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• The Library of Integrated Network-Based Cellular Signatures (LINCS) - NeuroLINCS

  The NeuroLINCS Center is part of the NIH Common Fund's Library of Integrated Network-based Cellular Signatures (LINCS) program, which aims to characterize how a variety of human cells, tissues and the entire organism respond to perturbations by drugs and other molecular factors. As Part of the LINCS program, the NeuroLINCS study concentrates on human brain cells, which are far less understood than other cells in the body. Our initial focus is to produce diseased motor neurons from patients by utilizing high-quality induced pluripotent stem cell (iPSC) lines from Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA) patients in addition to unaffected normal healthy controls. Using state-of-the-art OMICS methods (genomics, epigenomics, transcriptomics, and proteomics), we intend to create a wealth of cellular data that is patient-specific in the context of their baseline genetic perturbations and in the presence of other genetic and environmental perturbagens (e.g. endoplasmic reticulum stress). The primary data will be used to build cell signatures that convey the key features that distinguish the state of a cell and determine its behavior. Ultimately, the analysis of these datasets will lead to the identification of a network of unique signatures relevant to each of these motor neuron diseases. The datasets represented in this study are generated from assays interrogating RNA expression (RNA-seq), chromatin accessibility (ATAC-seq) and whole genome sequencing.

  Study phs001231

• Single Cell RNA-Seq Reveals Malignant and Stromal Programs Associated with Metastasis in Head and Neck Cancer

  This study of head and neck cancer aimed to profile individual malignant, stromal, and immune cells in treatment-naive oral cavity squamous cell carcinoma, with or without matched metastatic cervical lymph nodes. Clinical and pathologic information was collected on all patients, in addition to a fresh biopsy sample from the primary tumor and/or metastatic lymph node at the time of initial surgery. Biopsy specimens were processed for single cell RNA-seq (scRNA-seq) and/or whole exome sequencing (WES). A total of ~6,000 single cells from 18 participants were included in the final dataset. Stromal and immune cells had consistent expression programs across patients. Conversely, malignant cells varied within and between tumors in their expression of signatures related to cell cycle, stress, hypoxia, epithelial differentiation, and partial epithelial-to-mesenchymal transition (p-EMT). One of the top scoring genes in this program was TGFβ-induced (TGFBI), implicating the classic EMT regulator TGFβ. Cells expressing the p-EMT program spatially localized to the leading edge of primary tumors. By integrating single-cell transcriptomes with bulk expression profiles for hundreds of tumors, we refined Head and Neck Squamous Cell Carcinoma (HNSCC) subtypes by their malignant and stromal composition, and established p-EMT as an independent predictor of nodal metastasis, grade, and adverse pathologic features. Our results provide insight into the HNSCC ecosystem and define stromal interactions and a p-EMT program associated with metastasis.

  Study phs001474

• Space Associated Stem Cell Hallmarks of Aging in Astronauts

  This study examined the effects of the stress of space, specifically low earth orbit, on hematopoietic stem and progenitor cells (HSPCs) that maintain lifelong hematopoiesis and immune responses. Enriched CD34+ HSPCs were derived from 7 astronauts before, during and after 10 and 21-day ISS missions on the International Space Station. The samples were used as input to whole transcriptome sequencing by bulk RNA-Seq performed at The Scripps Research Institute Next Generation Sequencing Core on Illumina NextSeq 2000 sequencer and single cell RNA-Seq performed at The Salk Institute for Biological Studies on Illumina NovaSeq X Plus sequencer. Subsequent expression, RNA editing, and retrotransposon analyses were performed to assess HSPC and immune subpopulation survival dynamics. Overall, these analyses revealed space-associated stem cell hallmarks of aging (SASHA), including spaceflight dependent alterations in HSPC survival and self-renewal, ADAR1, telomere maintenance, mobilization and cell cycle gene expression, combined with space-induced clonal hematopoietic mutations, APOBEC3C activation and retrotransposon deregulation to warrant countermeasure development to enable long-duration spaceflight. Post-spaceflight analysis revealed increased C-to-T and clonal hematopoiesis-associated mutations, repetitive element and base deaminase deregulation, decreased telomere maintenance gene expression, and decreased self-renewal capacity compared to ground controls. These results demonstrate the space-associated aging effects in HSPCs after month-long exposure to LEO, providing insights into utilizing the LEO environment to model space-accelerated aging and other age-related malignancies.

