title: Very low protein diets lead to reduced food intake and weight loss, linked to inhibition of hypothalamic mTOR signaling, in mice

city: BEIJING

first: Yingga

last: Wu

state: BEIJING

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Purpose: To investigate graded levels of low protien dites effects on hypothalamic gene expression pattern, RNA-seq was performed on hypothalamus of mice treated with different levels of low protein and normal protein under both 60% fat and 20% fat conditions. Methods: There were 8 diets in total, the fat content of first 4 diets were fixed at 60% fat level by energy and protein was varied from 1% to 20% (1%, 2.5%, 5% and 20% respectively) by energy (D14121903, D14121904, D14071601,D14071604), another 4 kinds of diets contained the same graded levels of protein content as the first 4 diets but fat contents were fixed at 20% by energy (D14121905, D14121906, D14071607, D14071610). The remaining energy was compensated of carbohydrate which included corn starch and maltodextrose. Casein was used as the protein source in all diets. To mimic the typical western diet a mix of cocoa butter, menhaden oil, sunflower oil, palm oil and coconut oil was used as the fat source and was designed to generate a 47.5: 36.8: 15.8 proportion of saturated, mono-unsaturated and polyunsaturated fats and 14.7: 1 proportion of n-6 and n-3 fatty acids, the proportions of different fat compositions didn’t change under two different 60% and 20% fat conditions. Sucrose and cellulose were fixed at 5% level by energy and standard vitamin and mineral mix were also added to all diets as well (Hu et al., 2018). The two series were isocaloric within each series. Diets can be ordered direct from research diets (https://researchdiets.com) using the diet codes provided. The hypothalamus of 6 individuals were collected for each diet group, 3 of which were pooled together as one sample, resulting in each group having 2 pooled samples of 3 hypothalamus. Hypothalamic RNA was extracted using Trizol method described in star methods in paper and then sent to Beijing Genomic Institute (BGI) for RNA sequencing. All RNA sequencing was measured by using the BGI-seq 500 sequencer. To determine the sequencing quality of each sample, FASTQ raw data files were measured by using fastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) quality control tool, after confirmed sequencing quality of each sample, raw reads were aligned to the Mus musculus reference genome (GRCm38) using HISAT2-2.1.0 (Kim et al., 2015; Pertea et al., 2016) and Samtools-1.2 modules (Li et al., 2009), and then featureCounts (Liao et al., 2014) tool in Subread-5.0 (Liao et al., 2013) was used to get counts for each sample from BAM files which was obtained from alignment step. To exclude the low counts, only genes with counts per million (CPM) value > 1 were included in the further analysis. Counts were normalized by the trimmed means of M values (TMM normalization) (Robinson and Oshlack, 2010) method in the edgeR (Anders et al., 2013; Lund et al., 2012; McCarthy et al., 2012; Robinson et al., 2010; Robinson and Oshlack, 2010; Robinson and Smyth, 2007) package. To investigate different dietary protein contents under fixed two levels fat content effects on gene expression levels Generalized Linear Modelling (GLM) function in R-3.5.3 edgeR package was used, The GLM model used in this study were: ~P+F+P:F, which means regression against protein (P) and fat contents (F) of diets plus their interaction (P:F). If the interaction effect was not significant (p > 0.05), the interaction was not included in the analysis and a revised model (~P+F) was utilized (Hu et al., 2018). To explore significantly correlated genes with dietary protein content respectively under 60% fat and 20% fat conditions, Pearson correlation analysis was performed for normalized log counts of all genes by using Pearson correlation method in R-3.5.3. Then selected the significantly correlated genes with dietary protein content (GLM: p < 0.05) respectively in the GLM and Pearson correlation (Pearson: p < 0.05 for 60% fat and 20% fat conditions) analysis were loaded into the Ingenuity pathway analysis (IPA) program (Ingenuity Systems; http://www.ingenuity.com/) to observe the significantly affected pathways. Results: The most affected pathways by the dietary low protein included the mTOR signaling pathway, the hunger signaling pathway, eIF2a signaling pathway and regulation of eIF4 and p70S6K signaling pathway. In the hunger signal pathway, we found there were strong correlations for four key hunger signaling pathway genes Pomc, Cart, Npy and Agrp with the protein content in the diet across different protein content groups (from 1% protein to 20% protein group) with Pomc and Cart expression significantly reduced as protein level declined while Npy and Agrp expression increased as protein levels decreased.

overall_design: There are 8 groups in total, the fat content of first 4 diets were fixed at 60% fat level by energy and protein was varied from 1% to 20% (1%, 2.5%, 5% and 20% respectively) by energy , another 4 kinds of diets contained the same graded levels of protein content as the first 4 diets but fat contents were fixed at 20% by energy.  To investigate different dietary protein contents under fixed two levels fat content effects on gene expression levels Generalized Linear Modelling (GLM) function in R-3.5.3 edgeR package was used, The GLM model used in this study were: ~P+F+P:F, which means regression against protein (P) and fat contents (F) of diets plus their interaction (P:F). If the interaction effect was not significant (p > 0.05), the interaction was not included in the analysis and a revised model (~P+F) was utilized (Hu et al., 2018). To explore significantly correlated genes with dietary protein content respectively under 60% fat and 20% fat conditions, Pearson correlation analysis was did for normalized log counts of all genes by using Pearson correlation method

first: Y

first: B

last: Li

first: L

first: S

middle: E

last: Mitchell

first: C

last: Green

first: G

last: D'Agostino

last: Wang

first: M

first: J

last: Niu

first: Z

last: Jin

first: A

last: Douglas

last: Zheng

last: Speakman


title: Dux facilitates post-implantation development, but is not essential for zygotic genome activation

status: Public on Mar 04 2021

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

country: USA

institute: University of Minnesota

type: Expression profiling by high throughput sequencing

summary: Double homeobox genes are unique to eutherian mammals. It has been proposed that the DUXC clade of the double homeobox gene family, which is present in multicopy long tandem arrays, plays an essential role in zygotic genome activation (ZGA). We generated a deletion of the tandem array encoding the DUXC gene of mouse, Double homeobox (Dux), and found it surprisingly to be homozygous viable and fertile. We characterize the embryonic development and ZGA profile of knockout (KO) embryos, finding that zygotic genome activation still occurs, with only modest alterations in 2-cell embryo gene expression, no defect in in vivo preimplantation development, but an increased likelihood of post-implantation developmental failure, leading to correspondingly smaller litter sizes in the KO strain. While all known 2-cell specific Dux target genes are still expressed in the KO, a subset is expressed at lower levels. These include numerous genes involved in methylation, blastocyst development, and trophectoderm/placental development. We propose that rather than driving ZGA, which is a process common throughout the animal kingdom, DUXC genes facilitate a process unique to eutherian mammals, namely the post-implantation development enabled by an invasive placenta.

overall_design: 4 replicates of wild type and KO embryos analyzed by RNAseq

first: Michael

last: Kyba

first: Darko

last: Bosnakovski


title: Expression data with inducible silencing of HDAC9 in human mesenchymal stem cells (hMSCs)

status: Public on Mar 03 2021

city: Wuhan

first: Bo

address: No.215 Zhongshan Avenue, Wuhan City, Hubei Province

country: China

institute: Wuhan no1 hospital

summary:
In order to study the role of the HDAC9 in human mesenchymal stem cell differentiation, gene expression analysis was performed with inducible silencing of HDAC9 in human mesenchymal stem cell purchasing from Cyagen Biosciences (HUXMA-90011, Guangzhou, China).
Transcriptomic analysis performed on mRNA of human mesenchymal stem cells transfected with lentiviral knockdown HDAC9 (lenti-HDAC9) particles revealed down and up regulation of transcripts of hMSCs differentiation genes

overall_design: hMSCs were cultivated in vitro and transfection of lentiviral knockdown HDAC9 (lenti-HDAC9) particles and lentiviral GFP particles, used as the control group (lenti-control). Total RNA was used to produce microarray probes which were individually hybridized Affymetrix microarray.

first: Feng

last: Yong

first: Wang

last: Bo

first: Gong

last: Song

first: Han

last: Lizhi

first: Shao

last: Wenkai


title: Identification and characterization of amphibian SLC26A5 using RNA-Seq

city: Shanghai

first: Zhongying

address: No.639, Zhizaoju Road

department: Otolaryngology Head & Neck Surgery

institute: Shanghai Ninth People’s Hospital , School of medicine, Shanghai Jiao Tong University

summary: We mapped and sequenced the SLC26A5 of the American bullfrog from its inner ear cDNA using RNA-Seq. The frog SLC26A5 cDNA was 2,292 bp long, encoding a polypeptide of 763 amino acid residues, with 40% identity to mammals. After isolating the prestin gene of the frog, we generated a stable cell line transfected with this new coding gene and found it possessing similar electrophysiological features as the hair cells from the frog’s auditory organ. Our experiment demonstrated that the new coding gene could encode a functionally active protein conferring NLC to both frog HCs and the mammalian cell line.

overall_design: The SLC26A5 gene of bullfrog has been mapped, sequenced and cloned successively using RNA-Seq. We measured the nonlinear capacitance (NLC) of prestin both in the hair cells of frog’s inner ear and HEK293T cells transfected with this new coding gene.

first: Qixuan

first: Hao

last: Wu

first: Zhiwu

last: Huang


title: Unfolded protein response (UPR) and endoplasmic reticulum (ER) stress in acromegaly

city: Tokyo

first: Shigeharu

last: Kinoshita

state: Bunkyo

address: 1-1-1,Yayoi, Bunkyo, Tokyo, 113-8657 Japan room 251

department: Aquatic Bioscience

country: Japan

institute: The University of Tokyo

summary: Acromegaly is a growth hormone (GH) excess pathological condition in humans and is associated with somatic disfigurement and a wide variety of systemic manifestations such as arthritis, neuropathies, carpal tunnel syndrome, reproductive disorders, metabolic disorders, and gastrointestinal complications. Studying the effect of growth hormone (GH) excess at the cellular level could help in understanding the underlying causes of acromegaly complications. In our previous publications, we have shown that excess GH increases DNA damage and impairs DNA repair pathways in somatic cells. In addition, we revealed that excessive GH reduces the number of stem cells and causes premature aging. Exaggerated growth is one of the main features of acromegaly and therefore, in this research, we have focused on protein production and biogenesis in acromegaly and whether excess GH is associated with unfolded protein response (UPR) and endoplasmic reticulum (ER) stress. Acromegaly-associated abnormal growth can be caused by hypertrophy or hyperplasia. Using pathway enrichment analysis of RNA seq data from our Zebrafish Acromegaly Model and Flow Cytometry Analysis, here we show a progressive increase in hepatocyte cell size and enrichment of hypertrophy pathways in the muscle and liver. That was associated with a progressive enrichment of protein production pathways and ribosome biogenesis. Moreover, using GSEA (Gene Set Enrichment Analysis) of acromegaly RNA seq data, here we show that endoplasmic reticulum (ER) stress is an accompanying feature of acromegaly disease. Our model exhibited endoplasmic reticulum (ER) stress in various organs, especially in the brain.

overall_design:
Total mRNA obtained from 1-years old acromegaly zebrafish model muscle, brain, and liver compared to aged zebrafish (3-years-old) and wild-type (WT) zebrafish were generated by deep sequencing using Illumina.

