Matching Items (13)
Description
Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. We describe the establishment of primary dermal fibroblasts cells lines from 28 autopsy donors. These fibroblasts were used to examine the proliferative effects of establishment protocol, tissue amount, biopsy site, and donor age. As proof-of-principle, iPSCs were generated from fibroblasts from a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. To our knowledge, this is the first study describing autopsy donor-derived somatic cells being used for iPSC generation and subsequent neural differentiation. This unique approach also enables us to compare iPSC-derived cell cultures to endogenous tissues from the same donor. We utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, supported by (i) a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain, (ii) an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue, and (iii) a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. These studies support the utility of autopsy donors' somatic cells for iPSC-based neurological disease models, and provide evidence that in vitro neural differentiation can result in physiologically progression.
ContributorsHjelm, Brooke E (Author) / Craig, David W. (Thesis advisor) / Wilson-Rawls, Norma J. (Thesis advisor) / Huentelman, Matthew J. (Committee member) / Mason, Hugh S. (Committee member) / Kusumi, Kenro (Committee member) / Arizona State University (Publisher)
Created2013
Description
ABSTRACT Whole genome sequencing (WGS) and whole exome sequencing (WES) are two comprehensive genomic tests which use next-generation sequencing technology to sequence most of the 3.2 billion base pairs in a human genome (WGS) or many of the estimated 22,000 protein-coding genes in the genome (WES). The promises offered from WGS/WES are: to identify suspected yet unidentified genetic diseases, to characterize the genomic mutations in a tumor to identify targeted therapeutic agents and, to predict future diseases with the hope of promoting disease prevention strategies and/or offering early treatment. Promises notwithstanding, sequencing a human genome presents several interrelated challenges: how to adequately analyze, interpret, store, reanalyze and apply an unprecedented amount of genomic data (with uncertain clinical utility) to patient care? In addition, genomic data has the potential to become integral for improving the medical care of an individual and their family, years after a genome is sequenced. Current informed consent protocols do not adequately address the unique challenges and complexities inherent to the process of WGS/WES. This dissertation constructs a novel informed consent process for individuals considering WGS/WES, capable of fulfilling both legal and ethical requirements of medical consent while addressing the intricacies of WGS/WES, ultimately resulting in a more effective consenting experience. To better understand components of an effective consenting experience, the first part of this dissertation traces the historical origin of the informed consent process to identify the motivations, rationales and institutional commitments that sustain our current consenting protocols for genetic testing. After understanding the underlying commitments that shape our current informed consent protocols, I discuss the effectiveness of the informed consent process from an ethical and legal standpoint. I illustrate how WGS/WES introduces new complexities to the informed consent process and assess whether informed consent protocols proposed for WGS/WES address these complexities. The last section of this dissertation describes a novel informed consent process for WGS/WES, constructed from the original ethical intent of informed consent, analysis of existing informed consent protocols, and my own observations as a genetic counselor for what constitutes an effective consenting experience.
ContributorsHunt, Katherine (Author) / Hurlbut, J. Benjamin (Thesis advisor) / Robert, Jason S. (Thesis advisor) / Maienschein, Jane (Committee member) / Northfelt, Donald W. (Committee member) / Marchant, Gary (Committee member) / Ellison, Karin (Committee member) / Arizona State University (Publisher)
Created2013
Description
In 1997, developmental biologist Michael Richardson compared his research team's embryo photographs to Ernst Haeckel's 1874 embryo drawings and called Haeckel's work noncredible.Science soon published <“>Haeckel's Embryos: Fraud Rediscovered,<”> and Richardson's comments further reinvigorated criticism of Haeckel by others with articles in The American Biology Teacher, <“>Haeckel's Embryos and Evolution: Setting the Record Straight <”> and the New York Times, <“>Biology Text Illustrations more Fiction than Fact.<”> Meanwhile, others emphatically stated that the goal of comparative embryology was not to resurrect Haeckel's work. At the center of the controversy was Haeckel's no-longer-accepted idea of recapitulation. Haeckel believed that the development of an embryo revealed the adult stages of the organism's ancestors. Haeckel represented this idea with drawings of vertebrate embryos at similar developmental stages. This is Haeckel's embryo grid, the most common of all illustrations in biology textbooks. Yet, Haeckel's embryo grids are much more complex than any textbook explanation. I examined 240 high school biology textbooks, from 1907 to 2010, for embryo grids. I coded and categorized the grids according to accompanying discussion of (a) embryonic similarities (b) recapitulation, (c) common ancestors, and (d) evolution. The textbooks show changing narratives. Embryo grids gained prominence in the 1940s, and the trend continued until criticisms of Haeckel reemerged in the late 1990s, resulting in (a) grids with fewer organisms and developmental stages or (b) no grid at all. Discussion about embryos and evolution dropped significantly.