  Study phs004267

• Assessing mitochondrial bioenergetics in coronary artery disease: A translational left ventricular tissue study in humans (The AMBITION study).

  Severe or recurrent myocardial ischemia can lead to long-term left ventricular (LV) dysfunction and heart failure in patients with coronary artery disease (CAD). In this study, we assessed for chronic metabolomic and transcriptomic adaptations within LV myocardium of patients with evidence of preoperative inducible ischemia undergoing coronary artery bypass grafting (CABG). During surgery, paired transmural LV biopsies were acquired on the beating heart from a region of inducible ischemia (determined by stress perfusion cardiovascular magnetic resonance), and a remote LV segment. From 33 patients, 63 LV biopsies were acquired on the beating heart during CABG, comparing to analysis of LV samples from 11 donor hearts. The global myocardial ATP/ADP ratio was reduced in CAD patients as compared to donor LV tissue with increased expression of oxidative phosphorylation (OXPHOS) genes encoding the electron transport chain complexes across multiple cell types. Paired analyses of biopsies obtained during CABG from LV segments with or without inducible ischemia revealed no significant difference in the ATP/ADP ratio, broader metabolic profile or expression of ventricular cardiomyocyte genes implicated in OXPHOS. Finally, differential metabolite analysis suggested dysregulation of several intermediates in patients with impaired LVEF; this notably included the tricyclic acid cycle metabolite, succinate. Overall, our results suggest that viable human myocardium in patients with stable CAD has global alterations in bioenergetic and transcriptional profile without large regional differences between areas with or without inducible ischemia.

  Study EGAS00001007351

• Genetic variability in exon 1 of the glucocorticoid receptor gene NR3C1 is associated with postoperative complications

  Patients having major surgery experience inflammation post-operatively, which may contribute to post-operative morbidity. Endogenous glucocorticoids (GCs) are an essential part of the stress response, but this response varies between individuals, which may in turn affect clinical outcome in general, and post-operative inflammation, specifically. Exon 1 of the NR3C1 gene, encoding the glucocorticoid receptor, contains an established region of differential regulation. DNA methylation patterns in this region have been found to differ between individuals. We investigated the methylation status and genotype in the Cytosine-phosphate-Guanine (CpG) island in exon 1 of NR3C1 in 24 patients who underwent major abdominal surgery and correlated it with post-operative complications. DNA was extracted from peripheral blood leukocytes and underwent targeted bisulfite sequencing of the CpG island. Complications were graded according to the Clavien-Dindo classification and 14 out of 24 had post-operative complications. Multifactorial and partial least square methods were used to analyse the data. A homogenous demethylated pattern was observed in all patients and no single CpG methylation was associated with post-operative complications. Four single nucleotide polymorphisms (SNPs) were significantly correlated with higher Clavien-Dindo scores. Genetic variability in the chr5:143,402,505-143,405,805 region of exon 1 of the glucocorticoid receptor gene NR3C1, but not DNA methylation, was associated with more severe post-operative complications in patients having major abdominal surgery. This indicates that the response to GCs may be of clinical importance for inflammatory conditions.

