title: Single Cell Immunophenotyping of Lyme Erythema Migrans (Bulk TCR Repertoire Sequencing)

overall_design: Bulk TCR sequencing was performed on PBMCs from six subjects, all with confirmed cases of Lyme disease.


title: Multiomic analysis of the Arabian camel (Camelus dromedarius) kidney reveals a role for cholesterol in water conservation

status: Public on Jun 18 2021

city: Bristol

first: Fernando

last: Alvira Iraizoz

address: Dorothy Hodgkin Building, University of Bristol, Whitson Street

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

type: Expression profiling by high throughput sequencing

summary: The one-humped Arabian camel (Camelus dromedarius) is the most important livestock animal in arid and semi-arid regions and continues to provide basic necessities to millions of people. In the current context of global warming, there is renewed interest in the adaptive mechanisms that enable camelids to survive in arid conditions. Recent investigations described genomic signatures that revealed evolutionary adaptations to desert environments. We now present a comprehensive catalogue of the transcriptomes and proteomes of the dromedary kidney and describe how the gene expression profiles of Differentially Expressed Genes (DEGs) are modulated as a consequence of chronic dehydration and subsequent acute rehydration. We performed RNAseq and quantification of peptides in samples from 15 dromedaries (5 controls, 5 dehydrated and 5 rehydrated). Gene Ontology analyses suggested an enrichment of the cholesterol biosynthetic process and an overrepresentation of categories related to ion transmembrane transport in the camel kidney, and RTN analyses confirmed alterations in the transcriptional machinery involved in cholesterol synthesis. These data were validated by RT-qPCR. Based on our hypothesis of a role for cholesterol during dehydration, we identified DEGs with roles in the countercurrent multiplication process which are affected by changes in the level of cholesterol. Thus, we further validated differentially expressed genes with known roles in water conservation which are affected by changes in cholesterol levels. Our datasets suggest that suppression of cholesterol biosynthesis may facilitate water retention in the kidney by indirectly facilitating the AQP2-mediated water reabsorption.

overall_design: Nineteen male dromedary camels aged 4-5 years, body weight range 276-416 kg, were used in the present study. The camels were supplied with alfalfa hay as feed and ranch-housed in the United Arab Emirates. Veterinary supervision was provided throughout the experimental period and no signs of distress or illness were identified. After a short adaptive period, the camels were divided into 3 groups, control (n=5), dehydrated (n=8) and rehydrated (n=6). The control group had free access to food and water during the entire experimental period. The dehydrated group was water-deprived but had ad libitum access to food for 20 days. Meanwhile the rehydrated group was subjected to the same protocol as the dehydrated animals followed by ad libitum water supply for 3 additional days. After the experimental period, the camels were sacrificed in the local central abattoir for human consumption in April 2016. Kidney samples were harvested within 1 hour after killing the animals, immediately frozen in liquid nitrogen and kept at -80°C for later physiological, histological, morphological and molecular analysis. Samples were shipped frozen on dry ice to the University of Bristol under the auspices of a DEFRA Import Licence (TARP/2016/063). This study was approved by the Animal Ethics Committee of the United Arab Emirates University (approval ID: AE/15/38) and the University of Bristol Animal Welfare and Ethical Review Board. Total RNA was extracted from fresh frozen kidney medulla and cortex of 5 control, 5 dehydrated and 5 rehydrated camels (for a total of 30 samples). These 15 animals were randomly selected out of the 19 animals included in the experimental set up while the remaining 4 were used for preliminary analyses only. Frozen tissue was added to a pre-cooled mortar containing a small volume of liquid nitrogen. Tissue was then grounded to a fine powder using a pestle and the nitrogen was allowed to evaporate. The powdered tissue was placed into pre-chilled tubes on dry ice and stored at -80°C. For RNA extraction, 1ml of Qiazol (79306, Qiagen) was added to 100mg of powdered tissue, then immediately vortexed for 2 minutes, then incubated on ice for 10 minutes. Lysed samples were spun at 12000xg for 10 minutes at 4°C and the supernatant was transferred to a new tube. 1/5 volume Chloroform (22711.244, VWR) was added to each sample and vortexed for 15 seconds. Samples were then spun at 12000xg for 15 minutes at 4°C. 350ml of the upper phase was removed and mixed with an equal volume of absolute ethanol. RNA was extracted using ZymoTM Direct-Zol RNA miniprep (Zymo Research) as per the manufacturer’s instructions. Total RNA concentration and 260/280 ratios were measured using a Nanodrop 2000c (Thermo Scientific). Illumina Sequencing was performed by Bristol Genomics Facility, University of Bristol, using the poly-A selection method for library preparation and the Illumina NextSeq500 system. RIN were 8.1 (SD=0.5), 7.7 (SD=0.2) and 7.6 (SD=0.6) for control, dehydrated and rehydrated cortex samples, and 8.5 (SD=0.5), 8.8 (SD=0.2) and 8.7 (SD=0.4) for control, dehydrated and rehydrated medulla samples, respectively.

last: Alvira-Iraizoz

first: Ben

middle: T

last: Gillard

first: David

last: Murphy

first: Michael

middle: P

last: Greenwood

first: Abdu

last: Adem


title: Tissue-specific transcriptional profiling of plasmacytoid dendritic cells reveals a hyperactivated state in chronic SIV infection

status: Public on Jun 15 2021

city: Atlanta

first: Steven

middle: E.

last: Bosinger

address: 954 Gatewood Rd NE

country: USA

institute: Emory University

summary: HIV associated immune activation (IA) is associated with increased morbidity in people living with HIV (PLWH) on antiretroviral therapy, and remains a barrier for strategies aimed at reducing the HIV reservoir. The underlying mechanisms of IA have not been definitively elucidated, however, persistent production of Type I IFNs and expression of ISGs is considered to be one of the primary factors. Plasmacytoid DCs (pDCs) are a major producer of Type I IFN during viral infections, and are highly immunomodulatory in acute HIV and SIV infection, however their role in chronic HIV/SIV infection has not been firmly established. Here, we performed a detailed transcriptomic characterization of pDCs in chronic SIV infection in rhesus macaques, and in sooty mangabeys, a natural host non-human primate (NHP) species that undergoes non-pathogenic SIV infection. We also investigated the immunostimulatory capacity of lymph node homing pDCs in chronic SIV infection by contrasting gene expression of pDCs isolated from lymph nodes with those from blood. We observed that pDCs in LNs, but not blood, produced high levels of IFN transcripts, and upregulated gene expression programs consistent with T cell activation and exhaustion. We apply a novel strategy to catalogue uncharacterized surface molecules on pDCs, and identified the lymphoid exhaustion markers TIGIT and LAIR1 as highly expressed in SIV infection. pDCs from SIV-infected sooty mangabeys lacked the activation profile of ISG signatures observed in infected macaques. These data demonstrate that pDCs are a primary producer of Type I IFN in chronic SIV infection. Further, this study demonstrated that pDCs trafficking to LNs persist in a highly activated state well into chronic infection. Collectively, these data identify pDCs as a highly immunomodulatory cell population in chronic SIV infection, and a putative therapeutic target to reduce immune activation.

sample_organism:
Cercocebus atys
Macaca mulatta

platform_organism:
Cercocebus atys
Macaca mulatta

overall_design: RNA-Seq analysis of: (i) SIV+ vs SIV- rhesus macaque and sooty mangabey (n=4) (ii) PBMC vs LN in SIV+ rhesus macaques (n=9) (iii) spleen pDCs from H7N3+ vs H7N3- rhesus macaques (n=3)

first: Michelle

middle: Y

last: Lee

first: Amit

middle: A

last: Upadhyay

first: Hasse

last: Walum

first: Chi

middle: N

last: Chan

first: Reem

last: Dawoud

first: Christine

last: Grech

first: Justin

middle: L

last: Harper

first: Kirti

last: Karunakaran

first: Sydney

last: Nelson

first: Ernestine

last: Mahar

first: Kyndal

last: Goss

first: Diane

middle: G

last: Carnathan

first: Barbara

last: Cervasi

first: Kiran

last: Gill

first: Gregory

middle: D

last: Tharp

first: Elizabeth

middle: R

last: Wonderlich

first: Vijayakumar

last: Velu

first: Simon

middle: M

last: Barratt-Boyes

first: Mirko

last: Paiardini

first: Guido

last: Silvestri

first: Jacob

last: Estes

middle: E


title: Single-cell RNA sequencing reveals markers of disease progression in primary cutaneous T-cell lymphoma

status: Public on Sep 13 2021

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Background: In early-stage mycosis fungoides (MF), the most common primary cutaneous T-cell lymphoma, limited skin involvement with patches and plaques is associated with a favorable prognosis. Nevertheless, approximately 20-30% of cases progress to tumors or erythroderma, resulting in poor outcome. At present, factors contributing to this switch from indolent to aggressive disease are only insufficiently understood.
Methods: In patients with advanced-stage MF, we compared patches with longstanding history to newly developed plaques and tumors by using single-cell RNA sequencing, and compared results with early-stage MF as well as nonlesional MF and healthy control skin.
Results: Despite considerable inter-individual variability, lesion progression was uniformly associated with downregulation of the tissue residency markers CXCR4 and CD69, the heat shock protein HSPA1A, the tumor suppressors and immunoregulatory mediators ZFP36 and TXNIP, and the interleukin 7 receptor (IL7R) within the malignant clone, but not in benign T cells. This phenomenon was not only found in conventional TCR-αβ MF, but also in a case of TCR-γδ MF, suggesting a common mechanism across MF subtypes. Conversely, malignant cells in clinically unaffected skin from MF patients showed upregulation of these markers.
Conclusions: Our data reveal a specific panel of biomarkers that might be used for monitoring MF disease progression. Altered expression of these genes may underlie the switch in clinical phenotype observed in advanced-stage MF.

overall_design:
Single-cell RNA-seq investigation of patch, plaque/tumor, and follow up lesions and nonlesional skin in CTCL patients.
------------------------------
Authors state "raw data are missing due to patient privacy concerns".

