title: MHC class II inhibits the generation of IL-17A+ Vγ6 γδ T cells in the thymus at perinatal stage

city: Fukuoka

first: shinya

last: Hatano

address: 3-1-1, Maidashi, Higashi-ku,

institute: Kyushu University

summary: TCR γ chain loci of mice have seven variable (Vγ) gene segments (Vγ1, Vγ2, Vγ3, Vγ4, Vγ5, Vγ6, and Vγ7) using the Heilig and Tonegawa nomenclature. Vγ6+ γδ T cells, which develop in the thymus at the perinatal stage, are distributed within the mucosal tissues in the periphery. Vγ6+ γδ T cells are exclusive interleukin (IL)-17 producers among γδ T cells, and Vγ6+ IL-17A+ γδ T (γδT17) cells play important roles in protection against microbial infection and in the pathogenesis of inflammatory diseases, such as colitis and autoimmune diseases. We have previously reported that γδT17 cells develop from the CD4–CD8– (DN)2b stage in the thymus at the prenatal stage in a Bcl11b-dependent manner. However, details of the development of Vγ6+ γδT17 cells remain obscure. To analyze Vγ6+ γδ T cells in detail, we recently developed a monoclonal antibody (mAb; termed 1C10-1F7) specific to mouse Vg6 chain. Use of this mAb revealed that Vγ6+ γδ T cells in 0-day-old thymus were co-localized with medullary thymic epithelial cells (mTECs), which regulate T cell tolerance by self-antigen presentation using major histocompatibility complex (MHC) class II. Here, we report that MHC class II in the thymus inhibits the generation of Vγ6+ γδT17 cells.

overall_design: To assess differences in gene expression by Vγ6+ γδ T cells in the absence of MHC class II, we performed a microarray analysis and compared the transcriptome profiles of Vγ6+ γδT cells in the thymus of 0-day-old WT and MHC class II KO mice.

first: Shinya

first: Keichiro

last: Mine

first: Naoto

last: Noguchi

first: Mitsuru

last: Matsumoto

first: Yoshihiro

last: Baba

first: Yasunobu

last: Yoshikai


title: Ligand-independent integrin beta1 signaling supports lung adenocarcinoma development

status: Public on Aug 01 2022

city: Nashville

first: Scott

middle: Mattox

last: Haake

state: TN

address: 2220 Pierce Ave, PRB 606

department: Medicine, Division of Hematology/Oncology

country: USA

institute: Vanderbilt University Medical Center

type: Expression profiling by high throughput sequencing

summary: Integrins, the principal extracellular matrix (ECM) receptors of the cell, promote cell adhesion, migration, and proliferation, which are key events for cancer growth and metastasis. To date, most integrin-targeted cancer therapeutics have disrupted integrin-ECM interactions, which are viewed as critical for integrin functions. However, such agents have failed to improve cancer patient outcomes. We show that integrin b1, a highly expressed subunit in lung epithelium, is required for lung adenocarcinoma development in a carcinogen-induced mouse model. Likewise, human lung adenocarcinoma cell lines with integrin b1 deletion failed to form colonies in soft agar and tumors in mice. Mechanistically, we demonstrate that these effects do not require integrin b1-mediated adhesion to ECM but are dependent on integrin b1 cytoplasmic tail-mediated activation of focal adhesion kinase (FAK). Together, these studies support a critical role for integrin b1 in lung tumorigenesis that is mediated through constitutive, ECM-binding independent signaling involving the cytoplasmic tail.

overall_design: Examination of lung tumors and normal adjacent tissue from mice with and without integrin beta1 expression in type 2 alveolar epithelial cells.

middle: M


title: RNA seq analysis of Gpr56/Adgrg1 expressing 4T1 and TS/A cells cultured with type III collagen

city: Kanazawa

first: Soichiro

last: Sasaki

address: Kakuma-machi

country: Japan

institute: Cancer Research Institute, Kanazawa University

summary: We founed enhanced Gpr56/Adgrg1 mRNA expression in bone tropic mouse breast cancer cell lines, 4T1.3, grown in a bone cavity, compared with in vitro culture condition. Thus, we examined about the function of Gpr56/Adgrg1 in tumor growth of vitro culture condition with its ligand, type III collagen.

overall_design: Mouse breast cancer cell lines 4T1 and TS/A cells which were transduced Gpr56/Adgrg1 gene were cultured with type III collagen. After 72H, total RNAs was extracted. The resultant total RNAs were subjected to RNAseq.

first: So-ichiro

first: Sadahiro

last: Iwabuchi

first: Shin-ichi

last: Hashimoto

first: Naofumi

last: Mukaida


title: BAF1 and Brassinosteroid related mutant in Arabidopsis

city: Ames

first: Yanhai

last: Yin

state: Iowa

address: 1111 WOI Street

department: GDCB

institute: Iowa State University

summary: Brassinosteroids (BRs) regulate plant growth, development and stress responses by activating the core transcription factor BRI1-EMS-SUPPRESSOR1 (BES1). The E3 Ubiquitin ligase(s) that modify BES1 for autophagy-mediated degradation remain to be fully defined. In this study, we identified an F-box family E3 ubiquitin ligase termed BES1-ASSOCIATED F-BOX1 (BAF1). BAF1 interacts with and ubiquitinates BES1. Accordingly, BES1 stability and protein levels were reduced in BAF1 overexpression plants but increased in a baf1 loss-of-function mutant and in BAF1-DF (BAF1 with F-box deleted, dominant-negative form) overexpression lines. Selective autophagy of BES1, but not bulk autophagy, was significantly compromised in the baf1 mutant under sucrose starvation. BES1 degradation mediated by BAF1 could be blocked through autophagy but not proteasome inhibitors, suggesting that BAF1 mediates BES1 degradation largely through autophagy. baf1 and BAF1-DF overexpression plants had increased BR-regulated growth but were sensitive to long-term sucrose starvation, while BAF1 overexpression plants had decreased BR-regulated growth but were highly tolerant of sucrose starvation. Our results not only established BAF1 as a novel E3 ubiquitin ligase that targets BES1 for degradation through selective autophagy pathway, but also revealed a mechanism for plants to reduce growth during sucrose starvation by targeting this central growth regulator.

overall_design: 3 or 4 biological replicates samples of 250nM brassicanazole treated or untreated wild-type, bes1-D and baf1 seedlings were prepared for transcriptome profiling. Wild-type plants are control plants, and untreated plants are the reference condition.

first: Ping

last: Wang

first: Natalie

last: Clark

first: Hao

last: Jiang

first: Trevor

last: Nolan


title: Differential gene expression in mice with inducible loss of Bmal1 and HNF4α in the liver

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary:
Hepatocyte Nuclear Factor 4 alpha (HNF4α), a master regulator of hepatocyte differentiation, and circadian regulator Aryl Hydrocarbon-Like Receptor-Like 1 (ARNTL, or BMAL1) though robustly co-expressed in healthy liver, are incompatible within the context of HCC. Differential expression of Bmal1 and Hnf4α may control susceptibility to liver disease and ultimately, hepatocellular carcinoma. We compared gene expression profiles under conditions of  inducible loss of hepatic Hnf4α and inducible loss of Hnf4a and Bmal1 in this RNA-seq experiment.
Hepatic Hnf4a (H-KO) or Hnf4a and Bmal1 (BH-KO)  were inducibly knocked out after 5 days tamoxifen treatment in eight week-old mice (H-KO) or (BH-KO) followed by vivarium chow or high fat feeding (BH-HF-KO). Littermate control mice (H-WT, BH-WT and BH-HF-WT  ) were also treated with tamoxifen at eight weeks of age, but since they lacked the Cre transgene, Hnf4a and Bmal1 expression remained intact. Livers were harvested at 10 weeks of age (BH-WT/KO, H-WT/KO) or 45 weeks ( BH-HF-WT/KO) of age after high fat diet feeding, and liver tissue was flash frozen in liquid nitrogen.

overall_design: Liver RNA-seq samples were prepared from liver harvested at the ZT8 time point (3:00 PM). Three biological replicates were used for each of the six conditions, resulting in 18 total samples.

first: Baharan

last: Fekry

first: Kristin

last: Eckel-Mahan


title: Genome methylation defines EZH2 inhibitor resistance in neuroblastoma [II]

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: EZH2 is a H3K27 methylase and a target of cancer epigenetic treatments. We recently reported the oncogenic roles and NTRK1 (TRKA) epigenetic regulation by EZH2 in the MYCN-amplified aggressive neuroblastomas (NB) (Li et al., ONCOGENE, 2018). Here, we investigated the effects and function of small molecule EZH2 inhibitor (EZH2i) on aggressive NB model cell lines. We examined the antitumor effects of EZH2i using WST assay and colony formation assay. By EZH2i treatments, suppression of proliferation was observed in SK-N-SH and SK-N-BE cells (sensitive cells) dose-dependently, whereas it was not observed in IMR32 and NGP cells (resistant cells). FACS analysis showed apoptosis and G0/G1 cell cycle arrest in sensitive cells. Transcriptome analysis and GSEA indicated significant changes were observed in the gene set related to cell cycle arrest and differentiation in the sensitive cells. We selected genes induced at mRNA level by EZH2i only in the sensitive cells and confirmed tumor suppressor function in NB cells. Almost of the EZH2i-induced gene promoters were marked by H3K27me3 in MYCN-amplified NB cell lines. Interestingly, a part of the EZH2i-induced gene promoters have CpG islands and methylated in NB tumor samples registrated in databases. Further, combination of EPZ6438 and 5-aza-deoxycitide, resulted in effective suppression of proliferation in the EPZ6438-resistant 3 NB cell lines. Transcriptome/methylome analysis of the EPZ6438 and 5-aza-deoxycitide-treated NB cells revealed the combinational epigenetic regulation of the tumor suppressors and oncogene expression. Finally, methylome analysis of the promoter regions, e.g. VSTM2L, GPNMB, and TIMP3 CpG islands can be biomarkers of EPZ6438-registancy in unfavorable NB patients. These responsible CpG island methylation as biomarkers for the application of EZH2i/DNMTi combination therapy.

overall_design: RNA was extracted 4 days after drug treatment, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

first: Yuki

last: Endo

first: Ryuichi

middle: P

last: Sugino

first: Ryu

last: Okada

first: Yoshitaka

last: Shinno

first: Masayuki

last: Haruta

first: Shunpei

last: Satoh

first: Kyosuke

last: Mukae

first: Jesmin

last: Akter

first: Miki

last: Ohira

first: Takehiko

last: Kamijo


title: Genome methylation defines EZH2 inhibitor resistance in neuroblastoma [I]

overall_design: RNA was extracted 3 (SK-N-BE, SK-N-SH, NGP) or 4 (IMR32) days after EPZ-6438 1 µM treatment, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.


title: Genome methylation defines EZH2 inhibitor resistance in neuroblastoma

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

overall_design: Refer to individual Series


title: Platinum chemotherapy induces diverse evolutionary trajectories in high grade serous ovarian cancer

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Cisplatin- and carboplatin-resistant high-grade serous ovarian cancer (HGSC) cells were generated and new lines were created from single cell clones. All cells were derived from a common ancestral line, Ovcar4. RNA sequencing was performed to examine transcriptional changes related to acquisition of platinum resistance.

