title: Transcriptomic profiling of human senescent cells in the setting of curcumin intervention

first: Yu

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Aging and age-relataed pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using small molecules would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases. We report the potential of curcumin, a polyphenol constituent (up to ∼5%) of the traditional medicine known as turmeric, in targeting senescent cells via induction of programmed cell death. This study demonstrates the impact of curcumin as a medicinal compound on the expression profile of senescent cells and provides a strong rationale for its future application in geriatric medicine.

overall_design: Examination of in vitro efficacy of curcumin, a plant-derived polyphenol, in treating human senescent cells. This assay was performed beyond previous studies reporting curcumin's antioxidant, anti-inflammatory and anticancer properties as a traditional herbal medicine, as well as its efficacy in improvement of brain function, and control of obesity and diabetes.

first: Liu

last: Han


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCC cells with or without RNase7 treatment, and FIG-ROS1 Fusion Transcriptomes

status: Public on Dec 31 2022

city: Houston

first: Chunxiao

last: Liu

state: Texas

address: 7675 Phoenix Dr Apr623

country: USA

institute: MD Anderson

type: Expression profiling by high throughput sequencing

summary: The goals of this study are to compare RNase7-induced or fusion-driven HCC cell transcriptome profiling

overall_design: Gene expression profiling of HCC cell lines before and after RNase 7 treatment for 1h or with FIG-ROS1 fusion

first: Zhengyu

last: Zha

first: Chenhao

last: Zhou

first: Mien

middle: C

last: Hung


title: Transcriptome analysis of gene expression in MCF-7 cell upon circFAT1(e2) depletion

city: hefei

first: li

last: yong

state: anhui province

address: 安徽省合肥市经开区九龙路111号安大新区

country: China

institute: anhui university

summary: In previous study, we found circFAT1(e2) was highly expressed in breast cancer tissues and cell lines. And this factor is also a crucial role in breast cancer genesis and development. So in this study, we knocked down circFAT1(e2) in MCF-7 cells. The viability and metastasis was significantly inhibited with circFAT1(e2) depletion. In order to explore the potential down-stream gene of circFAT1(e2) in breast cancer cells. We extracted the total RNA from circFAT1(e2) knockdown MCF-7 cells and negative control group by using TriZol reagent. Then, toal RNA was subjected to transcriptome sequencing to determine the potential down-stream targets of circFAT1(e2). We expect to reveal the underlied mechanism of the regulatory effect on breast cancer of circFAT1(e2).

overall_design: CircFAT1(e2) was knocked down in siZ5 group to identify the down-stream genes of this circRNA in MCF-7 cell, and siNC was used as a knockdown control in this experiment.

first: Jialu

last: Shi

first: Yun

last: Wang

first: Mengqi

last: Yang

first: Yong

last: Li


title: Transcriptomic profiling of human senescent cells in the setting of pharmacological intervention (NAD+ and NMN)

city: Shanghai

last: Sun

summary: Aging and age-relataed pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using small molecules would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases. We report the potential of two metabolic molecules, NAD+ and NMN, to control the development of the pro-inflammatory phenotype of senescent human stromal cells. This study discloses the impact of NAD+ and NMN on the expression profile of senescent cells and provides a framework for future anti-aging administration with clear rationale.

overall_design: Examination of 2 different treatments of human senescent cells with mitochondrion-derived metabolic molecules.

first: Y

first: B

last: Zhang


title: Gene exprssion profile of hepatocellular carcinoma in the radiogenomic analysis

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

summary: Association of radiogenomic characteristics and gene expression profiles in hepatocellular carcinoma

overall_design:
Total 81 HCCs with PET information were sequenced to identify gene expressions.

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

first: Ju

middle: H

last: Shim

first: Jihyun

last: An

first: Chang

middle: O


title: Pulmonary effects of inhaled diesel particles in rats

city: Morgantown

first: Christina

middle: M

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

summary: The pulmonary response to inhalation exposure to diesel exhaust particles (DEP) was investigated in a rat model. Adult male Sprague-Dawley rats were exposed by whole-body inhalation to air or an aerosol containing DEP at concentrations of 200 or 1000 mg/m3, 6 hours/day for 4 days. The control and DEP-exposed rats were euthanized at post-exposure time intervals of 1, 7, or 27 days and pulmonary inflammatory, cytotoxic and oxidant responses were determined. Analysis of bronchoalveolar lavage parameters of toxicity such as lactate dehydrogenase activity, oxidant generation, and inflammation did not reveal any significant pulmonary toxicity in the DEP-exposed rats. The lung gene expression profiles did not change significantly in the DEP exposed rats compared with the controls. The data obtained from the present study demonstrated that DEP inhalation exposure under the conditions employed in the present study did not result in any significant lung toxicity in the rats.

overall_design: The rats were exposed by whole-body inhalation to filtered air or an aerosol containing DEP at concentrations of 200 or 1000 ug/m3, 6 hours/day for 4 days. The control and DEP-exposed rats were euthanized at post-exposure time intervals of 1, 7, or 27 days. Lung samples (n=6) were used to determine gene expression profiles by RNA sequencing.

first: Tina

last: Sager

first: Pius

last: Joseph


title: Tumor genes regulated in obesity-mediated breast cancer

city: Geneva

first: Isabelle

last: Dupanloup

address: Rue Michel-Servet, 1

country: Switzerland

institute: University of Geneva

summary: We developed a post-menopausal orthotopic ER+ breast cancer model that we used to investigate mechanisms of obesity mediated lung metastases. Obesity altered the immune cell composition and function in the primary tumor microenvironment. To identify tumor-derived genes associated with obesity mediated lung metastases we performed RNASeq on tumors grown in lean vs obese mice. From these results we identified a hepatocyte growth factor (HGF)-c-Met (HGF receptor)-CCL2 loop recruiting metastasis-promoting cells.

overall_design: 6 weeks-old female C57BL/6 mice were ovariectomized. Two week later mice were fed with high fat diet (5.1 kcal/g, 60% calories from fat) or regular diet (3.6 kcal/g, 10% calories from fat) for 6 weeks. In average HFD fed mice gained a 35% increase in body weight. 10E6 Py230 cells were injected in the 4th mammary gland, and 4 tumors per conditions were harvested at day 56 after tumor initiation.

first: Mélanie

last: Bousquenaud

first: Curzio

last: Rüegg


title: Transcriptome analysis of the rice response to Magnaporthe oryzae identified core genes involved in immunity

city: Fuzhou

first: Haitao

last: Cui

state: Fujian

address: Shangxiadian road 15

department: Plant Immunity Center

institute: Fujian Agriculture and Forestry University

summary: We carried out an time-series transcriptome study of susceptible rice cultivar Nipponbare and resistant cultivar Hui1586 in response to M. oryzae isolate Guy11 at 12, 24, 36 and 48 hpi. In total, 48 samples were subjected to RNA-seq, resulting in 6.8-gigabyte 100-bp paired-end reads per sample on average.

overall_design: mRNA of 14 days rice leaves infected by M. oryzae or water (mock) were subjected for RNA-sequcing and trancriptome profiling analysis.

first: Dewei

first: Dingzhong

last: Tang


title: Lung response to crystalline silica exposure in rats

summary: Exposure to crystalline silica results in serious health effects, most notably, silicosis and cancer. An understanding of the silica-induced lung toxicity is critical for the intervention and/or prevention of its adverse health effects. Rats were exposed by inhalation to air or crystalline silica (15 mg/m3, 6 hours/day for 5 days). At post-exposure time intervals of 1, 3, 6, 9, 12, and 18 months, the control and silica exposed rats were euthanized, and lung toxicity and gene expression profiles determined. Histological changes indicative of lung toxicity detected in the silica exposed rats included infiltration of neutrophils, thickening of alveolar epithelium, and fibrosis. Significant increases in lactate dehydrogenase activity, number of phagocytes, and inflammatory cytokine levels were detected in the bronchoalveolar lavage (BAL) obtained from the silica exposed rats compared with the corresponding time-matched controls. Significant changes in lung gene expression profiles, corresponding to the changes in the lung toxicity parameters analyzed, were detected in the silica exposed rats. The BAL parameters of toxicity and inflammation peaked at the 12-months post-exposure time interval and declined subsequently. However, lung fibrosis continued to progress being highest at the 18-month post-exposure time interval. These results suggest that inflammation may be required for the initiation but not for the progression and/or maintenance of lung fibrosis in response to silica exposure in the rats.

overall_design: For each post-exposure timepoint (1, 3, 6, 9, 12, and 18 months), rats (n=12) were exposed by whole body inhalation to air or crystalline silica (15 mg/m3, 6 hours/day for 5 days). At each post-exposure time point, lung tissue was collected, and Next Generation Sequencing was performed on the lungs of 5 rats per treatment group (air/crystalline silica).


title: Mutual regulation between GDF11 and TET2 prevents senescence in adipose tissue-derived mesenchymal stem cells

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: We implemented transcriptomic analyses of hADSCs treated with rGDF11 1, 2 and 6 days


title: Role of high fat diet on silica-induced lung toxicity in rats

summary: From an occupational standpoint, exposure to silica can have devastating consequences.  An estimated 2.3 million workers in the U.S. are exposed to dust containing crystalline silica, annually.  In addition, of the 140 million people over the age of 20, employed in the U.S., 30% are obese.  If and how diet-induced obesity modifies silica-induced pulmonary toxicity is unknown.  Therefore, the objective of this study was to determine the effect of diet-induced obesity, if any, on silica induced pulmonary toxicity. Rats (Fischer 344, male) were fed either a regular-fat diet (RFD; 18% kcal as fat) (Envigo, Indianapolis, IN) or a high-fat diet (HFD; 60% kcal as fat) (Envigo, Indianapolis, IN) and exposed by whole-body inhalation to either air or crystalline silica (15 mg/m3, 6 hours/day, 5 days). At designated post-exposure time intervals (1, 3, 6, and 9 months), pulmonary toxicity was determined. Silica inhalation resulted in pulmonary toxicity, which progressed across all post-exposure time points, as evidenced by enhanced neutrophil infiltration, increased LDH levels, enhanced oxidant production, and increased inflammatory cytokine levels. The incidence and severity of silica-induced lung pathology was similar between the two diet groups up to 6 months post-exposure. However, by 9 months post-exposure, silica-induced pathology tended to be slightly more severe in animals fed an RFD compared to those fed an HFD. Lung gene expression profiles were then determined in the rats euthanized at the 3- and 9-month post-silica exposure time intervals by RNA sequencing to identify transcript differences between the two timepoints.

