santos

first: Luis

last: Pinto


title: Meis2 ChIP-seq in palate

summary:
ChIP-Sequencing on Meis2-HA in E12.5 palate, to identify Meis2 binding chromatin regions and target genes.
Haploinsufficiency of MEIS2 is associated with cleft palate in humans and Meis2 inactivation leads to abnormal palate development in mice, implicating an essential role for Meis2 in palate development. However, its functional mechanisms remain unknown. In this study, we found widespread Meis2 expression in the developing palate in mice. Meis2 inactivation by Wnt1Cre in cranial neural crest cells led to the cleft of the secondary palate. Importantly, about half of Wnt1Cre;Meis2f/f mice exhibited submucous cleft, providing an excellent model for studying palatal bone formation and patterning. Consistent with a complete absence of the palatal bones, integrative analyses of Meis2 ChIP-seq, RNA-seq, and ATAC-seq results identified key osteogenic genes that are regulated directly by Meis2, indicating the fundamental role of Meis2 in palatal osteogenesis. De novo motif analysis discovered that the Meis2-bound regions possess highly enriched binding motifs of several key osteogenic transcription factors particularly Shox2. Comparison of Meis2 and Shox2 ChIP-seq analyses further revealed a genome-wide co-occupancy, in addition to their co-localization in the developing palate and physical interaction, suggesting that Shox2 and Meis2 act as partners. However, while Shox2 is required for proper palatal bone formation and is a direct downstream target of Meis2, Shox2 overexpression failed to rescue the palatal bone defects in Meis2 mutant background. These results, together with the facts that Meis2 expression is associated with high osteogenic potential and is required for the chromatin accessibility of osteogenic genes, support a vital function of Meis2 in setting up the ground state for palatal osteogenesis.

overall_design: Genome binding/occupancy profiling by high throughput sequencing


title: TGF-beta-activated cancer-associated fibroblasts limit cetuximab efficacy in preclinical models of head and neck cancer

city: Skolkovo

first: Ekaterina

last: Khrameeva

state: Moscow region

address: Novaya St., 100

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: Most head and neck cancer (HNC) patients are resistant to cetuximab, an antibody against the epithelial growth factor receptor. Such therapy resistance is known to be mediated, in part, by stromal cells surrounding the tumor cells; however, the mechanisms underlying such a resistance phenotype remain unclear. To identify the mechanisms underlying cetuximab resistance in an unbiased manner, RNA-sequencing (RNA-seq) of HNC patient-derived xenografts (PDXs) was performed. Comparing the gene expression of HNC-PDXs before and after treatment with cetuximab indicated that the TGF-beta signaling pathway was upregulated in the stromal cells of PDXs that progressed to cetuximab (CetuximabProg-PDX). However, in PDXs that were extremely sensitive to cetuximab, and when tumors shrunk following cetuximab treatment (CetuximabSen-PDX), the TGF-beta pathway was downregulated in the stromal compartment.  Histopathological analysis of PDXs showed that in CetuximabProg-PDX, TGF-beta-activation was detected in cancer-associated fibroblasts (CAFs). These TGF-beta-activated CAFs were sufficient to limit cetuximab efficacy in vitro and in vivo. Moreover, blocking the TGF-beta pathway using the SMAD3 inhibitor, SIS3, enhanced cetuximab efficacy and prevented the progression of CetuximabProg-PDX. Altogether, our findings indicate, for the first time, that TGF-beta-activated CAFs play a role in limiting cetuximab efficacy in HNC.

overall_design: Three tumors from each group (vehicle and cetuximab, a total of 6 samples for each PDX) were subjected to sequencing.