overall_design: RNA sequencing on HGSC cell lines OVCAR4, Ov4Cis and Ov4Carbo  as well as two cell lines derived from single cell Ov4Carbo clones (Ov4Carbo4 and Ov4Carbo7). The cells were cultured in vitro and three biological replicates were performed per cell line.

first: Joseph

last: Hoare

first: Helen

last: Hockings

first: Ashley

last: Browne

first: Jayeta

last: Saxena

first: Francesco

last: Nicolini

first: Michelle

last: Lockley


title: Illumina sequencing reveals conserved and novel microRNAs involved in dendrobine biosynthesis in Dendrobium nobile

city: Nanjing

first: Chen

last: Jishuang

state: Jiangsu

address: NO.30 Puzhu Road(S)

department: College of Biotechnology and Pharmaceutical Engineering

country: China

institute: Nanjing Tech University

type: Non-coding RNA profiling by high throughput sequencing

summary: Dendrobium plants are perennial herbs in the family Orchidaceae (Dendrobium Sw.). Due to protocorm can also produce plant-specific useful metabolites, protocorm is becoming a good substitute. MicroRNAs play essential roles in plant growth, development, and the response to environmental stresses, and they are widely used for prediction of molecular functions for biosynthesizing active comportments in medicinal plants. To obtain insight into the function of miRNAs in Dendrobium plants. Illumina sequencing of D. nobile protocorm, D. officinale protocorm and D. nobile leaf were conducted. A total of 439, 412 and 432 miRNAs were identified in three samples, and their expression levels were significantly different. Specially, 2, 12 and 4 specific miRNAs were identified. Through integrated GO and KEGG function annotation, miRNAs mainly involved in metabolic pathways, plant hormone signal transduction, biological regulation and protein binding. AACT, MK, DXR and HDS as important enzymes in synthesizing basic precursor isoprene pyrophosphate (IPP). were predicted controlled by 6 different miRNAs in terpenoid backbone biosynthesis pathway. 26 miRNAs participated in Auxin, Cytoklinine, Abscisic acid, Jasmonic acid and Salicylic acid signal transduction pathway. Our results could provide valuable information about miRNAs involved in terpenoid biosynthesis and plant hormone signal transduction pathway in D. nobile and candidate genes for increasing the yield of dendrobine.

sample_organism:
Dendrobium nobile
Dendrobium officinale

platform_organism:
Dendrobium nobile
Dendrobium officinale

overall_design: Illumina sequencing of D. nobile protocorm, D. officinale protocorm and D. nobile leaf were conducted to obtain insight into the function of miRNAs in Dendrobium plants.

first: Xu

last: Qian

first: Jishuang

last: Chen


title: Fine-Tuning of PGC1α Expression Regulates Cardiac Function and Longevity (RNA-seq: telomerase-deficient vs PGC1aOE)

city: Hangzhou

first: Xudong

last: Zhu

address: #2318 Yuhangtang Road

institute: Hangzhou Normal University

summary: PGC1alpha plays an important role in energy metabolism and mitochondrial function in the heart, multiple attempts have failed to upregulate PGC1alpha expression as a therapy, with the underlying mechanism to be answered. We used RNA sequencing to detail the global programme of gene expression in the hearts of third generation of telomerase-deficient mice with or without cardiomyocyte-restricted PGC1alpha overexpression.

overall_design: Heart mRNA profiles of 12-month old telomerase-deficient (G3) and PGC1alpha overexpressed G3 mice were generated by deep sequencing, using Illumina HiSeq.

first: Zhenyu

last: Ju


title: Fine-Tuning of PGC1α Expression Regulates Cardiac Function and Longevity (RNA-seq: WT vs PKI)

summary: PGC1alpha plays an important role in energy metabolism and mitochondrial function in the heart, multiple attempts have failed to upregulate PGC1alpha expression as a therapy, with the underlying mechanism to be answered. We used RNA sequencing to detail the global programme of gene expression in the hearts of wild-type mice with or without cardiomyocyte-restricted PGC1alpha overexpression.

overall_design: Heart mRNA profiles of 12-month old wild-type (WT) and PGC1alpha overexpressed (PKI) mice were generated by deep sequencing, using Illumina HiSeq.


title: Fine-Tuning of PGC1α Expression Regulates Cardiac Function and Longevity


title: Transcriptomic Profiling of Human Corneal Epithelial Cells Exposed to Airborne Fine Particulate Matter (PM2.5)

first: Danni

last: Lyu

address: 88 Jiefang Rd.

department: Eye Center

institute: 2nd Affiliated Hospital of Zhejiang University School of Medicine

summary: Objectives: To explore the molecular mechanisms of PM2.5-induced dysfunction in human corneal epithelial cells (HCECs). Methods: RNA-Seq was performed to identify the differentially expressed genes (DEGs) in PM2.5-exposed HCECs compared to unexposed condition, which was followed by validation via real-time PCR (qRT-PCR). Results: A total of 434 DEGs—240 up-regulated and 194 down-regulated—were identified in PM2.5-exposed HCECs rather than unexposed HCECs. The expression of a few genes related to proliferation, inflammation, and aryl hydrocarbon stimulation were significantly altered by PM2.5 exposure, which may contribute to PM2.5-related corneal diseases. Conclusion: The present study identified the altered expression of hundreds of genes in HCECs exposed to PM2.5, which suggests the importance of PM2.5 for cornea health.

overall_design:
To perform the transcriptomic analysis of PM2.5-exposed human corneal epithelial cells (HCECs) versus unexposed HCECs.
The PM2.5-exposed HCECs group and the control groups contained 3 replicats each.

first: Ke

last: Yao

first: Qiuli

last: Fu


title: Prediction of prognosis, immunogenicity and efficacy of immunotherapy based on glutamine metabolism in lung adenocarcinoma

status: Public on Jul 31 2022

city: Jinan

first: Jiajun

last: Du

address: 324 Jingwu Road

institute: Provincial Hospital Affiliated to Shandong University

summary: Glutamine (Gln) metabolism has been reported to play an essential role in cancer. However, a comprehensive analysis of its role in lung adenocarcinoma is still unavailable. This study established a novel system of quantification of Gln metabolism to predict the prognosis and immunotherapy efficacy in lung cancer. Further, the Gln metabolism in tumor microenvironment (TME) was characterized and the Gln metabolism-related genes were identified for targeted therapy. We comprehensively evaluated the patterns of Gln metabolism in 513 patients diagnosed with lung adenocarcinoma (LUAD) based on 73 Gln metabolism-related genes. Based on differentially expressed genes (DEGs), a risk model was constructed using Cox regression and Lasso regression analysis. The prognostic efficacy of the model was validated using an individual LUAD cohort form Shandong Provincial Hospital, an integrated LUAD cohort from GEO and pan-cancer cohorts from TCGA databases. Five independent immunotherapy cohorts were used to validate the model performance in predicting immunotherapy efficacy. Next, a series of single-cell sequencing analyses were used to characterize Gln metabolism in TME. Finally, single-cell sequencing analysis, transcriptome sequencing, and a series of in vitro experiments were used to explore the role of EPHB2 in LUAD. Patients with LUAD were eventually divided into low- and high-risk groups. Patients in low-risk group were characterized by low levels of Gln metabolism, survival advantage, “hot” immune phenotype and benefit from immunotherapy. Compared with other cells, tumor cells in TME exhibited the most active Gln metabolism. Among immune cells, tumor-infiltrating T cells exhibited the most active levels of Gln metabolism, especially CD8 T cell exhaustion and Treg suppression. EPHB2, a key gene in the model, was shown to promote LUAD cell proliferation, invasion and migration, and regulated the Gln metabolic pathway. Finally, we found that EPHB2 was highly expressed in macrophages, especially M2 macrophages. It may be involved in the M2 polarization of macrophages and mediate the negative regulation of M2 macrophages in NK cells. This study revealed that the Gln metabolism-based model played a significant role in predicting prognosis and immunotherapy efficacy in lung cancer. We further characterized the Gln metabolism of TME and investigated the Gln metabolism-related gene EPHB2 to provide a theoretical framework for anti-tumor strategy targeting Gln metabolism.

overall_design: PC-9 cells treated with EPHB2 siRNA or control siRNA for 36h. Total RNA was subsequently extracted for RNA-sequencing. There were three biological replicates for each group.

first: Jichang

last: Liu


title: EIF2AK2 selectively regulates the gene transcription in immune response and histones associated with systemic lupus erythematosus

city: Wuhan

first: Dong

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: We overexpressed EIF2AK2 in HeLa cells to study EIF2AK2-regulated genes using RNA-seq technology, followed by bioinformatic analysis of target genes of EIF2AK2-regulated transcriptional factors (TFs)

overall_design: transcrptional analysis of EIF2AK2 overexpression and control in Hela cells

first: Lan

last: Ge

first: Yuhong

last: Zhang


title: Viral Mimicry by Endogenous Y-RNAs Contributes to Antiviral Immunity [MVseq2]

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Pattern recognition receptors (PRRs) protect against host invasion by detecting specific molecular patterns found in pathogens and initiating an immune response. While microbial-derived PRR ligands have been extensively characterized, the contribution and relevance of endogenous ligands to PRR activation during viral infection remain overlooked. In this work, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors upon infection by a positive-sense RNA virus, a negative-sense RNA virus or a retrovirus. We found that several endogenous RNAs transcribed by RNA polymerase 3 (Pol3), and in particular the Y-RNA family of small non-coding repeats, bind and activate RIG-I. We show that this recognition is dependent on Y-RNA mimicking viral secondary structure and its 5’-triphosphate extremity. Further, we found that HIV-1 infection triggers a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, leading to an increase of Y-RNA 5’-triphosphorylation that enables their immunogenicity. Importantly, we show that altering DUSP11 expression is sufficient to induce a type-I interferon and T cell activation transcriptional program associated with HIV-1 infection. Overall, our work uncovers the critical contribution of endogenous RNAs ligands to antiviral immunity and demonstrates the role of this pathway in HIV-1 infection.

