title: Hypoxia controls the glycobiological signature and related pro-tumorigenic properties of metastatic melanomas

city: Miami

first: Anthony

last: Griswold

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: Metastatic melanoma (MM) has a five-year survival rate of only 37%.  The major causes of MM-related mortality are distant organ involvement and treatment resistance.  These metastatic activities are often potentiated by the persistence of tumor-initiating cells (TICs) thriving in areas of hypoxia.  To enhance therapy success, it is, thus, critical to understand MM TIC properties and devise MM TIC-specific treatment strategies.  Our recent data suggest that MM cells have a distinct MM glycome signature characterized by fetal i-linear poly-N-acetyllactosamines (poly-LacNAc) and loss of I-branching enzyme β1,6 N-acetylglucosaminyltransferase 2 (GCNT2) that promote tumorigenicity.  Whether hypoxia can instruct MM TIC development by modulating the MM glycome signature remains unknown.  Here, comparative analysis of GCNT2 levels on patient melanoma cells and clinical outcome confirmed the relationship between loss of GCNT2 and poor patient survival.  Moreover, MM cells with low GCNT2 showed elevated TIC marker expression and increased TIC potential, in vivo.  Under hypoxia, MM cells further lost GCNT2 and I-branched poly-LacNAc expression and showed corresponding elevations in TIC markers and other glycome-related alterations.  Galectin (Gal)-8, notably, was upregulated under hypoxia, preferred binding to i-linear poly-LacNAcs, increased TIC marker CD271, and was significantly elevated in sera of melanoma patients. Knockdown of Gal-8 in MM cells significantly decreased CD271 levels, even under hypoxia.  Results from this investigation reveal a key role for hypoxia in enforcing the MM glycome signature and for Gal-8 as a pro-tumorigenic lectin and putative biomarker of MM.

overall_design: Metastatic melanoma cell lines A375, A2058 and SKMEL-5 were used for analysis. Biological duplicates of each samples were used for analysis. For each cell line cells cultured under normoxic and hypoxic conditions (1% oxygen tension). The samples from the normoxic group were used as control/ reference group for analysis.

first: Asmi

last: Chakraborty

first: Mariana

last: Perez

first: Jordan

middle: D

last: Carroll

first: Aristotelis

last: Antonopoulos

first: Anne

last: Dell

first: Liettel

last: Ortega

first: Norhan

last: Mohammed

first: Michael

last: Wells

first: Caleb

last: Staudinger

first: Kevin

last: Chandler

first: Cristina

last: Marrero

first: Ramon

last: Jimenez

first: Yoshihiko

last: Tani

first: James

last: Wilmott

first: John

middle: F

last: Thompson

first: Wei

last: Wang

first: Robert

last: Sackstein

first: Richard

last: Scolyer

first: George

last: Murphy

first: Stuart

last: Haslam

first: Charles

last: Dimitroff


title: Dissecting the tumour microenvironment displays different genomic profile in patients treated with carmustine wafers.

status: Public on Aug 03 2022

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

type: Expression profiling by high throughput sequencing

summary:
Despite the state-of-the art treatment, consisting of surgery followed by chemo and radiotherapy, patients diagnosed for a glioblastoma multiforme (GBM), have a median overall survival of 14 months. The lack of therapeutic efficacy is due to the great inter- and intra-tumour cellular and molecular heterogeneity, the biological aggressiveness, the ability to develop drug resistance as well as the infiltrative nature of tumour cells into the surrounding brain parenchyma. Furthermore, it has been widely shown that GBM progression is supported not only by tumour cells, but also by their interaction with the surrounding microenvironment. In the late 90s, a novel adjuvant therapy has been approved involving the placement, in the resection cavity, of wafers delivering carmustine (CW). Although reported studies are contrasting a retrospective study, performed in our Institute, revealed that the treatment of 116 GBM patients by CW showed 17% of long-term survivors (OS >36 months).
We isolated glioma-associated stem cells (GASC), resident in the glioma microenvironment, from tumour samples of 3 patients responsive and 3 patients not responsive to CW implantation and we performed a transcriptomic analysis to identify differentially expressed genes. We found that GASC derived from the two classes of patients have distinctive transcriptomic profiles and we selected 78 differentially expressed genes to explore and validate their expression in more GASC cell lines. We identified four genes specifically downregulated in GASC isolated from patients with longer OS (>30 months). These genes showed a correlation with clinical data deposited in TCGA-GBM dataset.

overall_design: Given the crucial role of tumour microenvironment on the GBM progression, we here took advantage of our previously established in vitro model of glioblastoma microenvironment to characterize the transcriptomic profile of cells representing the tumour microenvironments of patients responsive and not responsive to CW implantation.

first: Ivana

last: Manini

first: Vera

last: Vendramin

first: Daniela

last: Cesselli

first: Miran

last: Skrap

first: Tamara

last: Ius


title: Comparative physiological and transcriptome analysis reveal the molecular mechanism of melatonin in regulating salt tolerance in alfalfa (Medicago sativa L.)

city: Yinchuan

first: Shuxia

last: Li

state: Ningxia

address: 489 Helan mountain West Road

department: College of Agriculture

country: China

institute: Ningxia University

summary: We established a regulatory network for melatonin-induced key signaling pathways and functional genes under salt stress.

overall_design: Physiological and gene expression of alfalfa leaves under melatonin, salt, and salt plus  melatonin treatments were examined.

first: Yuan

first: Jian

last: Lan

first: Bingzhe

last: Fu


title: Transcriptome sequencing data analysis of Bacillus subtilis NCIB 3610 wild-type strain, tmRNA mutant strain and MB revertant strain

city: Shenzhen

first: Shanshan

last: Xu

address: Xueyuan Avenue, No. 1066

institute: Shenzhen University

summary: In our study, we found that lack of tmRNA affects the biofilm formation in Bacillus subtilis, which has important research significance. Then, we obtained a revertant strain MB from tmRNA mutant strain. And MB strain could restore  biofilm production capacity. Therefore, the transcriptomes of the three strains were sequenced. Based on the statistical analysis of gene expression (P < 0.05), there were 756 genes up regulated while 992 genes down regulated by at least two folds when comparing TM to WT. Secondly, there were 974 genes up regulated while 563 genes down regulated by at least two folds when comparing MB to TM. And there were 179 genes up regulated while 307 genes down regulated by at least two folds when comparing MB to WT.

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: mRNA profiles of Bacillus subtilis NCIB 3610 wild type (WT), tmRNA mutant (TM) and  revertant strain (MB)

first: Ying

first: Bingyu


title: Gene expression profile of CD22 CAR T-cell products

city: Bethesda

first: LIPEI

last: SHAO

state: MD

address: 9000 Rockville Pike Bldg 10, 2C328

department: Center for Cellular Engineering

country: USA

institute: National Institutes of Health

summary: Cytokine release syndrome (CRS) is a strong immune system response that can occur as a result of the reaction of a cellular immunotherapy with malignant cells. While the frequency and management of CRS in CAR T-cell therapy has been well documented, there is emerging interest in pre-emptive treatment to reduce CRS severity and improve overall outcomes. Accordingly, identification of genomic determinants that contribute to cytokine release may lead to the development of targeted therapies to prevent or abrogate the severity of CRS. We examined CD22 CAR T-cells using the Nanostring nCounter platform and found that the expression of the PFKFB4 gene and glycolytic pathway activity were upregulated in CAR T-cells in those who developed CRS compared to those who did not have CRS.

overall_design: We collected 43 CD22 CAR T-cell pre-infusion products. All of them are cryoperserved in the liquid nitrogen. Each sample has related cytokine release syndrome grade (WithoutCRS, CRSgrade1, CRSgrade2, CRSgrade3, CRSgrade4).

first: Lipei

last: Shao

first: Alejandra

last: Pelayo

first: Rongye

last: Shi

first: Nirali

middle: N

last: Shah

first: David

last: Stroncek

first: Ping

last: Jin


title: Retinoic acid and FGF10 promote the differentiation of mESCs into induced embryonic salivary glands

city: Beijing

first: Siqi

last: Zhang

address: 22# Zhongguancun South Avenue, Haidian District

department: Department of Oral and Maxillofacial Surgery School and Hospital of Stomatology

institute: Peking University

summary: Salivary glands produce saliva and play essential roles in digestion and oral health. Pluripotent stem cell-derived (PSC) organoids provide a powerful platform for studying salivary gland development and developing new regenerative therapy. The previous protocol of PSC-derived salivary gland organoids required complicated manufacturing processes, which hampered the organoids for basic research and clinical application.Here, by mimicking the regulatory mechanism of developing salivary glands, we reported the differentiation of induced embryonic salivary glands (iE-SGs) from mouse embryonic stem cells by step-wise treatment of retinoic acid and FGF10. We showed that the iE-SGs recapitulated early morphogenetic events, including the thickening and invagination of the salivary gland placode, and then formed initial buds. The iE-SGs also differentiated into developing ducts structures and could develop to striated and excretory ducts when transplanted in vivo. RNA- seq revealed that iE-SGs had gene expression profiles similar to mouse embryonic SMGs. Thus, our study provided an easy and safe method to generate iE-SGs and offered possibilities for studying events during salivary gland morphogenesis in vitro

overall_design: Analysis of global transcriptomes of mouse embryonic stem cell derived iE-SGs.There are two  replicates in each group.

first: Zhang

last: Siqi

first: Wei

last: Shicheng


title: Differential regulation of flower transpiration during abiotic stress in plants

city: Columbia

first: Sidharth

last: Sen

state: Missouri

address: Agriculture Bldg, University of Missouri

department: The Division of Plant Sciences and Technology

institute: University of Missouri

summary: Soybean plants were subjected to water deficit, heat stress, and combination of water deficit and heat stress along with control condition for 10 days and unopened soybean buds were analysed for differential gene expression compared to control.

overall_design: Soybean plants (16-18 days old) were subjected to water deficit, heat stress, and combination of water deficit and heat stress for 10 days and unopened soybean buds were collected in liquid nitrogen. Total RNA was isolated and mRNA profile were generated by deep sequencing using NovaSeq 6000 PE150.

first: Ranjita

last: Sinha

first: Sara

middle: I

last: Zandalinas

first: Yosef

last: Fichman

first: Trupti

last: Joshi

first: Felix

middle: B

last: Fritschi

first: Ron

last: Mittler


title: Expression data in Wheat TGMS line BS366 under different conditions

first: Shiqing

last: Gao

address: Shuguang Garden Middle Street

institute: Beijing Academy of Agriculture and Forestry Sciences

summary:
The male sterility of a wheat thermosensitive genic male sterile (TGMS) line is strictly controlled by temperature.  We used microarrays to identify genes that play pivotal roles in anthers during cold-stress hypersensitivity.
The expression of genes in response to different temperature treatment were analyzed for anthers of BS366.

