title: Direct Induction of hemogenic endothelial progenitors from hPSCs by defined factors revealed by single-cell transcriptome analysis

city: University park

first: Yuqian

last: Jiang

state: PA

address: W345 millennium science complex

institute: PSU

summary: Transcription factors play critical roles in stem cell maintenance and differentiation.  Using single cell RNA sequencing, we investigated transcription factors expressed in endothelial progenitors differentiated from human pluripotent stem cells (hPSCs) and identified upregulated differential expression of SOXF subgroup members SOX7, SOX17, and SOX18. To test whether overexpression of these factors increases differentiation efficiency, we established inducible hPSC lines and found only SOX17 improved differentiation of CD34+VEC+ cells. Temporal expression analysis of SOX17 and VEC revealed that SOX17 was turned on immediately before VEC, indicating SOX17 may be a causative factor in determining hemogenic endothelial differentiation. Upon Cas13d mediated repression of SOX17, differentiation was significantly abrogated. We found SOX17 forward programming is sufficient to generate more than 50% CD34+VEC+CD73- cells. Further differentiation of SOX17 forward programmed cells generated hematopoietic progenitors that emerged via an endothelial to hematopoietic transition and significantly upregulated definitive hematopoietic transcriptional programs. Our analyses reveal an uncharacterized function of SOX17 in directing hPSCs differentiation towards hematopoietic lineages.

overall_design: One sample of hPSCs differentiated to day 5 endothelial progenitors was collected to sequence 2000-3000 cells via scRNAseq

first: Xiaojun

middle: L

last: Lian

first: Lauren

last: Randolph


title: The involvement of CdhR in Porphyromonas gingivalis during Nitric Oxide stress [RNA-seq]

status: Public on Feb 03 2023

city: Huntsville

first: Marie-Claire

last: Boutrin

address: 7000 Adventist Blvd NW

country: USA

institute: Oakwood University

type: Expression profiling by high throughput sequencing

summary: To understand the role of CdhR and its adjacent gene PG1236 in nitric oxide (NO) stress resistance, isogenic mutants P. gingivalis FLL457 (ΔPG1237::ermF), FLL458 (ΔPG1236::ermF) and FLL459 (ΔPG1236-37::ermF) were made by allelic exchange mutagenesis and their gene expression was studied under control and NO stress conditions. DNA microarray analysis of FLL457 showed that approximately 2% of the genes were up regulated and over 1% of the genes down regulated. Transcriptome analysis of FLL458 and FLL459 under NO stress showed similar modulation patterns in both mutants for a few genes. The PG1236-7 gene cluster seemed to be part of the same transcriptional unit that showed increased expression under NO stress. Recombinant CdhR showed binding activity to the predicted promoter regions of PG1459 and PG0495. Taken together, the data indicate that CdhR may play a role in NO stress resistance and be involved in a regulatory network in P. gingivalis.

overall_design:
Fresh cultures of P. gingivalis strains (mutants and wild type) were grown from overnight cell cultures under anaerobic conditions at 37ºC in BHI broth. P. gingivalis strains were grown to early exponential phase (OD600:~0.3) in BHI broth under anaerobic conditions at 37ºC. At that time point, the bacteria cultures were stressed with Diethylamine (DEA) NONOate (NO stress condition). Untreated wild type and mutant strains cell cultures grown under the same conditions were used as controls. Experiments were done in triplicates. After 15 minutes, stressed and control samples were taken from the fresh cultures. The library was generated using RiboMinus Transcriptome Isolation Kit (Life Technologies, CA) and NEXTflex RNA-Seq Kit (Bioo Scientific, TX) following the vendors’ protocols. Briefly, 2 μg total RNA (20 μl) was hybridized with 4 μl of RiboMinus probe in 100 μl hybridization buffer at 37 ºC for 5 min, which was then cooled on ice for at least 30 seconds. The sample was transferred into an Eppendorf tube containing RiboMinus Beads resuspended in 100 μl hybridization buffer, which was incubated at 37 ºC for 15 min to allow beads to bind with probes. The tube was placed on a magnetic separator for 1 min to pellet the rRNA-probe complex. The supernatant containing RiboMinus RNA was transferred into a new tube. The RiboMinus RNA was concentrated by ethanol precipitation and was resuspended in 14 μl nuclease free water. Five μl of NEXTflex RNA Fragmentation buffer (Bioo Scientific, TX) was mixed with the 14 μl RiboMinus RNA. The mixture was incubated at 95 ºC for 10 min and then chilled on ice immediately. The first and second strand cDNAs were synthesized following the Bioo Scientific protocol and the NEXTflex RNA-Seq barcode was ligated to double strand cDNA after the end repair and adenylation for multiplexing. The library was amplified by PCR. The quality of each RNA-Seq library was checked using Agilent Bioanaylzer and DNA 1000 Nano chip and the library was quantified using Qubit (Life Technology, CA). The libraries (20 samples) were loaded into a single lane of Illumina V3 flow cell for cluster generation and the sequencing was done on Illumina HiScanSQ with 100 x 100 BP of paired-end reads.
***Please note that raw data files have been lost and thus are not provided***

first: Arunima

last: Mishra

first: Charles

last: Wang

first: Yuetan

last: Dou

first: Hansel

middle: M

last: Flether


title: KDM8 epigenetically controls cardiac metabolism to prevent initiation of dilated cardiomyopathy [CUT&Tag]

status: Public on Dec 23 2022

city: Toronto

first: Paul

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cardiac metabolism is deranged in heart failure, but underlying mechanisms remain unclear. Lysine demethylase 8 (Kdm8) represses gene expression in the embryo and controls metabolism in cancer. However, its function in cardiac homeostasis is unknown. We show that Kdm8 maintains a mitochondrial gene network active by repressing Tbx15 to prevent dilated cardiomyopathy leading to lethal heart failure. Deletion of Kdm8 in mouse cardiomyocytes increased H3K36me2 with activation of Tbx15 and repression of target genes in the NAD+ pathway before dilated cardiomyopathy initiates. Moreover, NAD+ supplementation prevented dilated cardiomyopathy in Kdm8 mutant mice and TBX15 overexpression blunted NAD+-activated cardiomyocyte respiration. Furthermore, KDM8 was downregulated in human hearts affected by dilated cardiomyopathy and higher TBX15 expression defines a subgroup of affected hearts with the strongest downregulation of genes encoding mitochondrial proteins. Thus, KDM8 represses TBX15 to maintain cardiac metabolism. Our results suggest that epigenetic dysregulation of metabolic gene networks initiates myocardium deterioration towards heart failure and could underlie heterogeneity of dilated cardiomyopathy.

overall_design: CUT&Tag analysis of H3K36me2 deposition in WT and Kdm8 knockout isolated cardiomyocytes at 8 weeks of age.

first: Abdalla

last: Ahmed

first: Jibran

last: Syed

first: Yaxu

first: Lijun

last: Chi

first: Carmina

last: Perez-Romero

first: Dorothy

last: Lee

first: Etri

last: Kocaqi

first: Quetzalcóatl

last: Escalante-Covarrubias

first: Jielin

last: Yang

first: Akihiko

last: Ishimura

first: Takeshi

last: Suzuki

first: Lorena

last: Aguilar-Arnal

first: Gerard

middle: B

last: Gonzales

first: Kyoung-Han

last: Kim

last: Delgado-Olguín


title: KDM8 epigenetically controls cardiac metabolism to prevent initiation of dilated cardiomyopathy

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: TMAO treated human vascular smooth muscle cells

status: Public on Jan 02 2023

city: Cincinnati

first: Albert

middle: Phillip

last: Owens III

state: OH

address: 231 Albert Sabin Way, CVC Room 3925, ML: 542

department: Internal Medicine

institute: University of Cincinnati

summary: We utilized human aortic vascular smooth muscle cells (HAVSMCs) treated with saline or trimethylamine N-oxide (TMAO) for 5 hours

overall_design: RNA-seq from human aortic vascular smooth muscle cells treated with or without TMAO

middle: P


title: Multiomic characterization of WDR5 WIN site inhibition reveals actionable synergies for MLL-rearranged leukemia

status: Public on Jul 03 2023

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: In this study, we utilized a multi-omics approach to determine the transcriptional, translational, and proteomic responses to WIN Site inhibition in MLL-rearranged leukemia cells via RNA-Seq, Ribo-Seq, and quantitative proteomics, respectively. We also performed both a whole-genome targeting primary CRISPR screen and a secondary CRISPR screen targeting a currated collection of genes to determine genes important for sensitivity to WIN Site inhibition. These combined data sets rationally guided us in assembling a collection of compounds that, when combined with WIN Site inhibitor, synergistically inhibit growth of MLL-rearranged leukemia cells.

overall_design: MV4;11 cells were treated with either DMSO or one of two unique WIN Site inhibitors before performing RNA-Seq to determine transcriptome alterations and Ribo-Seq to determine translatome alterations. CRISPR screens were performed in MV4;11 cells to determine genes altering sensitivity to multiple WIN Site inhibitors.

first: Gregory

middle: C

last: Howard

first: William

last: Tansey

first: Qi

last: Liu


title: Rewiring the Mitochondrial Electron Transport Chain Enhances Tumor Antigen Presentation and Immunogenicity

status: Public on Dec 31 2022

city: San Diego

first: Yuqing

last: Hang

address: 10010 N Torrey Pines Rd

department: IGC Core

institute: Salk Institute for biological studies


title: KDM8 epigenetically controls cardiac metabolism to prevent initiation of dilated cardiomyopathy [RNA-seq]

first: Paul

last: Delgado-Olguin

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Kdm8 knockout mice hearts (whole ventricles) at 8, 16 and 24 weeks of age. Comparative gene expression profiling analysis of RNA-seq data for transfected Control and TBX15 overexpression plasmid in iPSC-CMs.

first: Abdalla

last: Ahmed

first: Jibran

last: Syed

first: Yaxu

first: Lijun

last: Chi

last: Perez-Romero


title: 10x genomics single cell sequencing of yak hair follicle

status: Public on Dec 10 2022

city: Lanzhou

first: qingbo

last: zheng

address: No.335, Jian 'gouyan, Xiaoxihu, Qilihe District, Lanzhou City, Gansu Province

country: China

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

summary: Hair follicles of the yak are in anagen and catagen , the hair follicles of healthy female yaks around 2 years old are collected for the preparation of single-cell suspension, the cells were sequenced by scRNA-seq on the 10x genome platform. A total of about 12000 single-cell transcriptome information were obtained. According to the reported marker genes, the main cell groups in anagen and catagen of yak were identified. Based on the analysis of pseudotime trajectory, the differentiation trajectory of epidermal cell lineage and dermal cell lineage during hair follicle development and the dynamic changes of genes during differentiation were described.