sample_organism:
Homo sapiens
Measles morbillivirus
Measles virus strain Schwarz

overall_design:
for each experimental condition three biological replicates were performed each time. No data were excluded for analysis
HEK293 cells described in DOI: 10.7554/eLife.11275

first: Nicolas

last: VABRET

first: Valérie

last: NAJBURG

first: Alexander

last: SOLOVYOV

first: Petr

last: ŠULC

first: Sreekumar

last: BALAN

first: Guillaume

last: BEAUCLAIR

first: Maxime

last: CHAZAL

first: Hugo

last: VARET

last: LEGENDRE

first: Odile

last: SISMEIRO

first: Raul

middle: Y

last: DAVID

first: Christopher

last: McCLAIN

first: Ramya

last: GOPAL

first: Lise

last: CHAUVEAU

first: Olivier

last: SCHWARTZ

first: Nolwenn

last: JOUVENET

first: Martin

last: MARKOWITZ

first: Frédéric

last: TANGY

first: Nina

last: BHARDWAJ

first: Benjamin

middle: D

last: GREENBAUM

first: Anastasia

middle: V

last: KOMAROVA


title: Primary specification of blastocyst trophectoderm by scRNA-seq: new insights into embryo implantation

city: BeiJing

first: Yidong

last: Chen

address: Yiheyuan Road

institute: Peking University

summary: Mechanisms of implantation such as determination of the attachment pole, fetal-maternal communication, as well as underlying causes of implantation failure are largely unexplored. Here we performed single-cell RNA sequencing (scRNA-seq) on peri-implantation embryos from both humans and mice to explore trophectoderm development and embryo–endometrium crosstalk. We found that the transcriptomes of polar and mural trophectoderm (TE) diverged after embryos hatched from the zona pellucida in both species, with polar TE being more mature than mural TE. The implantation poles show similarities in cell cycle activities, as well as in expression of genes critical for implantation and placentation. Embryos that either fail to attach in vitro or fail to implant in vivo, show abnormalities in pathways related to energy production, protein metabolism and 18S rRNA m6A methylation. These findings uncover the gene expression characteristics of humans and mice TE differentiation during the peri-implantation period and provide new insights into embryo implantation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcriptome of trophectoderm cells from peri-implantation human and mice embryos were analyzed by single cell RNA-seq

first: Dandan

last: Liu

first: Yixin

last: Ren

first: Liying

last: Yan

first: Jie

last: Qiao


title: ChIP-seq Analysis of Activation-Induced Cytidine Deaminase Distribution in Human B Cells: Insights for Targeting Mechanisms

first: David

middle: Jonathan

last: Fear

address: 5th Floor, Tower Wing, Great Maze Pond

department: Respiratory Medicine and Allergy

institute: Kings College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the analysis of genome wide distribution of activation induced cytidine deaminase by ChIP-seq in Human B cells. The resultant distribution of AID has then been compared to various histone modifications and transcription factors to shed insights into the mechanisms that target this enzyme.

overall_design: ChIP-Seq analysis of AID from human B cells isolated from 3 donors

middle: J


title: Adaptations in nucleus accumbens neuron subtypes mediate negative affective behaviors in fentanyl abstinence

city: Baltimore

first: Mahashweta

last: Basu

state: MD

address: 670 W. Baltimore Street

institute: Institute for Genome Sciences

summary: We used RNAseq to evaluate changes in  nucleus  accumbens (NAc) D1 and D2 translatomes from fentanyl abstinent mice.

overall_design: We performed gene expression profiling in ribosome-associated mRNA from two different mouse genotypes and drug conditions at a single time point

first: Megan

middle: E

last: Fox

first: Cali

middle: A

last: Calarco

first: Mary

middle: K

last: Lobo

first: Seth

last: Ament


title: Developmental exposure to low-level saxitoxin affects neuronal gene expression in zebrafish (Danio rerio)

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Increasing frequency and geographical distribution of harmful algal blooms (HABs) presents a growing threat to the public health. Saxitoxin (STX) is a potent neurotoxin naturally produced by dinoflagellates and cyanobacteria during HAB events. Consumption of seafood contaminated with STX is responsible for paralytic shellfish poisoning (PSP). STX inhibits voltage-gated sodium channels, affecting the propagation of action potentials. Humans are among the species most sensitive to PSP, and neurological symptoms of exposure range from tingling of the extremities to severe paralysis. To protect humans against PSP, there is a ban on harvesting of seafood when the STX levels reach 80 μg/100 g of shellfish tissue. However, shellfish with toxin levels below this regulatory limit often are harvested for consumption. Our objective is to understand the potential health effects of exposure to low levels of STX during sensitive windows of development. Zebrafish embryos were exposed to STX (24 or 48 pg) or vehicle (0.3 mM HCl) at 6 hours post fertilization (hpf) via microinjection. There was no overt toxicity, but starting at 36 hpf there was a temporary lack of pigmentation in STX-injected embryos, which resolved by 72 hpf. Using HPLC, we found that STX was retained in embryos up to 72 hpf in a dose dependent manner. We examined transcriptional profiles in embryos at 24, 36 and 48 hpf. There were no differentially expressed genes (DEGs) in STX-injected embryos at 24 hpf, but at 36 and 48 hpf there were_x000B_3547 and 3356 DEGs, respectively, in response to STX. KEGG pathway analysis revealed significant enrichment of genes related to focal adhesion, adherens junction and regulation of actin cytoskeleton, suggesting that cell-cell and cell-extracellular matrix interactions were affected by STX. The genes affected are critical for axonal growth and the development of functional neural networks. We also observed differential expression of axon guidance factors (netrins, semaphorins, and ephrins), which can control axon outgrowth. We are currently using immunohistochemistry to confirm these findings. Overall, these results suggest that STX exposure might affect axon outgrowth by modulating cell adhesion molecules. [NIH P01ES021923 and NSF OCE-1314642].

overall_design: Saxitoxin and vehicle (control) injected embryos were sequenced for profiling gene expression patterns. Three biological replicates per treatment and time point were sequenced.

first: Mark

last: Hahn

first: John

last: Stegeman


title: Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape

city: Santa Barbara

first: Siddharth

last: Dey

state: CA

address: 3008 BioEngineering Bldg. University of California, Santa Barbara

institute: University of California, Santa Barbara

summary: To understand ISR signaling we engineered photo-switchable control over the ISR stress sensor kinase PKR (opto-PKR), which allows virtual control of the ISR. Using controlled light inputs to activate opto-PKR we traced information flow in the ISR both globally, in the transcriptome, and for key ISR effectors

overall_design: To investigate transcriptomic dynamics of opto-PKR-induced ISR over time, H4-cells bearing opto-PKR were illuminated using the optoPlate device to collect 7 samples across 720 mins.

first: Taivan

last: Batjargal

first: Francesca

last: Zappa

first: Ryan

last: Grant

first: Robert

last: Piscopio

first: Alex

last: Chialastri

middle: S

first: Diego

last: Acosta-Alvear

first: Maxwell

middle: Z

last: Wilson


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ocular Adnexal B-cell Lymphoma Transcriptomes

city: Shanghai

first: Jiahao

last: Shi

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District,

department: Department of Ophthalmology

institute: Shanghai 9th Peoples Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to describe NGS-derived  transcriptome profiling (RNA-seq)  of ocular adnexal B-cell lymphomas (OABLs). Gene expression profiling of RNA was performed on OABL samples to identify  pathway alterations and expression changes affected by clinical traits

overall_design: mRNA profiles of 31 heterogenous samples from OABL patients were generated by deep sequencing using Illumina Novaseq 6000 according to the manufacturer's direction. RNA was extracted from cryopreserved lymphoma tumor specimens. The sequence reads that passed quality filters were analyzed at the transcript isoform level.

first: Tianyu

last: Zhu

first: Renbing

last: Jia

first: Yixiong

last: Zhou

first: Xianqun

last: Fan


title: WGBS of primary and recurrent ovarian cancer tumors with and without BRCA1/2 mutations

city: Los Angeles

first: Michelle

last: Jones

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

type: Methylation profiling by high throughput sequencing

summary: WGBS was generated for a cohort of ovarian cancer patients to identify DNA methylation changes between primary and recurrent ovarian cancer tumors from patients with and without BRCA1/2 mutations

overall_design: We performed whole genome bisulfite sequencing in 62 primary and  recurrent  tumors  from  28  patients  with  stage  III/IV  high  grade  serous  ovarian  cancer (HGSOC), of which 11 patients carried germline, pathogenic BRCA1and/or BRCA2mutations

first: Nicole

last: Gull

middle: R

first: Simon

last: Gayther


title: JAK inhibition selectively suppresses melanoma lacking IFN-γ pathway

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

summary: Immune checkpoint blockers (ICBs) showed unprecedented clinical benefits. But the overall efficacy of ICBs is limited to a small subset of cancer patients due to therapeutic resistance. Concerted efforts from our group and others have identified that loss of IFN-g signaling genes in melanoma is a major mechanism of resistance to ICBs. We therefore generated B16 melanoma model with IFNgR1 knocked out by CRISPR-Cas9. We sequenced the whole transcriptomes and identified activated PI3K-Akt-mTOR pathway in IFNgR1 knocked out cells. This may represent an attractive target for therapeutic interventions to bypassing ICB resistance in melanoma lacking functional IFN-g signaling.

overall_design: Scramble and IFNγR1KO B16 melanoma cells were sent for transcriptomic analysis by paired-end RNAseq analysis to find the activation of PI3K-Akt-mTOR pathway in IFNγR1 knocked out cells.

first: Hongxing

last: Shen

first: Fengyuan

last: Huang

first: Zechen

last: Chong

first: Lewis


title: MYC S146L is a context-dependent activating substitution in cancer development

city: Lebanon

first: Diwakar

last: Pattabiraman

state: New Hampshire

address: 1 Medical Center Drive

department: Molecular systems biology

institute: Geisel School of Medicine at Dartmouth

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

overall_design: Refer to individual Series


title: Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [ISO-seq]

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

institute: Institut Curie

summary: We explored the regulation of intronic polyadenylation isoforms by cisplatin, and its impact on the translatome. This was done in part by 3'-seq (see GSE119978) and Iso-Seq (this data set).

overall_design: To characterize intronic polyadenylation isoforms regulated by cisplatin, we performed Iso-seq analyses on cisplatin- and vehicle-treated non-small cell lung cancer cells.

first: Martin

last: DUTERTRE

first: Iris

last: TANAKA

first: Alexandre

last: DEVAUX

first: Mandy

last: CADIX

first: Sophie

last: MICHALLET

first: Ludovic

last: TESSIER

first: Hussein

last: MORTADA

first: Alina

last: CHAKRABORTY

first: Marc

last: DELOGER

first: Jean-Baptiste

last: CLAUDE

first: Pierre

last: GESTRAUD

last: LABBE

first: Sonia

last: LAMEIRAS

first: Virginie

last: RAYNAL

first: Sylvain

last: BAULANDE

first: Didier

last: AUBOEUF

first: Nicolas

last: SERVANT

first: Stéphan

last: VAGNER

first: Béatrice

last: EYMIN


title: Self-production of IFN-γ by acute myeloid leukemia cells remodels mesenchymal stromal bone marrow cells

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

summary: Acute myeloid leukemia (AML) cells can shape their niche to their own advantage, perturbing  bone marrow stromal and immune landscape. Indeed, AML cells provide the signals, among which inflammatory mediators are crucial, since they are able to subvert mesenchymal stromal cell (MSC) funtions. In particular, IFN-γhigh AML cells hold an inflammatory/immune modulating signature distinct from IFN-γlow cases. We analyzed changes in the gene expression profile of MSCs induced by co-culture with AML cells in vitro. IFN-γhigh but not IFN-γlow AML cells profoundly subverted the MSC transcriptome by inducing immune-modulating pathways, which, intriguingly, included IFN-γ-dependent genes related to regulatory T cell (Treg) differentiation and immune suppression.

overall_design: MSCs cultured with AML cells (on a transwell) for 24h (or control MSCs cultured without AML cells under the same conditions) were used for RNA extraction and hybridization on microarrays.

