title: Regulation of gene expression by the APP family in the adult cerebral cortex

first: Hye Ji

last: Cha

address: 1 Blackfan Circle

institute: Boston Children’s Hospital

summary: Amyloid precursor protein (APP) is associated with both familial and sporadic forms of Alzheimer’s disease. APP has two homologs, amyloid precursor-like protein 1 and 2 (APLP1 and APLP2), and they have functional redundancy. APP intracellular c-terminal domain (AICD), produced by sequential α- or β- and γ-secretase cleavages, is thought to control gene expression, similarly as the ICD of Notch. To investigate the role of APP family in transcriptional regulation, we examined gene expression changes in the cerebral cortex of APP/APLP1/APLP2 conditional triple knockout (cTKO) mice, in which APP family members are selectively inactivated in excitatory neurons of the postnatal forebrain. Of the 12 previously reported AICD target genes, only Nep and Npas4 mRNA levels were significantly reduced in the cerebral cortex of cTKO mice, compared to littermate controls. We further examined global transcriptional changes by RNA-seq and identified 189 and 274 differentially expressed genes in the neocortex and hippocampus, respectively, of cTKO mice relative to controls. Gene Ontology analysis indicated that these genes are involved in a variety of cellular functions, including extracellular organization, learning and memory, and ion channels. Thus, inactivation of APP family alters transcriptional profiles of the cerebral cortex and affects wide-ranging molecular pathways.

overall_design: mRNA expression profiles of control and APP/APLP1/APLP2 triple conditional knockout (cTKO) in the neocortex and hippocampus

first: Jongkyun

last: Kang

first: HyeJi


title: Induction of meiosis by embryonic gonadal somatic cells differentiated from pluripotent stem cells

status: Public on Jan 07 2022

city: Tianjin

first: Linlin

last: Liu

address: Weijin Road 97

country: China

institute: Nankai university

type: Expression profiling by high throughput sequencing

summary: ESCs of bulk RNA-Seq were harvested and total RNA extracted using Qiagen RNeasy Mini kit, according to the manufacturers’ instruction, including a DNAse digestion. Single-cell library was prepared using smart-seq2 or the 10 × Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v2 according to the manufacturer’s instructions.

overall_design: we did at least 2 repeats for each sample, and we use small molecules to get gonadal somatic cells  differentiating from pluripotent stem cells and the gonadal somatic cells can assist the primodial germ cells  starting normal meiosis.

first: Haiying

last: Wang

first: Chang


title: Non-microRNA Binding Competitively Inhibits LIN28 Regulation

city: La Jolla

first: Gene

last: Yeo

state: CA

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

country: USA

institute: UCSD

summary: RNA binding protein (RBP) expression is finite. For RBPs that are vastly outnumbered by their potential target sites, a simple competition for binding can set the magnitude of post-transcriptional control. Here we show that LIN28, best known for its direct regulation of let-7 miRNA biogenesis, is also indirectly regulated by its widespread binding of non-miRNA transcripts. Approximately 99% of LIN28 binding sites are found on non-miRNA transcripts, like protein coding and ribosomal RNAs. These sites are bound specifically and strongly, but they do not appear to mediate direct post-transcriptional regulation. Instead, non-miRNA sites act to sequester LIN28 protein and effectively change its functional availability, thus impeding the regulation of let-7 in cells. Together, these data show that the binding properties of the transcriptome broadly influence the ability of an RBP to mediate changes in RNA metabolism and gene expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of LIN28B binding using enhanced CLIP via 2 biological replicates of RNA fragments derived from LIN28B immunoprecipitation and 2 control input replicates for 4 LIN28B expression conditions in HEK293A (LIN28B_X1, LIN28B_X2, LIN28B_X3, LIN28B_X4). Examination of LIN28B binding using enhanced CLIP via 2 biological replicates of RNA fragments derived from Lin28A immunoprecipitation and 2 control input replicates in mouse ESCs with (HPK_mESCs) and without (V6_5_mESCs) sponge expression. Examination of changes in transcriptome-wide ribosome occupancy in mouse ESCs via total RNA (2 replicates, T) and ribosome-bound RNA (2 replicates, P) for several experimental conditions: (dd-Cit = double Dicer knockout ESCs expressing mock Citrine), (dd-HpK = double Dicer knockout ESCs expressing LIN28 sponge), (V6_5_mock = V6.5 ESCs expressing mock Citrine), (Hpk_mock = V6.5 ESCs expressing LIN28 sponge).

first: Frederick

middle: E

last: Tan

first: Shashank

last: Sathe

first: Emily

middle: C

last: Wheeler

middle: W


title: Raver2 and Setd2 knockdown of mouse mTECs in a 3D orgonatypic co-culture system

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

summary: Aire-sensitive genes escape the inclusion of alternative splicing events that Raver2 and Setd2 promote in mTECs

overall_design: Two shRNAs against Raver2 and Setd2 were cloned into the pLKO.3G vector containing an eGFP cassette (Addgene #14748). Ultra-high titer lentiviruses were produced into HEK293T cells by using the calcium phosphate co-transfection method for each specific subcloned lentiviral pLKO.3G. Primary mouse mTECs (CD45- EpCAM+ Ly51- I-A/E+) were seeded at the top of the 3D organotypic co-culture setup that we prepared in seeding human dermal fibroblasts into a fibrin gel made of fibrinogen, thrombin and aprotinin. The infection was directly performed with the addition of the concentrated shRNA-bearing lentiviruses that we produced against Raver2, Setd2 or the Ctr LacZ. Five days after infection, the fibrin gel was processed to evaluate the impact of Raver2 and Setd2 knockdown on the inclusion of alternative splicing events of Aire-sensitive and neutral genes by RNA-seq. We sorted by flow cytometry DAPI- I-A/E+ GFP+ cells corresponding to viable lentivirus-infected mTECs.

first: Francine

last: Padonou


title: WT and Aire-KO B6 MEChi RNAseq profiling

summary: Aire-sensitive genes exhibit a weak inclusion of alternative splicing events

overall_design: Total RNA isolated by Trizol extraction from MHC-II high mTECs (pool of mice) was used to generate poly-A-selected transcriptome libraries using the TruSeq stranded mRNA library Prep following the manufacturer's protocols. Paired-end (2 × 100 bp) sequencing was performed using the Illumina HiSeq2000 machine.


title: AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: We identified enrichment of a disease-enhancing, proinflammatory subpopulation of microglia in human AD patient brains with the R47H-TREM2 mutation, and uncovered that enhanced Akt signaling in microglia underlies the proinflammatory cytokine state and synaptic toxicity in our R47H-TREM2 tauopathy mouse model.

overall_design: Droplet-based single nuclear RNA sequencing of mouse hippocampus with and without the TREM2-R47H mutation and MK-2206 treatment.

first: Faten

middle: A

last: Sayed

first: Lay

last: Kodama

last: Fan

first: Gillian

middle: K

last: Carling

first: Joe

last: Udeochu

first: David

last: Le

first: Qingyun

last: Li

first: Lu

last: Zhou

first: Man

last: Wong

first: Rose

last: Horowitz

first: Pearly

last: Ye

first: Hansruedi

last: Mathys

first: Minghui

first: Xiang

last: Niu

first: Linas

last: Mazutis

first: Xueqiao

last: Jiang

first: Xueting

first: Fuying

last: Gao

first: Matthew

last: Brendel

first: Maria

last: Telpoukhovskaia

first: Tara

last: Tracy

first: Georgia

last: Frost

first: Yungui

first: Yaqiao

first: Zuolin

last: Cheng

first: Guoqiang

last: Yu

first: John

last: Hardy

first: Giovanni

last: Coppola

first: Shiaoching

last: Gong

first: Fei

first: Michael

last: DeTure

first: Bin

last: Zhang

first: Lei

last: Xie

middle: Q

last: Trajnowski

first: Virginia

middle: M

last: Lee

first: Subhash

last: Sinha

first: Dennis

last: Dickson

first: Wenjie

last: Luo


title: H3K36me3 profiling in mTEClo

first: Matthieu

last: Giraud

type: Genome binding/occupancy profiling by high throughput sequencing

summary: AIRE-sensitive genes are marked with low levels of H3K36me3 in mTEClo

overall_design: Nano-ChIP-seq on H3K36me3 was performed as previously described (Adli and Bernstein, 2011) on 5*10^4 purified mTEClo (EpCAM+ UEA-1+ Ly51lo CD80lo) from individual B6 mice. ChIP-seq libraries were prepared with the TruSeq ChIP Sample Preparation Kit (Illumina) and 2x75-bp paired-end reads were sequenced on an Illumina HiSeq 2000 machine.

first: Magali

last: Irla


title: Transciptional profiling of human mTEChi

overall_design: Thymi from cardiac surgery pediatric patients were minced in 1xPBS to release the thymocytes. Then treated four times with collagenase/dispase (1:200) and DNaseI (1:1000) digestion, and the cell fractions were further dissociated with gentleMACS treatment. All fractions were combined and filtered through the 100μm Falcon cell strainer. The cells were collected by centrifugation, washed, and transferred to Optiprep density gradient. The upper cell layer was combined into one tube, washed, and counted resulting in 0.4-6.5x 10^8 thymic cells. The cell fraction was then depleted with human CD45 beads (100ul beads per 2x10^8 cells; Miltenyi Biotec) using autoMACS. After the CD45 depletion, the cells were sorted with BD FACSAria for mTEC MHChi (CD45- CDR2- EpCAM+ HLA-DRhi) directly into TRIzol (ThermoFisher) solution.

first: Pärt

last: Peterson


title: Tbx-2

city: Oxford

first: Sizhu

last: Lu

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research, Oxford branch

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

overall_design: Refer to individual Series


title: Integrative analysis of the salt stress response in cyanobacteria

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

summary: In many habitats, microorganisms are exposed to high or fluctuating salinities and evolved specific acclimation strategies to thrive in those environments. Euryhaline microorganisms can grow in a broad range of salinities, from low ionic strength like freshwater up to twofold seawater salinities. Here, we analyzed the salt acclimation process of the euryhaline model cyanobacterium Synechocystis sp. PCC 6803 in a multi-omics approach by combining transcriptomic, proteomic and metabolomic analyses. The Overall, the comparison of salt-induced proteome and transcriptome changes revealed a good correleation between the proteome and transcriptome that as most the majority of stably up-regulated proteins also showed elevated mRNA transcript levels. However, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably also involves the action of small regulatory RNAs acting at the post-transcriptional level. In addition to the rapid and stable steady upregulation of compatible solute biochemistry, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably involves the action of small regulatory RNAs. Moreover, the coordinated induction of several stress proteins known to be involved in iron and oxidative stress responses as well as of mechano-sensitive channels was observed. Based on these data, an extended salt stimulon can be defined comprising many proteins directly or indirectly related to compatible solute metabolism, ion and water movements as well as a defined set of small regulatory RNAs. Moreover, the massive accumulation of the compatible solute glucosylglycerol had large impact on the overall carbon and nitrogen metabolism. Our comprehensive data set provides the basis for future attempts to engineer cyanobacterial salt tolerance and to search for processes regulating this important environmental acclimation process.

overall_design: We analyzed gene expression in Synechocystis sp. PCC 6803 WT 0.5, 2 and 24 hours after a shift from 0% NaCl to 4% NaCl. For each sampling point, 2 biological replicates were analyzed.