overall_design: Lung RNA profiles of rats exposed to air, crystalline silica (full body inhalation exposure), a high fat diet, or a high fat diet and crystalline silica were generated by deep sequencing, 4 ≤ n ≤ 6, using Illumina HiSeq.


title: Efficacy of small molecule inhibitors and genetic interference of cGAS-STING axis on development of the senescence-associated secretory phenotype (SASP) in human stromal cells

first: Yu

summary: Rapid advancements in next generation sequencing (NGS) have revolutionized system-based analysis of genome-wide expression, cellular pathways and stress responses. We performed this cGAS-STING-associated study to streamline the transcriptomic profiling (RNA-seq) of human stromal cells manifesting a typical senescence-associated secretory phenotype (SASP) in a DNA damage setting.

overall_design: Overall transcript profiles of primary normal human prostate stromal cells (PSC27) were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Qixia

last: Xu


title: To identify novel targets of a histone acetyltransferase Gcn5 in Pichia pastoris

city: Bangalore

first: Aditi

last: Gupta

state: Karnataka

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

country: India

institute: Indian Institute of Science

summary: The regulation of gene expression in Pichia pastoris has so far involved study of transcription factors. However, there are factors other than transcription factors affecting mRNA synthesis such as coactivators, enhancers, and chromatin modifiers. This study is a first ever report on epigenetic regulation in Pichia pastoris where, a histone acetyltransferase is reported to regulate transcription of genes involved in utilization of alternate carbon sources. We employed RNA Seq to identify new targets of Gcn5 in methanol medium.

overall_design: Wild type and knockout cells were cultured in minimal medium with methanol as a carbon source. Cells were harvested after 14 hours followed by RNA preparation using QIAGEN RNEASY Mini Kit which was then subjected to RNA-SEQ.

first: P

middle: N

last: Rangarajan


title: Microarray mRNA expression profiling of peripheral blood samples in PCOS patients

first: madavan

last: vasudevan

address: Kasturi Nagar

institute: Theomics International Private Limited

summary:
In the present study through microarray analysis we looked into the mRNA differential expression in peripheral blood of PCOS patients v/s control women. The results implicated that many signalling networks as  MAPK pathway, Androgen signaling, Insulin signaling and Immune signaling are regulated in peripheral blood of PCOS patients. The data indicate that there is generic PCOS specific gene expression in  peripheral blood of PCOS subjects which can reflect the same from other PCO tissues.
Total RNA was extracted from peripheral blood of  4 PCOS patients and 4 control subjects and compared for mRNA diferential expression through microarray.

overall_design: Laloraya, Malini

first: Krishna

middle: B

last: Meera


title: Landscape profiling of small RNAs in extracellular vesicles secreted by senescent human stromal cells after DNA damage treatment

last: Sun

type: Non-coding RNA profiling by high throughput sequencing

summary: Blooming advancements in next generation sequencing (NGS) have revolutionized system-based analysis of genome-wide expression, cellular pathways and stress responses. We performed this non-coding RNA-associated milestone study to document comprehensively the small RNA molecules carried by extracellular vesicles (EVs) from human stromal cells, which develop typical cellular senescence and manifest the senescence-associated secretory phenotype (SASP) after genotoxic stress in culture.

overall_design: Transcript profiles of primary normal human prostate stromal cells (PSC27) were generated by deep sequencing, in triplicates, using Illumina HiSeq X10. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.

first: Liu

last: Han


title: Analysis of Primary and Expanded NK Cells for Future Clinical Use

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyi Biotec GmbH

summary: Clinical Natural Killer (NK) cell therapy for the treatment of leukemia is currently limited by the availability of larger numbers of functional NK cells. In vitro NK cell expansion can be used to generate higher numbers of NK cells and shows the potential to improve the cytotoxicity against tumor cells. A critical need for the clinical application of manufactured NK cells is their molecular and functional characterization.  In order to characterize primary and expanded NK cells of all donors the cells were analyzed on the surfaceome level by using CSC technology in combination with total gene expression analysis using whole human genome oligo microarrays.

overall_design: The dataset comprises four samples of primary and four samples of expanded NK cells. Each sample consists of pooled NK cells from 5-7 donors. Samples were processed in pairs with equal numbers of pooled donors.

first: Markus

last: Granzin

first: Sabine

last: Müller

first: Andrea

last: Jacobs

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

first: David

last: Agorku

first: Jürgen

last: Schmitz

first: Volker

last: Huppert

first: Bernd

last: Wollscheid


title: GDF11 rejuvenates neural stem cells via Smad2/3-PI3K-AKT-mTOR and reverses aged-dependent cognitive decline

first: Hailiang

last: Liu

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

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Liensinine improves AngII induced vascular remodeling via MAPK/TGF-β/Smad signaling pathway

status: Public on Dec 30 2022

first: Jia

middle: pei

last: zhi

address: Shangjie Town, Minhou County, Fuzhou City, Fujian Province

institute: Fujian University of Chinese Medicine

summary: The objective of this study was to compare blank control mice (NS V) with AngII-induced hypertensive mice (AngII V). Angii-induced hypertensive mice (AngII V) and liensinine intervention group (Lien V); Different genes expressed in vascular tissue and identify new targets for reversing hypertension-induced vascular remodeling.

overall_design: RNA sequencing was performed on the vascular tissues of NS, AngII and Lien groups (n = 5 in each group) at 10 weeks of age to identify different expression genes and related pathways.

first: Shan

last: Lin

first: Wei

first: Jun

last: Peng

first: Peizhi

last: Jia

first: Daxin

last: Chen

first: Ling

last: Zhang

first: Qiaoyan

last: Cai

first: Chunyu

last: Zhao

first: Meiling

last: Wang

first: Yaoyao

last: Xu


title: Structural and Genome-wide Analysis Support a Role for SETMAR in Transcriptional Regulation

city: Indianapolis

first: Millie

last: Georgiadis

state: Indiana

address: 635 Barnhill Drive

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: Approximately 50 million years ago, the Hsmar1 transposon entered the primate lineage giving rise to a new protein, a chimeric fusion of a SET domain and the Hsmar1 transposase. This protein, SETMAR or Metnase, is broadly expressed in human tissues and has been shown to retain its ancestral sequence-specific binding to Hsmar1 terminal inverted repeat (TIR) sequences found at the ends of the transposons. Despite the fact that there were estimated to be anywhere from 1500-7000 TIR sites within the human genome, the relevance of SETMAR-TIR interactions was unknown. Here, we report the crystal structure of the SETMAR DNA-binding domain (DBD) complexed with TIR DNA at 2.37 Å. The DBD structure includes two helix-turn-helix motifs (HTH1 and HTH2), which dimerize through HTH1, and confer sequence-specific recognition of the TIR through nucleobase-specific interactions with R371 in HTH1 and R417, H427, S428, and R432 in HTH2. The extent of genome-wide binding was determined by chromatin immunoprecipitation sequencing (ChIP-seq) analysis yielding a total of 7457 SETMAR bound sites. The effect of SETMAR on the transcriptome was assessed by RNA-seq analysis; among the 177 differentially regulated transcripts, a cluster of histones on chromosome 6 were found to be repressed. The dimeric SETMAR structure with each DBD bound to TIR DNA, the presence of eleven TIR sites within the histone gene cluster, and previously reported DNA looping activity are consistent with a direct regulatory mechanism in which SETMAR represses mRNA expression for specific genes through chromatin looping.

overall_design: HEK293T cells were transfected with either empty vector or vector containing full length wild type SETMAR gene and differential gene expression was determined by Next Gen RNA sequencing

first: Alison

last: Bates


title: Assessing the effects of transcription factor knockouts on growth in high-density fed-batch cultures

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

summary: We used RNA-seq to investigate the effects of single transcription factor knockouts on growth of E. coli BW25113 in fed-batch cultures at multiple timepoints. Cells were grown in an ambr automated bioreactor and maintained at 30 degrees and pH 6.5 in Medium C.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Growth of E. coli was performed with biological duplicates. Total RNA was extracted from fed-batch culture at specified time points for RNA-Seq library preparation. For batch cultures, total RNA was extracted at mid-log phase.

first: Suresh

last: Sudarsan


title: GDF11 rejuvenates neural stem cells via Smad2/3-PI3K-AKT-mTOR and reverses aged-dependent cognitive decline [human blood]

summary: We implemented transcriptomic analyses of  blood from young and aged people

overall_design: transcriptome analysis of human blood from young and aged people


title: GDF11 rejuvenates neural stem cells via Smad2/3-PI3K-AKT-mTOR and reverses aged-dependent cognitive decline [monkey blood]

summary: We implemented transcriptomic analyses of  blood from young and aged monkey

overall_design: transcriptome analysis of blood from young and aged monkeys


title: GDF11 rejuvenates neural stem cells via Smad2/3-PI3K-AKT-mTOR and reverses aged-dependent cognitive decline [mice tissue]

summary: We implemented transcriptomic analyses of different tissues of 10M and 15M mice; These mice with the treatment of rGDF11 for 30 days.


title: Expression data form PI3K Knockout colon cancer cell lines (HCT116 and DLD1)

city: Ioannina

first: Carol

last: Murphy

address: Panepistimioupoli

department: Biomedical reseach

country: Greece

institute: FORTH-IMBB

summary:
Whole transciptome analysis of colon cancer mutated cell lines(HCT116 and DLD1) under serum starvation conditions (19hrs-0.5%FBS)
We used microarrays to compare gene regulation of truncated cell lines, knocked-out of either the wild type or mutated allele of PI3K, for two independent colon cancer cell lines

overall_design: Vogelstein's lab generated two truncated cell lines, knocked-out of either the wild type or mutated allele of PI3K, for two independent colon cancer cell liness (HCT116 and DLD1). These 4 cell lines were selected for RNA extraction under serum starvation conditions and RNA was used for hybridization on Affymetrix microarrays. We sought to identify potent regulators of carcinogenesis and metastases under these conditions

first: Athena

last: Kyrkou


title: GBA1 regulates the CLEAR network through Calcineurin and TFEB in cellular models of Parkinson´s disease

city: Basel

first: Jitao David

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

institute: F. Hoffmann-La Roche

summary: The GBA1 gene encodes the lysosomal enzyme acid-β-glucocerebrosidase (GCase). GBA1 mutations cause the lysosomal storage disorder Gaucher disease (GD) and are a genetic risk factor for Parkinson´s disease (PD). Many GBA1 mutations cause aberrant GCase folding and processing but how these impinge on PD pathogenesis remains unclear. We addressed GCase functions in human dopaminergic (DA) neurons derived from engineered GBA1-deficient (GBA1-/-) embryonic stem cells (hESCs) and GBA1N370S PD patient-derived induced pluripotent cells (hiPSCs). GBA1-mutant DA neurons displayed aberrant morphologies and gene expression that were rescued by recombinant GCase treatment. GBA1-/- neurons have hyperactive Calcineurin (CaN) and nuclear localization of the Transcription Factor EB (TFEB). Expression of TFEB targets and lysosomal CLEAR network components were increased in GBA1-/- DA neurons and rescued by GCase replacement and CaN inhibition. Our findings reveal a link between increased CaN activity and loss of GCase, providing a mechanism for the disturbed lysosomal/autophagy pathways in GBA1-associated PD.