ContributorsWellner, Karen L (Author) / Maienschein, Jane (Thesis advisor) / Ellison, Karin D. (Committee member) / Creath, Richard (Committee member) / Robert, Jason S. (Committee member) / Laubichler, Manfred D. (Committee member) / Arizona State University (Publisher)
Created2014
Description
Biology textbooks are everybody's business. In accepting the view that texts are created with specific social goals in mind, I examined 127 twentieth-century high school biology textbooks for representations of animal development. Paragraphs and visual representations were coded and placed in one of four scientific literacy categories: descriptive, investigative, nature of science, and human embryos, technology, and society (HETS). I then interpreted how embryos and fetuses have been socially constructed for students. I also examined the use of Haeckel's embryo drawings to support recapitulation and evolutionary theory. Textbooks revealed that publication of Haeckel's drawings was influenced by evolutionists and anti-evolutionists in the 1930s, 1960s, and the 1990s. Haeckel's embryos continue to persist in textbooks because they "safely" illustrate similarities between embryos and are rarely discussed in enough detail to understand comparative embryology's role in the support of evolution. Certain events coincided with changes in how embryos were presented: (a) the growth of the American Medical Association (AMA) and an increase in birth rates (1950s); (b) the Biological Sciences Curriculum Study (BSCS) and public acceptance of birth control methods (1960s); (c) Roe vs. Wade (1973); (d) in vitro fertilization and Lennart Nilsson's photographs (1970s); (e) prenatal technology and fetocentrism (1980s); and (f) genetic engineering and Science-Technology-Society (STS) curriculum (1980s and 1990s). By the end of the twentieth century, changing conceptions, research practices, and technologies all combined to transform the nature of biological development. Human embryos went from a highly descriptive, static, and private object to that of sometimes contentious public figure. I contend that an ignored source for helping move embryos into the public realm is schoolbooks. Throughout the 1900s, authors and publishers accomplished this by placing biology textbook embryos and fetuses in several different contexts--biological, technological, experimental, moral, social, and legal.
ContributorsWellner, Karen L (Author) / Maienschein, Jane (Thesis advisor) / Ellison, Karin D. (Committee member) / Robert, Jason S. (Committee member) / Arizona State University (Publisher)
Created2010
Description
Since the 1950s, scientists have developed interspecies blastocysts in laboratory settings, but not until the 1990s did proposals emerge to engineer interspecies blastocysts that contained human genetic or cellular material. Even if these embryos were not permitted to mature to fetal stages, their ethical and political status became debated within nations attempting to use them for research. To study cell differentiation and embryonic development and causes of human diseases, interspecies-somatic-cell-nuclear-transfer -derived (iSCNT) humanesque blastocysts provided opportunities for research and therapy development. Such a technology also involved ethical debates.