first: Stefan

last: Mikkat

first: Matthias

last: Riediger

first: Jens

last: Georg

first: Wolfgang

middle: R

last: Hess

first: Martin

last: Hagemann


title: Expression data of LX2 transfected with Adenoviruses overexpressing Gata4 or GFP

city: Seville

first: Anabel

last: Rojas

state: Seville

address: Avda. Américo Vespucio

department: Stem Cell

country: Spain

institute: CABIMER

summary:
Deactivation of aHSCs has emerged as a novel and promising therapeutic approach for liver fibrosis. However, our knowledge of the master regulators involved in the deactivation of fibrotic HSCs is still limited. The transcription factor GATA4 has been previously shown to play an important role in embryonic hepatic stellate cells quiescence. We aim to evaluate whether GATA4 is able to revert the active phenotype of LX2 cells.
Adenoviruses approaches were used to genetically manipulate Gata4 expression in adult hepatic stellate cells. To analyze changes in gene expression mediated by GATA4  we overexpressed Gata4 in  LX2 cells and performed Affimetrix analyses

overall_design: 2 samples per triplicate. GFP as control and G4 as experimental. LX2 were transfected with each adenoviruses at MOI100 and RNA was collected after 72h of transfection


title: Transcriptional repression and apoptosis influence the effect of APOBEC3A/3B functional polymorphisms on biliary tract cancer risk

city: Shanghai

first: Wenbin

last: Liu

address: 800 Xiangyin Rd..

institute: Second Military Medical University

summary: APOBEC3s-related somatic mutations are the predominant burden in biliary tract cancers (BTCs). Here, we reveal the effects and mechanisms of APOBEC3A/3B functional polymorphisms on cholangiocarcinoma and gallbladder cancer (GBC). rs2267401-G at the APOBEC3B promoter decreases cholangiocarcinoma risk but increased GBC risk. rs2267401-G confers a decreased APOBEC3B promoter activity in cholangiocarcinoma cells but an increased activity in GBC cells. rs12157810-C at the APOBEC3A promoter decreases the risk of BTCs. rs12157810-C up-regulated the promoter activity in both cells. APOBEC3A overexpression attenuates cancer evolution via causing apoptosis, in contrast to APOBEC3B. Inflammatory factors promote cancer evolution via interacting with transcriptional repressors regulating the APOBEC3A/3B promoters. ATAC-seq was used to identify the difference between transcriptional networks of cholangiocarcinoma and GBC.

overall_design: 4 Cell lines were involved in the single-cell ATAC-seq analysis: the cholangiocarcinoma cell line RBE, the RBE with stimulation of TNF-a, GBC, and GBC with stimulation of TNF-a

first: Hongxiang

last: Ji

first: Jiahui

last: Song

first: Guangwen

last: Cao


title: Human Embryonic Stem Cell Spheroids exosomal miR-6766-3p alleviate activation of hepatic stellate cells and liver fibrosis by targeting TGFβRII in CCl4-induced liver fibrosis

city: Guangzhou

first: Ning

last: Wang

address: No.382 Waihuan East Road, Guangzhou 510006, P.R. China.

department: School of Biomedical Sciences and Engineering

institute: South China University of Technology

summary: To further explore the gene expression between 2D-hESCs-Exosomes and 3D-hESCs-Exosomes, we have employed MiRNA microarray expression profiling as a discovery platform to identify.

overall_design: To screen and identify the candidate miRNAs in 3D-hESCs-Exosomes that enhanced the antifibrotic efficacy of 2D-hESCs-Exosomes in CCL4-induced fibrosis, a miRNA microarray was used to profile the simultaneously upregulated or downregulated miRNAs between 2D-hESCs-Exosomes and 3D-hESCs-Exosomes.


title: Molecular Determinants of Response to Anti–PD-1 Immunotherapy in Syngeneic Tumor Mouse Models

city: Boston

first: Eric

last: Muise

state: MA

address: 33 Ave. Louis Pasteur

department: GPGX

institute: Merck

summary: Targeting the PD-1/PD-L1 pathway has changed the landscape of cancer immunotherapy, revolutionizing the treatment of many cancers. Somatic tumor mutational burden (TMB) and T-cell–inflamed gene expression profile (GEP) are clinically validated pan-tumor genomic biomarkers that predict responsiveness to anti-PD-1/anti-PD-L1 monotherapy in a variety of tumor types.  Here we analyze the association between these biomarkers and efficacy in 11 commonly used preclinical murine syngeneic models using a rodent surrogate antibody (muDX400) of pembrolizumab, a humanized monoclonal antibody against PD-1. Response to muDX400 treatment was broadly classified in these models into 3 categories: highly responsive, partially responsive, and intrinsically resistant to therapy. Molecular and cellular profiling validated differences in immune-cell infiltration and activation in the tumor microenvironment of muDX400 responsive tumors. Baseline and post-treatment genomic analysis showed an association between murine-GEP and TMB and response to muDX400 treatment. To better understand the limitations, predictive nature and role of these models in guiding treatment options at the bedside, we extended our analysis to investigate a canonical set of cancer and immune biology-related gene expression signatures, including signatures of angiogenesis, monocytic myeloid derived suppressor cell (mMDSC) and stromal/EMT/TGF-β biology   previously shown to have potential negative impact on immunotherapy efficacy in the clinic. Finally, reverse translation studies were performed to evaluate the association between murine-GEP and preclinical efficacy with standard of care and anti-angiogenic combinations with muDX400 which show promising clinical activity. These efforts begin to elucidate which biological mechanisms can and cannot be appropriately and productively tested in these preclinical models to facilitate the development of rational orthogonal combination strategies with checkpoint blockade as well as the evaluation of underlying biological mechanisms associated with response in the clinic

overall_design: Total RNA from tumors from 11 syngeneic mouse models treated with either isotype control mIgG1 or anti-PD1 antibody muDX400 for 8 days, was sequenced.

middle: S

first: Elaine

last: M. Pinheiro


title: Single cell RNA sequencing data of Side Population and Non-Side Population tumor cells from a mouse model of undifferentiated pleomorphic sarcoma

city: Durham

first: Benjamin

last: Alman

state: NC

address: Levine Science Research Center,308 Research Drive

institute: Duke university

summary: We report the application of single-cell RNA sequencing data on Side Population (SP) cells and their Non-Side Population (NSP) counterparts in a mouse model of undifferentiated pleomorphic sarcoma (UPS). SP cells exhibit tumor propagting cell properties characterized by enhanced tumorigenicity and self-renewal potential.  The purpose of this experiment is to investigate cellular heterogeneity at the gene expression level in UPS tumors and lineage relationships between different subpopulation of tumor cells.  We generated the gene expression profiles of individual cells in the SP and NSP compartments of mouse UPS.

overall_design: Mouse UPS tumors are sorted into SP and NSP populations using flow cytometery and the single-cell RNA sequencing is performed for the sorted populations

first: Yuning

middle: J

last: Tang

first: Yu

last: Xiang

first: Yarui

last: Diao


title: Humans PBMCs: Balanced constitution vs. Phlegm-dampness constitution

city: 北京

first: Lidan

last: Dong

state: 北京

address: 北京北三环东路11号

institute: 北京中医药大学

summary: We investigated the expression profiles of lncRNAs and mRNAs in peripheral blood mononuclear cells (PBMCs) from subjects with 13 Phlegm-dampness constitution (PDC) and nine balanced Balanced constitution (BC). The differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified by the “limma” method. Goal was to determine whether long non-coding RNAs (lncRNAs) play a regulatory role in metabolic disease in subjects with PDC.

overall_design: Two-condition experiment, BC vs. PDC. Peripheral blood mononuclear cells (PBMCs). Biological replicates:9 subjects with Balanced constitution (BC), 13 subjects with Phlegm-dampness constitution samples (PDC). This experiment was performed technically as a dual channel. Cy3 is used to the label of the PDC and the BC. Besides, RNA from all samples was as reference_RNA. And Cy5 is used to label the reference_RNA in each chip. Normalized log2 ratio (Cy3/Cy5) representing test/reference.

first: Lingru

last: Li


title: Multiplex 5mC Marker Barcode Counting (MMBC-seq): A sensitive detection method for cell-free DNA methylation

city: CHICAGO

first: JI

last: NIE

state: IL

department: Chemistry

institute: The University of Chicago

type: Methylation profiling by high throughput sequencing

summary: The detection of hypermethylation markers on cell-free DNA (cfDNA) in biological fluids is a promising and non-invasive approach for early diagnosis and monitoring of human diseases. However, it is challenging to detect hypermethylation markers in a high-throughput, sensitive, and cost-effective manner. Here we presented a multiplex 5-methylcytosine marker barcode counting (MMBC-seq) technique and reported its clinical application for cfDNA from peripheral plasma samples. We identified an MMBC cancer detection panel and developed a scoring system to differentiate cancer versus healthy controls. In a multiple-cancer case-control study, the panel achieved a sensitivity and specificity of 80.2% and 95.7% respectively (AUC 0.906, 95% CI 0.846-0.948). The results suggest that MMBC-seq has great potential to realize non-invasive, flexible and clinically applicable cancer detection.

overall_design: A total of 58 healthy individuals, 121 cancer patients, 19 patients with benign disease from China.

first: Chuan

last: He

first: Ji

last: Nie


title: XIST modulates mammary stem cell homeostasis and tumor fate II

status: Public on Jan 06 2022

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

institute: Institut Curie


title: XIST modulates mammary stem cell homeostasis and tumor fate [WT and KO RNA-seq]

summary: Disruption of XIST expression in mammary epithelial cells leads to chromatin changes on the inactive X chromosome, transcriptional reactivation of X-linked genes, and defective luminal differentiation.

overall_design: Cells from both luminal (ML) and mammary stem cell (MaSC) compartments were isolated from wild-type (WT) and XIST-KO HMLE (Human Mammary Epithelial cells) by FACS sorting based on their positivity for the cell surface antigen ESA (Epithelial Specific Antigen) (ML: ESA+; MaSC: ESA-). Three replicates were generated per compartment and genotype. Total RNA was isolated and sequenced to perform gene expression and allele-specific analyses.

first: L

first: M

middle: L

last: Picod

first: E

last: Charafe

last: Heard

first: R

last: Margueron

first: C

last: Ginestier


title: Liver transcriptome analysis of mice with ASirs2 suppression

city: Tokyo

first: Motoharu

last: Awazawa

address: 1-21-1 Toyama, Shinjuku

country: Japan

institute: National Institute for Global Health and Medicine

summary:
Purpose: We show that the Irs2 locus, a critical regulator of insulin actions, encodes an antisense transcript ASIrs2, whose expression increased  after refeeding in liver, reciprocally to that of Irs2. In order to elucidate the functions of ASIrs2, the liver transcriptome was analyzed under ASIrs2 suppression in wild type mice after refeeding.
Methods:  C57BL/6 mice were injected with AAV encoding shRNA for ASIrs2 via the via tail vein at 8 weeks of age, and the mice were sacrificed for organ collection after overnight fasting and subsequently 6 hours of refeeding on the 27th or 28th day after AAV injection.

overall_design: Liver mRNA profiles of wild type mice after refeeding under ASirs2 suppression.