title: ATAC-seq of wildtype and Meis2 mutant  in the developing palate

summary:
We use ATAC-seq to identify chromatin accessibility in the palatal mesenchyme of wildtype and Wnt1Cre;Meis2f/f mice at E12.5.
Haploinsufficiency of MEIS2 is associated with cleft palate in humans and Meis2 inactivation leads to abnormal palate development in mice, implicating an essential role for Meis2 in palate development. However, its functional mechanisms remain unknown. In this study, we found widespread Meis2 expression in the developing palate in mice. Meis2 inactivation by Wnt1Cre in cranial neural crest cells led to the cleft of the secondary palate. Importantly, about half of Wnt1Cre;Meis2f/f mice exhibited submucous cleft, providing an excellent model for studying palatal bone formation and patterning. Consistent with a complete absence of the palatal bones, integrative analyses of Meis2 ChIP-seq, RNA-seq, and ATAC-seq results identified key osteogenic genes that are regulated directly by Meis2, indicating the fundamental role of Meis2 in palatal osteogenesis. De novo motif analysis discovered that the Meis2-bound regions possess highly enriched binding motifs of several key osteogenic transcription factors particularly Shox2. Comparison of Meis2 and Shox2 ChIP-seq analyses further revealed a genome-wide co-occupancy, in addition to their co-localization in the developing palate and physical interaction, suggesting that Shox2 and Meis2 act as partners. However, while Shox2 is required for proper palatal bone formation and is a direct downstream target of Meis2, Shox2 overexpression failed to rescue the palatal bone defects in Meis2 mutant background. These results, together with the facts that Meis2 expression is associated with high osteogenic potential and is required for the chromatin accessibility of osteogenic genes, support a vital function of Meis2 in setting up the ground state for palatal osteogenesis.

overall_design: Chromatin assessibility of wildtype (WT) and Wnt1Cre;Meis2f/f palatal mesenchyme cells were asseyed by Tn5 transposase and sequencing, in triplicate.


title: Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing

city: Hangzhou

first: li

last: lei

address: xiashas street num 6

summary: Background: Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new glyphosate-tolerant varieties is a research focus of seed companies and researchers. The glyphosate stress-responsive genes were used for the development of genetically modified crops, while only the EPSPS gene has been used currently in the study on glyphosate-tolerance in rice. Therefore, it is essential and crucial to intensify the exploration of glyphosate stress-responsive genes, to not only acquire otherglyphosate stress-responsive genes with clean intellectual property rights but also obtain non-transgenic glyphosate-tolerant rice varieties. This study is expected to elucidate the responses of miRNAs, lncRNAs, and mRNAs to glyphosate applications and the potential regulatory mechanisms in response to glyphosate stress in rice.  Results: Leaves of the non-transgenic glyphosate-tolerant germplasm CA21 sprayed with 2 mg•ml-1 glyphosate (GLY) and CA21 plants with no spray (CK) were collected for high-throughput sequencing analysis. A total of 1197 DEGs, 131 DELs, and 52 DEMs were identified in the GLY samples in relation to CK samples. Genes were significantly enriched for various biological processes involved in detoxification of plant response to stress. A total of 385 known miRNAs from 59 miRNA families and 94 novel miRNAs were identified. Degradome analysis led to the identification of 32 target genes, of which, the squamosa promoter-binding-like protein 12 (SPL12) was identified as a target of osa-miR156a_L+1. The lncRNA-miRNA-mRNA regulatory network consisted of osa-miR156a_L+1, two transcripts of SPL12 (LOC_Os06g49010.3 and LOC_Os06g49010.5), and 13 lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1).   Conclusion: Large-scale expression changes in coding and noncoding RNA were observed in rice mainly due to its response to glyphosate. SPL12, osa-miR156, and lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1) could be a novel ceRNA mechanism in response to glyphosate stress in rice.

overall_design: In this study, we first constructed cDNA libraries, sRNA libraries, and degradome libraries from the leaves of glyphosate-tolerant rice CA21. Through high-throughput sequencing analysis, a systematic and integrated analysis of the potential lncRNA-miRNA-mRNA regulatory network was performed in leaves of glyphosate-tolerant rice.

first: Rongrong

last: Zhai

first: Shenghai

last: Ye

first: Guofu

last: Zhu

first: Yanting

last: Lu

first: Jing

first: Faming

last: Yu

first: Xiaoming

last: Zhang


title: The miRNA microarray data after UVB exposure to human keratinocyte HaCaT cells

city: Seoul

first: Donghwa

last: Kim

state: Seoul

address: Gwanakro-1, Gwanakgu

institute: Seoul National University

summary:
UVB plays a key role in inflammation and DNA damage in human skin. Human keratinocyte HaCaT cells were utilized to determine the up- and down-regulated miRNA after UVB exposure.
We used microarrays to identify the miRNA affected after UVB (15 mJ/cm^2) exposure to HaCaT cells

overall_design: HaCaT cells were exposed to UVB (15 mJ/cm^2) and incubated for 6 hours. The cells were collected usign TRI reagent, RNA was extracted, and subjected to Affymetrix microarrays. We sought to investigate miRNA regulating UVB-induced inflammation.