first: Constanze

last: Jonak

first: Natalia

last: Alkon

first: Felix

last: Thaler

first: Harald

last: Kurz

first: Lisa

last: Shaw

first: Georg

last: Stingl

first: Wolfgang

last: Weninger

first: Florian

last: Halbritter

last: Bauer

first: Matthias

last: Farlik

first: Patrick

last: Brunner


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

status: Public on Apr 26 2021

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Cohesin regulates homology search during recombinational DNA repair [Hi-C]

status: Public on Jul 21 2021

city: PARIS

first: Helene

last: Bordelet

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

summary: Homologous recombination (HR) is an ubiquitous DNA double-strand break (DSB) repair mechanism. It entails a homology search step, carried out along a conserved RecA/Rad51-ssDNA nucleoprotein filament (NPF) assembled on each DSB ends. In contrast to the extensive knowledge of DNA damage checkpoint (DDC)-induced changes in chromatin composition and mobility,  the questions of if, how, and to what extent a DSB impacts the spatial organization of chromatin, and whether this organization in turn influences the homology search process, remain ill-defined. Here we characterize two layers of spatial chromatin reorganization following DSB formation in S. cerevisiae. While cohesin folds chromosomes into cohesive arrays of ~20 kb-long chromatin loops as cells arrest in G2/M, the DSB-flanking regions interact locally in a resection- and 9-1-1 clamp-dependent manner, independently of cohesin, Mec1ATR, Rad52 and Rad51. This local structure blocks cohesin progression, constraining the DSB region at the base of a loop. Functionally, cohesin promotes DSB-dsDNA interactions and donor identification in cis, while inhibiting them in trans. This study identifies multiple direct and indirect ways by which cohesin regulates homology search during HR repair.

overall_design: Global and local genome organisation upon DSB damage was assessed by collecting cells for Hi-C 2, 4 and 6 hours after DSB induction. Some Hi-C were also performed before DSB induction. These experiments were performed in WT and mutants to determine the factors responsible for these global and local genome organisation upon DSB induction.

first: Piazza

last: Aurele

first: Bordelet

last: Helene

first: Dumont

last: Agnes

first: Thierry

first: Savocco

last: Jerome

first: Girard

last: Fabien

first: Koszul

last: Romain


title: Reactivation of multiple fetal miRNAs in lung adenocarcinoma

status: Public on May 29 2021

city: Vancouver

first: Wan

last: Lam

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) play vital roles in the regulation of normal developmental pathways. However, cancer cells can co-opt these miRNAs, and the pathways that they regulate, to drive pro-tumourigenic phenotypes. Characterization of the miRNA transcriptomes of fetal organs is essential for identifying these oncofetal miRNAs, but it has been limited by fetal sample availability. As oncofetal miRNAs are absent from healthy adult lungs, they represent ideal targets for developing diagnostic and therapeutic strategies. We conducted small RNA sequencing of a rare collection of 25 human fetal lung (FL) samples, and compared them to two independent cohorts (n = 140, n = 427), each comprised of adult non-neoplastic lung (ANL) and lung adenocarcinoma (LUAD) samples. We identified 13 oncofetal miRNAs that were expressed in FL and LUAD but not in ANL. These oncofetal miRNAs are potential biomarkers for LUAD detection (AUC = 0.963). Five of these miRNAs are derived from the imprinted C14MC miRNA cluster at the 14q32 locus, which has been associated with cancer development and abnormal fetal and placental development. Additionally, we observed the pulmonary expression of 44 previously unannotated miRNAs. The sequencing of these fetal lung samples also provides a baseline resource against which aberrant samples can be compared.

overall_design: We used a sequencing-based approach to profile the miRNA transcriptomes of a group of 165 samples, consisting of 25 fetal lung (FL) samples, 77 adult non-malignant lung (ANL) samples, and 63 lung adenocarcinoma (LUAD) samples, in order to identify lung oncofetal miRNAs. The miRNA expression of 73/77 ANL and 59/63 LUAD samples in this study was previously analyzed using different methods, and that resulting data was deposited in GEO (GSE62182). Sample titles for these samples directly correspond to those used in GSE62182. Samples from GSE62182 that yielded less than 5 million sequencing reads were excluded from this study.


title: Single Cell Immunophenotyping of Lyme Erythema Migrans [Single-Cell BCR Repertoire Sequencing]

status: Public on Jun 07 2021

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: Erythema migrans (EM) is a skin lesion caused by the spirochete B. burgdorferi (Bb) and is a hallmark initial sign of Lyme disease. Previous studies have demonstrated that T cells and innate immune cells mediate local inflammatory cytokine production that promote the reaction. Despite the established importance of B cells and antibodies in preventing Bb infection and resolving disease, the role of B cells in the skin immune response to Bb is incompletely defined. In this study, we characterized the immunophenotype of EM lesions and used single cell RNA-Seq to investigate B cell receptor (BCR) and T cell receptor (TCR) repertoires in the EM skin lesions and peripheral blood of patients with Lyme disease. We hypothesized that B cells from the circulation, potentially primed by exposure to Bb antigens in regional draining lymph nodes, are recruited into EM lesions and play an active role in the local response to infection. We found that B cells are more abundant in the EM lesion in comparison to autologous uninvolved skin and possess distinct characteristics, including abundant expression of MHCII genes and preferential IgM isotype usage. A subset exhibited low levels of somatic hypermutation despite a gene expression profile more consistent with memory than naïve B cell subsets. Moreover, infiltrating B cells were clonally expanded and a large fraction could be directly traced to circulating relatives. By leveraging single cell gene expression with paired BCR and TCR repertoire sequencing, we demonstrate, for the first time, that B cells are recruited to the skin infection site in early Lyme disease and express a phenotype suggesting that they could play a role in local antigen presentation and antibody production.

overall_design: Six subjects were studied, all with confirmed cases of Lyme Disease. Five of six had samples from both EM rash and unaffected skin. One subject had sample only from EM rash. One subject had an additional PBMC sample. Sequencing of BCR was performed using the 10X Genomics platform.

first: Tony

last: Melillo

first: Ruoyi

last: Jiang

first: Steven

middle: H

last: Kleinstein

first: Linda

middle: K

last: Bockenstedt


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [ATAC-Seq]

summary: Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression within these networks is sufficiently perturbed it can lead to disease. To understand how gene expression disruptions percolate through a network, we must first map the connections between regulatory genes and their downstream targets. However, it has been challenging to identify the upstream regulators for genes of interest. Here we develop a system for systematic discovery of upstream regulators of critical immune factors – IL2RA, IL-2, and CTLA4 – in primary human T cells. Then, CRISPR perturbations coupled with RNA-Seq, and ATAC-Seq, allowed us to map the full network of these regulators’ target genes and enhancers. These regulators form highly interconnected networks with extensive feedback loops. Furthermore, this network is highly enriched for autoimmune-associated disease variants and genes. These results provide insight into how autoimmune associated disease genes are regulated in T cells as well as broader principles about the structure of human gene regulatory networks.

overall_design: ATAC-Seq of CD4+CD25- human T cells after CRISPR KO of 24 genes or AAVS1 controls

first: Jacob

middle: W

last: Freimer

first: Oren

last: Shaked

first: Sahin

last: Naqvi

first: Nasa

last: Sinnott-Armstrong

first: Arwa

last: Kathiria

first: Amy

middle: F

last: Chen

first: Jessica

last: Cortez

first: William

middle: J

last: Greenleaf

first: Jonathan

last: Pritchard


title: Grouping of UVCB Substances with Dose-Response Transcriptomics Data from Human Cell-Based Assays

status: Public on Jan 01 2022

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

summary: Six human cell lines were treated in a log dose response to 141 petroleum substance extracts containing unknown or variable composition, complex reaction products and biological materials (UVCBs) to be used for grouping and read across strategies.   The six cell lines consisted of human induced pluripotent stem cell (iPSC)-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, as well as the human MCF7 and A375 cell lines. All transcriptomics were targeted with BioSpyder S1500+ gene list.

overall_design: Transcriptomic Dose Response Characterizations Across Petroleum Based UVCBs

middle: S

first: Fabian

last: Grimm

last: Klaren

first: Abigail

last: Dalzell

first: Srikeerthana

last: Kuchi

first: Shu-Dong

last: Zhang

first: Klaus

last: Lenz

first: Peter

last: Boogaard

first: Hans

middle: B

last: Ketelslegers

first: Timothy

last: Gant

first: Ivan

last: Rusyn

first: Fred

last: Wright


title: NOCICEPTRA: Gene and microRNA signatures and their trajectories characterizing human iPSC-derived nociceptor maturation

status: Public on Sep 06 2021

city: Innsbruck

first: Kai

last: Kummer

address: Schoepfstrasse 41/Eg

department: Institute of Physiology

institute: Medical University of Innsbruck

summary: Nociceptors are specialized sensory neurons implicated in the reception and transduction of painful stimuli. Many pain disorders directly affect nociceptors but mechanistic insight into underlying pathway regulations is limited by the translational paresis from animal models to human pain disorders. Although transcriptomic data are available for rodent and post-mortem patient samples, no comprehensive transcriptomic data are currently available for human nociceptor development. Here, we performed paired long and small RNA sequencing for six timepoints during nociceptor differentiation from three different human iPSC cell lines. Complex bioinformatics analyses for differential gene expression, protein-protein interactions and mRNA targeting by microRNAs revealed five distinct differentiation stages with critical hub genes and microRNAs guiding nociceptor development. The online resource platform NOCICEPTRA was specifically developed to visualize respective mRNA and microRNA trajectories, as well as query disease specific pathways, thereby enabling researchers to determine susceptibility windows for nociceptor-associated disorders as well as possible new treatment targets.

overall_design: 108 high troughput mRNA (54 samples) and miRNA (54 samples) were analyzed at 6 different time-points for 3 different cell lines (AD3, AD2, 840) with three replicates per time point

first: Zeidler

last: Maximilian

first: Clemens

last: Schoepf

first: Zameel

last: Cader

first: Michaela

last: Kress


title: miRNA, mRNA and lncRNA expression in colorectal cancer

status: Public on Aug 01 2021

city: Dongguan

first: Guangxian

last: Xu

state: Guangdong

address: No.1 Xincheng Blvd, Songshan Lake National High-tech Industrial Development Zone

department: College of Medical Technology

country: China

institute: Guangdong Medical University

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


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [CRISPR]

first: Alexander

last: Marson

overall_design: Pooled CRISPR screen followed by FACS to sort CD25 (IL2RA), IL-2, and CTLA4 high or low expressing cells.

first: Jacob

last: Freimer

first: Oren

last: Shaked

first: Sahin

last: Naqvi

first: Nasa

last: Sinnott-Armstrong

first: Arwa

last: Kathiria

first: Amy

last: Chen

first: Jessica

middle: T

last: Cortez

first: William

last: Greenleaf

first: Jonathan

last: Pritchard


title: Elevated N-linked glycosylation of IgG variable regions in myasthenia gravis disease subtypes

status: Public on Aug 13 2021

first: Hailong

last: Meng

summary: Elevated N-linked glycosylation of immunoglobulin G variable regions (IgG-VN-Glyc) is an emerging molecular phenotype associated with autoimmune disorders. To test the broader specificity of elevated IgG-VN-Glyc, we studied patients with distinct subtypes of myasthenia gravis (MG), a B cell-mediated autoimmune disease. Our experimental design included adaptive immune receptor repertoire sequencing to quantify and characterize N-glycosylation sites in the global B cell receptor repertoire, proteomics to examine glycosylation patterns of the circulating IgG, and production of human-derived recombinant autoantibodies, which were studied with mass spectrometry and antigen binding assays to confirm occupation of glycosylation sites and determine whether they alter binding. We found that the frequency of IgG-VN-Glyc motifs was increased in the B cell repertoire of MG patients when compared to healthy donors. Motifs were introduced by both biased V gene segment usage and somatic hypermutation. IgG-VN-Glyc could be observed in the circulating IgG in a subset of MG patients. Autoantigen binding, by patient-derived MG autoantigen-specific monoclonal antibodies with experimentally confirmed presence of IgG-VN-Glyc, was not altered by the glycosylation. Our findings extend prior work on patterns of variable region N-linked glycosylation in autoimmunity to MG subtypes. Although occupied IgG-VN-Glyc motifs are found on MG autoantigen-specific monoclonal antibodies, they are not required for binding to the autoantigen in this disease.