overall_design: Anthers were selected at five developmental stages from BS366 unde four conditions for hybridization with the Affymetrix GeneChip Wheat Genome Arrays

first: Liping


title: Tendon methylation microarray after particulate matter inhalation

city: Daejeon

first: Minhyeok

last: Lee

address: 158, Gwanjeodong-ro, Seo-gu

department: Department of Internal Medicine

country: South Korea

institute: Konyang university hospital

summary:
Open tenotomy of the Achilles tendon of 6 rats was performed. The animals were divided into two groups according to exposure of PM2.5 (particulate matter less than 2.5 µm): control group (Non-PM group) or PM exposure group (PM group). After 6 weeks of PM exposure, the tendon DNA was extracted and anlyzed.
Genome-wide DNA methylation profiles were determinen. DNA amplicons were prepared using Differential Methylation Hybridization (DMH) method, subsequently hybridized on to the Customized Agilent Rat CpG island Microarray. The goal was to unravel the DNA methylation patterns in different subgropus of tendon tissue according to partciulate matter exposure.

overall_design: 3 PM exposure group group/3 control group

first: Jae-Hwang

last: Song

first: Ji

middle: W

last: Son


title: RNA-seq of primary human keratinocytes : Effects of IL-20 on gene expression

city: Kaifeng

first: ruizhen

last: wang

address: Jinming Avenue, Kaifeng City, Henan Province

institute: Henan University

summary: In the  present study, RNA-seq were performed To explore biological significance of IL-20 in the neuro-cutaneous signaling network of chronic itch. mRNA profiles were generated by deep sequencing, in triplicate, using MGISEQ-2000. We found that human keratinocytes responded to IL-20, resulting in enrichment of genes promoting itch and inflammation. IL-20 activation promotes cutaneous inflammation and itch, both leading into an aggravation of AD. This finding might help us to better understand the immune-neuro-modulatory mechanism in itch circuits

overall_design: primary human keratinocytes were stimulated with IL-20 (500 ng/ml) or vehicle control. gene expression of these cells were investigated utilizing MGISEQ-2000.

first: Zhiping

last: Lu

first: Jianghui

last: Meng


title: Unveiling co-infection in cystic fibrosis airways: Transcriptomic analysis of Pseudomonas aeruginosa and Staphylococcus aureus dual-species biofilms

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

summary: Staphylococcus aureus and Pseudomonas aeruginosa are the most prevalent pathogens that colonize structurally abnormal airways such as those in Cystic Fibrosis (CF) and other chronic obstructive lung diseases. Although these bacteria seem to succeed one another, CF patients acquire coinciding P. aeruginosa and S. aureus pulmonary infections, being co-infection usually associated with decreased lung function and increased frequency of pulmonary exacerbations. In addition, P. aeruginosa and S. aureus pathogens adopt a biofilm mode of growth, which contributes to high tolerance to antibiotic treatment and the recalcitrant nature of these chronic coinfections, leading to significant patient morbidity and mortality. Interactions between P. aeruginosa and S. aureus have been widely studied and it is commonly admitted that P. aeruginosa outcompetes S. aureus, perhaps outcompeting S. aureus for limited nutrients or producing anti-staphylococcal compounds, having S. aureus a minimal contribution to the overall course of the infection. However, the molecular mechanisms behind these interactions are largely unknown. Herein, we decided to characterize the full transcriptome of these dual-species biofilms, to unveil important molecular interactions that can occur between these two bacterial species that are relevant for the pathogenesis of the entire consortia. Our data provide novel insights into the role of interspecies interactions in the pathogenesis of P. aeruginosa and S. aureus co-infections and will contribute to future studies by the research community.

sample_organism:
Pseudomonas aeruginosa
Staphylococcus aureus

overall_design:
Briefly, transcriptional profiles of P. aeruginosa and S. aureus were obtained after 24-h of growth as dual-species biofilms and compared to the respective single-species biofilms, using high-throughput RNA-sequencing (RNA-seq) from six independent biological samples, pooled into two independent RNA-sequencing libraries (pool of 3 independent samples/libraries).

Please note that the dual-species biofilm raw data were aligned with either S. aureus or P. aeruginosa genomes and then compared with S. aureus or P. aeruginosa single biofilms data.

first: Andreia

middle: P

last: Magalhães

first: Angela

first: Maria

middle: O

last: Pereira

first: Nuno

last: Cerca


title: Identification of candidate regulatory elements controlling transcriptome during the formation of interphalangeal joints

city: Rotterdam

first: Karol

last: Nowosad

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the ChIPseq derived Candidate Enhancer (CE) atlas generated for interphalangeal interzone and phalange, tissues collected during synovial joint formation. Three replicates for interzone and three replicated for phalange were immunoprecipitated (IP) with the H3K27ac antibodies. Also, two replicates for interzone and two replicates for phalange were immunoprecipitated with H3K4me1 antibodies. The IP samples for both histone marks were sequenced and used for annotation of CEs. Further, the CEs were functionally annotated. In parallel, the total RNA for three interzone and three phalange replicates was isolated and mRNA sequencing libraries were constructed. Next the identification of differentially expressed genes (DEGs) and integrative analysis of DEGs and CEs was performed.

overall_design: Integrative analysis of ChIPseq derived candidate enhancers (CEs) defined by enrichment of 2 different histone modifications (H3K27ac and H3K4me1) and transcriptome profiles (RNAseq) in dissected interdigital interzone and phalange.

first: Rutger

last: Brouwer

first: Adrian

last: Odrzywolski

first: Anne

middle: L

last: Korporaal

first: Bartłomiej

last: Gielniewski

first: Bartosz

last: Wojtaś

first: Wilfred

last: van IJcken

first: Frank

last: Grosveld

first: Danny

last: Huylebroeck

first: Przemko

last: Tylzanowski


title: Induced endothelial cell integrated liver assembloids promotes hepatic maturation and therapeutic effect on cholestatic liver fibrosis

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary:
Transplantation of pluripotent stem cell (PSC) derived liver organoids have been studied to solve the donor shortage. However, differentiation of unintended cell populations, challenges in generating multi-lineage organoids, and tumorigenicity hinder its uses in clinics. Here, liver assembloids (iHEA) were generated by integrating induced endothelial cells (iEC) and induced hepatic stem cells (iHepSC). iHEA showed enhanced functional maturity iHepSCs derived liver organoids (iHLO) in vitro and had improved therapeutic effects on cholestatic liver fibrosis animals in vivo. Mechanistically, FN1 expressed from iECs led to up-regulation of Itgalph5/beta1 and Hnf4alpha in iHEA and were correlated to decrease of hepatic stellate cells activation genes such as Lox, and Spp1 in the cholestatic liver fibrosis animals. In conclusion, our study demonstrates that directly converted cells can be a promising source for generating transplantable assembloids.
This study is designed to generate liver organoids (iHLO) and liver assembloids (iHEA) using induced stem cells generated by direct conversion. Hepatic maturity of iHLO and iHEA were compared by measuring gene expression, albumin/urea secretion and CYP1A2 activity. The experiments were repeated at least three times, and the replicates are indicated in each figure and legend. N values represent the number of animals in the experiment. All animal experimental procedures were approved and conducted under a protocol (UNISTIACUC-20-49) by the Animal Care and Use Committee of Ulsan National Institute of Science and Technology (UNIST, Ulsan, South Korea). The experiments were carried out in accordance with documented standards of the Institutional Review Board of Ulsan National Institute of Science and Technology (UNIST) (UNISTIRB-15–17 C) for human cell experiments.

overall_design:
The data Fib (Fibroblast) is performed with 1 replicate
The data 2D-iHepSC (2 Dimensional induced Hepatic Stem Cells (2D-iHepSCs)) is performed with 1 replicate
The data 2D-iHepSCiEC (2 Dimensional induced Hepatic Stem Cells integrating induced endothelial cells (2D-iHepSCECs)) is performed with 1 replicate
The data 3D-iHA (3 Dimensional Hepatic Assembloids (3D-iHAs)) is performed with 1 replicate
The data 3D-iHEA (3 Dimensional Hepatic Endothelial Assembloids (3D-iHEAs)) is performed with 1 replicate
The data Adult-Liver (Adult-Liver1) is performed with 1 replicate
The data Fetal-Liver (Fetal-Liver1) is performed with 1 replicate

first: Donggyu

last: Nam

first: Myung

middle: R

last: Park

first: Hyunah

last: Lee

first: Sung

middle: C

last: Bae

first: Daniela

last: Gerovska

middle: J

first: Holm

last: Zaehres

first: Hans

last: Schöler

first: Jeong

last: Kim


title: Differential Neuropathology, Genetics, and Transcriptomics in two kindred cases with Alzheimer’s Disease and Lewy Body Dementia

city: Pavia

first: Ilaria

last: Palmieri

state: PV

address: Via Mondino 2

institute: IRCCS Mondino Foundation

summary: Alzheimer’s disease (AD) and Lewy body dementia (LBD) are two different forms of  dementia but their pathology may involve the same cortical areas with overlapping cognitive  manifestation. Dementia cases within the same family share a common genetic background.  Nonetheless, the clinical phenotype may be different due to the different underlying molecular  processes that come-up apart from genetics, causing diverse neurodegeneration. Through  neuropathological, genetic and transcriptomic comparison of four different brain areas  (substantia nigra, hippocampus, parietal lobe and basal ganglia), we defined commonalities  and differences in the pathological processes of dementia in two kindred cases, a mother and a  son, who developed a classical AD and an aggressive form of AD/LBD respectively. Genetic  analysis did not reveal any pathogenic variants in the principal AD/LBD-causative genes.  RNA sequencing highlighted high transcriptional dysregulation within the substantia nigra in  LBD pathology, while AD underwent lower degree of transcriptional dysregulation, with the  parietal lobe being the most involved brain area. Conversely, hippocampus (the most  degenerated area) and basal ganglia (lacking specific lesions) expressed the lowest level of  dysregulation. Our data suggest that there is a link between the transcriptional dysregulation  and the amount of tissue damage accumulated across time, assessed through neuropathology.  Moreover, we highlight that the molecular bases of AD and LBD follow very different  pathways, which underlie their neuropathological signatures. Indeed, the transcriptome  profiling through RNA sequencing may be an important tool in flanking the  neuropathological analysis for a deeper understanding of AD and LBD pathogenesis.

overall_design: Frozen slices from four brain areas (substantia nigra, hippocampus, parietal lobe and basal ganglia) of the two kindred cases (mother and son) and of the  non-demented control were used to perform deep RNA sequencing.

first: Tino

middle: E

last: Poloni

first: Velentina

last: Medici

first: Susanna

last: Zucca

first: Annalisa

last: Davin

first: Orietta

last: Pansarasa

first: Mauro

last: Ceroni

first: Livio

last: Tronconi

first: Antonio

last: Guaita

first: Cristina

last: Cereda

first: Stella

last: Gagliardi


title: Next Generation Sequencing Quantitative Analysis of Wild Type and NONO Knock Down Glioblastoma Cell Line (GSC P3) Transcriptomes

city: jinan

first: Xu

last: Wang

state: State...