overall_design:
Single-cell RNA sequencing was performed on a single cell in the hair follicle anagen and catagen of Tianzhu white yak scapula skin.
Single-cell RNA sequencing was performed on a single cell in the hair follicle telogen of Tianzhu white yak scapula skin.

first: Heping

last: Pan

first: Ping

last: Yan

first: Qingbo

last: Zheng

last: Ye


title: Gene expression profile at single cell level of islet cells from CD and HFD mice

status: Public on Nov 30 2022

city: Nanjing

first: Hemin

last: Jiang

address: Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China

summary: High-throughput scRNA-seq transcriptionally profiled an estimated 15093 cells from CD islets and 18906 from HFD islets. The mean number of reads per sequenced cell was 43,301 for CD islets and 33,867 for HFD islets, while the median number of genes per sequenced cell was 2105 and 1775, respectively.

overall_design: We performed scRNA-seq to identify α, β, and δ cell subpopulation in a high-fat diet (HFD)-induced prediabetes mouse model.

last: Fu

first: Heming

first: Yu

last: Qian


title: Transcriptome profiling reveals of a new cell line based model system of Amyotrophic Lateral Sclerosis model

status: Public on Dec 02 2022

city: New York

first: Shuvadeep

last: Maity

state: NY

address: 12 waverly place

department: Center for Genomics and Systems Biology

institute: New york University

summary: To address the motor neuron-specific degeneration in Amyotrophic lateral sclerosis, a fatal neurodegenerative disease, we used a unique mouse stem cell differentiation system to induce cranial (NIP) and spinal motor neuron (NIL) populations. The differentiation method is published at PMID: 31157617.  We monitored transcriptome changes in the two cell lines  in the presence and absence of endoplasmic reticulum (ER) stress (mock and cyclopiazonic acid treatment). We used Nextseq 500 for sequencing and our data comprises expression profiles for ~13,800 transcripts.

overall_design: Stem cell derieved motor neurons were subjected to protein misfolding stress.  We generated transcript profiles at different time points (0hr, 6hr , 12hr) and for two replicates by deep sequencing using Illumina NextSeq500 highthroughput mode.

first: Christine

last: Vogel


title: Single-Cell RNA Sequencing Reveals the Difference of Human Normal and Degenerative Nucleus Pulposus Tissue Profiles and Cellular Interactions

status: Public on Dec 11 2022

city: Zhanjiang

first: Zhencong

last: Li

address: 57 South Renmin Avenue, Xiashan District, Zhanjiang City, Guangdong Province, China

institute: Affiliated Hospital of Guandong Medical University

summary: Background: The nucleus pulposus is a constituent structure of the human intervertebral disc, and its degeneration can cause Intervertebral disc degeneration (IDD). However the cellular molecular mechanisms involved remain elusive.     Methods: Through bioinformatics analysis, the single-cell transcriptome sequencing expression profiles of human normal nucleus pulposus cells (NNP) and human degenerative nucleus pulposus cells (DNP) were compared to clarify the transcriptome differential expression profiles of human normal and human degenerative nucleus pulposus cells. The single-cell sequencing results of the two samples were analyzed using bioinformatics methods to compare the differences in histiocytosis between human normal nucleus pulposus and human degenerated nucleus pulposus, map the histiocytes of NNP and DNP, perform cell differentiation trajectories for the cell populations of interest and predict cell function, and explore their heterogeneity by pathway analysis and Gene ontology analysis.    Results: Nine cell types were identified, which were Chondrocyte1, Chondrocyte2, Chondrocyte3, Chondrocyte4, Chondrocyte5, Endothelial, Macrophage, Neutrophil, and T cells. Analysis of the proportion of chondrocytes in different tissues revealed that chondrocyte 1 accounted for a higher proportion of normal nucleus pulposus cells and highly expressed COL2A1 compared with degenerated nucleus pulposus cells; chondrocyte 2, chondrocyte 3, chondrocyte 4, and chondrocyte 5 accounted for a higher proportion of degenerated nucleus pulposus cells compared with normal nucleus pulposus cells. Among them, chondrocyte 2 was an inhibitory calcified chondrocyte with high expression of MGP, Chondrocytes 3 were fibrochondrocytes with high expression of COL1A1, Chondrocytes 4 are chondrocytes that highly express pain inflammatory genes such as PTGES, Chondrocytes 5 were calcified chondrocytes with high expression of FN1. (Chondrocytes 4 and chondrocytes 5 were found for the first time in a study of single-cell transcriptome sequencing of disc tissue.) Cell trajectory analysis revealed that chondrocyte 1 was at the beginning of the trajectory and chondrocyte 3 was at the end of the trajectory, while chondrocyte 5 appeared first in the trajectory relative to chondrocyte 2 and chondrocyte 4.    Conclusion: After functional identification of the specifically expressed genes in five chondrocytes, it was found that chondrocyte 1 was a chondrocyte with high expression of COL2A1, COL9A2, COL11A2, and CHRDL2 in a high proportion of normal nucleus pulposus cells, and chondrocyte 3 was a fibrochondrocyte with high expression of COL1A1, COL6A3, COL1A2, COL3A1, AQP1, and COL15A1 in an increased proportion during nucleus pulposus cell degeneration. Through cell trajectory analysis, it was found that chondrocytes 5 specifically expressing FN1, SESN2, and GDF15 may be the key cells leading to degeneration of nucleus pulposus cells. Chondrocytes 2 expressing MGP, MT1G, and GPX3 may play a role in reversing calcification and degeneration, and chondrocytes 4 expressing PTGES, TREM1, and TIMP1 may play a role in disc degeneration pain and inflammation.

overall_design: A total of two human samples were analyzed including one human normal nucleus pulposus tissue and one human degenerative nucleus pulposus tissue

first: Dongping

first: Libing

last: Dai

first: Yude

last: Xu

first: Hao

last: Wu

first: Wei

last: Luo

first: Yiming

last: Liu

first: Xiguan

last: Yao

first: Peigeng

last: Wang

first: Haixiong

last: Miao

first: Jiake

first: Weiguo

last: Liang


title: Hfq RIL-seq analysis

status: Public on Nov 15 2022

city: Jena

first: Malte

last: Siemers

address: Winzerlaer Straße 2

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University

summary: In this study we used RIL-seq (RNA interaction by ligation and sequencing) to identify Hfq-mediated RNA-RNA interactions in V. cholerae.

overall_design: V. cholerae wild-type and hfq::3XFLAG-tagged strains were cultivated in LB medium to low (OD600 of 0.2) and high (OD600 of 2.0) cell densities. Cells were subjected to RIL-seq analysis. Two biological replicates for each condition are provided.

first: Michaela

last: Huber

first: Sahar

last: Melamed

first: Gisela

last: Storz

first: Kai

last: Papenfort


title: FHL3 promotes the formation of fast glycolytic muscle fibers by interacting with YY1 and muscle glycolytic metabolism

status: Public on Nov 17 2022

city: wuhan

first: wei

last: bai

address: hongshan District

institute: Huazhong Agricultural University

summary: Composition of distinct muscle fiber types plays an important role in the regulation of skeletal muscle metabolism, as well as animal meat production.Four and a half LIM domain protein 3 (FHL3) is highly expressed in fast glycolytic muscle fibers and differentially regulates the expression of MyHC isoforms at cellular levels.Here we knocked out FHL3 in C2C12 cells by CRISPR/Cas9 technology.RNA sequencing analyses revealed that the expression of MYH7 in KO cells was significantly increased, while the expression of MYH1,MYH2 and MYH4 was significantly decreased.Further comfirm FHL3 regulates the transformation of muscle fiber types.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and FHL3 KO C2C12 cells which were differentiated for 4 days.

last: Bai


title: Genome-wide methylation studies in nasal epithelial cells.

status: Public on Nov 07 2022

city: Chicago

first: Emma

last: Thompson

state: IL

address: 920 E 58th St, CLSC Rm 501

department: Human Genetics

institute: The University of Chicago

type: Methylation profiling by genome tiling array

summary: We performed an epigenome-wide association study (EWAS) of allergic sensitization using nasal epithelial cell DNA from 280 subjects.

overall_design: Nasal epithelial methylation patterns were assessed from 280 children at age 11.

first: Carole

last: Ober

first: William

last: Wentworth-Sheilds


title: Towards a mechanistic understanding of patient response to neoadjuvant SBRT with anti-PDL1 in human HPV-unrelated locally advanced HNSCC: Phase I/Ib trial results

status: Public on Nov 02 2022

city: Aurora

first: Sana

middle: D

last: Karam

state: CO

address: 1665 Aurora Ct.

department: Radiation Oncology

institute: CU Denver Anschutz

summary: Five-year survival for HPV-unrelated head and neck squamous cell carcinomas (HNSCC) remains below 50%. We assessed the safety of administering combination hypofractionated stereotactic body radiation therapy (SBRT) with anti-PDL-1 neoadjuvantly followed by adjuvant anti-PDL-1 with standard of care therapy (n=21) (NCT03635164). The primary endpoint of the study was safety, which was met. Secondary endpoints included radiographic, pathologic, and objective response, locoregional control (LRC), progression-free survival (PFS), and overall survival (OS). Among evaluable patients at early median follow-up of 16 months (448 days, or 64 weeks), OS was 80.1% with 95% C.I. (62.0%, 100.0%), LRC and PFS were 75.8% with 95% C.I. (57.5%, 99.8%), and major pathological response (MPR) or complete response (CR) was 75% with 95% exact C.I. (51.6%, 100%). Circulating CD8/Treg ratio, CD4 effector memory T cells, and TCR repertoire at time of surgery emerged as biologic correlates of response to therapy. Using high-dimensional multi-omics and spatial data as well as biological correlatives pre- and post-treatment, three major changes were noted in responders within the tumor microenvironment (TME) (and within the blood) post-treatment: 1) an increase in effector T cells; 2) a decrease in immunosuppressive cells; and 3) an increase in antigen presentation. Non-responders appeared to fail due to a lack of one of these three identified steps needed for priming and maintaining activation of T cells. Multiple correlates for response, along with subsets of non-responders that may benefit from additional or alternative immunotherapies, were identified. This treatment is being tested in an ongoing phase II trial with a similar design, where we hope to confirm and expand on our understanding of the mechanisms underlying resistance to therapy.

overall_design: Tumor tissue collected from patients at time of initial biopsy and at time of surgery were used for RNA sequencing.

first: Darragh

last: Laurel

first: Karam

last: Sana


title: SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle

status: Public on Oct 31 2022

city: Copenhagen

first: Haiyue

last: Liu

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: We combined RNA metabolic labeling and alkylation with droplet-based sequencing to detect newly synthesized mRNAs in single cells. With the classification of labeled and unlabeled precursor and mature mRNAs, we modeled and analyzed the time-dependent RNA kinetic rates associated with the cell cycle. We found both transcription and degradation rates are highly dynamic over the cell cycle and different kinetic regulation types were observed for cycling genes.