overall_design: A MuSK MG cohort (N=3) was defined using BCR repertoire sequencing derived from a previous study. Another n = 11 AChR MG and n = 9 heathy control subjects were selected for BCR based adaptive immune receptor repertoire-sequencing or AIRR-Seq using PBMC derived RNA for this study. In total, serum samples from all 3 MuSK MG subjects and 9 AChR MG subjects (8 overlapping with paired AIRR-Seq) cohort were also investigated for the presence of VH gene glycosylation-specific signatures in the serum. For patients with MuSK MG diagnoses and patient AChR MG-1 with an AChR MG diagnosis, longitudinal serum samples were collected. A patient with Rheumatoid Arthritis (RA) (n = 1) was enrolled in a research study at University of California San Francisco (UCSF) for pathogen and autoantibody detection.

first: Caleigh

last: Mandel-Brehm

first: Miriam

last: Fichtner

first: Ruoyi

last: Jiang

first: Valerie

last: Winton

first: Sara

last: Vazquez

first: Minh

middle: C

last: Pham

first: Kenneth

last: Hoehn

first: Neil

last: Kelleher

first: Richard

last: Nowak

first: Steven

last: Kleinstein

first: Michael

last: Wilson

first: Joseph

last: DeRisi

first: Kevin

last: O’Connor


title: Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks [RNA-Seq]

first: Alexander

last: Marson

overall_design: RNA-Seq of CD4+CD25- human T cells after CRISPR KO of 24 genes or AAVS1 controls

first: Jacob

last: Freimer

first: Oren

last: Shaked

first: Sahin

last: Naqvi

first: Nasa

last: Sinnott-Armstrong

first: Arwa

last: Kathiria

first: Amy

last: Chen

first: Jessica

last: Cortez


title: Single Cell Immunophenotyping of Lyme Erythema Migrans Identifies IgM-Switched Memory B Cells (10X Single-Cell Gene Expression)

first: Hailong

last: Meng

overall_design:
Six subjects were studied, all with confirmed cases of Lyme Disease. Five of six had samples from both EM rash and unaffected skin. One subject had sample only from EM rash. One subject had an additional PBMC sample.

UPDATE [Apr-27-2025] The .rds file was replaced.

first: Tony

last: Melillo

first: Ruoyi

last: Jiang

first: Linda

last: Bockenstedt


title: Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19

status: Public on Apr 05 2021


title: Differentially expressed miRNAs in colorectal cancer

first: Guangxian

last: Xu

summary: Colorectal cancer (CRC) is one of the most malignant cancers with high morbidity and mortality. MicroRNAs (miRNAs) are small noncoding RNAs that affect biological processes by binding to mRNAs and regulating their expression, and epigenetic alterations including miRNA dysregulation are significantly involved in CRC development. Here we report significantly up-regulated as well as down-regulated miRNAs in CRC tissues compared with their matched non-tumoral tissues.

overall_design: Examination of  Differential expression of miRNAs between 3 pairs of colorectal tumor tissues and normal tissues

first: Dan


title: Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19 [single-cell RNA-seq]

summary: A dysregulated immune response against the SARS-CoV-2 virus plays a critical role in severe COVID-19. However, the molecular and cellular mechanisms by which the virus causes lethal immunopathology are poorly understood. Here, we utilize multi-omics single-cell analysis to probe dynamic immune responses in patients with stable or progressive manifestations of COVID-19, and assess the effects of tocilizumab, an anti-IL-6 receptor monoclonal antibody. Coordinated profiling of gene expression and cell lineage protein markers reveals a prominent type-1 interferon response across all immune cells, especially in progressive patients. An anti-inflammatory signature in monocytes and a pre-exhaustion phenotype in activated T cells are hallmarks of progressive disease. Single-cell T and B cell receptor repertoire analysis reveal a skewed clonal distribution of CD8 T cells and a primary B cell response with possible contribution from memory B cells. Our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19, which may contribute to delayed virus clearance and has implications for therapeutic intervention.

overall_design: 18 PBMC samples from 10 patients at various time points were studied. Age and sex matched healthy subjects (n=13) whose samples were collected before the COVID-19 pandemic were used as controls. Single-cell RNA sequencing (scRNA-seq) was performed, as well as surface protein libraries (CITE-seq), T cell receptor (TCR) libraries and B cell receptor (BCR) libraries. The processed data for the control samples exist solely within the Seurat Rds file. There are no additional metadata or processed data files for the control samples, as there are for the COVID-19 samples.

first: Avraham

last: Unterman

first: Tomokazu

last: Sumida

first: David

middle: A

last: Hafler

first: Naftali

last: Kaminski

first: Charles

last: Dela Cruz


title: Single Cell Immunophenotyping of Lyme Erythema Migrans

relation:
SuperSeries of: GSE166796
SuperSeries of: GSE169437
SuperSeries of: GSE169438
SuperSeries of: GSE171087
SuperSeries of: GSE171215
SuperSeries of: GSE172225


title: Mouse lung DC RNA-Seq after allergic sensitization

status: Public on Jun 25 2021

city: Research Triangle Park

first: Sara

last: Grimm

address: 111 TW Alexander Dr

institute: NIEHS

summary: Transcriptome analysis of mouse lung Ly-6C+ and other DC populations with or without allergic sensitization

overall_design: Lung APCs and BM preDCs were purified before or after instillation of house dust extract and ovalbumin

first: Gentaro

last: Izumi

first: Hideki

last: Nakano

first: Keiko

first: Donald

middle: N

last: Cook


title: Expression landscape of human stromal cells in preclinical trials involving chemotherapeutic and histone demethylase KDM4-targeting agents

status: Public on Mar 23 2021

city: Shanghai

first: Yu

last: Sun

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

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Aging and age-related pathologies including multiple cancer types can be controlled by specifically targeting senescent cells, or more specifically, their hallmark feature, the senescence-associated secretory phenotype (SASP). Lysine methylation is one of the most common histone posttranslational modifications that regulate chromatin structure in mammalian cells. Changes in histone lysine methylation status have been observed during cancer progression, a consequence of dysregulation of histone lysine methyltransferases and/or their opposing demethylases. KDM4 (or JMJD2) encompasses demethylases that target histone H3 on lysines 9 and 36 sites. Frequently overexpressed in breast, colorectal, lung, prostate, and other tumor types and required for efficient cancer cell proliferation, KDM4 proteins represent novel drug targets. However, emerging studies are beginning to uncover the functional roles of KDM4 in epigenomic regulation during cellular senescence and organismal aging, thus providing a new angle to understand human aging and allowing expansion of the existing list of epigenetic targets, the drugs of which are currently limited to the pharmacological arsenal against DNA methyltransferases and histone deacetylases.

overall_design: Examination of in vivo efficacy of a KDM4 inhibitor, ML324, when combined with conventional chemotherapy in reducing the SASP and promoting tumor regression under prelinical conditions. Experimental mice xenografted with human stromal cells and cancer cells were exposed to mitoxantrone (MIT), ML324 or MIT plus ML324, agents delivered via intraperitoneal injection. Drugs were administered in a metronomic manner, given biweekly from the 3rd week of a 8 week regimen.

first: Boyi

last: Zhang


title: A deep learning approach to identify new gene targets of a novel therapeutic for human splicing disorders

status: Public on Mar 29 2021

city: Boston

first: Susan

last: Slaugenhaupt

state: Massachusetts

address: 185 Cambridge Street, CPZN-5254

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Pre-mRNA splicing is a key control point in human gene expression. Disturbances in splicing due to mutation or aberrant splicing regulatory networks lead to dysregulated protein expression and contribute to a substantial fraction of human disease. Several classes of active and selective splicing modulator compounds (SMCs) have been recently identified and establish that pre-mRNA splicing represents a viable target for therapy. This also raises the intriguing possibility that SMCs may have broad capabilities to ameliorate aberrant splicing across multiple human disorders. We describe herein the identification of BPN-15477, a novel SMC that restores correct splicing of exon 20 in the Elongator complex protein 1 (ELP1) gene carrying the major IVS20+6T>C mutation responsible for familial dysautonomia.   Given that BPN-15477 corrects splicing and increases full-length ELP1 protein in vivo, we developed a machine learning approach to evaluate the therapeutic potential of BPN-15477 to correct splicing in other human genetic diseases. Using transcriptome sequencing from compound-treated fibroblast cells, we identified treatment responsive sequence signatures, the majority of which center at the 5' splice site of exons whose inclusion or exclusion is modulated by SMC treatment. We then leveraged this model to identify 155 human disease genes that harbor ClinVar mutations predicted to alter pre-mRNA splicing as potential targets for BPN-15477 treatment. Using in vitro splicing assays, we validated representative predictions by demonstrating successful correction of splicing defects caused by mutations in the genes responsible for cystic fibrosis (CFTR), cholesterol ester storage disease (LIPA), Lynch syndrome (MLH1) and familial frontotemporal dementia (MAPT). Importantly, we also validated these predictions in two disease relevant cellular models for LIPA and CFTR, confirming that treatment increases functional protein and confirming the clinical potential for our model predictions. Our study shows that deep learning techniques can identify a complex set of sequence signatures and predict response to pharmacological modulation, strongly supporting the use of in silico approaches to expand the therapeutic potential of drugs that modulate splicing.

overall_design: Both placebo and BPN-15477 treatment were applied on six human WT fibroblast lines. Paired-end RNASeq were applied to generate twelve libraries.