first: Giulia

last: Corradi

first: Giovanni

last: Martinelli

first: Marilena

last: Ciciarello

first: Antonio

last: Curti


title: Global profiling of genes expressed in silk glands of Philippine-reared mulberry silkworm (Bombyx mori)

city: Quezon City

first: Ma. Anita

last: Bautista

address: Ma. Regidor St., National Science Complex

department: National Institute of Molecular Biology and Biotechnology

country: Philippines

institute: University of the Philippines Diliman

summary: This study aims to bridge the gap in our knowledge of Philippine-reared silkworm by analyzing the gene expression profiles in the silkworm silk glands through next generation sequencing. RNA was isolated from the silk glands of 5th instar larvae and mRNA-enriched libraries were sequenced with NextSeq 500 (Illumina). To compare gene expression profiles of strains from CAR (Benguet) and TCMO (Misamis Oriental), DESeq2 analysis was performed. DESeq2 found 476 differentially expressed genes (222 upregulated, 254 downregulated) in CAR strains when compared to TCMO strains. Genes were mapped to protein IDs from the NCBI nr database and GO terms were assigned by mapping to the latest annotation data from KAIKObase. Enrichment of GO terms was analyzed using R package goseq. Among the top DEGs are myrosinase, heat shock proteins, serine protease inhibitors, dehydrogenases, and regulators of juvenile hormone. GO term enrichment analysis reveals overrepresentation of GO terms related to the biological processes nucleotide metabolism and biosynthesis, lipid and carbohydrate metabolic processes, regulation of transcription, and molecular functions related to nucleotide binding, protein binding, and metal binding, catalytic activity, oxidoreductase activity, and hydrolase activity. This study provides for the first time valuable information on the transcriptome of B. mori strains in the Philippines, which are adapted to the tropical environment. The transcriptome assemblies may serve as a resource for studies intended to improve local strains, particularly for increasing silk production.

overall_design: Silk gland mRNA profiles of 3 Philippine silkworm strains, 3 bioreplicates each strain

first: Pauline-Nicole

middle: O

last: de la Peña


title: MYC S146L is a context-dependent activating substitution in cancer development [CUT&TAG]

first: Diwakar

last: Pattabiraman

summary: MYC is one of the most dysregulated oncogenes and is thought to be fundamental to tumor formation and/or maintenance in many cancer types. This dominant pro-tumor activity makes MYC an attractive target for cancer therapy. However, MYC is a transcription factor lacking enzymatic activity, and the structure of one of its two domains is unknown e.g., its transactivation domain. Consequently, few direct MYC-targeting therapies have been developed, and none have been successful in the clinic. Nevertheless, significant effort has been devoted to understanding the mechanisms of oncogenic MYC activity with the objective of uncovering novel vulnerabilities of MYC-dependent cancers. These extensive investigations have revealed in detail how MYC translocation, amplification, and other upstream perturbations contribute to MYC activity in cancer. However, missense mutations of the MYC gene have remained relatively understudied for their potential role in MYC-mediated oncogenesis. While the function of several low-frequency mutations in MYC have been described, our understanding of other equally or more frequent mutations is incomplete. Herein, we define the function of a recurrent missense mutation in MYC resulting in the substitution S146L. This mutation reinforces the interaction between MYC and its cofactor TRRAP and may enhance oncogenic MYC activity in certain cellular contexts. Implication: our results fortify the mechanistic understanding of oncogenic MYC and may indicate a novel prognostic marker for patients whose tumors harbor the somatic mutation resulting in MYC S146L.

overall_design: Paired-end CUT&RUN of four cell lines expressing specified vectors (or empty vector). Two replicates per cell line.

first: Owen

last: Wilkins

first: Michael

last: Cole


title: P. angusta DL1 strain: Control vs. heat stress

city: Seoul

first: Hye Yun

last: Moon

state: Seoul

address: , 221 Heukseok-dong, Dongjak-gu

department: Department of Life Science

country: South Korea

institute: Chung-Ang university

summary: Transcriptional profiling of heat stress condition comparing control and 55 degree temperature condition on P. angusta DL1 strain.

overall_design: three-condition experiment, normal condition vs. heat stress condition (55 degree temperature 15, 30, 60min) in P. angusta DL1 strain. independently grown and harvested. Dye swapping per array.

first: Hye

first: Hyun

last: Kang


title: MYC S146L is a context-dependent activating substitution in cancer development [RNA-seq]

overall_design: Single-end 3'-end RNA-sequencing of four cell lines expressing specified vectors (or empty vector). Three replicates per cell line.


title: Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes [total RNA-seq]

first: Céline

last: Labbé

summary: We explored the regulation of intronic polyadenylation isoforms by cisplatin, and its impact on the translatome. This was done in part by 3'-seq (see GSE119978) and Total-RNA-Seq (this data set).

overall_design: To characterize intronic polyadenylation isoforms regulated by cisplatin, we performed Total-RNA-seq analyses on cisplatin- and vehicle-treated non-small cell lung cancer cells.

first: Martin

last: DUTERTRE

first: Iris

last: TANAKA

first: Alexandre

last: DEVAUX

first: Mandy

last: CADIX

first: Sophie

last: MICHALLET

first: Ludovic

last: TESSIER

first: Hussein

last: MORTADA

first: Alina

last: CHAKRABORTY

first: Marc

last: DELOGER

first: Jean-Baptiste

last: CLAUDE

first: Pierre

last: GESTRAUD

last: LABBE

first: Sonia

last: LAMEIRAS

first: Virginie

last: RAYNAL

first: Sylvain

last: BAULANDE

first: Didier


title: Communication between corpus callosum and SVZ mediated by locally controlled circadian clocks during demyelination

city: Nanjing

first: Hao

last: Huang

address: Dongnandaxue Road

department: Department of Bioinformatics

institute: Southeast University

summary: We report two sets of potential circadian clock target genes by high-throughput transcriptome profiling (RNA-sequencing): one set from the corpus callosum of the adult mouse brain and the other set from adult neural stem cell cultured from the SVZ (neurospheres) of the mouse brain. First, the corpus callosum was dissected from three adult wild-type and two Bmal1 knockout (Bmal1-/-) mice, mRNA profiles were generated by deep sequencing using BGISEQ-500 RNA-Seq platform. The sequence reads that passed quality control were analyzed: we mapped more than 21 million total clean reads, more than 96% total Mapping Ratio, more than 86% Uniquely Mapping Ratio per sample to mouse genome. qRT-PCR validation with primers covering at least 3 known housekeeping genes and at least 5 well-known circadian clock genes were performed with SYBR Green assay. 103 differentially expressed genes (DEGs) were identified in the corpus callosum of Bmal1-/- mice (58 up-regulated and 45 down-regulated genes; |log2FC| > 1 & adjusted P-value < 0.05). Hypergeometric test revealed that potential functions of circadian clock target genes in the corpus callosum are secreted proteins as signaling molecules. For the second set of data, neurospheres were cultured from the SVZ of three adult wild-type and three adult Bmal1-/- mice, mRNA profiles were generated by deep sequencing using BGISEQ-500 RNA-Seq platform. The sequence reads that passed quality control were analyzed: we mapped more than 28 million total clean reads, more than 97% total Mapping Ratio, more than 68% Uniquely Mapping Ratio per sample to mouse genome. qRT-PCR validation with at least 3 known housekeeping genes and at least 5 well-known circadian clock genes using SYBR Green assay. 30 DEGs were identified in neurospheres cultured from Bmal1-/- mice (17 up-regulated and 13 down-regulated genes; |log2FC| > 1 & adjusted P-value < 0.05). Gene Set Enrichment Analysis (GSEA) revealed that potential circadian clock associated functions in the SVZ (neurospheres) are controlling diverse signal transductions.

overall_design: mRAN profiles in the corpus callosum of adult wild-type and Bmal1 knockout (Bmal1-/-) mice; mRNA profiles in adult neural stem cells (neurospheres) cultured from the SVZ of wild-type and Bmal1-/- mice

first: Jin

last: Kim


title: Profiling DNA copy number alterations of 44 lung cancer cell lines

city: Taipei

first: yi-chiung

last: hsu

address: 128 Academia Road, Section 2

country: Taiwan

institute: academia sinica

type: Genome variation profiling by genome tiling array

summary: We established and characterized 24 lung cancer cell lines from Taiwan lung cancer specimens or pleural effusions. Three EGFR-mutant TKI-sensitive parental cell lines were cultured in gefitinib following well-established TKI dose-escalation protocols. 20 Caucasian lung cancer cell lines are purchased from the American Type Culture Collection and National Cancer Institute. We conducted 44 lung cancer cell lines with copy number variation, EGFR status and invasion ability.

overall_design: 44 lung cancer cell line samples

first: Yi-Chiung

last: Hsu

first: Cin-Di

last: Wang


title: High depth profiling of miRNA targets with chimeric eCLIP [eCLIPseq]

status: Public on Jul 30 2022

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Growing demand in RNA-targeted therapies and promise of miRNA-based drugs creates a need for tools that can accurately identify and quantify miRNA:target interactions at scale. The experimental capture of miRNA:mRNA interactions by ligation into chimeric RNA fragments provides a direct read out of miRNA targets by enabling profiling of miRNA targets with high-throughput sequencing. However, integration of chimeric CLIP-seq into wide practical use has been limited because the inefficiency of the miRNA:mRNA ligation step (resulting in a low rate of chimeric reads in final libraries) combined with the technical complexity of the method makes it challenging to apply to miRNAs of interest at scale. Here we describe chimeric eCLIP, in which we integrate a chimeric ligation step into AGO2 eCLIP to enable chimeric read recovery, and show that removal of the cumbersome polyacrylamide gel and nitrocellulose membrane transfer step common to CLIP techniques can be omitted for chimeric AGO2 eCLIP to create a simplified high throughput version of the assay that maintains high signal-to-noise. With the increased yield of recovered miRNA:mRNA interactions in no-gel chimeric eCLIP, we show that simple enrichment steps using either PCR or on-bead probe capture can be added to chimeric eCLIP in order to target and enrich libraries for chimeric reads specific to one or more miRNAs of interest in both cell lines and tissue samples, resulting in 30- to 175-fold increases in recovery of chimeric reads for miRNAs of interest. We further show that the same probe-capture approach can be used to recover miRNA interactions for a targeted gene of interest, revealing both distinct miRNA targeting as well as co-targeted by several miRNAs from the same seed family. RNA-seq analysis of gene expression following miRNA overexpression confirmed miRNA-mediated repression of chimeric eCLIP identified targets, and indicated that chimeric eCLIP can provide additional sensitivity to detect regulated targets among genes that either contain or lack computationally predicted miRNA target sites. Thus, we believe that chimeric eCLIP will be a useful tool for quantitative profiling of miRNA targets in varied sample types at scale, and revealing a deeper picture for regulatory networks for miRNAs of biological interest.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Chimeric eCLIP performed with gel and without gel in human HEK293T, mouse liver, rat C9 and HEK293T+C9 mix cells.