overall_design: The experiment follows a two-factor design: two genotypes (GBA+/+ and GBA-/-) and three treatments (vehicle, 1 μg/ml rGCase, and 10 μg/ml  rGCase). Two biological replicates are available for each sample group. All together, 12 samples were available and profiled.

first: Jitao

middle: D

first: Erich

last: Kueng

first: Ulrich

last: Certa

first: Stefania

last: Fedele

first: Anna

middle: L

last: Gündner

first: Ravi

last: Jagasia

first: Ginetta

last: Collo

first: Verdon

last: Taylor


title: Umbilical Cord Mesenchymal Stem Cells Derived Exosomal microRNA-148a-3p Inhibits Neointimal Hyperplasia by Targeting Serpine1

city: Guangzhou

first: Xiaoyu

last: Zhang

address: number 58, Zhongshan er road

institute: The first affiliated hospital of sun yat-sen unversity

summary: Restenosis is an inescapable problem when patients underwent percutaneous transluminal angioplasty because of intimal hyperplasia. Human umbilical cord mesenchymal stem cells derived exosomes (HucMSC-Exo) have been proved to promote reendothelialization to restrain the process of intimal hyperplasia. However, aberrant vascular smooth muscle cell (VSMC) proliferation, migration and dedifferentiation play more important roles in intimal hyperplasia, the effects and mechanisms of HucMSC-Exo upon VSMC are elusive

overall_design: Three samples from untreated mouse vascular smooth muscle cells and three samples from exosome treated mouse vascular smooth muscle cells

first: Yu

last: Zhou

first: Chen

last: Yao

first: Shenming


title: TLDA miRNA expression profiling of peripheral blood samples in PCOS patients

first: madavan

last: vasudevan

summary:
In the present study through TLDA analysis we looked into the miRNA differential expression in peripheral blood of PCOS patients v/s control women. The results implicated that many signalling networks as  MAPK pathway, Androgen signaling, Insulin signaling and Immune signaling are regulated in peripheral blood of PCOS patients. The data indicate that there is generic PCOS specific gene expression in  peripheral blood of PCOS subjects which can reflect the same from other PCO tissues.
Total RNA was extracted from peripheral blood of  4 PCOS patients and 4 control subjects and compared for miRNA diferential expression through TLDA

first: Krishna

last: Meera


title: The microbiome buffers tadpole hosts from the deleterious effects of heat stress: a hologenomic approach to understand host-microbe interactions under warming conditions.

city: Pittsburgh

first: Samantha

last: Fontaine

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

overall_design:
Refer to individual Series
Please note a related set of metagenomic data is available via BioProject PRJNA853287


title: RNA-Seq analysis of Col-0, VQ28OE9 and VQ28KO12

city: Yangling

first: Xingjie

last: Lan

state: Shaanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

summary: The goal of the RNA sequencing is to find out the signal pathway the VQ28 gene  involved in. Uninfected 30-day-old detached Arabidopsis rosette leaves of wild type Col-0, knock-out line VQ28KO12 and overexpression line VQ28OE9 were collected to isolate total RNA. Then, we created a final cDNA library and performed the 2×150bp paired-end sequencing on an Illumina Novaseq™ 6000. After removed the low quality bases and undetermined bases, we mapped reads to the genome.  The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05, and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs. In comparison with Col-0, constitutively overexpressing VQ28 caused the enrichment of most genes in MAPK signaling pathway and plant hormone signal transduction. Among the 11 genes up-regulated in VQ28OE9 but down-regulated in VQ28KO12, examining their expression by querying the Arabidopsis eFP Browser which contains an extensive collection of gene expression microarray data, six of them were involved in the response to abscisic acid (ABA). qRT-PCR analyses of expression presented that the six ABA-related genes were up-regulated in VQ28OE9 without infection.

overall_design: Examination of mRNA level in Col-0,VQ28KO12 and VQ28OE9 detached leaves

first: Xiaoxia

last: Wang

first: Quandan

last: Tao

first: Hua

last: Cao

first: Jinyang

last: Li

first: Yuling

last: Meng

first: Weixing

last: Shan


title: Cluster thinning effect on Pinot noir berry ripening.

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

summary: The impact of yield on fruit and wine quality has been studied extensively; vine response to increased yield is well known, but responsible mechanisms – including the regulation of pathways responsible for color, aroma and mouthfeel – have not been characterized at the level of genetic regulation. To examine the impact of crop load on transcriptomic and metabolomic changes during grape berry maturation vines from two cluster thinning treatments (50% or 75% of clusters removed following fruit set) were compared to control vines (no cluster thinning).  Treatments were applied to mature Pinot noir grapevines over three consecutive vintages. Agronomic parameters, including yield per vine and the yield to pruning weight ratio, as well as fruit and wine composition, were determined at harvest.  Fruit transcriptomic and metabolomic changes were measured in berry samples collected from each treatment at 7 to 10 day intervals from fruit set to harvest. The patterns of berry development by weight, sugar accumulation, and malic acid degradation indicated that vines responded differentially to crop load reduction by accelerating berry maturation progress. RNA-Seq analysis, and untargeted GC-MS and UHPLC-QTOF-MS -based metabolomic approaches were used. The indication of the acceleration of maturation transcriptional programs and of metabolite accumulation in the treated vines was suggested by multivariate analyses. To identify the transcriptional key triggers of this response we applied a two-regression step statistical approach which identified genes modulated over development dependent on the crop load. Comparing vintages we were able to estimate the environmental influence on the crop load treatments among years. The application of this multifaceted approach allowed the construction of robust models describing the impact of crop load on the genetic regulation of grape maturation.

overall_design: Cluster thinning treaments were applied removing 50% or 75% of clusters following fruit set. Grape berries were collected at ten-day intervals in 2012, and weekly in 2013 and 2014 beginning at fruit set until harvest (24.5 °Brix) at the same time of day (8:00 am). Samples were collected in randomized 8-vine block designs along nine rows (3 rows/treatment). Each sample entailed the collection of 26 clusters from each vine block. 60 berries, selected from 6 isolated clusters randomly selected from the vine blocks, were ground under liquid nitrogen. Seeds were removed in the grinding process. Frozen powder was aliquoted in 100mg and 400 mg samples for metabolite and RNA extractions respectively. Transcriptomic and metabolomic approaches were used to monitor the expression of all grapevine genes and to elucidate grape berry metabolome during development.

first: Chandra

last: Richter

first: Sara

last: Zenoni

first: Giovanni

last: Tornielli

first: Nicola

last: Vitulo

first: Silvia

last: Dal Santo

first: Nick

last: Dokoozlian

first: Mario

last: Pezzotti


title: Supranutritional Maternal Organic Selenium Supplementation During Different Trimesters of Pregnancy in Beef Cattle

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

summary: We used an RNA-Seq transcriptomic approach to investigate Longissimus dorsi muscle gene expression profiles of calves from cows receiving weekly Se-yeast boluses at supranutritional concentrations during different trimesters of gestation. Pregnant beef cows received, except the control group (CTR), weekly supranutritional selenium-yeast boluses (105 mg Se/wk) during the first (TR1), second (TR2), or third (TR3) trimester of gestation. Within 12 to 48 h of birth, muscle samples were collected from the Longissimus dorsi using a Bergstrom biopsy needle (inner diameter: 5 mm). Muscle biopsies were placed into sterile vials, stored on ice and frozen at – 80 ºC until total RNA isolation was performed. After sequencing and read quality control, we identified 3,048 unique differentially expressed genes (DEGs) across all group comparisons (FDR < 0.05 and |log2FC| > 1.5). Furthermore, we predicted 237 unique transcription factors that putatively regulate the DEGs. Our findings suggest a beneficial effect of supranutritional maternal organic Se supplementation during late gestation on Se-status and muscle development and function of newborn calves.

overall_design: Angus-cross cows that had calved at least once previously were assigned to one of four groups at conception (control and groups 1, 2, and 3 corresponding to trimester of Se-treatment: CTR, TR1, TR2, and TR3, respectively), using a randomized complete block design. Except in the CTR group, cows received Se-supplementation during their corresponding pregnancy trimester in the form of three Se-yeast (Phibro Selenium Yeast 2000, Prince Agri Products, Inc., Quincy IL) boluses per week for 13 weeks, equaling 105 mg Se/wk throughout their treatment trimester. Thus, cows received Se-yeast during the first (TR1), second (TR2), or third (TR3) trimester of gestation. In addition, cows had access to a mineral supplement containing 120 mg/kg Se (US FDA regulations) from Na selenite. Within each group of cows, ten were chosen for repeated measures based on uniform genetic background (black color), medium size, and middle aged (5 – 9 years). The resulting calf group demographics from these cows were as follows: CTR group n = 10 (3 females, 7 males), TR1 n = 9 (2 females, 7 males), TR2 n = 11 (3 females, 8 males), TR3 n = 10 (6 females, 4 males).   Within 12 to 48 h of birth, muscle samples were collected from the Longissimus dorsi using a Bergstrom biopsy needle (inner diameter: 5 mm). Muscle biopsies were placed into sterile vials, stored on ice and frozen at – 80 ºC until total RNA isolation was performed.  Total RNA was isolated using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MA), following the manufacturer's protocol. After RNA quality control, strand-specific libraries (poly-A enrichment) were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA). Paired-end sequencing (150-bp reads) at a depth of 20 M reads/sample was carried out on the Illumina NovaSeq 600 platform. RNA isolation, library preparation, and RNA sequencing were performed by Novogene Co. (Nanjing, China).  Read quality control was performed with FastQC v0.11.8 (https://bit.ly/3pCUvar) and MultiQC v1.9 (https://multiqc.info/) software. After QC, clean reads (38 samples) were mapped to the Bos taurus reference genome (ARS-UCD 1.2) using the STAR aligner v. 2.7.3a (https://rb.gy/dlgdva). The –quantMode GeneCounts flag from STAR and the annotation information (release 100, Ensembl) were used to determine the number of raw counts per gene in each sample. MultiQC was used for post-mapping quality control. Furthermore, exploratory data analyses were based on Principal Component Analysis (PCA) and clustering using the R-packages NOISeq v.2.31.0 (10.18129/B9.bioc.NOISeq), edgeR v.3.30.3 (10.18129/B9.bioc.edgeR), and factoextra v.1.0.7 (https://bit.ly/3s2fZPA).   The gene expression normalization procedure was performed through the DESeq2 v.1.28.1 (10.18129/B9.bioc.DESeq2) using the VST function. The DESeq2 design model included the dam’s age, offspring sex, and treatment group. Differentially expressed genes (DEGs) were identified between the treatments considering the t-test method proposed by Reverter et al. and implemented in the R-package CeTF v.1.0.7 (10.18129/B9.bioc.CeTF. The differences between the treatments, i.e., TR1 vs. CTR, TR2 vs. CTR, TR3 vs. CTR, were tested, and DEGs were considered significant at an FDR adjusted P-value < 0.05 and |log2 FC| > 1.5. The treatments were used as the reference group, and DEGs were classified as up or downregulated based on the log2 fold change direction. Gene annotation was performed using biomaRt v.2.38.0 (10.18129/B9.bioc.biomaRt) based on the B. taurus Ensembl database.