  Study EGAS00001005737

• Whole genome sequencing with linked reads of pediatric glioblastoma samples

  Pediatric glioblastoma (pGBM) is a lethal cancer with no effective therapies. To understand mechanisms of tumor evolution in this cancer, we performed whole genome sequencing with linked reads on longitudinally resected pGBM samples. Our analyses showed that all diagnostic and recurrent samples were collections of genetically diverse subclones. Clonal composition rapidly evolved at recurrence, with less than 8% of non-synonymous single nucleotide variants being shared in diagnostic-recurrent pairs. In order to track the origins of the mutational events we observed in pGBM, we generated whole genome datasets for two patients and their parents. These trios showed that genetic variants could be (i) somatic, (ii) inherited from a healthy parent, or (iii) arose de novo in the germlines of pGBM patients. Analysis of variant allele frequencies supported a model of tumor growth involving slow-cycling cancer stem cells that give rise to fast-proliferating progenitor-like cells and to non-dividing cells. Interestingly, radiation and anti-mitotic chemotherapeutics did not increase overall tumor burden upon recurrence. These findings support an important role for slow-cycling stem cell populations in contributing to recurrences, since slow-cycling cell populations are expected to be less prone to genotoxic stress induced by these treatments and to accumulate few mutations. Our results highlight the need for new targeted treatments that account for the complex functional hierarchies and genomic heterogeneity of pGBM.

  Study EGAS00001003432

• The Environmental Determinants of Diabetes in the Young Study (TEDDY)