first: Maya

last: Matsushita

first: Masafumi

last: Muratani

first: Kohjiroi

last: Ueki


title: CGGBP1-dependent CTCF-binding sites restrict ectopic transcription

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

summary: CGGBP1-dependent CTCF-binding sites identified in Patel et. al. 2019 [PMID 31547883] serve as barrier elements consistent with asymmetrical levels of H3K9me3 in the flanks and asymmetrical RNA levels at these sites in the genome. In this study we have characterised the function of such CGGBP1-depenedent CTCF binding sites which are usually repeat rich in nature. By cloning one such CTCF-binding site in an episomal system, we have studied the barrier activity of this CGGBP1-dependent CTCF-binding sites in the prsesnce and absence of CGGBP1 in HEK293T cells through various molecular assays and RNA-sequencing. Our results show that these sites act as barrier for the ectopic transcription as the depletion of CGGBP1 lead to starnd-specific bidirectional transcription as a result of loss of barrier activity concomitant with the loss of CTCF-binding. Further, analysing the RNA-seq revealed that weakly transcribed sites are flanked by the CTCF-binding at transcription start and end sites in the presence of CGGBP1. However, CGGBP1 depletion leads to loss of barrier activity maintained by CGGBP1 with dispersed CTCF binding and a loss of transcription restriction. Such CGGBP1-dependent CTCF-binding sites prevents ectopic transcription.

overall_design: RNA sequencing was done to identify the trancripts regulated by CGGBP1-dependent CTCF-binding sites in HEK293T CT and KD cells. Briefly, RNA isolated from the cells was subjected to polyA-tailing and ribo-depletion followed by sequencing.

first: Divyesh

last: Patel

first: Manthan

first: Subhamoy

last: Datta


title: Transcriptome analysis of multiple obese mouse models to identify commonly unregulated genes in liver

summary:
Purpose: RNAseq analyses were conducted to screen for the genes undergoing transcriptional changes either in the liver of high-fat-diet (HFD)-induced obese mice or in the liver of Lepr-deficient db/db mice compared to the livers of the respective control mice
Methods:  C57BL/6 wild-type male mice were fed on high-fat diet (HFD) or a low-fat diet (NCD) for 18 weeks starting from 6 weeks of age, and the livers were collected at 24 weeks of age at ad libitum-fed condition.Misty/misty or db/db were sacrificed at ad libitum-fed condition at 10weeks and the liver was collected.
Results: 2079 genes and 1085 genes were identified in high-fat-diet fed mice and db/db mice, respectively.

overall_design: Liver mRNA profiles of obese mouse moldels.


title: Tissue-resident FOLR2+ macrophages associate with tumor-infiltrating CD8+ T cells and with increased survival of breast cancer patients

first: Julie

last: HELFT

state: Ile-de-France

address: 26 Rue d'Ulm

department: U932 - Immunity and Cancer

summary: Macrophage infiltration is a hallmark of solid cancers and overall macrophage infiltration correlates with lower patient survival and resistance to therapy. Tumor- associated macrophages, however, are phenotypically and functionally heterogeneous. Specific subsets of tumor-associated macrophage might be endowed with antagonistic roles on cancer progression and on the development of anti-tumor immunity. Here, we identify a discrete population of FOLR2 + tissue-resident macrophages in healthy mammary gland and breast cancer primary tumors. FOLR2 + macrophages localize in perivascular areas in the tumor stroma, where they interact with CD8 + T cells. Moreover, FOLR2 + macrophages efficiently prime effector CD8 + T cells ex vivo . The density of FOLR2 + macrophages in tumors positively correlates with better patient survival. This study highlights antagonistic roles for tumor-associated macrophage subsets and paves the way for subset-specific therapeutic interventions in macrophages-based cancer therapies.

overall_design: Tumor infiltrating myeloid cells were isolated from human and murine breast tumors for single cell RNA-seq or bulk RNA-seq analysis

last: Helft

first: Rodrigo

middle: N

last: Ramos

first: Yoann

last: Missolo-Koussou


title: XIST modulates mammary stem cell homeostasis and tumor fate [CHIP-seq]

first: Laia

last: Richart

overall_design: Mammary stem cells (MaSC) were isolated from wild-type and XIST-KO HMLE (Human Mammary Epithelial cells) by FACS sorting based on their positivity for the cell surface antigen EpCAM (ESA) (MaSC: ESA-). Two replicates were generated per genotype. Cells were processed for ChIP-Seq against MED1.


title: Microarray analysis of lncRNA and mRNA expression profiles in sinonasal inverted papilloma

status: Public on Jan 05 2022

city: Hangzhou

first: Yaoshu

last: Teng

state: China

address: No. 261, Huansha Road

institute: Hangzhou First People' Hospital

summary: To explore the expression profile, potential functions, and diagnostic and clinicopathological significance of lncRNAs in sinonasal inverted papilloma (SNIP).The expression profiles of lncRNAs and mRNAs were analyzed using a microarray. The potential functions and clinical implications of specific lncRNAs were further analyzed by bioinformatics and statistical methods.

overall_design: SNIP tissue samples were obtained from 4 patients with SNIP.The diagnosis of SNIP was confirmed by histopathological examination.A total of 12 patients with only nasal septum deviation were selected to provide nasal mucosal tissue samples as the control group.


title: Time series data of chromatin and transcription throughout the cell cycle

first: Yulong

last: Li

address: 208 Research Dr

institute: Duke University

summary: The occupancy states of DNA-binding nucleosomes and subnucleosome-sized proteins (e.g.  transcription factors, replication proteins, etc.) determine the chromatin accessibility landscape and provide additional regulatory context for DNA-templated processes including transcription and DNA replication. Throughout the mitotic cell division cycles, the transcriptome undergoes periodic reprogramming along with replication- and mitosis-induced global chromatin reconfiguration; however, profiling of the cell cycle-specific chromatin dynamics and understandings of its regulatory mechanisms remain limited. Here we employed high-resolution MNase-seq to factor-agnostically map the genome-wide chromatin occupancy with synchronized Saccharomyces cerevisiae cell populations, in parallel with transcriptome profiling by RNA-seq. Throughout the cell cycles, the occupancy of gene-body nucleosomes and promoter subnucleosomes (presumably TFs and polymerase) exhibit both transcription- dependent and independent periodicity, suggesting a decoupling between transcription and chromatin occupancy dynamics. The “phased” positioning of nucleosomes within gene bodies, however, is pervasively disorganized by replication fork progression, and also regulated by the intensity and cell cycle phase of transcriptional activation. Finally, we profiled the chromatin organization around replication origins throughout the complete cell cycle and revealed the chromatin context for origin efficiency.

overall_design: Time course of yeast released from α-factor and collected every 10 min from T=0 min (prior to release) to 150 min (Replicate 1) or 140 min (Replicate 2) post release. Because the recovery time from α-factor arrest for Replicate 1 is about one time point longer than Replicate 2, T=10 min for Replicate 1 is discarded and all later time points are shifted one time point earlier when  aligning the cell cycle timeline with Replicate 2.  Two biological replicates are conducted which include 30 samples of MNase chromatin and 29 samples of RNA (T=110 min for Replicate 2 is of bad quality and discarded).

first: David

last: MacAlpine

first: Alexander

last: Hartemink


title: Single Cell RNA Sequencing Reveals a Unique Monocyte Population in Bronchoalveolar Lavage Cells of Mice Challenged with Afghanistan Particulate Matter and Allergen

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Upon returning from deployment to Afghanistan, increasing numbers of United States service personnel are reporting symptoms consistent with an asthma-like airways disease, thought to be caused by prolonged inhalation of toxic desert particulate matter. Deployment Related Lung Disease (DRLD) symptoms persist in the post-deployment setting, where soldiers are then exposed to common household allergens. The goal of this study was to define the transcriptomic responses of leukocytes found in the airway lumen and airspace in a post-deployment setting, mimicked by inhalation of Afghanistan desert particulate matter (APM) and subsequent challenge with house dust mite (HDM) in mice. C57BL/6 mice (n=15/group) were exposed to filtered air or aerosolized APM for 6 hours per day for 12 consecutive days using a whole body exposure system, followed by intranasal PBS or HDM allergen challenges. One day after the last HDM challenge, mice were euthanized to collect bronchoalveolar lavage (BAL) cells for single cell RNA sequencing (scRNAseq) using the 10x Genomics Platform and assessment of inflammation and airway hyperresponsiveness (AHR). Unsupervised clustering of BAL cell scRNAseq data revealed a unique monocyte population induced only by both APM and allergen treatments. This population of monocytes is characterized by expression of genes involved in allergic asthma, including ALOX15, which is involved in airway obstruction and promoting the inflammatory response. We validated ALOX15 expression in monocytes via immunohistochemistry and immunofluorescence staining of lung tissue. APM pre-exposure, followed by HDM challenge lead to significantly increased total respiratory system resistance compared to filtered air controls. Using this post-deployment mimic in mice, we demonstrated that inhalation of desert PM while on deployment to Afghanistan may prime airways to be more responsive to allergen exposure after returning home. DRLD symptoms in post deployment setting may involve induction of a unique lung monocyte population that has the ability to regulate AHR and inflammation, possibly through increased expression of ALOX15.

overall_design: Single cell RNA-Seq of BAL fluid from mice stimulated with various allergens

first: Harry

last: Smith

first: Reena

last: Berman

first: Hong

last: Chu

first: Brian

last: Day


title: Changes in DNA methylation during pregnancy and after delivery

city: Taipei City

first: Shin-yu

last: Lin

state: Taipei

address: Zhongzheng Dist.

country: Taiwan

institute: National Taiwan University Hospital

type: Methylation profiling by genome tiling array

summary: Peripheral whole blood DNA methylation profiles of pregnant women with normal pregnancy from the 10th-14th weeks of gestation (average at the 10th week), 24th-28th weeks of gestation (average at the 25th week), 38th-40th weeks of gestation (average at the 38th week) and after delivery status (average at the 10th month after delivery)

overall_design: Comparing the  dynamic changes in whole blood DNA methylation from the four pregnany status of 10 mothers with normal pregnancies.

first: Ming-Wei

first: Mong-Hsun

last: Tsai

first: Ching-Yu

last: Shih

first: Yi-Yun

last: Tai

first: Chien-Nan

last: Lee

first: Shin-Yu


title: Gene expression signatures after immunisation with Boostrix - alum adsorbed tetanus toxoid, reduced diphtheria toxoid and acellular pertussis vaccine (BIOVACSAFE protocol 305D2)

city: London

last: Lewis

address: Du Cane Road

department: ICRF

institute: Imperial College London

summary: The time course of whole blood gene expression was determined in healthy adult human participants who were randomised to receive either a single intramuscular immunisation with Boostrix vaccine (characteristics: treatment = BOOSTRIX) or equivalent volume saline control (characteristics: treatment = PLACEBOD2). Participants are identified who reported having had an immunisation with Boostrix within the past 5 years (characteristics: recent boostrix = 1).

overall_design: Participants attended a single outpatient unit (CEVAC, Gent, Belgium). Pre-immunisation baseline samples were drawn on day 0, and further samples collected on days 1, 7 and 28. Half the participants were allocated to also attend on day 2 whereas the other half attended on day 3 instead. All samples were collected into PaxGene tubes. Immunisations were given on day 0 after baseline blood draw.