address: wenhua west road

institute: shandong university

summary: We identified non-POU domain-containing octamer-binding protein (NONO), a Drosophila behavior human splicing (DBHS) protein, among the most upregulated mRNA splicing factors in glioblastoma multiforme (GBM). NONO was associated with poor prognosis in GBM patients, and overexpression of NONO promoted GBM cell proliferation, invasion and tumorigenesis in a GBM orthotopic xenograft model. Through RNA sequencing based transcriptomic profiling, we found that knockdown of NONO resulted in global changes in alternative splicing-intron retention, and identified GPX1 and CCN1 as two pre-mRNAs targeted by NONO. NONO directly bound to the intron of GPX1 pre-mRNA through the RNA-recognition motifs 2 (RRM2) domain and required interaction with another DBHS protein family member, PSPC1. Knockdown of NONO interfered with redox homeostasis in cells, at least partially, through abnormal splicing of GPX1. Finally, Auranofin, a small-molecule inhibitor targeting NONO, inhibited GBM growth in an orthotopic xenograft model in mice. Taken together, our data revealed that NONO was a key regulator of mRNA splicing in GBM, and that targeting NONO represents a novel and effective therapeutic strategy for the treatment of GBM.

overall_design: Glioblastoma cell line P3 mRNA profiles of wild type (siNC) and NONO Knock Down (siNONO) cell line


title: Next Generation Sequencing Quantitative Analysis of Wild Type and NONO Knock Down Glioblastoma Cell Line(U251) Transcriptomes

overall_design: Glioblastoma cell line U251 mRNA profiles of wild type (siNC) and NONO Knock Down (siNONO) cell line


title: RNA-seq analysis of follicular (FO), marginal zone (MZ) and aged-associated B cells (ABC) across three TLR9 genotypes (TLR9WT, TLR9-/- and non-signaling TLR9P915H/P915H) isolated from a mixed chimeric setting in the MRL/lpr murine model of SLE

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary:
Purpose: The goal of this study was to assess if TLR9 deficiency (TLR9-/-) or TLR9 incapacity to signal through MyD88 would differentially influence the gene programs of B cell subsets, in a B cell intrinsic manner.
Methods : Mixed bone marrow chimeras of one-third each TLR9+/+ CD45.1/2, TLR9-/- CD45.1/1 and TLR9P915H/P915H CD45.2/2 were generated on the MRL/lpr background.  From each recipient, three B cell subsets, FO, MZ and ABC were sorted with respect to the CD45 congenic markers at [x weeks] post chimerism. RNA was isolated using the RNeasy Plus Micro Kit (QIAGEN). Samples were sequenced using NovaSeq 6000 flowcell (Illumina, Inc, California, USA) with 100 bp paired-end reads (20 million reads per sample) and aligned to the mm10 genome using the STAR aligner.
Results: ABCs showed the most transcriptional differences among TLR9 genotypes. TLR9P915H and TLR9WT ABC transcriptomes were much more similar to each other than to those of TLR9-/- mice, sharing 246 of 381 DEGs, even though TLR9P915H B cells could not signal via MyD88. These included a number of genes encoding for inhibitory or anti-inflammatory pathways, suggesting that TLR9 could induce a regulatory signal independently of MyD88.

overall_design: mRNA profiles of TLR9 deficient (TLR9-/-), mutant TLR9 (P915H/P915H) and intact TLR9 (WT) FO, MZ and ABC of 19-week-old (3-way-mixed) BM chimera MRL/lpr mice were generated in four replicates by sequencing, using NovaSeq 6000 flowcell.

first: Claire

last: Leibler

first: Shuchi

last: Smita


title: The signalling axis ERK5/KLF2 is a major determinant of chemical sarcomagenesis

city: Madrid

first: Luis

last: del Peso

state: Madrid

address: Arzobispo Morcillo

department: Biochemistry

country: Spain

institute: Universidad Autonoma de Madrid

summary: Sarcomas are a heterogeneous group of tumors in which the role of ERK5 is poorly studied. To clarify the role of this particular MAPK in sarcomatous pathology, we used a murine 3-methyl-cholanthrene (3MC)-induced sarcoma model. Our data show that 3MC induces pleomorphic sarcomas with muscle differentiation, showing an increased expression of ERK5. Indeed, this upregulation was also observed in human sarcomas of muscular origin such as leiomyosarcoma or rhabdomyosarcoma. Moreover, in cell lines derived from these 3MC-induced tumors, abrogation of Mapk7 expression by using specific shRNAs decreased in vitro growth, colony-forming capacity, and caused a marked loss of tumor growth in vivo. Indeed, the transcriptomic profile in ERK5 abrogated cell lines by RNAseq showed a deregulated gene expression pattern for key biological processes such as angiogenesis, migration or motility, among others. Finally, among the various differentially expressed genes, Klf2, a direct target of the ERK5 pathway, is a key mediator of the biological effects of ERK5 in vitro and in vivo, as indicated by its specific interference. Therefore, our data suggest that the ERK5KLF2 signaling axis is an important determinant of 3MC-induced sarcomas and should be further studied in human sarcomas, especially those of muscular origin.

overall_design: mRNA profile of Ek5-defficient/prficiebt 3MC-induced tumor cell lines

first: Ricardo

last: Sanchez-Prieto

first: Maria

last: Ruiz-Hidalgo


title: Assaying peroxisome proliferator-activated receptor activation in the peripartum using precision-cut bovine liver slices reveals novel putative PPAR targets in dairy cows.

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: Weniger Hall

department: Animal Sciences

institute: Oregon State University

summary: Metabolic challenges experienced by dairy cows during the transition between pregnancy and lactation (also known as peripartum), are of considerable interest from a nutrigenomic perspective. The mobilization of large amounts of non-esterified fatty acids (NEFA) leads to an increase in NEFA uptake in the liver, the excess of which can cause hepatic accumulation of lipids and ultimately fatty liver. Interestingly, peripartum NEFA activate the peroxisome proliferator-activated receptor (PPAR), a transcriptional regulator with known nutrigenomic properties. The study of PPAR activation in the liver of periparturient dairy cows is thus crucial; however, current in vitro models of the bovine liver are inadequate, and the isolation of primary hepatocytes is prohibitive and error-prone. The objective of the current study was to evaluate the use of precision-cut liver slices (PCLS) from liver biopsies as a model for PPAR activation in periparturient dairy cows. Four cows were enrolled in the experiment, and PCLS from each were prepared prepartum (-10 DIM) and postpartum (+10 DIM) and treated with a variety of PPAR agonists and antagonist. Gene expression was assayed through RT-qPCR and RNAseq, and intracellular triglyceride concentration was measured. PCLS treated with PPARγ agonist rosiglitazone displayed upregulation of canonical PPAR targets ACADVL and LIPC in the postpartum, while a PPARδ agonists increased expression of PPAR target PDK4; no gene expression changes were detected in the prepartum, and triglyceride concentrations were unchanged between treatments. Transcriptome sequencing revealed considerable differences in response to PPAR agonist, mainly related to pathways involved with lipid metabolism and the immune response. Among differentially expressed genes, a subset of 91 genes were identified as novel putative PPAR targets in the bovine liver, by cross-referencing our results with a publicly-available dataset of predicted PPAR target genes, and supplementing our finding with prior literature. Our results provide important insights on the use of PCLS as a model for assaying PPAR activation in the peripartum.

overall_design: Gene expression profiling on precision-cut liver slices from 4 early postpartum cows treated with PPAR agonists. Precision-cut liver slices (PCLS) from each animal were treated with 100 µM of the PPARα agonist WY-14643, or 50 µM of the PPARδ agonist GW-501516, or 100 µM of the PPARγ agonist rosiglitazone, or were left untreated. RNA was isolated and sequenced after 18 hours of incubation

first: Busato

last: Sebastiano

first: Abdelatty

last: Alzahraa

first: Ford

last: Hunter

first: Estill

last: Charles

first: Bionaz

last: Massimo


title: Cellular Recovery After Prolonged Warm Ischemia of the Whole Body

city: New Haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar Street

department: Neuroscience

institute: Yale University

summary: Here we use single-cell transcriptome analysis in healthy and varying ischemic conditions across 4 vital organs such as brain (hippocampus), heart, liver and kidney to better understand the changes occurring following the cessation of the blood flow. Furthermore, we use these datasets as references to characterize changes on the single-cell transcriptome level that are induced by re-introduction of the blood flow to the same organs.

overall_design: Restoring molecular and cellular functions after a period of ischemia of the whole body

first: David

last: Andrijevic

first: Zvonimir

last: Vrselja

first: Taras

last: Lysyy

first: Shupei

last: Zhang

first: Mario

last: Skarica

first: Ana

last: Spajic

last: Dellal

first: Stephanie

last: Thorn

first: Robert

last: Duckrow

first: Shaojie

last: Ma

first: Phan

middle: Q

last: Duy

first: Atagun

middle: U

last: Isiktas

first: Dan

last: Liang

first: Mingfeng

last: Li

first: Suel-Kee

last: Kim

first: Stefano

middle: G

last: Daniele

first: Khadija

last: Banu

first: Sudhir

last: Perincheri

first: Madhav

last: Menon

first: Anita

last: Huttner

first: Kevin

last: Sheth

middle: T

last: Gobeske

first: Gregory

last: Tietjen

first: Hitten

last: Zaveri

first: Stephen

last: Latham

first: Albert

last: Sinusas


title: TRIM28 keeps the time of mitotic gene expression sustaining proliferation and progression of Malignant Pleural Mesothelioma (MPM).

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

institute: Azienda USL- IRCCS di Reggio Emilia

summary: RNA extracted from tumor samples of 86 patients affected by MPM was analyzed on the nCounter system using a custom panel called MPM_C9073 (Nanostring Technologies).

overall_design: Evaluation of gene expression profile associated to overall survival in MPM.

first: Alessia

last: Ciarrocchi


title: Transcriptome profiling of glycosyltransferase knockouts using CRISPR in Poplar

city: Victoria

first: Harley

last: Gordon

state: BC

address: 3800 Finnerty Rd

department: Biology

country: Canada

institute: University of Victoria

summary: Comparison of UGT71L1 knock-out genes with empty vector and wild-type controls in Populus tremula x alba

overall_design: Mature leaf mRNA profiles of Greenhouse grown plants.


title: Comparative profiling of microRNA transcriptome in different developmental phases  and analysis of microRNAs associated with reproductive development in the Brown Planthopper, Nilaparvata lugens

city: Hangzhou

first: Ni

last: Wang

address: Sundun Street

institute: Institute of Insect Sciences, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province

type: Non-coding RNA profiling by high throughput sequencing

summary: In the present study, small RNA libraries derived from three developmental phases (1st day after eclosion, 3rd day after eclosion and 5th day after eclosion) of short-winged morphs female adults were constructed and sequenced. A total of 15,571,298, 16,362,568 and 15,147,276 raw reads were obtained from three BPH small RNA libraries, respectively. Moreover, we identified 905 miRNAs, including 263 conserved (belonging to 37 families) and 642 novel miRNAs. In addition, the expression profiles of these miRNAs were assessed across different developmental stages Specifically, 22, 19, and 12 miRNAs were differentially expressed between3d and 1d, 5d and 1d, and 5d and 3d, respectively. A total of 43 miRNAs were differentially expressed in the three developmental phases, and 7 miRNAs were validated using quantitative RT-PCR. Target Scan and miRanda predicted14568 putative targets for 43 differentially expressed miRNAs within the 3’UTRs sequences of BPH transcriptome. Moreover, GO and KEGG pathway analysis of the predicted miRNA targets further illustrate the likely roles for these differentially expressed miRNAs in reproduction.