first: Dadi

last: Gao

first: Elisabetta

last: Morini

first: Monica

last: Salani


title: Integrative analysis of microRNA-mRNA of muscle tissues in Qianhua Mutton Merino and Small Tail Han sheep

status: Public on Apr 16 2021

city: Changchun

first: Limin

state: Jilin

address: Xincheng Street 2888,Jingyue Distric

institute: Jilin Agricultural University

summary: We aimed to evaluated the key microRNA-mRNA network associated with sheep muscle growth and development. We used RNA-Seq to obtain the smallRNA profiles of the longissimus muscle from the QHMM and STH. The results showed that a total of 153 known sheep miRNAs were identified, and 4 known sheep miRNAs were differently expressed. Combining mRNA library data, 26 target genes of 4 known miRNAs were selected and the miRNA–mRNA network was successfully built. GO and KEGG analysis showed that 26 target genes were significantly enriched in 86 biological processes, including muscle organogenesis, myoblast migration, cell proliferation, and adipose tissue development, and nine metabolic pathways, including carbohydrate, nucleotide, and amino acid metabolic pathways. The oar-miR-655-3p and target gene ACSM3, and oar-miR-381-5p and target gene ABAT were selected for subsequent analysis based on GO and KEGG analyses. The results suggested that the DEmiRNAs, especially oar-miR-655-3p and oar-miR-381-5p play crucial roles in muscle growth and development processes. This Integrative analysis of microRNA-mRNA analysis of QHMM and STH muscle is reported for the first time.

overall_design: Muscle miRNA profiles of Qianhua Mutton Merino (QHMM) and  Small Tail Han (STH) sheep were generated by deep sequencing, three replicates in each sheep breed, using ABI Ion Proton instrument .

first: Huaizhi

last: Jiang


title: USP7 shRNA knock-down in T-ALL cells [Jurkat_HSB2_shRNA_RNA-seq]

status: Public on Mar 09 2021

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: RNAseq analysis of USP7 shRNA KD in T-ALL cell lines. USP7 shRNAs lentivirus was generated by co-transfecting 293T cells with shRNA vectors (OriGene or Sigma). T-ALL cells were transduced with USP7 shRNA lentivirus and sorted for GFP positive cells five days after transduction or selected by puromycin.

overall_design: USP7 shRNA in Jurkat (n = 4); shRNA scramble in Jurkat (n = 2); Wild-type Jurkat (n = 2); USP7 shRNA in HSB-2 (n = 4); shRNA scramble in HSB-2 (n = 2); Wild-type HSB-2 (n = 2)

middle: I

first: Dong

last: Li

first: Jinghui


title: Heterozygous and Homozygous Knock-Out of USP7 mouse models [mouse_RNA-seq]

summary: RNAseq analysis of USP7 conditional knock-out (cKO) mice. They were designed to flox exon 6 of USP7 and to allow deletion of exon 6 upon expression of Cre recombinase 27. USP7FL/FL mice were bred with Vav1-Cre mice to obtain USP7FL/wt-Vav1-Cre mice (heterozygote). USP7FL/FL-Vav1-Cre mice (homozygote) were obtained via breeding of heterozygous cKO mice.

overall_design: Single allele KO (n = 3), bi-allelic KO (n = 3), wild-type with cre-induced (n = 2), wild-type without cre-induction (n = 2)


title: Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19 [CITE-seq]

first: Hailong

last: Meng

overall_design: 18 PBMC samples from 10 patients at various time points were studied. Age and sex matched healthy subjects (n=13) whose samples were collected before the COVID-19 pandemic were used as controls. Single-cell RNA sequencing (scRNA-seq) was performed, as well as surface protein libraries (CITE-seq), T cell receptor (TCR) libraries and B cell receptor (BCR) libraries. Detailed sample metadata are included in the tar archive with the processed data. The processed data for the control samples exist solely within the Seurat Rds file. There are no additional metadata or processed data files for the control samples, as there are for the COVID-19 samples.

first: Avraham

last: Unterman

first: Tomokazu

last: Sumida

first: David

first: Naftali

first: Charles


title: Control of the anterior pituitary cell lineage regulator POU1F1 by the stem cell determinant Musashi

status: Public on Jan 11 2021

city: LITTLE ROCK

first: Melanie

last: MacNicol

state: Arkansas

address: 4301 W Markham St

department: Neuroscience

institute: UAMS

summary: The high energetic cost of reproduction requires that female fertility be closely linked to metabolic status. However, the mechanisms by which the metabolic and reproductive systems communicate is still largely undefined.  We have previously reported that signaling through the major metabolic cytokine leptin controls levels of the pituitary maturation determinant POU1F1 (also referred to as Pit1) that is required for optimal reproductive function. These studies further indicated that leptin increases POU1F1levels in females by promoting Pou1f1 mRNA translation, although the mechanism ofPou1f1 mRNA translation control is unknown.  In this study, we report that the stem cell marker and mRNA translational control protein, Musashi, represses translation of the Pou1f1 mRNA. In FACS-sorted purified female somatotropes, Msi1 mRNA and Musashi protein levels are increased in the mouse model that lacks leptin signaling (Gh-CRE leprLepr-null), coincident with the observed attenuation of Pou1f1 mRNA translation. Single-cell RNA sequencing of pituitary cells from control female animals indicates that Msi1 and Pou1f1 mRNAs are co-expressed in Gh-expressing cells and immunocytochemistry analyses of these cells confirms that Musashi protein is present in the GH-containing somatotrope population. We demonstrate that Musashi interacts directly with the Pou1f1 mRNA 3’ UTR and exerts translational repression of a Pou1f1 mRNA translation reporter in vitro, and interacts with the Pou1f1 mRNA in vivo.  These findings indicate a critical role for Musashi-mediated mRNA translational regulation in the coordination between metabolic status and the maturation of pituitary somatotropes that is required for optimized reproductive function .

overall_design: single cell RNA sequencing (scRNA-seq) on pooled pituitary samples from 8-week old, virgin, diestrous female mice. Three animals were pooled to generate two scRNA-seq control samples for sequencing.  After sequencing and bioinformatics clustering using the 10x Genomics cellular barcodes and unique molecular identified (UMI) counts (see Methods), the predominant pituitary cell types (somatotropes, lactotropes, thyrotropes, gonadotropes, corticotropes and melanotropes) were identified primarily based on established pituitary endocrine expression markers (Pou1f1, Gh, Prl, Tshb, Lhb, Fshb, Pomc, Pax7),

first: Melody

last: Allensworth-James

first: Angela

last: Odle

first: Jewel

last: Banik

first: Linda

last: Hardy

first: Alex

last: Lagassse

first: Jordan

last: Bird

first: Christian

middle: L

last: Thomas

first: Nathan

last: Avaritt

first: Stephanie

middle: D

last: Byrum

first: Gwen

middle: V

last: Childs

first: Angus


title: Maastricht Human Plaque Study (MaasHPS)

status: Public on Dec 15 2020

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

summary: Microarray transcriptional profiling of carotid atherosclerotic plaques taken from symptomatic patients undergoing carotid endarterectomy surgery.

overall_design: In order to better identify processes associated with intraplaque haemorrhage (IPH) and plaque instability, in this study we compared gene makeup of low- vs high-risk atherosclerotic lesion segments from carotid endarterectomy patients, as judged from absence or presence of intraplaque haemorrhage, respectively.

first: Erik

last: Biessen


title: USP7 CRISPR knock-out in T-ALL cells [Molt4_CRISPR_RNA-seq]

first: Timothy

last: Shaw

summary: RNAseq analysis of USP7 CRISPR KO in T-ALL cell lines. Genetically modified T-ALL cells were generated using CRISPR-Cas9 technology.  Briefly, the sgRNA was designed with at least 3bp of mismatch to any other site in the human genome to mitigate the risk of off-target editing. To generate the modified cells, 400,000 cells were transiently co-transfected with / without 0.5 ug pmaxGFP plasmid (Lonza), with 33 pmol spCas9 protein, 100 pmol chemically modified sgRNA (Synthego), and 100 pmol of blocking ssODN (IDT) via nucleofection (Lonza), using solutions and programs according to the manufacturer’s recommended protocol. Five days post-nucleofection, cells were single-cell sorted by FACs into 96-well plates. Cells were clonally expanded and verified the desired modification via targeted deep sequencing

overall_design: Partial CRISPR KO of USP7 in Molt4 (n = 2); 100% CRISPR KO of USP7 in Molt4 (n = 2); Wild-type Molt4 (n = 1);

first: Dong

last: Li

first: Jinghui

last: Zhang


title: Genome-wide mapping to profile histone H3-associated epigenetic marks and chromatin conformation in senescent human stromal cells

first: Yu

last: Sun

summary:
Cellular senescence, one of the major driving forces of organismal aging and age-related pathologies, is modulated by interconnected molecular changes. Combinational analysis of high-throughput 'multi-omics' datasets can provide a multi-dimensional and integrated profile of cellular senescence to unravel the heterogeneous aging process with unprecedented throughput and details.
Linear chromatin is compacted into eukaryotic nucleus through a complex and multi-layered architecture. Consequently, chromatin conformation in a local or long-distance manner is strongly correlated with gene expression. Epigenetic study approaches such as chromosome conformation capture (3C) technology, together with its variants like 4C/5C/Hi-C, have been well developed to characterize chromatin looping and whole genome structure. DNA-binding proteins, including transcription factors, epigenetic and chromatin modifiers, govern gene expression in a highly intricate manner. To pinpoint the binding sites of DNA-binding proteins is crucial for decoding gene regulatory networks. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a widely used technique to identify DNA regions bound by a specific protein. Information derived from ChIP-seq has tremendously advanced the research of mechanisms of transcription factors, cofactors and histone modifications in regulating gene expression during cellular senescence.

overall_design: Using the ChIP-seq strategy to establish epigenome signatures and generate a wide-spectrum chromatin landscape of senescent human stromal cells, the major components of tissue microenvironment in diverse solid organs. To profile the genomic DNA sequences associated with histone H3-specific alterations including H3K9me3 and H3K36me3, and to identify epigenomes that are highly occupied by these H3 sites but potentially subject to significant changes in the course of cellular senescence. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of human stromal cells. We find that lysine 9 and lysine 36 trimethylation of histone H3 effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect a distinct cellular state between proliferation and senescence or cell cycle arrest, and image overall expression status. Finally, we show that chromatin state can be read in a spatiotemporal and cell lineage-specific manner when systematically taking advantage of ChIP-seq, ATAC-seq and RNA-seq data. This study provides a basic framework for future application of comprehensive chromatin profiling towards characterization of human senescent cells in the course of organismal aging.

first: Boyi


title: Global landscape mapping of chromatin accessibility in DNA damage-induced senescent human stromal cells

summary: We report the application of an improved assay for transposase-accessible chromatin with high-throughput sequencing in profiling changes of chromatin openning state in senescent human stromal cells. By obtaining over four billion bases of sequence from Tn5 transposase-processed chromosome DNAs, we generated genome-wide chromatin-state maps of human primary stromal cells (with a starting cell number of 50,000). This study provides a framework for the application of ATAC-Seq technique towards spatiotemporal chromatin configuration of human stromal cells upon DNA damage-induced senescence.

overall_design: Examination of 3 different cellular states in a primary normal human prosate stromal cell strain.