ContributorsTaddeo, Sarah (Author) / Robert, Jason S. (Author) / Diehnelt, Nicole (Author) / Arizona State University. School of Life Sciences. Center for Biology and Society. Embryo Project Encyclopedia. (Publisher) / Arizona Board of Regents (Publisher)
Created2017-06-23
Description
To educate its citizens about research into chimeras made from human and non-human animal cells, the United Kingdom's Human Fertilisation Embryology Authority published the consultation piece Hybrids and Chimeras: A Consultation on the Ethical and Social Implications of Creating Human/Animal Embryos in Research, in 2007. The document provided scientific and legal background, described ethical and social issues associated with research using part-human part-animal embryos, supplied a questionnaire for citizens to return to the HFEA with their opinions, and offered a list of resources for further reading to stimulate public debate. The strategy of surveying the public provided a template for developing further policy in the United Kingdom and other countries, as well as for educating citizens on embryological research.
ContributorsTaddeo, Sarah (Author) / Robert, Jason S. (Author) / Newkirk, Nicole (Editor) / Bartlett, Zane N. (Editor) / Arizona State University. School of Life Sciences. Center for Biology and Society. Embryo Project Encyclopedia. (Publisher) / Arizona Board of Regents (Publisher)
Created2014-11-04
Description
In 2007, the Human Fertilisation and Embryology Authority in London, UK, published Hybrids and Chimeras: A Report on the Findings of the Consultation, which summarized a public debate about research on, and suggested policy for, human animal chimeras. The HFEA formulated the report after conducting a series of surveys and debates from earlier in 2007. The HFEA issued a statement in September 2007, followed by an official report published on 1 October 2007. Their report on human-animal chimeras set a worldwide precedent for discussions of the ethical use of those embryos in labs. The HFEA's report led the UK government to pass legislature about the use of human-animal cytoplasmic hybrid embryos for research in the UK.
ContributorsRobert, Jason S. (Author) / Taddeo, Sarah (Author) / Bartlett, Zane N. (Editor) / Arizona State University. School of Life Sciences. Center for Biology and Society. Embryo Project Encyclopedia. (Publisher) / Arizona Board of Regents (Publisher)
Created2014-11-22
Description
Rapid advancements in genomic technologies have increased our understanding of rare human disease. Generation of multiple types of biological data including genetic variation from genome or exome, expression from transcriptome, methylation patterns from epigenome, protein complexity from proteome and metabolite information from metabolome is feasible. "Omics" tools provide comprehensive view into biological mechanisms that impact disease trait and risk. In spite of available data types and ability to collect them simultaneously from patients, researchers still rely on their independent analysis. Combining information from multiple biological data can reduce missing information, increase confidence in single data findings, and provide a more complete view of genotype-phenotype correlations. Although rare disease genetics has been greatly improved by exome sequencing, a substantial portion of clinical patients remain undiagnosed. Multiple frameworks for integrative analysis of genomic and transcriptomic data are presented with focus on identifying functional genetic variations in patients with undiagnosed, rare childhood conditions. Direct quantitation of X inactivation ratio was developed from genomic and transcriptomic data using allele specific expression and segregation analysis to determine magnitude and inheritance mode of X inactivation. This approach was applied in two families revealing non-random X inactivation in female patients. Expression based analysis of X inactivation showed high correlation with standard clinical assay. These findings improved understanding of molecular mechanisms underlying X-linked disorders. In addition multivariate outlier analysis of gene and exon level data from RNA-seq using Mahalanobis distance, and its integration of distance scores with genomic data found genotype-phenotype correlations in variant prioritization process in 25 families. Mahalanobis distance scores revealed variants with large transcriptional impact in patients. In this dataset, frameshift variants were more likely result in outlier expression signatures than other types of functional variants. Integration of outlier estimates with genetic variants corroborated previously identified, presumed causal variants and highlighted new candidate in previously un-diagnosed case. Integrative genomic approaches in easily attainable tissue will facilitate the search for biomarkers that impact disease trait, uncover pharmacogenomics targets, provide novel insight into molecular underpinnings of un-characterized conditions, and help improve analytical approaches that use large datasets.