overall_design: Single cell and bulk RNA-seq of 4sU labeled, fixed and alkylated transcripts in HEK293 cells.

first: Roberto

last: Arsiè

first: Marcel

last: Schilling

first: Daniel

last: Schwabe

first: Igor

last: Minia

first: Jonathan

last: Alles

first: Christine

last: Kocks

first: Anastasiya

last: Boltengagen

first: Martin

last: Falcke

first: Nir

last: Friedman

first: Markus

last: Lanthaler

first: Nikolaus

last: Rajewsky


title: Dynamics of DNA hydroxymethylation and methylation during mouse embryonic and germline development

status: Public on Oct 28 2022

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: In mammals, DNA 5-hydroxymethylcytosine (5hmC) is involved in methylation reprogramming during early embryonic development. Yet, to what extent 5hmC participates in genome-wide methylation reprogramming remains largely unknown. Here, we characterize the 5hmC landscapes in mouse early embryos and germ cells with parental allele specificity. DNA hydroxymethylation was most strongly correlated with DNA demethylation as compared with de novo or maintenance methylation in zygotes, while 5hmC was targeted to particular de novo methylated sites in postimplantation epiblasts. Surprisingly, DNA replication was also required for 5hmC generation, especially in the female pronucleus. More strikingly, aberrant nuclear localization of Dnmt1/Uhrf1 in mouse zygotes due to maternal deficiency of Nlrp14 led to defects in DNA-replication-coupled passive demethylation and impaired 5hmC deposition, revealing the divergency between genome-wide 5-methylcytosine (5mC) maintenance and Tet-mediated oxidation. In summary, our work provides insights and a valuable resource for the study of epigenetic regulation in early embryo development.

overall_design: ACE-Seq, RNA-seq and Bisulfite sequecing of mouse germline cells.

first: Rui

last: Yan

first: Xin

last: Cheng

first: Chan

last: Gu

last: Long


title: An inflammatory state remodels the immune microenvironment and improves risk stratification in acute myeloid leukemia

status: Public on Nov 01 2022

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

summary: Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. We characterize unique inflammation signatures in a subset of AML patients, and derive an inflammation-associated gene score (iScore) that associates with poor survival outcomes in AML patients. The addition of the iScore refines current risk stratifications for AML patients and may enable the identification of patients in need of more aggressive treatment. This work provides a framework for classifying AML patients based on their immune microenvironment and a rationale for consideration of the inflammatory state in clinical settings.    This submission represents the adult RNA-Seq component of study.

overall_design: Gene expression profiling at time of AML diagnosis

first: Ann-Kathrin

last: Eisfeld

first: Deedra

last: Nicolet

last: Selen Yilmaz

first: Bettina

last: Nadorp


title: Single-cell RNA sequencing reveals the impact of CD34+ cells in heart failure

status: Public on Oct 06 2022

city: Hangzhou

first: Qingbo

last: Xu

state: Zhejiang

address: 79 Qingchun Road

department: Department of Cardiology

institute: First Affiliated Hospital, Zhejiang University School of Medicine

summary: CD34+ cells have been used to treat the patients with heart failure, but the outcome is variable. It is of great significance to scrutinize the fate and the mechanism of CD34+ cell differentiation in vivo during heart failure and explore its intervention strategy. By analyzing the transcriptomes of single cells from the Cd34-CreERT2;R26-tdTomato heart, we illustrated the dynamics of cell landscape during the progression of heart hypertrophy, including CD34+ cells, fibroblasts, endothelial cells and immune cells. And Our study also provides a cellular landscape of CD34+ cell-derived cells in the hypertrophy heart of animal models.

overall_design: scRNA-seq for total non-cardiomyocytes and CD34+ cells from Cd34-CreERT2;R26-tdTomato mice hearts

first: L

last: Du

first: X

last: SUN

first: Q


title: Dietary intake of α-ketoglutarate ameliorates α-synuclein pathology in a Parkinson’s disease mouse model

status: Public on Oct 02 2022

city: Guangzhou

first: Wenlong

last: Zhang

address: Yuexiu

institute: The First Affiliated Hospital of Guangzhou Medical University

summary: In order to investigate the effect of Alpha-Ketoglutarate (AKG) on p-α-synuclein in substantia nigra of Parkinson's disease (PD) model mice (C57BL/6), we profiled substantia nigra from wild-type (WT), AAV-α-synuclein (α-Syn), AKG and α-Syn-AKG in male mice by RNA sequencing (RNA-seq).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of wild-type (WT), AAV-α-synuclein (α-Syn), AKG and α-Syn-AKG mice.

first: Liuyan

last: Ding

first: Mengran

first: Yunlong


title: Blocking common gamma chain cytokine signaling ameliorates T-cell-mediated pathogenesis in disease models

status: Public on Oct 04 2022

city: Tarrytown

first: Kaitlyn

last: Gayvert

address: 777 Old Saw Mill River Rd

department: Molecular Profiling & Data Science

institute: Regeneron Pharmaceuticals

summary: The common γ chain (γc; IL2RG) is a subunit of the interleukin (IL) receptors for the γc cytokines IL2, IL4, IL7, IL9, IL15, and IL21. Because of the lack of appropriate neutralizing antibodies recognizing IL2RG, it has been difficult to thoroughly interrogate the role of γc cytokines in inflammatory and autoimmune disease settings. To determine whether γc cytokines might be targeted for T-cell-mediated disease prevention and treatment, we generated a new γc cytokine receptor antibody, REGN7257. Biochemical, structural and in vitro analysis showed that REGN7257 binds with high affinity to IL2RG and potently blocks signaling of all γc cytokines. In nonhuman primates, REGN7257 efficiently suppressed T-cells without impacting granulocytes, platelets or red blood cells. Using REGN7257, we showed that γc cytokines drive T-cell-mediated disease in mouse models of graft-versus-host disease (GVHD) and multiple sclerosis, by impacting multiple aspects of the pathogenic response. Importantly, we discovered that our xenogeneic GVHD mouse model recapitulates hallmarks of both acute and chronic GVHD, with T-cell expansion/infiltration into tissues and liver fibrosis, as well as hallmarks of immune aplastic anemia, with bone marrow aplasia and peripheral cytopenia. And we showed that γc cytokines contribute to disease pathology by driving all of these features. Overall, by demonstrating that broad inhibition of γc cytokine signaling with REGN7257 protects from immune-mediated disorders, our data provide evidence of γc cytokines as key drivers of pathogenic T-cell responses, offering a potentially novel strategy for the management of T-cell-mediated diseases.

overall_design: Freshly isolated human PBMCs were activated with beads coated with anti-CD3 and anti-CD28. PBMCs with and without activation are incubated with REGN7257 (anti-IL2RG) or isotype for 3 days. PBMCs from 5 unique donors were isolated. Each condition was tested in duplicate.     Experimental autoimmune encephalomyelitis (EAE) is the mouse model of human MS and is useful to investigate immune cell infiltration into the central nervous system. EAE was induced in all test animals. Three treatment groups: PBS treatment (n=8), IgG4 isotype control treatment (n=9), and REGN7257 treatment (n=10).

first: Wei

middle: K

last: Lim

first: Audrey

last: Le Floc'h

first: Kirsten

last: Nagashima


title: The integrated single cell RNAseq analysis of bone marrow cells produced by mouse-mouse intraspecies blastocyst complementation and mouse-rat interspecies blastocyst complementation

status: Public on Oct 14 2022

city: Cincinnati

first: Guolun

last: Wang

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: We report the application of single cell RNAseq analysis of bone marrow cells from mouse-mouse intraspecies blastocyst complementation and mouse-rat interspecies blastocyst complementation.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
Both interspecies and intraspecies samples were prepared from P10 mouse or rat.  The Bone marrow cells were collected from tibia and femur of P10 interspecies or intraspecies and were dissociated into single cell suspension. The GFP+ Lineage- (561317, BD) cells were purified by flow cytometry  to prepare single cell RNA 3' v3 library for sequencing with 10X Genomics platform.

All *P5 samples were prepared from P5 mouse or rat.  The Bone marrow cells were collected from tibia and femur of P5. The cells were purified by flow cytometry  to prepare single cell RNA 3' v3 library for sequencing with 10X Genomics platform.

first: Vladimir

last: Kalinichenko

first: Bingqiang

last: Wen


title: Effect of knockout of SOX9 on gene expression profile in Huh7 cells

status: Public on Oct 01 2022

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

summary: To investigate the effect of SOX9 on the expression profile of Huh-7 cells, we established SOX9 knockout (SOX9KO)Huh-7 cells by crisper-cas9 system.We then performed gene expression profiling analysis using data obtained from RNA-seq of Huh-7 and SOX9KO Huh-7 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  Huh-7 and SOX9KO Huh-7 cells.

first: Hui

last: Qian

first: Chenhong

first: Fang

last: Liu

first: Shijie

last: Chen


title: RNA Sequencing and Bioinformatics Analysis of Differentially Expressed Genes in the Peripheral Serum of Ankylosing Spondylitis patients

status: Public on Oct 16 2022

city: Qingdao

first: yongchen

last: Bie

address: No. 16, Jiangsu Road, Shinan District, Qingdao

department: Spinal Surgery

institute: The Affiliated Hospital of Qingdao University

summary: We randomly selected three serum samples each from an AS and a normal control (NC) group for high-throughput sequencing followed by using edgeR to find differentially expressed genes (DEGs). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome pathway analyses and gene set enrichment analysis (GSEA)were used to comprehensively analyze the possible functions and pathways involved with these DEGs. Protein–protein interaction (PPI) networks were constructed using the STRING database and Cytoscape. The modules and hub genes of these DEGs were identified using MCODE and CytoHubba plugins. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to validate the expression levels of candidate genes in serum samples from AS patients and healthy controls.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Serum of Ankylosing Spondylitis patients and normal controls.

first: Jianqiang

last: Kou

first: Yongchen


title: Pulmonary epithelial and endothelial cell damage, loss of repair, inhibition of fibrinolysis and cellular senscence in fatal COVID-19

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Key pulmonary findings included: 1) Loss or damage to respiratory epithelial basal cells, alveolar epithelial cells, 2) Impaired clot fibrinolysis with increased levels of plasma and lung PAI-1,  and 3) modulation of cellular senescence markers.