first: Jiyoung

last: Hwang

first: Sang

last: Lee


first: rong

middle: rong

last: zhai

address: 198, Shiqiao Road, Hangzhou, Zhejiang, 310021, China

department: Institute of Crop and Nuclear Technology Utilization

institute: Zhejiang Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing


title: The HDAC Inhibitor Sodium Butyrate Prevents Allergic Rhinitis and Alters lncRNA and mRNA Expression Profiles in the Nasal Mucosa of Mice

city: Xi’an

first: jie

middle: wang

last: wang

state: shanxi

address: 17 Changle Western Road

department: Department of Otolaryngology-Head and Neck Surgery

institute: Xijing Hospita,Air Force Military Medical University

summary: Our previous research confirmed that histone deacetylase inhibitor sodium butyrate (NaB), delivered intranasally, has exhibits therapeutic effects on a mouse model of allergic rhinitis (AR). However, whether it is effective on AR when administered orally and prophylactically, as well as its potential effects on gene expression, remained unknown. Methods: In this study, we investigated the preventive effect of NaB on AR when added to the diet of newly weaned mice and evaluated changes in lncRNA and mRNA expression profiles in the nasal mucosa. Mice were randomly divided into three groups as follows: C group (control group, no treatment), AR group (treated with ovalbumin [OVA]), and NaB+AR group (treated with both OVA and NaB). The NaB+AR group was given NaB in their feed (30 g/kg), whereas the other two groups were fed normal feed from 3 weeks to 6 weeks of age. At 7 weeks of age, OVA administration was initiated to induce AR in the AR and NaB+AR  groups. Then, behavioral assessments, western blotting, and gene analysis were performed.

overall_design: Mice were randomly divided into three groups(n = 30 per group)  as follows: C group (control group, no treatment), AR group (treated with ovalbumin [OVA]), and NaB+AR group (treated with both OVA and NaB). The NaB+AR group was given NaB in their feed (30 g/kg), whereas the other two groups were fed normal feed from 3 weeks to 6 weeks of age. mice were sacrificed under anesthesia, and the nasal mucosa was preserved in liquid nitrogen for further analysis.

first: Jie

last: Wang


title: Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing [degradome]


title: Interleukin-4/STAT6 signaling impairs the survival of mouse astroglia in vivo but not in vitro

city: New York

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

summary: Neurogenesis is limited in mammalian brains and Alzheimer’s disease conditions further reduce the neurogenic output. Recent findings suggest that reduced neurogenesis could be one of the reasons underlying the exacerbated neuropathology in humans, and restoring the neural stem cell proliferation and neurogenesis could help circumventing some pathological aspects of Alzheimer’s disease. We recently identified Interleukin-4/STAT6 signaling as a neuron-glia crosstalk mechanism that enables glial proliferation and neurogenesis in adult zebrafish brain and 3D cultures of human astroglia, which manifest neurogenic properties. In this study, we tested whether activating IL4/STAT6 signaling in adult mouse astroglia would enhance cell proliferation and neurogenesis in health and disease conditions. By using single cell sequencing in APP/PS1dE9 mouse model of AD, we found that IL4 receptor (Il4r) is not expressed in mouse astroglia. Lentivirus-mediated expression of IL4R or constitutively active STAT6V impaired the survival capacity of mouse astroglia in vivo but not in vitro. Our findings suggest that adult mouse brain generates a non-permissive environment that dictates a negative effect of IL4 signaling on astroglial survival and neurogenic properties in contrast to zebrafish brains and in vitro mammalian cell cultures.

overall_design: single-cell sequencing performed from 12 months old mice (single-mice) dentate gyrus

first: Violeta

last: Mashkaryan

first: Mehmet

middle: I

last: Cosacak


title: Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing [miRNA-Seq]

overall_design:
In this study, we first constructed cDNA libraries, sRNA libraries, and degradome libraries from the leaves of glyphosate-tolerant rice CA21. Through high-throughput sequencing analysis, a systematic and integrated analysis of the potential lncRNA-miRNA-mRNA regulatory network was performed in leaves of glyphosate-tolerant rice.

