Single-Cell, Human Sperm Transcriptomes and Variants from Fathers of Autistic and Healthy Children
Year: 2019
Type: preprint
Study design: Observational Study
Abstract: The human sperm is one of the smallest cells in the body, but also one of the most important, as it serves as the entire paternal genetic contribution to a child. This is especially relevant for diseases such as Autism Spectrum Disorders (ASD), which have been correlated with advance paternal age. Historically, most studies of sperm have focused on the assessment of a bulk sperm, wherein millions of individual sperm are present and only high-frequency variants can be detected. Using 10X Chromium single cell sequencing technology, we have assessed the RNA from >65,000 single sperm cells across 6 donors (scsperm-RNA-seq), including two of whom have autistic children and four that do not. Using multiple RNA-seq methods for differential expression and variant analysis, we found clusters of sperm mutations in each donor that are indicative of the sperm being produced by different stem cell pools. Moreover, by comparing the two groups, we have found expression changes that can separate out the two sets of donors. Finally, through our novel variant calling from single-cell RNA-seq methods, we have shown that we can detect mutation rates in sperm from ASD donors that is distinct from the controls, highlighting this method as a new means to characterize ASD risk.
DOI: 10.1101/640607
Language: English
Subfield: Reproductive Medicine
Field: Medicine
Domain: Health Sciences
Open Access status: green
Funders: National Aeronautics and Space Administration, Vallee Foundation, Pershing Square Sohn Cancer Research Alliance, WorldQuant Foundation, National Institutes of Health, Weill Cornell Medical College, National Institute of Neurological Disorders and Stroke, National Institute of Environmental Health Sciences, National Institute of Biomedical Imaging and Bioengineering
Awards: G1284901464, (1) SUMMARYMASSIVELY PARALLEL DNA SEQUENCING CONTINUES TO PROVIDE ASTONISHING INSIGHTS INTO THE REGULATORY COMPLEXITY OF THE MAMMALIAN GENOME REVEALING HERITABLE AND DE NOVO OCCURRING RISK FACTORS PREDISPOSING HUMANS TO A WIDE VARIETY OF DISEASES AND DISORDERS. NOTABLY MEMBERS OF THE ENCYCLOPEDIA OF DNA ELEMENTS (ENCODE) CONSORTIUM INCLUDING CO-INVESTIGATORS DRS. MASON AND SNYDER HAVE RECENTLY MAPPED THOUSANDS OF NON-CODING REGULATORY ELEMENTS IN THE HUMAN GENOME THAT SPECIFY RISK AND PROTECTIVE SITES FOR MANY DISEASE. THESE NONCODING GENETIC VARIATIONS ALSO SHOW DIFFERENTIAL IMPACT DEPENDING ON THE EPIGENETIC CHANGES OF THE GENOME INCLUDING METHYLATION OF DNA AND CHROMATIN STATES INSIDE CELLS. YET THESE QUESTIONS HAVE NOT BEEN COMPREHENSIVELY EXAMINED IN HUMAN ASTRONAUTS DUE TO THE FACT THAT THE VERY FIRST DATA SETS THAT CAN DELINEATE THE PUTATIVE IMPACT OF GENOME-WIDE NONCODING VARIATION AND EPIGENETIC CHANGES FROM SPACE TRAVEL ARE ONLY NOW BEING GENERATED IN THE NASA TWINS STUDY.HOWEVER WITH THIS DATA FROM NASA TWINS STUDY THERE IS A UNIQUE OPPORTUNITY TO BOTH GENERATE NEW COMPUTATIONAL TOOLS FOR THE INTEGRATION OF THE DATA FROM THESE SAMPLES AND ALSO TO UTILIZE NOVEL