first: January

last: Weiner

first: Jeroen

last: Maertzdorf


title: Transcriptome sequencing of bristol strain (wild-type), metl-9 KO strain and metl-9 mutation strain upon P.aeruginosa infection

city: Beijing

first: Guan

last: Jialiang

state: Beijing

address: China, Beijing, Haidian district, Peking University, 1000871

institute: Peking University

summary: We challenge bristol strain (wild-type), metl-9 KO strain (short as KO, has a 101bp insertion, leads to a truncated protein of 258aa) and metl-9 catalytic-activity mutated strain (short as mut, has N172K, D274G mutations in full-length protein) with P.aeruginosa (P.A14), and observe a discrepant transcriptome pattern between wild-type and KO/mut strains. Plenty of innate immune response genes show different expression patterns upon P.A14 infection between the wild-type strain and KO/mut strain. It indicates the important role of metl-9 and 6mA in worm innate immune response modulation.

overall_design: RNA-seq of wild-type, KO or mut strain upon P.A14 infection, or normal condition (OP50).

first: Chengchuan

last: Ma

first: Jialiang

last: Guan

first: Wanqiu

last: Ding

first: Chuanyun


title: Profiling of DHOK targets through transcriptome sequencing

first: Yuhan

last: Shu

address: Ling Yin Street, Road 38 West Lake District

institute: Zhejiang University

summary: DHOK (14,15β-dihydroxyklaineanone) is a novel diterpene isolated from roots of Eurycoma longifolia Jack, a traditional herb widely applied in Southeast Asia. It is reported that DHOK has cytotoxic effect on cancer cells, but its anti-cancer mechanism has still been not clear. To elucidate the anti-cancer mechanism of DHOK, we used transcriptome sequencing (RNA-seq) to identify cancer-associated gene signatures in human CRC cells treated with DHOK. The differential expression of genes in SW620 cells treated with or without DHOK (12.5 μM, 24 h) was significant. Compared with the control, there were totally 4083 genes with their expression levels significantly altered following DHOK treatment. Among these differentially expressed genes, 2857 genes were downregulated and 1226 genes were upregulated. Subsequently, we performed GO (gene ontology) analysis of DHOK targets. It was shown that the distribution of these targets was in different parts of the cell, and especially in the nucleus, cytoplasm, mitochondria, lysosome, endoplasmic reticulum, Golgi apparatus etc.To understand the inhibitory effect of DHOK on human CRC cells, the differentially expressed genes identified were subjected to functional enrichment analysis. The significantly enriched GO terms were mainly associated with autophagy, including autophagosome formation, lysosomal transport, mitophagy, regulation of autophagy, metabolic stress etc. KEGG (kyoto encyclopedia of genes and genomes) analysis showed that the targets of DHOK participated in various signaling pathways, including VEGF (vascular endothelial growth factor), mTOR, P53, TNF-α (tumor necrosis factor), MAPK (mitogen activated protein kinase), Ras, Wnt, FoxO (forkhead box) etc.

overall_design: Examination of a compound on cell transcriptome.

first: Jianbin

last: Zhang


title: RNA-seq for dual BET/p300 inhibitors in pancreactic cancer cells

city: Chicago

first: Rui

last: Xiong

address: 833 S Wood St, room 335

institute: University of Illinois at Chicago

summary:
The goals of this study are to compare transcriptome profiling (RNA-seq) of seletive BET inhibitior, combiantion of BET and p300 inhibitor, and dual BET/p300 inhibitor in pancreatic cancer model (PANC1 cells) and study the anticancer mechanism.
Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the human genome (build hg38) using Burrows Wheeler Aligner- Maximum Exact Match (BWA MEM) algorithm. The raw count for each gene was quantified using the general purpose read summarization function, featureCounts gainst ENSEMBL genes. Differential analysis was performed using edgeR, including a batch effect correction for batch effects. Geneset enrichment analysis based on the differential analysis idenfied few essential pathways that was the mechansim of action, including KRAS, TGFb, etc.

overall_design: Retinal mRNA profiles of 21-day old wild type (WT) and Nrl-/- mice

first: Danny

last: Principe

first: Fei

last: Huang

first: Gregory

last: Thatcher

first: Ajay

last: Rana


title: Genome-wide Analysis of Smad7-Mediated Transcription in Mouse Embryonic Stem Cells [RNA-Seq]

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

summary: Smad7 has been identified as a negative regulator of the transforming growth factor TGF-β pathway by direct interaction with the TGF-β type I receptor (TβR-I).  Although Smad7 has also been shown to play TGF-β unrelated functions in the cytoplasm and in the nucleus, a comprehensive analysis of its nuclear function has not yet been performed. Here we show that in ESCs Smad7 is mainly nuclear and acts as a general transcription factor regulating a number of genes unrelated to the TGF-β pathway. Loss of Smad7 results in the downregulation of several key stemness master regulators, including Pou5f1 and Zfp42, and in the upregulation of developmental genes, with consequent loss of the stem phenotype. Integrative analysis of genome-wide mapping data for Smad7 and ESC self-renewal and pluripotency transcriptional regulators revealed that Smad7 co-occupies promoters of highly expressed key stemness regulators genes, by binding to a specific consensus response element NCGGAAMM. Altogether, our data establishes Smad7 as new integral component of the regulatory circuitry that controls ESC identity.

overall_design: RNA-seq transcriptome profiling of Control and Smad7 silenced mouse Embryonic Stem Cells (ESC). 8 samples, 2 different shRNAs were used for the knockdown of Smad7, 2 biological replicates for each condition.

first: Guohua

last: Meng

first: Mara

last: Maldotti

first: Francesca

last: Anselmi

first: Isabelle

last: Polignano

first: Stefania

last: Rapelli

first: Daniela

last: Donna

first: Salvatore

last: Oliviero


title: Genome-wide Analysis of Smad7-Mediated Transcription in Mouse Embryonic Stem Cells

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

overall_design: Refer to individual Series


title: RNA-sequencing of epicardial adipose tissue of heart failure patients with preserved ejection fraction

first: Shan

last: He

address: Jingyuan Road No.5

institute: Beijing Chaoyang Hospital Jingxi Branch

type: Non-coding RNA profiling by high throughput sequencing

summary: Recent studies have suggested that epicardial adipose tissue (EAT) play an important role in the pathogenesis of heart failure with preserved ejection fraction (HFpEF), but few have characterized the underlying mechanism between their interactions. Recent evidence suggested that molecules secreted from EAT, including exosomes carrying non-coding RNAs (ncRNAs), may participate in the development of HFpEF. The aim of the present study was to investigate the expression profile of mRNAs and ncRNAs in EAT with HFpEF.

overall_design: Epicardial adipose samples collected from patients with HFpEF (n=5) and without heart failure (n=5) were profiled using RNA-sequencing on Illumina Hiseq 6000.

first: Huagang

last: Zhu

first: Lei

last: Zhao

first: Xinchun

last: Yang


title: The histone H3 K4me3, K27me3 and K27ac genome-wide dis-tributions are differently influenced by sex in brain cortexes and gastrocnemius of the Alzheimer’s disease PSAPP mouse model

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

institute: UNIVERSITA' DI PADOVA

summary: Background: Women represent the majority of Alzheimer’s disease patients and show typical symptoms. Genetic, hormonal and behavioral mechanisms have been proposed to explain gender differences in dementia prevalence. Whether sex differences exist in the epigenetic landscape of neuronal tissue during the progression of the disease is unknown. Methods: To investigate the differences of histone H3 modifications important for transcription we determined the ge-nome-wide profiles in K4me3, K27ac and K27me3 from brain cortexes of an Alzheimer mouse model (PSAPP). Gastrocnemius muscles were also tested since they are known to be different in the two sexes and are affected during the disease progression. Results: Correlation analysis dis-tinguished the samples based on sex for H3K4me3 and H3K27met3 but not for H3K27ac. The analysis of TSS signal distribution and of bounding sites revealed that the epigenetic landscape of gastrocnemius is more influenced than brain by sex, with the exception of H3K27me3 distribution on the X chromosome which showed sex-related differences in promoters belonging to behavior and cellular/ neuronal spheres in mice cortexes. Conclusions: The epigenetic landscape is slightly affected by sex in brain, with the exception of H3K27me3. On the other hand, a higher number of differences can be found in gastrocnemius.

overall_design: Exanation of H3K4me3 and H3K27met3 and H3K27ac profiles in brain cortexes and gastrocnemius muscles of an Alzheimer mouse model (PSAPP)

first: Casciaro

last: Francesca

first: Persico

last: Giuseppe

first: Rusin

last: Martina

first: Amatori

last: Stefano

first: Montgomery

last: Claire

first: Rutkowsky

last: Jennifer M.

first: Ramsey

last: Jon

first: Fanelli

last: Mirco

first: Giorgio

last: Marco


title: Genome-wide Analysis of Smad7-Mediated Transcription in Mouse Embryonic Stem Cells [ChIP-Seq]

first: Andrea

last: Lauria

overall_design: ChIP-seq profiling of Bio-Smad7 in mouse Embryonic Stem Cells (ESC). 3 samples, 2 ChIP and 1 Mock as control.

first: Guohua

last: Meng

first: Mara

last: Maldotti

first: Francesca

last: Anselmi

first: Isabelle

last: Polignano

first: Stefania

last: Rapelli


title: Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Phaseolus vulgaris L.

city: Harbin city

first: mengdi

last: li

state: Heilongjiang Province, China

address: Heilongjiang University, Nangang District, Harbin city, Heilongjiang Province

institute: Heilongjiang University

summary: Cold tolerance of crop plants influences survival and productivity under low-temperature conditions. Elucidation of molecular mechanisms underlying low temperature tolerance could be helpful in breeding.  In this study, based on transcriptome and metabolomic analysis, we successfully identified a number of candidate genes and metabolites involved in key biological pathways during cold stress response. During cold stress, a total of 22335 differentially expressed genes were detected in each group (093Cvs120C, 093Tvs120T, 093Cvs093T, 120Cvs120T), of which 12978 were up-regulated and 9357 were down-regulated. A total of 18,166 metabolites were detected and 7,670 metabolites were annotated, among which 654 were secondary metabolites with significant differences. Under cold stress, the petC gene in both common bean cultivars was down-regulated, which led to the decrease of photosynthetic efficiency. Transcriptome and metabolome results under cold stress showed that the synthesis pathways of various unsaturated fatty acids including alpha-linolenic acid were significantly up-regulated and their contents were enriched. In addition, leukotriene-A4 hydrolase in the catabolic pathway of 120 arachidonic acid was inhibited under cold stress. Furthermore, the content of arachidonic acid was increased. A variety of amino acids in both 093 and 120 were enriched under cold stress, which was beneficial to the resistance of bean to osmotic stress caused by cold stress. However, in addition to a few amino acids that were enriched together, 093 was mainly positively charged and 120 was negatively charged among the amino acids that were enriched differently. This is an interesting phenomenon that needs to be further studied. In addition, under cold stress, we found that genes in multiple metabolic pathways, including ABA, GA, JA and other hormone metabolism pathways, were differentially expressed in 093 and 120.