overall_design: Inregration of lung gene expression and viral load, pathology and plasma protein from autopsy tissue from COVID-19 patients was compared normal lung tissue

first: Kathie-Anne

last: Walters

first: John

last: Kash

first: Jeffery

last: Taubenberger


title: miR-486 is an epigenetic modulator of Duchenne muscular dystrophy pathologies [RNA-seq]

city: Birmingham

first: Matthew

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

department: Pediatrics

institute: University of Alabama at Birmingham

summary: Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle disorder resulting in muscle weakness and cardiomyopathy. MicroRNAs have shown to play a significant role in muscle development, metabolism, and disease pathologies. We demonstrated that miR-486 expression is reduced in DMD muscles and its expression levels correlate with dystrophic disease severity. miR-486 knockout mice developed disrupted myofiber architecture, decreased myofiber size, decreased locomotor activity, increased fibrosis, and metabolic defects that were exacerbated on the dystrophic mdx5cv background. We integrated RNA-sequencing and chimeric eCLIP-sequencing data to identify direct in vivo targets of miR-486 and associated dysregulated gene signatures in skeletal muscle. Together, our studies identify miR-486 as a driver of muscle remodeling in DMD, a useful biomarker for dystrophic disease progression, and highlight chimeric eCLIP-sequencing as a useful tool to identify direct in vivo microRNA target transcripts.

overall_design: Whole TA muscles were isolated from male 6-month wild type (C57/Bl6) and mdx5cv (DMD mouse model on B6 strain background)

first: Rylie

last: Hightower

first: Adrienne

last: Samani

first: Andrea

last: Reid

first: Katherine

last: English

first: Michael

last: Lopez

first: J

last: Doyle

middle: J

last: Conklin

first: David

middle: A

last: Schneider

first: Marcas

last: Bamman

first: Jeffrey

last: Widrick

last: Crossman

first: Min

last: Xie

last: Jee

first: Eric

last: Lai


title: Epigenome-wide association analysis of pancreatic exocrine cells from High Fat dietary and normal dietary mice.

status: Public on Sep 24 2022

city: moroyama-machi

first: Tomoyuki

last: Araki

country: Japan

institute: Saitama medical university

summary: Genomo wide DNA methylation analysis of isolated pancreatic exocrine cells from high fat dietary and normal dietary mice. The illumima Infinium MethylationEPIC was used to obtain DNA methylatoin profiles across approximately 287K CpGs in isolated cultured cells. Total twelve samples (seven controls and five obese cases) were included in the file.

overall_design: Bisulphite converted DNA from the twelve samples were hybridized to the lllumina Infinium MethylationEPIC.

first: T

first: N

last: Miwa


title: Acute exercise mobilizes NKT-like cells with a cytotoxic transcriptomic profile but does not augment the potency of cytokine-induced killer (CIK) cells

status: Public on Sep 12 2022

city: Tucson

first: Tiffany

middle: Marie

last: Zuniga

state: AZ

address: 1501 N Campbell Ave.

department: School of Nutritional Health and Wellness

institute: University of Arizona

summary: CD3+/CD56+ Natural killer (NK) cell-like T-cells (NKT-like cells) represent <5% of blood lymphocytes, display a cytotoxic phenotype, and can kill various cancers. NKT-like cells can be expanded ex vivo into cytokine-induced killer (CIK) cells, however this therapeutic cell product has had mixed results against hematological malignancies in clinical trials. The aim of this study was to determine if NKT-like cells mobilized during acute cycling exercise could be used to generate more potent anti-tumor CIK cells from healthy donors. An acute exercise bout increased NKT-like cell numbers in blood 2-fold. Single cell RNA sequencing revealed that exercise mobilized NKT-like cells have an upregulation of genes and transcriptomic programs associated with enhanced anti-tumor activity, including cytotoxicity, cytokine responsiveness, and migration. Exercise, however, did not augment the ex vivo expansion of CIK cells or alter their surface phenotypes after 21-days of culture. CIK cells expanded at rest, during exercise (at 60% and 80% VO2max) or after (1h post) were equally capable of killing leukemia, lymphoma, and multiple myeloma target cells with and without cytokine (IL-2) and antibody (OKT3) priming in vitro. We conclude that acute exercise in healthy donors mobilizes NKT-like cells with an upregulation of transcriptomic programs involved in anti-tumor activity, but does not augment the ex vivo expansion of CIK cells.

overall_design: Blood samples were collected from 3 healthy volunteers (age 27-41 yrs) at rest, during graded exercise at 80% VO2max, and at 1hr post exercise (+1H). Isolated PBMCs underwent single cell RNA sequencing (scRNAseq) and gene expression analysis was performed on NKT-like cell clusters from resting samples

first: Forrest

last: Baker

first: Kyle

last: Smith

first: Helena

last: Batatinha

first: Branden

last: Lau

last: Gustafson

first: Emmanual

last: Katsanis

first: Richard

last: Simpson


title: Epigenetic regulation of profibrotic macrophages in systemic sclerosis- associated interstitial lung disease

status: Public on Sep 02 2022

city: Pittsburgh

first: Tracy

last: Tabib

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

summary: Systemic sclerosis-associated interstitial lung disease (SSc-ILD) is the leading cause of death in patients with systemic sclerosis (SSc) with unclear pathogenesis and limited treatment options. Evidence strongly supports an important role for profibrotic, SPP1-expressing macrophages in SSc-ILD. We sought to define the transcriptome and chromatin structural changes of SPP1 SSc-ILD macrophages, so as to better understand their role in promoting fibrosis and to identify transcription factors associated with open chromatin driving their altered phenotype.

overall_design: We performed single cell RNA-sequencing on 11 explanted SSc-ILD and healthy control lung samples, as well as single cell ATAC-sequencing on a subset of lung samples to define altered chromatin accessibility of SPP1 macrophages. We predicted transcription factors regulating SPP1 macrophages using SCENIC and determined transcription factor binding sites associated with global alterations in SPP1 chromatin accessibility using Signac/Seurat.

first: Anna

last: Papazoglou

first: Mengqi

last: Huang

first: Melissa

last: Bulik

first: Annika

last: Lafyatis

first: Christina

last: Morse

first: John

last: Sembrat

first: Mauricio

last: Rojas

first: Eleanor

last: Valenzi

first: Robert


title: Whole-genome bisulfite sequencing and histone 3.3 ChIP-seq of microdissected developing mouse lens

city: Bronx

first: William

last: Chang

address: 1301 Morris Park Ave

department: Ophthalmology

institute: Albert Einstein College of Medicine

summary: Using whole genome bisulfite sequencing (WGBS), we investigated dynamics of DNA methylation and chromatin changes during mouse lens fiber and epithelium differentiation between embryos (E14.5) and newborns (P0.5) using microdissected lenses. Histone H3.3 variant chromatin landscapes were also generated by ChIP-seq using microdissected newborn lenses.

overall_design: Whole-genome bisulfite sequencing (WGBS) of DNA methylation in microdissected mouse lens epithelium and fiber in embryonic (E14.5) and newborn (P0.5) mice, and histone 3.3 ChIP-seq of microdissected lens epithelium and fiber in newborn mice (P1)

first: Yilin

last: Zhao

first: Danielle

last: Rayee

first: Qing

last: Xie

first: Masako

last: Suzuki

first: Deyou

last: Zheng

first: Ales

last: Cvekl


title: Targeted epigenetic induction of mitochondrial biogenesis enhances antitumor immunity in mouse model

city: Kyoto

first: Madhu

last: Malinee

state: Kyoto

address: Kitashirakawa-Oiwakecho,

department: Graduate School of Science

institute: Kyoto University

summary: Cancer immunotherapy using monoclonal antibodies (mAbs) to immune checkpoint (e.g., PD-1) has revolutionized the cancer treatments with long-term clinical benefits and being applicable to a wide range of tumors. However, a significant fraction of cancer patients does not respond to PD-1 blockade-based monotherapy. Considering the potential of combinatorial therapies in overcoming existing limitations of cancer immunotherapy, there is an increasing need to identify small-molecule modulators of immune cells capable of augmenting the effect of PD-1 blockade, leading to better cancer treatment. Although epigenetic drugs have shown potential in combination therapy, the lack of sequence specificity is a major concern. Pyrrole–imidazole polyamide (PIP), a selective DNA-binding small molecule, can guide epigenetic modulators to enable targeted gene activation.  Here, we prepared and screened a library of PIPs encompassing the distinct PIPs conjugated with P300/CBP-selective bromodomain inhibitor (BI), which acts as a P300/CBP recruiter, and identified a PIP called BI-PIP-R that can trigger the targeted induction of the peroxisome proliferator-activated receptor-gamma coactivator 1 alpha/beta (PGC-1a/b), a regulator of mitochondrial activation and biogenesis. We further improved the chemical architecture of BI-PIP-R using a tri-arginine vector for better nuclear accumulation. This designer dual-functional molecule termed EnPGC-1 that enhanced mitochondrial activation, energy metabolism, proliferation of CD8+ T cells in vitro, and, in particular, enhanced oxidative phosphorylation (OXPHOS), a feature of long-lived memory T cells. Genome-wide gene analysis also suggested that EnPGC-1 and not the control compounds can regulate of T cell activation as a major biological process. EnPGC-1 also synergized with PD-1 blockade to enhance antitumor immunity and improved the survival. Together, this study represents the first example of a programmable DNA-based epigenetic drug with the potential to overcome the existing issues in cancer immunotherapy.

overall_design: Murine primary CD8+ T cells TCR stimulated (with anti-CD3+CD28 mAb) and treated with PIPs (EnPGC-1, Ctrl PIP, SGC-CBP30) or DMSO vehicle.

first: Ganesh

middle: N

last: Pandian

first: Hiroshi

last: Sugiyama


title: Genome-wide expression profiling reveals novel biomarkers in epithelial ovarian cancer

status: Public on Sep 13 2022

city: Teliyarganj, Prayagraj

first: Priyanka

last: Gautam

state: Uttar Pradesh

address: Department of Biotechnology, MNNIT Allahabad

department: Biotechnology

country: India

institute: Motilal Nehru National Institute of Technology

summary: This study sought to identify hub genes and prospective pathways that would help in comprehending the molecular mechanisms involved in the development of EOC.

overall_design: Gene expression profiling of 2 normal and 4 ovarian cancer samples.