overall_design: Small RNA libraires from three developmental stages (1st day after eclosion, 3rd day after eclosion and 5th day after eclosion)

first: Zengrong

last: Zhu


title: mRNAseq in control(WT) and Dst-b mutant mouse heart

city: Niigata

first: Nozomu

last: Yoshioka

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

department: Graduate School of Medical and Dental Sciences

country: Japan

institute: Niigata university

summary: We sequenced mRNA from mouse heart to compare gene expression level between 3 control(WT) and 3Dst-b mutant.

overall_design: mRNA profiles obtained from 3 different control(WT) and 3 Dst-b mutant were generated by deep sequencing using Illumina NovaSeq6000.

first: Masato

last: Yano

first: Hirohide

last: Takebayashi


title: Genetic characterization of a missense mutation in the X-linked TAF7L gene in an oligozoospermic man

city: Nanjing

first: Li

last: Fangfang

address: 101 Longmian Avenue, Jiangning District, Nanjing, Jiangsu Province,

institute: Nanjing Medical University

summary: We carried out genome-wide expression profiling by RNA-seq to determine whether the mutation brings about a certain influence to the transcriptomic homeostasis. Indeed, there were some differential expressions of mRNA and noncoding genes in comparison of the Taf7lD144G and wide-type testis, lending support to mutation-caused defects at molecular level.

overall_design: Examination of transcriptome profiling coding and noncoding gene of adult wild type(WT) and taf7l mutant mice testis

last: Ling

first: Fangfang

last: Li


title: The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [THP-1]

city: Ann Arbor

first: Joseph

last: Holoshitz

state: MI

address: 1150 W Medical Center Dr

department: Internal Medicine - Rheumatology

institute: University of Michigan

summary: We report RNA sequencing data that shows the differential effects of HLA-DRb1*0301 (LE), HLA-DRb1*0401 (SE) and HLA-DRb1*0402 (PE) on macrophage gene expression under IFNγ cell culture conditions.

overall_design: mRNA profiles obtained from THP-1 cells cultured in presence of synthetic peptides coding the 65-79 region of HLA-DRb1*0301 (LE), HLA-DRb1*0401 (SE) or HLA-DRb*0402 (PE) and IFNγ.

first: V

last: van Drongelen

first: B

last: Miglioranza Scavuzzi

last: Kaur

first: J

last: Liu

first: R

middle: A

last: Mesquita-Ferrari

first: A

middle: H

last: Sawalha

middle: M

last: Kahlenberg

first: E

last: Farkash

first: F

last: Miller


title: The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [RAW264.7]

overall_design: mRNA profiles obtained from RAW264.7 cells cultured in presence of synthetic peptides coding the 65-79 region of HLA-DRb1*0301 (LE), HLA-DRb1*0401 (SE) or HLA-DRb*0402 (PE) and IFNγ.


title: Transcriptomic insights into differential cold tolerance of two tobacco cultivars

first: zhenyu

last: luo

state: Jiangsu

address: Xuanwu

department: College of Agricuture

institute: Nanjing Agricultural University

summary:
Purpose: we conducted a six time-point transcriptomic analysis using two tobacco cultivars with contrasting cold responses, Taiyan8 tobacco (TT, cold susceptibility) and Yanyan97 tobacco (YT, cold resistance).
Methods: mRNA profiles of Tobacco seedlings from CK and cold-treated plants were generated by deep sequencing, in triplicate, usingIllumina Hiseq4500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with methods: hisat2 (v2.0.5), SAMtools (v1.9). StringTie (v1.3.4d) and FeatureCounts (v1.6.4)
Results: We found that both cultivars had common mechanisms to cope with cold stress, including common differentially expressed genes (DEGs), similar time-point-related differential expression profile of genes, and similar NtCBF gene co-expression modules, suggesting conservation of adaptation   strategies for cold responses. Importantly, we found that YT experienced DEGs even under   normal growth condition and had less DEGs in early stage of cold stress (0.5-2 h) when   compared to TT, reflecting occurrence of genotype-dependent gene transcription. Moreover, a   gene co-expression module (brown) with stress-related genes up-regulated in YT instead of   TT at late stage (4-8 h), which might contribute to contrasting phenotypic changes during   cold stress between TT and YT.
Conclusions: our study provides valuable resources for   transcriptomic studies of cold responses in plants. It also helps to identify key cold responsive genes for genetic manipulation for breeding of tobacco cultivars in the future.

overall_design: Tobacco seedlings at the five-leaf stage were used for cold treatment at 4℃. Leaves from CK and cold-treated (0.5h,1h,2h,4h and 8h) plants were collected at different time points and immediately frozen in liquid nitrogen for RNA preparation. Each sample was biologically triplicated for transcriptomic analyses.

first: Zhenyu

last: Luo


title: Response of unmodified and TGFBR2 knockout tumor infiltrating lymphocytes (TIL) to TGF-B stimulation

city: Tampa

first: Yunfei

last: Wang

state: FL

address: 12902 USF Magnolia Drive

department: Clinical Science

institute: H. Lee Moffitt Cancer Center & Research Institute

summary: TGFBR2 was deleted in ovarian cancer TIL via CRISPR/Cas9 gene editing. Response of unmodified and TGFBR2 knockout TIL to TGF-B stimulation was evaluated via RNA sequencing.

overall_design: Unmodified and TGFBR2 knockout TIL were exposed to 10ng/mL TGF-B1 for 24hrs before collection and RNA-sequencing. TGFBR2 knockout was achieved using two different CRISPR gRNAs: gRNA #3 and gRNA #4. CRISPR gene knockout with each gRNA was performed in triplicate using a single patient TIL sample. Thus, three technical replicates were studied for unmodified TIL (WT), TGFBR2 knockout TIL with gRNA #3, and TGFBR2 knockout TIL with gRNA #4. Each sample was subjected to 24hr exposure to TGF-B1 or vehicle for a total of 18 samples.

first: Samantha

last: Fix

first: Marie-Andrée

last: Forget

first: Donastas

last: Sakellariou-Thompson

first: Patrick

last: Hwu

first: Chantale

last: Bernatchez

first: Amir

last: Jazaeri


title: Colorectal liver metastases-specific lncRNA CRLM1 inhibits apoptosis and promotes metastasis through transcriptional regulation cooperated with hnRNPK [CRLM1_OE]

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: The survival rate of colorectal liver metastases remains low. Long noncoding lncRNAs is emerging as a novel class of master regulators of cell invasion and metastasis. In this study, analysis of the lncRNA expression dynamics in the colorectal liver metastases, primary colorectal tumor and normal tissues led to the identification of the metastasis-specific expression of a set of lncRNAs including CRLM1. CRLM1 inhibited apoptosis and promoted metastasis and invasion of colorectal cancer cells, and also promoted tumor growth in nude mice. CRLM1 weakly associated with chromatin regions of genes involved in cell adhesion and DNA damage, correlated with CRLM1-regulated gene expression bidirectionally. CRLM1 physically interacts with and promotes the nuclear localization of the metastasis protein hnRNPK. CRLM1 effectively promotes hnRNPK promoter occupancy, and co-regulate gene expression. These findings suggest a potential biomarker and druggable target for treatment of colorectal liver metastases.

overall_design: To further explore the biological functions of lncRNA-CRLM1 in colorectal cancer cells, we established a HCT116 cell line with stable CRLM1 overexpression (CRLM1-OE). Two negative control cell lines were prepared in parallel, including empty plasmid (Ctrl) and plasmid with CRLM1 antisense sequences (CRLM1-anti, see methods for detail information). Three biological replicates were prepared for each sample.

first: Zhe


title: Colorectal liver metastases-specific lncRNA CRLM1 inhibits apoptosis and promotes metastasis through transcriptional regulation cooperated with hnRNPK [CRLM1_CHIRP]

overall_design: To decipher how lncRNA-CRLM1 regulates gene expression in HCT116 cells, Chromatin Isolation by RNA Purification (ChIRP) method was performed to identify the potential CRLM1-chromatin interaction sites by sequencing the CRLM1 associated chromatin DNA fragments (ChIRP-seq). Anti-LacZ and Input samples were used as control. Two biological replicates were obtained for each sample.


title: APE1 controls DICER expression through functional regulation of miRNA33a: a novel hypothesis for NSCLC cancer progression

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

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

overall_design: Refer to individual Series


title: APE1 controls DICER1 expression through functional regulation of miRNA33a and miRNA130b: a novel hypothesis for NSCLC cancer progression [NanoString]

summary: Lung cancer is the leading cause of cancer death worldwide. The lack of specific and sensitive methods for early diagnosis as well as inadequate targeted therapies contribute to poor outcomes. A growing body of evidences suggests different roles of microRNAs including development and progression of lung cancer.  The overexpression of the DNA repair protein apurinic/apyrimidinic endonuclease 1 (APE1) is an important cause of poor chemotherapeutic and its expression is able to predict the progression-free and overall survival in patients receiving platinum-containing chemotherapy. Recently, we have demonstrated APE1 involvement in miRNA biogenesis related to cancer progression.   In this article, we report the identification of miRNAs that are modulated in lung cancer cells upon APE1 silencing. We defined a miRNA signature consisting of the 13 miRNAs, which strongly correlates with APE1 expression in lung cancer: miR-1246, miR-4488, miR-24, miR-183, miR-660, miR-130b, miR-543, miR-200c, miR-376c, miR-218, miR-146a, miR-92b and miR-33a. Gene ontology annotation and pathway analysis of the miRNA signature revealed its biological significance in cancer proliferation and survival. Among the miRNAs downregulated by APE1 is miRNA-33a-5p which targets Dicer, a major miRNA biogenesis gene whose expression is found to be downregulated in several tumours. We here validated Dicer as a direct functional target of miR-33a and profiled miR-33a, DICER and APE1 expression in clinical samples. Our findings suggest that APE1 may promote lung cancer progression through modulation of Dicer expression via miR-33a regulation. Our findings reveal new mechanistic insight into how APE1 functions in tumor biology.

overall_design: In the study presented here, miRNA expression profiling was performed with 100 ng of total RNAs from A549 silenced for APE1–protein expression. The experiment was performed in triplicates.

first: Giulia

last: Antoniali

first: Emiliano

last: Dalla

first: Giovanna

last: Mangiapane

first: Xiaolong

last: Zhao

first: Yi

last: Cheng

first: Veronica

last: De Sanctis

first: Dilara

last: Ayyildiz

first: Mengxia

last: Li

first: Gianluca

last: Tell


title: Colorectal liver metastases-specific lncRNA CRLM1 inhibits apoptosis and promotes metastasis through transcriptional regulation cooperated with hnRNPK [HNRNPK_CHIP]

overall_design: We performed chromatin immunoprecipitation and sequencing method (ChIP-seq) for hnRNPK in HCT116 cells with hnRNPK overexpression under CRLM1-OE and control (empty control and antisense control)conditions. Genomic DNA (Input) was used as negative control for each IP sample. Two biological replicates were prepared for each sample.