middle: J

first: Gerd

last: Bobe

first: Jean

middle: A

last: Hall


title: Comparative gene expression in mature egg cell, fertilized egg cell (1-1.5 hap) and fertilized zygote (2.5-3 hap)

city: Norman

first: Scott

last: Russell

state: OK

address: 770 Van Vleet Oval

department: Dept of Microbiology and Plant Biology

institute: University of Oklahoma

summary:
Egg cells represent the female partner that fuses with the sperm cell during fertilization in all multi-cellular eukaryotic organisms—and, in flowering plants, is a founder of the embryo.  We examined the transcriptome of Oryza sativa ssp. japonica (cv Katy) using the Affymetrix 57K rice genome GeneChip to provide an overview of genes activated in the maternal gamete, transcripts transmitted by the paternal genome, and changes in transcript up- and down-regulation during fertilization.
We used microarrays to detail the global program of gene expression in the egg cell at anthesis, complementing prior data on the male germ lineage, and following gene expression during fertilization and gamete fusion.

overall_design:
Female gametophytic cells consisting of isolated unfertilized egg cells (0 hr after pollination = 0 hap = anthesis), in vivo pollinated 1-1.5 hap fertilized egg cells, and in vivo pollinated 2.5-3 hap fertilized zygotes were compared before and soon after plasmogamy (cellular fusion) and karyogamy (nuclear fusion).
keywords: tissue expressional profile, female gametophyte germline, anthesis unfertilized egg cell, fertilized egg cell, fertilized zygote

first: Xiaoping

last: Gou


title: Paracrine Secretion of IL8 by Breast Cancer Stem Cells Promotes Therapeutic Resistance and Metastasis

city: Heifei

first: Mingming

last: Wu

state: Anhui

address: inZhai Road Baohe District

institute: University of Science and Technology of China

summary: Breast cancer stem cells (CSCs) play pivotal roles in cancer therapeutic failure and metastasis. However, it remains indeterminate how CSCs determine the progression of the bulk cancer cell population. Using a co-culture system in vitro and a co-implantation system in vivo, it is demonstrated herein that the breast cancer stem cell (BCSC) secretome rendered the bulk cancer cell population resistant to anti-estrogen and CDK4/6 inhibitor therapy; as well as increased the metastatic burden attributable to bulk cancer cells. Screening of BCSC secretome identified IL8 as a pivotal factor that potentiated ERα activity, endowed tamoxifen resistance and enhanced metastatic burden by regulation of bulk cancer cell behavior. Pharmacological inhibition of IL8 increased the efficacy of fulvestrant and/or palbociclib by reversing tamoxifen resistance and abrogated metastatic burden. Hence, this study has delineated the mechanism by which BCSCs determine the therapeutic response and metastatic of bulk cancer cells; and thereby suggests novel therapeutic strategies to ameliorate breast cancer outcomes.

overall_design: The BCSCs isolated from flow cytometry sorting or mammospheres culturing were seeded with the regular medium in monolayer culture for 48 hours. The medium from parallelly cultured parental cells was used as the control medium. The conditioned medium was centrifuged at 4,000 g for 3 minutes and filtered with a 0.22 μm filter unit (Millipore) to deplete any cell debris.the BCSCs isolated from flow cytometry sorting or mammospheres culturing were seeded with the regular medium in monolayer culture for 48 hours. The medium from parallelly cultured parental cells was used as the control medium. The conditioned medium was centrifuged at 4,000 g for 3 minutes and filtered with a 0.22 μm filter unit (Millipore) to deplete any cell debris. The MDA-MB-231 cells were cultured with the CM derived from BCSCs or parental cells for 48 hours, and the RNA was isolated and sequenced.

first: Xiao

last: Zhang

first: Tao

last: Zhu


title: Metabolic subgroups of Diversity Outbred mice show distinct phenotypic and transcriptomic signatures of obesity and insulin resistance

city: Durham

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

summary: Clinicians and researchers are turning towards precision medicine to treat and prevent obesity and diabetes, given the known contributions of genetics to these metabolic diseases and the wide variability reported in response to treatments. Animal models that incorporate the genetic diversity present in the human population may help discover novel genetic contributors to metabolic disease and test potential treatments. We characterized the Diversity Outbred (DO) mouse population as a model in which to study interindividual variability in metabolic disease and investigated the presence of metabolic subgroups within the population. Glucose metabolism was assessed in male Diversity Outbred (DO) mice after consumption of a high-fat diet for 14 weeks and profiled transcriptomic changes in liver, adipose, and muscle—key tissues involved in glucose homeostasis. To identify metabolic subgroups, we applied classification and regression tree analyses to metabolic phenotype measures as well as transcriptomic data. These findings suggest that DO mice exhibit a diversity of metabolic phenotypes that can be segmented into subgroups using a machine learning approach. The metabolic subgroups observed in the DO may be a useful for probing the phenotypic variability in metabolic disease observed in humans.

overall_design: Male DO mice received either control or high-fat diet (HFD) for 14 weeks. At study start animals were randomized and half of the mice (N=75) were placed on the High Fat diet (60 kcal %, D12492/D12492N; Research Diets, New Brunswick, NJ)  while the other half (N=75) continued receiving control diet ad libitum. Animals were examined for morbidity and clinical observation twice daily on weekdays and once daily on weekends and holidays. Body weight was measured prior to blood collection on week 1 and then weekly for the remainder of the study. Feed consumption was monitored weekly. During Week 1, 5, 9, and 14, mice were fasted for a period of 4-5 hours and resting-state glucose levels were measured. After 12 weeks, an oral glucose tolerance test was also conducted after mice were fasted overnight (approximately 16-18 hours). Serum insulin and leptin content as well as routine clinical chemistry were also measured. After 14 weeks animals were necropsied and tissues collected. Samples of liver, muscle, and adipose (abdominal) tissue were frozen in liquid nitrogen and stored at or below -70 degrees C. Total RNA was extracted from small sub-samples of these three tissues and gene expression was measured to investigate potential molecular changes driving variability among mice to allow subgroupings. Metabolic subgroups were identified using a machine-learning algorithm.

first: Madelyn

last: Huang

first: Matt

last: Ehinger

first: Margarita

last: Gruebbel

first: Yuanyuan

last: Li

first: Dahea

last: You

first: Natalie

last: Bell

first: Daven

last: Jackson-Humble

first: Dhiral

last: Phadke

first: Michele

last: Balik-Meisner

first: Ruchir

last: Shah

first: Keith

last: Shockley

first: Leah

last: Zorrilla

first: Leping

first: Alison

last: Harrill


title: Transcriptome analysis of SFRS8 siRNA (R_si_5d) and WT(R_WT_5d) in RAW264.7 cells

city: Nanjing

first: Yuanjiao

state: China

address: Xianlin Road

institute: nanjing university of chinese medicine

summary: Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expression in RAW264.7 cells when SFRS8 was interfered.

overall_design: Examination  in RAW264.7 cells.

first: YuanJiao

first: Ye

last: Yang

first: Chunyang

last: Gu


title: Desiccation-driven senescence in the resurrection plant Xerophyta schlechteri

city: Cape Town

first: Astrid

middle: Lillie

last: Radermacher

address: University Ave

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

summary: RNA-Seq data from the resurrection plant Xerophyta schlechteri during desiccation in three tissues: non-senescent, senescent and pre-senescent during dehydration and rehydration.

overall_design: Leaf blades were sampled from the plant at full turgor, 75%, 55%, 35%, <10% RWC and 48h after rehydration. RNA from the non-senescent, senescent and pre-senescent was extracted using a modified Trizol/RNEasy kit method. Library preparation was performed using the Illumina RNA-Seq kit as per manufacturer instructions, and sequencing was conducted on the Illumina MiSeq500 (San Diego, California) platform at Queensland University of Technology’s Central Analytical Research Facility. The Tuxedo suite (Trapnell et al., 2014) was used for annotation and mapping to the reference genome for this species (Costa et al., 2017).

first: A

first: J

last: Farrant

first: B

last: Williams

first: S

middle: G

last: Mundree


title: Global alternative RNA splicing and mRNA expression analysis of Epstein-Barr Virus EBNA2-regulated cells

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

summary:
Purpose: To identify the effect of EBV EBNA2 on cellular mRNA alternative splicings
Methods: HEK293 cells were transfected with either GFP-EBV EBNA2 vector or empty vector (NC)  for 48 hours. Then the cell RNA was sequenced by the Illumina NovaSeq 6000 high-throughput sequencing (RNA-seq, the second generation sequencing); and by the PacBio Sequel II platform (SMRT-seq, the third generation sequencing).
Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05.
Conclusions: Our study describes the mRNA changes (including mRNA expression and mRNA alternative splicing) induced by EBV-EBNA2 in HEK293 cells

overall_design: HEK293 cells were transfected with either GFP-EBV EBNA2 vector or empty vector (NC)  for 48 hours, and cellular RNA was used for RNA-sequencing (the second generation sequencing) and SMRT-sequencing (the third generation sequencing) to show the gene expression profile and mRNA splicing profile changes induced by EBV-EBNA2 transfection.