>>>Raw data are unavailable for this series due to file loss<<<

first: Abdalla

middle: A

last: Elbialy


title: Integrative microRNAome analysis of muscle tissue of Colossoma macropomum (tambaqui), Piaractus mesopotamicus (pacu) and the hybrid, tambacu, based on next-generation sequencing data.

city: Botucatu

first: Bruno

middle: Evaristo de Almeida

last: Fantinatti

state: São Paulo

address: Prof Antonio Celso Wagner Zanin

department: Morphology

country: Brazil

institute: Unesp

type: Non-coding RNA profiling by high throughput sequencing

summary: Muscle miNRA analysis over two parental and the hybrid genotype

sample_organism: Piaractus mesopotamicus x Colossoma macropomum

overall_design: MicroRNAs were extracted from muscle samples of juvenile individuals using Trizol, prepared with truseq-small-rna-sample-prep and sequenced in a HiSeq_2500FastMode (50 cycles – single end)

first: Érika

middle: S

last: Perez

first: Bruna

middle: T

last: Zanella

first: Jéssica

last: Valente

first: Tassiana

middle: G

last: Paula

first: Edson

last: Mareco

first: Robson

middle: F

last: Carvalho

first: Silvano

last: Piazza

first: Michela

last: Denti

first: Maeli

last: Dal-Pai-Silva


title: Comparison of gene expression profiles human mesenchymal stromal cells (MSC) cultured in 5% oxygen atmosphere and 19.95% oxygen

city: Houston

first: Maria da Graca

last: Cabreira

state: TX

address: 6770 Bertner Ave

department: Regenerative Medicine Research

institute: Texas Heart Institute

summary:
Gene expression in passage 3 human healthy donor-derived MSC that had been simultaneously cultured in 5% AND 20% oxygen were compared to determine its effects on survival and proliferation
The data supported some of our findings based upon functional proteome analysis showing relative increased activity in MAPK and mTOR pathways and shifting of energy metabolism from oxidative phosphorylation to glycolysis.

overall_design: Passage 3 cultures from donor samples, simultaneously expanded at the described oxygen conditions, were collected during subconfluency (70-80%). RNA and other biological samples (DNA, protein, etc…) were extracted in the lab

first: Maria

last: da Graca Cabreira

first: Emerson

last: Perin


title: A genome-wide screen for essentiality upon telomerase inhibition identifies a novel p53 regulator, C16ORF72/TAPR1 [RNA-seq]

city: Montreal

first: Lea

last: Harrington

state: Quebec

address: 2950 chemin de Polytechnique, Pavillon Marcelle-Coutu

department: Department of Medicine

country: Canada

institute: University of Montreal

summary: Telomere erosion in cells with insufficient levels of the telomerase reverse transcriptase, TERT, contributes to age-associated tissue dysfunction and senescence, and p53 plays a crucial role in this response. We undertook a genome-wide screen to identify gene deletions that sensitized p53-positive human cells to telomerase inhibition. We uncovered a previously unannotated gene, C16ORF72, which we term Telomere Attrition and p53 Response 1, TAPR1, that exhibited a synthetic-sick relationship with TERT loss. A genome-wide screen in TAPR1-disrupted cells also identified TERT as a sensitizing gene deletion. Additional genetic and transcriptome analysis of TAPR1-disrupted cells revealed that TAPR1 tapered p53 activation in response to eroded telomeres, p53 stabilization with nutlin-3a, or DNA damage. Importantly, deletion of TP53 rescued the fitness defect in TAPR1-disrupted cells. These findings identify C16ORF72/TAPR1 as new regulator at the nexus between telomere integrity and p53 regulation.

overall_design: RNA-seq analysis of wild-type, TERT-disrupted or TAPR1/C16orf72-disrupted NALM-6 cells

first: Yahya

last: Benslimane

first: María

last: Sánchez-Osuna

first: Jasmin

last: Coulombe-Huntington

first: Thierry

last: Bertomeu

first: Danielle

last: Henry

first: Caroline

last: Huard

first: Éric

last: Bonneil

first: Pierre

last: Thibault

first: Mike

last: Tyers


title: A genome-wide screen for essentiality upon telomerase inhibition identifies a novel p53 regulator, C16ORF72/TAPR1 [BIBR_screen]

overall_design: Genome-wide screen to test for gene deletions that affect fitness in cells treated with an inhibitor of telomerase reverse transcriptase, BIBR1532


title: Integration of transcriptome, small RNAs and degradome sequencing uncovers a tissue-specific regulatory network of paeoniflorin biosynthesis in Paeonia Lactiflora Pall. [RNA-seq]

city: Hangzhou

first: Pan

last: Xu

address: 132 Tianmushan Road

institute: Zhejiang Academy of Traditional Chinese Medicine

summary: The study of paeoniaflorin biosynthesis in Paeonia lactiflora Pall.at a molecular level is scarce, and the regulatory network between small RNAs and mRNAs in paeoniaflorin biosynthesis has not been assessed. Here, we attempt to combine mRNA and miRNA expression data with degradome analysis to reveal the tissue-specific regulatory network of miRNAs and their targets in Paeonia, especially the complex network of paeoniaflorin biosynthesis.The results will advance our understanding of the miRNA-mediated molecular mechanisms of paeoniaflorin and monoterpenoids biosynthesis, and provide a valuable resource for further study on Paeonia.

overall_design: Four tissues of root, leaf, flower and fruit, which showed different paeoniflorin acculumation were employed. The root, leaf and flower were collected at the blossom period and the fruit was collected at young fruit period, immediately frozen in liquid nitrogen and stored at -80℃. Each tissue has two biological replicates. we did a transcriptome-wide study on different tissues of Paeonia by combining RNA, sRNA and degradome sequencing to uncover a tissue-specific regulatory network of paeoniflorin biosynthesis in Paeonia Lactiflora Pall.

first: Jinbao

last: Pu


title: SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes [10x]

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control. Here, we identified non-synonymous mutations in MHC-I restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding, which was associated with a loss of recognition and functional responses by CD8+ T cells isolated from HLA-matched COVID-19 patients. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through sporadically emerging escape mutations in MHC- I restricted viral epitopes.

overall_design:
Single-cell RNA-sequencing (10x Genomics Immune Profile 5') of expanded T cells from two patients. Four separate samples were collected per patient and pooled after labelling with hashtag oligos: WT YLQ-, WT YLQ+, MUT YLQ-, MUT YLQ+.

*** Raw sequence data submission to the European Genome-Phenome Archive (EGA) to protect patient privacy - in progress.

first: Benedikt

last: Agerer

first: Luis

last: Montaño-Gutierrez

first: Anna-Maria

last: Husa

first: Lisa

last: Shaw

first: Thomas

last: Penz

first: Daniele

last: Barreca

first: Wolfgang

last: Paster

first: Rene

last: Geyeregger

first: Matthias

last: Farlik

first: Judith

middle: H

last: Aberle

first: Andreas

last: Bergthaler


title: Transcriptome sequencing of PCV2 ORF5 overexpressed PK15 cells

city: Seoul

first: Chang-Yong

last: Choi

address: 145, Anam-ro, Seongbuk-gu

department: Department of Biotechnology

country: South Korea

institute: Korea University

summary: This study investigated the immunological function of PCV2 ORF5 by ectopic expression of PCV2 ORF5 in PK15 cell line. Identifying the functional role of each PCV2 ORF associated with host cell modulation may provide better knowledge about the pathogenesis of postweaning multisystemic wasting syndrome (PMWS). PCV2 ORF5 is recently identified and the functional role of ORF5 during the pathogenesis after PCV2 infection is largely unknown.

overall_design: A Pig kidney epithelial cell line, PK15, was transfected with pLNCX2 (Mock-PK15) or PCV2ORF5/pLNCX2 (ORF5-PK15). Cloned PCV2 ORF5 cDNA sequence (GenBank accession FR823451.1) is derived from PCV2a type contained 180 bp encoding 59 amino acids. To identify differentially expressed mRNAs in the PCV2 ORF5 transfectant and mock, three cDNA libraries from each transfectant group (PCV2 ORF5 transfectant and mock) were generated and sequenced using the Illumina HiSeq4000 sequencer.


title: High-plex spatial RNA profiling reveals cell type-specific biomarker expression during melanoma development

city: Seattle

first: Michelle

last: Kriner

state: WA

address: 500 Fairview Ave North

institute: NanoString Technologies

summary:
Early diagnosis of melanoma is critical for improved survival. However, biomarkers of early melanoma evolution and their origin within the tumor and its microenvironment, including the keratinocytes, are poorly defined. To address this, we used spatial transcript profiling that maintains the morphological tumor context to measure expression of >1,000 RNAs in situ in patient-derived formalin-fixed, paraffin-embedded tissue sections in primary melanoma and melanocytic nevi. We profiled 134 200µm-diameter regions of interest enriched in melanocytes, neighboring keratinocytes or immune cells. This approach captured distinct expression patterns across cell types and tumor types during melanoma development. Unexpectedly, we discovered that S100A8 is expressed by keratinocytes within the tumor microenvironment during melanoma growth. Immunohistochemistry of 252 tumors showed prominent keratinocyte-derived S100A8 expression in melanoma but not in benign tumors and confirmed the same pattern for S100A8’s binding partner S100A9, suggesting that injury to the epidermis may be an early and easily detectable indicator of melanoma development Together, our results establish a framework for high-plex, spatial and cell type-specific resolution of gene expression in archival tissue applicable to the development of biomarkers and characterization of tumor-microenvironment interactions in tumor evolution.
In this dataset, we capture the GeoMx DSP RNA profiling data associated with this study. The files here represent patients with melanocytic tumors (n = 16) which were profiled with the NanoString GeoMx pilot panel (n=4 patients, n=108 gene targets) or CTA developmental panel v1.0 (n=12 patients, n=1,412 gene targets). These panels were read out using Illumina sequencing according to manufacturer protocols. For access to high resolution (single channel, composite, or ROI) images please contact mkriner@nanostring.com.

overall_design: This dataset contains expression data from patient FFPE samples collected during skin biopsy. Up to 16 ROIs were collected from each patient sample. H&E-stained serial sections were used to guide ROI selection by an experienced dermatopathologist.