overall_design: Transcriptome analysis was conducted on cold-tolerant common bean variety 120 and cold-sensitive common bean variety 093. 120C and 093C were the control group under non-cold stress, and 120T and 093T were the 4℃ cold stress groups. The specific test conditions are：Sow the seeds in a pot with an inner diameter of 10cm. Sow 6 pots for each variety, one treatment for each 3 pots, and 4 seeds for each pot. After sowing, place the seeds on the culture rack (12h light and 12h darkness every day) for culture. The cold treatment group was then moved to an incubator at 4 °C (12h daily light, 12h dark) for a period of 3 days. The true leaves of the plants were selected for sampling. All leaf samples were immediately frozen in liquid nitrogen and stored at -80°C.

first: Mengdi

last: Li

first: Xiaoxu

last: Yang

first: Guojun

last: Feng

first: Dajun

last: Liu


title: GPTransformer: A transformer-based deep learning method for predicting Fusarium related traits in barley.

city: Brandon

first: James

middle: Raymond

last: Tucker

state: MB

address: 2701 Grand Valley Rd.

country: Canada

institute: Agriculture and Agri-Food Canada

summary:
Fusarium head blight (FHB) incited by Fusarium graminearum Schwabe is a devastating disease of barley and other cereal crops worldwide. Fusarium head blight is associated with trichothecene mycotoxins such as deoxynivalenol (DON), where contaminated grains are unfit for malting or animal feed industries. While genetically resistant cultivars offer the best economic and environmentally responsible means to mitigate disease, parent lines with adequate resistance are limited in barley. Resistancebreeding based upon quantitative genetic gains has been slow to date, due to intensive labour requirements of disease nurseries. The development of high throughput genome-wide molecular markers, allow application in genomic prediction models. A diverse genomic panel consisting of 400 two-row spring barley lines was assembled to focus on Canadian barley breeding programs. The panel was evaluated for FHB and DON content in three environments and over two years. Moreover, it was genotyped using an Illumina Infinium HTS iSelect custom beadchip array of single nucleotide polymorphic molecular markers (50K SNP), where over 23K molecular markers were polymorphic. Genomic prediction has been successfully demonstrated for reducing FHB and DON content in cereals using various statistically-based models of different underlying assumptions. Herein, we have studied an alternative method basedon machine learning and compare it with a statistical approach. Two encoding techniques were utilized (categorical or Hardy-Weinberg frequencies), followed by selecting essential genomic markers for phenotype prediction. Subsequently, we applied a transformer-based deep learning algorithm to predict FHB and DON. Apart from the transformer method, we also implemented a Residual Fully Connected Neural Network (RFCNN). Pearson correlation coefficients were calculated to compare true vs. predicted outputs. Under most model scenarios, the use of all markers vs. selected markers marginally improved prediction performance except for RFCNN method for FHB (27.6%). Hardy-Weinberg encoding generally improved correlation for FHB (6.9%) and DON (9.6%) for transformer. This study suggests the potential of the transformer based method for genomic prediction of complex traits such as FHB or DON, having performed better or equally compared with existing machine learning and statistical method.
To genomic prediction in barley for Fusarium head blight and deoxynivalenol content using a custom Illumina Infinium array (BarleySNP50-JHI) (www.illumina.com). Sample types included leaves from 400 barley genotypes mostly of Canadian origin. This series includes 400 genotypes assayed on an Illumina infinium HTS platform 50K BeadChip.

overall_design: 400 samples of barley genotypes were evaluated

first: Sheikh

last: Jubair


title: Effect of NAM on the TGFβ1-induced hESC-derived corneal endothelial progenitor cells

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

summary: To further explore the effect of NAM on the TGFβ1-induced hESC-derived corneal endothelial progenitor cells, we have employed whole RNA microarray expression profiling as a discovery platform to identify genes and mechanism of NAM on the EnMT and senescence. hESC-derived endothelial progenotors were culured under 30ng/ml TGFβ1 with or without 50 mM NAM. The cultures were incubated for 72 hours at 37 ºC in a humidified incubator with 5% CO2.

overall_design: hESC-derived endothelial progenitors were cultured under 30ng/ml TGFβ1 with or without 50 mM NAM for 72 hours. Three independent experiments were performed.

first: Zongyi

first: Weiyun

last: Shi


title: Long-Term Consumption Of Poultry Egg Products Provided Stable Growth Demographics, Body Composition, Glucose Control, And Liver Gene Expression In The Zebrafish Danio rerio

city: Birmingham

first: Melissa

last: Harris

state: AL

address: 1300 University Blvd, CH464

department: Biology

institute: University of Alabama at Birmingham

summary: Background: Poultry eggs are a low cost, high protein nutrient package that can be consumed as part of a quality diet. However, consumption of poultry egg products has been historically contentious, which highlights the importance of investigating impacts of long-term egg consumption on metabolic health. Objective: Our study utilized the zebrafish Danio rerio, a newly-defined model of human metabolic health, to understand the metabolic consequence of consuming egg products in lieu of other well-described protein sources. Methods: Reference diets were formulated to contain multi-source protein with casein and fish protein hydrolysate (CON; control protein sources), the protein sources of which have been vetted in numerous reference diets. These proteins were then replaced in part with either whole egg (WE; protein and lipid source), egg white (EW; protein source), wheat gluten (WG; cereal protein source), or a high lipid content diet containing a multi-source protein with casein and fish protein hydrolysate (HFCON; isonitrogenous and isolipidic with the WE diet) in a 34-week trial. Daily feeding was initiated at early juvenile life stage and terminated at late reproductive adult stage. Results: The amino acid composition of control vs egg product diets did not vary substantially, although methionine and lysine were apparently limiting in fish fed WG. At termination, fish fed EW as the protein source had similar weight gain and body composition to those fed the CON diet. Blood glucose, both fasting and postprandial, did not differ among any dietary treatment. Assessment of the liver transcriptome using RNAseq revealed no differential gene expression between zebrafish fed CON or WE diets. Zebrafish fed WG had lower weight gain in males. Conclusions: Long-term consumption of egg products promoted metabolic health equal to that of historically-relevant proteins. These data support the value of egg products for maintaining long-term metabolic health in animal diets.

overall_design: Zebrafish housed in standard conditions were fed either a control diet or a whole egg-based diet starting at 21 days of age and continuing to 36 weeks of age. At 36 weeks, the livers from these fish were harvested for RNA sequencing.

first: Stephen

last: Watts


title: Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System

city: Albany

first: Ben

middle: Gregory

last: Szaro

state: NY

address: 1400 Washington Avenue

department: Biological Sciences

institute: University at Albany, SUNY


title: Gasdermin D inhibition confers antineutrophil mediated cardioprotection in acute myocardial infarction

city: Shanghai

first: Yaozu

last: Xiang

address: 1239 Siping Road, Yangpu District

institute: Tongji University

summary: Acute myocardial infarction (AMI) induces blood leukocytosis, which correlates inversely with patient survival. The molecular mechanisms leading to leukocytosis, and recruitment to the infarcted heart, remain poorly understood. Using an AMI mouse model, gasdermin D (GSDMD) was identified in activated neutrophils early in AMI. We demonstrated that GSDMD is required for enhanced recruitment of neutrophils and monocytes to the infarcted heart. Loss of GSDMD resulted in reduced release of IL-1β from neutrophils and reduced recruitment of neutrophils and monocytes to the infarcted heart. Knockout of GSDMD in mice significantly reduced infarct size, improved cardiac function and increased survival post AMI. Through a series of bone marrow transplantation studies and leukocytes depletion experiments, we further demonstrated that excessive bone marrow derived and GSDMD-dependent neutrophil recruitment, contributes to the detrimental immunopathology after AMI. Pharmacological inhibition of GSDMD also conferred cardioprotection post AMI, through reduction of scar size and enhancement of heart function. Our study provides new mechanistic insights into molecular regulation of neutrophil generation and recruitment after AMI, and supports GSDMD as a new target for improved ventricular remodeling and reduced heart failure after AMI.

overall_design: Heart mRNA profiles of 12 samples including post AMI (Day1), AMI (Day7) and Sham

first: Kai

last: Jiang

first: Feng

last: Chen

first: Yue

last: Xu

first: Dandan

last: Wang


title: Salivary ZG16B expression loss marks onset of oral Chronic Graft-Versus-Host Disease and exocrine gland dysfunction

city: Bethesda

first: Jacqueline

middle: W.

last: Mays

state: MD

address: 30 Convent Dr, Room 303

institute: NIDCR, NIH

summary: Chronic graft-versus-host disease (cGVHD) targets include the oral mucosa and salivary glands after allogeneic hematopoietic stem cell transplant (HSCT). Without incisional biopsy, no diagnostic test exists to confirm oral cGVHD. Consequently, therapy is often withheld until severe manifestations develop. This proteomic study examined saliva and human salivary gland for a biomarker profile at first onset of oral cGVHD prior to initiation of topical steroid therapy. Whole saliva collected at onset of biopsy-proven oral GVHD was assessed using liquid chromatography coupled tandem mass spectrometry with identification of 569 proteins, of which 77 significantly changed in abundance. ZG16B, a secretory lectin protein, was reduced 2-fold in oral cGVHD saliva (p < 0.05), and significantly decreased in salivary gland secretory cells affected by cGVHD. Single-cell RNAseq analysis of healthy MSG localized ZG16B expression to two discreet acinar cell populations. Reduced expression of ZG16B may indicate specific cGVHD activity, general salivary gland dysfunction.

overall_design: In this study, we used whole saliva to search for salivary biomarkers of oral cGVHD at disease onset and prior to initiation of topical steroid therapy.

first: Ana

last: Costa da Silva

first: Joshua

last: Dodge

first: Marit

middle: H

last: Aure

first: Daniel

last: Martin

first: Susan

last: Dhamala

first: Monica

last: Cho

first: Jeremy

last: Rose

first: Carol

last: Bassim

first: Kiran

last: Ambatipudi

first: Frances

middle: T

last: Hakim

first: Steven

middle: Z

last: Pavletic


title: Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System assayed by 5hmC MeDIP and by ChIP-seq for Histone Markers

first: Ben

last: Szaro

summary: Xenopus is uniquely suited for identifying core features of successful CNS axon regeneration, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. To aid in the interpretation of  bisulfite whole genome methylation sequencing (WGBS) on juvenile frog eye after optic nerve injury,  and on hindbrain samples from tadpole and juvenile frog after spinal cord injury during the peak phase of axon regeneration, we performed ChIP-seq for histone modifications associated with active gene expression (H3K4me3 & H3K27ac) and repressed gene expression (H3K27me3 & H3K9me3) on these same tissues, as well as DNA-immunoprecipitation sequencing (DIP seq) for 5-hydroxymethyl cytosine (5hmC) on eye samples during optic nerve regeneration.

overall_design: Histone ChIP seq: Two biological replicates for each of the tissues and conditions used previously for WGBS (6 pooled eyes after optic nerve crush, from the operated side and contralateral unoperated side, plus 6 pooled eyes from unoperated animals; 5 pooled hindbrains from tadpoles and 5 from frogs subject to spinal cord injury (SCI) plus 5 pooled hindbrains from age-matched, uninjured tadpoles and frogs each. 5hmC DIP seq: performed on eye samples only, otherwise collected as for WGBS and histone ChIP-seq, with replicates (2) pooled for sequencing.