first: Sameer

last: Gupta

first: Manisha

last: Sachan


title: MUC1-C ACTIVATES THE SET1A/WDR5 COMPASS COMPLEX AND H3K4 TRIMETHYLATION IN CANCER STEM CELLS

status: Public on Aug 24 2022

city: Boston

first: Atrayee

last: Bhattacharya

state: Massachusetts

address: 450 Brookline Avenue, Boston 02215

institute: Dana Farber Cancer Institute, Harvard Medical School

summary: MUC1-C activates the COMPASS SET1A/WDR5 complex in integrating the induction of genes that promote chronic inflammation, pluripotency and the cancer stem cell state

overall_design: RNA-seq in BT549 cell line


title: Single-cell transcriptomics and analysis for new molecular regulators of sleep

city: Philadelphia

first: Utham Kashyap

last: Valekunja

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

institute: University of Pennsylvania

summary: The molecular mechanisms governing sleep are largely unknown. Here, we used a combination of single-cell RNA sequencing to interrogate the molecular and functional underpinnings of sleep. Different cell types in three important brain regions for sleep (brainstem, cortex and hypothalamus) had a similar transcriptional response to sleep need, with a large proportion of cells changing during recovery sleep. In contrast, sleep deprivation regulated expression of different functions in each brain region. This includes antigen processing, synaptic transmission and cellular metabolism in brainstem, cortex and hypothalamus, respectively. Increased sleep need enhances expression of the transcription factors Sox2, Mafb, and Zic1 in brainstem; Hlf, Cebpb and Sox9 in cortex, and Atf3, Fosb and Mef2c in hypothalamus. In turn, these transcription factors regulate downstream gene expression during sleep deprivation and recovery. In cortex, we also interrogated the proteome of two major cell types: neurons and astrocytes. We found surprising functional overlap of proteins that mediate vesicle and neurotransmitter transport in both cell types. In contrast, other functions were specific to each cell type.

overall_design: To assess how 12-h of sleep deprivation affected the sleep/wake behaviours, 3 days baseline EEG/EMG were recorded after mice were acclimatized for a week. Mice were recorded from for next 3-4 days (which encompassed sleep deprivation and recovery phases). Sleep deprivation was initiated at lights on [Zeitgeber Time 0 (ZT0)] by switching on the motors, choosing the continuous sweeping mode. Post sleep deprivation, animals were allowed to recover for 24-h. Baseline recording 1-day before sleep deprivation was used as the control condition (normal sleep). Following sacrifice by cervical dislocation, whole brains were isolated at ZT12 (i.e. lights off) for ad libitum Normal Sleep (NS, ZT0-12), Sleep Deprivation (SD, ZT0-12) and 12-h sleep deprivation followed by 12-h of Recovery Sleep (RS, ZT12-12) groups. Brainstem, cortex and hypothalamus were quickly dissected and tissue collected for preparation of single cell suspensions. The single cell suspensions preparation procedure for all the three brain regions was adapted from Holt and colleagues. Briefly, tissues were dissociated with Papain in the manufacturer supplied medium followed by manual trituration using a fire polished silanized Pasteur pipette and filtration through 70µm cell strainer. Cells were pelleted at 300 x g, 10 min, the supernatant was discarded, and cells resuspended in a minimal volume of PBS with 0.5% of BSA. To reduce the debris, we incubated the cell suspensions with myelin removal beads and passed it through an LS Column with 70µm pre-separation filter. Flow-through containing single cell suspension were collected and estimated the yield and viability. Single cell suspension were diluted in PBS with 0.5% of BSA to obtain ~ 350 cells/ µl and followed the 10X Genomics Chromium Single Cell Kit Version 2 manual for the capture, cDNA synthesis, library preparation, and sequencing.

first: Utham


title: Mapping the glucocorticoid gene regulatory network and alterations that contribute to steroid resistance in childhood acute lymphoblastic leukemia

status: Public on Aug 25 2022

city: Memphis

first: Daniel

last: Savic

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Independent phenotypic plasticity axes define distinct obesity sub-types [RNA-seq, mouse]

status: Public on Jul 13 2022

city: Grand Rapids

first: Luca

last: Fagnocchi

state: MI

address: 333 Bostwick AVE NE

institute: VAI

summary: Studies in genetically ‘identical’ individuals indicate that as much as 50% of complex trait variation cannot be traced to genetics or to the environment. The mechanisms that generate this ‘unexplained’ phenotypic variation (UPV) remain largely unknown. Here, we identify neuronatin (NNAT) as a conserved factor that buffers against UPV. We find that Nnat deficiency in isogenic mice triggers the emergence of a bi-stable polyphenism, where littermates emerge into adulthood either ‘normal’ or ‘overgrown’. Mechanistically, this is mediated by an insulin-dependent overgrowth that arises from histone deacetylase (HDAC)-dependent β-cell hyperproliferation. A multi-dimensional analysis of monozygotic twin discordance reveals the existence of two patterns of human UPV, one of which (Type B) phenocopies the NNAT-buffered polyphenism identified in mice. Specifically, Type-B monozygotic co-twins exhibit coordinated increases in fat and lean mass across the body; decreased NNAT expression; increased HDAC-responsive gene signatures; and clinical outcomes linked to insulinemia. Critically, the Type-B UPV signature stratifies both childhood and adult cohorts into four metabolic states, including two phenotypically and molecularly distinct types of obesity.

overall_design: We performed bulk RNA-seq on at least 3 biological replicates of primary islets isolated from 3- or 6-weeks old mice, taken from Nnat+/-p-Light, Nnat+/-p-Heavy, and wild type littermates.

first: Chih-Hsiang

last: Yang

first: J

last: Pospisilik

first: Stefanos

last: Apostle


title: Independent phenotypic plasticity axes define distinct obesity sub-types


title: Myostatin is a negative regulator of adult neurogenesis in zebrafish

status: Public on Oct 20 2022

city: St. Louis

first: Mayssa

middle: H

last: Mokalled

state: MO

address: 4523 Clayton Ave, CB 8103

department: Developmental Biology

institute: Washington University in St. Louis

summary: Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord (SC) repair in mammals. In contrast, adult zebrafish achieve functional recovery after SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism, how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b (mstnb) in a niche of dorsal ependymal progenitors after complete SC transection in zebrafish. Genetic loss-of-function in mstnb impaired functional recovery, although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines, we quantified the numbers of stem, progenitor, and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced, while newborn neurons were increased in mstnb null tissues, suggesting mstnb is a negative regulator of neurogenesis. Molecularly, neuron differentiation genes were upregulated, while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally, we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish, and establish the importance of local neurogenesis for functional SC repair.

overall_design: Gene expression profiling of mstn mutants and wildtype at control and one week post injury.

first: Vishnu

last: Saraswathy

first: Lili

last: Zhou

first: Brooke

last: Burris

first: Deepika

last: Dogra

first: Sven

last: Reischauer


title: Independent phenotypic plasticity axes define distinct obesity sub-types [RNA-seq, human]

overall_design: The Leipzig Childhood adipose tissue cohort comprises Caucasian children aged 0-18 years who underwent elective orthopedic surgery, herniotomy/orchidopexie, or other surgeries. Exclusion criteria were severe diseases and medication that might affect adipose tissue biology, such as: diabetes, generalized inflammation, malignant diseases, genetic syndromes, or permanent immobilization. Written informed consent was obtained from all parents and study protocols were approved by the local Ethics Committee (265–08, 265– 08-ff) and registered in the National Clinical Trials database (NCT02208141). BMI data were standardized to age- and sex- specific centiles by applying German reference data, and are represented as BMI standard score (SDS). Overweight and obesity are defined by a cutoff of 1.28 and 1.88 SDS (90th or 97th centile), respectively. Subcutaneous adipose tissue samples were excised during surgery, washed three times in PBS, and immediately frozen in liquid nitrogen for RNA isolation.

first: Steffen

last: Heyne

first: Antje

last: Körner


title: Identification of collateral RNA cleavage mediated by Type VI CRISPR-Cas system from Leptotrichia shahiii

status: Public on Aug 31 2022

city: Skolkovo

first: Matvei

last: Kolesnik

address: 3 Nobel str

department: Life Sciences

country: Russia

institute: Skoltech

summary: We investigated the in vivo and in vitro specificity of collateral RNA degradation mediated by LshCas13a protein encoded by Type VI CRISPR-Cas system derived from L. shahii. In our experimental system, we used Escherichia coli strain harboring Type VI spacer matching inducible transcript ("targeting" cells) or strain that does not encode spacers matching any E. coli transcripts ("nontargeting" cells). After the induction of the target transcription, cells were collected, total RNA samples were extracted from the cells and subjected to high throughput RNA sequencing with a specific protocol allowing to capture RNA degradation products. To investigate the influence of RNase toxins encoded in E. coli genome on the observed RNA degradation pattern, we repeated the described experiment on E. coli strain lacking ten known ribonuclease-encoding toxin-antitoxin loci. To investigate in vitro specificity of LshCas13a protein, we analyzed products of the degradation on total E. coli RNA by purified LshCas13a supplemented with crRNA and targeted or nontargeted transcripts. The obtained samples were processed as it was described above. All experiments were independently performed in triplicate. To detect transcript degradation sites, the obtained read pairs were filtered using trimmomatic tool and then mapped onto reference sequences using bowtie2. Next, for each nucleotide position of each strand of reference sequences the number of 5’ ends of aligned fragments were counted producing corresponding tables. The differences between the numbers of mapped 5’ ends in targeting and nontargeting samples were analyzed using edgeR package. Using this data, we identified target preferences for collateral RNA degradation by LshCas13a effectors.

overall_design: The differences between targeting and nontargeting samples were analyzed. Each experiment was performed in triplicate, i. e. each analysis included six samples (3 targeting + 3 nontargeting).

first: Matvey

first: Ishita

last: Jain

first: Ekaterina

last: Semenova

first: Konstantin

last: Severinov


title: Mapping the glucocorticoid gene regulatory network and alterations that contribute to steroid resistance in childhood acute lymphoblastic leukemia [ChIP-seq]

first: Daniel

last: Savic

summary: Glucocorticoids (GCs) are a mainstay of contemporary, multi-drug chemotherapy in the treatment of acute lymphoblastic leukemia (ALL). Although overall survival rates of childhood ALL have improved, resistance to antileukemic agents remains a major clinical concern. In particular, resistance to GCs is predictive of ALL relapse and poor clinical outcome, and it therefore represents a major hurdle limiting further improvements in survival rates. While advances have been made in identifying genes and transcriptional signatures implicated in ALL GC resistance, there remains an insufficient understanding of the impact of glucocorticoid response element (GRE) alterations in GC resistance. To therefore better understand the role of gene regulatory alterations in GC resistance, we comprehensively mapped the GC gene regulatory network in two ALL cell lines using orthogonal functional genomic assays and identified tens of thousands of GREs in the ALL genome. A closer examination revealed binding profiles that were consistent with the long-range flexible billboard model of gene regulation. GCs also induced the formation of over 250 super-enhancers, and these GC-responsive super-enhancers control the expression of genes mediating GC resistance. By further integrating our results with genetic and epigenetic data in primary ALL cells from patient cohorts at St. Jude, we identified 45 DNA sequence variants associated with ex vivo GC resistance that map to GREs and validated an associated variant within the TLE1 gene locus. We also uncovered that 1929 accessible chromatin sites associated with ex vivo GC resistance were significantly enriched at GREs. A CRISPR interference screen of these elements validated their effects on GC resistance. Overall, these data suggest that GCs initiate pervasive, genome-wide effects on the leukemia epigenome and transcriptome, while genetic and epigenetic alterations to GREs are mechanisms contributing to GC resistance in childhood ALL.