first: Sergei

last: Manakov

first: Brian

last: Yee

first: Kylie

last: Shen

first: Diana

last: Cox

first: Samuel

last: Park

first: Alexander

last: Shishkin

middle: W

first: Eric

middle: L

last: Van Nostrand


title: Transcriptome of NK-92 cells with pharmacological inhibition of SUPT16H, a subunit of FACT complex, by using its inhibitor curaxin 137 (CBL0137)

status: Public on Jul 29 2022

city: Columbus

first: Dawei

last: Zhou

state: OH

address: 400 W 12th Ave, Wiseman Hall 351C

department: Pathology

institute: The Ohio State University Wexner Medical Center

summary:
Purpose: This study aims to evaluate the effect of FACT complex inhibitor CBL0137 to the total transcriptome of NK-92 cells through RNA-seq assay.
Methods: NK-92 cells were treated with CBL0137 (500 nM) or DMSO for 24 h. RNA samples were extracted and submitted to GENEWIZ (South Plainfield, NJ 07080) for quality control and subsequent rRNA removal through polyA selection, followed by the library preparation. Sequencing was carried out on an Illumina HiSeq platform with the configuration of 2 × 150 bp (paired end), and > 20 million reads per sample were achieved. Differential expression of genes was analyzed by DESeq2.
Results: R packages, pheatmap and clusterProfiler, were used for heatmap construction and pathway analysis, respectively. 917 genes were enriched based on the fold-change > 1.5 as well as the adjusted P-value < 0.05. GO biological process (BP) analysis shows that inteferon signaling and anti-viral responses are among top enriched pathways. Expression of interferons and interferon-stimulated genes (ISGs) are increased based on heatmap, which was further validated through quantitative reverse transcription PCR (RT-qPCR) assay.
Conclusions: CBL0137 causes the systemic upregulation of IFNs and ISGs with statistical significance in NK-92 cells, which shows the potential of CBL0137 to trigger the anti-viral innate immunity. In addition, due to the upragulation of IFN-gamma pathways, CBL0137 also shows the ability to increase the NK cytotoxicity.

overall_design: NK-92 cells were treated with either DMSO as a control, or CBL0137 (500 nM) for 24 h. Four independent experiments were performed. Totally 8 samples were subjected to RNA-seq assay.

first: Zhenyu

last: Wu

first: Jian

last: Zhu


title: 5/6 nephrectomy (5/6Nx) effect on the splenic monocytes in mouse

city: fukuoka

first: Naoya

last: Matsunaga

address: maidashi 3-1-1, higashi-ku

institute: kyushu university

summary: Chronic kidney disease (CKD) is a very important problem in global health treatment. CKD increases the disease risk of apoplexy, cardiac failure and cardiac infarction. Cardiovascular disease is especially the most serious problem. In this study, the expression of mRNA in 5/6 nephrectomy (5/6Nx) mouse  splenic monocytes was investigated.

overall_design: Differential gene expression between 5/6 nephrectomized and sham-operated mouse was measured on the splenic monocytes.

first: Yuya

last: Yoshida

first: Kaori

last: Yasuda

first: Atsushi

last: Doi

first: Koyanagi

last: Satoru

first: Ohdo

last: Shigehiro


title: Transformed cells after senescence give rise to more severe tumor phenotypes than transformed non-senescent cells

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

institute: Inserm 1052

summary: Oncogenic stress-induced senescence initially inhibits tumor initiation by blocking proliferation. If these cells are not eliminated they may resume proliferation upon loss-of-tumor suppressors, and be at risk of transformation. During tumor formation, depending on the sequence of events of gain-of-oncogenes and/or loss-of-tumor suppressors, cancer cells may emerge from senescent cells. The goal of this study is to determine if transformed cells after senescence (TS) display more aggressive tumorigenic features, with a greater capacity to migrate and a higher resistance to anti-tumoral drugs than cells having undergone transformation without senescence. Here, we modeled cell transformation using mouse embryonic fibroblasts (MEFs) subjected to an inverse sequence of events: i) gain-of-RasV12 oncogene and loss-of-p53 tumor suppressor, leading to transformed cells after senescence (TS), or ii) the opposite, resulting in transformed (T) non-senescent cells.

overall_design: This study is based on transciptome analysis of Mouse Embrionic Fibroblasts (MEFs) expressing 4 different combination of viral vectors: Oncogenic form of RAS (RASV12); short hairpin RNA targeting mouse p53 mRNA (shp53); first shp53 plus RASV12 (T cells); or first RASV12 plus shp53 (TS cells) .For each condition three independent biological replicates were analysed.

first: Alberta

last: Palazzo

first: David

last: Bernard

first: Jean-Michel

last: Flaman


title: High depth profiling of miRNA targets with chimeric eCLIP

first: Gene

last: Yeo

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: High depth profiling of miRNA targets with chimeric eCLIP [small RNA-seq]

overall_design: Each miRNA over-expression was performed in duplicate, and was compared against either mock transfection or untransfected for differential expression analysis as indicated.

first: Sergei

last: Manakov

first: Brian

last: Yee

first: Kylie

last: Shen

first: Diana

last: Cox

first: Samuel

last: Park


title: A maternal high-fat diet induces fetal origins of NASH-HCC in mice

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: Maternal overnutrition affects offspring susceptibility to nonalcoholic steatohepatitis (NASH). Male offspring from high-fat diet (HFD)-fed dams developed a severe form of NASH, leading to highly vascular tumor formation. The cancer/testis antigen HORMA domain containing protein 1 (HORMAD1), one of 146 upregulated differentially expressed genes in fetal livers from HFD-fed dams, was overexpressed with hypoxia-inducible factor 1 alpha (HIF-1alpha) in hepatoblasts and in NASH-based hepatocellular carcinoma (HCC) in offspring from HFD-fed dams at 15 weeks old. Hypoxia substantially increased Hormad1 expression in primary mouse hepatocytes. Despite the presence of three putative hypoxia response elements within the mouse Hormad1 gene, the Hif-1alpha siRNA only slightly decreased hypoxia-induced Hormad1 mRNA expression. In contrast, N-acetylcysteine, but not rotenone, inhibited hypoxia-induced Hormad1 expression, indicating its dependency on nonmitochondrial reactive oxygen species production. Synchrotron-based phase-contrast micro-CT of the fetuses from HFD-fed dams showed significant enlargement of the liver accompanied by a consistent size of the umbilical vein, which may cause hypoxia in the fetal liver. Based on these findings, a maternal HFD induces fetal origins of NASH/HCC via hypoxia, and HORMAD1 is a potential therapeutic target for NASH/HCC.

overall_design: Comaprison between fetal livers from HFD-fed dams and those from CD-fed dams. There are two biological replicates for each conditions.

first: Takao

last: Takiyama

first: Toshihiro

last: Sera

first: Masanori

last: Nakamura

first: Masato

last: Hoshino

first: Kentaro

last: Uesugi

first: Makiko

last: Meguro-Horike

first: Ryoichi

last: Bessho

first: Yuri

first: Hiroya

last: Kitsunai

first: Yasutaka

last: Takeda

first: Kazuki

last: Sawamoto

first: Naoto

last: Yagi

first: Yuji

last: Nishikawa

first: Yumi


title: Transcriptional effects of catalytic mTOR inhibiton among LPS-stimulated primary human monocytes

city: Chicago

first: Richard

middle: Thomas

last: D'Aquila

state: IL

address: 303 E Superior St Lurie Research 9-220

department: Medicine (Infectious Diseases)

institute: Northwestern University Feinberg School of Medicine

summary: To better understand the role of mTOR in regulation of the monocyte response to LPS, we obtained mRNA-seq profiles of primary human monocytes stimulated ex vivo through TLR4, with and without pretreatment with a catalytic mTOR inhibitor (mTORi)

overall_design: We obtained primary human monocytes from six independent donors and stimulated with LPS (1 ng/mL) or vehicle for 6h following pretreatment with an mTORi (AZD2014 at 5μM) or DMSO for 6h ex vivo, prior to extraction of RNA and library prep.

middle: T

first: Harry

last: Taylor

first: Nina

last: Calantone


title: High depth profiling of miRNA targets with chimeric eCLIP [RNA-seq]

first: Gene

last: Yeo

first: Sergei

last: Manakov

first: Brian

last: Yee

first: Kylie

last: Shen

first: Diana

last: Cox

first: Samuel

last: Park

first: Alexander

last: Shishkin

first: Eric

last: Van Nostrand


title: miRNA profiling of sacral chordoma and nucleus pulposus cells

status: Public on Jul 28 2022

city: Debrecen

first: Beáta

last: Scholtz

address: Nagyerdei krt. 98

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen, Faculty of Medicine

summary: Next-generation RNA sequencing (NGS) was used for the combinatorial analysis of mRNA-miRNA gene expression profiles in sacral chordoma and nucleus pulposus samples, and to predict miRNA-mRNA regulatory networks with altered activity in chordoma. We identified a gene set including key regulators of the Hippo pathway, which is targeted by differently expressed miRNAs, and validated their altered expression by RT-qPCR. These newly identified miRNA/RNA interactions are predicted to have a role in the self-renewal process of chordoma stem cells, which might sustain the high rate of recurrence for this tumor.

overall_design: 8 chordoma (CH) and 8 nucleus pulposus (NP) tissue samples were collected from surgically treated Caucasian patients. The chordoma samples were frozen in lN2 immediately after removal and stored at -80 ºC until processing. NP tissues were surgically removed from patients diagnosed with degenerative disc disease (Pfirrmann grade III), undergoing lumbar intervertebral fusion surgery. We established primary NP cell cultures from the NP tissue samples, applying the explantation method without any enzymatic digestions.

first: Arpad

last: Bozsodi

first: Gergo

last: Papp

first: Adam

last: Biczo

first: Peter

middle: P

last: Varga

first: Aron

last: Lazary


title: Gene expression changes in cerebellar meninges in Pdgfc and Pdgfra mutant mice at P0

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: Platelet-derived growth factor-C (PDGF-C) is one of three known ligands for the tyrosine kinase receptor PDGFRα. We generated mice that were double mutants for Pdgfc -/- and Pdgfra GFP/+, and have previously shown how cerebral meninges are affected resulting in developmental neuronal overmigration. Other severe phenotypes displayed in these mice include cerebellar malformation, spina bifida and lung emphysema. We focused our analysis on the central nervous system (CNS) and the cerebellum, where PDGF-C was identified as a critical factor during development.

overall_design: Meninges overlying the cerebellum of P0 mouse were freely dissected and stored in RNA later® (Ambion). RNA was isolated using RNeasy micro kit (Qiagen) and quality checked in a 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Transcription profiling was performed with Gene Chip Mouse Gene 1.0 ST array. We compared mice with a cerebellar phenotype (Pdgfc-/-; Pdgfra GFP/+) with a control group consisting of all littermates (Pdgfc+/+, Pdgfc+/-, Pdgfc-/-, Pdgfc+/+; Pdgfra GFP/+ and Pdgfc+/-; Pdgfra GFP/+).

first: Johanna

last: Andrae


title: Blood transcriptional profiles distinguish different clinical stages of cutaneous leishmaniasis in humans

status: Public on Jul 27 2022

city: Tehran

first: Fariborz

last: Bahrami

address: 69 Pasteur Ave.