first: Maija

last: Kiuru

first: John

middle: D

last: McPherson

first: Guannan

last: Zhu

first: Jessica

middle: R

last: Terrell

first: Samantha

last: Wong

first: Qian

last: Li

first: Margaret

last: Hoang

first: Joseph

last: Beechem


title: Non-coding RNAs in the transcriptional network that differentiates skeletal muscles of sedentary from long-term endurance- and resistance-trained elderly (RNA-Seq)

city: Bologna

first: Valentina

last: Indio

state: Bologna

address: via Giuseppe Massarenti,11

country: Italy

institute: University of Bologna

summary: In a previous study, the whole transcriptome of the vastus lateralis muscle from sedentary elderly and from age-matched athletes with an exceptional record of high-intensity, life-long exercise training was compared, the two groups representing the two ends of a physical activity scale. Exercise training enabled the skeletal muscle to counteract age-related sarcopenia by inducing a wide range of adaptations, sustained by the expression of protein-coding genes involved in energy handling, proteostasis, cytoskeletal organization, inflammation control, and cellular senescence. Building on the previous study, we examined here the network of non-coding RNAs participating in the orchestration of gene expression and identified differentially expressed micro- and long-non-coding RNAs and some of their possible targets and roles. Unsupervised hierarchical clustering analyses of all non-coding RNAs were able to discriminate between sedentary and trained individuals, regardless of the exercise typology. Validated targets of differentially expressed miRNA were grouped by KEGG analysis, which pointed to functional areas involved in cell cycle, cytoskeletal control, longevity, and many signaling pathways, including AMPK and mTOR, which had been shown to be pivotal in the modulation of the effects of high-intensity, life-long exercise training. The analysis of differentially expressed long-non-coding RNAs identified transcriptional networks, involving lncRNAs, miRNAs and mRNAs, affecting processes in line with the beneficial role of exercise training.

overall_design: all subjects were aged men (65 to 80 years); 5 were fully sedentary subjects; 4 were exceptionally trained subjects practicing mostly resistance exercise; 5 were exceptionally trained subjects practicing mostly endurance exercise

first: Paola

last: De Sanctis

first: Giuseppe

last: Filardo

first: Provvidenza

middle: M

last: Abruzzo

first: Annalisa

last: Astolfi

first: Alessandra

last: Bolotta

first: Alessandro

last: Di Martino

first: Christian

last: Hofer

first: Helmut

last: Kern

first: Stefan

last: Lofler

first: Maurilio

last: Marcacci

first: Marina

last: Marini

first: Sandra

last: Zampieri

first: Cinzia

last: Zucchini


title: Gene expression data of the subcutaneous adipose tissue from entire male, immunocastrated and surgically castrated pigs

city: Ljubljana

first: Klavdija

last: Poklukar Žnidaršič

state: Ljubljana

address: Hacquetova ulica 17

department: Animal Science department

country: Slovenia

institute: Agricultural Institute of Slovenia

summary: Differences in adipose tissue deposition and properties between pig male sex categories, i.e., entire male, immunocastrated and surgically castrated pigs are relatively well characterized, whereas the underlying genetic mechanisms are still not fully understood. To gain the knowledge about the genetic regulation of the differences in adipose tissue deposition, RNA-sequencing approach was used. A total of 83 differentially expressed genes were identified between entire male and immunocastrated pigs, 15 between immunocastrated and surgically castrated pigs and 48 between entire male and surgically castrated pigs by RNA-sequencing of the subcutaneous adipose tissue. Comparing entire male with immunocastrated or surgically castrated pigs, upregulated genes related to extracellular matrix dynamics, and downregulated genes involved in the control of lipid and carbohydrate metabolism were determinated. Moreover, differential gene expression in general indicated a high similarity between immunocastrated and surgically castrated pigs in contrast to entire males, except for several heat shock protein genes which were upregulated in entire male and immunocastrated pigs compared with surgically castrated pigs.

overall_design: Pigs originating from one slaughter batch (12 entire males, 12 immunocastrated and 12 surgically castrated pigs) of the commercial Landrace x Pietrain crosses were used. Surgically castrated pigs were castrated within the first week of life, while immunocastrated pigs were vaccinated at the age of 12 and 21 weeks with a vaccine against GnRH (Improvac® vaccine, Zoetis). At the age of 26 weeks, animals were slaughtered and the inner layer of subcutaneous fat at withers (i.e., between first thoracal and last cervical vertebra) was sampled.

first: Martin

last: Škrlep

first: Marjeta

last: Čandek-Potokar

last: Poklukar


title: Non-coding RNAs in the transcriptional network that differentiates skeletal muscles of sedentary from long-term endurance- and resistance-trained elderly (microarray)

first: Valentina

last: Indio

last: De Sanctis


title: Expression profiling by small RNA-seq for identifying miRNAs associated with pathological classifications in thyroid cancer.

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: There are no reliable small molecules to accurately differentiate indolent thyroid tumors from more aggressive thyroid cancers. This study aimed to develop new micro RNA (miRNA) markers for diagnosis and recurrence risk stratification of papillary thyroid carcinoma (PTC). Thyroid tumor-specific miRNA profiling was investigated in 34 fresh frozen tissues, which included nontumor (n = 7), noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP, n = 6) and PTC (n = 21), based on small RNA-seq technique. The PTC samples also consists of a number of pathological sub-cateories including classic (n = 11), tall cell (n = 7), and encapsulated follicular variant (EFV, n = 3) subtypes. By applying unsupervised hierarchical clustering with miRNAs, we found that thyroid tumor samples were well differentiated from normal thyroid tissues. When the histological data were compared among the tumor samples, patients with NIFTP or EFV were found to be differently clustered from those with classic or tall cell, indicating that micro-environment displayed by miRNAs well reflect pathological characteristics.

overall_design: miRNA-seq data of 34 samples including nontumor (n = 7), NIFTP (n = 6), classic (n = 11), tall cell (n = 7), and EFV (n = 3) subtypes were generated. Total RNA was isolated using the mirVana miRNA isolation kit (Ambion). Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified. Sequencing was performed in single end reads (75 bp) using NextSeq 500 platform (Illumina).

first: Jeong-Hwan

first: Jong-Lyul

last: Park

first: Chan

middle: K

last: Jung

first: Yong


title: Plasma miR-9-3p and miR-136-3p levels as novel diagnostic biomarkers for mild traumatic brain injury

city: Kuopio

first: Shalini

last: Das Gupta

address: Neulaniementie 2, P.O.B. 1627

department: A.I.Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary:
Purpose: High throughput small RNA-Seq analysis from circulating biofluids is crucial in driving the discovery of non-invasive miRNA biomarkers for TBI. In this study, we focused our analysis on acute post-TBI alterations in plasma miRNA profiles in adult, male Sprague-Dawley rats. We compared the plasma miRNA profiles from naive, sham-operated controls and rats with mild and severe TBI. The aim was to identify a miRNA signature that would distinguish the rats with mTBI from the naive and sham-operated controls. Next, we compared the rats with mild and severe TBIs to investigate if a dose-dependent increase would occur in the plasma miRNA levels with corresponding increase in injury severities. Finally, we analysed if the sham surgery itself results in alterations in circulating miRNA profiles, by comparing the naive and sham-operated controls.
Methods: TBI was induced with the lateral fluid percussion injury (FPI) model. Tail-vein plasma was collected at 2 days post-TBI from 31 adult male, Sprague-Dawley rats (5 naive, 8 sham-operated controls, 10 mTBI and 8 sTBI) under inhalation of isoflurane anesthesia. Small RNA-Seq was performed from plasma samples of a subset of 20 rats (5 cases each from naive, sham-operated controls, mTBI and sTBI groups). For each case, RNA was isolated from 200 µL plasma using the miRNeasy serum/plasma kit. The extracted RNA was subjected to qPCR-based quality control (QC). Small RNA library preparation was performed with the QIASeq miRNA library kit for Illumina NGS systems. Single-end sequencing of 75 bp reads was performed at a depth of 12M, with one sample/lane in the Illumina NextSeq 550. One naive plasma sample failed at the library preparation step. Hence, small RNA-Seq was succesful for 19/20 cases. The raw fastq files obtained from small RNA-Seq were first manually inspected with FastQC (v0.11.3) to check the overall quality of the sequencing data. For primary quantification of read counts, the fastq files were then uploaded to the Qiagen Geneglobe Data analysis center (DAC), a freely available web resource to analyze data from Qiagen’s QIASeq NGS library kits (https://geneglobe.qiagen.com/in/analyze/). Mapping was performed in the DAC portal with bowtie, using the rat reference genome RGSC Rnor_6.0. Annotation of miRNAs was performed with miRBase v21. Following primary quantification, differential expression analysis for miRNAs was performed with DESeq2 (v1.22.2) in R environment (v3.5.3). Logistic regression (LR) with feature selection utilizing nested leave-one-out cross-validation was also performed to identify miRNAs (“features”) contributing most to groupwise differences (differences between naïve, sham, mTBI, sTBI, sTBI + mTBI and naïve + sham).
Results: A total of 748 miRNAs were detected across all samples, out of which 723 (97%) were expressed in all the four groups (naive, sham-operated, mTBI and sTBI). Based on the differential expression and logistic regression analyses, we identified five miRNA candidates that contributed most to the seperation between the mTBI and naive groups: rno-miR-9a-3p, rno-miR-153-3p, rno-miR-15a-3p, rno-miR-136-3p and rno-miR-434-3p. We validated the small RNA-Seq data for these miRNA candidates with miRCURY reverse transcriptase quantitative PCR (RT-qPCR). We could succesfully validate elevated levels of miR-9a-3p, miR-136-3p and miR-434-3p in the mTBI group in comparison to naive. When analysed from the whole cohort, the elevated levels of these miRNAs were consistently observed in the mTBI group compared to the naive, both with RT-qPCR and droplet digital PCR (ddPCR). Further, all the three miRNAs revealed elevated plasma levels in the sTBI group in comparison to the mTBI.
Conclusions: Elevated plasma miRNA signature of miR-9a-3p, miR-136-3p and miR-434-3p distinguishes rats with mTBI from the naive, in the lateral FPI model of TBI. Further, all these miRNAs exhibit a dose-dependent increase in plasma levels with increase in injury severities.

overall_design: Small RNA-Seq analysis from rat tail-vein plasma samples at 2 days post-TBI

first: Robert

last: Ciszek

first: Mette

last: Heiskanen

first: Niina

last: Lapinlampi

first: Ville

last: Leinonen

first: Noora

last: Puhakka

first: Asla

last: Pitkänen


title: Down-regulation of SRD5A1 induces autophagy and apoptosis in multiple myeloma

city: Nanjing

first: Ye

last: Yang

address: 138 Xianlin Road

institute: Nanjing University of Chinese Medicine

summary: Steroid 5α-reductase type I (SRD5A1) is a validated oncogene in many sex hormone-related cancers, but its role in multiple myeloma (MM) remains unknown. Based on gene expression profiling of sequential MM samples during disease course, we found that high SRD5A1 expression was correlated with progression and poor prognosis in MM patients. In this study, we assessed the SRD5A1 function in promoting MM cell growth, cell cycle and tumorigenesis by using different human MM cell lines, the xenograft mouse and 5TMM mouse models. Applying lentivirus-mediated short-hairpin RNA (shRNA) method, inducible knockdown of SRD5A1 inhibited myeloma cell growth and induced cell apoptosis as well as autophagy. Meanwhile, the SRD5A1 knockdown-induced apoptosis was aggravated by the autophagy inhibitor 3-methyladenine. Mechanistically, SRD5A1 downregulation simultaneously regulated both the Bcl-2 family proteins mediated apoptosis and the autophagic process via PI3K/Akt/mTOR signaling pathway in MM cells. We also evaluated the therapeutic effect of SRD5A1 inhibitor, Dutasteride, on improving the survival rate of MM mouse model. To summarize, our findings demonstrate that SRD5A1 may serve as a biomarker for MM progression and prognosis, indicating that the dual autophagy-apoptosis regulatory SRD5A1 is a potential target for future therapies in MM patients.