overall_design: ChIP-seq for CTCF, GR, and H3K27ac was performed in Nalm6 and 697 cells with or without prednisolone treatment. Cells grown in standard culture conditions were treated with prednisolone (10uM for 697 cells and 5uM for Nalm6 cells) for 2, 6, 12, or 24 hours. Thirty million cells were cross-linked for each replicate and time point. 5ug of specified antibody were used for IP. Independent experiments were conducted for each condition and time point.


title: Tissue-resident Memory and Circulating T cells are Early Responders to Pre-surgical Cancer Immunotherapy

status: Public on Jul 07 2022

first: Shengbao

last: Suo

state: MA

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

summary: Pre-surgical (neoadjuvant) immune checkpoint blockade has shown promising activity in multiple cancer types, but the molecular mechanisms are not well understood. Here, we characterized early kinetic changes in tumor-infiltrating and circulating immune cells in oral cancer patients treated with neoadjuvant anti-PD-1 or anti-PD-1/CTLA-4 in a phase 2 clinical trial. Tumor-infiltrating CD8 T cells that clonally expanded during immunotherapy expressed elevated tissue-resident memory and cytotoxicity programs compared to non-responding cells. These programs were already active in pre-treatment T cells that later responded, reflecting a capacity for rapid response. Treatment also induced a systemic immune response, including expansion of pre-existing and emergent T cell clonotypes undetectable prior to therapy. The frequency of activated blood CD8 T cells, including pretreatment PD-1-positive KLRG1-negative T cells, was strongly associated with intra-tumoral pathological response, and these activated cells were enriched for tumor-infiltrating T cell clonotypes. These results demonstrate how neoadjuvant checkpoint blockade induces local and systemic tumor immunity.

overall_design: Samples from 30 patients from 2 different cohorts (anti-PD-1  monotherapy, anti-PD-1+anti-CTLA-4 combination therapy)

first: Kai

middle: W

last: Wucherpfennig


title: ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome

status: Public on Jul 06 2022

city: Nashville

first: Tyler

last: Hansen

address: 2215 Garland Ave

department: Biochemistry

institute: Vanderbilt University

summary: Massively parallel reporter assays (MPRAs) test the capacity of putative gene regulatory elements to drive transcription on a genome-wide scale. Most gene regulatory activity occurs within accessible chromatin, and recently described methods have combined assays that capture these regions—such as assay for transposase-accessible chromatin using sequencing (ATAC-seq)—with self-transcribing active regulatory region sequencing (STARR-seq) to selectively assay the regulatory potential of accessible DNA (ATAC-STARR-seq). Here, we report an integrated approach that quantifies activating and silencing regulatory activity, chromatin accessibility, and transcription factor (TF) occupancy with one assay using ATAC-STARR-seq. Our strategy, including important updates to the ATAC-STARR-seq assay and workflow, enabled high-resolution testing of ~50 million unique DNA fragments tiling ~101,000 accessible chromatin regions in human lymphoblastoid cells. We discovered that 30% of all accessible regions contain an activator, a silencer or both. Although few MPRA studies have explored silencing activity, we demonstrate silencers occur at similar frequencies to activators, and they represent a distinct functional group enriched for unique TF motifs and repressive histone modifications. We further show that Tn5 cut-site frequencies are retained in the ATAC-STARR plasmid library compared to standard ATAC-seq, enabling TF occupancy to be ascertained from ATAC-STARR data. With this approach, we found that activators and silencers cluster by distinct TF footprint combinations and these groups of activity represent different gene regulatory networks of immune cell function. Altogether, these data highlight the multi-layered capabilities of ATAC-STARR-seq to comprehensively investigate the regulatory landscape of the human genome all from a single DNA fragment source.

overall_design: We examined regulatory activity, chromatin accessibility, and TF binding in GM12878 B cells using ATAC-STARR-seq. For all replicates, we sequenced reisolated plasmid DNA and reporter RNA. We also sequenced the ATAC-STARR plasmid library to check library complexity.

first: Emily

last: Hodges


title: Targeted epigenetic induction of mitochondrial biogenesis enhances antitumor immunity in mouse model [ChIP-seq]

first: Madhu

last: Malinee

summary: Cancer immunotherapy using monoclonal antibodies (mAbs) to immune checkpoint (e.g., PD-1) has revolutionized the cancer treatments with long-term clinical benefits and being applicable to a wide range of tumors. However, a significant fraction of cancer patients does not respond to PD-1 blockade-based monotherapy. Considering the potential of combinatorial therapies in overcoming existing limitations of cancer immunotherapy, there is an increasing need to identify small-molecule modulators of immune cells capable of augmenting the effect of PD-1 blockade, leading to better cancer treatment. Although epigenetic drugs have shown potential in combination therapy, the lack of sequence specificity is a major concern. Pyrrole–imidazole polyamide (PIP), a selective DNA-binding small molecule, can guide epigenetic modulators to enable targeted gene activation.  Here, we prepared and screened a library of PIPs encompassing the distinct PIPs conjugated with P300/CBP-selective bromodomain inhibitor (BI), which acts as a P300/CBP recruiter, and identified a PIP called BI-PIP-R that can trigger the targeted induction of the peroxisome proliferator-activated receptor-gamma coactivator 1 alpha/beta (PGC-1a/b), a regulator of mitochondrial activation and biogenesis. We further improved the chemical architecture of BI-PIP-R using a tri-arginine vector for better nuclear accumulation. This designer dual-functional molecule termed EnPGC-1 that enhanced mitochondrial activation, energy metabolism, proliferation of CD8+ T cells in vitro, and, in particular, enhanced oxidative phosphorylation (OXPHOS), a feature of long-lived memory T cells. Genome-wide gene analysis also suggested that EnPGC-1 and not the control compounds can regulate T cell activation as a major biological process. EnPGC-1 also synergizes with PD-1 blockade that enhances antitumor immunity and improves the survival. Together, this study represents the first example of a programmable DNA-based epigenetic drug with the potential to overcome the existing issues in cancer immunotherapy.

overall_design: Murine primary CD8+ T cells were TCR stimulated (with anti-CD3+CD28 mAb) and treated for 48 hours with PIPs EnPGC-1 or DMSO vehicle. Following the treatment, cells were prepared for ChIP assay. H3K27Ac ChIP was performed and sequenced further to get insight about the genome-wide acetylation.

first: Malinee

last: Madhu

first: Pandian

last: Ganesh N

first: Sugiyama

last: Hiroshi


title: Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression

status: Public on Jul 28 2022

city: SAINT LOUIS

first: Parker

last: Wilson

address: 660. S Euclid Ave., CB 8118

summary:
Purpose: Single cell sequencing has advanced our understanding of kidney biology. The goals of this study are to compare single nucleus RNA (snRNA-seq) and single nucleus assay for transposase accessible chromatin sequencing (snATAC-seq) from healthy control donors and donors with type 2 diabetic kidney disease to identify altered signaling pathways and chromatin accessibility patterns observed in diabetic kidney disease.

Methods: Nuclear dissociation of human kidney cortex samples was performed on samples obtained from patients undergoing tumor nephrectromy or deceased organ donors. snRNA-seq and snATAC-seq libraries were prepared using 10X Genomics kits according to manufacturers instructions. For this study, two healthy control libraries from one donor were prepared with the following chemistries (1 - single cell 3-prime v3, 1 - single cell ATAC v1) and nine DKD libraries from seven donors were prepared with the following chemistries (2 - single cell 5-prime v2 paired-end, 7 - single cell ATAC v1).

Raw data for three healthy control and three DKD snRNA-seq libraries sequenced with single nucleus 5-prime R2 only can be found in GSE13188213. Raw data for two healthy control snRNA-seq sequenced with single nucleus 5-prime paired-end and five snATAC-seq single nucleus ATAC v1 libraries can be found in GSE151302. snRNA-seq and snATAC-seq libraries from these earlier studies were recounted with cellranger (v4.0) or cellranger-atac (v2.0) to provide consistency across processed data files.

overall_design: snRNA-seq and snATAC-seq of human kidney cortex from patients with and without type 2 diabetic kidney disease

first: Yoshiharu

last: Muto

first: Benjamin

last: Humphreys


title: Single-cell RNA sequencing of human hypopharynx

status: Public on Jun 19 2022

city: Jinan

first: Rui

last: Guan

state: Shandong

address: West Wenhua Road

institute: Shandong University

summary: Cellular origins of hypopharynx diseases are crucial for further diagnosis and treatments, and the immune microenvironment in tissues may also be associated with specific cell types simultaneously. For the above reasons, we should rapidly investigate the classification and transcriptomic information of the human hypopharynx. Thus, we obtained a single-cell suspension of normal hypopharynx and conducted single-cell RNA sequencing (scRNA-seq). Here, we present the scRNA-seq data of 39315 high_x0002_quality cells from the hypopharynx of five human donors. In this dataset, we show 9 clusters of normal human hypopharynx cells. Due to the high quality of single-cell transcriptomic information, hypopharynx cells were classifed into two large groups, non-immune cells and immune. Collectively, our data provide a reliable reference for studies on hypopharynx cell biology and related diseases.

overall_design:
Examination of the expression  of cells and genes in 5 normal hypopharyngeal tissues

Please note that both raw and processed data files have been updated for the GSM6239363 sample records on April 6, 2023.

first: Dapeng

last: Lei

first: Ce

last: Li


title: Chemical, molecular, and single cell analysis reveal chondroitin sulfate proteoglycan aberrancy in fibrolamellar carcinoma

status: Public on May 20 2022

city: Ithaca

first: Praveen

last: Sethupathy

address: T7 006D Veterinary Research Tower, Box 17

department: Biomedical Sciences

institute: Cornell University

summary: Fibrolamellar carcinoma (FLC) is an aggressive liver cancer that predominantly afflicts adolescents and young adults. Patients with FLC are characterized by a heterozygous deletion on chromosome 19 that creates an oncogenic gene fusion, DNAJB1-PRKACA. The extracellular environment of FLC tumors is poorly characterized and may contribute to cancer progression, metastasis, and/or drug resistance. To bridge this knowledge gap, we propose to assess pathways relevant to proteoglycans, a major component of the extracellular matrix. We leveraged single-cell ATAC-seq to analyze the diversity of VCAN accessibility across different cell types.

overall_design: Human primary tumor and adjacent nonmalignant liver samples were resected and flash frozen. We used single cell ATAC-seq to assess genome accessibility across three types of samples; non-malignant liver (n=2), primary fibrolamellar carcinoma tumor (n=2), and metastatic fibrolamellar carcinoma (n=2).