department: Immunology

country: Iran

institute: Pasteur Institute of Iran

summary: Cutaneous leishmaniasis (CL) is prevalent in many low-income countries. Although CL is considered non-fatal, it has a major impact on public health systems of affected nations, causing social and economic problems due to disfiguration, morbidity, loss of productivity and medical costs for the public sector. Since no effective human vaccine against CL exists, it is crucial to understand better factors that may affect the outcome of the disease, including the impact of the pathogen on the host immune system. While transcriptomics analyses of the skin lesion in CL patients were recently reported, there is a dearth of information on the expression of immune-related genes in the blood of CL patients. We herein sought to profile the expression of immune-related genes in the blood of healed, asymptomatic and active CL patients.

overall_design: Using a dual-color reverse-transcription multiplex ligation-dependent probe amplification (dcRT-MLPA) assay, the transcriptomic profile of innate, adaptive and inflammatory immune-related genes in whole blood PAXgene samples obtained from two Leishmania tropica endemic areas were investigated. The blood samples were obtained from healthy individuals with positive leishmanin skin test, but without history of CL lesions (i.e., asymptomatic), and those with cured previous CL lesions (i.e., healed). We also investigated the same profile in individuals with active lesions (i.e., patients) and healthy residents of endemic areas with no history of CL and with a negative leishmanin skin test.

first: Nasrin

last: Masoudzadeh

first: Suzanne

last: Van Veen

first: Josefine

last: Persson

first: Arezou

last: Lari

first: Hamzeh

last: Sarvnaz

first: Yasaman

last: Taslimi

first: Malin

last: Östensson

first: Björn

last: Andersson

first: Iraj

last: Sharifi

first: Vahid

last: Mashayekhi-Goyonlo

first: Tom

middle: H

last: Ottenhoff

first: Mariëlle

middle: C

last: Haks

first: Ali

middle: M

last: Harandi

first: Sima

last: Rafati


title: Gene expression of cardiomyocytes exposed to L-lactate

city: Barcelona

first: Elisabeth

last: Engel

address: C\ Baldiri Reixac 15-21, Helix Building

country: Spain

institute: Institute for Bioengineering of Catalonia

summary: We evaluated the effect of L-lactate supplementation in cell culture media on cardiomyocyte gene expression

overall_design: Human iPSC were differentiated to cardiomyocytes until day 15. Three biological replicates were incubated with 6mM of L-lactate in cell culture media for 7 days, while three more replicates were incubated with L-lactate and 1mM of α-Cyano-4-hydroxycinnamic acid (α-CHC), an inhibitor of the lactate transporter MCT1. Three replicates of untreated cardiomyocytes were used as gene expression control.

first: Jesús

last: Ordoño

first: Soledad

last: Pérez-Amodio

first: Kristen

last: Ball

first: Aitor

last: Aguirre


title: Dynamically Upregulated Mast Cell CPA3 Patterns in lung disease

city: Lund

first: Mattias

last: Magnusson

address: BMC A12

department: Molecular Medicine and Gene Therapy

institute: Lund university

summary:
The mast cell-specific metalloprotease CPA3 has been given important roles in lung tissue homeostasis and disease pathogenesis. However, the dynamics and spatial distribution of mast cells CPA3 expression in lung diseases remains unknown.
Methods: Using a histology-based approach for spatial and quantitative simultaneous decoding of mRNA and protein expression at a single cell level, this study investigates the dynamics of CPA3 expression across mast cells residing in lungs from healthy controls and patients with severe chronic obstructive pulmonary disease (COPD) or idiopathic lung fibrosis (IPF).
Results: Mast cells in COPD lungs had increased CPA3 mRNA (bronchioles p<0.001, pulmonary vessels p< 0.01, alveolar parenchyma p< 0.01) compared to controls, while granule stored CPA3 protein was unaltered. IPF lungs had a significant upregulation of both CPA3 mRNA (p<0.001) and protein (p<0.05) in the fibrotic alveolar tissue. IPF was also characterized by highest density of distal lung mast cells. As an indication of disease relevant increased CPA3 turnover, spatial expression maps revealed altered mast cell mRNA/protein quotients in lung areas subjected to disease-relevant histopathological alterations. Single cell RNA sequencing of bronchial mast cells confirmed CPA3 as a top expressed gene with potential links to both inflammatory and protective markers.
Conclusion: This study shows that lung tissue mast cell populations in COPD and IPF-affected lungs have spatially complex and markedly up-regulated CPA3 expression profiles that correlates with sites of structural pathologies. Given the proposed roles of CPA3 in tissue homeostasis, remodeling and inflammation, these alterations are likely to have clinical consequences.

overall_design:
Comparing primary human mast cells from healthy donors
***Please note that raw data are not provided due to subject privacy concerns***

first: Pavan

last: Prabhala


title: The endogenous HBZ interactome in ATL leukemic cells reveals an unprecedented complexity of host interacting partners involved in RNA splicing

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

institute: oncovirology and Biotherapies, UMR5239, LBMC

summary: Five percent of HTLV-1 infected subjects develops an untreatable form of cancer designated Adult T cell leukemia (ATL). The HTLV-1-encoded HBZ protein is believed to act as a viral oncogene by disarranging crucial pathways in the infected cells. Key to thisfunction is a progressive cytoplasmic-to-nuclear dislocation of HBZ and its interaction with nuclear factors whose complexity wasnot assessed until now. In this investigation we unveiled for the first time such complexity by studying the endogenous HBZinteractome in a leukemic cell line derived from an ATL patient. A high number of nuclear interactors, represented by at least 249members, were found. Among the various family of interactors, we found predominant the family involved in RNA splicing and RNAstability. A disarrangement of the splicing mechanism was demonstrated both in ATL cells and in non HTLV-1-derived leukemic cellsexpressing HBZ after genetic transfer, strongly suggesting that a major mechanism leading to HTLV-1-mediated transformationand persistence of the oncogenic state is related to this event. Our unprecedented results shed new light on the mechanisms bywhich a human retrovirus can alter the infected cell metabolism and strongly predispose and/or maintain neoplastictransformation

overall_design: To assess the effects of HBZ on gene expression and alternative splicing, we performed RNA-seq analysis of Jurkat cells stably expressing HBZ, HTLV-1-transformed ATL2 cells, and uninfected Jurkat and MOLT4 cells used as controls.

first: Mariam

last: Shallak

first: Tiziana

last: Alberio

first: Mauro

last: Fasano

first: Maria

last: Monti

first: Ilaria

last: Iacobucci

first: Julien

last: Ladet

first: Franck

last: Mortreux

first: Roberto

last: Accolla

first: Greta

last: Forlani


title: The role of core circadian component BMAL1 or CLOCK in human bone marrow mesenchymal stem cells osteogenic capacity

status: Public on Jul 26 2022

city: Shenzhen

first: Peitao

last: Xu

address: No.3025, Shennan Middle Street

institute: The Eighth Affiliated Hospital of Sun Yat-sen University

summary: To elucidate how the core circadian component BMAL1 and clock regulate the osteogenic capacity of human bone marrow MSCs, RNA-seq was performed to study the impact of diminishing core component BMAL1 or CLOCK in MSCs by lentiviruses.

overall_design: Examination of the mRNA profiles in human bone marrow MSCs with diminishing  BMAL1 or CLOCK during osteogenic differentiation

first: Huiyong

last: Shen

first: Zhongyu

last: Xie

first: Wenhui

last: Yu


title: Cerebellar gene expression changes in Pdgfc and Pdgfra mutant

first: L.

last: He

summary: Platelet-derived growth factor-C (PDGF-C) is one of three known ligands for the tyrosine kinase receptor PDGFR-alpha. Analysis of Pdgfc null mice has demonstrated roles for PDGF-C in palate closure and the formation of cerebral ventricles, but redundancy with other PDGFR-alpha ligands might hide additional functions. In search of further developmental roles for PDGF-C, we generated mice that were double mutants for Pdgfc -/- and Pdgfra GFP/+. These mice display a range of severe phenotypes including cerebellar malformation, neuronal over-migration in the cerebral cortex, spina bifida and lung emphysema. We focused our analysis on the central nervous system (CNS), where PDGF-C was identified as a critical factor for the formation of meninges and assembly of the glia limitans basement membrane.

overall_design: Cerebellum from E13.5 and E14.5 embryos were freely dissected. Tissues were stored in RNA later® (Ambion), RNA was isolated using RNeasy micro kit (Qiagen) and quality checked in a 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Transcription profiling was performed with Gene Chip Mouse Gene 1.0 ST array. We compared mice with a cerebellar phenotype (Pdgfc-/-; Pdgfra GFP/+) with a control group consisting of all littermates (Pdgfc+/+, Pdgfc+/-, Pdgfc-/-, Pdgfc+/+; Pdgfra GFP/+ and Pdgfc+/-; Pdgfra GFP/+). One litter from E13.5 (3 mutants and 5 controls) and one litter from E14.5 (2 mutants and 7 controls) were used.

first: Johanna

last: Andrae


title: Transcriptomic in grain and leaf tissues of a low-gluten RNAi wheat line.

city: Córdoba

first: Francisco

last: Barro Losada

state: Córdoba

address: Alameda Del Obispo

institute: Institute of Sustainable Agriculture

summary: Gluten proteins are responsible for the unique viscoelastic properties of wheat dough, but they also trigger the immune response in celiac disease patients. RNA interference (RNAi) wheat lines with strongly silenced gliadins were obtained to reduce the immunogenic response of wheat. The E82 line presents the highest reductions of gluten, but other grain proteins increased, maintaining a total nitrogen content comparable to that of the wild type. To better understand the regulatory mechanisms in response to gliadin silencing, we carried out a transcriptomic analysis of grain and leaf tissues of the E82 line during grain filling. A network of candidate transcription factors (TFs) that regulates the synthesis of the seed storage proteins (SSPs), α-amylase/trypsin inhibitors, lipid transfer proteins, serpins, and starch in the grain was obtained. Moreover, there were a high number of differentially expressed genes in the leaf of E82, where processes such as nutrient availability and transport were enriched. The source-sink communication between leaf and grain showed that many down-regulated genes were related to protease activity, amino acid and sugar metabolism, and their transport. In the leaf, specific proline transporters and lysine-histidine transporters were down- and up-regulated respectively. Overall, the silencing of gliadins in the RNAi line is compensated mainly with lysine-rich globulins, which are not related to the proposed candidate network of TFs, suggesting that these proteins are independently regulated to the other SSPs. Results reported here can explain the protein compensation mechanisms and contribute to decipher the complex TF network operating during grain filling.

overall_design: Examination of 12 samples of grain and leaf tissues of a wild-type and a RNAi line of wheat with three biological replicates.

first: Miriam

last: Marín Sanz

last: Barro


title: Convergent pathways underlying the Kallmann syndrome-linked genes Hs6st1 and Fgfr1

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

summary: Kallmann syndrome (KS) is a congenital disorder characterized by idiopathic hypogonadotropic hypogonadism and olfactory dysfunction. KS is linked to variants in more than 24 genes, which are scattered across the human genome and show disparate biological functions. Although the genetic basis of KS is well studied, the mechanisms by which disruptions of these diverse genes cause KS are not fully understood.