overall_design: Transcriptomic RNA-Seq to profile differentially expressed mRNAs in ARP1 cells when SRD5A1 gene was knocked donw by a (Dox)-inducible lentivirus-mediated shRNA (AK_SRD5A1 vs AKdox_SRD5A1).

first: Renjie

last: Dou

first: Jinjun

last: Qian


title: NGS of small RNA reads in sampled potato plants from the highlands of Colombia

city: Madrid

first: Tomas

last: Canto

state: Madrid

address: Ramiro de Maeztu 9

department: Environmental Plant Biology

country: Spain

institute: CSIC

summary: Potato yellow vein virus (PYVV) was detected by RT-PCR in potatoes grown in the Central Colombian highlands, north of Bogotá (~3000 mt height).  At this altitude viral whitefly vectors are largely absent, but infection persists because of the use of uncertified tubers.  Plants with typical PYVV-induced yellowing symptoms, as well as with atypical yellowing or non-symptomatic were sampled at three separate geographical locations.  And five of them were subjected to Next Generation Sequencing (NGS) of their small RNA (sRNA) populations.  Contigs to any virus were assembled, and complete or almost complete sequences of four PYVV isolates were thus re-constructed, all from symptomatic plants.  Three viral isolates infected plants singly, while the fourth one co-infected the plant together with a potyvirus (potato virus Y, PVY).  Relative proportions of sRNAs to each of the three viral genomic RNAs were assessed and found to remain comparable between the four infections.  Genomic regions were identified as hotspots to sRNA formation, or as regions that induced poorly sRNAs.  Furthermore, PYVV titers in the mixed vs. the single infections were found to be remained comparable, indicating absence of synergistic/antagonistic effect of the potyvirus on the accumulation of PYVV.

sample_organism:
Solanum tuberosum
Solanum phureja

platform_organism:
Solanum tuberosum
Solanum phureja

overall_design: 5 different potato plant samples analysed by NGS of their small RNA (sRNA) populations

first: Liliana

last: Franco-Lara

first: Francisco

last: Javier del Toro


title: Integration of transcriptome, small RNAs and degradome sequencing uncovers a tissue-specific regulatory network of paeoniflorin biosynthesis in Paeonia Lactiflora Pall. [miRNA-seq]

first: Pan

last: Xu

first: Jinbao

last: Pu


title: Integration of transcriptome, small RNAs and degradome sequencing uncovers a tissue-specific regulatory network of paeoniflorin biosynthesis in Paeonia Lactiflora Pall.

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

overall_design: Refer to individual Series


title: P53-dependent Genes in Human Pulmonary Smooth Muscle Cells

city: Stanford

first: Jan

last: Hennigs

state: California

address: 269 Campus Dr

department: Wall Center for Pulmonary Vascular Diseases, Cardiovascular Institute and Pediatrics - Cardiology

institute: Stanford University

summary: We report differentially expressed genes in human pulmonary arterial smooth muscle cells under genotoxic stress (Doxorubicin) or pharmacological p53-activation by Nutlin-3.

overall_design: Examination of DEGs under genotoxic stress (Doxorubicin) or pharmacological p53-activation by Nutlin-3 in human pulmonary arterial smooth muscle cells isolated from healthy donor controls.

first: Julia

last: Mienert

first: Anika

last: Witten


title: Bromodomain testis-specific protein BRDT directs ΔNp63 function and super enhancer activity in a distinct subset of esophageal squamous cell carcinomas [RNA-seq]

status: Public on Mar 05 2021

city: Shenzhen

first: Xin

last: Wang

state: Guangdong

address: 1068, Xueyuan Road

department: Institute of Synthetic Biology

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

summary: Using an unbiased method, we found a testis-specific epigenetic reader protein BRDT to be expressed and functional active in a significant portion of ESCC patients. Mechanistically, BRDT co-localizes with ΔNp63, a defining transcription factor for squamous subtype, at selected super-enhancers to regulate ΔNp63-dependent transcription programs to promote cell migration. Pharmacologically depleting BRDT resembles the effects of knock-down of BRDT, thus providing a promising clinical approach for precision medicine in a subset of ESCC.

overall_design: We performed siRNA-mediated knock-down of BRDT in KYSE180 and TE6 cells as well as knock-down of p63 in KYSE150, KYSE180 and TE6 cells. The transfected cells were cultured for 48 hours and the RNA was isolated for library preparation using commercial kits.

first: Steven

last: Johnsen

first: Ana

middle: P

last: Kutschat


title: Antagonistic roles for Ataxin-2 structured and disordered domains in RNP condensatation

city: Mandi

first: Baskar

last: Bakthavachalu

state: Himachal Pradesh

address: Kamand

department: School of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology

summary: Ataxin-2 is a conserved translational control protein as well as an important target for ALS therapeutics under development. Despite its clinical and biological significance, Ataxin-2’s activities, mechanisms and functions are not well understood.  Using Drosophila Ataxin-2 (Atx2) we investigate how Ataxin-2 IDRs work with structured (Lsm, Lsm-AD and PAM2) domains to enable positive and negative regulation of target mRNAs. Using TRIBE (Targets of RNA-Binding Proteins Identified by Editing) technology, we identified and analysed Atx-2 target mRNAs in the Drosophila brain.

overall_design: We generated transgenic Drosophila melanogaster containing Atx2-ADARcd fusion protein (WT and domain deletions) controlled by Gal4-responsive UAS promoter. Using elav-Gal4 the Atx2 fusion protein was expressed in nervous system and the expression was restricted to adult flies with the use of the temperature sensitive Gal4 inhibitor, GAL80ts. Fly brains were dissected, and mRNA was sequenced using Illumina HiSeq 2500. RNA edits sites were identified using TRIBE pipeline (https://github.com/rosbashlab/TRIBE).

first: Arvind

last: Kandi

first: Mani

last: Ramaswami


title: Transcriptomes of Effector Memory T cells undergoing lymphopenia induced proliferation

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

summary:
Purpose: T cells undergo intense proliferation in the setting of lymphopenia and chemotherapy pre-conditioning is therefore an essential component of CAR-T therapy. Lymphopenia-induced proliferation (LIP) is thought to be mediated primarily by homeostatic cytokines such as IL-7 and IL-15 but little is known regarding the underlying mechanisms in human subjects
Methods: We undertook transcriptional analysis of CD4+ and CD8+ T cells following myeloablative autograft stem cell transplantation.
Results: T cells at day 12 after transplant were undergoing intense proliferation and the proportion of naïve T cells was markedly reduced and replaced by an effector pool.The proportion of FoxP3+ regulatory cells was almost doubled by day 12 and the global effector T cell pool also displayed a transcriptional profile typical of activated regulatory cells. Transcriptional analysis further revealed intense cell cycle activation driven by fatty acid metabolism and strong signalling responses to interferon. In contrast, TGF- signalling, a major negative regulator of T cell proliferation, was strongly suppressed
Conclusions: The human LIP response is thus characterised by intense cytokine and TCR-driven proliferation which drives global T cell activation but also preferentially triggers a regulatory cell expansion which may limit induction of tumour-specific immunity. These features indicate a range of potential therapeutic opportunities to manipulate immunotherapy regimens that incorporate LIP conditioning protocols.

overall_design: Total RNA profiles of Effector Memory CD8 and CD4 T cells from the peripheral blood of healthy donors and patients at Day 12 post autograft stem cell transplantation

first: Wayne

last: Croft

first: Kriti

last: Verma

first: Suzy

last: Eldershaw


title: Defining the  transcriptomic  fingerprints of benzo[a]pyrene exposure in Caenorhabditis elegans

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

summary: Polycyclic aromatic hydrocarbons (PAHs) are abundant organic compounds and are anthropogenically produced by the incomplete combustion of organic matter (e.g. fossil fuels and tobacco smoke). One notable model PAH is benzo[a]pyrene (BaP), which is listed as a Group 1 human carcinogen by the International Agency of Research on Cancer (IARC). Although the mode of action for BaP is well known in higher organisms, limited knowledge is available regarding the consequence of BaP exposure in the model organism Caenorhabditis elegans. The objective of this study was to define the the global transcriptome of wild-type C. elegans exposed to BaP (0, 5 and 20 μM). The most responsive transcripts were linked to redox processes and xenobiotic responses, including P450 enzymes (CYPs) (mainly members of the CYP35 family), epoxide hydrolases (EHs), glutathione S-transferases (GSTs), and UDP-glucuronosyltransferases (UGTs), all of which are linked to the metabolism (phase I & II) of xenobiotic substances. In summary, although the dominant CYP1A1/2 & CYP1B1 metabolic pathway is absent in C. elegans, BaP still induced a strong transcriptomic response. This provides strong evidence that parallel pathway(s) are implicated in BaP metabolism, and possibly, in its detoxification.

overall_design: The global transcriptome was compared in wild type N2 raised in the presence or absence of benzo[a]pyrene  at the concentration of 0,5 or 20 μM for  for 48 hours from L1 stage to L4 stage.

first: Mustafa

last: Abbass

first: Yuzhi

last: Chen

first: Volker

last: Arlt


title: Genome-wide mapping of p53-transcriptional activity in the pulmonary endothelium

first: Jan

last: Hennigs

type: Genome binding/occupancy profiling by high throughput sequencing


title: Berberine ameliorates vascular dysfunction by a global modulation of mRNA and lncRNA expression profiles in hypertensive mouse aortae

city: BeiJing

last: Tan

address: No. 38 Xue Yuan Road

institute: Peking University Health Science Center

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

summary: To investigated the mechanism underlying the therapeutic effects of berberine in the vasculature in hypertension,  we performed systematical analyses on the expression profiles of message RNAs (mRNAs) and long noncoding RNAs (lncRNAs) in the aortae from Ang Ⅱ-induced hypertensive mice with or without berberine treatment.

overall_design: The animals were divided to the following three group (3 mice per group): (ⅰ) C57BL/6J as vehicle group; (ⅱ) Ang II infused C57BL/6J (1000μg/kg/24h) with oral berberine treatment (100mg/kg/d) (Ang Ⅱ+ Berberine); (ⅲ) Ang II infused C57BL/6J without oral berberine treatment (Ang Ⅱ).