This dataset is the miRNA component only

first: R

first: S

first: G

first: Y

first: J

first: F

first: X


title: α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer [RNA-seq III]

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

summary: Genetic-driven deregulation of the Wnt pathway is crucial but not sufficient for colorectal cancer (CRC) tumourigenesis. Here, we show that environmental glutamine restriction further augments Wnt signaling in APC mutant intestinal organoids to promote stemness and leads to adenocarcinoma formation in vivo via decreasing intracellular alpha-ketoglutarate (aKG) levels. aKG supplementation is sufficient to rescue low-glutamine induced stemness and Wnt hyperactivation. Mechanistically, we found that aKG promotes hypomethylation of DNA and histone H3K4me3, leading to an upregulation of differentiation-associated genes and downregulation of Wnt target genes, respectively. Using CRC patient-derived organoids and several in vivo CRC tumour models, we show that aKG supplementation suppresses Wnt signaling and promotes cellular differentiation, thereby significantly restricting tumour growth and extending survival. Together, our results reveal how the low glutamine metabolic microenvironment impacts Wnt signaling and identify aKG as a potent antineoplastic metabolite for potential differentiation therapy for CRC patients.

overall_design: 6 samples are analyzed RNA sequencing (3 biological replicates for control samples and 3 biological replicates for low glutamine treated samples)

first: Mei

last: Kong


title: α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer [RNA-seq II]

overall_design: 6 samples are analyzed for RNA sequencing (3 biological replicates for control samples and 3 biological replicates for DM-aKG treated samples)


title: α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer [RRBS]

overall_design: 6 samples are analyzed for RRBS sequencing ( 3 biological replicates for control samples and 3 biological replicates for DM-aKG treated samples)


title: α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer [methylation array]

overall_design: 4 samples are analyzed for DNA methylation microarray ( 2 biological replicates for control samples and 4 biological replicates for DM-aKG treated samples)


title: α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer [RNA-seq I]

overall_design: RNA sequencing, 7 control APC Min mouse samples, 6 DM-aKG treated  APC Min mouse samples, 7 untreated WT mouse samples


title: Secondhand smoke induces liver steatosis through deregulation of genes involved in lipid metabolism.

city: Los Angeles

first: Stella

last: Tommasi

state: California

address: 1450 Biggy St

institute: University of Southern California

summary: In this study, we have investigated the role of secondhand smoke (SHS) in the development of metabolic liver disease by characterizing the global regulation of genes and molecular pathways  in SHS-exposed mice after termination of exposure  (SHS 4M) and following one-month recovery in clean air (SHS 4M +1M RECOVERY).

overall_design: In total 12 samples: 4

first: Jae-In

last: Yoon

first: Ahmad

last: Besaratinia


title: Abiotic stress response and adaptive phenology in fruit trees

city: Knoxville

first: Margaret

last: Staton

email: mestato@gmail.com, mstaton1@utk.edu

state: Tennessee

address: 2505 EJ Chapman Blvd, 370 PBB

institute: University of Tennessee

summary: Due to the broad climate adaptation of perennial trees, phenological traits (e.g. chilling requirement-CR, bloom date-BD) exhibit complex inheritance patterns. Conceptually, these are adaptive responses to abiotic stress. As production depends on traits like CR, breeders have developed varieties that are phenotypically/genotypically matched to particular geographic/temperature zones. These genotypes are ideal for study of gene networks governing these climate-critical traits. Using genetic approaches, genome-wide association analyses, functional and comparative genomics in fruit and forest trees, we identified a foundational network of genetic activity (phenylpropanoid pathway) linking winter cold stress response to control of the endodormancy-ecodormancy transition (EET) and seed stratification. Our goal is to examine during endodormancy the allelic effects of genes controlling the production of stress related metabolic intermediates that regulate seed stratification, thus linking these two cold temperature responses. Our objective is to use a transcriptome sequencing approach to characterize genotypic effects on the phenylpropanoid gene network transcriptome during endodormancy and the EET. These adaptive genes and gene networks will be targets for knowledge based breeding strategies of fruit and forest trees to sustain and improve these resources to meet the challenges of rapid environmental change

sample_organism:
Prunus persica
Prunus armeniaca

platform_organism:
Prunus persica
Prunus armeniaca

overall_design: Floral bud mRNA from four apricot genotypes collected at 0, 100, 400 and 800 chill hours (CH) and sepal visible, petal visible stages with two or three replicates. Floral buds mRNA from four peach genotypes collected at 0, 100, 600, and 1000 chill hours and pre-bloom stage with four replicates.

