Prediction of Gene Function by Genome-Scale Expression Analysis: Prostate Cancer-Associated Genes

Edited by Xiao-Fan WangProper neural commitment is essential for ensuring the appropriate development of the human brain and for preventing neurodevelopmental diseases such as autism spectrum disorders, schizophrenia, and intellectual disorders. However, the molecular mechanisms underlying the neural commitment in humans remain elusive. Here, we report the establishment of a neural differentiation system based on human embryonic stem cells (hESCs) and on comprehensive RNA sequencing analysis of transcriptome dynamics during early hESC differentiation. Using weighted gene co-expression network analysis, we reveal that the hESC neurodevelopmental trajectory has five stages: pluripotency (day 0); differentiation initiation (days 2, 4, and 6); neural commitment (days 8 -10); neural progenitor cell proliferation (days 12, 14, and 16); and neuronal differentiation (days 18, 20, and 22). These stages were characterized by unique module genes, which may recapitulate the early human cortical development. Moreover, a comparison of our RNA-sequencing data with several other transcriptome profiling datasets from mice and humans indicated that Module 3 associated with the day 8 -10 stage is a critical window of fate switch from the pluripotency to the neural lineage. Interestingly, at this stage, no key extrinsic signals were activated. In contrast, using CRISPR/ Cas9 -mediated gene knockouts, we also found that intrinsic hub transcription factors, including the schizophrenia-associated SIX3 gene and septo-optic dysplasia-related HESX1 gene, are required to program hESC neural determination. Our results improve the understanding of the mechanism of neural commitment in the human brain and may help elucidate the etiology of human mental disorders and advance therapies for managing these conditions. Brain development is one of the most complicated and hierarchical events in mammals. A series of temporal processes, including neural commitment, patterning and sub-regionalization, neurogenesis, and neuronal network formation, are required to generate a functional brain (1-4). Defects in any of these processes will lead to neurodevelopmental diseases such as autism spectrum disorders, schizophrenia, depression, and epilepsy. Neural commitment occurs after gastrulation and initiates the program to form neural epithelium (5-7). Many studies on amphibians and rodents reveal that the inhibition of BMP 3 signaling is an evolutionally conserved mechanism for neural induction; in addition, intrinsic factors play pivotal roles to direct fate transition from pluripotency to neural lineage (8 -11). Nonetheless, how the neural commitment is ensured in human brain has not been clearly elucidated. Systematically understanding the critical role of signaling pathways and transcriptional factors in modulating and shaping human brain development is hindered by limited accessibility to early embryos and inadequate amounts of stage-specific and cell type-specific materials. These problems may now be solved by the use of human embryonic stem cells (h...

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“…We performed Guilt-byAssociation analysis (24,32) to identify putative sub-stagespecific markers (Fig. 4E).…”

Section: Comparative Analysis Validates Module 3 Associated Day 8/10 mentioning

confidence: 99%

Transcriptome analysis reveals determinant stages controlling human embryonic stem cell commitment to neuronal cells

Wang

Qiao³

et al. 2017

Journal of Biological Chemistry

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“…54 Recent studies using complementary DNA microarray analysis have demonstrated widespread differences in gene expression patterns between benign and malignant growth of the prostate gland. [55][56][57][58][59][60][61][62][63][64][65] Such gene expression analysis of prostate tissues should help to disclose the molecular mechanisms underlying prostate malignant growth and identify molecular markers for diagnosis, prognosis, and therapy. Recent studies from our institution have focused on the gene for AMACR.…”

Section: ␣-Methylacyl-coenzyme a Racemase: A New Molecular Marker Formentioning

confidence: 99%

Human prostate cancer precursors and pathobiology

Marzo

Meeker

Zha

et al. 2003

Urology

171

103

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“…Similarly, aggressive technological innovation is required for the field of comparative genomics to reach its full potential (4). Finally, mRNA sequencing is valuable to determine exon splicing patterns (9) and as a tool to discover gene function from context-specific expression data (10).…”

mentioning

confidence: 99%

Sequence information can be obtained from single DNA molecules

Braslavsky

Hébert

Kartalov

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

427

245

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The completion of the human genome draft has taken several years and is only the beginning of a period in which large amounts of DNA and RNA sequence information will be required from many individuals and species. Conventional sequencing technology has limitations in cost, speed, and sensitivity, with the result that the demand for sequence information far outstrips current capacity. There have been several proposals to address these issues by developing the ability to sequence single DNA molecules, but none have been experimentally demonstrated. Here we report the use of DNA polymerase to obtain sequence information from single DNA molecules by using fluorescence microscopy. We monitored repeated incorporation of fluorescently labeled nucleotides into individual DNA strands with single base resolution, allowing the determination of sequence fingerprints up to 5 bp in length. These experiments show that one can study the activity of DNA polymerase at the single molecule level with single base resolution and a high degree of parallelization, thus providing the foundation for a practical single molecule sequencing technology.T he Sanger method of DNA sequencing (1) and subsequent developments in automation (2) and computation (3) revolutionized the world of biological sciences and eventually led to the sequencing of the consensus human genome (4, 5). The successes of this and other genome projects have only whetted the appetite of the scientific community, and many applications of DNA sequencing have been proposed that will require cheaper, faster, or more sensitive sequencing technology than conventional methods currently provide. After the determination of the consensus human genome, there is a desire to sequence many individual human genomes to provide highresolution genotypes that can be used to determine the complex relationships among disease, pharmaceutical efficacy, and genetic variability (6-8). Similarly, aggressive technological innovation is required for the field of comparative genomics to reach its full potential (4). Finally, mRNA sequencing is valuable to determine exon splicing patterns (9) and as a tool to discover gene function from context-specific expression data (10).There have been many proposals to develop new sequencing technologies based on single molecule measurements, generally either by observing the interaction of particular proteins with DNA (6, 11-13) or by using ultra high-resolution scanned probe microscopy (14). Although none of these methods has been demonstrated experimentally, they are interesting because they promise high sensitivity, low cost, and in some cases a high degree of parallelization (15). Unlike conventional technology, their speed and read length would not be inherently limited by the resolving power of electrophoretic separation. Single molecule sensitivity might permit direct sequencing of mRNA from rare cell populations or perhaps even individual cells.A major obstacle in the development of single molecule sequencing schemes is that DNA has an extraordinarily ...

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Prediction of Gene Function by Genome-Scale Expression Analysis: Prostate Cancer-Associated Genes

Cited by 148 publications

References 33 publications

Transcriptome analysis reveals determinant stages controlling human embryonic stem cell commitment to neuronal cells

Transcriptome analysis reveals determinant stages controlling human embryonic stem cell commitment to neuronal cells

Human prostate cancer precursors and pathobiology

Sequence information can be obtained from single DNA molecules

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