last: Wang


title: Transcriptome analysis by RNA sequencing after treatment with JIB-04 in hepatocellular carcinoma

city: Seoul

first: Jina

last: Lee

address: 50, Yonsei-ro, Seodaemun-gu

department: Department of systems biology

institute: Yonsei university

summary: Our RNA sequencing analysis revealed that the JIB-04 treatment altered the expression of genes that are involved in the cell cycle, p53 signaling pathway, and apoptosis, and are also related to several cancers including hepatocellular carcinoma. JIB-04 also altered the expression of genes involved in various signaling pathways such as the FoxO signaling pathway, the PI3K-Akt signaling pathway, which is crucial for the proliferation and maintenance of hepatocellular carcinoma cells.

overall_design: Examination of RNA sequencing profile in DMSO or 6µM of JIB-04 treated PLC/PRF/5 cells.

first: Ji

middle: S

last: Kim


title: Colorectal liver metastases-specific lncRNA CRLM1 inhibits apoptosis and promotes metastasis through transcriptional regulation cooperated with hnRNPK


title: Glutamate pathway dysfunction in MELAS syndrome is alleviated by ketogenic diet

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: The development of mitochondrial medicine is greatly impaired by the lack of knowledge and identification of efficient therapeutic routes targeting mitochondria. To better understand the pathophysiology of MELAS syndrome, neuronal cybrid cells, carrying different mutant loads of the m.3243A>G mutation, were investigated by a metabolomics and transcriptomics combined approach. Specific signatures, identifying MELAS biochemical biomarkers, disclosed the glutamate pathway as a culprit mechanism, establishing a strong correlation between glutamate concentrations and the m.3243A>G heteroplasmy levels. Transcriptomic analyses further revealed peculiar gene clusters, including glutamate, gamma-aminobutyric acid (GABA) and tricarboxylic acid (TCA) cycle pathways. These results were supported by post-mortem brain tissue analysis of a MELAS patient, confirming the dysregulation of the glutamate metabolic pathway. Ketogenic diet known to reduce glutamate toxicity, induced a significant reduction of glutamate level after 48h of ketone body treatment, improved mitochondrial functions alleviating the accumulation of several intermediate metabolites of the TCA cycle in MELAS cells. Thus, the integrated approach using a multi-OMICs strategy on MELAS cybrid cells, disclosed novel insights in the mitochondrial energy failure, identifying glutamate as a potential biomarker of the disease, while highlighting ketogenic diet, a nutrition based strategy, to treat MELAS patients

overall_design: gene expression profiling of neuronal cells for 8 samples in two groups, control and Mutant.

first: David

last: Goudenège


title: APE1 controls DICER expression through functional regulation of miRNA33a: a novel hypothesis for NSCLC cancer progression [RNA-Seq]

summary: The overexpression of the DNA repair protein apurinic/apyrimidinic endonuclease 1 (APE1) is an important cause of poor outcome and its expression is able to predict the progression-free and overall survival in patients receiving platinum-containing chemotherapy. Recently, we have demonstrated APE1 involvement in miRNA biogenesis related to cancer progression.

overall_design: In this work, through the use of NGS and Nanostring strategies, we report the identification of miRNAs that are modulated in lung cancer cells upon APE1 silencing. We defined a miRNA signature consisting of the 13 miRNAs, which strongly correlates with APE1 expression in lung cancer: miR-1246, miR-4488, miR-24, miR-183, miR-660, miR-130b, miR-543, miR-200c, miR-376c, miR-218, miR-146a, miR-92b and miR-33a. Gene ontology annotation and pathway analysis of the miRNA signature revealed its biological significance in cancer proliferation and survival. Among the miRNAs regulated by APE1, miRNA-33a-5p targets DICER, a major miRNA biogenesis gene whose expression is found to be downregulated in several tumours. We here validated DICER as a direct functional target of miR-33a and profiled miR-33a, DICER and APE1 expression in clinical samples.


title: Colorectal liver metastases-specific lncRNA CRLM1 inhibits apoptosis and promotes metastasis through transcriptional regulation cooperated with hnRNPK [HNRNPK_OE]

overall_design: We overexpressed hnRNPK in HCT116 cells with stable overexpression of lncRNA-CRLM1 and in those without (antisense control and empty control). Transcriptome sequencing (RNA-seq) was conducted to identify CRLM1 and hnRNPK regulated genes. Three biological replicates were prepared for each sample


title: Dimorphic H3K27 methylation guides germline or vegetative cell fate dichotomy in male gametophytes [RNA-seq]

first: Xiaorong

last: Huang

address: Bayi Road

institute: College of Life Science, Wuhan university

summary: During angiosperm male gametogenesis, microspores divide to produce a vegetative cell (VC) and a male germline (MG), each with a distinct cell fate. How the MG cell/VC fate is determined remains largely unknown. Here, we report that the VC-targeted H3K27me3 erasure resulted in VC fate transition towards a gamete destination. Multi-omics and cytologic analysis reveal that H3K27me3 is essential for VC fate commitment and contributes to suppress the MG cell fate initiation in VC, whereas MG cells require H3K27me3 reprograming for the gamete cell fate. This work suggests that the MG cell/VC fate is epigenetically regulated. The dimorphic H3K27 methylation acts as a core switch to determine their distinct cell fates and ensure the functional specification of both VC and MG for pollen fertility. This work also provides direct evidences for the proposal that VC maintains the default developmental program of microspore, whereas MG requires reprogramming.

overall_design: Examination of H3K27me3 modification (CUT&Tag), chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq). This dataset includes the RNA-seq data.

first: Meng-xiang

last: Sun


title: The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope

first: Joseph

last: Holoshitz

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Dimorphic H3K27 methylation guides germline or vegetative cell fate dichotomy in male gametophytes [ATAC-seq]

overall_design: Examination of H3K27me3 modification (CUT&Tag), chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq). This dataset includes the ATAC-seq data.


title: The dependency factor RRM2 at the nexus of a copy number driven regulatory network and a target for synthetic lethal interactions with replication stress checkpoint addiction in high-risk neuroblastoma [3AP or the combination 3AP-prexasertib]

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

summary: Neuroblastoma is a pediatric tumor originating from the sympathetic nervous system responsible for 10-15% of all childhood cancer deaths. Half of all neuroblastoma patients present with high-risk disease at diagnosis despite intensive multi-modal therapies of which nearly 50% relapse and die of their disease. In contrast to the overall paucity of mutations, high-risk neuroblastoma nearly invariably present with recurrent somatic segmental chromosome copy number variants. For several focal aberrations (e.g. MYCN and LIN28B amplification), the direct role in tumor formation has been established. However, for recurrent aberrations, such as chromosome 2p and 17q gains, the identification of genes contributing to tumor initiation or progression has been challenging due to the scarcity of small segmental gains or amplifications. In this study, we identified and functionally evaluated the ‘ribonucleotide reductase regulatory subunit 2’ (RRM2) as a top-ranked 2p putative co-driver and therapeutic target in high-risk neuroblastoma enforcing replicative stress resistance. RRM2 dependency was shown in vitro through knockdown in neuroblastoma cells, with transcriptome analysis revealing downregulation of pediatric tumor markers. Transgenic zebrafish lines expressing RRM2 in immature sympathoblasts were crossed with a dh-MYCN transgenic zebrafish line, with RRM2 overexpression dramatically increasing tumor penetrance from 20% to nearly 100%, accelerating neuroblastoma formation with tumors formed as early as 5 weeks of age in the double positive fish.  Through CasID, we aimed to identify RRM2 promotor bound proteins. and enriched amongst others HEXIM1 and the NurRD complex. Importantly, adaptive responses regulating RRM2 expression are also controlled by ATR/CHK1 and WEE1 cell cycle checkpoint kinases, as shown by pharmacological inhibition with small molecule inhibitors. We provide in vitro and in vivo data showing that RRM2 inhibition with triapine strongly sensitizes neuroblastoma cells to CHK1 inhibition and that combined treatment could robustly induce upregulated PD-L1 surface expression. Altogether, we propose RRM2 as a bona fide target to explore novel synergistic drug combinations through phase I clinical trials.

overall_design: Human neuroblastoma cell lines SHSY5Y, SK-N-BE(2)-C IMR32 and CLBGA were grown in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS), 100 IU/mL penicillin/streptomycin and 2mM L- Glutamine. All cell lines were grown at 37°C and 5% CO2. TThe adherent cell lines were seeded in a T-75 flask at density of 2x106 – 2.25x106 cells per flask, depending on the cell line. Cells were allowed to adhere for 48h, after which the medium was replaced by fresh medium and DMSO or 3AP or the combination 3AP-prexasertib was added. After 48h of treatment the cells were scraped, centrifuged, for 5 minutes at 1200 rpm, and the pellet was washed twice with ice-cold PBS.

first: Carolina

last: Nunes

first: Lisa

last: Depestel

first: Louis

last: Delhaye

first: Kaylee

last: Keller

first: Liselot

last: Mus

first: Emmy

last: Dolman

first: Volodimir

last: Olexiouk

first: Christoph

last: Bartenhagen

first: Fanny

last: De Vloed

first: Ellen

last: Sanders

first: Aline

last: Eggermont

first: Wouter

last: Van Loocke

first: Julie

last: Morscio

first: Siebe

last: Loontiens

first: Pauline

last: Depuydt

first: Bieke

last: Decaesteker

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: de Force

first: Bram

last: De Wilde

first: Pieter

last: Van Vlierberghe

first: Vanessa

last: Vermeirssen

first: Sven

last: Eyckerman

first: Christophe

last: Van Neste

first: Matthias

last: Fischer

first: Jan

last: Molenaar

first: Kaat

last: Durinck

first: Frank

last: Speleman


title: Secretory Leukocyte Peptidase Inhibitor (SLPI) is a Novel Predictor of Tubulointerstitial Injury and Renal Outcome in Patients with Diabetic Nephropathy

city: nanjing

first: shen

last: li

state: jiangsu

address: Xianlin Avenue №163, Qixia District

institute: Nanjing University

summary: Tubulointerstitial injury plays an important role in diabetic nephropathy (DN) progression; however, no reliable urinary molecule has been used to predict tubulointerstitial injury and renal outcome of DN clinically. In this study, based on tubulointerstitial transcriptome, we identified secretory leukocyte peptidase inhibitor (SLPI) as the molecule associated with renal fibrosis and prognosis of DN. In tubular cells, high glucose could upregulate SLPI, which bound with β-catenin and GSK-3β reciprocally, abolished the interaction between β-catenin and GSK-3β, diminished GSK-3β-regulated β-catenin phosphorylation and the subsequent ubiquitination and degradation, thus led to β-catenin signaling activation and renal fibrosis. Db/db mice injected with adenovirus carrying Slpi-3xflag-GFP (Ad-Slpi-GFP) developed β-catenin signaling activation in the proximal tubule, worse albuminuria and tubulointerstitial fibrosis. Conversely, Slpi knockout (KO) mice with STZ-induced DN developed less albuminuria, tubulointerstitial fibrosis and β-catenin signaling activation. Furthermore, clinical studies showed that urinary SLPI protein level (uSLPI/Cr) had significant correlation with intrarenal SLPI mRNA and interstitial fibrosis. In an independent prospective cohort enrolled 711 patients with biopsy proven DN, uSLPI/Cr level was significantly associated with eGFR slope and improved the prediction value of renal outcome. Together, our study identified SLPI as a novel critical regulator for the progression of tubulointerstitial injury, which may be used as an independent risk predictor of DN progression.