middle: G

first: Sergei

last: Reverdatto

first: Xiang

last: Zhang

first: Morgan

last: Sammons

first: Kurt

last: Gibbs


title: Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate (Xenopus laevis) Central Nervous System Characterized by Whole Genome Bisulfite Sequencing (WGBS)

summary: Xenopus is uniquely suited for identifying core features of successful CNS axon regeneration, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. We performed bisulfite whole genome bisulfite methylation sequencing (WGBS) on juvenile frog eye after optic nerve injury,  and on hindbrain samples from tadpole and juvenile frog after spinal cord injury during the peak phase of axon regeneration, to compare tissue-related and injury-induced differences in DNA methylation among them.

overall_design: Whole Genome Bisulfite Sequencing (WGBS: 15XGenome coverage per sample) was performed on 21 samples (3 biological replicates; 7 tissues/conditions): operated juvenile frog eye and contralateral unoperated eye after optic nerve injury at 11 days post optic nerve crush, plus surgically naïve frog eyes, with 6 pooled eyes for each sample; tadpole hindbrain after spinal cord transection plus age-matched unoperated controls at 7 days post spinal cord transection, with 5 pooled hindbrains for each sample; juvenile frog hindbrain at 7 days after spinal cord transection, plus unoperated hindbrain control, with 5 pooled hindbrains for each sample.

middle: A


title: Single-cell transcriptional analyses reveal tissue-driven segregation of T cell function in secondary antiviral response

city: New York

first: Donna

last: Farber

address: 650 West 168th Street

institute: Columbia University Medical Center

summary: Virus-specific memory T cells generated during primary infection and maintained in tissues and circulation are capable of initiating a quick and robust response upon secondary exposure to viral antigens. To understand the nature of this recall response and the factors that determine antiviral T cell function, we performed single-cell transcriptome profiling of virus-specific CD8+ T cells across diverse tissue sites following stimulation with viral antigens using pooled library amplification for transcriptome expression sequencing (PLATE-seq)(Bush et al., 2017). From this analysis, we found that antigen-responsive cells primarily cluster based on tissue and not virus specificity, with the exception of CMV-specific T cells from the BM. These findings suggest tissue-regulated antiviral T cell function, with specific CMV-driven influences in the BM.

overall_design: Single-cell suspensions from blood, BM, spleen, lung, and LLN from a deceased human donor were stimulated in vitro with either Flu or CMV CD8+ T cell epitopes synthesized in the form of megapools (MPs) that allow simultaneous presentation of a large number of virus-specific epitopes predicted utilizing the Immune Epitope Database and Analysis Resource (IEDB) and bioinformatic approaches. After 24 hr in vitro stimulation with MPs, antigen-responding CD8+ T cells (CD69+ IFN-γ+) were individually sorted into wells of 96-well plates, followed by single-cell RNA sequencing (scRNA-seq) using pooled library amplification for transcriptome expression sequencing (PLATE-seq)(Bush et al., 2017).

first: Maya

last: Poon

first: Eve

last: Byington

first: Yufeng

last: Shen


title: CircRNA sequencing in peripheral blood mononuclear cells from Ankylosing Spondylitis patients and healthy controls

city: Guangzhou

first: Jun

last: Xiao

state: Guangdong

address: Department of Orthopaedic Surgery, Nanfang Hospital, Southern Medical University, No.1838 Guangzhou North Avenue, Baiyun District, Guangzhou, Guangdong Province, P.R.C

department: Department of Orthopaedic Surgery

summary: To identify the expression profiles of circRNAs in peripheral blood mononuclear cells (PBMCs) from Ankylosing Spondylitis (AS) patients and healthy controls, we used circRNA sequencing to detect circRNA in 3 samples of PBMCs from AS patients and 3 samples of PBMCs from healthy controls. In brief, total RNA was extracted and purified using Magen Hipure Total RNA Mini Kit (Magen, Guangzhou, China), followed by constructing RNA sequencing libraries with KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Inc., MA, USA). After the construction of RNA sequencing libraries, Qubit 3.0 fluorometer (Invitrogen, CA, USA) and the Agilent 2100 bioanalyzer (Applied Biosystems, CA, USA) were used for quality control. Then, the PE150 mode of HiSeq X10 (Illumina Inc., CA, USA) was used for sequencing. Differentially expressed circRNAs were screened with criteria of fold-change>1.5 and p<0.05.

overall_design: CircRNAs expression profiles of peripheral blood mononuclear cells (PBMCs) from Ankylosing Spondylitis (AS) patients and healthy controls

first: Chao

first: Minkai

last: Song

first: Jiawen

last: Gao

first: Tao

last: Yan


title: Single-cell RNA sequencing Highlights Cell Diversity in Odontogenic Keratocysts

city: Wuhan

first: qiwen

last: man

state: Hubei

address: Luyu road

institute: wuhan university

summary: Here, we performed single cell RNA sequencing (scRNA-seq) analysis for 14,072 cells from 2 donors with primary OKC and 1 donor with recurrent OKC.

overall_design: Single cell RNA sequencing (scRNA-seq) analysis of odontogenic keratocyst

first: Qi-Wen

last: Man

first: Bing

last: Liu


title: Effect of Titanium Nanoparticles on Differentially Activated Human Primary Macrophages

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: Long term use of titanium implants generates wearing particles off. Titanium nanoparticles (TiNP) favor a pro-inflammatory macrophage polarization (M1) and lower the tolerogenic activation (M2). Our previous Affymetrix data showed that TiNP upregulate GDF15 and downregulate STAB1 expression in macrophages. GDF15 is a cytokine that regulates energy expenditure and fibrosis, and is endocytosed by the scavenger receptor Stabilin-1. Our study aim was to investigate the effect of TiNP on GDF15 and STAB1 expression, on GDF15 secretion and on endocytosis efficiency in macrophages. We used the model system of primary human macrophages derived from CD14+ monocytes. After 6 days of incubation with TiNP, we quantified GDF15 and STAB1 expression, and GDF15 secretion in INF-γ stimulated (M1) and IL-4 stimulated (M2) macrophages using RT-PCR and ELISA, respectively. Flow cytometry assessed the effect of TiNP on endocytosis based on the uptake of fluorescently labelled acLDL, a known ligand of stabilin-1, and MS-1, an antibody directed against the extracellular portion of stabilin-1 in M1 and M2. Our results revealed a strong up-modulating effect of TiNP on GDF15 expression and secretion in all subtypes of macrophages. In contrast, stabilin-1 expression was significantly suppressed by TiNP. acLDL and MS-1 uptake by macrophages was also significantly suppressed under the treatment with TiNP. Our findings highlight a consistent ex vivo stimulatory effect of TiNP on GDF15 production and inhibitory effect on STAB1 expression and Stabilin-1-mediated endocytosis. Our results suggest an important implication of TiNP on macrophage healing functions.

overall_design: 60 samples are analyzed, no duplicates, control are considered the samples without titanium nanoparticles treatment

first: Julia

last: Kzhyshkowska

first: Lina

last: Bermudez

first: Tatyana

last: Sevastyanova


title: Targeting Cytoplasmic SAM by Expressing Slc25a26 Inhibits Protein Synthesis in Cardiac Hypertrophy via SAMTOR/mTOR signaling

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

summary: Excess protein synthesis is the major pathological manifestation of cardiac hypertrophy; however, the underlying mechanism remains elusive. Here we found that a SAM transporter Slc25a26 translocated to mitochondria during cardiac hypertrophy. Silencing Slc25a26 aggravated phenylephrine-induced cardiomyocyte hypertrophy in neonatal rat ventricular myocytes. Transcriptome analysis revealed a specific regulation of ribosome genes by Slc25a26. Puromycin incorporation assay showed a negative regulation of protein synthesis rate by Slc25a26. The translational regulation was independent of ribosome assembly, but abolished by mTOR inhibitor rapamycin. Administration of SAM, or silencing Samtor, reversed the inhibitory impact of Slc25a26 on protein synthesis. AAV9-mediated Slc25a26 overexpression in mouse heart increased the SAM level in mitochondria, but reduced that in nucleus and cytoplasm. Transaortic-constriction-induced hypertrophic pathologies, including pathological gene induction, cardiomyocyte enlargement, myocardial remodeling and heart dysfunction were significantly alleviated by Slc25a26 overexpression. Our data demonstrate a crucial role of subcellular SAM homeostasis in translational control during cardiac hypertrophy.

overall_design: NRVMs were first transfected with siSlc25a26 or siNeg, then treated with PE for 36h after 12h of transfection. NRVMs were used to extracted RNA according to the manufacturer's instructions. Transcriptome sequencing of RNA was completed by Beijing Genomics Institution (BGI). Three independent biological replicate samples were sequenced for each group.

first: Ningning

last: Guo

first: Jian

last: Lv

first: Yingying

first: Shun

first: Shuai

last: Mao

first: Yu

last: Fang

first: Lili

last: Li

first: Gang

last: Wu

first: Jingjing

last: Tong


title: Heterogeneous phenotypes of Pten-null hepatocellular carcinoma in hepatitis B virus transgenic mice parallels liver lobule zonal gene expression patterns

first: Mark

last: Maienschein-Cline

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

summary: Chronic HBV infection is a major cause of hepatocellular carcinoma (HCC) worldwide.  The phenotypes of HCC are diverse, in part, due to mutations in distinct oncogenes and/or tumor suppressor genes.  These genetic drivers of HCC development have generally been considered as major mediators of tumor heterogeneity.  Using the liver-specific Pten-null HBV transgenic mouse model of chronic viral infection, a critical role for liver lobule zone-specific gene expression patterns in determining HCC phenotype is demonstrated.  These observations suggest that the position of the hepatocyte within the liver lobule, and hence its intrinsic gene expression pattern at the time of cellular transformation, make critical contributions to the properties of the resulting liver tumor.  These results may explain why therapies targeting pathways modulated by specific identified tumor driver genes display variable treatment efficacy.

overall_design: Amplicon bisulfite-sequencing data: 12 samples. RNA-seq: 8 samples. Samples are DNA (for methylation analysis) and RNA (for RNA-seq analysis) samples from control HBV(+/-)Pten(fl/fl)Cre(+/-) [normal liver] and HBV(+/-)Pten(fl/fl)Cre(+/-) [paired Pten-null non-tumor and tumor HCC samples] livers.

first: Claudia

middle: E

last: Oropeza

first: Caitlin

last: Ondracek

first: Grant

last: Tarnow

first: Stefan

last: Green

first: Alan

last: McLachlan


title: Human Astrocytes Exhibit Tumor Microenvironment, Age- and Sex-Related Transcriptomic Signatures

city: Los Angeles

first: Mitchell

last: Krawczyk

state: CA

address: 635 Charles E Young Dr S

institute: UCLA

summary: Human astrocytes were purified from cortical surgical resections from consenting patients; Astrocytes were purified by immunopanning with HepaCAM. Total RNA of purified astrocytes was isolated and sequenced by Illumina HiSeq 4000.

overall_design: mRNA profiles of human astrocytes from control, epileptic, or tumor-surrounding cerebral cortex

middle: C

first: Ye

last: Zhang


title: Expression profilling of C. glabrata response to fluconazole and the role of the transcription factor Mar1 in such response

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Avenida Rovisco Pais 1

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Tecnico

summary: The goals of this study are to compare C. glabrata transcriptome profiling (RNA-seq) upon exposure to the antifungal fluconazole in order to assess antifungal response. The role of the transcription factor Mar1 is clarified through comparison of the transcrptome profiles of WT and Mar1 mutant cells. mRNA profiles of WT and ∆mar1 were generated by deep sequencing, in duplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed with TopHat followed by HTSeq.