title: Genome-wide mapping of p53-transcriptional activity in the pulmonary endothelium [RNA-seq]

summary: We report a pharmacologically inducible vasculoprotective mechanism in pulmonary arterial endothelial cells (PAEC) in response to DNA damage by p53 and a novel PPARgamma/p53 transcription factor complex.

overall_design: Examination of p53 and PPARγ/p53 TF complex target genes human pulmonary arterial endothelial cells under genotoxic stress (Doxorubicin) or pharmacologiocal p53-activation by Nutlin-3.

first: Minyi

last: Shi

first: Michael

last: Snyder

first: Marlene

last: Rabinovitch


title: Non-coding RNAs in the transcriptional network that differentiates skeletal muscles of sedentary from long-term endurance- and resistance-trained elderly

first: Valentina

last: Indio

platform_organism:
Homo sapiens
synthetic construct


title: Transcriptome analysis of human erythroid cells differentiated from iPSCs, cord blood and adult peripheral blood

city: Singapore

first: Alison

last: Lee

address: 20 Biopolis Way

country: Singapore

institute: Bioprocessing Technology Institute

summary:
The aim of the study is to develop a scalable continuous agitation suspension culture bioprocess for differentiation of hiPSCs towards erythroid cells. Using process optimization, we developed the entire process completely in agitation suspension culture condition starting from hiPSC expansion through to hematopoietic induction and erythroid differentiation.
Transcriptome profiling was carried out to facilitate comparisons between erythroid cells differentiated from hiPSCs using this bioprocess, and erythroid cells differentiated from cord blood and adult CD34+ cells.

overall_design: A total of 11 samples were analyzed, consisting of 5 replicates of erythroid cells differentiated from hiPSCs in stirred spinner flasks, 3 replicates of cord blood differentiated erythroid cells, and 3 replicates of adult peripheral blood differentiated erythroid cells.

first: Jaichandran

last: Sivalingam

first: Steve

last: Oh


title: Altered drug response of recovered human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from cryopreservation

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

summary: We conducted RNA sequcing of the fresh and 1-week recoverd human induced pluripotent stem cell-derived caridomyocytes (hiPSC-CMs) undergo cryopreservation

overall_design: Examimation of 3 lines of hiPSC-CMs without cryopreservation and 1 week recovery after cryopreservation

first: Joe

last: Zhang


title: Genome-wide mapping of p53-transcriptional activity in the pulmonary endothelium [ChIP-seq]

overall_design: Examination of p53 and PPARγ/p53 TF complex target genes in human pulmonary arterial endothelial cells under genotoxic stress conditions.


title: Cannibalized Erythroblasts Accelerate Developmental Neurogenesis by Regulating Mitochondrial Dynamics

city: Sydney

first: Ramin

last: M Farahani

state: NSW

address: Westmead Hospital, Darcy Road

department: molecular biomedicine

country: Australia

institute: University of Sydney

summary: In this study, we disclose a mechanism triggered during neurulation that programs brain development by donation of sacrificial yolk sac erythroblasts to neuroepithelial cells. At embryonic day (E) 8.5, neuroepithelial cells transiently integrate with the endothelium of yolk sac blood vessels and cannibalize intravascular erythroblasts as transient heme-rich endosymbionts. This cannibalistic behavior instructs precocious neuronal differentiation of neuroepithelial cells in the proximity of blood vessels. By experiments in vitro, we show that access to erythroblastic heme accelerates the pace of neurogenesis by induction of a truncated neurogenic differentiation program from a poised state.

overall_design: mRNA profiles of Control, Heme-treated, and NIM (post-neural induction) mouse neural progenitor cells, Biological replicates: 2/group

last: Farahani


title: Adaptation of Cupriavidus metallidurans CH34 to toxic zinc concentrations involves an uncharacterized ABC-type transporter

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary: Cupriavidus metallidurans CH34 is a well-studied metal-resistant β-proteobacterium and contains a battery of genes involved in the resistance and processing of numerous metals. Here, we performed a directed evolution experiment to obtain derivatives adapted to grow in the presence of zinc at concentrations above the minimal inhibitory concentration for the parental strain. Genetic characterization of one derivative, CH34ZnR, which was also more resistant to cadmium, revealed seven mutations, including inactivation of glpR coding for a DeoR-type transcriptional repressor by insertion of IS1088. The latter resulted in the constitutive expression of the neighboring ABC-type transporter. GlpR and the adjacent ABC transporter are highly similar to the glycerol operon regulator and ATP-driven glycerol importer of Rhizobium leguminosarum bv. viciae VF39, respectively. Deletion of glpR or the ABC transporter and complementation of CH34ZnR with the parental glpR gene further demonstrated that loss of GlpR function, with concomitant induction of the adjacent ABC transporter, is pivotal in the observed phenotype. Moreover, addition of glycerol, presumably by glycerol-mediated reduced GlpR activity, also promoted increased zinc and cadmium resistance. Thus, the ABC-type transporter is proposed to be a new adaptation route during exposure to toxic zinc concentrations.

overall_design: Expression profiling of CH34ZnR compared to parental CH34 strain.

first: R

first: P

last: Monsieurs

first: J

last: Vandecraen

first: N

last: Leys

first: A

last: Aertsen


title: Transcriptional Profile of Mycobacterium tuberculosis Colony Morphotype Variants

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

summary: Transcriptional profiling of Mycobacterium tuberculosis mc2 7000 spread and raised colony morphotypes

overall_design: Two condition experiment, pooled spread colonies vs. pooled raised colonies.

first: Tsungda

last: Hsu


title: NRG1 as a regulator of pH adaptation in the Basidiomycota Ustilago maydis

city: Monterrey

first: Jose

middle: Alejandro

last: Sánchez-Arreguin

state: Nuevo León

address: Pedro de Alba S/N

department: Facultad de ciencias Biológicas

country: Mexico

institute: Universidad Autónoma de Nuevo León

summary: A homologue of the transcriptional repressor ScNrg1 described previously in the budding yeast and Candida albicans NRG1 wich plays an essential role in repressing hyphal development in both Saccharomyces cerevisiae and C. albicans, was found in Ustilago maydis. In S. cerevisiae it regulates a set of stress-responsive genes, also in Cryptococcus neoformans is involved in pathogenesis. In this work, we describe the effect of the absence of the U. maydis NRG1 gene in cell response to acid pH, mannosylerithritol lipids production, and cellular response to several stressful conditions. In U. maydis, NRG1 is required for filamentous growth and appears to be essential to respond to pH changes, and oxidative stress accurately. By comparing gene expression in a wild type strain versus nrg1 mutant strain of the fungus trough RNA_Seq analyses, it turned out to act as transcriptional factor altering the expression of 368 genes (205 up-regulated, 163 downregulated). Most relevant cellular processes affected by NRG1 are osmotic stress pathway, pH response, internal environmental sensor mechanism, represented by the genes Hog1, Rim101, and WCO1 respectively, also, all the genes present in the mannosylerithritol lipids production pathway, even under conditions not favorable for the production of glycolipids. Among previous specific functions described before for this transcriptional regulator as a glucose repressor, it seems to have an important role in metabolic adaptation, cellular transport, cell rescue defense and interaction with the environment.

overall_design: Transcriptomic comparison between wild type and NRG1 mutant of Ustilago maydis, replicates were analyzed.

first: José

last: Ruiz-Herrera

first: Felipe

last: Mares-Rodríguez

first: Claudia

last: León-Ramírez

first: Lino

last: Sánchez-Segura

first: Patricio

last: Zapata-Morín

first: Jordan

last: Coronado-Gallegos

first: Elva

last: Teresa Aréchiga-Carvajal


title: Comprehensive genomic, phenotypic and transcriptomic approaches to enhance Bifidobacterium animalis subsp. animalis growth and survival in milk

city: Cork

first: Francesca

last: Bottacini

address: Western Road

department: APC Microbiome Institute & School of Microbiology

country: Ireland

institute: University College Cork

summary:
Bifidobacterium animalis subsp. animalis CNCM I-4602 was tested for its ability to grow in reconstituted skimmed milk (RSM). Strain CNCM I-4602 grows and survives poorly in reconstituted skimmed milk (RSM), although this was partially countered by the addition of certain compounds, including yeast extract, uric acid, glutathione, cysteine, ferrous sulfate and a combination of magnesium sulfate and manganese sulfate. Microarray analysis of the strain grown in RSM revealed a number of up-regulated amino acid biosynthetic pathways, as well as stress-related genes.
Expression profiling by array

overall_design: Bifidobacterial cells were isolated from milk-based medium (RSM) according to a previously described method (de Jong et al., 2013). In brief, a 15 ml sample of a bifidobacterial culture in RSM was harvested by centrifugation at 6,000 x g for 10 mins at 4°C. Following centrifugation, the pellet was resuspended in 1-4 ml of 3 M guanidium chloride (depending on the level of coagulation of the milk), and then solubilized by 5 cycles of vortex mixing and chilling on ice, each for one minute. Cells were collected from the solution by centrifugation at 3,500 x g for 15 mins at 4°C, then washed twice with 0.9 % (wt/vol) saline solution, after which cells were frozen at -80°C or used directly for RNA extraction. RNA was extracted using a combination of the Macaloid method and the Roche High Pure RNA isolation kit (Zomer et al. 2009). RNA quality control, complementary DNA synthesis and labelling were performed as described previously (Zomer et al., 2009). DNA microarrays containing oligonucleotide primers representing each of the identified open reading frames on the genome of B. animalis subsp. animalis CNCM I-4602 were designed and obtained from Agilent Technologies (Palo Alto, Ca., USA). Two separate microarray experiments were performed. The first compared gene expression of B. animalis subsp. animalis CNCM I-4602 in mMRS supplemented with glucose (used as the reference condition) to the strain in gRSM (test condition). The second microarray experiment compared the strain in mMRS with glucose (reference condition) compared to gRSM supplemented with cysteine (test condition). Each transcriptome experiment was performed as a dye swap so as to account for any dye bias. Hybridization, washing of the slides and processing of the DNA microarray data was performed as previously described (Pokusaeva et al., 2010).