overall_design: Here we show that disruptions of KS-linked genes affect the same biological pathways, indicating a convergent mechanism underlying KS. We disrupted two KS-linked genes, Heparan sulfate 6-O-sulfotransferase 1 (Hs6st1) and fibroblast growth factor receptor 1 (Fgfr1), in mouse neuronal cells. We found that disruptions of Hs6st1 and Fgfr1 altered the same biological processes, the upregulation of extracellular pathways and the downregulation of nuclear pathways. Moreover, we found that Hs6st1 and Fgfr1 regulate gene transcription likely via the transcription factor Sox9/Sox10 and the chromatin regulator Chd7, which are also associated with KS.

first: Sohyun

last: Moon


title: Using the Daphnia magna Transcriptome to Distinguish Water Source: Wetland and Stormwater Case Studies

city: Seattle

first: Mark

last: Jankowski

state: WA

address: 1200 6th Ave

institute: USEPA

summary: Investigation of mRNA expression (using HiSeq 2500) in response to treatment of Daphnia magna to pyriproxyfen, wetland water, or stormwater samples.

overall_design: Four day treatment of D.magna to wetland waters with and without pyriproxyfen or stormwaters collected seasonally and with and without in situe water treatment controls. RNA was extracted from whole organism treated and control D.magna and mRNA was sequenced to assess gene expression in response to the experimental treatments.

first: David

last: Fairbairn

first: Joshua

last: Baller

first: Benjamin

last: Westerhoff

first: Heiko

last: Schoenfuss


title: Comprehensive evaluation of MEK inhibitors for malignant peripheral nerve sheath tumors reveals differences in efficacy and drug resistance development

city: Shanghai

first: Zhichao

last: Wang

address: 639 Zhizaoju Road, Shanghai 200011, P.R. China

department: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

institute: Department of Plastic and Reconstructive Surgery

summary: Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft-tissue sarcomas which lack effective drugs. Previous studies support the usefulness of MEK inhibitors (MEKis) for treating RAS-driven tumors, however, the lack of preclinical assessment of MEK inhibitors in MPNSTs limit the clinical application as well as the development of combination therapy. In this study, we comprehensively evaluated 8 MEK inhibitors in terms of efficiency, safety and mechanisms of resistance for treating MPNSTs. We identified the most promising MEK inhibitor, trametinib, for the treatment of MPNSTs. Through high-throughput transcriptomic sequencing and drug screening, we discovered the upregulation of integrin signaling contributing to MEK inhibitor resistance, termed as cell adhesion-mediated drug resistance (CAM-DR). We also confirmed MET overactivation in MEKi-resistant MPNST cells. These targets are potential solutions to overcome MEKi- resistance in clinical applications.

overall_design: The mRNA profiles of resistant and non-resistant MPNST cell lines were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Yihui

last: Gu

first: Wei

first: Chengjiang

last: Wei

first: Qingfeng

last: Li


title: Digital spatial profiling of pancreatic ductal adenocarcinoma, acinar ductal metaplasia and adjacent normal pancreas tissue

status: Public on Jul 25 2022

city: Beijing

first: Bo

last: Gao

address: No.11 Xizhimen South Street, Beijing, China

department: Department of General Surgery

institute: Peking university people's hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) is the most important histological subtype of pancreatic cancer, accounting for approximately 90% of all pancreatic cancers.Acinar to ductal metaplasia (ADM) is a recently recognized, yet less well-studied, precursor lesion of PDAC developed in the setting of chronic pancreatitis. Through digital spatial mRNA profiling, we compared ADM and adjacent PDAC tissues from patient samples to unveil the bridging genes, bridging signaling pathway and bridging molecular function during the malignant transformation of pancreatitis.

overall_design: A total of 8 sets of PDAC tissue samples were obtained from 8 patients with a history of chronic pancreatitis who underwent surgical resection in McGill University Health Centre. In each case, formalin fixed paraffin embedded (FFPE) tissue blocks that contain normal acini, ADM tissue and PDAC on the same tissue section were selected. None of the patients with pancreatic cancer received any pre-operative treatments, including radiotherapy, chemotherapy, or biological treatments. All specimens were histopathologically diagnosed by two pathologists according to the WHO diagnostic criteria for PDAC. We selected several regions of interest (ROIs) from each PDAC sample, including normal, ADM and PDAC ROIs. NanoString Technologies’ newly developed GeoMx digital spatial profiling (DSP) technology allows for morphology-driven, high-plex spatial analysis of FFPE samples.  Using the GeoMx Cancer Transcriptome Atlas, a panel of RNA probes designed for comprehensive profiling of the tumor, tumor microenvironment, and tumor immune status with 1860 RNA targets, we directly analyzed the in situ RNA expression of a total of 48 ROIs from 8 PDAC samples.

first: Julia

last: Messina-Pacheco

first: Zu-hua


title: Interleukin-1b in Tendon Injury Enhances Reparative Gene and Protein Expression in Mesenchymal Stem Cells

city: Raleigh

first: Lauren

middle: V

last: Schnabel

state: North Carolina

address: 1060 William Moore Dr

institute: North Carolina State University

summary:
Intralesional mesenchymal stem cell (MSC) therapy has improved tissue architecture and reinjury rates in equine tendon injury; however, the mechanisms by which they promote repair are still being investigated.
Therefore, the objectives of this study were to determine how the predominate pro-inflammatory cytokines present in a surgically induced model of equine tendon injury modulate MSC gene and protein expression.

overall_design: Comparative gene expression analysis (RNA-seq) of paired (naïve or licensed) equine mesenchymal stem cells (n=6) following IL-1b or IL-6 licensing.

first: Drew

last: Koch


title: RNA Sequencing of H520 cells treated with ML355 or NVR and their controls treated with DMSO

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: We uncovered the retrotransposon L1-FGGY exhibited an oncogenic role via activating 12-LOX metabolic pathway in this study. In order to elucidate the underlying oncogenic roles of L1 and 12-LOX in tumorigenesis and tumor progression, we treated the H520 cells overexpressing L1-FGGY with NVR (reverse transcriptase inhibitor) and NVR (12-LOX inhibitor) and performed RNA sequencing for them.The results showed decrease of L1 level after treatment in both NVR and ML355, suggesting their potential effects on L1 suppress. Genes downregulated in NVR and ML355 treatment were enriched in cell cycle, cell growth and ATP metabolic process, which we showed to be related to LCT activity.

overall_design: mRNA profiles of H520 cells overexpressing L1-FGGY treated with NVR (reverse transcriptase inhibitor) or NVR (12-LOX inhibitor) and their controls treated with DMSO

first: Rui

last: Zhang


title: Re-expression of tafazzin isoforms in TAZ-deficient C6 glioma cells restores cardiolipin composition but not proliferation rate and alterations in gene expression

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

summary: Tafazzin an acyltransferase is involved in cardiolipin (CL) remodeling. CL is associated with mitochondrial function, structure and more recently with cell proliferation. Various tafazzin isoforms exists in humans. The role of these isoforms in cardiolipin remodeling is unknown. Aim of this study is to investigate if isoform Δ5, which is lacking exon 5, full length rat TAZ, and mutant full-length rat Taz (enzymatically dead H69L) could restore wild type phenotype in C6 TAZ cells with respect to CL composition, cellular proliferation and gene expression profile. In addition, we aim to determine the molecular mechanism by which tafazzin can modulate gene expression by applying promoter analysis and IPA to genes regulated by TAZ-deficiency. Expression of Δ5 and rat full length TAZ in C6-TAZ- cells can fully restore CL composition and – as proven for 5 – this is naturally associated with restoration of mitochondrial respiration. A similar restoration of CL-composition could not be observed after re-expression of an enzymatically dead full-length rat TAZ (H69L; TAZmut3). The re-expression of none of the TAZ isoforms used led to the restoration of the proliferation rate and gene expression profiles. Very likely TAZ-deficiency provokes substantial long-lasting changes in cellular lipid metabolism which contribute to changes in proliferation and gene expression, and are not or only very slowly reversible.

overall_design: C6 (3 pooled samples) and C6 TAZ (3 pooled samples)

first: Gayatri

last: Jagirdar

first: Matthias

last: Elsner

first: Christian

last: Scharf

first: Katrin

last: Borucki

first: Michael

last: Lalk

first: Karen

last: Methling

last: Linnebacher

first: Mathias

last: Krohn

first: Oliver

last: Otto

first: Carmen

last: Wolke

first: Uwe

last: Lendeckel


title: High-throughput renal transcriptome profiling in mice infected with Leptospira spp.

city: Taoyuan

first: Li-Fang

last: Chou

address: 5 Fu-Shing St., Kueishan

department: Department of Medical Research and Development

institute: Chang Gung Memorial Hospital, Linkou

summary: Leptospirosis is a globally important infectious disease caused by an infection with pathogenic Leptospira spp. and associated with kidney injury due to sustained tubulointerstitial inflammation. We apply the high-throughput Illumina sequencing platforms to determine the murine renal transcriptome and investigate gene expression alterations and biological pathways associated with kidney damage induced by leptospiral infection. The goal of this study is to investigate a global analysis of renal gene expression associated with renal damage that was induced by leptospiral infection in experimental mice models.

overall_design: C57BL/6 female mice were inoculated using intraperitoneal challenge with a high infective dose of L. interrogans serovar Copenhageni Fiocruz L1-130 (ATCC number BAA-1198) and L. biflexa serovar Patoc (ATCC number 23582), respectively. The control groups were inoculated with sterile EMJH medium. The mice were sacrificed at 7 days post-infection, and the kidneys were harvested. Total RNA was extracted from kidneys and subjected to high-throughput RNA sequencing analysis (n=3 per each group).

first: Chih

last: Yang

first: Li

middle: F


title: Decitabine-induced T cell remodeling facilitates a high antitumor response to PD-1 blockade therapy by promoting the expansion and effector function of CD8+ progenitor exhausted T cells

first: Jing

last: Nie

state: Beijing

address: No.28, Fuxing Road

institute: Chinese PLA General Hospital

summary: CD8+ exhausted T (Tex) cells are heterogeneous with distinct transcriptional and epigenetic landscapes. PD-1 inhibitors reinvigorate progenitor Tex cells, which subsequently differentiate into irresponsive terminal Tex cells and impair the longlasting antitumor response of PD-1 blockade therapy. How to maintain durable proliferative capacity of progenitor Tex cells is important but remains largely unknown. Here, we showed that low-dose DNA demethylating agent decitabine-pretreated CD8+ progenitor Tex cells had enhanced cytolytic activity against tumors after anti-PD-1 treatment in vitro and could not reactivate the terminal Tex cells. Decitabine-plus-anti-PD-1 treatment promoted the activation and expansion of endogenous tumor-infiltrated CD8+ progenitor Tex cells and efficiently suppressed tumor growth in multiple mice tumor models. The single-cell RNA-sequencing, TCR-sequencing and ATAC-sequencing demonstrated that decitabine-plus-anti-PD-1 combination altered the transcriptional and epigenetic status of CD8+ Tex cells and markedly elevated the clonally expansion and effector function of progenitor Tex cells as compared with anti-PD-1 monotherapy, presenting increased expression of genes associated with T cell activation, proliferation, cytolytic activity, memory and mitochondrial metabolism. Strikingly, decitabine-plus-anti-PD-1 combination sustained the expression and activity of AP-1 transcription factor JunD, which was reduced following PD-1 blockade therapy. Suppressing JNK/AP-1 signaling in CD8+ T cells blunted decitabine-plus-anti-PD-1-induced activation of CD8+ T cells. Together, our findings show that the epigenetic therapy remodels CD8+ progenitor Tex subset, improves responsiveness to anti-PD-1 therapy and suppresses CD8+ T cell terminal differentiation.