first: Qiu

last: Peng


title: Genome wide mapping of Nr1d1 (Reverb α) binding sites in Th1 (T-helper type 1) cells

city: Chandigarh

first: Pawan

last: Gupta

state: Chandigarh

address: Department of Cell Biology and Molecular Immunology, CSIR-Institute of Microbial Technology, Sector-39A

institute: CSIR-Institute of Microbial Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of this study was to identify all the sites to which our nuclear receptor Nr1d1 binds to and how this interaction with these various genes is influencing the programming of Th1 cells. Naive T-cells were isolated from C57BL/6 mice and programmed into Th1 cells. The cells were harvested after 3-4 days and to characterize the regions bound by Nr1d1, genome wide ChIP-sequencing using an Nr1d1 antibody was carried out. Short reads from IgG were used as a control for peak detection.

overall_design: Examination of Nr1d1 binding sites in genome of programmed Th1 cells.

first: Drishti

last: Tiwari


title: Histone methylation regulator PTIP orchestrates inflammatory responses via modulating acetylation state of cis-regulatory elements [BMDM-RNA-seq]

city: wuhan

first: Haojian

last: Zhang

state: Hubei

address: Donghu Rd

department: Medical Research Institute

institute: Wuhan university

summary: Innate immune cells including myeloid cells exhibit dynamic cellular switches during inflammatory and immune responses against infection. These processes are tightly regulated at different levels including the cis-regulatory elements of immune cells. However, it remains unclear how the dynamic states of cis-regulatory elements of innate immune cells are controlled during inflammatory responses. Here we found that histone methylation regulator PTIP orchestrates inflammatory responses of macrophages through regulating acetylation state of enhancers and promoters. Rapid elevated expression of PTIP is observed in primary human and mouse macrophages upon lipopolysaccharide (LPS) stimulation. Loss of PTIP represses transcription of pro-inflammatory genes, and activates expression of anti-inflammatory genes. Mechanistically, we found that, independent of its function in histone methylation, PTIP interacts with acetyltransferase p300 and deacetylase HDACs, and serves as a beacon to recruit them to specific sites of inflammatory genes respectively. PTIP deficiency alters H3K27 acetylation state of cis-regulatory elements of inflammatory genes. Moreover, PTIP and c-JUN shape a positive and feedforward regulatory circuit. In addition, PTIP deletion sustains immunosuppressive function of tumor-associated macrophages (TAMs) and promotes tumor growth. Overall, our findings uncover a critical role of PTIP in altering the acetylation state of cis-regulatory regions and fine-tuning the inflammatory responses of innate immune cells.

overall_design: [BMDM-RNA-seq] This dataset contains RNAseq experiments of in vitro polarized bone marrow derived macrophages (BMDMs), with wildtype (PtipWT) or PtipcKO genotype. BMDMs were treated with LPS (100 ng/ml) for 0 or 6 hours. Cells were harvested for RNA for RNAseq with two biological replicates.

first: Qifan

last: Wang

first: Jin

last: Hu

first: Guoqiang

last: Han


title: Histone methylation regulator PTIP orchestrates inflammatory responses via modulating acetylation state of cis-regulatory elements [TAM- RNA-seq]

overall_design: [TAM- RNA-seq] This dataset contains RNA-seq experiments of tumor associated macrophages (TAMs) isolated from PtipWT or PtipcKO mice. For TAM experiments, MC38 cell line was injected into PtipWT or PtipcKO mice. TAMs were harvested from the resultant tumors for RNAseq analysis with three biological replicates.


title: Transcriptomic analysis of fungus Penicillium oxalicum 114, laeA deletion strains and histone H2B point mutant strains

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

institute: shandong university

summary: RNA-seq was used to compare the responses of laeA deletion strain and histone H2B point mutant strains . The wild-type strain were also studied.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and mutant strains. qRT–PCR validation was performed using SYBR Green assays.

first: Xiujun

first: Yuqi

last: Qin

first: Yinbo

last: Qu


title: Expression of the MET oncogene correlates with upregulation of coagulation factor XII and procoagulant disorders in colorectal cancer

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary: Cancer patients often develop hemostasis disorders whose pathogenesis is poorly understood.  Previous work in mouse models has shown that these disorders can be sustained by the MET oncogene by transcriptional upregulation of hemostasis genes. Here we investigated the correlation between the procoagulant state of colorectal cancer patients, and overexpression of MET and hemostasis genes in the tumor. We found that, in a patient subset, blood levels of D-dimer and coagulation factor XII (F12) were frequently elevated, and reverted towards normality after surgery. Global expression profiling of tumor tissues and adjacent mucosae revealed a significant correlation between high  D-dimer levels in the blood, and overexpression of MET in the tumor. An “hemostasis gene signature”, including F12, cyclo-oxygenase 2, thromboxane synthase-1, plasminogen activator inhibitor-1, urokinase-type plasminogen activator and protein C receptor was associated with MET overexpression. This association was confirmed in an independent 173-sample CRC dataset. The mechanistic link between MET signaling and F12 expression was established experimentally in cell lines. These data indicate that MET contributes to the pathogenesis of coagulation disorders in CRC by upregulation of hemostasis genes including F12, and provide a candidate biomarker for the CRC-associated procoagulant state.

overall_design: Surgical samples from 23 colorectal cancer partients. From each patient, one sample from neoplastic tissue and one sample from adjacent normal mucosa were taken and analyzed.

first: Claudio

last: Isella

first: Carla

last: Boccaccio


title: Improving Risk Assessment for Metastatic Disease in Endometrioid Endometrial Cancer Patients Using Molecular and Clinical Features: an NRG Oncology / Gynecologic Oncology Group Study

city: Annandale

first: Kathleen

last: Darcy

state: VA

address: 3289 Woodburn Road Suite 370

department: Gynecologic Cancer Center of Excellence

institute: Henry M Jackson Foundation for the Advancement of Military Medicine

summary:
Accurate methods to predict nodal and distant metastasis are needed in endometrioid endometrial cancer (EEC) patients to advance personalized care and reduce both overtreatment and undertreatment.  A transcript-based classifier for predicting risk of nodal and distant metastasis in EEC patients was developed, and shown to outperform a panel of clinical and molecular features
We used microarrays to detail the gene expression in EEC patients and identified a classifer to predict nodal and distant metastasis

overall_design:
Frozen primary endometioid endometrial cancer tissues acquired at the time of primary surgical staging undrwent transcriptomic analysis using the Affymetrix U133 Plus 2.0 microarray platform.
contributor: GYNCOE
contributor: GOG


title: RNA-Seq Provides Insights into VEGF-Induced Signaling in Human Retinal Microvascular Endothelial Cells: Implications in Retinopathy of Prematurity [RNA-seq_2]

status: Public on Dec 29 2022

city: Salt Lake City

first: Mary Elizabeth

last: Hartnett

state: Utah

address: 65 Mario Capecchi Dr

department: Ophthalmology and Vision Sciences

institute: University of Utah

summary: The pathophysiology of retinopathy of prematurity (ROP) is postulated to first involve delayed intraretinal vascularization, followed by intravitreal neovascularization (IVNV). Although intravitreal agents that reduce the bioactivity of vascular endothelial growth factor (VEGF) are used to treat IVNV, concerns exist regarding their effects on intraretinal vascularization. In an experimental ROP model, VEGF receptor 2 (VEGFR2) knockdown in retinal endothelial cells reduced IVNV and promoted intraretinal vascularization, whereas knockdown of a downstream effector, signal transducer and activator of transcription 3 (STAT3) in retinal endothelial cells only reduced IVNV. In this study, we tested the hypothesis that the different pathways involved in VEGF-triggered VEGFR2 signaling and VEGF-triggered STAT3 signaling in retinal endothelial cells would allow us to delineate signaling pathways involved in IVNV from those involved in intraretinal vascularization in ROP. To address our hypothesis, we used RNA-sequencing and pathway enrichment analysis to determine changes in the transcriptome of cultured human retinal microvascular endothelial cells (HRMECs). Of the enriched pathways, inactivation of oncostatin M signaling was predicted by either KDR or STAT3 knockdown in the presence of VEGF. Activation of kinetochore metaphase signaling was predicted by KDR knockdown, whereas inactivation was predicted by STAT3 knockdown in the presence of VEGF. Inactivation of signaling by the Rho family of GTPases was predicted by KDR knockdown, but activation was predicted by STAT3 knockdown in the presence of VEGF. Taken together, our data identified unique signaling pathway differences between VEGF-triggered VEGFR2 and VEGF-triggered STAT3 in HRMECs that might have implications in ROP.

overall_design: Human retinal microvascular endothelial cells (HRMECs, Cell Systems, Krikland, WA, USA), passages 3–5, were cultured in attachment factor (Cell Systems) coated cultureware with the Endothelial Growth Medium BulletKit (EGM, Lonza, Walkersville, MD, USA) supplemented with 10% fetal bovine serum (FBS). Cultured HRMECs were transfected with equal concentrations of control small interfering RNA (siRNA) or STAT3 siRNA oligos (Thermo Fisher Scientific, Waltham, MA, USA) using Targefect Solution A and Virofect (Targeting Systems, El Cajon, CA, USA). Twenty-four hours after transfection, HRMECs were serum starved in Endothelial Basal Media (EBM, Lonza) for eight hours and then treated with either VEGF (25 ng/mL, R&D Systems, Minneapolis, MN, USA) or an equal volume of phosphate-buffered saline (PBS) as vehicle control for four hours. Overall, this study had four experimental groups and 3 biological replicates per group for a total of 12 samples from one independent experiment.

first: Mary

middle: E

first: Aniket

last: Ramshekar


title: RNA-Seq Provides Insights into VEGF-Induced Signaling in Human Retinal Microvascular Endothelial Cells: Implications in Retinopathy of Prematurity [RNA-seq_1]

overall_design: Human retinal microvascular endothelial cells (HRMECs, Cell Systems, Krikland, WA, USA), passages 3–5, were cultured in attachment factor (Cell Systems) coated cultureware with the Endothelial Growth Medium BulletKit (EGM, Lonza, Walkersville, MD, USA) supplemented with 10% fetal bovine serum (FBS). Cultured HRMECs were transfected with equal concentrations of control small interfering RNA (siRNA) or KDR siRNA oligos (Thermo Fisher Scientific, Waltham, MA, USA) using Targefect Solution A and Virofect (Targeting Systems, El Cajon, CA, USA). Twenty-four hours after transfection, HRMECs were serum starved in Endothelial Basal Media (EBM, Lonza) for eight hours and then treated with either VEGF (25 ng/mL, R&D Systems, Minneapolis, MN, USA) or an equal volume of phosphate-buffered saline (PBS) as vehicle control for four hours. Overall, this study had four experimental groups and 3 biological replicates per group for a total of 12 samples from one independent experiment.