first: Jiali

first: Meg


title: α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer [exome-seq]

overall_design: 2 samples are analyzed for DNA variation using Exome Seq (control sample and low glutamine treated sample)


title: The choroid plexus in progressive multiple sclerosis presents hypoxia and secretory changes that may be related to neuroprotection

city: Amsterdam

first: Helga

middle: E

last: de Vries

address: De Boelelaan 1108

department: MCBI

institute: Amsterdam UMC

summary: The choroid plexus (CP) is a key regulator of central nervous system (CNS) homeostasis through its secretory, immunological and barrier properties. Accumulating evidence suggests that the CP plays a pivotal role in the pathogenesis of multiple sclerosis (MS), but the underlying mechanisms remain largely elusive. To get a comprehensive view on the role of the CP in MS pathogenesis, we studied transcriptomic alterations of the human CP in progressive MS compared to controls using an RNA sequencing approach. We identified 17 genes with significantly higher expression in progressive MS patients relative to that in controls. Among them is the newly described long non-coding RNA HIF1A-AS3. Next to that, we uncovered disease-affected pathways related to hypoxia, secretion and neuroprotection, while only subtle immunological and no barrier alterations were observed. Three of the differentially expressed genes encode for secreted proteins, namely ADM, PAI-1 (SERPINE1) and STC2. Together, these findings provide novel insights to target the CP during MS and promote the secretion of neuroprotective factors into the CNS of progressive MS patients.

overall_design: Post-mortem samples from Whole Choroid Plexus of Primary Progressive Multiple Sclerosis patients and non-neurological controls were sequenced using Illumina Hiseq 3000 and differential expression was assesed using DESeq2

first: Sabela

last: Rodríguez-Lorenzo

first: David

last: Ferreira-Francisco


title: Transcriptome of control and FTO-knockdown HOC313 cells

city: Sendai

first: Fan-Yan

last: Wei

address: Seiryo-machi 4-1

institute: Tohoku University

summary: N6-methyladenosine (m6A) modification is the major post-transcriptional modification present in mammalian mRNA. m6A controls fundamental biological processes including cell proliferation, but the molecular mechanism remains unclear. Herein, we demonstrate that the m6A demethylase fat mass and obesity-associated (FTO) controls the cell cycle by targeting cyclin D1, the key regulator required for G1 phase progression. FTO silencing suppressed cyclin D1 expression and induced G1 arrest. FTO depletion upregulated cyclin D1 m6A modification, which in turn accelerated the degradation of cyclin D1 mRNA. Importantly, m6A modification of cyclin D1 oscillates in a cell cycle-dependent manner; m6A levels were suppressed during the G1 phase and enhanced during other phases. Low m6A levels during G1 were associated with nuclear translocation of FTO from the cytosol. Furthermore, nucleocytoplasmic shuttling of FTO is regulated by Casein Kinase II-mediated phosphorylation at Thr 150 of FTO. Our results highlight the role of m6A in regulating cyclin D1 mRNA stability, and add a new layer of complexity to cell cycle regulation.

overall_design: Examination of RNA expression in 3 control and 3 FTO-knockdown cells, Examination m6A modification in control and FTO-knockdown HOC313 cells

first: Mayumi

last: Hirayama


title: Expression data from the hepatic stellate cell line LX-2 after treatment with DMOG and from the liver sinusoidal endothelial cell line TRP3 after incubation with conditioned medium of DMOG-treated LX-2

city: Zürich

first: Konstantin

last: Dirscherl

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

summary:
Expression data from the hepatic stellate cell line LX-2 after treatment with the prolylhydroxylase inhibitor dimethyloxalylglycine (DMOG) and from the liver sinusoidal endothelial cell line TRP3 after incubation with conditioned medium of DMOG-treated LX-2
Prolyl-hydroxylase inhibitors such as dimethyloxalylglycine (DMOG) stabilize HIF-1α, thereby chemically inducing hypoxia, which also accelerates liver volume increase when given with portal rerouting.
We used microarrays to clarify the cellular crosstalk of the different cell types in accelerated liver regeneration by examining the role of hepatic stellate cells (HSC) and liver sinusoidal endothelial cells (LSEC).