overall_design: Yeast mRNA profiles after 1h fluconazole exposure of WT and ∆mar1 cells were generated by RNA-Seq, in duplicate (each duplicate made of triplicate samples pooled together) using Illumina HiSeq

first: Pedro

last: Pais

first: Mónica

last: Galocha

first: Raquel

last: Califórnia

first: Romeu

last: Viana

first: Mihaela

last: Ola

first: Michiyo

last: Okamoto

first: Hiroji

last: Chibana

first: Geraldine

last: Butler


title: Charged tRNA profiling of mcf10a, HCC1806 cells, polysome profiling, RNA-Seq and Ribo-Seq in 4T07 cells upon LARS knockdown by shRNA, and RNA-Seq of ribosome-associated RNAs in Lars depleted PyMT tumors

first: Maria

last: Passarelli

state: New York

address: Rockefeller University, 1230 York Ave

institute: Rockefeller University

summary: In this study, we identify leucyl-tRNA synthetase (LARS) as a breast tumor suppressor. To identify the mechanism underlying LARS-mediated breast tumor suppression, we first conducted charged tRNA profiling to assess charged and total tRNA-Leu expression in cell lines with high and low LARS expression. Expression of select charged and total tRNA-Leu isoacceptors were reduced in cell lines with lower LARS expression. We then conducted RNA-Seq and translation profiling including ribosome profiling (Ribo-Seq), polysome profiling in LARS-depleted cell lines. To test our hypothesis in vivo, we also performed RNA-Seq of ribosome-associated RNAs in Lars depleted PyMT tumors within RiboTag mice. The analyses implicate LARS as a regulator of leucine-rich translation.

overall_design: To identify changes in tRNA-Leu expression, charged tRNA profiling was conducted in LARS-high non-transformed mcf10a cells compared to LARS-low HCC1806 breast cancer cells using charged tRNA profiling. To identify the impact of LARS on protein translation, RNA-Seq, Ribo-Seq and Polysome profiling were conducted in LARS-depleted 4T07 breast cancer cells. To assess the effects of LARS on translation in vivo, RNA-Seq was conducted on ribosome-associated mRNAs isolated from RiboTag mice harboring PyMT tumors, with and without monoallelic LARS deletion in the mammary tumor compartment.

first: Sohail

last: Tavazoie


title: Effect of prenatal sulforaphane (SUL) on Nrf2+/+ and Nrf2-/- placenta

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Results: In Nrf2+/+ placenta, genes involved in estrogen receptor signaling and reproductive system development (e.f., Med subfamily, Igf1r, Ncor2), vasculature and embryonic development (e.g., Adamdec1, Pdgfrb, Col8a2, Sema3g, Krt5, Lce1a1), and inhibition of prenatal death and cell morbidity (e.g., Dnmt3a, Col4a2) were regulated by SFN. Multiple granzyme isozymes (Gzmd, Gzmg, Gzmf, Gzmc) and oxidoreduction genes (e.g., Gstt1, Gstt2, Prdx5, Hao3, Hsd17b10, Pecr) were suppressed in Nrf2+/+ placenta treated with SFN. SFN-altered transcriptome changes in Nrf2-/- placenta were predicted to inhibit prenatal death via regulation of genes including Igf2r, Tgfb2, Arid5b, and Il6st and to activate angiogenesis and cell growth by alteration of genes such as Timp3, Kdr, and Il6ra.
Conclusion: Overall transcriptome changes indicated reduced cytotoxicity and activated feto-placenta barrier functions in both Nrf2+/+ and Nrf2-/- mice.

overall_design: PARALLEL study design with 12 samples comparing 48 groups of prenatal treatment (PBS, SUL) and gene (Nrf2-WT, Nrf2-KO). (2 groups of Nrf2-WT; PBS, SUL),  (2 groups of Nrf2-KO; PBS, SUL) Biological replicates: 3 per group

first: Steven

last: Kleeberger

first: Hye-Youn

last: Cho


title: Effect of prenatal sulforaphane (SUL) on hyperoxia-induced lung injury in Nrf2+/+ and Nrf2-/- neonates

summary:
Results: Prenatal SUL altered baseline lung genes involved in organ/cell development and grow (e.g., Ibsp, Ctsk, Igfbp5) and ARE responses (e.g., Aldh3a1, Maff, Mafg) in Nrf2+/+ neonates and in cell morphogenesis and cell death and organismal injury/abnormality inhibition (e.g., Neat1, Nox4, Vegfa, Igfbp2, Trp53) in Nrf2-/- neonates. In hyperoxia-exposed lung, prenatal SULincreased organogenesis/development genes (e.g., Prss35, Cep128) and decreased inflammatory genes (H2-D1, Cd40, Lcn2, Cdh22) in Nrf2+/+ pups. In Nrf2-/- mice exposed to hyperoxia, prenatal SFN decreased hyperoxia-upregulated many immune and inflammatory response genes (e.g., Ccl9, Btla, Ncf4, Ltb, Selplg, Csf2rb) and upregulated many DNA repair/damage checkpoint genes (e.g., Uimc1, Neil3, Nbn, Smc4, Smc6).
Conclusion: Overall, prenatal maternal SUL altered genes differentially in Nrf2+/+ and Nrf2-/- lungs. However, SUL-mediated transcriptome changes affected similar biological functions benificial to host defense and organ development in both strain. Compensatory differential lung transcriptome changes in Nrf2-/- neonates may resulted in the manifest protection of their severe hyperoxic lung injury.

overall_design: PARALLEL study design with 21 samples comparing 8 groups of prenatal treatment (PBS, SUL), gene (Nrf2-WT, Nrf2-KO), and postnatal exposure: (air, O2)  (4 groups of Nrf2-WT; PBS/air, SUL/air, PBS/O2, SUL/O2),  (4 groups of Nrf2-KO; PBS/air, SUL/air, PBS/O2, SUL/O2) Biological replicates: 2 or 3 per group


title: The expression of microRNA Induced by HIV-1 Infection

first: Jialu

last: Qiao

address: Sanjiaohu Road No.8

institute: Jianghan University

summary: To investigate whether and what miRNAs expression might be regulated by HIV-1 challenge, we analyzed the miRNA expression profile of MT4 cells inoculated with HIV-1-GFP for 48h using an array-based miRNA profiling and the infectivity was over 90% by analyzing with flow cytometer.

overall_design: MiRNA expression profile of MT4 cells inoculated with or without pseudotyped HIV-1-GFP for 48h was measured.Three independent experiments were performed using different samples for each.

first: Binlian

last: Sun


title: RNA-Sequencing to identify the transcriptional targets of Rai1

first: Jin

last: Xu

state: Guandong

address: No. 135 Xingang Xilu

department: School of Life Sciences

institute: Sun Yat-Sen University

summary:
The goals of this study are to harvest adult-onset Rai1-deficient mouse brains from hypothalamus and compare the transcriptome with their wild-type littermates.
Methods:  mRNA profiles from Rai1 conditional knockouts and wild-type mice were generated by deep sequencing, in duplicate using Illumina system.
Conclusions: Our study suggests that Rai1 preferentially regulate genes involved in cell communication

overall_design: Hypothalamic mRNA profiles of wild-type and Rai1 conditional knockout mice were generated by deep sequencing, in duplicates.

first: Wei-Hsiang

last: Huang


title: Differential expression and pathway enrichment in neutrophils treated with Ruxolitinib and vehicle

status: Public on Jan 04 2022

city: Tianjin

first: Shan

last: Jiang

address: Tianjin NanjingRoad

institute: Public Union Medical College

summary: We report the effect of rexolitinib on neutrophil function, by extracting mouse bone marrow neutrophils, and after treatment with Ruxolitinib and vehicle, extracting neutrophil RNA from each group for RNA-seq. Finally, we show that Ruxolitinib produces functional effects on neutrophils mainly through inflammatory signaling pathways, amplifying the immune effects of neutrophils in an inflammatory environment and accelerating neutrophil death.

overall_design: The changes of Neutrophil RNA expression in Ruxolitinib-treated and vehicle treated groups were detected

first: Shiyue

last: Zhang

first: Lu

first: Tong

last: Wang

first: Yigeng

last: Cao

first: Shuquan

last: Rao

first: Yuanfu


title: Effects of the SLICK1 mutation in PRLR on regulation of core body temperature and global gene expression in liver in cattle

city: Gainesville

first: Peter

middle: James

last: Hansen

state: FL

address: 2250 SW Shealy Drive

department: Animal Sciences

institute: University of Florida

summary: Determine the effect of 0,1, or 2 copies of the slick mutation in the PRLR on gene expression

overall_design: For one exp, liver was obtained from daughters of slick bulls (Blanco or Lone Ranger) ; daughters inherited 0 (FREE) or 1 (SLICK) copies of the SLICK allele. For the other study, liver was obtained from animals with 1 (S1) or 2 (S2) copies of the SLICK allele

first: Froylan

last: Sosa

first: J

last: Santos

first: D

middle: O

last: Rae

first: C

last: Larson

first: M

last: Macchietto

last: E Abrahante

first: T

middle: F

last: Amaral

first: A

last: Denicol

last: Sonstegard

first: P


title: Genome-wide maps of chromatin state in HCT116 colorectal cancer cell. [RNA-Seq]

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

summary: Identification of the genome-wide gene transcription in Auxin untreated and Auxin treated HCT116 CTCF Degron cells.

overall_design: RNA-seq in Auxin untreated and Auxin treated HCT116 CTCF Degron cells

first: Jung-Sik

last: Joo

first: Yong-Jin


title: Histologic and molecular patterns in responders and non-responders with chronic-active antibody mediated rejection

city: Zurich

first: Thomas

middle: F.

last: Müller

address: Rämistrasse

country: Switzerland

institute: University Hospital Zurich

summary: Endothelial, inflammatory, cellular, interferon gamma and calcineurin inhibitor related genes were analyzed in 10 therapy responders and 6 non responders in chronic active antibody mediated rejection (caABMR) in kidney transplantation.

overall_design: Sixteen kidney transplant biopsies taken between 2008 and 2016 with only pure, unquestonable caABMR and no other pathologic features were analyzed in respect to 44 target genes and 4 house-keeping genes.

first: Onur

last: Sazpinar

last: Mueller


title: Well-paired-seq: a Size-exclusion and Locally Quasi-static Hydrodynamic Microwell Chip for Single-cell RNA-seq

city: Xiamen

first: Li

last: Lin

state: Fujian

address: 422 Road, Siming District,  Xiamen, China

institute: Xiamen University

summary: High throughput single-cell RNA sequencing (scRNA-seq) is a powerful technology for revealing new cell types and cellular states. However, the existing droplet or well-based methods are primarily based on the stochastic pairing of single cells and barcoded beads, resulting in a large number of empty microreactors and a low cell/bead utilization efficiency. Here, we present Well-paired-seq, consisting of thousands of size-exclusion and quasi-static hydrodynamic dual wells to address these limitations. The size-exclusion based dual-well structure allowed one cell and one bead to be trapped in the bottom well (cell-capture-well) and the top well (bead-capture-well), respectively, while the quasi-static hydrodynamic principle ensured that the trapped cells were unable to escape from cell-capture-wells, achieving cumulative capture of cells and buffer exchange in the Well-paired-seq chip. By the integration of quasi-static hydrodynamic and size-exclusion principles, the structure of the dual-well ensures one cell and one bead pairing with high density, acheiving high efficiency of cell/bead pairings (~80%) and low cell doublets.  The high utilization of microreactors and single cells/beads enable us to achieve an ultra-high throughput (~105 cells ) with low collision rates (6.2%). We demonstrate the technical performance of Well-paired-seq by collecting transcriptome data from around 200,000 cells across 21 samples including various cell lines, peripheral blood mononuclear cells, and drug-treated cells, successfully revealing the heterogeneity of single cells and showing the wide applicability of Well-paired-seq for basic or clinical biomedical research.