title: The transcriptional signature for Hepatocyte Growth Factor-driven invasive growth predicts poor prognosis of human hepatocellular carcinoma.

summary: During embryogenesis, Hepatocyte Growth Factor (HGF) elicits a distinctive morphogenetic program, the invasive growth, by the activation of MET, whose aberrant activation in cancer drives metastatic progression.  Aim of this work is to define and characterize the transcriptional signature of invasive growth, and to verify its activation in human cancers. Global expression profiling was carried out on mouse liver stem/progenitor cells (MLP-29) stimulated for different times, one, six and twenty-four hours, in vitro with HGF to define the invasive growth signature. Meta-analysis of human cancer microarray data was carried out to dissect the transcriptional modules of the invasive growth that are aberrantly activated during carcinogenesis of hepatocellular carcinoma. Differential expression analysis identified 2643 regulated genes by HGF, the invasive growth signature, subdivided in 11 gene expression clusters revealing waves of time coded transcriptional regulation. Those waves have been in-silico associated with the regulative role of the transcriptional unit of Rela/Nfkbia and Fos/Jun and biological features recapitulating the physiological invasive growth phenotype observed in cell line, such as cell motility and scattering, cellular proliferation and protection from apoptosis, cytoskeletal rearangement. Genomic meta-analysis on hepatocellular carcinoma identified of a core genes set (323 gene symbols), consistently regulated between MLP-29 and human tumors and significantly associated with cancer aggressiveness and metastasis p.val < 1*10-6, HR=5.404 CI= 2.570-11.365. The invasive growth signature recapitulates the physiopatological program driven by the stimulation of HGF in normal embryonic liver cells and its activity is observed in HCC as well as in several other tumors. This signature is associated with neoplastic progression and reliably predicts human HCC disease outcome, suggesting the involvement of the invasive growth and cancer in cancer progression. These results prompt the future application of anti-met target therapies in HCC and the application of the signature for both prognostic and predictive purposes.

overall_design: TimeCourse, 3 experimental points, one reference, 2 biological replicates per experiment

first: Tommaso

last: Renzulli


title: Comparative gene expression in synergid cells and antipodal cells at anthesis

first: Scott

last: Russell

summary:
Synergid cells represent the receptor cell type of angiosperm gametophytes that attract and receive the male pollen tube and are implicated in the transfer of the sperm cells to the target egg and central cells prior to double fertilization.  The antipodals represent an accessory cell type that typically degenerates after fertilization; in rice it may initially have a short-lived nutritional role prior to endosperm establishment.  We examined the transcriptome of these two cell types using Oryza sativa ssp. japonica (cv Katy) using the Affymetrix 57K rice genome GeneChip to provide an overview of genes activated at receptivity in the synergid and antipodal cells and transcript up- and down-regulated at female gametophyte maturity just prior to fertilization.
This is part of a larger microarray paroject to examine the global program of gene expression during sexual reproduction in Oryza sativa which serves as a model angiosperm in which male and female gametophytic and embryonic cells may be readily isolated and characterized.

overall_design: Two female gametophytic accessory cell types were isolated from living embryo sacs, consisting of isolated synergid cells and antipodal cells collected at floral anthesis.

first: Xiaoping

last: Gou


title: Pleiotropic architectures of porcine immune and growth trait pairs revealed by a self-product-based transcriptome method

city: Wuhan

first: Pingping

address: Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary:
Pleiotropy is an important biological phenomenon with complicated genetic architectures for multiple traits. To date, pleiotropy was mainly identified by multi-trait GWAS, but GWAS method has its disadvantages, and new developments for pleiotropy detection methods are needed. Here we defined a novel metric, self-product, and based on it, we developed a transcriptome method to identify candidate pleiotropic genes and revealed the genetic architectures of immune and growth trait pairs in pigs.
In statistics, the well-known covariance is used to quantify the co-variation between two variables. Suppose that X and Y represent two traits with individual records of xi and yi and corresponding means of μx and μy. We defined the individual-level product (xi − μx)(yi − μy) as self-product. Obviously, self-product is an individual-level measurement for the co-variation between two traits of the ith individual, and the covariance Cov(X , Y) is the mean of the self-product (xi − μx)(yi − μy).
The self-product-based transcriptome method was tested using immune and growth trait pairs in pigs.We identify candidate pleiotropic genes using the Affymetrix Porcine Genechip.
Result:Comparative transcriptome analyses identified dozens of candidate pleiotropic genes related to 8 trait pairs from two tails of self-product distribution. GO enrichment analysis indicated that most of identified pleiotropic genes were involved in both immune- and growth-related biological processes. We established pleiotropic genes interaction network to exhibit core genes shared by 8 trait pairs, of which CCL5 and IL-10 genes were hub genes. Genetic association analyses showed that SmaI-polymorphisms of CCL5 and IL-10 genes had significant associations with phenotypic co-variations of multiple trait pairs, indicating that the variants in pleiotropic genes were also pleiotropic variants.
Conclusions:The validity of our proposed method was preliminarily verified, and our findings provide new insights into the genetic basis of pleiotropic architectures of immune and growth trait pairs in pigs.

overall_design:
A total of 8 immune and growth trait pairs were selected, including CD4+--W35, CD8+--W35, IFN-alpha--W35, IL-10--W35, CD4+--IFN-alpha, CD4+--IL-10, CD8+--IFN-alpha, and CD8+--IL-10, where W35 refers to the weight on day 35. After calculation, each trait pair has a self-product measurement. For each trait pair, all individuals were ordered according to the values of self-product. Five extreme individuals were separately selected from two tails of the self-product distribution in each trait pair, and the selected individuals were divided into high and low groups for subsequent transcriptome experiments. The total RNAs were extracted from blood samples with Trizol reagent following supplier’s recommendation. RNA tagging and hybridization were performed at a commercial Affymetrix array service company (GeneTech Biotechnology Limited Company, Shang Hai, China).
In our study, CEL files were one-to-one with individuals, because the same individuals appeared repeatedly in different experimental groups, so the same CEL files were also shared by multiple experimental groups. CEL files have been named so that all CEL files have unique names but the raw data contained in these files are identical. For example, raw data in CD4+--W35_low_2240.CEL are identical to raw data contained in IFN-alpha--W35_low_2240.CEL.

first: Chao

first: Wei

first: Yalan

last: Wu

first: Daoyuan

first: Shuhong

last: Zhao

first: Mengjin

last: Zhu


title: Zinc finger protein 251 deficiency impairs glucose metabolism through adipocyte hypertrophy

city: Seoul

first: Han Geuk

last: Seo

address: 120 Neungdong-ro, Gwangjin-gu

institute: Konkuk University

summary: To investigate glucose intolerance and white adipocyte hypertrophy shown in ZFP251 knockout (KO) mice, We performed gene expression profiling analysis using data obtained from the RNA-seq of epididymal white adipose tissue (eWAT).

overall_design: We performed RNA-seq from ZFP251 KO and its littermate wild-type mice to understand ZFP251 function in eWAT.

first: Eunsu

last: Kim

first: Sun

last: Ham

first: Jung

middle: S

last: Hwang

first: Jun

middle: P

last: Won

first: Hyuk

last: Lee

first: Jinwoo

last: Hur

first: Han


title: The interplay between SRC kinase and Caspase-8 phosphorylation on Y380 sustains the aberrant activation of NFkB signaling and promotes angiogenesis and resistance to therapy in glioblastoma

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

institute: Italian National Cancer Institute "Regina Elena"

summary:
Caspase-8 is a cysteine protease that plays an essential role in apoptosis. Consistently with its canonical proapoptotic function, cancer cells may genetically or epigenetically downregulate its expression, or may dampen its enzymatic activity by promoting the expression of FLIP protein.
However, unexpectedly, Caspase-8 expression is often retained in cancer even in the absence of FLIP up regulation, suggesting that alternative mechanisms may be exploited by cancer cells to cope with Caspase-8 expression. In this regard, we reported that SRC tyrosine kinase, which is aberrantly activated in many tumors, promotes Caspase-8 phosphorylation on Tyr380 and this event impairs Caspase-8 autoprocessing and full activation. Here, we investigated the significance of Caspase-8 expression in the modulation of gene expression in glioblastoma, a brain tumor where both Caspase-8 expression and SRC activity are often aberrantly upregulated. Transcriptomic analyses identified inflammatory response as a major target of Caspase-8 expression, and in particular, the NFkB signaling as one of the most affected pathways. More importantly, we could show that SRC kinase activity promotes Caspase-8 phosphorylation on Tyr380 in this context and that this event drives the assembly of a multiprotein complex that triggers NFkB activation, thereby inducing the expression of inflammatory and pro-angiogenetic factors. Moreover Caspase-8 phosphorylation on Tyr380 sustains neoangiogenesis and resistance to radiotherapy. In summary, our work identifies a novel interplay between SRC kinase and Caspase-8 that allows cancer cells to hijack Caspase-8 to sustain tumor growth.

overall_design: 3 biological replicates for shCTR (sc_U87) and 3 biological replicates for shC8 (shC8_U87)

first: Claudia

last: Contadini

first: Alessandra

last: Ferri

first: Marta

last: Di Martile

first: Donatella

last: Del Bufalo

first: Francesca

last: De Nicola

first: Maurizio

last: Fanciulli

last: Sacco

first: Gloria

last: Donninelli

first: Alessia

last: Capone

first: Elisabetta

last: Volpe

first: Nadine

last: Keller

first: Dwayne

last: Stupack

first: Daniela

last: Barilà


title: mRNAseq in forebrain and cerebellum of wild-type mice at postnatal 2 weeks age

city: Niigata

first: Nozomu

last: Yoshioka

address: 1－757, Asahimachi-dori, Chuo-ku

department: Graduate School of Medical and Dental Sciences

country: Japan

institute: Niigata university

summary: We sequenced mRNA from mouse brain to compare gene expression level between 2 forebrain and 2 cerebellum.

overall_design: mRNA profiles obtained from 2 differet wild-type mice were generated by deep sequencing using Illumina NovaSeq6000.

first: Dang

last: Tran

first: Masato

last: Yano

first: Hirohide

last: Takebayashi


title: Cell type specific transcriptomic alterations in prefrontal deep-layer pyramidal neurons in individuals with a history of childhood abuse