overall_design: We examined the effect of SLPI overexpression by gene expression profiling in HK-2 cells.

first: Shen

last: Li

first: Song

last: Jiang

first: Jinsong

last: Shi

first: Mingchao

last: Zhang

first: Yue

last: Lang

first: Chunxia

last: Zheng

first: Caihong

last: Zeng

first: Wenju

first: Daoyuan

last: Lv

first: Hui

last: Wang

first: Chunsun

last: Dai

first: Zhihong

last: Liu


title: TIC regulates hypocotyl growth in Arabidopsis by inhibiting PHYA signal

city: Beijing

first: Lei

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

institute: insitute of botany, chinese academy of sciences

summary: Functional analysis of TIC1 in Arabidopsis

overall_design: We analyzed the transcriptomic profile of Col-0 and tic-2 mutant using 10-day-old seedlings. Three biological replicates were performed with the tissues harvesting at predawn and postdusk respectively.

first: Yan

first: Chen

last: Su

first: Yingjun

last: Yu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Normal human keratinocytes and IL-13 receptor alpha 1 and 2 knockdown human keratinocytes Transcriptomes

city: Dublin

first: Jianghui

last: Meng

address: Glasnevin Avenue

country: Ireland

institute: Dublin City University

summary:
Purpose: The goals of this study are to investigate the influence of human keratinocyte IL-13 receptor knockdown on transcriptome profiling (RNA-seq)
Methods: A total of 18 samples were tested using the DNBSEQ platform, with an average yield of 1.13G data per sample. The average alignment ratio of the sample comparison genome was 95.24%, which was comparative The average alignment of the gene set was 83.86%; a total of 19022 genes were detected.
Conclusions: Our study represents the first detailed analysis of transcriptoms after human keratinocyte with IL-13 receptor alpha 1 and 2 knockdown transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that numerous gene transcription were affected after knockdown of each IL-13 receptor.

overall_design: Human keratinocyte mRNA profiles after knockdown of IL-13 receptor alpha 1 and 2

last: Xiao


title: Loss of the centrosomal protein Cenpj leads to dysfunction of the hypothalamus and obesity in mice

city: beijing

first: wenyu

last: ding

address: 15 Datun Road Chaoyang District

institute: University of Chinese Academy of Sciences

summary: Here, we identified distinct transcription factor expressed in specific cellular region. We precisely microdissected hypothalamus to isolate VZ, medial MZ and lateral MZ tissue at E12.5, which then were dissociated for RNA sequencing and three biological repeats were included. (GO) analysis of Nkx2-1-associated genes showed a significant enrichment of terms related to neuron differentiation, including neuron fate commitment, pattern specification process, stem cell development, neurotransmitter biosynthetic process, positive regulation of cell proliferation, neuropeptide hormone activity, and particularly type 4 melanocortin receptor binging.

overall_design: Identification of regional specific genes in mice developing hypothalamus

first: W

last: Ding

first: Q

last: Wu

first: X


title: Dimorphic H3K27 methylation guides germline or vegetative cell fate dichotomy in male gametophytes

first: Xiaorong

last: Huang


title: The dependency factor RRM2 at the nexus of a copy number driven regulatory network and a target for synthetic lethal interactions with replication stress checkpoint addiction in high-risk neuroblastoma [siRNA_RRM2]

first: Laurentijn

last: Tilleman

overall_design: IMR32 and CLBGA neuroblastoma cells were transfected with 100 nM of two independent RRM2 targeting siRNAs (s12361 and s12362, Ambion, Thermo Fischer Scientific) or a control siRNA  (#AM4635, Ambion, Thermo Fischer Scientific) using the Neon transfection Kit (Cat. No. MPK10096). RNA was collected 72h post-transfection. RNA extraction was performed according to  the manufacturer’s instructions of miRNeasy kit (Qiagen) including on-column DNase treatment and nanodrop (Thermo Scientific) was used to determine the concentration.

first: Carolina

last: Nunes

first: Lisa

last: Depestel

first: Louis

last: Delhaye

first: Kaylee

last: Keller

first: Liselot

last: Mus

first: Emmy

last: Dolman

first: Volodimir

last: Olexiouk

first: Christoph

last: Bartenhagen

first: Fanny

last: De Vloed

first: Ellen

last: Sanders

first: Aline

last: Eggermont

first: Wouter

last: Van Loocke

first: Julie

last: Morscio

first: Siebe

last: Loontiens

first: Pauline

last: Depuydt

first: Bieke

last: Decaesteker

first: Filip

last: Van Nieuwerburgh

first: Dieter

last: de Force

first: Bram

last: De Wilde

first: Pieter

last: Van Vlierberghe

first: Vanessa

last: Vermeirssen

first: Sven

last: Eyckerman

first: Christophe

last: Van Neste

first: Matthias

last: Fischer

first: Jan

last: Molenaar

first: Kaat

last: Durinck

first: Frank

last: Speleman


title: Dimorphic H3K27 methylation guides germline or vegetative cell fate dichotomy in male gametophytes [CUT&Tag]

first: Xiaorong

last: Huang

overall_design: Examination of H3K27me3 modification (CUT&Tag), chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq). This dataset includes the CUT&Tag data.

first: Meng-xiang

last: Sun


title: The dependency factor RRM2 at the nexus of a copy number driven regulatory network and a target for synthetic lethal interactions with replication stress checkpoint addiction in high-risk neuroblastoma [compound_3AP]

first: Laurentijn

last: Tilleman

overall_design: Human neuroblastoma cell lines SHSY5Y, SK-N-BE(2)-C IMR32 and CLBGA were grown in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS), 100 IU/mL penicillin/streptomycin and 2mM L- Glutamine. All cell lines were grown at 37°C and 5% CO2. TThe adherent cell lines were seeded in a T-75 flask at density of 2x106 – 2.25x106 cells per flask, depending on the cell line. Cells were allowed to adhere for 48h, after which the medium was replaced by fresh medium and 3AP (or DMSO) was added. After 48h of treatment the cells were scraped, centrifuged, for 5 minutes at 1200 rpm, and the pellet was washed twice with ice-cold PBS.

first: Carolina

last: Nunes

first: Lisa

last: Depestel

first: Louis

last: Delhaye

first: Kaylee

last: Keller

first: Liselot

last: Mus

first: Emmy

last: Dolman

first: Volodimir

last: Olexiouk

first: Christoph

last: Bartenhagen

first: Fanny

last: De Vloed

first: Ellen

last: Sanders

first: Aline

last: Eggermont

first: Wouter

last: Van Loocke

first: Julie

last: Morscio


city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

summary: To identify genes for radioresistance in lung cancer, unbiased CRISPR/Cas9 library knockout screening was performed by constructing stable cells in A549 containing a pooled genome-wide human sgRNA library containing 12, 3411 sgRNAs targeting 19,050 unique human genes. Two populations of cells were either nonirradiated or irradiated at 4 Gy, and they were cultured in vitro for 4 days. Then genomic DNA was acquired to readout the sgRNA representation by deep sequencing.

first: Chun

last: Cheng


title: Real-time quantitative PCR analysis of Nannochloropsis gaditana

status: Public on Aug 02 2022

city: Cuernavaca

first: Daniela

last: Morales Sanchez

state: Morelos

address: Av. Universidad 2000

department: Instituto de Biotecnologia

country: Mexico

institute: Universidad Nacional Autonoma de MExico

summary:
Nannochloropsis gaditana cells were cultivated under continuous light as a control condition versus 3 different flashing light conditions (FL5, FL50 and FL500). This study is complementary to Lima et al. (2020) where physiology and photosynthetic capacity were assesed. Here we analyzed the mRNA expression level of key genes related to photoshynthesis, lipid and starch synthesis, and nitrogen assimilation.
Total cell RNA was extracted from cultures of N. gaditana at a concentration of 1x106 cells/mL using the E.Z.N.A® total DNA/RNA isolation kit (Omega Bio-tek, Inc., USA). Reverse transcription reactions were performed using SuperScript™ IV VILO™ Master Mix with the enzyme ezDNase (Invitrogen™, ThermoFisher scientific, USA) according to the manufacturer’s protocol. The qPCR reactions were performed by mixing 5L of FastStart Universal SYBR Green Master mix (Rox) (Roche Molecular Systems, Inc., USA) with 1 L of primer mix (consisting of forward and the reverse primers) at a concentration of 300 nM and 4 L of the cDNA. The conditions of thermocycling were: 95 C for 600 s (preincubation), followed by 40 cycles of denaturation at 95 C for 10 s, annealing/extension at 60 C for 30 s. qPCR were performed in the LightCycler 96 Roche Life Science instrument.

overall_design: qPCR gene expression profiling. Procedure were conducted as described in the summary. Equal amount total RNA from each donor was pooled prior to gene.

last: Morales-Sánchez


title: Effect of ILB on Gene expression in Schwann like cells

city: Birmingham

first: Zsuzsanna

last: Nagy

address: Medical School

country: United Kingdom

institute: University of Birmingham

summary: The experiments were carried out to further understand the mechanism of action of ILB, a low molecular weight dextran sulphate, in glial cell. The experiments were carried out with ILB concentrations that are relevant to the therapeutic concentrations of the drug. The results indicate that ILB regulates the expression of genes to enhance cell survival and differentiation is a dose dependent manner. Upstream regulator analysis indicates that the gene expression changes are due to enhanced activity of growth factors and cytokines.

overall_design: Human Schwann-like cells (CRL-2884, ATCC) were cultured in high-glucose DMEM supplemented with 10% of FCS for 48 hours (day 0 timepoint). ILB was added to the cultures (final concentration: 0.01, 0.1, 1.0 and 10 µg/ml; n=3 for each concentration). Control cultures received only vehicle (0.9% NaCl in water added to culture medium 1:10,000; n=2). Cells were cultured for another 48 hours (day 2 timepoint).  Samples were [reserved in RNAlater. RNA was extracted using the Agilent RNA Isolation Kit. Expression analysis was performed using the SurePrint G3 Human Unrestricted GE 8x60K array (G4858A- 028004).


title: ATAC-seq for Pantr2 knockout cortical neurospheres

city: Baltimore

first: Jonathan

middle: Joseph

last: Augustin

state: MD

address: 733 N. Broadway Rm#332

institute: Johns Hopkins Medical Institute

summary: We used assay for transposase accessible chromatin with sequencing (ATAC-seq) to discover changes in chromatin accessibility in Pantr2 KO cortical neurospheres

overall_design: The dorsal telencephalon of E14.5 wildtype and Pantr2 knockout mice were dissected used to generated cortiacl neurospheres for ATAC-seq profiling

first: Loyal

last: Goff


title: Effect of ILB on Gene expression in SHSY5Y neuroblastoma cells

summary: The experiments were carried out to further understand the mechanism of action of ILB, a low molecular weight dextran sulphate, in neuronal cell. The experiments were carried out with ILB concentrations that are relevant to the therapeutic concentrations of the drug. The results indicate that ILB regulates the expression of genes to enhance cell survival and differentiation is a dose dependent manner. Upstream regulator analysis indicates that the gene expression changes are due to enhanced activity of growth factors and cytokines.