title: Whole transcriptome sequencing in human cervical adenocarcinoma and normal cervical tissues

status: Public on Oct 13 2020

city: Hangzhou

first: Junfen

last: Xu

state: Other (Non U.S.)

address: No.1 Xueshi Road

department: Department of Gynecologic Oncology

institute: Women’s Hospital, Zhejiang University School of Medicine

summary: mRNA, lncRNA, and miRNA signatures were identified to discriminate cervical adenocarcinoma from normal cervix by whole transcriptome sequencing. We confirmed the RNA-seq data in another cohort of clinical cervical tissue samples by qRT-PCR.We demonstrated that miR-192-5p/HNF1A-AS1/VIL1 panel could accurately discriminates adenocarcinoma from normal cervix. Moreover,we also identified the circRNA expression profiles in cervical adenocarcinoma tissues and explored the function roles and mechanisms of circular RNA circEYA1 and circSPIDR in cervical adenocarcinoma cells.

overall_design: Examination of mRNA, lncRNA, miRNA, and circRNA signatures in 4 cervical adenocarcinoma tissues and 4 normal cervical tissues

first: Weiguo

last: Lu


title: Increased IL-6 Trans-Signaling in the Airways After an Allergen Challenge

status: Public on Oct 22 2020

city: Madison

first: Yury

last: Bochkov

state: WI

address: 600 Highland Ave, K4/945 CSC

department: Pediatrics

institute: University Of Wisconsin-Madison

summary: The pro-inflammatory cytokine IL-6 is elevated in both blood and airways in asthma. IL-6 signaling is regulated by its receptor composed of two proteins, IL-6R and GP130, that are found in both membrane and soluble forms. The interaction of IL-6 with soluble IL-6R (sIL-6R) can trigger IL-6 trans-signaling in cells such as epithelial cells and fibroblasts, which express GP130, but do not produce sufficient IL-6R. We aimed to analyze IL-6 trans-signaling in the airways after an allergen challenge and to examine the potential source of sIL-6R and sGP130. In addition to protein analysis of bronchoalveolar lavages by ELISA and flow cytometry, we performed next-generation RNA sequencing (RNA-seq) to study the expression of the IL-6R subunits by eosinophils activated by IL-3 in vitro. RNA-seq and proteomic analyses confirmed that eosinophils do not produce GP130 but produce both IL-6R and ADAM10, a metalloproteinase that cleaves membrane IL-6R into sIL-6R.

overall_design: Gene expression profiles of blood eosinophils from three subjects with allergy and mild asthma that were cultured in RPMI and 10% serum with or without IL-3 (2 ng/ml) for 4 h and 20 h.

first: Stephane

last: Esnault


title: RNA sequencing of the ventral rhombomere 1 of the developing mouse

status: Public on Oct 10 2020

city: Helsinki

first: Kaia

last: Achim

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

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

overall_design: Refer to individual Series


title: mRNA transcriptome analysis of bone in a mouse model of implant-associated Staphylococcus aureus osteomyelitis

status: Public on Feb 11 2021

city: Guangzhou

first: Yihuang

last: Lin

address: No.1838 North of Guangzhou Avenue

department: Orthopaedics

institute: Nanfang Hospital, Southern Medical University

summary:
Objective: To investigate the molecular pathogenesis of bone with implant-associated osteomyelitis (IAOM) in early and chonic stages.
Methods: After a 2 mm sterile stainless pin (0.3 mm in diameter) was inserted into the bone marrow cavity, 2 μl S. aureus solution at 1 × 10e6 CFU/ml was slowly injected into the bone marrow cavity using a micro-syringe to create IAOM mice while only an equal volume of sterile PBS to create controls. Transcriptomic sequencing was performed on day 3 and 14 post-operation, respectively. Differential expression analyses of IAOM_3D vs Ctrl_3D and of IAOM _14D vs Ctrl_14D were performed using the DESeq2 R package (1.16.1); P-values were adjusted using the Benjamini and Hochberg’s approach to control the false discovery rate. The genes with an adjusted P-value < 0.05 and |log2 (Fold Change)| > 1 were recognized as differentially expressed genes (DEGs). GO, KEGG and PPI analysis of DEGs were performed to identify key genes.
Results: Differential expression analyses detected a total of 101 DEGs, among which 96 were up-regulated and 5 down-regulated in the femur, when the IAOM and control groups were compared by day 3 post-infection. The number of DEGs significantly increased up to 1,702 by day 14 post-operation, with 1,065 up-regulated and 637 down-regulated in the IAOM femurs compared with controls. Further GO, KEGG and PPI analyses of DEGs suggested that IL-6, CXCL10, IFN-γ and CXCL9 were associated with early development of IAOM.
Conclusions: Our study has revealed transcriptomic characteristics of IAOM and suggested that IL-6, CXCL10, IFN-γ and CXCL9 might play an important role in the early stage of IAOM.

overall_design: 3 mice in the IAOM group and the control group were performed total RNA sequencing on the days 3 and 14 post-operation, respectively.

first: Jianwen

last: Su

first: Yutian

last: Wang

first: Daorong

first: Xianrong

first: Bin

last: Yu


title: Lipid remodeling in response to methionine stress in MDA-MBA-468 triple-negative breast cancer cells

status: Public on Aug 11 2020

city: Irvine

first: Peter

last: Kaiser

address: Department of Biological Chemistry, 829 Health Sciences Rd

institute: University of California, Irvine

summary: Methionine is an essential amino acid and critical precursor to the cellular methyl donor S-adenosylmethionine. Unlike non-transformed cells, cancer cells have a unique metabolic requirement for methionine and are unable to proliferate in growth media where methionine is replaced with its metabolic precursor, homocysteine. This metabolic vulnerability is common among cancer cells regardless of tissue origin and is known as “methionine dependence”, “methionine stress sensitivity”, or Hoffman effect. Here, we characterize the response of lipids to methionine stress in the triple negative breast cancer cell line MDA-MB-468 and its methionine stress insensitive derivative, MDA-MB-468res-R8. Lipidome analysis identified an immediate, global decrease in lipid abundances with the exception of triglycerides and an increase in lipid droplets in response to methionine stress specifically in MDA-MB468 cells. Furthermore, specific gene expression changes were observed as a secondary response to methionine stress in MDA-MB-468, resulting in a down-regulation of fatty acid metabolic genes and up-regulation of genes in the unfolded protein response pathway. We conclude that the extensive changes in lipid abundance during methionine stress is a direct consequence of the modified metabolic profile previously described in methionine stress sensitive cells. The changes in lipid abundance likely results in changes in membrane composition inducing the unfolded protein response we observe.

overall_design: RNA profiles of the triple-negative, methionine-sensitive breast cancer line MDA-MB-468 and its methionine-insensitive derivitive cell line MDA-MB-468res-R8 during methionine stress.

first: Stacey

last: Borrego


title: Methylation and Hydroxymethylation profile of zebrafish tet2 mutant

status: Public on Sep 01 2020

city: North York

first: Vinothkumar

last: Rajan

state: ON

address: 2075 Bayview Ave, Room # M7-413

department: Biological Sciences

institute: Sunnybrook Research Institute

type: Methylation profiling by high throughput sequencing

summary: Zebrafish hematopoietic cells from kidney marrow from zebrafish tet2 mutants were compared to wild-type

overall_design: MeDIP and hmeDIP  performed across three biological replicates and 2 genotypes

first: Sergey

last: Prykhozhij

first: Jason

last: Berman

first: Martin

last: Hirst

first: Annaick

last: Carles

first: Michelle

last: Moksha


title: miRNA expression data from primary central nervous system lymphomas (PCNSL) [miRNA-4]

status: Public on Jun 05 2020

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: Expression profiling of miRNA was performed on 20 PCNSLs. A gene classifier was developed.

overall_design: Twenty PCNSL patients were selected for miRNA extraction and hybridization on Affymetrix microarrays.

last: YAMANAKA


title: Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [miRNA-array]

status: Public on Jul 01 2020

city: Glendale

first: Crystal

last: Marconett

address: 1856 Kirkby Rd

department: Translational Genomics

institute: Keck School of Medicine

summary: The alveolar epithelium is comprised of two cell types, alveolar type 1 (AT1) and type 2 (AT2) cells, the latter being capable of self-renewal and transdifferentiation into AT1 fate to establish alveolar function. Micro-RNAs (miRNAs) re critical regulators of developmental pathways, including branching morphogenesis. To determine if miRNAs also play a crucial role in establishment/maintenance of cellular identity within the alveolar epithelium, we performed genome-wide analysis of miRNAs alongside transcriptomic alterations during transdifferentiation of human AT2 (hAT2) into AT1-like cells in vitro . Our results indicated that miRNAs are tightly correlated to known gene expression pattern changes during AEC differentiation. We were able to define three phases of miRNA expression during the trans differentiation process, “early”, “late” and “consistently” changed, which further sub-classified as up- or downregulated. miRNAs with altered expression at all time points during AT1-like differentiation were the largest subgroup, suggesting the need for consistent regulation of signaling pathways to mediate transdifferentiation .  Target prediction analysis and integration with previously published gene expression data identified glucocorticoid signaling as the top pathway regulated by miRNAs. Serum/glucocorticoid kinase 1 (SGK1) emerged as a central regulatory factor with temporally-correlated loss of expression and gain of hsa-miR-424 and hsa-miR-503 expression. Functional validation demonstrated specific targeting of these miRNAs to the 3’UTR of SGK1. Taken together, our data show the time-related contribution of miRNAs to the alveolar transdifferentiation process and suggest the need for inhibition of glucocorticoid pathway signaling to achieve the AT1-like cell phenotype in vitro. The miRNA-mRNA interactions identified herein may help to establish AT2 to AT1 cell differentiation in vivo.

overall_design: human alveolar epithelial type 2 (hAT2) cells were isolated from remnant transplant lungs and differentiated into alveolar type 1 (AT1-lik cells over the course of 8 days in culture. miRNA was isolated and profiled on the Agilent miRNA and normalized using the AgiMicroRNA package in R.