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

summary: Childhood abuse significantly increases the lifetime risk of negative mental health outcomes, including psychiatric disorders, such as depression and suicide. While clinical and epidemiological associations are well characterized, the molecular mechanisms through which adverse experiences in early life influence mental health outcomes over the lifespan remain unclear. In this study, we employed laser capture microdissection followed by RNA sequencing (LCM-seq) to investigate transcriptomic alterations to prefrontal deep-layer pyramidal neurons in individuals with a history of childhood abuse (N=24) in comparison to controls (N = 21). We first showed that LCM-seqproduced high-quality transcriptomic data that was strongly enriched for our cell type of interest (95.8% contribution).  Differential expression analysis revealed119 genes that were altered between cases versus controls. Using weighted correlation network analysis (WGCNA) we next identified a network of downregulated genes, in individuals with a history of childhood abuse (r = -0.30, p = 0.04), that was enriched in pathways related to nervous system development and plasticity. The eigengene of this network was significantly correlated (r(23) = 0.490, p = 0.021) with average cell body volume of deep-layer pyramidal neurons. Of the 1042 mRNA genes within this network, 81 were differentially expressed between cases and controls. Using high-throughput qPCR, and comparing with an additional group of depressed subjects who died by suicide without a history of childhood abuse (N = 29), we found 7 genes whose expression levels were significantly (p < 0.05) predicted by a history of childhood abuse but not major depressive disorder and suicide.Our study, therefore, advances our understanding of the long term impact of childhood abuse and points to some of the molecular pathways that may underly previously observed alterations innervous system development and plasticity.

overall_design: The cohort used for RNA sequencing consisted of frontopolar cortex tissue (Brodmann area 10) from subjects who had a history of severe childhood abuse (N=24), as well as control subjects with no psychiatric histories (N=21).

first: Daniel

last: Almeida

first: Gary

last: Chen

first: Jean-François

last: Théroux

first: Laura

last: Fiori

first: Dominique

last: Mirault

first: Cynthia

last: McMahan

first: Maria-Antionietta

last: Davoli

first: Naguib

last: Mechawar


title: Mediating a host cell signaling pathway linked to the overwinter mortality offers a promising therapeutic approach for improving bee health

city: Beltsville

first: Judy

email: judy.chen@usda.gov, george.liu@usda.gov

state: Maryland

address: 306 Powder Mill Road

department: Agriculture

institute: USDA-ARS-BARC

summary: Overwintering mortality is the greatest threat to the supply of healthy bee colonies available for pollination of spring-blooming crops, but efforts to mitigate colony losses are hindered because underlying mechanisms remain poorly understood. In the present study, we identified that sirtuin signaling pathway is the most significantly affected pathway in collapsing overwintering colonies that carried a high prevalence of pathogens and is a convergent signaling hub that links mitochondrial dysfunction and metabolism alterations. We showed that the expression of SIRT1, a major sirtuin regulating energy and immune metabolism, was significantly downregulated in diseased overwintering bees and bees exposed to cold challenge alone. We demonstrated that activation of SIRT1 expression by SRT1720, a SIRT1 activator, could result in increased robustness and lifespan extension of cold-stressed bees. The novel information gained from this study provides a promising avenue for the development of therapeutic strategies for mitigating colony losses, both overwinter and annually.

overall_design: The study is divided into four distinct phases. Phase I involved continuous pathogen screening of overwintering bees for four years. Phase II was where RNA-Seq transcriptional profiling of overwintering honey bee host responses to pathogenic infection was conducted. qRT-PCR was performed in Phase III to confirm the results of the differential expression analysis of transcriptome data of selected genes. Lastly, laboratory bioassays were conducted in Phase IV to measure the effects of cold challenges on bee survivorship and stress responses and to assess the effect of SRT1720, an activator of sirtuin 1 (Sirt1) which is a crucial modulator of energy and immune metabolism, on lifespan extension of cold-challenged honey bees.

first: Yan

first: Yi

last: Zhang


title: Whole-transcriptome analysis and construction of a leaf and petiole development-related ceRNA regulatory network in baby Chinese cabbage (Brassica campestris L. ssp. pekinensis)

city: shenyang

first: jun

last: zhang

address: liaoning

institute: Shenyang Agricultural University

summary: Background: The growth and development of leaf and petiole have an important influence on the photosynthesis of plants. The research on molecular mechanism of leaf and petiole development is of great significance, whether it is to improve plant photosynthetic efficiency, cultivate varieties with high photosynthetic efficiency, or improve the yield of crops using leaves as food organs. In this study, we aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). These data were then used to construct competitive endogenous RNA (ceRNA) networks, which can provide valuable information for better understanding the mechanism of leaf and petiole development.  Results: In this study, the leaf and petiole of the baby Chinese cabbage inbred line ‘PHL’ were used as research materials for whole-transcriptome sequencing. A total of 10646 differentially expressed (DE) mRNAs, 303 DE lncRNAs, 7 DE circRNAs, and 195 DE miRNAs were identified between the leaf and petiole. Some transcription factors or proteins that play important roles in leaf and petiole development were identified, such as xyloglucan endotransglucosylase/hydrolase (XTH) protein, expansion protein, TCP15 transcription factor, bHLH transcription factor, LOB domain protein, cellulose synthase (CESA), MOR1-like protein, and plant hormone biosynthesis related genes. Additionally, we constructed a leaf and petiole development-related ceRNA regulatory network, and obtained 85 pairs of ceRNA relationships, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA and 2 DEmiRNA-DEcircRNA. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaf and petiole of baby Chinese cabbage were screened from transcriptome data for subcellular localization analysis and overexpression transgenic verification. The results showed that BrLSH1, BrLSH2 and BrLSH3 were nucleoprotein and BrLSH2 has an obvious inhibitory effect on the growth and development of Arabidopsis thaliana.  Conclusions: Our results revealed the potential mRNAs and non-coding RNAs (ncRNAs) involved in leaf and petiole development, which laid a foundation for further research on the molecular mechanism of leaf and petiole development in Chinese cabbage.

overall_design: In this study, whole-transcriptome sequencing was performed on leaf and petiole samples of baby Chinese cabbage. A total of 10646 DEmRNAs, 303 DElncRNAs, 7 DEcircRNAs, and 195 DEmiRNAs were identified as being differentially expressed between ‘leaf’ and ‘pet’. GO annotation and KEGG pathway enrichment analyses were performed on the differentially expressed RNAs, revealing their important roles in the regulation of leaf and petiole development. Some transcription factors and proteins that play important roles in leaf and petiole development were identified, such as XTH protein, expansion protein, TCP15 transcription factor, bHLH transcription factor, LOB domain protein, CESA, MOR1-like protein, and plant hormone biosynthesis related genes. Moreover, we constructed the first leaf and petiole development-related ceRNA‒miRNA–target gene regulatory network in Chinese cabbage, comprising 41 DEmRNAs, 18 DEmiRNAs, 9 DElncRNAs, and 1 DEcircRNAs. The subcellular localization analysis and over expression transgenic verification of BrLSH1, BrLSH2 and BrLSH3, which were differentially expressed between the leaf and petiole, were carried out. The results showed that BrLSH1, BrLSH2 and BrLSH3 were nucleoproteins, and BrLSH2 significantly inhibited the growth and development of Arabidopsis thaliana. Our findings provide a systematic recognition of mRNA and ncRNA related to leaf and petiole development, and lay a foundation for further exploring the molecular regulation mechanism of leaf and petiole development in Chinese cabbage.

first: Zhiyong

last: Liu

first: Fengyan

last: Shi

first: Zifan

last: Zhao

first: Yang

last: Jiang


title: Cell autonomous expression of Bcl6 is required to maintain lineage identity of mouse CCR6+ ILC3s [16s rDNA]

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: Innate lymphoid cells (ILC) are similar to T helper (Th) cells in expression of cytokines and transcription factors. For example, RORγt is the lineage-specific transcription factor for both ILC3 and Th17 cells. However, the ILC counterpart for BCL6-expressing T follicular helper (Tfh) cells has not been defined. Here, we report that in the ILC compartment, BCL6 is selectively co-expressed with not only CXCR5, but also RORγt and CCR6 in ILC3 from multiple tissues. BCL6-deficient ILC3 produce enhanced levels of IL-17A and IL-22. More importantly, phenotypic and single-cell ATAC-seq analysis show that absence of BCL6 in mature ILC3 increases the numbers of ILC1 and transitional cells co-expressing ILC3 and ILC1 marker genes. A lineage-tracing experiment further reveals BCL6+ ILC3 to ILC1 trans-differentiation under steady state. Lastly, microbiota promote BCL6 expression in colonic CCR6+ ILC3, and thus reinforce their stability. Collectively, our data have demonstrated that CCR6+ ILC3 have both Th17 and Tfh programs and that BCL6 expression in these cells functions to maintain their lineage identity.

overall_design: 16s rDNA sequencing of colonic feces matter from WT (Bcl6^fl/fl Rag^-/-) and KO (Vav1^cre Bcl6^fl/fl Rag^-/-) mice

first: Yuling

last: Li


title: Transcriptional changes in human palate and skin healing

city: Chicago

first: Trevor

middle: R

last: Leonardo

state: Illinois

address: 801 South Paulina Street

department: Medicine

institute: University of Illinois at Chicago

summary: Most human tissue injuries lead to the formation of a fibrous scar and result in the loss of functional tissue. One adult tissue that exhibits a more regenerative response to injury with minimal scarring is the oral mucosa. We generated a microarray gene expression dataset to examine the response to injury from human palate and skin excisional biopsies spanning the first seven days after wounding. Differential expression analyses over time were performed in each tissue to identify genes overexpressed or underexpressed compared to baseline unwounded tissue. To attribute biological processes of interest to these gene expression changes, gene set enrichment analysis was used to identify core gene sets that are enriched over the time-course of the wound healing process with respect to unwounded tissue. This analysis identified gene sets uniquely enriched in either palate or skin wounds and gene sets that are enriched in both tissues in at least one time point after injury. Finally, a cell-deconvolution analysis was performed to better understand the cell type distribution in these tissues and how it changes over the time course of wound healing. This dataset provides a source of human wound gene expression data that includes two tissue types with distinct regenerative and scarring phenotypes.

overall_design: 96 samples across 18 subjects, 9 male, 9 female, 5 time points (Day 0, 6 hours, Day 1, Day 3, Day 7).