first: Adam

last: Francisco

first: Jine

first: Alaa

middle: R

last: Farghli

first: Matt

last: Kanke

first: Bo

last: Shui

first: Paul

last: Munn

first: Jennifer

last: Grenier

last: Soloway

first: Zhangjie

last: Wang

first: Lola

last: Reid

first: Jian

last: Liu


title: Whole transcriptomics analysis of lacrimal gland during chronic inflammation progression.

status: Public on Sep 23 2022

city: La Jolla

first: Helen

last: Makarenkova

state: CA

address: 10550 N Torrey Pines Rd, MB-218

department: Molecular Medicine

institute: The Scripps Research Institute

summary: To identify the molecular pathways altered during the progression of chronic inflammation in the lacrimal gland, we compared the transcriptome of NOD.B10.H2b vs BALB/cJ mice at different time points

overall_design: We sequenced RNA from lacrimal glands of BALB/cJ (control) and NOD.H2b (disease) mice aged of 2, 4 and 6 months in triplicates.

first: Olivier

last: Mauduit

first: Vanessa

last: Delcroix

first: Takeshi

last: Umazume

first: Cintia

last: S de Paiva

first: Darlene

last: A Dartt

last: P Makarenkova


title: Immune system modulation by the adjuvants Poly (I:C) and Montanide ISA 720

status: Public on May 22 2022

city: Sao Paulo

first: Filipe

last: Menegatti de Melo

state: Sao Paulo

address: Avenida Professor Lineu Prestes, 1374

department: Microbiology

country: Brazil

institute: University of Sao Paulo

summary: We investigated the immune phenotypes induced by Poly (I:C) and Montanide ISA 720 in the context of mice immunization with a recombinant protein based on the Plasmodium vivax circumsporozoite protein sequence.

overall_design: We performed RNA-Seq from lymphocyte populations (B, T CD4+ and T CD8+) isolated 14 days after the last immunization.

first: Rodolfo

middle: F

last: Marques

last: De Melo

first: Alba

last: Gimenez


title: Transcriptomic profiling of kidney organoids treated with QNZ

status: Public on Jun 23 2022

city: Los Angeles

first: Tracy

last: Tran

address: 1425 San Pablo

institute: University of Southern California

summary:
We performed RNA-Seq on wildtype or PDK2-null human kidney organoids treated with various concentration of QNZ or control. For WT organoid we started QNZ treatment on day8 and harvested the samples on day28. For PKD2 null organoids we started treatment on day13 and harvested the samples on day20
We performed RNA-Seq on PDK2-null human organoid derived cysts treated with various concentration of QNZ or control. We started QNZ treatment on day3 and harvest on day9.

overall_design: cyst and organoid mRNA profiles of QNZ treatment vs. DMSO treatment

first: Cheng

last: Song

first: Qiuyu

last: Guo

first: Andrew

last: McMahon


title: Australian sugarcane soldier fly’s salivary gland transcriptome in response to starvation and feeding on sugarcane crops

status: Public on Jun 29 2022

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

summary: The soldier fly is an endemic pest of sugarcane in Australia. Small numbers of larvae can cause significant damage to roots and reduce the crop yields. Little is known about the composition and function of the soldier fly salivary gland, its secretions, and their roles in insect-plant interactions. In this study, we performed transcriptome analysis of the salivary glands of starved and sugarcane root-fed soldier fly larvae. A total of 31,119 highly expressed assembled contigs were identified in the salivary glands and almost 50% of them showed high levels of similarity to known proteins in Nr databases. Of all the obtained contigs, only 9,727 sequences contain an open reading frame of over 100 amino acids. Around 31% of contigs were predicted to encode secretory proteins, including some digestive and detoxifying enzymes and potential effectors. Some known salivary secreted peptides such as serine protease, cysteine proteinase inhibitors, antimicrobial peptides and venom proteins were among the top 100 highly expressed genes. Differential gene expression analysis revealed significant modulation of 850 transcripts in salivary glands upon exposure to plant roots or starvation stress. Here, we identified some venom proteins which were significantly upregulated in the salivary glands of soldier fly larvae exposed to sugarcane roots. In other insects and nematodes some of these proteins have been used to manipulate host plant defense systems and facilitate the invasion of the host plant. These findings provide a further insight into the identification of potential effector proteins involved in soldier fly- sugarcane interactions.

overall_design: in total 6 samples (3 biological replicates starved and 3 replicates exposed to food)

first: Michael

last: Furlong


title: RNA-seq for understanding effects of vitamin B12 removal on astrocyte culture

status: Public on May 17 2022

first: Yasuyuki

last: Kihara

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Astrocytes express a vitamin B12 uptake receptor, CD320/TCblR, that is regulated by S1P1 signaling. In search of genes controlled under B12 deficiency in astrocytes, we employed RNA-seq using RNA of astrocytes cultured in normal or B12 deficient media.

overall_design: Primary cultures of astrocytes were maintained on either serum-free normal or serum- and B12-free media for 2 weeks and RNA was isolated. RNA-seq was performed starting with 150 ng of RNA from each sample in biological duplicates.

first: Aran

last: Groves

first: Deepa

last: Jonnalagadda

first: Jerold

last: Chun


title: RNA-seq for understanding effects of vitamin B12 removal on astrocyte culture and understanding astrocyte S1P1 signaling

overall_design: Refer to individual Series


title: RNA-seq for understanding astrocyte S1P1 signaling

summary: Astrocytic S1P1 has been previously shown to be essential for FTY720 (an orally delivered drug for MS) efficacy (CNS), in addition to its well-known immunological mechanisms of action. FTY720-P (an analogue of S1P) is a functional antagonist to S1P1. TetTag c-Fos reporter mice displayed temporal and spatial GFP-labeling of astrocytic nuclei under experimental autoimmune encephalomyelitis (EAE) pathology. We generated astrocyte conditional S1P1-KO mice in c-Fos background (S1P1-AsCKOfos). In search of essential factors controlled by S1P-S1P1 signaling in astrocytes, we employed nuclear RNA-seq using RNA of DAPI+NeuN-GFP+ nuclei isolated from spinal cords (SCs) of EAE-induced WTfos, S1P1-AsCKOfos, and FTY720-treated WTfos mice.

overall_design: A sequencing library was produced using 0.75 ng of the amplified cDNA from WTfos, S1P1-AsCKOfos and FTY720-treated WTfos EAE induced mice astrocytic nuclei. Each group had 4, 3 and 3 samples, respectively. Their transcript profiles were generated by deep sequencing using Illumina NextSeq500.


title: EpiMatch DNA Methylation Resource

status: Public on Apr 25 2022

city: London

first: Stephan

last: Beck

address: 72 Huntley Street

department: Department of Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

summary: Genome-wide DNA Methylation Data from Illumina HumanMethylationEPIC arrays for whole blood samples from 570 healthy individuals. Raw IDAT files are available for a subset of 403 samples on EGA. Raw data (IDAT files) and associated phenotype information are available for all individuals included in this study (n=570) directly from CIBMTR. Data are available under controlled access release upon reasonable request and execution of a data use agreement. Requests should be submitted to CIBMTR at info-request@mcw.edu and include the study reference IB17-04.

overall_design: Bisulfite converted DNA from 570 whole blood samples from healthy individuals were hybridised to the Illumina Infinium MethylationEPIC array

first: Amy

last: Webster

first: Stephen

last: Spellman


title: Genome-wide maps of chromatin state in patient-derived model (PDX) of AR-positive or negative CRPC

status: Public on Apr 20 2022

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary: We investigated the global OCT1 genomic signals using high-throughput chromatin immunoprecipitation sequencing (ChIP-seq) in a patient-derived model (PDX) of androgen receptor (AR)-negative or positive castration resistant prostate cancer (CRPC).

overall_design: OCT1 and Acetyl-Histone H3 (Lys27) (AcH3K27) ChIP-seq with AR negative CRPC organoid or AR positive CRPC cells derived from PDX established from metastatic CRPC tissues were performed. We also used polyamide targeting OCT1 (OCT1-PI) (Oncogene. 2016 Dec 8;35(49):6350-6358.) to inhibit OCT1 genomic binding in CRPC cells.

first: Daisuke

last: Obinata


title: Analysis of the effects of deafening on gene expression in birdsong neural circuitry

status: Public on Apr 15 2022

city: San Francisco

last: Brainard

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

overall_design: 18 Bengalese finch (Lonchura striata domestica) adult males were either deafened by bilateral cochlea removal (9 birds) or underwent a sham surgery (9 birds). Birds were allowed to survive for 4, 9, or 14 days post-procedure (3 hearing and 3 deaf birds for each time point) before euthanasia.

first: Bradley

middle: M

last: Colquitt


title: The neuronal tyrosine kinase receptor ligand ALKAL2 mediates persistent pain

status: Public on Apr 22 2022

city: Calgary

first: Christophe

last: Altier

address: 3300 Hospital Drive NW

institute: University of Calgary

summary:
To identify putative genes that could contribute to the phenotypic plasticity of TRPV1 nociceptors in inflammation-induced sensitization, we used the Complete Freund’s Adjuvant (CFA) model of chronic inflammatory pain. Three days post intraplantar injection of CFA, ipsilateral and contralateral lumbar DRG neurons were separated, and TRPV1-pHluorin neurons were purified by FACS and analyzed through the GeneChip™ Mouse Gene 2.0 ST Array.
The array analysis provided a complete expression profile of mRNA between contralateral and ipsilateral TRPV1 neurons following inflammatory insult. In inflammatory condition, we found >100 genes to be up or down regulated in TRPV1 neurons.

overall_design: 6 samples were analysed. Primary data analysis was carried out with the Affymetrix Expression Console 1.4.1.46 software including the Robust Multiarray Average module for normalization. Gene expression data were log-transformed. A change was considered significant when the FDR-corrected p-value/q-value thresholds met the criterion q < 0.01 at fold changes > 2 (expression increments or declines larger than two).

first: Manon

last: Defaye


title: RNA-seq analysis of various strains of Mycobacterium tuberculosis under normal and acidic stress.

status: Public on Jul 15 2022

city: CHANDIGARH

first: Dibyendu

last: Sarkar

address: SECTOR 39A

institute: CSIR-IMTECH

summary: We have performred RNA-seq analysis of WT and ∆phoR Mtb H37Rv under normal and acidic stress, to investigate the role of PhoR in maintaning the pH homoeostasis of bacterium. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. For acid stress, cells at OD600 of 0.6 were pelleted, washed twice with 7H9 medium buffered with 100 mM MOPS or 2N HCl for pH 7.0 or pH 4.5, respectively, re-suspended in media of indicated pH, and finally the cells were grown further for 2 hours at 37°C. After incubation cells were combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen). RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies). Library construction, RNA-sequencing and data analysis have been carried out by Agrigenome Labs Private Limited (Cochin), India. The main purpose of this study is to understand how mycobacteria can sense acidic stress conditions and mount an appropriate stress response.