ContributorsSzelinger, Szabolcs (Author) / Craig, David W. (Thesis advisor) / Kusumi, Kenro (Thesis advisor) / Narayan, Vinodh (Committee member) / Rosenberg, Michael S. (Committee member) / Huentelman, Matthew J (Committee member) / Arizona State University (Publisher)
Created2015
Description
In 2014, the Centers for Medicare and Medicaid Services (CMS), which oversees the federal Clinical Laboratories Improvement Amendments (CLIA) program, issued guidance that the CLIA requirements apply when researchers seek to return individual-level research findings to study participants or their physician (Centers for Medicare & Medicaid Services, 2014). The present study explores the stance of U.S. Institutional Review Boards (IRBs) toward the applicability of and compliance with the CLIA regulations when studies plan to return individual research results (RIRR). I performed a document content analysis of 73 IRB policies and supporting documents from 30 United States (U.S.) institutions funded for biomedical research by the National Institutes of Health in 2017. Documents analyzed included policies, procedures, guidance, protocol and consent templates, and miscellaneous documents (such as IRB presentations) found to address the RIRR to study participants. I used qualitative content and document analysis to identify themes across institutions related to the CLIA regulations and the RIRR. Basic descriptive statistics were used to represent the data quantitatively. The study found that 96.67% (n=29) of institutions had documents that addressed the RIRR to participants. The majority of the institutions had at least one document that referenced the CLIA regulations when discussing the practice of disclosing participant-specific results [76.67% (n=23)]. The majority of institutions [56.67% (n=17)] indicated that they require compliance with the CLIA regulations for returning individual study findings to participants, while 13.33% (n=4) recommended compliance. The intent of two (6.67%) institutions was vague or unclear, while seven (26.67%) institutions were silent on the topic altogether. Of the 23 institutions that referenced “CLIA” in their documents, 52.17% only mentioned CLIA in a one or two-sentence blurb, providing very little guidance to investigators. The study results provide evidence that the majority of U.S. biomedical institutions require or recommend compliance with CLIA stipulations when investigators intend to return individual research results to study participants. However, the data indicates there is heterogeneity and variation in the quality of the guidance provided.
ContributorsBuchholtz, Stephanie (Author) / Robert, Jason S. (Thesis advisor) / Ellison, Karin D. (Committee member) / Carpten, John D. (Committee member) / Craig, David W. (Committee member) / Marchant, Gary E. (Committee member) / Arizona State University (Publisher)
Created2021
Description
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT), is a rare and understudied cancer with a dismal prognosis. SCCOHT's infrequency has hindered empirical study of its biology and clinical management. However, we and others have recently identified inactivating mutations in the SWI/SNF chromatin remodeling gene SMARCA4 with concomitant loss of SMARCA4 protein in the majority of SCCOHT tumors. Here we summarize these findings and report SMARCA4 status by targeted sequencing and/or immunohistochemistry (IHC) in an additional 12 SCCOHT tumors, 3 matched germlines, and the cell line SCCOHT-1. We also report the identification of a homozygous inactivating mutation in the gene SMARCB1 in one SCCOHT tumor with wild-type SMARCA4, suggesting that SMARCB1 inactivation may also play a role in the pathogenesis of SCCOHT. To date, SMARCA4 mutations and protein loss have been reported in the majority of 69 SCCOHT cases (including 2 cell lines). These data firmly establish SMARCA4 as a tumor suppressor whose loss promotes the development of SCCOHT, setting the stage for rapid advancement in the biological understanding, diagnosis, and treatment of this rare tumor type.
ContributorsRamos, Pilar (Author) / Kamezis, Anthony N. (Author) / Hendricks, William P. D. (Author) / Wang, Yemin (Author) / Tembe, Waibhav (Author) / Zismann, Victoria L. (Author) / Legendre, Christophe (Author) / Liang, Winnie S. (Author) / Russell, Megan L. (Author) / Craig, David W. (Author) / Farley, John H. (Author) / Monk, Bradley J. (Author) / Anthony, Stephen P. (Author) / Sekulic, Aleksandar (Author) / Cunliffe, Heather E. (Author) / Huntsman, David G. (Author) / Trent, Jeffrey M. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2014-11-03