overall_design: Human SHSY5Y neuroblastoma cells (CRL-2266, ATCC) were cultured in DMEM:F12 medium supplemented with 10% FCS and 1% GlutaMAX™-I for 48 hours (day 0 timepoint). ILB was added to the cultures (final concentration: 0.01, 0.1, 1.0 and 10 µg/ml; n=3 for each concentration). Control cultures received only vehicle (0.9% NaCl in water added to culture medium 1:10,000; n=2). Cells were cultured for another 48 hours (day 2 timepoint).  Samples were preserved in RNAlater. RNA was extracted using the Agilent RNA Isolation Kit. Expression analysis was performed using the SurePrint G3 Human Unrestricted GE 8x60K array (G4858A- 028004).


title: CD4 cells re-educate tumor associated macrophages.

city: Bethesda

first: Ainhoa

last: Perez-Diez

address: 9000 Rockville Pike

institute: NIAID, NIH

summary: Tumor Associated Macrophages (TAMs) are known to release cytokines/chemokines that promote tumor survival and angiogenesis. Little is known, however, about their ability to present tumor antigens to CD4 T cells, nor whether such presentation might switch their tumor supporting function. Here we show that TAMs present tumor antigens to CD4 T cells and that upon antigen recognition, the T cells re-educate the TAMs to produce lower amounts of tumor nurturing proteins and greater amounts of anti-angiogenic proteins. The CD4-educated-TAMs display a gene signature characterized by upregulation of INFgamma esponsive genes that have anti-viral and anti-bacterial function. This phenotypic switch is INF-gamma dependent, and necessary for CD4-mediated tumor rejection. CD4-based immunotherapies could take advantage of this re-education process to improve cancer treatment.

overall_design: The experiment consisted of six untreated Tumor Associated Macrophages (TAMs) and six CD4-treated Tumor Associated Macrophages (TAMs) for a total of 12 samples. For each of the treated and untreated samples, two were technical replicates and four were biological replicates.


title: Tunicamycin-induced Endoplasmic Reticulum-Quality Control Pathway and Endoplasmic Reticulum-Associated Degradation Mechanism in the diatom Phaeodactylum tricornutum

city: shantou

first: jichen

last: chen

address: university road

institute: shantou university

summary: Tunicamycin inhibits the first step of protein N-glycosylation modification. However, the physiological, transcriptomic, and N-glycomic effects of tunicamycin on important marine diatom Phaeodactylum tricornutum are still unknown. In this study, comprehensive approaches were used to study the effects. The results showed that cell growth and photosynthesis were significantly inhibited in P. tricornutum under the tunicamycin stress. The soluble protein content was significantly decreased, while the soluble sugar and neutral lipid were dramatically increased to orchestrate the balance of carbon and nitrogen metabolism. 0.3 μg m-1 tunicamycin could not complete inhibited the N-glycosylation of protein, but it resulted in the differentially expression of ERQC and ERAD related genes. The upregulation of genes involved in ERQC and the activation of anti-oxidases were speculated to alleviate the tunicamycin stress. The differentially expression of genes related to ERAD was suggested to degrade the unfolded and/or incorrect N-glycoproteins induced by tunicamycin. The identification of mannose-type and complex-type N-glycan structures enriched the N-glycan database of diatom P. tricornutum and provided important information for studying the function of N-glycosylation modification on proteins. All in all, the proposed working models of ERQC and ERAD will provide a solid foundation for further in-depth study the related mechanism and the diatom expression system.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type and wild type under 0.3ug/ml tunicamycin

first: J

last: Chen

first: X

last: Liu

first: M

last: Assam

first: H

last: Du

first: Z

last: Luo

last: Fang


title: miRNA sequencing of Mesenchymal stem cells-derived exosomes and MRC-5 cell-derived exosomes

first: liu

last: peipei

address: No. 2, Cherry Blossom Garden East Street, Chaoyang District

department: Department of Pulmonary and Critical Care Medicine

institute: China-Japan FriendshipHospital

summary: To investigate the differential miRNA between Mesenchymal stem cells-derived exosomes and MRC-5 cell-derived exosomes.

overall_design: Mesenchymal stem cells (MSCs) were isolated from the umbilical cord and expanded in culture. MSCs and Medical Research Council cell strain 5 (MRC-5) cells were cultured in exosomes-free complete medium. We isolated exosomes from the cell culture supernatant. Then we compared the differential miRNA between Mesenchymal stem cells-derived exosomes and MRC-5 cell-derived exosomes by using miRNA sequencing.

first: Peipei

first: Shengnan

last: Yang

first: Xuecheng

last: Shao

first: Chen

last: Li

first: Zai

last: Wang

first: Huaping

last: Dai


title: CRMP2 derived from cancer associated fibroblasts facilitates progression of ovarian cancer via HIF-1α-glycolysis signaling pathway

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

summary: To investigate the external CRMP2 function of triggering which signaling pathway in A2780 cells. We treated A2780 cells with human recombinant CRMP2 (r-CRMP2) for RNA-seq to compare deferential genes between two different samples.

overall_design: RNA-seq

first: Yunfeng

last: Jin

first: Hua

last: Jiang


title: Transcriptional analysis of THP-1 cells stimulated by bacterial extracellular vesicles enriched by ultracentrifugation and an ε-poly- L-lysine-based method

first: Dian

last: Jiao

state: Beijing

address: Tsinghua University Beijing China

institute: Tsinghua University

summary: We propose an isolation strategy based on a broad-spectrum antimicrobial epsilon-poly-L–lysine (ε-PL) to precipitate bacterial extracellular vesicles (BEVs) at a relatively low centrifugal speed (10,000 × g). Compared to the standard ultracentrifugation (UC) strategy, our method can enrich BEVs from large volumes of media inexpensively and rapidly. The precipitated BEVs can be recovered by adjusting pH and ionic strength of the media, followed by ultrafiltration step to remove ε-PL and achieve buffer exchange. To address whether BEVs isolated by these two methods lead to different host responses, we isolated Escherichia coli (E. coli) and Staphylococcus aureus BEVs from bacterial culture media using ultracentrifugation and our ε-poly- L-lysine-based method, respectively. Then we stimulated THP-1 cells with the isolated BEVs and the global transcript profiles were evaluated by the RNA-seq technique. Compared with the unstimulated THP-1 cells, BEV isolated by both methods could trigger a striking alteration in the gene expression pattern. Among the functions significantly enriched by these DEGs were immune response and leucocyte chemotaxis. The results indicated that the BEVs isolated by the ε-PL-based method also retained the in vitro biological activity as the commonly used ultracentrifugation.

overall_design: Totally 15 samples were analyzed, including unstimulated THP-1 cells as controls, THP-1 cells treated with E. coli BEVs isolated by ultracentrifugation/ε-PL-based method and S. sureus BEVs isolated by ultracentrifugation/ε-PL-based method.

first: Wanli

last: Xing

first: Shujin

last: Wei


title: Transcriptome analysis of Intestinal epithelial cells after Heligmosomoides polygyrus bakeri (Hpb) infection

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: RNAseq on intestinal epithelial cells 24hrs  after Hpb inoculation in WT- villinCre and VillinCre-A2BARfl/fl mice

overall_design: WT- villinCre and VillinCre-A2BARfl/fl mice were infected with Hpb for 24hrs, small intestinal duodenum IECs were sorted on DAPI-, CD45-, EpCAM+ cells and subjected to RNAseq. Naïve mice from  both strains were used as controls

first: D

middle: W

last: El-Naccache


title: Gene expression profiling in 3 different melanoma cells under adhesion and suspension

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

department: School of Medicine

country: Taiwan

institute: FuJen Catholic University

summary: Analysis of gene expression and compare the significant changed genes with associated phenotypes

overall_design: Total RNA extracted from adherent or suspended melanoma cells

first: ShihSheng

first: ShaoChen


title: Effects of ARHGEF2 knockdown on gene expression in Hepatocellular Carcinoma HepG2 cells

city: Hefei

first: Yue

last: Zhu

address: The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China

summary: To investigate the role of ARHGEF2 in HCC cells and to search for downstream targets, we established the ARHGEF2 knockdown cell line, in which ARHGEF2 was silenced by lentivirus technology. Then, we used two groups of cells (n=3) for gene expression profile analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells  (shNC, shARHGEF2).

first: Weiwei

last: Liu

first: Zishu

first: Guoping

last: Sun


title: Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features in Breast Cancer

city: Chuo-ku

first: Jun

last: Nakayama

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center

summary: Ductal carcinoma in situ (DCIS) is a nonobligate precursor of invasive breast cancer. Its biological features, particularly its intratumoral heterogeneity, remain obscure. Moreover, mechanism of lymph node metastasis is unclear. To address this deficiency, we performed single-cell transcriptome profiling of DCIS, invasive ductal carcinoma (IDC) and lymph node metastasis. Single-cell transcriptome analysis revealed that breast cancer exhibits intratumoral heterogeneity at the transcriptional level, defining specific functions, and that DCIS has similar heterogeneity to IDC.

overall_design: Single-cell transcriptome profiling from 13 human breast cancer tissues, 6 lymph node metastasis and 1 normal breast tissue. 13 breast cancer tissues include 7 ductal carcinoma in situ (DCIS) and 6 invasive ductal carcinoma (IDC). All cases of IDC are accompanied by lymph node metastasis, and lymph node metastasis was collected from each case of IDC.

first: Momoko

last: Tokura

first: Marta

last: Prieto-Vila

first: Yusuke

last: Yamamoto


title: Epigenome analysis of gliomas arising in the setting of neurofibromatosis type 1

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of 32 NF1-associated gliomas. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 32 gliomas.

overall_design: Bisulfite converted genomic DNA extracted from the 32 glioma tumor samples was hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips


title: Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection [RNA-Seq]

city: New York

first: Julia

last: Brown

state: New York

address: 413 E 69th Street, 1252A

institute: Weill Cornell Medicine

summary: The gut microbiome is intricately coupled with immune regulation and metabolism, but its role in Coronavirus Disease 2019 (COVID-19) is not fully understood. Severe and fatal COVID-19 is characterized by poor anti-viral immunity and hypercoagulation, particularly in males. Here we define multiple pathways by which the gut microbiome protects mammalian hosts from SARS-CoV-2 intranasal infection, both locally and systemically, via production of short-chain fatty acids (SCFAs). SCFAs reduced viral burdens in the airways and intestines by downregulating the SARS-CoV-2 entry receptor, angiotensin-converting enzyme 2 (ACE2), and enhancing adaptive immunity in male animals. In order to identify other mechanisms by which SCFAs influence the outcome of SARS-CoV-2 infection, we performed RNA-seq on lungs from male GF mice given control or SCFA water for two weeks. We identified a novel role for the gut microbiome in regulating systemic coagulation response by limiting megakaryocyte proliferation and platelet turnover via the Sh2b3-Mpl axis. Taken together, our findings have unraveled novel functions of SCFAs and fiber-fermenting gut bacteria that might be leveraged as pan-coronavirus therapeutics to dampen viral entry and hypercoagulation and promote adaptive anti-viral immunity.