overall_design: mRNA profiles of K562/3T3 mixing, five lung adenocarcinoma cell lines, PBMCs, and vorinostat-exposed A549

first: Kun

last: Yin

first: Meijuan

last: Zhao

first: Jia

last: Song

first: Chaoyong

last: Yang


title: Recent Cis-Trans Coevolution Driven by the Emergence of A Novel Gene in Drosophila

city: Chicago

first: Manyuan

last: Long

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

summary: Young, or newly evolved, genes arise ubiquitously across the tree of life, and can rapidly acquire novel functions that influence a diverse array of biological processes (Chen et al. 2013)1.  Previous work identified a young regulatory gene in Drosophila, Zeus, which diverged rapidly from its parent Caf40 and took on roles in the male reproductive system.  This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome Chen et al. 2012)2.  However, the way in which new DNA-binding proteins acquire and co-evolve with their targets in the genome is not understood. Here, by comparing Zeus ChIP-seq data from D. melanogaster and D. simulans to the ancestral Caf40 binding events from D. yakuba, a species that diverged before the duplication event, we find a dynamic pattern in which Zeus binding rapidly co-evolved with a previously unknown DNA motif under the influence of positive selection.  Interestingly, while both copies of Zeus acquired targets at male-biased and testis-specific genes, D. melanogaster and D. simulans proteins have specialized binding on different chromosomes, a pattern echoed in the evolution of the associated motif.  Our results suggest that evolution of young regulatory genes can be coupled to substantial re-wiring of the transcriptional networks into which they integrate, even over short evolutionary timescales.  Our results thus uncover dynamic, genome-wide evolutionary processes associated with new genes.

overall_design:
Generation of Transgenic Drosophila Lines: Expression vectors were constructed for each gene of interest and were transformed into white-eyed D. melanogaster. Briefly, each coding sequence (Dmel Zeus, Dsim Zeus, and Dyak Caf40) was cloned so as to be linked to an Actin5C promoter and FLAG tag, and then inserted into the piggyBac MWpBacFPNS vector (Bloomington Drosophila Genomics Resource Center, Stock Number 1289). Transformations of D. melanogaster were performed by Rainbow Transgenics, Inc. (Camarillo, CA)
ChIP-seq Data Production:  ChIP-seq experiments were performed using standard modEncode protocols after collecting adults in each species. Four (4) technical replicates were performed for each transgenic Drosophila line. Sequencing data was generated by the High-Throughput Genome Analysis Core (HGAC) at the Institute for Genomics and Systems Biology, University of Chicago

first: Benjamin

last: Krinsky

first: Robert

middle: K

last: Arthur

first: Kevin

middle: P

last: White


title: To perform a standard RNAseq experiment to evaluate the impact of the knockout of Zeus gene(CG9573) in D. melanogaster

summary:
This experiment was designed to study the transcriptional alternations using RNA-seq technique. RNA materials were collected and sequenced with multiple experimental groups in tri-plicates as follows: control-knockout-replicate 1~3 (KO-Ctrl__1~3), Zeus-knockout-replicate 1~3 (KO-Zeus__1~3), for RNA-sequencing. In total, 6 sequencing files were downloaded from the genomic core facility, University of Chicago. The aims of this analysis are to 1) conduct quality control (QC) assessment on the original raw sequencing data, 2) map sequencing reads to target species, 3) identify differentially expressed (DE) protein-coding genes per comparison.
Through assessing the quality of original raw sequencing data, good base-wise quality was revealed in average in all samples, indicating a high confidence on the base call. Adapter/primer sequences are absent from reads; therefore, trimming of sequencing reads was skipped prior to downstream RNA-seq analysis. Overall, around 94.89% of reads were successfully mapped to the fruit fly genome model in RNA-seq data. All RNA samples were used for further downstream identification of differentially expressed (DE) mRNA genes in individual pairwise comparison.
Several commonly used tools (DESeq2, edgeR, and limma) were utilized for the identification of DE mRNA between pairwise groups. Using the criteria of fold change no less than 1.5 and FDR (False Discovery Rate) less than 0.1). Pairwise comparison, KO-Zeus/KO-Ctrl, were conducted. Overall, we find Zeus regulated the expression of 661 differentially expressed genes (DEGs) based on combination of three tools. Venn diagram was further depicted to present the consensus/overlapped DE gene sets detected across different methods.

overall_design: Identification of DEGs between Zeus-KO mutant and WT in testis in Drosophila melanogaster.

first: Shengqian

last: Xia


title: Transcriptome analysis after DOT1L inhibitors treatment in uveal melanoma cells.

first: gu

last: xiang

address: No.833 Zhizaoju Road

institute: Shanghai Jiao Tong University school of medicine

summary: To disclose the regulatory role of H3K79me2 in gene expression, we performed  RNA-seq of  cells treated with DOT1L inhibitor or not and RNA-seq of normal and uveal melanoma cells.

overall_design: Examination the target genes of H3K79me2 in uveal melanoma cells.

first: X

last: Gu

last: Chai

first: J

last: Yu


title: Genome-wide maps of H3K79me2 in uveal melanoma cells.

summary: To investigate the role of H3K79me2 in tumorgenesis of uveal melanoma.

overall_design: Examination of H3K79me2 in uveal melanoma cells.

first: P


title: Genome-wide maps of chromatin state in HCT116 colorectal cancer cell

first: Hyoung-Pyo

last: Kim

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

overall_design: Refer to individual Series


title: Genome-wide maps of chromatin state in HCT116 colorectal cancer cell (HiC)

summary: Identification of the genome-wide pair-wise chromatin interaction in Auxin untreated and Auxin treated HCT116 CTCF Degron cells.

overall_design: Examination of genome-wide chromatin interaction in WT and CTCF KD HCT116 colorectal cancer cells

first: Bobae

first: Yong-Jin


title: Genome-wide maps of chromatin state in HCT116 colorectal cancer cell (HiChIP)

summary: Identification of the genome-wide RNA polymerase II mediated chromatin interaction  in Auxin untreated and Auxin treated HCT116 CTCF Degron cells.

overall_design: Examination of RNA Pol. II mediated chromatin interaction in WT and CTCF KD HCT116 colorectal cancer cells


title: Genome-wide maps of chromatin state in HCT116 colorectal cancer cell (ChIP-Seq)

summary: Identification of the genome-wide landscape of transcription factors(CTCF, SMC1, RNA Pol. II) and histone modification(H3K27Ac) in Auxin untreated and Auxin treated HCT116 CTCF Degron cells.

overall_design: CTCF, SMC1, RNA Pol. II, H3K27Ac ChIP-seq in Auxin untreated and Auxin treated HCT116 CTCF Degron cells


title: EMSY inhibits homologous recombination repair and the interferon response promoting lung cancer immune evasion

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Non-small cell lung cancers (NSCLCs) harboring KEAP1 mutations are characterized by worse overall outcomes and resistance to immunotherapy.  Here, we identified a molecular mechanism by which KEAP1 targets EMSY for ubiquitin-mediated degradation to regulate homologous recombination repair (HRR) and anti-tumor immunity.  Loss of KEAP1 in NSCLC induces stabilization of EMSY producing a BRCAness phenotype characterized by HRR defects and sensitivity to PARP inhibitors (PARPis).  Defective HRR increases genomic instability leading to high tumor mutational burden (TMB), which prompts an innate immune response.  Notably, EMSY accumulation also suppresses the type I interferon response and impairs innate immune signaling, fostering cancer immune evasion.  Activation of the type I interferon response in the tumor microenvironment using a STING agonist results in the engagement of innate and adaptive immune signaling, impairing the growth of KEAP1-mutant tumors.  Our results suggest that targeting the PARP and STING pathways, individually or in combination, represent a novel therapeutic strategy in NSCLC patients harboring alterations in KEAP1.

overall_design: All samples were generated by deep sequencing

first: Antonio

last: Marzio

first: Emma

last: Kurz


title: Preclinical model of anti-PDL1 Immune-checkpoint blockade (ICB) resistance in breast cancer associated to low antigen presentation machinery (APM)

city: Barcelona

first: Antoni

last: Celià-Terrassa

address: Carrer Dr.Aiguader 88

institute: IMIM

summary: Immune-checkpoint blockade (ICB) immunotherapy has emerged as one of the most effective therapies in oncology by unleashing anti-tumor response. However, despite the improvement in the clinical outcome of TNBC patients, most patients do not respond yet. Thus, to understand the underlying mechanisms of ICB resistance is necessary. With this purpose, we generated a preclinical immunocompetent syngeneic model of anti-PD-L1 ICB resistance. Mouse breast cancer 4TO7 cells were orthotopically implanted by MFP and at 0.5 x 0.5 cm tumor size mice were treated with anti-PD-L1 (10mg/Kg every 3 days). Though tumors initially responded, they eventually developed resistance to anti-PD-L1 treatment. Immunotherapy resistant tumor (IRT) cells and control tumor cells were isolated and validated again for anti-PDL1 resistance in vivo. RNA from isolated resistant tumor cells was obtained using Qiagen RNA extraction kit. Samples were analyzed by bioanalyzer. Poly-A sequencing was selected for library preparation, and samples were sequenced using Illumina Hi-Seq 2500 platform with 1x50 bp settings in the Centre of Genomic Regulation (CRG). Quality raw data was performed with FastQC software. Raw reads were then aligned with the STAR mapper to the Mus musculus genome and raw counts of reads per gene was additionally obtained with STAR. Differentially expression was assessed using DESeq2 version 1.30.1 package from R/Bioconductor. Among all the results, we have seen that those IRT cells have a downregulation of the antigen presentation machinery (APM) and an enrichment of stemness signatures. Overall, the results support the notion that ICB resistance emerge from low APM activity cell populations with associated stem cell-like phenotype.

overall_design: Transcriptomic profile of 2 individual biological replicates of cells from ICB resistant to anti-PD-L1 tumors vs control tumors

first: Iván

last: Pérez Núñez


title: Transcriptome profiling of bone marrow-derived macrophages from wilde type mice and EndoV knockout mice

city: Oslo

first: Kuan

address: Sognsvannsveien 20

department: Research Institute of Internal Medicine

country: Norway

institute: Oslo University Hospital

summary: We performed high-throughput RNA sequencing to characterize possible differences in the transcriptome of bone marrow-derived macrophages from wilde type mice and EndoV knockout mice to further examine how ENDOV affect the CCL2 signaling. we stimulated both type of BMDMs with recombinant CCL2 and analyzed the transcriptome using mRNA sequencing analysis

overall_design: RNA-sequencing performed on bone marrow-derived macrophages from three wilde type mice and three EndoV knockout mice using Illumina NovaSeq 6000

first: Tuva

middle: B

last: Dahl