first: Muireann

last: Egan


title: The XPB Subunit of the TFIIH Complex Plays a Critical Role in HIV-1 Transcription, and XPB Inhibition by Spironolactone Prevents HIV-1 Reactivation from Latency

status: Public on Mar 02 2021

city: Jupiter

first: Adam

last: Getzler

state: FL

address: 130 Scripps Way

country: USA

institute: TSRI-FL

summary: Human immunodeficiency virus (HIV) transcription requires assembly of cellular transcription factors at the human immunodeficiency virus type 1 (HIV-1) promoter. The TFIIH general transcription factor facilitates transcription initiation by opening the DNA strands around the transcription start site and phosphorylating the C-terminal domain of RNA polymerase II (RNAPII) for activation. Spironolactone (SP), an FDA approved aldosterone antagonist, triggers the proteasomal degradation of the XPB subunit of TFIIH and concurrently suppresses acute HIV infection in vitro. Here, we investigated SP as a possible block-and-lock agent for a functional cure, aimed at the transcriptional silencing of the viral reservoir. The long-term activity of SP was investigated in primary and cell line models of HIV-1 latency and reactivation. We show that SP rapidly inhibits HIV-1 transcription by reducing RNAPII recruitment to the HIV-1 genome. Short hairpin RNA (shRNA) knockdown of XPB confirmed XPB loss as the mechanism of action of HIV inhibition. Unfortunately, long-term pretreatment with SP does not result in long-term epigenetic suppression of HIV upon SP treatment interruption, since the virus rapidly rebounds when XPB reemerges; however, SP alone without antiretroviral therapy (ART) maintains transcriptional silencing of HIV. Importantly, SP inhibits HIV reactivation from latency in both cell line models and resting CD4+ T cells isolated from aviremic individuals living with HIV upon cell stimulation with latency-reversing agents. Furthermore, long-term treatment with concentrations of SP that potently degrade XPB does not lead to global dysregulation of cellular mRNA expression. Overall, these results suggest that XPB plays a key role in HIV transcriptional regulation, and XPB degradation by SP strengthens the potential of HIV transcriptional inhibitors in block-and-lock cure approaches.

overall_design: 8 samples, 2 replicates each

first: L

last: Mori

first: S

last: Valente


title: Genome-wide mapping of p53-binding in 293T cells

first: Jan

last: Hennigs

summary: We report p53-target genes in response to DNA damage in 293T cells

overall_design: Examination of p53 target genes in 293T cells at baseline vs. Doxorubicin-induced DNA stress.

first: Minyi

last: Shi

first: Michael

last: Snyder

first: Marlene

last: Rabinovitch


title: Targeting the eIF4A dependent translation of KRAS and other oncoproteins in pancreatic cancer

city: Bronx

first: Kamini

last: Singh

address: 1300 Morris Park Ave, Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: New and effective therapeutics are urgently needed for the treatment of pancreatic ductal adenocarcinoma (PDAC). The eIF4A/DDX2 RNA helicase drives translation of mRNAs with highly structured 5’UTRs. The natural compound silvestrol and synthetic analogues are potent and selective inhibitors of eIF4A1/2 that show promising activity in models of hematological malignancies. Here, we show silvestrol analogues have nanomolar activity against PDAC cell lines and organoids in vitro. Moreover, we see single agent activity in the KRAS/p53 mouse PDAC model and also against PDAC xenografts and primary, patient derived PDAC tumors. These therapeutic effects occur at non-toxic dose levels. Transcriptome-wide ribosome profiling, analyses of protein and gene expression, and translation reporter studies reveal that eIF4A inhibitors block an oncogenic translation program in PDAC cells that includes G-quadruplex containing mRNAs such as KRAS, MYC, YAP1, MET, SMAD3, TGFβ and others. Together, our data indicate that pharmacological inhibition of eIF4A disrupts oncoprotein production and shows efficacy across several PDAC models.

overall_design: We performed ribosome footprinting and RNA sequencing on six samples of PANC1 cells including three untreated samples (DMSO) and three samples that were collected 45 minutes after treatment with CR31B (25 nM). DMSO treated samples are indicated as CT and CR31B treated samples are indicate as S.

first: Jianan

last: Lin

first: Nicolas

last: Lecomte

first: Prathibha

last: Mohan

first: Askan

last: Gokce

first: Viraj

last: Sanghvi

first: Grbovic-Huezo

last: Olivera

first: Man

last: Jiang

first: Antonija

last: Burčul

first: Stefan

last: Stark

first: Agnes

last: Viale

first: Paul

middle: B

last: Romesser

first: Elisa

last: de Stanchina

first: Rachel

last: Bagni

first: Gunnar

last: Rätsch

first: Steve

last: Leach

first: Zhengqing

last: Ouyang

first: Hans-Guido

last: Wendel


title: A novel gene signature associated with poor response to chemoradiotherapy in patients with locally advanced cervical cancer

city: Seoul

first: Kyung Hwan

last: Kim

address: 50-1 Yonsei-ro

institute: Yonsei University College of Medicine

summary: Purpose: We aimed to investigate the distinct transcriptional landscape in the poor responders to concurrent chemoradiotherapy (CCRT) and to gain mechanistic insights on treatment resistance in cervical cancer.  Methods: RNA sequencing was performed using archived pre-treatment tissue biopsies of patients with locally advanced cervical cancer treated with concurrent platinum-based CCRT. Transcriptome data of patients with no durable benefit (NDB; progression-free period < 3 years) and durable clinical benefit (DCB; progression-free period > 5 years) after were compared. NDB score was estimated for each patient using the differentially expressed genes between NDB and DCB patients. Three independent cohorts, including The Cancer Genome Atlas cervical cancer (TCGA-CESC) cohort, were utilized for validation of NDB score. Potential response to PD-1 blockade was estimated with Tumor Immune Dysfunction and Exclusion (TIDE) score and T-cell-inflamed gene expression profile (GEP).  Results: Patients with NDB exhibited a distinct transcriptional profile compared to those with DCB such as higher signatures of extracellular matrix organization and epithelial-to-mesenchymal transition. The fraction of cancer-associated fibroblasts (CAFs) within the tumor was significantly higher in NDB than DCB patients. Higher NDB score was significantly associated with poor survival in the TCGA-CESC cohort (n = 274; P = 0.015), but only in patients that received curative aim radiotherapy (P = 0.002) and not in patients who received other treatments (P = 0.57). The transcriptomic characteristics of patients with NDB were recapitulated in patients with high NDB score in TCGA-CESC. Patients with high NDB score displayed significantly higher TIDE prediction score and lower T-cell-inflamed GEP score compared to patients with low NDB scores.  Conclusion: Cervical cancer patients with poor treatment outcome following CCRT exhibited a distinct gene signature that was able to predict treatment outcomes. For poor responders, immune checkpoint inhibitors may be less effective and CAF-targeting treatments may be a promising approach.

overall_design: patients with durable clinical benefit vs. no durable benefit

first: Kyung

first: Yong


title: P53-dependent Genes in Human Pulmonary Adventitial Fibroblasts

first: Jan

last: Hennigs

summary: We report differentially expressed genes in human pulmonary arterial adventitial fibroblasts under genotoxic stress (Doxorubicin) or pharmacological p53-activation by Nutlin-3.

overall_design: Examination of DEGs under genotoxic stress (Doxorubicin) or pharmacological p53-activation by Nutlin-3 in human pulmonary arterial adventitial fibroblasts isolated from healthy donor controls.

first: Julia

last: Mienert

first: Anika

last: Witten


title: Cerebrospinal fluid (CSF) boosts metabolism and virulence expression factors in Acinetobacter baumannii

city: Fullerton

first: M. S.

last: Ramirez

address: 800 N. State College Blvd

institute: California State University Fullerton

summary: Analysis of the effect of cerebrospinal fluid on the transcriptome of Acinetobacter baumanii A118

overall_design: Total mRNA of Acinetobacter baumanii A118 was isolated from bacteria incubated in LB with or without 4% human cerebrospinal fluid

first: Maria

first: Rodrigo

last: Sieira


title: RNA sequencing of mesenchymal stem cells reveals a blocking of differentiation and immunomodulatory activities under inflammatory conditions in rheumatoid arthritis patients

city: Madrid

first: Luis

last: Rodriguez-Rodriguez

address: Calle Prof Martin Lagos

department: Rheumatology

institute: Instituto de Investigación Sanitaria San Carlos

summary: We identified the differentially expressed genes in bone marrow mesenchymal stem cells after exposure to an inflammatory environment. The transcriptome profiling was evaluated by means of the precise measurement of transcripts provided by the RNA-Seq technology. Our results evidenced the existence of blocking of both regenerative (differentiation) and immunomodulatory phenotypes under inflammatory conditions characterized by an upregulation of genes involved in immune processes and a simultaneous downregulation of genes mainly involved in regenerative or cell differentiation functions.

overall_design: Bone marrow mesenchymal stem cells from healthy donors were co-cultured with activated OR non activated pefipheral blood mononuclear cells from rheumatoid arthritis patients

first: J

first: A

last: Mucientes

first: L


title: Vascular fate in misidentified pluripotent-derived blood-brain-barrier endothelial cells rescued by transcriptional reprogramming

city: New York

first: Tyler

last: Lu

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: Total RNA, greater than 100ng, from cultured cells was isolated in TRIzol L and purified using Qiagen RNeasy Mini Kit per manufacturer’s protocols. Agilent Technologies 2100 Bioanalyzer was used to assess the RNA quality. RNA libraries were prepared and multiplexed using Illumina TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection) and 10 nM of cDNA was used as the input for high-throughput sequencing via Illumina’s HiSeq 2500 platform, producing 50 bp paired end reads.

overall_design: Cell samples were harvested from  in vitro culture conditions and sequenced using Illumina HiSeq 2500

first: Sean

last: Houghton

first: Shahin

last: Rafii

first: Dritan

last: Agalliu

first: David

last: Redmond

first: Raphael

last: Lis


title: Expression data from microglia in Abeta and TAU mouse models of Alzheimer Disease

city: Seville

first: Carmen

last: Romero-Molina

state: Seville

address: Profesor Garcia Gonzalez, 2

department: Faculty of Pharmacy. Biochemistry and Molecular Biology

institute: University of Seville. Institute of Biomedicine of Seville

summary:
Microglia activation is a hallmark in Alzheimer Disease. Non-active and Active microglia were isolated from young and aged WT mice and before- and after- pathology mouse models of Alzheimer Disease.
Microarray analysis was used to determine the global gene expression programe in microglia during pathological (Abeta or TAU pathology) versus control state.

overall_design: Cortical plus hippocampal microglia (CD45+ and CD11b+) were isolated from WT, APP and TAU mice at 3 and 9-12 month-old. Active microglia were isolated as Clec7a+ microglia.

last: Virtudes Sanchez-Mico

first: Marisa

last: Vizuete

first: Javier

last: Vitorica


title: IRF4 genome wide binding and transciptomic profile in 501Mel melanoma cell line

city: reykjavik

first: Ramile

last: Dilshat

address: Sturlugata 8

department: Biochemistry and Molecular biology

country: Iceland

institute: University of Iceland

summary: To map genome wide binding sites of IRF4, we performed ChIP-seq against eGFP tagged IRF4 in human melanoma cells. To assess whether IRF4 binding influences its target gene expression, RNA-seq was performed after siRNA mediated depletion of IRF4 in 501Mel cells. Subsequently, target genes of IRF4 obtained from ChIP-seq and RNA-seq studies were used to interrogate melanocyte meQTL and identified 131 candidate downstream target CpGs of IRF4, which were validated by cis-/trans-meQTL mediation analysis, suggesting transcription factor mediated expression changes reflected in methylation changes.