overall_design: 8-week-old male germ-free C57BL/6 mice were given normal drinking water (n=3) or drinking water containing SCFAs (acetate, propionate, and butyrate; n=3) for two weeks, and bulk RNAseq was performed on the lung tissue.

first: Katherine

middle: Z

last: Sanidad

first: Serena

last: Lucotti

first: Aparna

last: Ananthanarayanan

first: Srijani

last: Basu

first: Justin

last: Chen

first: Mengrou

last: Shan

first: Mohammed

last: Amir

first: Fabian

last: Schmidt

first: Yiska

last: Weisblum

first: Michele

last: Cioffi

first: Tingting

last: Li

first: Florencia

last: Rowdo

first: M

middle: L

last: Martin

first: Chun-Jun

last: Guo

first: Costas

last: Lyssiotis

first: Brian

last: Layden

first: Andrew

last: Dannenberg

first: Paul

middle: D

last: Bieniasz

first: Benhur

first: Naohiro

last: Inohara

first: Irina

last: Matei

first: Melody

middle: Y

last: Zeng


title: TP53-Status-Dependent Oncogenic EZH2 Activity in Pancreatic Cancer

city: Goettingen

first: Lennart

middle: Viktor

last: Versemann

address: Robert-Koch-Strasse 40

department: Department of Gastroenterology, gastrointestinal Oncology and Endocrinology

institute: University Medical Center Goettingen

summary: Transcriptomic analysis of p53-wildtype and -mutant murine PDAC cells in the presence and absence of EZH2 revealed p53-status determined EZH2-dependent target gene regulation. We found that among others p53-pathway and apoptosis-related gene sets are enriched in p53wt PDAC cells upon EZH2 depletion but not in cells bearing a mutation in the Trp53 gene.

overall_design: mRNA expression profiles of murine p53wt (KrasG12D (KC), caNFATc1;KrasG12D (NKC)) and p53mut (KrasG12D;Trp53R173H/+ (KPC), KrasG12D;caNFATc1;Trp53R173H/+ (KNPC)) PDAC cells upon siRNA- (KC, KPC, KNPC) or shRNA- (NKC) mediated knockdown of EZH2 (48h)

first: Shilpa

last: Patil

first: Zhe

last: Zhang

first: Elisabeth

last: Hessmann


title: Genome-wide analysis of DNA replication stress in the Human Neuroblastoma Cell Line IMR32 by TrAEL-seq

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

institute: Ghent University

summary: TrAEL-seq was used to assess the impact of Triapine (3AP), a RRM2 inhibitor, on replication fork accumulation and changes to the replication profile of IMR32 cells.

overall_design: TrAEL-seq was performed on IMR32 cells cultured (as described below) in duplicate, in either untreated media or in media containing 0.1% DMSO with or without 3AP treatment (689.5 nM).

first: Ellen

last: Sanders

first: Carolina

last: Nunes

first: Alex

middle: J

last: Whale

first: Neesha

last: Kara

first: Simon

middle: R

last: Andrews

first: Jonathan

last: Houseley

first: Kaat

last: Durinck

first: Frank

last: Speleman


title: Effect of Parathyroid Hormone Analog Treatment on Gene Expression

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: The effect of parathyroid hormone (PTH) analog treatment was tested on osteoblasts prepared from calvaria of C57BL/6J mice 7-10 days old. Osteoblasts were treated for 4 hr with either human parathyroid hormone (1-34) (hPTH(1-34), bovine (D-Trp12,Tyr34)-PTH(7-34) amide (bPTH(7-34)), bPTH(3-34), hPTH(1-31), or hPTH(7-34). Gene expression effects were evaluated by DNA microarray.

overall_design: Mouse osteoblasts were prepared independently for each biological replicate. Three biological replicates were used for each treatment. Osteoblasts were treated for 4 hr with either vehicle or different PTH analogs. Total RNAs were collected and 100 ng analyzed for gene expression using Affymetrix Mouse Gene 2.0 ST GeneChips.

first: Louis

last: Luttrell


title: Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis III

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

summary: The treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor, we found that expression of the hominid-restricted retrogene POU5F1B through aberrant activation of a primate-specific endogenous retroviral promoter is a strong negative prognostic CRC biomarker. Correlating this observation, we could demonstrate that POU5F1B fosters the proliferation and metastatic potential of CRC cells. We further determined that POU5F1B, in spite of its phylogenetic relationship with the POU5F1/OCT4 transcription factor, is a membrane-enriched protein that associates with protein kinases and known targets or interactors as well as with cytoskeleton-related molecules, and induces intracellular signaling events and the release of trans-acting factors involved in cell growth and cell adhesion. As POU5F1B is an apparently non-essential gene only lowly expressed in normal tissues, and as POU5F1B-containing TcGTs are detected in other tumors besides CRC, our data provide interesting leads for the development of cancer therapies.

overall_design: RNA-sequencing analysis of LS1034 cells transduced with sh-scramble, POU5F1B-targeting shRNA3, or POU5F1B-targeting shRNA5.

first: Laia

last: Simo-Riudalbas


title: Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis II

overall_design: RNA-sequencing analysis of POU5F1B- and GFP-overexpressing HT29 cells.


title: Transcriptional profiles predict treatment outcome in patients with tuberculosis and diabetes at diagnosis and at two weeks after initiation of anti-tuberculosis treatment

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

institute: London School of Hygiene & Tropical Medicine

summary: Globally, the anti-tuberculosis (TB) treatment success rate is approximately 85%, with treatment failure, relapse and death occurring in a significant proportion of pulmonary TB patients. Treatment success rates are lower among people with diabetes mellitus (DM). Predicting treatment failure early after diagnosis would allow early treatment adaptation and may improve global TB control.  Methods  Samples were collected in a longitudinal cohort study of adult TB patients with or without concomitant DM from South Africa and Indonesia to characterize whole blood transcriptional profiles before and during anti-TB treatment, using unbiased RNA-Seq and targeted gene dcRT-MLPA.  Findings  We report differences in whole blood transcriptome profiles between patients with a good versus poor anti-TB treatment outcome, which were observed before initiation of treatment and throughout treatment. An eight-gene and 22-gene blood transcriptional signatures distinguished patients with a good treatment outcome from patients with a poor treatment outcome at diagnosis (AUC=0·815) or two weeks (AUC=0·834) after initiation of anti-TB treatment, respectively. Importantly, high accuracy was obtained by cross-validating this signature in an external cohort (AUC=0·749).  Interpretation  These findings suggest that transcriptional profiles can be used as a prognostic biomarker for treatment failure and success, even in patients with concomitant DM.

overall_design: Whole blood was collected from patients with TB-only, TB-DM throughout anti tuberculosis treatment at four time points: Diagnosis, Week 2, Month 2 and Month 6 from two field sites; South Africa and Indonesia. Treatment outcome data were collected at Month 12

first: Clare

last: Eckold

first: Jacqueline

first: Hazel

last: Dockrell

first: Cassandra

last: van Doorn

first: Tom

last: Ottenhoff

first: Eleonora

last: Vianello


title: Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection [16S rRNA]

first: Julia

last: Brown

summary: The gut microbiome is intricately coupled with immune regulation and metabolism, but its role in Coronavirus Disease 2019 (COVID-19) is not fully understood. Severe and fatal COVID-19 is characterized by poor anti-viral immunity and hypercoagulation, particularly in males. Via 16S sequencing of antibiotic-treated mice, we found that Clostridia species protect mammalian hosts from SARS-CoV-2 intranasal infection, both locally and systemically, via production of short-chain fatty acids (SCFAs). SCFAs reduced viral burdens in the airways and intestines by downregulating the SARS-CoV-2 entry receptor, angiotensin-converting enzyme 2 (ACE2), and enhancing adaptive immunity in male animals. In order to identify other mechanisms by which SCFAs influence the outcome of SARS-CoV-2 infection, we performed RNA-seq on lungs from male GF mice given control or SCFA water for two weeks. We identified a novel role for the gut microbiome in regulating systemic coagulation response by limiting megakaryocyte proliferation and platelet turnover via the Sh2b3-Mpl axis. Taken together, our findings have unraveled novel functions of SCFAs and fiber-fermenting gut bacteria that might be leveraged as pan-coronavirus therapeutics to dampen viral entry and hypercoagulation and promote adaptive anti-viral immunity.

overall_design: 8-week-old male C57BL/6 mice were given normal drinking water (n=2) or drinking water containing antibiotics (gentamicin or vancomycin; n=5 each) for two weeks.  DNA was extracted from fecal pellets and the V4 region of the 16S rRNA gene was amplified using universal primers and sequenced on an Illumina MiSeq sequencer.

first: Katherine

last: Sanidad

first: Serena

last: Lucotti

first: Aparna

last: Ananthanarayanan

first: Srijani

last: Basu

first: Justin

last: Chen

first: Mengrou

last: Shan

first: Mohammed

last: Amir

first: Fabian

last: Schmidt

first: Yiska

last: Weisblum

first: Michele

last: Cioffi

first: Tingting

last: Li

first: Florencia

last: Rowdo

first: M

last: Martin

first: Chun-Jun

last: Guo

first: Costas

last: Lyssiotis

first: Brian

last: Layden

first: Andrew

last: Dannenberg

first: Paul

last: Bieniasz

first: Benhur

last: Lee

first: Naohiro

last: Inohara

first: Irina

last: Matei

first: Melody

last: Zeng


title: Tumor-derived Lysophosphatidic Acid Blunts Protective Type-I Interferon Responses in Ovarian Cancer

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Lysophosphatidic acid (LPA) is a bioactive lipid enriched in highly immunosuppressive neoplasms like ovarian cancer (OvCa). While LPA is known to enhance the tumorigenic capacity of malignant cells, the immunomodulatory role of this phospholipid in cancer remains largely unexplored. Here, we report that LPA operates as a negative regulator of type-I interferon (IFN) responses in OvCa. Ablation of the LPAgenerating enzyme autotaxin in OvCa cells reprogrammed the tumor immune microenvironment, extended host survival, and improved the effects of therapies that elicit protective responses driven by type-I IFN. Mechanistically, LPA sensing by dendritic cells triggered PGE2 synthesis that suppressed type-I IFN signaling via autocrine EP4 engagement. Moreover, we identified an LPA-controlled, immune-derived gene signature associated with weak responses to combined PARP inhibition and PD-1 blockade in OvCa patients. Controlling LPA production or sensing in tumors may therefore be useful to improve cancer immunotherapies that rely on robust induction of type-I IFN.

overall_design: RNA-seq experiment in bone marrow derived dendritic cells under control and LPA treated conditions

first: Chang-Suk

last: Chae

first: Juan

last: Cubillos-Ruiz