SINGLE-CELL APPROACHES FOR EPIGENETIC STATES IN THE HUMAN CELLS TAKEN FROM SPACE. WE PROPOSE TO EXPAND AND FURTHER INTEGRATE OUR TOOLS FOR EXAMINING THE REGULATORY CHANGES TO DNA AND RNA TOGETHER CALLED "EPISUITE " WHICH WILL PROVIDE LONG-SOUGHT SOLUTIONS TO PROBLEMS IN INTEGRATIVE GENOMICS AND ESTABLISH A MORE SYSTEMS-LEVEL VIEW OF HUMAN PHYSIOLOGY DURING SPACE TRAVEL. SPECIFICALLY WE WILL OPTIMIZE AND INTEGRATE OPEN-SOURCE AND PUBLISHED BIOINFORMATICS TOOLS BETWEEN BOTH LABORATORIES (HUGE-SEQ METHYLKIT EDMR R-MAKE) EXPAND OUR CODE BASE WITH TWO NEW TOOLS (METHCLONE AND CEMBASE) AND THEN CREATE A WEB-INTERFACE FOR USERS TO UPLOAD ORGANIZE AND ANALYZE THESE DATA RELATIVE TO ENCODE PUBLIC DATA. THEN WE WILL USE NOVEL SINGLE-CELL EXPERIMENTAL METHODS (SCATAC-SEQ) TO CONFIRM AND CHARACTERIZE THE IMPACT AND SCOPE OF SUCH NONCODING AND EPIGENETIC CHANGES. TOGETHER THE DATA AND TOOLS IN EPISUITE CONCOMITANT WITH THE NEW SINGLE-CELL CHROMATIN DATA WILL ENABLE DISCOVERY AND VALIDATION OF SPECIFIC LOCI THAT REPRESENT THE GENETIC AND EPIGENETIC RISKS FACED BY ASTRONAUTS AND ALSO AN IMPROVED UNDERSTANDING OF THE REGULATORY AND GENETIC IMPACT (BMED5) OF THESE MOLECULAR CHANGES.(2) HYPOTHESISWE HYPOTHESIZE THAT SPECIFIC AREAS OF THE GENOME ARE EPIGENETICALLY DYSREGULATED AS A RESULT OF SPACE TRAVEL AND THAT SOME OF THESE AREAS DIFFER BETWEEN ASTRONAUTS. MOREOVER WE HYPOTHESIZE THAT THE ENRICHMENT OF NON-CODING VARIANTS IN DISTINCT BIOLOGICAL PATHWAYS WILL ALSO DIFFER BETWEEN ASTRONAUTS AND ANALYSIS AND INTEGRATION OF THESE DATA WILL REVEAL THE FIRST REGIONS OF "EPIGENETIC SPACE RISK" FOR THE ASTRONAUTS DELINEATED IN BMED5. TO VALIDATE THESE PREDICTIONS WE WILL PERFORM SINGLE-CELL ATAC-SEQ (ASSAY FOR TRANSPOSASE ACCESSIBLE CHROMATIN) ON CELL FRACTIONS FROM EARTH-BASED CONTROL SAMPLES AND THOSE TAKEN FROM SPACE.(3) SPECIFIC AIMSAIM 1. CREATE A WEB-BASED FRAMEWORK FOR INTEGRATING NON-CODING GENOMIC VARIATION AND DIFFERENTIAL EPIGENETIC STATES. THIS EPISUITE INTERFACE AND SET OF MACHINE-LEARNING ALGORITHMS WILL HELP ONGOING WORK WITH THE NASA TWINS STUDY AND AID FUTURE INVESTIGATIONS THAT LEVERAGE MULTI-OMICS DATA SETS FROM ASTRONAUTS. THESE DATA WILL ALSO BE LINKED TO GENE EXPRESSION DATA TO GAUGE THE IMPACT OF GENETIC AND EPIGENETIC CHANGES ON SPECIFIC BIOLOGICAL NETWORKS.AIM 2. VALIDATE THE ALTERED CHROMATIN STATES IN CELLS FROM SPACE TRAVEL AND MEASURE THE PROPORTION OF CELLS CHANGED WITH SINGLE-CELL ATAC-SEQ. WE WILL USE AN ASSAY CALLED SINGLE CELL (SCATAC-SEQ) WHICH CAN MEASURE THE SITES OF OPEN AND CLOSED CHROMATIN ON A CELL-BY-CELL BASIS. THIS WILL VALIDATE THE SITES WHERE WE OBSERVE EPIGENETIC CHANGES AND ALSO PROVIDE THE FIRST ESTIMATE OF THE PROPORTION OF CELLS EPIGENETICALLY IMPACTED BY SPACE TRAVEL., NEXT-GENERATION SEQUENCING (NGS) TECHNOLOGIES HAVE RECENTLY BEEN USED TO DETECT AND CLASSIFY EPIGENETIC CHANGES AT AN UNPRECEDENTED LEVEL. EPIGENETIC, Community Research Education and Engagement for Data Science (CREEDS), Study of Neural Tube Defects Etiology: Genome and Exposome, G6375568880, G6978705394, G7535378661, Epigenome Interactions in Complex Neurogenetic Disorders, G8216312950, G9000163900
OpenAlex ID: W2946079736