overall_design: RNA-seq experiments were performed in triplicates respectively for siCTRL and siIRF4 in 501Mel cells. ChIP-seq experiments were performed in biological duplicates for eGFP tagged IRF4 in 501Mel cells.

first: Berglind

middle: O

last: Einarsdóttir


title: Naked mole rat TRF1 safeguards glycolytic capacity and telomere replication under low oxygen

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

summary: The naked mole rat (NMR), a long-lived and cancer resistant rodent, is highly resistant to hypoxia. Here, using robust cellular models wherein the mouse telomeric protein TRF1 is substituted by the NMR TRF1 or its mutant forms, we show that TRF1 supports maximal glycolytic capacity under low oxygen, shows increased nuclear localization and association with telomeres, and protects telomeres from replicative stress. We pinpoint this evolutionary gain of metabolic function to specific amino acid changes in the homodimerization domain of this protein. We further find that NMR TRF1 accelerates telomere shortening. These findings reveal an evolutionary strategy to adapt telomere biology for metabolic control under an extreme environment.

overall_design: mRNA profiles of tMEF cells (transformed mouse embryonic fibroblasts), cultured in normoxia and hypoxia conditions, wherein the mouse telomeric protein TRF1 is substituted by the NMR TRF1 or its mutants forms: mutGLAD (Glu69Lys, Val70Ala, and Ala75Thr), mutTIN (Ala105Thr) or both mutGLAD/TIN. The experiments were performed in duplicate using the sequencer Illumina NovaSeq 6000.

first: Adeline

last: Augereau

first: Marco

last: Mariotti

first: Mélanie

last: Pousse

first: Doria

last: Filipponi

first: Frédérick

first: Benjamin

last: Beck

first: Vera

last: Gorbunova

first: Eric

last: Gilson

first: Vadim

middle: N

last: Gladyshev


title: Gene expression signatures for rat liver grafts

city: Tianjin

first: Hongli

last: Song

state: Tianjin

address: No. 24 Fukang Road, Nankai District

department: Department of Organ Transplantation

country: China

institute: Tianjin First Central Hospital

summary: Acute rejection remains an important risk factor affecting the survival of recipients following transplantation. Bone marrow mesenchymal stem cells (BMMSCs) are used in the treatment of organ transplantation due to their immunomodulatory ability. BMMSCs were isolated from rat bone marrow and modified with the adenovirus for heme oxygenase 1 (HO-1) gene. Saline solution, BMMSCs or HO-1/BMMSCs were perfused into the donor liver in vitro using a normothermic machine perfusion (NMP) system, followed by liver transplantation. The liver grafts were collected at 7 days post-transplantation. Gene chip technology was used to detect differential gene expression.

overall_design: The rats were divided into the following five groups according to the different liver treatments: sham operated (Sham) group; static cold storage (SCS) group; NMP group; NMP combined with BMMSCs (BMP) group; and NMP combined with HO-1/BMMSCs (HMP) group.The rats were subjected to the orthotopic liver transplantation. On day 7 after liver transplantation, the recipient was euthanized and liver grafts were obtained. One independent experiments were performed at each time.

first: Huan

last: Cao


title: Claudin-10a deficiency shifts proximal tubular Cl- permeability to cation selectivity via claudin-2 translocation

city: Berlin

first: Oliver

last: Nagel

address: Hindenburgdamm 30

department: Department of Gastroenterology, Rheumatology and Infectious Diseases

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: The tight junction (TJ) proteins claudin-2 and -10a form paracellular cation and anion channels, respectively, and have both been reported to be expressed in the proximal tubule (PT). However, the physiological role of claudin-10a in the kidney is yet obscure. Mice deficient in claudin-10a were generated and successful knockout was confirmed by Southern Blot, Western Blot and immunofluorescence staining. The functionality of isolated PTs was investigated electrophysiologically. Compensatory regulation was studied by pharmacological intervention, RNA-Seq analysis, Western Blot and immunofluorescence staining.

overall_design: 7 samples from proximal tubule (4 WT, 3 Cldn10a KO), 8 samples from distal convoluted tubule (4 WT, 4 Cldn10a KO)

first: Tilman

last: Breiderhoff

first: Nina

last: Himmerkus

first: Luca

last: Meoli

first: Anja

last: Fromm

first: Natalia

last: Kriuchkova

first: Yury

last: Ladilov

first: Susanne

last: Krug

first: Cosima

last: Merkel

first: Merle

last: Brinkhus

first: Janine

last: Altmüller

first: Michal

last: Schweiger

first: Dominik

last: Müller

first: Kerim

last: Mutig

last: Milatz

first: Markus

last: Bleich

first: Dorothee

last: Günzel


title: Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature [array]

city: London

first: Samah

last: Alimam

address: Great Maze Pond

department: Cancer Genetics

institute: KCL

type: Methylation profiling by genome tiling array

summary: Using gene expression analysis in combination with genome-wide methylation profiling, we discovered  a unique signature pattern that is consistent across the essential thrombocythaemia population regardless of mutation status.

overall_design: Infinium Human-Methylation 850K array on a total of 32 patient samples with essential thrombocythemia and 2 healthy controls.

first: William

last: Villiers


title: Modular gene analysis reveal distinct molecular signatures for cutaneous lupus patient subsets

city: Dallas

first: Jane

last: Zhu

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: We utilized RNA-seq to investigate the molecular heterogenity of cutaneous lupus patients compared to controls.

overall_design: Examining molecular hetereogenity of cutaneous lupus patients

first: Benjamin

last: Chong

first: Judith

last: James

first: Joel

last: Guthridge


title: Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature [RNA-seq]

summary: There is a unique signature pattern that is consistent across the essential thrombocythaemia (ET) population regardless of mutation status. ET phenotype may therefore, at least in part and regardless of mutation type, be driven by transcriptional mis-regulation and may propagate downstream via the MAPK, TNF and NFκB pathways with resultant JAK/STAT activation.

overall_design: RNA-Sequencing on a total of 18 patient samples with essential thrombocythemia and 4 healthy controls.


title: Triple negative, JAK2V617F and CALR mutated essential thrombocythaemia patients share a unique gene expression signature

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

overall_design: Refer to individual Series


title: Effect of 14 hours of starvation on gene expression in the WM983B cell line using RNA-seq / Effect of HA15 resistance on gene expression in the WM983B cell line using RNA-seq

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

summary:
In order to examine the effect of starvation on gene expression and its contribution to the elevated ER stress, autophagy and apoptotic mechanisms we performed RNA-seq experiment on starved melanoma cells and on cells growing under normal cell conditions.The highest expression difference were seen for the RP11-134F2.8 gene (217 fold change) and the RP11-618G20.1 gene (64 fold change). Two starvation related genes including the SLCO4C1 (32 fold change), and PIK3IP1 (14 fold change) genes were also highly expressed in the starved WM983B cell population.
We are the first who successfully established HA15 resistant melanoma cell lines (WM983BHA15RES) against 30uM HA15. In order to define gene expression alterations associated with the HA15 resistant phenotype we performed RNAseq analysis on the newly developed resistant melanoma cell line and compared the gene expression signature to the original WM983 cell line.

overall_design: Examination of 14 hours of starvation on gene expression in the WM983B cell line. / Examination of HA15 resistance on gene expression in the WM983B cell line.

first: Margit

last: Balázs


title: Epigenome analysis of brochoscopic paired biopsy specimens from tumoral sites and the contralateral bronchus.

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

summary: Genome wide DNA methylation profiling of brochoscopic paired biopsy samples from tumoral sites and the contralateral bronchus (controls). The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in bronchoscopic biopsy samples. In 37 patients (74 samples) a difinite histological diagnosis could be reached. In the remaining 36 samples the diagnosis remained indefinite, the assumption of the pathologists is stated.

overall_design: Bisulphite converted DNA from 110 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Escherichia coli segments its controls on carbon-dependent gene expression into global and specific regulations

city: Shenzhen

first: Conghui

last: You

address: No. 1066 Xueyuan Road

department: College of Life Sciences and Oceanology

institute: Shenzhen University

summary: We investigated the way global gene expression changed in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways with features varying in: carbon influx flow rate; entry points in the metabolic network; modes of transport. Quantitative coarse-grained expression-pattern analysis demonstrated that the gene expression trend following immediately the reduction of carbon influx flow rate was determined by its initial expression level. Subsequent fine-grained expression-pattern analysis demonstrated that the Crp regulator, associated to a change in growth rate, governed the response of most carbon influx-dependent genes. By contrast, the Cra, Mlc and Fur regulators governed the expression of genes responding to non-glycolytic substrates, glycolytic substrates or PTS (phosphotransferase system) transported sugars following an idiosyncratic way, with the function of each of these regulators being titrated by the metabolism of the corresponding substrates. This work also allowed us to expand the extent of the gene complement regulated by each regulator with additional genes (27 genes in the Crp regulon, 49 genes in the Cra regulon, 1 gene in the Mlc regulon and 2 genes in Fur regulon) and to elucidate the regulatory functions of each regulator comprehensively. Strikingly, Crp and Cra worked in concert to coordinate central carbon metabolism with amino acids biosynthesis. Together, these results demonstrated the power of physiology-based interperation of global data in revealing regulatory networks of bacteria.

overall_design: Examination of the gene expression when E. coli NCM3722 grew in 7 different carbon sources (Ace, G6P, Glc, Gly, Lac, Sor, Suc), as well as its crp- & cyaA- mutant (CY104) grew in Glc.

first: Qing

last: Pan


title: Mouse preimplantation imprinting

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

type: Methylation profiling by high throughput sequencing


title: Novel long non‐coding RNA 005620 induces epirubicin resistance of triple-negative breast cancer via regulating ITGB1 expression

city: Nanjing

first: Jing

last: Yu

address: No.101 Longmian Avenue, Jiangning District

institute: Nanjing Medical University, China P.R

summary: In this study, a total of 12 differentially expressed lncRNAs were established through lncRNA sequencing analysis. Lnc005620 is one of the novel intronic lncRNAs which is highly expressed in Epi-R MDA-MB-231. Lnc005620 is an important lncRNA that leads to the resistance of Epirubicin in triple negative breast cancer by integrin β1.

overall_design: Wild-type MDA-MB-231 cell and ADR resistant MDA-MB-231 cell were conducted，using lncRNA sequencing to find some relevant resistant lncRNA and target genes

first: Fengliang

last: Wang

first: Mingming

last: Lv

first: Jinhai

last: Tang


title: Mouse preimplantation imprinting [RNA-seq]

summary: In mammals, chromatin marks at imprinted genes are asymmetrically inherited from each parent to control gene expression. Many genomic imprints are determined by differentially methylated regions (DMRs), but these have not been comprehensively mapped physically or functionally in mouse preimplantation embryos. We here address this by integrating transcriptomic and epigenomic approaches. Transcriptome analysis of blastocysts from genetically distinguishable crosses identified 106 genes with previously unknown parent-of-origin-specific allelic bias (nBsX genes), and 71 novel imprinted genes with parent-of-origin-specific expression with an allelic ratio of 70:30 or greater (nBiX genes). Uniparental expression of tested nBsX and nBiX transcripts disappeared soon after implantation.