sample_organism:
Mycobacterium tuberculosis
Mycobacterium tuberculosis H37Rv

overall_design: Investigating the importance of phoP/phoR system against acidic stress.

first: Harsh

last: Goar

first: Prabhat

last: Singh


title: Time dependence of volume overload on left ventricular remodeling during preadolescence

status: Public on Apr 07 2022

city: Shanghai

first: Yuqing

last: Hu

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine

summary: We reported the RNAseq analyses of left ventricualr free wall myocardium in young volume overload (VO)  C57/BL6 mice.VO was induced by the fistula between abdominal aorta and inferior vena cava (AVF) on postnatal day 7(P7). RNAseq analyses of LV free wall at P14 and P21from VO and sham-operated mice revealed that there were 378 differentially expressed genes between VO and sham group at P14, this number decreased to 184 at P21, there were 1374 differentially expressed genes between P21 and P14 sham group, and the number chenged to 1167 at the presence of VO. GO analysis showed that in the VO and sham comparison, the upregulated genes mainly mediated cell−cell junction  and the downregulated genes mainly mediated regulation of immune response at P14, and the upregulated genes mainly mediated cell growth, and downregulated genes mainly mediated response to interferon−beta at P21. As expected, in the normal LV development during preadolescence (from P14 to P21), upregulated genes mainly mediated muscle system process  and regulation of membrane potential and the downregulated genes mainly mediated regulation of mitotic cell cycle. VO changed the LV development, the upregulated genes mainly mediated regulation of protein catabolic process and the down regulated genes mainly mediated antigen processing and presentation. KEGG pathway analysis revealed that glucagon signaling pathway was upregulated and phagosome pathway and chemokine signaling pathway were downregulated between VO and sham group at P14, protein processing in endoplasmic reticulum was upregulated and antigen processing and presentation were downregulated at P21 between VO and sham group. In the normal LV development, calcium signaling pathway  and cardiac muscle contraction pathway were upregulated while VO changed that to the arginine and proline metabolism . All the above changes were further confirmed by the functional tests.

overall_design: RNAseq analyses of left ventricular free wall myocardium in young volume overload and sham-operated C57/BL6 mice

first: Sijuan

last: Sun

first: Lincai

last: Ye

first: Fen

last: Li


title: Single-cell eQTL mapping identifies cell type specific genetic control of autoimmune disease [Genotype_data]

status: Public on Apr 08 2022

city: Darlinghurst

first: Joseph

middle: E

last: Powell

state: NSW

address: 384 Victoria Street

institute: Garvan Institute of Medical Research

summary: The human immune system displays remarkable variation between individuals, leading to differences in susceptibility to autoimmune disease. We present single cell RNA sequence data from 1,267,768 peripheral blood mononuclear cells from 982 healthy human subjects. For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs) and 990 trans-eQTL, with the majority showing cell type specific effects on gene expression. We subsequently show how eQTLs have dynamic allelic effects in B cells transitioning from naïve to memory states and demonstrate how commonly segregating alleles lead to inter-individual variation in immune function. Finally, utilizing a Mendelian randomization approach, we identify the causal route by which 305 risk loci contribute to autoimmune disease at the cellular level. This work brings together genetic epidemiology with scRNA-seq to uncover drivers of inter-individual variation in the immune system.

overall_design:
To investigate celltype specific eQTLs in PBMCs, we have genotyped blood samples from over 1000 individuals. 18 replicates were included.
Genomic DNA extracted from blood samples was genotyped using Infinium Global Screening Array-24 v2.0 Genotyping BeadChips (Illumina).

first: Seyhan

last: Yazar

first: Alex

last: Hewitt


title: Single-cell eQTL mapping identifies cell type specific genetic control of autoimmune disease

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


title: System genetics in rat HXB/BXH reference population identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose

status: Public on Mar 16 2022

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Neurogenesis in the adult hippocampus contributes to learning and memory in the healthy brain and is dysregulated in metabolic and neurodegenerative diseases, but the molecular relationships between neural stem cells activity, adult neurogenesis and global metabolism are largely unknown. We applied unbiased systems genetics to reveal genetic correlations between adult neurogenesis and metabolism of peripheral tissues in a genetic reference population of 30 HXB/BXH recombinant inbred (RI) strains, derived from a cross between spontaneously hypertensive (SHR/OlaIpcv) and Brown Norway (BN-Lx/Cub) rats. We measured the rates of precursor cell proliferation, survival of new neurons, and gene expression profiles in the hippocampi of RI and parental strains and combined them with published metabolic phenotypes to reveal a “neuro-metabolic” quantitative trait locus (QTL) for serum glucose and neuronal survival, which was further narrowed down to the Tti2 (Telo2 interacting protein 2) gene, which is a regulator of activity and stability of PIKK kinases. To validate Tti2 as a causal QTL gene, we generated a targeted frameshift mutation on the SHR/OlaIpcv background. Heterozygous SHR-Tti2+/- rats showed decreased hippocampal neurogenesis and hallmarks of dysglycemia when compared to wild-type littermates. Here we present gene expression profiling of hippocampus, liver, soleus muscle and peritoneal fat in SHR-Tti2 heterozygous rats and wild-type SHR control littermates.  Our findings suggest that Tti2 may represent a direct molecular link between glucose metabolism and structural brain plasticity.

overall_design: Gene expression profiling (RNA-Seq) of  multiple tissues (peritoneal fat, hippocampus, liver, soleus muscle) extracted from six wild type and six heterozygous Tti2 knock-out rats on the spontaneously hypertensive rat genetic background (SHR/OlaIpcv-Tti2+/+ and SHR/OlaIpcv-Tti2+/- respectively). For each tissue, five samples with the best RNA quality (the highest rin number) were sequenced.

first: Anna

last: Grzyb

first: Michal

last: Pravenec


title: Genome wide expression from esophageal biopsies of subjects with EoE-like inflammatory diseases, eosinophilic esophagitis, gastroesophageal reflux disease and healthy controls

status: Public on Feb 28 2022

city: Bern

first: Shida

last: Yousefi

state: Bern

address: Inselspital, INO-F

department: Pharmacology

country: Switzerland

institute: University of Bern

summary: Esophageal biopsy RNA was isolated from proximal esophageal biopsied RNA from patients with EoE-like inflammatory diseases (EoE-like esophagitis, lymphocytic esophagitis, non-specific esophagitis), patients with active EoE, patients with GERD, and unaffected healthy controls. EoE-like inflammatory disease patients were clinically active at the time when biopsies were taken. None of the patients (EoE-like inflammatory diseases, EoE, GERD and controls) were under anti-eosinophil treatment (including dietary restrictions).  The quality of the RNA-seq data was assessed using fastqc v. 0.11.5 1) and RSeQC v. 2.6.4 2). The reads were mapped to the reference genome using HiSat2 v. 2.1.0 3). FeatureCounts v. 1.6.0 4) was used to count the number of reads overlapping with each gene as specified in the genome annotation (Homo_sapiens.GRCh38.94). The Bioconducture package DESeq2 5) was used to test for differential gene expression between the experimental groups. TopGo 6) was used to identify gene ontology terms containing unusually many differentially expressed genes. An interactive Shiny application was set up to facilitate the exploration and visualisation of the RNA-seq results. All analyses were run in R version 3.4.4 (2018-03-15)

overall_design: RNA sequencing of esophageal biopsy RNA

first: T

last: Greuter

first: H

middle: U

last: Simon


title: Single-cell eQTL mapping identifies cell type specific genetic control of autoimmune disease [scRNAseq_data]

summary: The human immune system displays remarkable variation between individuals, leading to differences in susceptibility to autoimmune disease. We present single cell RNA sequence data from 1,267,768 peripheral blood mononuclear cells from 982 healthy human subjects. For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs) and 990 trans-eQTL, with the majority showing cell type specific effects on gene expression. We subsequently show how eQTLs have dynamic allelic effects in B cells transitioning from na√Øve to memory states and demonstrate how commonly segregating alleles lead to inter-individual variation in immune function. Finally, utilizing a Mendelian randomization approach, we identify the causal route by which 305 risk loci contribute to autoimmune disease at the cellular level. This work brings together genetic epidemiology with scRNA-seq to uncover drivers of inter-individual variation in the immune system.

overall_design: Human PBMC mRNA profiles at single cell resolution


title: Stem cell and developmental hierarchies in rhabdomyosarcoma

status: Public on Feb 05 2022

city: Cambridge

first: Qian

last: Qin

address: 24 Peabody Terrace, Unit 2002

department: Molecular Pathology Unit

institute: Massachusetts General Hospital

summary: Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood and is comprised of two major molecular subtypes. Despite sharing features with skeletal muscle, the conservation of underlying cellular hierarchy with human muscle development and the identification of molecularly-defined tumor-propagating cells have not been reported. Using single-cell RNA sequencing of patient-derived RMS, DNA-barcode cell fate mapping, and antibody enrichment and functional stem cell assays using in vitro culture and mouse xenografts, we have uncovered tumor cell hierarchies in Fusion-negative (FN-) RMS that are shared with normal human muscle development.  We also identified common developmental stages at which tumor cells become arrested.  FN-RMS resemble early muscle found in embryonic and larval development, while fusion-positive (FP-)RMS express a highly specific developmental gene program found in muscle cells transiting from embryonic to fetal development at 7-7.75 weeks of age.  FP-RMS also have neural-pathway enriched cell states, suggesting less-rigid adherence to muscle development hierarchies in this disease.  Finally, we identify a molecularly-defined tumor-propagating cell in FN-RMS that shares remarkable similarity to the newly described bi-potent, muscle mesenchyme stem/progenitor cell that makes both muscle and osteogenic cells.

overall_design: Single cell RNA-seq profiling and lineage tracing of Rhabdomyosarcoma PDX, cell line and primary patient samples

first: Yun

last: Wei

first: Chuan

last: Yan

first: David

last: Langenau


title: RNAseq facilitates quantitative analysis of wildtype, pdia6 -/- and focad -/- zebrafish livers transcriptome

status: Public on Apr 01 2022

city: SINGAPORE

first: Tze Shin

last: Teoh

address: 8A, BIOMEDICAL GROVE

country: Singapore

institute: Genome Institute of Singapore

summary: pdia6 knockout zebrafish and focad knockout zebrafish were generated to model liver diseases observed in human patient.   Livers were harvested from wt, pdia6 -/- and focad -/- adult zebrafish for RNASeq to study its transcriptome profile.

overall_design: Liver transcriptome profile of wt, pdia6 knockout and focad knockout zebrafish.

first: Bruno

last: Reversade

first: Ricardo

last: Traspas