first: Luisa

last: DiPietro

first: Phillip

middle: T

last: Marucha


title: Methylome and transcriptome sequencing to study epigenetic alterations in colon associated fibroblasts from normal, colitis and cancer associated fibroblasts

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

type: Methylation profiling by high throughput sequencing

summary: The colon cancer associated fibroblasts are part of the tumor microenvironment and has been shown to facilitate colon cancer progression by secretion of various signaling molecules and growth hormones. Similarly, the fibroblasts associated with colitic colons secrete pro-inflammatory cytokines that promote inflammation of the colon.  However, the molecular mechanisms that underlie these gene expression changes in these fibroblasts is unclear. To characterize the epigenetic mechanisms that may contribute to the gene expression changes in these fibroblasts, we performed RNA-seq and MBD-isolated genome sequencing (MiGS or MBD-seq) on colon associated fibroblasts isolated from normal, colitis and cancer patients.

overall_design: DNA and RNA were extracted from cultured colon associated fibroblasts from normal, colitis and cancer patients using Qiagen Allprep Kit. The DNA samples were used for MBD-isolated genome sequencing (MiGS), followed by addition of illumina adapters for high-throughput sequencing. The RNA samples were used for paired end Stranded RNA-seq.

first: Nagarajavel

last: Vivekananthan

first: Emina

last: Huang

first: Steven

last: Signs


title: Differential expression of miRNA in ischemia-reperfusion myocardium

city: Zunyi

first: Song

last: Cao

address: 149 Dalian Street

institute: Affiliated Hospital of Zunyi Medical University

summary: To detect the differential expression of miRNA in normal rat myocardium and ischemic hypoxic myocardium

overall_design: The samples were normal rat hearts and the hearts that recovered blood flow for half an hour after ligation of the left anterior descending coronary artery for half an hour. The miRNAs expressed in the hearts of the two groups were detected.

first: Haiying

last: Wang

first: Tian

last: Yu


title: Next generation sequencing to determine alternative cleavage and polyadenylation events among prostate and prostate cancer cell lines

summary: Alternative cleavage and polyadenylation (APA) is a form of transcriptional regulation via shifts in how frequently multiple polyadenylation (polyA) sites within genes are used across biological conditions. APA can result in transcripts with varying length and information content, and has been linked to gene regulation in both cancer and development. To provide a reference for investigating APA in the context of prostate cancer, we performed a genome-wide quantification of polyA site usage using a next generation sequencing technique. By priming the polyA-tails of an RNA library, we mapped cleavage sites and abundances with base-pair resolution across the genomes of one normal prostate and two prostate cancer cell lines. This data can be used to detect APA events among these cell line models, and integration of these data with APA events from clinical prostate cancer samples can lead to candidate genes for future mechanistic studies of the regulation and function of APA in cancer.

overall_design: Biological quadruplicates of the PrEC (normal prostate), LNCaP (prostate cancer), and DU145 (prostate cancer) cell lines were subjected to polyA-site sequencing.

first: Thomas

last: Sweet


title: Next generation sequencing to determine polyadenylation events in DICER hypomorph cells

summary: Alternative cleavage and polyadenylation (APA) is a form of transcriptional regulation via shifts in how frequently multiple polyadenylation (polyA) sites within genes are used across biological conditions. APA can result in transcripts with varying length and information content, and has been linked to gene regulation in both cancer and development. We performed a genome-wide quantification of polyA site usage using a next generation sequencing technique. By priming the polyA-tails of an RNA library, we mapped cleavage sites and abundances with base-pair resolution across the genomes of the DICER(ex5) hypomorph cells. The DICER cell line is derived from the parental HCT116 colon cancer cell line, but has an ablation of DICER function. This polyA sequencing data may be used to interrogate any cross-talk between DICER function and APA.

overall_design: Biological quadruplicates of the DICER cell line were subjected to polyA-site sequencing.

first: Jeffrey

middle: M

last: Bhasin


title: Transcriptome-Wide Profiling of mRNA N6-Methyladenosine Modification in Rice Panicles and Flag Leaves

city: Xinxiang

first: Li

address: No.46, Jianshe East Road

department: College of Life Science

institute: Henan Normal University

summary: N6-methyladenosine (m6A) modification is essential for plant growth and development. However, the spatiotemporal dynamics of m6A methylation in rice organ differentiation and development remain largely unknown. We profiled transcriptome-wide m6A landscapes from panicle at booting stage (PB) and flowering stage (PF), and flag leaf at flowering stage (LF), the global m6A level significantly differed among three tissues, which was closely associated with the expression of writer and eraser genes. The methylated gene ratio was higher in flag leaf than in panicle. Compared with common methylated genes, tissue-specific methylated genes showed both lower m6A modification and expression level, and the preference of m6A deposition in CDS region. The m6A profiles varied more between different organs than the same organ at different stages. Negative correlation between m6A level and gene expression was observed in PF vs. PB, but not in PF vs. LF, indicting the complicated regulation of m6A on gene expression. The distinct expression pattern of m6A reader genes imply they may affect gene stability through binding. Overall, our findings demonstrate the crucial roles of m6A in panicle development and photosynthesis feature of the flag leaf, and provide new insights into molecular mechanism of organ differentiation and development in rice.

overall_design: Examination of  m6A modification patterns in rice panicles and flag leaves at two different stages.

first: Yong-Fang

first: Chenhui

last: Yang


title: Cell autonomous expression of Bcl6 is required to maintain lineage identity of mouse CCR6+ ILC3s

status: Public on Dec 28 2022

first: Chen

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

sample_organism:
Mus musculus
feces metagenome

platform_organism:
Mus musculus
feces metagenome

overall_design: Refer to individual Series


title: Cell autonomous expression of Bcl6 is required to maintain lineage identity of mouse CCR6+ ILC3s [RNA-seq in vivo]

overall_design: bulk RNA-seq of total intestinal BCL6+ ILC3 and BCL6- ILC3 from B6 background Bcl6^RFP/RFP Rorc^GFP/+ double reporter mice

first: Yuling


title: Gene expression analysis of control and Dnd1-cKO germ cells at E11.5.

city: Yokohama

first: Atsuki

last: Imai

state: Japan

institute: Yokohama National University

summary: The present investigation was to identify transcriptomic changes of control and Dnd1-cKO PGCs at E11.5 by RNA-seq analysis. We identified 181 upregulated and 141 downregulated genes in Dnd1-cKO PGCs.

overall_design: There were gene expression data of Nanog-EGFP positive PGCs from testes of control and Dnd1-cKO embryos at E11.5. Each contains five replicates of transcriptome data.

first: Kazuya

last: Matsuda

first: Yuki

last: Niimi

first: Atsushi

last: Suzuki


title: Transcriptomic analysis of colorectal cancer cells treated with Oil Production Waste Products (OPWPs) reveals enrichment of pathways of mitochondrial functionality

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

institute: University of Verona

summary: Oil Production Waste Products (OPWPs) derive from olive mill and represent a crucial environmental problem due to the high polyphenolic content able to pollute the ground. One option to reduce the OPWPs’ environmental impact is to exploit polyphenols biological properties. We sought to analyze the transcriptomic variations of colorectal cancer cells exposed to the OPWPs extracts and hydroxytyrosol, the major component, to recognize unknown and ill-defined characteristics. Among the top affected pathways identified by GSEA, we focused on oxidative phosphorylation in an in vitro system. Colorectal cancer HCT116 and LoVo cells treated with hydroxytyrosol or OPWPs extracts showed enhancement of the respiratory chain complexes protein levels, ATP production and membrane potential, suggesting stimulation of mitochondrial functions. The major proteins involved in mitochondrial biogenesis and fusion events of mitochondrial dynamics were positively affected, as by western blot, fostering increase of the mitochondrial mass organized in a network of elongated organelles. Mechanistically, we proved that PPAR mediates the effects as they are mimicked by a specific ligand and impaired by its inhibition. OPWPs extracts and hydroxytyrosol, thus, promote mitochondrial functionality via a feed-forward regulatory loop involving the PPAR/PGC-1 axis. These results support their use in functional foods and as adjuvants in cancer therapy.

overall_design: In all experiments, HCT116 cells were treated with 0.0154 mg mL−1 HTyr or 0.0154 mg mL−1 OPWPs extracts for 72 h; LoVo cells were treated with 0.0231 mg mL−1 HTyr or 0.0231 mg mL−1 OPWPs extracts for 72 h

first: Manuela

last: Leo

first: Livio

last: Muccillo

first: Erica

last: Pranzini

first: Giovannina

last: Barisciano

first: Matteo

last: Parri

first: Giulia

last: Lopatriello

first: Marco

last: Carlomagno

first: Maria

last: Taddei

first: Lina

last: Sabatino


title: Shading Effects on Leaf Color Conversion and Biosynthesis of Three Major Secondary Metabolites in the Albino Tea Cultivar ‘Yujinxiang’

city: Hangzhou

first: Xu

last: Ping

state: Zhejiang

address: 866 Yuhangtang Road

department: Tea Research Institute

institute: Zhejiang University

summary: An increasing amount of evidence attest that the tea made by albino tea cultivars processes characteristic aroma and taste, which has been considered as a new potential product in the market. Therefore, flavor formation mechanism of albino tea cultivars have drawn exceeding attention from researchers. In this study, transcriptome, metabolomics, and whole-genome bisulfite sequencing (WGBS) were employed to investigate shading effects on leaf color conversion and biosynthesis of three major secondary metabolites in the Albino tea cultivar ‘Yujinxiang’. The increase of leaf chlorophyll level is the major cause of shaded leaf greening from young pale or yellow leaf. Transcriptome analysis showed differentially expressed genes (DEGs) mainly participated in biosynthesis of amino acids, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, sulfur metabolism, purine metabolism, and pentose and glucuronate interconversions in shading period compared with control group. The result of metabolomics indicated the total catechins level of shading group was significantly decreased than the control; however, the abundance of caffeine was markedly increased, and theanine level was nearly not influenced. Whole-genome DNA methylation analysis revealed that the global genomic DNA methylation patterns of shading period were remarkably altered compared with the control. Furthermore, differentially methylated regions (DMRs) and the DMR-related DEGs between shading and non-shading analysis indicated the DMR-related DEGs were the critical participants in biosynthesis of three major secondary metabolites. To sum up, these findings suggested that the altered levels of DNA methylation may be the main cause for biosynthesis changes of three major secondary metabolites in ‘Yujinxiang’.

overall_design: mRNA expression profile of tea plants' leaves after 5-day shading (SD) and followed 5-day regaining (RD) light treatment and normal leaves

first: Ping

last: Xu