first: Alessandra

last: Castaldi

first: Masafumie

last: Horie

first: Megan

middle: E

last: Rieger

first: Mickael

last: Dubourd

first: Mitsuhiro

last: Sunohara

first: Kusum

last: Pandit

first: Naftali

last: Kaminski

first: Beiyun

last: Zhou

first: Ite

last: Offringa

first: Zea

last: Borok


title: Epithelial membrane protein 2 (EMP2) regulates hypoxia induced angiogenesis in retinal epithelial cells

status: Public on Jun 03 2020

city: Los Angeles

first: Michel

middle: M

last: Sun

address: 675 Charles E Young Dr S

department: Ophthalmology

institute: UCLA

summary: Pathologic retinal neovascularization is a potentially blinding consequence seen in many common diseases including diabetic retinopathy, retinopathy of prematurity, and retinal vascular occlusive diseases, among others. The use of therapeutics targeting pro-angiogenesis factors such as vascular endothelial growth factor (VEGF) has proven to be highly effective, however considerable side effects exist and serial anti-VEGF treatment has been shown to decrease effectiveness over time. Characterization of additional regulators of neovascularization is needed to further understand neovascular disease and identify possible new therapeutic targets. This study investigates epithelial membrane protein 2 (EMP2) and its role as a possible modulator of angiogenesis in human retinal pigment epithelium (RPE) under hypoxia. EMP2 is highly expressed in human RPE and RPE cell lines. Adult retinal pigment epithelial cell line-19 (ARPE-19) cells were genetically modified to either overexpress EMP2 (OE) or knock down EMP2 (KD) and expression at the RNA and protein level was evaluated using RNA sequencing and western blot respectively. Protein expression was evaluated under both normoxic conditions and conditions of hypoxic stress with 0.5% O2. EMP2 expression was found to positively correlate with expression of the pro-angiogenesis factors hypoxia inducible factor 1-alpha (HIF-1a) and VEGF for both RNA and protein. EMP2 mediated changes in ARPE-19 cells was also found to alter the secretion of a paracrine factor(s) in conditioned media that can regulate human umbilical vein endothelial cells (HUVEC) endothelial cell migration and capillary tube formation in in vitro functional angiogenesis assays. This study identifies EMP2 as a potentially important mediator of angiogenesis in the human RPE, a tissue involved in abnormal retinal neovascularization in a number of diseases. EMP2 levels positively correlate with those of the potent pro-angiogenesis mediators HIF-1a and VEGF, however the mechanism of this relationship remains to be clarified. This study supports further investigation of EMP2 as a promising novel target for therapeutic treatment of pathologic neovascularization in the retina.

overall_design: mRNA profiles of ARPE-19 cell panel consisting of EMP2 knock down, EMP2 overexpressing, vector control, and WT ARPE-19 cells under hypoxic and normoxic conditions

first: Nina

last: Cherian

first: Ann

last: Chan

first: Alison

last: Chu

first: Madhuri

last: Wadehra

first: Lynn

middle: K

last: Gordon


title: Murine B cell response to immunization with SARS-CoV-2

status: Public on Jun 09 2020

city: New Haven

first: Hailong

last: Meng

address: 300 George Str

institute: Yale University

summary: We performed single-cell gene expression and V(D)J profiling to interrogate the blood plasmablast response in mice immunized with the receptor binding domain of the SARS-CoV-2 spike protein.

overall_design: Examination of one scRNA-seq sample of total antibody-secreting cells sorted from pooled draining lymph nodes of two C57BL/6 mice.

first: Jackson

last: Turner

first: Julian

middle: Q

first: Aaron

last: Schmitz

first: Steven

middle: H

last: Kleinstein

first: Ali

last: Ellebedy


title: Human B cell response to influenza vaccination

status: Public on Aug 13 2020

summary: We used ultrasound-guided fine needle aspiration of the draining axillary lymph nodes to interrogate influenza vaccine-induced GC responses in humans.

overall_design: Examination of 21 single-cell RNA-seq samples from PBMC and lymph node taken at multiple time points pre- and post-vaccination.

first: Julianna

last: Han

middle: J

first: Amena

last: Rizk

first: Wafaa

last: Al-Soussi

first: Tingting

last: Lei

first: Mostafa

last: Amor

first: Ketherine

last: McIntire

first: Philip

last: Meade

first: Shirin

last: Strohmeier

first: Rafael

last: Brent

first: Bassem

last: Mohammed

first: Sara

last: Richey

first: Alem

last: Haile

first: Yuhe

middle: R

last: Yang

first: Michael

last: Klebert

first: Teresa

last: Suessen

first: Sharlene

last: Teefey

first: Rachel

last: Presti

first: Florian

last: Krammer

first: Andrew

last: Ward


title: Analysis of tumor-bearing Farnesoid X Receptor and Small heterodimer Partner double knockout and control WT mice in both sexes

status: Public on Jun 15 2020

city: Houston

first: Yun Seong

last: Jeong

state: TX

address: 6565 MD Anderson Blvd.

institute: MD Anderson Cancer Center

summary: Mice were aged to a year and their livers were collected and analyzed at the end of the experiment. All the mice used in this study are on C57/B6 background.

overall_design: Since double knockout of Fxr and Shp develop spontaneous liver tumors by one year of age only in the male mice, we decided to examine their transcription profile and compare it to the female livers. WT male and female mice were used as controls.

first: Sayee

last: Anakk

first: Kangho

last: Kim

first: Ju

middle: S

last: Lee

first: Yun

first: Sung


title: Id1 in mutant KRAS lung adenocarcinoma

status: Public on Dec 14 2020

city: Pamplona

first: Silvestre

last: Vicent

address: Avenida Pío XII 55

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

summary: Analysis of global gene expression changes in mutant KRAS lung adenocarcinoma cells upon Id1 inhibition

overall_design: H1792 cell were infected with an inducible GFP shRNA or a Id1 shRNA. Cell were grown with 1 ug/ml doxuxycline for 3 days. Then, cells were trypsinized and the same amount of cells was plated for 24 hours before RNA harvesting.

first: Ignacio

last: Gil-Bazo


title: Global Analysis of the dermatophyte Trichophyton rubrum when shifted from glucose to keratin

status: Public on Sep 19 2019

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

summary:
Purpose: We evaluated T. rubrum transcriptome using high-throughput RNA-sequencing (RNA-seq) technology aiming to identify metabolic pathways modulated  the development in keratin.
Methods: T. rubrum strain CBS118892 was inoculated into 100 mL Sabouraud dextrose broth, and incubated under agitation at 28 °C for 96 h. Mycelia were aseptically transferred into 100 mL minimal medium (MM) at pH 5.0 containing 70 mM nitrate and 50 mM glucose (control) or 0.5% (w/v) bovine keratin (treatment) as the carbon source. The cultures were incubated under agitation at 28 °C for 24 h, 48 h, or 96 h. Equal amounts of RNA from three independent biological replicates of keratin or glucose cultures were sequenced with a Hiseq 2000 sequencer. Paired-end reads 150 bp in size were generated. Raw read data obtained were filtered for quality control by FastQC tool and trimmed with Trimmomatic to remove adapters and Illumina-specific sequences. Trimmed paired-end reads from each sample were aligned to the T. rubrum reference genome. Gene-level read counts were quantified with STAR’s ‘-quantModeGeneCounts’ parameter. Differential expression was analyzed with the DESeq2 bioconductor package. A Benjamini-Hochberg correction adjusted the P threshold and was applied to reveal statistically significant changes in gene expression levels. It was set to 0.05, with a log2 fold change ± 1.5 and postulated as a significantly modulated transcript abundance level. Genes surpassing these thresholds are hereinafter referred to as differentially expressed genes (DEG). They were functionally categorized with the Gene Ontology (GO) terms assigned by the Blast2GO algorithm. Highly represented categories were determined by enrichment analysis with the BayGO algorithm.
Results: Our results present adaptive strategies in response to culture media. The global modulation in response to keratin supports fungal virulence and proper adaptation to the environment, in comparison to the availability of glucose as a carbon source.
Conclusions: Our results revealed a profile of the adaptive events to the host environment, crucial to the establishment and maintenance of the infection. The observed metabolic modulation is necessary for fungus survival and perpetuation in the initial steps of the infective process in their host.

overall_design: We examined at the transcriptomic level the effects of carbon source switching from glucose to keratin in Trichophyton rubrum metabolism. We aimed to evaluate the transcriptional pattern during the early stages of the infection in the host.

first: Maíra

middle: P

last: Martins

first: Larissa

middle: G

last: Silva

first: Antonio

last: Rossi

last: Souza

first: Nilce

last: Martinez-Rossi


title: Conformation of the budding yeast pericentromere in metaphase

status: Public on Jan 13 2020

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

institute: University of Edinburgh

summary: High-resolution Hi-C in metaphase in wild type cells with and without tension, chl4Δ with tension, and sgo1-3A and sgo1Δ without tension

overall_design: Purpose: To determine how pericentromeric chromosome conformation changes in response to spindle tension and to the absence of pericentromeric cohesin and condensin.

first: Flora

last: Paldi

first: Adele

last: Marston


title: Single-cell RNAsequencing of the ventral rhombomere 1 of the developing mouse [10X Genomics]

first: Kaia

last: Achim

summary: Sequencing of the mouse ventral rhombomere 1 tissues and cells to characterize the Tal1-dependent and -independent neuronal precursor groups. The data allowed to describe the cell types in the R1 brain region, and map gene expression dynamics during bifurcation of the GABAergic and glutamatergic lineagesOur results provide a framework for understanding the development of cellular diversity in the tegmental nuclei.

overall_design: Unlabelled single cells were dissociated from selected brain regions and collected on 10xgenomics Chromium platform.

first: Juha

last: Partanen

last: Borshagovski

first: Ogli

last: Samir-Sadik


title: Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503

first: Crystal

last: Marconett


title: Downregulation of polycomb repressive complex 2 mediates cisplatin acquired resistant in testicular germ cell tumors

status: Public on Nov 11 2019

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

summary: A greater understanding of the hypersensitivity and curability of testicular germ cell tumors (TGCTs) has the potential to inform strategies to sensitize other solid tumors to conventional chemotherapies.  More than 80% of metastatic TGCT patients are cured with cisplatin-based chemotherapy. However, resistance can occur, which results in poor outcomes. The mechanisms of cisplatin hypersensitivity and resistance in these tumors and embryonal carcinoma (EC), the stem cells of TGCTs, remain largely undefined. To study the mechanisms of cisplatin acquired resistance we generated a large panel of independently derived, acquired resistant clones from three distinct parental EC models employing a protocol designed to match standard of care regimens of TGCT patients.  Transcriptomics revealed highly significant alterations shared between resistant cells regardless of their parental origin. This included a highly significant enrichment of genes normally repressed by H3K27 methylation and the polycomb repressive complex 2 (PRC2) which correlated with a substantial decrease in global H3K27me3, H2AK119 ubiquitination and expression of BMI1.  Importantly repression of H3K27 methylation with the EZH2 inhibitor GSK-126 conferred cisplatin resistance to parental cells while induction of H3K27 methylation with the histone lysine demethylase inhibitor GSK-J4 resulted in increased cisplatin sensitivity to resistant cells. A gene signature based on H3K27me gene enrichment was associated with an increased rate of recurrent/progressive disease in testicular cancer patients.  Our data indicates that repression of H3K27 methylation may be a mechanism of cisplatin acquired resistance in TGCTs and that restoration of PRC2 complex function could be a viable approach to overcome treatment failure.