overall_design: The human hepatic stellate cell line LX-2 was treated with 1 mM DMOG for 24 hours, RNA was extracted and hybridized on Clariom S microarrays. Supernatants of DMOG-treated LX-2 were given as conditioned medium to the human liver sinusoidal endothelial cell line TRP3, after 24 hours incubation RNA was extracted and hybridized on Clariom S microarrays.

first: Dirscherl

last: Konstantin

first: Beck

last: Beatrice

first: Schadde

last: Erik

first: Moehle

last: Christoph


title: Comparison of human isogeneic Wharton’s Jelly MSCs and iPSC-derived MSCs responses to interferon-gamma (IFNG) stimulation

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
To explore differences between native MSCs (nMSCs) and iPSC-derived MSCs (iMSCs), we developed isogeneic lines from Wharton’s Jelly (WJ) from the umbilical cords of two donors (#12 and #13) under xeno-free conditions. Next, we reprogrammed them into iPSCs (iPSC12 and iPSC13) and subsequently differentiated them back into iMSCs (iMSC12 and iMSC13) using two different protocols, which we named ARG and TEX. As an additional control, we used human embryonic stem cell line KCL034 to differentiate the cells into eMSC following ARG and TEX protocols. We assessed IFNG-induced changes in all lines.
Our data suggest that, following a careful selection and screening of donors, nMSCs from umbilical’s cord WJ can be easily reprogrammed into iPSCs providing an unlimited source of material for differentiation into iMSCs. However, the differentiation protocol should be chosen depending on their clinical use.

overall_design: To assess effects of IFNG on MSCs, recombinant human IFNG (Peprotech) was added to the media at 10 ng/ml and cells were cultured for 18 h prior to collection for RNA extraction

first: Dusko

last: Ilic

first: Liani

last: Devito


title: Pancreatic Epithelial Single Cell RNAseq in OGT-deficient cells

city: Minneapolis

first: emilyn

middle: U

last: alejandro

department: Integrative Biology and Physiology

institute: University of Minnesota

summary: Single Cell RNAseq was performed to identify cell types and upstream regulators in pancreatic epithelial cells with or without OGT.

overall_design: Embryonic pancreas was collected on embryonic day 15.5. Pancreatic epithelial cells were picked via FACS of endogenous GFP (in PdxCre;OGTflox/flox;CAG GFP mice) or E-cadherin GFP (in control OGTflox/flox).

first: Emilyn

last: Alejandro


title: Gene Expression Profiling in ovaries and association analysis reveal HEP21 as a candidate gene for chicken sexual maturity

city: Nanchang

first: Chen

last: Biao

state: Jiang Xi

address: Zhimin main street 1101#

department: College of animal science and technology

institute: Jiangxi Agricultural University

summary: The objective of this study was to identify candidate genes associated with sexual maturity and ovary development of chicken. Gene expression profiling sequencing analysis was employed using pre-laying (P-F-O1, L-F-O1) and laying ovaries (P-F-O2, L-F-O2) from two sub-breeds of Ningdu Yellow chicken. RNA-seq data and qPCR showed that HEP21 significantly differential expressed between the pre-pubertal ovary and pubertal ovary. A total of 23 variations were detected on HEP21. Association analysis between SNP in HEP21 and chicken reproductive traits showed that rs315156783 was significantly related to chicken comb height at 84 and 91 days.

overall_design: Examination of mRNA profiles  in  32-day-old early sexual maturity pre-laying-hen (P-F-O1), 103-day-old early sexual maturity laying-hen (P-F-O2), 32-day-old late sexual maturity pre-laying-hen (L-F-O1), and 153-day-old late sexual maturity pre-laying-hen (L-F-O2).

first: Biao

last: Chen

first: Min

last: Zhou

first: Sanfeng

last: Liu