  Study Overview The Environmental Determinants of Diabetes in the Young (TEDDY) Study is a longitudinal study that investigates genetic and genetic-environmental interactions, including gestational events, childhood infections, dietary exposures, and other environmental factors after birth, in relation to the development of islet autoimmunity and type 1 diabetes (T1D). A consortium of six clinical centers assembled to participate in the development and implementation of the study to identify environmental triggers for the development of islet autoimmunity and T1D in genetically susceptible individuals. Beginning in 2004, the TEDDY study screened over 400,000 newborns for high-risk HLA-DR, DQ genotypes from both the general population and families already affected by T1D. The TEDDY study enrolled around 8,676 participants across six clinical centers worldwide (Finland, Germany, Sweden and three in the United States) in the 15-year prospective follow-up. Participants are followed every three months for islet autoantibody (IA) measurements with blood sampling until four years of age and then at least every six months until the age of 15. After the age of four, autoantibody positive participants continue to be followed at three month intervals and autoantibody negative participants are followed at six-month intervals. In addition to the analysis of autoantibodies, additional data and sample collection are performed at each visit. Parents collect monthly stool samples in early childhood. The parents also fill out questionnaires at regular intervals in connection with study visits and record information about diet and health status in the child's TEDDY Book between visits. Continued long-term follow-up of the currently active TEDDY participants will provide important scientific information on early childhood diet, reported and measured infections, vaccinations, and psychosocial stressors that may contribute to the development of type 1 diabetes and islet autoimmunity. Additional information on the TEDDY study is available in the following articles: Rewers et al., 2008, PMID: 19120261 and Hagopian et al., 2006, PMID: 17130573. Details of the TEDDY protocol can be found in Hagopian et al., 2011, PMID: 21564455. TEDDY data currently available in dbGaP include: gene expression, SNPs, exome, microbiome (gut, nasal, and plasma), RNA sequencing, and whole genome sequencing. For more information on TEDDY Study version history please refer to TEDDY Study dbGaP README File. ImmunoChip SNP DNA from whole blood samples on study participants and their family members (mothers, fathers, and siblings) was obtained and used for SNP genotyping. Genotyping was performed by the Center for Public Health Genomics at the University of Virginia using the Illumina ImmunoChip SNP array, which contains around 196,000 SNPs from 186 regions associated with 12 autoimmune diseases (Hadley et al., 2015, PMID: 26010309). Data cleaning and validation included the removal of subjects with a low call rate (< 5% SNPs missing) and differences in reported sex and prior genotyping at the TEDDY HLA laboratory. Additionally, SNPs with a low call rate or Hardy-Weinberg equilibrium P value < 10-6, except for chromosome 6 due to HLA eligibility requirements, were removed from the final dataset (Törn et al., 2015, PMID: 25422107).TEDDY-T1DExome ArrayDNA from whole blood samples on study participants and their family members (mothers, fathers, and siblings) was obtained and used for genotyping. Genotyping was performed by the University of Virginia using the Illumina TEDDY-T1DExome array. The TEDDY-T1DExome array is a custom chip that contains 550,601 markers from the Infinium CoreExome-24 v1.1 BeadChip and an additional 90,214 tagSNPs specifically selected by the TEDDY investigators based on their associations with nutrients, vitamins, type 2 diabetes, autoimmune diseases, body-mass index, or other exposures and phenotypes measured by TEDDY study.The Illumina GenTrain2 algorithm was used for genotype calling. Sample quality control metrics included sample call rate, heterozygosity rate and concordance of gender between the information reported and genotyped. Gene Expression The TEDDY study collected peripheral blood for the extraction of total RNA from enrolled children starting at 3 months of age, and then at 3 month intervals up to 48 months and then biannually. Total RNA was extracted using a high throughput (96-well format) extraction protocol using magnetic (MagMax) beads technology at the TEDDY RNA Laboratory, Jinfiniti Biosciences in Augusta, GA. Purified RNA (200 ng) was further used for cRNA amplification and labeling with biotin using Target Amp cDNA synthesis kit (Epicenter catalog no. TAB1R6924). Labeled cRNA was hybridized to the Illumina HumanHT-12 Expression BeadChips based on the manufacturer's instructions. The HumanHT-12 Expression BeadChip provides coverage for more than 47,000 transcripts and known splice variants across the human transcriptome. Microbiome The TEDDY microbiome study aimed to characterize the longitudinal development of the microbiome, including bacteria, viruses and other microorganisms in the gut, plasma, and nasal cavity of prediabetic and diabetic subjects compared to autoantibody negative non-diabetic subjects. Stool samples used were collected monthly from 3 to 48 months, after which stool samples were collected every 3 months. Nasal swab samples were collected every 3 months starting at 9 months of age until 48 months, after which nasal swabs were collected every 6 months. Plasma samples were collected every 3 months starting at 3 months of age until 48 months, after which plasma samples were collected every 6 months. If the subject was autoantibody positive at 48 months then they remained on the 3 month collection interval for nasal swab and plasma samples. Samples underwent 16s rRNA gene sequencing, DNA and viral RNA metagenomics shotgun sequencing, and sequencing of the internal transcribed spacer (ITS) regions. Additional information on the TEDDY microbiome data is available in the following articles: Vatanen et al., 2018, PMID: 30356183, Stewart et al., 2018, PMID: 30356187, and Vehik et al., 2020, PMID: 31792456. RNA Sequencing The TEDDY study aimed to characterize the transcriptome in subjects with islet autoimmunity and type 1 diabetes compared to matched control subjects. Peripheral blood was collected to extract total RNA from enrolled children starting at 3 months of age, and then at 3 month intervals up to 48 months and then biannually. Total RNA was extracted using a high throughput (96-well format) extraction protocol using magnetic (MagMax) beads technology at the TEDDY RNA Laboratory, Jinfiniti Biosciences in Augusta, GA. Purified RNA was then sent to the Broad Institute for the generation of the TEDDY RNA sequencing (RNA-Seq) data. The RNA samples were prepped using Superscript III reverse transcriptase and Illumina's TruSeq Stranded mRNA Sample Prep Kit. The TruSeq libraries were run on the Illumina HiSeq2500 platform. Whole Genome Sequencing The TEDDY study aimed to conduct deep whole genome sequencing and examine the genomic variations in subjects with islet autoimmunity and type 1 diabetes compared to matched autoantibody negative and non-diabetic children. DNA from whole blood was obtained from TEDDY children for whole genome sequencing. The WGS data were generated on the Illumina HiSeq X Ten system.

  Study phs001442

• Use_of_Deep_Sequencing_to_Dectect_Clonal_Mutations_In_Sun_Exposed_Skin_Epidermis

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Study EGAS00001000515

• Use_of_Deep_Sequencing_to_Dectect_Clonal_Mutations_In_Sun_Exposed_Skin_Epidermis_PART2

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Study EGAS00001000603

• Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation

  Raw sequencing files from scRNA-seq dataset used in Schmassmann et al. 2023. Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation. Elife 12 (https://elifesciences.org/articles/92678) Dataset content: 14 samples from 5 donors File type: paired-end fastq files Technology: Illumina sequencing Experimentation used: scRNA-seq using the 10X technology

  Dataset EGAD50000000434