overall_design: gene expression of parental and cisplatin resistant cell lines in biological triplicate were analysed


title: RNA sequencing of the left ventricle from non-failing donors and heart failure samples from the MAGNet consortium

status: Public on Dec 13 2019

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: The Myocardial Applied Genomics Network (MAGNet; www.med.upenn.edu/magnet), collects and banks human cardiac tissue for genomic research.  All subjects or next of kin provided written informed consent for tissue donation and analyses and all study protocols were approved by relevant institutional review boards. Left ventricular free-wall tissue was harvested at the time of cardiac surgery from subjects with heart failure undergoing transplantation and from unused donor hearts with apparently normal function. The heart was perfused with cold cardioplegia prior to cardiectomy to arrest contraction and prevent ischemic damage, and tissue specimens were frozen in liquid nitrogen.

overall_design:
Resource of  left ventricular transcriptomes of non-failing healthy donors, Peripartum cardiomyopathy (PPCM), Hypertrophic cardiomyopathy (HCM) and Dilated cardiomyopathy (DCM) samples
----------------------------
MAGnet Consortium

Additional processing information can be found at:
https://github.com/mpmorley/MAGNet
https://github.com/mpmorley/MAGNet/wiki

first: Kenneth

middle: B

last: Margulies

first: Thomas

last: Cappola


title: DNA methylation profiling of normal, precursor lesion and cholangiocarcinoma samples

status: Public on Jan 05 2021

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

country: Germany

institute: Heidelberg University Hospital

type: Methylation profiling by genome tiling array

summary: A detailed understanding of the molecular alterations in the course of cholangiocarcinogenesis is crucial for a better understanding of this disease and may pave the way to early diagnosis and better treatment options for cholangiocarcinoma (CCA) patients.  We analyzed a clinicopathologically well-characterized patient cohort with intraductal papillary (IPNB) or tubulopapillary biliary (ITPN) precursor lesions of the biliary tract. For a large subset of patients, the triplet sample set of non-neoplastic biliary epithelium, IPNB or ITPN, and invasive CCA was available.

overall_design: We conducted genome wide DNA methylation analyses of non-neoplastic bile duct, IPNB or ITPN and invasive CCA.

first: Reka

last: Toth

first: Damian

last: Stichel


title: Single-cell transcriptomic phenotyping combined with lineage tracing using paired B cell receptor repertoires identified both persistent antibody-secreting cell as well as memory B cell subsets after immunotherapy.

status: Public on Aug 03 2020

first: Hailong

last: Meng

summary: Disease relevant B cells during post-rituximab (RTX)relapseemerge from the unsuccessfuldepletion of pre-existing B cell clones; single-celltranscriptomic phenotyping combined with lineage tracing using paired B cell receptor repertoires identified both persistent antibody-secreting cell as well as memory B cellsubsets.

overall_design: Examination of gene expression in B-lymphocytes utilizing 10X Genomics single-cell technology, deep sequenced on Illumina NovaSeq.

first: Ruoyi

last: Jiang

first: Steven

last: Kleinstein

first: Kevin

middle: C

last: O’Connor


title: Transcriptomic profiling of adipose tissue in periparturient dairy cows

status: Public on Oct 09 2020

city: East Lansing

first: David

last: Salcedo-Tacuma

state: Mi

address: 567 Wilson road

department: Physiology

institute: Michigan State University

summary: Periparturient cows rely on adipose tissue fatty acid reserves released by lipolysis to offset the negative energy balance induced by physiological changes related to  parturition and the onset of lactation. However, lipolysis causes inflammation and structural remodeling in excess predisposes cows to disease. The objective of this study was to determine effects of the periparturient period on the transcriptomic profile of AT using NGS RNAseq

overall_design: mRNA profile of 12 mammary glands from cows  before and at two time points after parturition. Subcutaneous adipose biopsies were collected on day -11, day 6 and day 13 relative to parturition

first: Jair

last: Parales

last: Prom

first: Miguel

last: Chirivi

first: Juliana

last: Laguna

first: Adam

middle: L

last: Lock

first: G

middle: A

last: Contreras


title: Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [RNA-Seq]

first: Crystal

last: Marconett

state: CA

overall_design: Total RNA was isolated from primary alveolar epithelial cells taken from human remnant transplant lung and purified as described previously (Marconett et al., 2013).

first: Alessandra

last: Castaldi

first: Masafumie

last: Horie

first: Megan

last: Rieger

first: Mickael

last: Dubourd

first: Mitsuhiro

last: Sunohara

first: Kusum

last: Pandit

first: Naftali

last: Kaminski

first: Beiyun

last: Zhou

first: Ite

last: Offringa

middle: N

first: Zea

last: Borok


title: Convergent genes shape budding yeast pericentromeres

first: Daniel

last: Robertson

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

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Refer to individual Series


title: Hyperglycemia promotes an aggressive phenotype in breast cancer cells

status: Public on Aug 24 2019

city: Estado de Mexico

first: Rubi

last: Viedma

state: Estado de Mexico

address: Av. de los Barrios 1, Los Reyes Ixtacala,  Tlalnepantla,

department: bioquimica

country: Mexico

institute: unam

summary: Diabetes and breast cancer are common diseases with a major impact on the health sector in Mexico and worldwide. Epidemiological and experimental works support the link between type 2 diabetes and breast cancer; these data support that insulin resistance, hyperglycemia, hyperinsulinemia, and elevated levels of IGF-1 in patients with type II diabetes mellitus promote growth and invasiveness of tumor cells. The aim of the present work was to determine, by microarray, the mechanisms of action and signaling of a hyperglycemic microenvironment in the cell line (MDA-MB-231) and its effect to treatment with cisplatin (CCP). MDA-MB-231 breast cancer cells were cultured in DMEM medium, supplemented with 10% fetal bovine serum and antibiotics at 5% CO2, at 37 ˚C. We proceeded to extract total RNA for the analysis of microarrays under LG (low glucose) and HG (high glucose) conditions; for the cDNA synthesis, it was labeled with dUTP-Cy3 or dUTP-Cy5 fluorophores, using a CyScribe Firs-Strand cDNA kit. The analysis was carried out through the KEGG pathways program; some bioenergetic metabolism processes (glycolysis, biosynthesis of purines and pyrimidines, and metabolism of glycerol phospholipids) were found altered, which fulfill the feedback function to the cellular microenvironment, activating some signaling processes, such as the Hippo route, PI3K-Akt, Jak-STAT, MAPK, Ras, Wnt/β-catenin, apoptosis, and favoring an aggressive phenotype and drug resistance in a hyperglycemic microenvironment. The microarray analysis was validated by qRT-PCr of the tetraspanin and Frizzled genes.

overall_design: The cells were cultured in BG and HG media; 10 μg of total RNA were obtained and used for cDNA synthesis and labeling with a Super Script II kit Invitrogen, using the dUTP-Cy3 incorporation array for BG (control) and dUTP-Cy5 for HG. Incorporation efficiency was analyzed measuring absorbance at 555 nm for Cy3 and 655 nm for Cy5. Similar quantities of fluorophores labeled cDNA were hybridized on the oligonucleotides collection 50-mer Human10K from MWG Biotech Oligo Bio Sets (Germany). Images of the microarrays were acquired and quantified in a Scan Array 4000 using the Quant Array software from Packard BioChips (USA). A first analysis of the images and the data was performed using the Array-Pro Analyzer software from Media Cybernetics (USA).  Microarray data analysis was performed using the free software program genArise, allowing background correction, normalization, intensity filter, replicate analysis, and selection of differentially expressed genes; this program was developed in the Computing Unit of the Cellular Physiology Institute of the UNAM.

first: Luis

last: Arturo Baiza Gutman

first: Araceli

last: Rubí Vietma Rodriguez


title: Dissecting the Individual and Collective Regenerative Behavior of Muscle Stem Cells During Aging

status: Public on Aug 30 2019

city: Ann Arbor

first: Carlos

last: Aguilar

state: MI

address: 2800 Plymouth Rd.,

department: Biomedical Engineering

institute: University of Michigan - Ann Arbor

summary: We utilize an integrative genomics approach (bulk RNA-Seq, ATAC-Seq)  to show how  Muscle Stem Cells (MuSCs) from distinct age groups (young and aged) are significantly altered during the regenerative response. Transcriptional landscapes during quiescence, activation, proliferation and differentiation from young and aged mice are profiled and chromatin accessibility is compared.

overall_design: Bulk RNA-Seq and ATAC-Seq at timepoints 0, 1 day, 3 day, 5 day, day 7, and day 21 post-injury for both young and aged mouse MuSCs

first: Anna

last: Shcherbina


title: Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [ATAC-seq]

status: Public on Jul 29 2019

city: Montreal

first: Amandine

last: Bemmo

state: QC

address: 110 Avenue des Pins

institute: IRCM

summary: Pioneer transcription factors are coined as having the unique property of “opening closed chromatin sites” for implementation of cell fates. We previously showed that the pioneer Pax7 specifies melanotrope cells through deployment of an enhancer repertoire: this allows binding of Tpit, a nonpioneer factor that determines the related lineages of melanotropes and corticotropes. Here, we investigated the relation between these two factors in the pioneer mechanism. Cell-specific gene expression and chromatin landscapes were defined by scRNAseq and chromatin accessibility profiling. We found that in vivo deployment of the melanotrope enhancer repertoire and chromatin opening requires both Pax7 and Tpit. In cells, binding of heterochromatin targets by Pax7 is independent of Tpit but Pax7-dependent chromatin opening requires Tpit. The present work shows that pioneer core properties are limited to the ability to recognize heterochromatin targets and facilitate nonpioneer binding. Chromatin opening per se may be provided through cooperation with nonpioneer factors.

overall_design: ATACseq in pituitary cells and pituitary-derived cell lines

first: Alexandre

last: Mayran

first: Konstantin

last: Khetchoumian

first: Jacques

last: Drouin


title: Gene expression profile of zebrafish tet2 mutant

status: Public on Sep 01 2020

first: Vinothkumar

last: Rajan

summary: Zebrafish hematopoietic cells from kidney marrow from zebrafish tet2 mutants were compared to wild-type

overall_design: RNAseq in three biological replicates and 2 genotypes

first: Sergey

last: Prykhozhij

first: Jason

last: Berman


title: Influence of histone lysine demethylase JMJD2-specific inhibition on the senescence-associated secretory phenotype developed in human stromal cells upon DNA damage

status: Public on Nov 24 2020

city: Shanghai

first: Yu

last: Sun

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

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Recent advances in next generation sequencing (NGS) has revolutionized system-based analysis of genome-wide expression, cellular pathways and responses. We performed this epigenetic study to streamline the transcriptome profiling (RNA-seq) of human stromal cells developing a typical senescence-associated secretory phenotype (SASP) upon stress induced by DNA damage or DNA damage together with pharmacological targeting of JMJD2, a trimethylation-specific demethylase of histone H3K9 and H3K36.