overall_design: scRNA-seq, scTCR-seq, ATAC-seq, and WGBS of T cells in the Control (C), decitabine(D), anti-PD-1(P), and decitabine-plus-anti-PD-1(DP) group.

first: Xiang

last: Li

first: Yaru

first: Hebing

last: Chen

first: Weidong

last: Han


title: RNA Sequencing of L1-FGGY- and L1-FGGY+ lung squamous cell carcinoma tissues

first: Zeguo

last: Sun

summary: We uncovered the roles of Long Interspersed Nuclear Element-1 (LINE-1, L1) in cancer development in this study. In order to elucidate the underlying oncogenic roles of L1-FGGY in tumorigenesis and tumor progression, we collected an independent Chinese cohort of 109 LUSC tumor samples (52 L1-FGGY+ vs. 57 L1-FGGY-) from Tianjin Medical University Cancer Institute and Hospital (TJMUCH) and performed RNA sequencing for them.The functional Gene Ontology enrichment of those genes in L1-FGGY+ tissues revealed the significant functions in multiple metabolic processes, including glutathione metabolism, arachidonic acid (AA) metabolism, and drug metabolism.

overall_design: Tissue mRNA profiles of 52 L1-FGGY- and 57 L1-FGGY+ lung squamous cell carcinoma samples

first: Rui

last: Zhang


title: The DEAD-box helicase Hlc regulates basal transcription and chromatin opening of stress-responsive genes

status: Public on Jul 24 2022

city: Chongqing

first: jin

last: you

address: Huxi Campus

institute: Chongqing University

summary: Stress-responsive genes are lowly transcribed under normal conditions and robustly induced in response to stress. The significant difference between basal and induced transcription indicates that the general transcriptional machinery requires a mechanism to distinguish each transcription state. However, what factors specifically function in basal transcription remains poorly understood. Using a classic model stress-responsive gene (Drosophila MtnA), we found that knockdown of the DEAD-box helicase Hlc resulted in a significant transcription attenuation of MtnA under normal, but not stressed, conditions. Mechanistically, Hlc directly binds to the MtnA locus to maintain the accessibility of chromatin near the transcriptional start site, which allows the recruitment of RNA polymerase II and subsequent MtnA transcription. Using RNA-seq, we then identified plenty of additional stress-responsive genes whose basal transcription was reduced upon knockdown of Hlc. Taken together, these data suggest that Hlc-mediated transcription regulation is an essential and widespread mechanism for precise control of stress-responsive genes.

overall_design: Two biological replicates for both beta-gal dsRNA and Hlc dsRNA (dsRNA#2 and #3) treated samples.

first: J

last: You

first: C

last: Huang


title: Analysis of cellular transcripts targeted by ZAPL or  ZAPS  in HEK293T cells

city: Singapore

first: Phuong Thao

last: Ly

address: SBS-02S-88D, 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: To investigate the differential functions of two major ZAP variants, ZAPL and ZAPS, in the regulation of cellular RNA abundance, we established HEK293T cell lines in which either ZAPL or ZAPS has been knockout with CRISPR-mediated deletion.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 genotypes (3 batches of WT; 2 and 1 batches of ZAPS-KO1 and 2, respectively; and 2 and 1 batches of ZAPL-KO1 and 2, respectively) and 2 treatments (medium-only and IFN-b treatment for 24h).
Transcriptome profiles of HEK293T cell lines with either wild-type, ZAPL-KO or ZAPS-KO, using CRISPR/Cas9-mediated deletion

first: Phuong

first: Xavier

last: Roca


title: Epigenetic dependencies of interferon gamma-induced gene expression [RNA-Seq]

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

summary: Interferon gamma (IFNy) is a pro-inflammatory cytokine that directly activates the JAK/STAT pathway. However, the temporal dynamics of chromatin remodeling and transcriptional activation initiated by IFNy have not been systematically profiled in an unbiased manner. Herein, we integrated transcriptomic and epigenomic profiling to characterize the acute epigenetic changes induced by IFNy stimulation in a murine breast cancer model. We identified de novo activation of cis-regulatory elements bound by Irf1 that were characterized by increased chromatin accessibility, differential usage of pro-inflammatory enhancers, and downstream recruitment of BET proteins and RNA polymerase II. To functionally validate this hierarchical model of IFNy-driven transcription, we applied selective antagonists of histone acetyltransferases P300/CBP or acetyl-lysine readers of the BET family. This highlighted that histone acetylation is an antecedent event in IFNy-driven transcription, whereby targeting of P300/CBP but not BET inhibition, could curtail the epigenetic remodeling induced by IFNy through suppression of Irf1 transactivation. These data highlight the utility for epigenetic therapies to reprogram pro-inflammatory gene expression, which may have therapeutic implications for anti-tumor immunity and inflammatory diseases.

overall_design: Examination of changes in gene expression by 3'-mRNA-seq (QuantSeq) following stimulation of AT3 cells in technical triplicate with interferon gamma (IFNy) alone and in combination with catalytic inhibitors of P300/CBP, A-241 or A-485, for 3 hours.


title: Epigenetic dependencies of interferon gamma-induced gene expression

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

overall_design: Refer to individual Series


title: Epigenetic dependencies of interferon gamma-induced gene expression [ChIP-Seq]

summary: Interferon gamma (IFNy) is a pro-inflammatory cytokine that directly activates the JAK/STAT pathway. However, the temporal dynamics of chromatin remodeling and transcriptional activation initiated by IFN have not been systematically profiled in an unbiased manner. Herein, we integrated transcriptomic and epigenomic profiling to characterize the acute epigenetic changes induced by IFNy stimulation in a murine breast cancer model. We identified de novo activation of cis-regulatory elements bound by Irf1 that were characterized by increased chromatin accessibility, differential usage of pro-inflammatory enhancers, and downstream recruitment of BET proteins and RNA polymerase II. To functionally validate this hierarchical model of IFNy-driven transcription, we applied selective antagonists of histone acetyltransferases P300/CBP or acetyl-lysine readers of the BET family. This highlighted that histone acetylation is an antecedent event in IFNy-driven transcription, whereby targeting of P300/CBP but not BET inhibition, could curtail the epigenetic remodeling induced by IFNy through suppression of Irf1 transactivation. These data highlight the utility for epigenetic therapies to reprogram pro-inflammatory gene expression, which may have therapeutic implications for anti-tumor immunity and inflammatory diseases.

overall_design: Examination of changes in Histone H3 Lysine 27 acetylation (H3K27ac) and IRF1 genomic localization by ChIP-seq following stimulation of AT3 cells treatedwith interferon gamma (IFNy) alone and in combination with catalytic inhibition of P300/CBP for 3 hours.


title: Single-cell Transcriptomic Profiling Unveils Cardiac Cell-type Specific Response to Maternal Hyperglycemia Underlying the Risk of Congenital Heart Defects

status: Public on Jul 22 2022

city: Columbus

first: Madhumita

last: Basu

state: Ohio

address: 700 Children's Drive

department: Center for Cardiovascular Research

institute: Nationwide Children's Hospital

summary: Congenital heart disease (CHD) is the most prevalent structural malformations of the heart affecting ∼1% of live births. To date, both damaging genetic variations and adverse environmental exposure such as maternal diabetes have been found to cause CHD. Clinical studies show ∼fivefold higher risk of CHD in the offspring of mothers with pregestational diabetes. Maternal pregestational diabetes affects the gene regulatory networks key to proper cardiac development in the fetus. However, the cell-type specificity of these gene regulatory responses to maternal diabetes and their association with the observed cardiac defects in the fetuses remains unknown. To uncover the transcriptional responses to maternal diabetes in the early embryonic heart, we used an established murine model of pregestational diabetes. In this model, we have previously demonstrated an increased incidence of CHD. Here, we show maternal hyperglycemia (matHG) elicits diverse cellular responses during heart development by single-cell RNA-sequencing in embryonic hearts exposed to control and matHG environment. Through differential gene-expression and pseudotime trajectory analyses of this data, we identified changes in lineage specifying transcription factors, predominantly affecting Isl1+ second heart field progenitors and Tnnt2+cardiomyocytes with matHG. Using in vivo cell-lineage tracing studies, we confirmed that matHG exposure leads to impaired second heart field-derived cardiomyocyte differentiation. Finally, this work identifies matHG-mediated transcriptional determinants in cardiac cell lineages elevate CHD risk and show perturbations in Isl1-dependent gene-regulatory network (Isl1-GRN) affect cardiomyocyte differentiation. Functional analysis of this GRN in cardiac progenitor cells will provide further mechanistic insights into matHG-induced severity of CHD associated with diabetic pregnancies.

overall_design: Comparison of differential transcriptional response in developing embryonic hearts exposed to matrenal control and hyperglycemic environment at single cell resolution

first: Vidu

last: Garg

first: Sathiyanarayan

last: Manivannan

first: Corrin

last: Mansfield


title: Sleep Disturbance and Activation of Cellular and Transcriptional Mechanisms of Inflammation in Older Adults

city: Los Angeles

first: Donald

last: Lamkin

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

institute: UCLA

summary: Genome-wide transcriptional profiling results were used to systematically assess the extent to which transcriptomes of older adults with insomnia show expression of genes that are different from those without insomnia

overall_design:
Total RNA obtained from peripheral blood mononuclear cells (PBMCs) of older adults with insomnia disorder who participated in the Behavioral Treatment of Insomnia in Aging study (n = 17) and older adults without insomnia disorder who participated in the Sleep Health and Aging Research (SHARE) study (n = 25) at UCLA.

**Please note that raw data was lost and thus is not included in the records**

first: Joshua

last: Cho


title: Epigenetic dependencies of interferon gamma-induced gene expression [ATAC-Seq]

overall_design: Examination of changes in chromatin accessability by ATAC-seq following stimulation of AT3 cells treated in technical duplicate with interferon gamma (IFNy) alone and in combination with catalytic inhibition of P300/CBP for 3 hours.


title: RNA-seq identifies the gene differential expression after LINC01186 knockdown in hepatocellular carcinoma cell line HepG2

city: Guangzhou

first: Xingyuan

last: Liu

state: Guangdong

address: Guangzhou, Guangdong, China

department: Public Health

institute: Southern Medical University

summary: To figure out the role of long non-coding RNA LINC01186 in HCC and the underlying mechanism, we performed RNA-seq analysis after LINC01186 knockdown by RNA interference in HepG2 cells. Here, we conducted LINC01186 knockdown in 2 HepG2 cells as a parallel experiment and have 2 HepG2 cells treated with siNC as control.

overall_design: Performed LINC01186 knockdown in HepG2 to identify the gene differential expression and find LINC01186 regulated genes.

first: Yi

last: Jin

first: Xiaoting

last: Liang

first: Ke

last: Wang

first: Liang

last: Zhou

first: Fei

last: Zou