overall_design: Allele-specific RNA-sequencing (SMART-Seq2) on E3.5 embryos obtained without in vitro culture from reciprocal Mus musculus musculus C57BL/6 (B6) x Mus musculus castaneus (cast) natural mating. 3 and 5 embryos were analysed from the B6 x cast (forward cross) and the cast x B6 (reverse cross) matings, respectively.

first: Laura

last: Santini

first: Florian

last: Halbritter

first: Toru

last: Suzuki

first: Fabian

last: Titz-Teixeira

first: Matthias

last: Farlik

first: Maki

last: Asami

first: Julia

last: Ramesmayer

first: Xiaoyan

last: Ma

first: Andreas

last: Lackner

first: Nick

last: Warr

last: Pauler

first: Simon

last: Hippenmeyer

first: Ernest

last: Laue

first: Christoph

last: Bock

last: Beyer

first: Antony

last: Perry


title: Mouse preimplantation imprinting [WGBS]

first: Martin

last: Leeb

summary: In mammals, chromatin marks at imprinted genes are asymmetrically inherited from each parent to control gene expression. Many genomic imprints are determined by differentially methylated regions (DMRs), but these have not been comprehensively mapped physically or functionally in mouse preimplantation embryos. To address this, we measured genome-wide DNA methylation in individual haploid uniparental parthenogenetic haploid (ph) and androgenetic haploid (ah) E3.5 blastocysts by micro-whole-genome bisulfite sequencing (µWGBS). For comparison, we also included ahESC and phESC lines in the analysis.Comparison of DNA methylomes from uniparental blastocysts with those of control blastocysts (produced by intracytoplasmic sperm injection) identified 859 DMRs. Haploid ES cells showed overall erosion of those DMRs, in contrast to diploid ES cells that relatively maintained differential methylation.

overall_design: DNA methylation profiling (using micro-WGBS) of mouse E3.5 blastocysts (2 androgenotes, 2 parthenogenotes, 2 ICSI), embyronic stem cells (3 female, 2 male, 4 parthenogenotes, 3 androgenotes), and somatic tissue (kidney, n = 1). Haploid embryos offer the advantage to reduce noise that might have been generated by different alleles in diploid uniparental embryos.


title: Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

institute: Newcastle University

summary: Genome-wide methods for examining chromatin modification provide detailed information on regulatory regions of the genome.  Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression.  Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding.

overall_design: Gene expression microarray SW1353 cells treated with IL-1 (n = 3) vs controls (n = 3)

first: Matt

last: Barter

first: Kathleen

last: Cheung


title: M1/M2 polarization of Lyz2Cre+ or C57Bl/6 BMDMs yield unique phenotypes when polarized in the presence/absence of EGFR inhibitor Erlotinib

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

state: MI

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

summary: We report the gene expression (obtained by next generation RNAseq) of bone marrow derived macrophages from Lyz2Cre+ or C57Bl/6 mice that have been polarized to an M1 or M2 phenotype in the presence of absence of EGFR inhibitor, Erlotinib. This study provides data on how M1 and M2 BMDMs differ in their overall gene expression profiles in mice as well as how gene expression is influenced by EGFR inhibition during polarization.

overall_design: BMDMs derived from Lyz2Cre+ or C57Bl/6 mice were treated with LPS (100ng/ml)+IFNg (50ng/ml) to achieve an M1 phenotype and with IL-4 (10ng/ml)+IL13 (10ng/ml) to achieve an M2 phenotype. BMDMs receiving erlotinib treatment were given erlotinib (1uM) at time of M1/M2 polarization

first: Elissa

last: Hult

middle: J

first: Bethany

last: Moore


title: Transcriptional profiling of metastatic tumor cells in liver of a mouse pancreatic cancer model

first: Jinyang

last: Li

address: 1230 York Ave

institute: The Rockefeller University

summary: Cancer patients presenting with surgically resectable disease often harbor occult metastases, a potential source of relapse that is targetable only through systemic therapy. Studies of this occult fraction have been limited by a lack of tools with which to isolate cells based on spatial grounds. We developed a photoconversion-based isolation technique allowing efficient recovery of cell clusters of any size including solitary disseminated tumor cells (DTCs), which are largely inaccessible otherwise. In a mouse pancreatic cancer model, transcriptional profiling of spontaneously arising DTCs revealed considerable heterogeneity, functionally reduced propensity to proliferate and enrichment for inflammatory-response phenotype associated with NF-κB signaling.

overall_design: Cel-seq2 was utlized as transcriptional profiling strategy to compare the gene expression programs between DTCs and macrometastatic tumor cells. DTCs and macropmetastatic tumor cells were sorted from liver in an orthotopically implantation based mouse pancreatic cancer model.

first: Yogev

last: Sela

first: Ben

last: Stanger


title: Development of MeTA-inducible system in LNCaP cells

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: Epigenetic gene silencing induced by aberrant DNA methylation is an important mechanism leading to the loss of key cellular pathways in tumorigenesis. Although DNA demethylating agents reverse DNA methylation and have significant cytostatic and cytotoxic effects, it remains elusive whether their effects on cellular phenotypes are solely on reactivation of hypermethylated genes. To address this issue, we constructed LNCaP-derived human prostate cancer cell lines that can pharmacologically induce the expression of fusion gene comprising NFkB transcriptional activation domain (AD) and methyl-CpG binding domain (MBD). Tetracycline induction of NFkB (AD)-MBD protein led to so-called methyl-CpG targeted transcriptional activation (MeTA), as demonstrated by the reactivation of hypermethylated genes such as MT1M, NEFH, and NEFM. The cell proliferation assay indicated that MeTA suppressed the growth of LNCaP cells. Furthermore, both flow cytometry and TUNEL assay clearly demonstrated that MeTA induced apoptosis. In order to search genes responsible for apoptosis, we performed gene expression microarray analysis of MeTA-uninduced and -induced LNCaP cells: Several tumor necrosis factor receptor superfamily (TNFRSF) genes upregulated in accordance with the induction of MeTA. These results suggest that DNA methylation confers cancer cells the ability to avoid apoptosis and MeTA may provide an efficient mean to analyze the change in cancer cell phenotypes by DNA methylation alterations. This is the first report showing that the reactivation of hypermethylated genes by the method other than DNMT inhibition induces growth arrest and apoptosis in cancer cells.

overall_design: Two LNCaP prostate cancer-derived cell lines, TR9-MeTA14 and TR15-MeTA5, that allow tetracycline-regulated NFkB (AD)-MBD expression were constructed. The RNAs from TR9-MeTA14 and TR15-MeTA5 with (4 days treatment) or without tetracycline were prepared and analyzed by using Agilent whole human genome microarray (4×44K).

first: Toshiya

last: Miyauchi


title: High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways II

city: Santa Cruz

first: Sergio

last: Covarrubias

address: Thimann Receiving/Department Carpenter Lab/Biomed 125, 1156 High St., Thimann Labs

department: MCD

institute: UCSC

summary:
Here we compare gene expression profiles of un-stimulated vs 6hour Pam3CSK4-stimulated THP1 (ATCC) cells
The goal of this experiment was to define differentially expressed coding genes.

overall_design: Un-stimulated or Pam3CSK4-stimulated THP1 were collected and placed directly in Trizol. RNA was isolated and sequenced

first: Susan

last: Carpenter


title: Genomic properties of variably-methylated retrotransposons in mouse

city: Cambridge

first: Anne

last: Ferguson-Smith

address: 20 Downing Place

department: Genetics

institute: Cambridge University

summary: Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. Two examples of TEs that escape this regulation are the murine-specific intracisternal A particle (IAP) elements Avy and AxinFu, which exhibit inter-individual variability in methylation associated with phenotypic variation. To determine the frequency of this phenomenon, its underlying mechanisms, and its effects on gene expression, we previously conducted a screen identifying variably methylated IAPs (VM-IAPs). Here, we fully validate these elements, categorising VM-IAPs for the first time into those exhibiting tissue specificity (tsVM-IAPs) and those showing uniform methylation among tissues (constitutive- or cVM-IAPs) with both types having the potential to regulate the genome in cis. Using our validated set of VM-IAPs, we explore how variable methylation is established and identify sequences enriched within cVM-IAPs, implicating genetics as a determinant of variability. CTCF, a methylation-sensitive transcription factor known for its role in facilitating chromatin interactions, is enriched at VM-IAPs and we show that CTCF binding is inversely correlated with methylation at cVM-IAPs. We uncover dynamic physical interactions between lowly-methylated cVM-IAPs and other genomic loci, suggesting that VM-IAPs have the potential for long-range genomic regulation. Lastly, screening for variably methylated regions in other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We propose that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs has the potential to cause inter-individual variability in transcriptional outcomes with implications for phenotypic variation.

overall_design: CTCF ChIP-seq of eight individual mouse livers and 4C-seq of five genomic loci across five individual mouse livers

first: Jessica

middle: L

last: Elmer

first: Amir

last: Hay

first: Noah

last: Kessler

first: Eve

last: Ainscough

middle: C


title: Study on Low temperature Mechanism via  SMRT-based RNA-seq in Chrysanthemum leaves

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary: The mixed sample was obtained from the salt stress treatment and the control,  then we obtained one cDNA library. In total, 3,717,516 subreads and 141,445 Consensus reads were constructed.

overall_design: Dendranthema grandiflorum var. jinba was used in this study. The buds raised from tissue-cultured seedlings were grown on MS medium (16 h photoperiod, 25 °C/22 °C day/night temperature) for thirty days. Then thirty-day old chrysanthemum seedlings were transferred to pots filled with a 1:1 mixture of peat and perlite, and acclimated for five days at normal condition. Then the seedlings were subjected to following treatments: (CK) normal condition as control, (T) 4 °C for 24 h, followed by − 4 °C for 4 h. Each treatment collected a mixture of three biologically replicated leaves, then samples rapidly frozen with liquid nitrogen and stored at − 80 °C. There were two samples in total used for RNA-Seq.

first: Ling

last: He


title: High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways I

summary:
Whole-genome pooled sgRNA screen using immortalize bone marrow-derived mouse macrophages with Cas9 and an NFKB-GFP reporter system (iBMDM-NFKB-Cas9)
The goal of this experiment was to 1) identify regulators of NFKB signaling 2) identify genes important for viability

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: iBMDM-NFKB-Cas9 cells were infected with a custom whole-genome sgRNA library and were stimulated with 200ng/ml LPS and FACS sorted for collect top/bottom 20% of cells. For the viability screen, cells were collected at day 0 and day20.


first: David

last: Young

overall_design: ATAC-seq SW1353 cells treated with IL-1 (n = 3) vs controls (n = 3)

first: Matt

last: Barter

first: Kathleen

last: Cheung


title: High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways

sample_organism:
Homo sapiens
Mus musculus
synthetic construct