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

first: Boyi

last: Zhang


title: Role of iron in the regulation of the epithelial-to-mesenchymal transition (RNA-seq)

status: Public on Oct 01 2019

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: The biological process termed Epithelial-to-Mesenchymal Transition (EMT) plays a central role in cancer cell invasion, metastasis, self-renewal and resistance to therapy1,2. Here, we characterize using RNA sequencing  the mRNA levels changes occurring during EMT induced by epidermal growth factor in breast cancer MDA-MB-468 cells.  1. Nieto, M. A., Huang, R. Y., Jackson, R. A. & Thiery, J. P. EMT: 2016. Cell 166, 21–45 (2016). 2. Puisieux, A. & Brabletz, T. & Caramel, J. Oncogenic roles of EMT-inducing transcription factors. Nat. Cell Biol. 16, 488–494 (2014).

overall_design: Analyses of 6 samples: (i) untreated (ii) EGF 72h. Experiment was performed in 3 independent biological replicates

first: Fabien

last: Sindikubwabo

first: Sylvain

last: Baulande

first: Rodriguez

last: Raphael


title: Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening


title: Deep Multiple-omics Profiling of Brain Tumors Identifies Signaling Networks Downstream of Cancer Driver Genes

status: Public on Jun 22 2019

city: Memphis

first: Timothy

middle: Isham

last: Shaw

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: We profiled the transcriptome in two high-grade glioma (HGG) mouse models driven by mutated receptor tyrosine kinase (RTK) oncogenes, platelet-derived growth factor receptor alpha (PDGFRA), neurotrophic receptor tyrosine kinase 1 (NTRK1). In addition, transcriptome for normal mouse cortex was also profiled. The transcriptome was used to define transcription factor activity by integrating with whole proteome and phosphoproteome datasets.

overall_design:
7 samples with PDGFRA Mutant, 7 samples with TPM3-NTRK1 fusions, 4 normal mouse cortex samples;
[1] A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
[2] A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
[3] Normal brain cortex of athymic nude mice

middle: I

first: Alexander

last: Diaz

first: Suzanne

last: Baker


title: NYGC ALS Consortium data

status: Public on Sep 20 2019

city: New York

first: Hemali

last: Phatnani

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

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

Consortium contacts:
Maria Pedersen: mpedersen@nygenome.org
Hemali Phatnani: hphatnani@nygenome.org
NYGC ALS Consortium: cgndhelp@nygenome.org

overall_design:
Refer to individual Series:
GSE116622
GSE124439
GSE153960


title: Microarray expression profiling data for Trp53/Brca1-null mammary tumors derived from K8+ luminal cells

status: Public on Jun 27 2019

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

summary: BRCA1 mutation-carriers are predisposed to develop Basal-like breast cancer (BLBC), and p53 mutations are present in the majority of human BLBC cases, suggesting loss of these two tumor suppressors play key roles in development of BLBC.  Recent studies suggest that the majority of human breast cancers, including BLBC, may originate from mammary epithelial cells (MECs) in the luminal lineage.  However, how loss of p53 and BRCA1 contributes to development of BLBC from luminal MECs remains largely elusive.  We developed a novel genetic targeting and lineage tracing approach based on intraductal injection of Cre-expressing adenovirus under the control of the pan-luminal Keratin 8 (K8) promoter (Ad-K8-Cre).  We performed intraductal injection of Ad-K8-Cre to female mice carrying conditional knockout alleles of Brca1 and Trp53.  The injected females developed mammary tumors within 12 months after injection.  Microarray expression profiling of these tumors showed that they most closely resembled human BLBC.

overall_design: Total RNAs from YFP+ wild-type luminal mammary epithelial cells (i.e., cells of origin) sorted from Rosa26-Stop-YFP female mice 10-14 days after intraductal induction of Ad-K8-Cre adenovirus, or from mammary tumors developed in Trp53L/L;Brca1L/L females several months after intraductal injection of Ad-K8-Cre, were prepared and subjected to microarray expression profiling.

first: Dongxi

last: Xiang


title: miRNA expression data from primary central nervous system lymphomas (PCNSL)

status: Public on Jan 17 2019

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

institute: Kyoto Prefectural University of Medicine

summary: Expression profiling of miRNA was performed on 27 PCNSLs. A gene classifier was developed.

overall_design: Twenty-seven PCNSL patients were selected for miRNA extraction and hybridization on Affymetrix microarrays.


title: Genetic disarray follows mutant KLF1-E325K expression in a congenital dyserythropoietic anemia patient

status: Public on Mar 23 2019

first: James

last: Bieker

address: One Gustave Levy Place

department: Cell, Developmental, and Regenerative Biology

institute: Mount Sinai School of Medicine

summary: Congenital dyserythropoietic anemia (CDA) type IV is caused by a heterozygous mutation, Glu325Lys (E325K), in the KLF1 transcription factor. A molecular understanding of this disease is absent, partly due to its rarity. We expanded erythroid cells from a patient’s peripheral blood and analyzed its global expression pattern. We find that a large number of erythroid pathways are disrupted, particularly those related to membrane transport, globin regulation, and iron utilization. The altered genetics lead to significant deficits in differentiation. Glu325 is within the KLF1 zinc finger domain at an amino acid critical for site specific DNA binding. The change to Lys is predicted to significantly alter the target site recognition sequence, both by subverting normal recognition and by enabling interaction with novel sites. Consistent with this, we find high level ectopic expression of genes not normally present in the red cell. These altered properties explain the patients’ clinical and phenotypic features and elucidate the dominant character of the mutation.

overall_design: Samples from one patient and one healthy individual; each analyzed at three different time points of erythroid expansion/differentiation

first: Antanas

last: Planutis


title: ELP1 splicing correction reverses proprioceptive sensory loss in familial dysautonomia

status: Public on Mar 21 2019

first: Susan

last: Slaugenhaupt

state: Massachusetts

address: 185 Cambridge Street, CPZN-5254

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Familial dysautonomia (FD) is a recessive neurodegenerative disease caused by a splice mutation in Elongator complex protein 1 (ELP1, also known as IKBKAP) which leads to variable skipping of exon 20 and to a drastic reduction of ELP1 levels in the nervous system. Clinically, many of the debilitating aspects of the disease are related to a progressive loss of proprioception, which leads to severe gait ataxia, spinal deformities and respiratory insufficiency due to neuromuscular incoordination. There is currently no effective treatment for FD and the disease is ultimately fatal. Development of a drug that targets the underlying molecular defect provides hope that the drastic peripheral neurodegeneration characteristic of FD can be halted. We demonstrate herein that the FD mouse, TgFD9; IkbkapΔ20/flox, recapitulates the proprioceptive impairment observed in individuals with FD, and we provide the in vivo evidence that postnatal correction of mutant ELP1 splicing promoted by the small molecule kinetin can rescue neurological phenotypes in FD. Daily administration of kinetin starting at birth improves sensory-motor coordination and prevents the onset of spinal abnormalities by stopping the loss of proprioceptive neurons. These phenotypic improvements correlate with increased levels of full length ELP1 mRNA and protein in multiple tissues including the peripheral nervous system (PNS). Our results show that postnatal correction of the underlying ELP1 splicing defect can rescue devastating disease phenotypes and is therefore a viable therapeutic approach for persons with FD.

overall_design: Both placebo and kinetin treatments were applied on six human FD fibroblast lines. Paired-end RNASeq was performed on these twelve fibroblast lines.

first: Elisabetta

last: Morini

first: Dadi

last: Gao

first: Connor

middle: M

last: Montgomery

first: Monica

last: Salani


title: Identification of Functional Lung Adenocarcinoma Susceptibility Loci through Positional Integration with Human Alveolar Cell Epigenomes

status: Public on Mar 18 2019

city: Glendale

first: Crystal

last: Marconett

address: 1856 Kirkby Rd

institute: Keck School of Medicine

summary: Lung adenocarcinoma (LUAD) is the predominant lung cancer subtype. To date, 15 single nucleotide polymorphisms (SNPs) have been reproducibly associated with LUAD susceptibility. However, as most SNPs identified in genome-wide association studies (GWAS) are not located in the coding regions of genes and are co-inherited with hundreds of SNPs in linkage disequilibrium (LD), mechanistic links to disease outcomes remain largely unexplored. We hypothesized that some SNPs increase LUAD risk by affecting enhancers of gene transcription in alveolar epithelial cells (AECs), the purported cells of origin for LUAD.  Forty-six LUAD risk-associated SNPs mapped to putative AEC enhancers, and 11 of these were located in FAIRE peaks. Of those, seven were predicted to form transcription factor binding motifs. For four of these, ChIPseq data confirmed the binding of the predicted transcription factors. We chose rs452384, rs6942067 and rs11364096 for functional validation. The reference (risk) allele for rs452384 forms an NKX2-1 binding site that is disrupted by the alternate allele, elicited a 42% increase in activity in H1648 LUAD cells relative to the alternative allele (P = 6.7 x 10-3), and was associated with elevated TERT levels in esophageal tissue (P = 6 x 10-8). The reference (risk) allele for rs6942067 forms an EP300 binding site disrupted by the alternate allele, elicits a 94% increase in enhancer activity relative to the alternative allele in H1648 LUAD cells (P = 2.7 x 10-2), and was associated with higher expression of potential oncogene DCBLD1 in blood (P = 5.2 x 10-16). Lastly, the alternate (risk) allele for rs11364096 disrupts binding sites for FOXA1, HDAC2 and SP1, elicits a 32% decrease in enhancer activity in A549 LUAD cells relative to the reference allele (P = 5.7 x 10-3), and LUAD data from The Cancer Genome Atlas indicates that this SNP is associated with altered expression in LUAD of four genes on other chromosomes. Our analyses provide possible mechanisms for the genetic susceptibility to LUAD, with the identification of three strong functional SNP candidates that appear to affect AEC enhancers. Further investigation of these enhancers and their target genes may ultimately yield more effective and personalized strategies for LUAD risk assessment, prevention and treatment.

overall_design: To test this hypothesis, we performed ChIP-seq for enhancer histone marks using purified primary human AECs, and carried out formaldehyde-assisted identification of regulatory elements (FAIRE) to identify transcription factor accessible DNA. We integrated this data with LUAD index SNPs and SNPs in high LD (r^2≥0.5). We performed transcription factor binding site predictions to identify SNPs likely to affect transcription factor binding. Next, we used luciferase reporter assays to test whether selected SNPs confer allele-specific enhancer activity in LUAD cell lines. Lastly, we performed expression quantitative trait locus (eQTL) analysis to identify potential target genes affected by selected SNPs.

first: Chenchen

last: Yang

first: Theresa

last: Steuve

first: Suhn

middle: K

last: Rhie

first: Jiao

last: Luo

first: Kim

last: Siegmund

first: Beiyun

last: Zhou

first: Zea

last: Borok

first: Ite

last: Offringa